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House cleaning for phreeqcpp

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git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@787 1feff8c3-07ed-0310-ac33-dd36852eb9cd
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David L Parkhurst 2006-02-16 15:40:24 +00:00
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ReadClass.cpp → ReadClass.cxx
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SAXPhreeqc.cpp → SAXPhreeqc.cxx
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Sun/examples/ex1.log
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Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex1
Output file: ex1.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 1.--Add uranium and speciate seawater.
SOLUTION 1 SEAWATER FROM NORDSTROM ET AL. (1979)
units ppm
pH 8.22
pe 8.451
density 1.023
temp 25.0
redox O(0)/O(-2)
Ca 412.3
Mg 1291.8
Na 10768.0
K 399.1
Fe 0.002
Mn 0.0002 pe
Si 4.28
Cl 19353.0
Alkalinity 141.682 as HCO3
S(6) 2712.0
N(5) 0.29 gfw 62.0
N(-3) 0.03 as NH4
U 3.3 ppb N(5)/N(-3)
O(0) 1.0 O2(g) -0.7
SOLUTION_MASTER_SPECIES
U U+4 0.0 238.0290 238.0290
U(4) U+4 0.0 238.0290
U(5) UO2+ 0.0 238.0290
U(6) UO2+2 0.0 238.0290
SOLUTION_SPECIES
U+4 = U+4
log_k 0.0
U+4 + 4 H2O = U(OH)4 + 4 H+
log_k -8.538
delta_h 24.760 kcal
U+4 + 5 H2O = U(OH)5- + 5 H+
log_k -13.147
delta_h 27.580 kcal
U+4 + 2 H2O = UO2+ + 4 H+ + e-
log_k -6.432
delta_h 31.130 kcal
U+4 + 2 H2O = UO2+2 + 4 H+ + 2 e-
log_k -9.217
delta_h 34.430 kcal
UO2+2 + H2O = UO2OH+ + H+
log_k -5.782
delta_h 11.015 kcal
2UO2+2 + 2H2O = (UO2)2(OH)2+2 + 2H+
log_k -5.626
delta_h -36.04 kcal
3UO2+2 + 5H2O = (UO2)3(OH)5+ + 5H+
log_k -15.641
delta_h -44.27 kcal
UO2+2 + CO3-2 = UO2CO3
log_k 10.064
delta_h 0.84 kcal
UO2+2 + 2CO3-2 = UO2(CO3)2-2
log_k 16.977
delta_h 3.48 kcal
UO2+2 + 3CO3-2 = UO2(CO3)3-4
log_k 21.397
delta_h -8.78 kcal
PHASES
Uraninite
UO2 + 4 H+ = U+4 + 2 H2O
log_k -3.490
delta_h -18.630 kcal
END
-----
TITLE
-----
Example 1.--Add uranium and speciate seawater.
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1. SEAWATER FROM NORDSTROM ET AL. (1979)
-----------------------------Solution composition------------------------------
Elements Molality Moles
Alkalinity 2.406e-03 2.406e-03
Ca 1.066e-02 1.066e-02
Cl 5.657e-01 5.657e-01
Fe 3.711e-08 3.711e-08
K 1.058e-02 1.058e-02
Mg 5.507e-02 5.507e-02
Mn 3.773e-09 3.773e-09
N(-3) 1.724e-06 1.724e-06
N(5) 4.847e-06 4.847e-06
Na 4.854e-01 4.854e-01
O(0) 3.746e-04 3.746e-04 Equilibrium with O2(g)
S(6) 2.926e-02 2.926e-02
Si 7.382e-05 7.382e-05
U 1.437e-08 1.437e-08
----------------------------Description of solution----------------------------
pH = 8.220
pe = 8.451
Activity of water = 0.981
Ionic strength = 6.748e-01
Mass of water (kg) = 1.000e+00
Total carbon (mol/kg) = 2.180e-03
Total CO2 (mol/kg) = 2.180e-03
Temperature (deg C) = 25.000
Electrical balance (eq) = 7.936e-04
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 0.07
Iterations = 7
Total H = 1.110147e+02
Total O = 5.563047e+01
---------------------------------Redox couples---------------------------------
Redox couple pe Eh (volts)
N(-3)/N(5) 4.6750 0.2766
O(-2)/O(0) 12.3893 0.7329
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 2.674e-06 1.629e-06 -5.573 -5.788 -0.215
H+ 7.981e-09 6.026e-09 -8.098 -8.220 -0.122
H2O 5.551e+01 9.806e-01 1.744 -0.009 0.000
C(4) 2.180e-03
HCO3- 1.514e-03 1.023e-03 -2.820 -2.990 -0.170
MgHCO3+ 2.195e-04 1.640e-04 -3.658 -3.785 -0.127
NaHCO3 1.667e-04 1.948e-04 -3.778 -3.710 0.067
MgCO3 8.913e-05 1.041e-04 -4.050 -3.982 0.067
NaCO3- 6.718e-05 5.020e-05 -4.173 -4.299 -0.127
CaHCO3+ 4.597e-05 3.106e-05 -4.337 -4.508 -0.170
CO3-2 3.821e-05 7.959e-06 -4.418 -5.099 -0.681
CaCO3 2.725e-05 3.183e-05 -4.565 -4.497 0.067
CO2 1.210e-05 1.413e-05 -4.917 -4.850 0.067
UO2(CO3)3-4 1.255e-08 1.184e-10 -7.901 -9.927 -2.025
UO2(CO3)2-2 1.814e-09 5.653e-10 -8.741 -9.248 -0.506
MnCO3 2.696e-10 3.150e-10 -9.569 -9.502 0.067
MnHCO3+ 6.077e-11 4.541e-11 -10.216 -10.343 -0.127
UO2CO3 7.429e-12 8.678e-12 -11.129 -11.062 0.067
FeCO3 1.952e-20 2.281e-20 -19.709 -19.642 0.067
FeHCO3+ 1.635e-20 1.222e-20 -19.786 -19.913 -0.127
Ca 1.066e-02
Ca+2 9.504e-03 2.380e-03 -2.022 -2.623 -0.601
CaSO4 1.083e-03 1.266e-03 -2.965 -2.898 0.067
CaHCO3+ 4.597e-05 3.106e-05 -4.337 -4.508 -0.170
CaCO3 2.725e-05 3.183e-05 -4.565 -4.497 0.067
CaOH+ 8.604e-08 6.429e-08 -7.065 -7.192 -0.127
CaHSO4+ 5.979e-11 4.467e-11 -10.223 -10.350 -0.127
Cl 5.657e-01
Cl- 5.657e-01 3.528e-01 -0.247 -0.452 -0.205
MnCl+ 9.582e-10 7.160e-10 -9.019 -9.145 -0.127
MnCl2 9.439e-11 1.103e-10 -10.025 -9.958 0.067
MnCl3- 1.434e-11 1.071e-11 -10.844 -10.970 -0.127
FeCl+2 9.557e-19 2.978e-19 -18.020 -18.526 -0.506
FeCl2+ 6.281e-19 4.693e-19 -18.202 -18.329 -0.127
FeCl+ 7.786e-20 5.817e-20 -19.109 -19.235 -0.127
FeCl3 1.417e-20 1.656e-20 -19.849 -19.781 0.067
Fe(2) 6.909e-19
Fe+2 5.205e-19 1.195e-19 -18.284 -18.923 -0.639
FeCl+ 7.786e-20 5.817e-20 -19.109 -19.235 -0.127
FeSO4 4.845e-20 5.660e-20 -19.315 -19.247 0.067
FeCO3 1.952e-20 2.281e-20 -19.709 -19.642 0.067
FeHCO3+ 1.635e-20 1.222e-20 -19.786 -19.913 -0.127
FeOH+ 8.227e-21 6.147e-21 -20.085 -20.211 -0.127
FeHSO4+ 3.000e-27 2.242e-27 -26.523 -26.649 -0.127
Fe(3) 3.711e-08
Fe(OH)3 2.841e-08 3.318e-08 -7.547 -7.479 0.067
Fe(OH)4- 6.591e-09 4.924e-09 -8.181 -8.308 -0.127
Fe(OH)2+ 2.118e-09 1.583e-09 -8.674 -8.801 -0.127
FeOH+2 9.425e-14 2.937e-14 -13.026 -13.532 -0.506
FeSO4+ 1.093e-18 8.167e-19 -17.961 -18.088 -0.127
FeCl+2 9.557e-19 2.978e-19 -18.020 -18.526 -0.506
FeCl2+ 6.281e-19 4.693e-19 -18.202 -18.329 -0.127
Fe+3 3.509e-19 2.796e-20 -18.455 -19.554 -1.099
Fe(SO4)2- 6.372e-20 4.761e-20 -19.196 -19.322 -0.127
FeCl3 1.417e-20 1.656e-20 -19.849 -19.781 0.067
Fe2(OH)2+4 2.462e-24 2.322e-26 -23.609 -25.634 -2.025
FeHSO4+2 4.228e-26 1.318e-26 -25.374 -25.880 -0.506
Fe3(OH)4+5 1.122e-29 7.679e-33 -28.950 -32.115 -3.165
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.436 -44.369 0.067
K 1.058e-02
K+ 1.042e-02 6.495e-03 -1.982 -2.187 -0.205
KSO4- 1.627e-04 1.216e-04 -3.789 -3.915 -0.127
KOH 3.137e-09 3.665e-09 -8.503 -8.436 0.067
Mg 5.507e-02
Mg+2 4.742e-02 1.371e-02 -1.324 -1.863 -0.539
MgSO4 7.330e-03 8.562e-03 -2.135 -2.067 0.067
MgHCO3+ 2.195e-04 1.640e-04 -3.658 -3.785 -0.127
MgCO3 8.913e-05 1.041e-04 -4.050 -3.982 0.067
MgOH+ 1.084e-05 8.100e-06 -4.965 -5.092 -0.127
Mn(2) 3.773e-09
Mn+2 2.171e-09 4.982e-10 -8.663 -9.303 -0.639
MnCl+ 9.582e-10 7.160e-10 -9.019 -9.145 -0.127
MnCO3 2.696e-10 3.150e-10 -9.569 -9.502 0.067
MnSO4 2.021e-10 2.360e-10 -9.695 -9.627 0.067
MnCl2 9.439e-11 1.103e-10 -10.025 -9.958 0.067
MnHCO3+ 6.077e-11 4.541e-11 -10.216 -10.343 -0.127
MnCl3- 1.434e-11 1.071e-11 -10.844 -10.970 -0.127
MnOH+ 2.789e-12 2.084e-12 -11.555 -11.681 -0.127
Mn(NO3)2 1.375e-20 1.607e-20 -19.862 -19.794 0.067
Mn(3) 5.993e-26
Mn+3 5.993e-26 4.349e-27 -25.222 -26.362 -1.139
N(-3) 1.724e-06
NH4+ 1.609e-06 9.049e-07 -5.794 -6.043 -0.250
NH3 7.326e-08 8.558e-08 -7.135 -7.068 0.067
NH4SO4- 4.157e-08 3.106e-08 -7.381 -7.508 -0.127
N(5) 4.847e-06
NO3- 4.847e-06 2.846e-06 -5.314 -5.546 -0.231
Mn(NO3)2 1.375e-20 1.607e-20 -19.862 -19.794 0.067
Na 4.854e-01
Na+ 4.791e-01 3.387e-01 -0.320 -0.470 -0.151
NaSO4- 6.053e-03 4.523e-03 -2.218 -2.345 -0.127
NaHCO3 1.667e-04 1.948e-04 -3.778 -3.710 0.067
NaCO3- 6.718e-05 5.020e-05 -4.173 -4.299 -0.127
NaOH 3.117e-07 3.641e-07 -6.506 -6.439 0.067
O(0) 3.746e-04
O2 1.873e-04 2.188e-04 -3.727 -3.660 0.067
S(6) 2.926e-02
SO4-2 1.463e-02 2.664e-03 -1.835 -2.574 -0.740
MgSO4 7.330e-03 8.562e-03 -2.135 -2.067 0.067
NaSO4- 6.053e-03 4.523e-03 -2.218 -2.345 -0.127
CaSO4 1.083e-03 1.266e-03 -2.965 -2.898 0.067
KSO4- 1.627e-04 1.216e-04 -3.789 -3.915 -0.127
NH4SO4- 4.157e-08 3.106e-08 -7.381 -7.508 -0.127
HSO4- 2.089e-09 1.561e-09 -8.680 -8.807 -0.127
MnSO4 2.021e-10 2.360e-10 -9.695 -9.627 0.067
CaHSO4+ 5.979e-11 4.467e-11 -10.223 -10.350 -0.127
FeSO4+ 1.093e-18 8.167e-19 -17.961 -18.088 -0.127
Fe(SO4)2- 6.372e-20 4.761e-20 -19.196 -19.322 -0.127
FeSO4 4.845e-20 5.660e-20 -19.315 -19.247 0.067
FeHSO4+2 4.228e-26 1.318e-26 -25.374 -25.880 -0.506
FeHSO4+ 3.000e-27 2.242e-27 -26.523 -26.649 -0.127
Si 7.382e-05
H4SiO4 7.110e-05 8.306e-05 -4.148 -4.081 0.067
H3SiO4- 2.720e-06 2.032e-06 -5.565 -5.692 -0.127
H2SiO4-2 7.362e-11 2.294e-11 -10.133 -10.639 -0.506
U(4) 1.034e-21
U(OH)5- 1.034e-21 7.725e-22 -20.985 -21.112 -0.127
U(OH)4 1.652e-25 1.930e-25 -24.782 -24.715 0.067
U+4 0.000e+00 0.000e+00 -46.997 -49.022 -2.025
U(5) 1.622e-18
UO2+ 1.622e-18 1.212e-18 -17.790 -17.916 -0.127
U(6) 1.437e-08
UO2(CO3)3-4 1.255e-08 1.184e-10 -7.901 -9.927 -2.025
UO2(CO3)2-2 1.814e-09 5.653e-10 -8.741 -9.248 -0.506
UO2CO3 7.429e-12 8.678e-12 -11.129 -11.062 0.067
UO2OH+ 3.385e-14 2.530e-14 -13.470 -13.597 -0.127
UO2+2 3.019e-16 9.409e-17 -15.520 -16.026 -0.506
(UO2)2(OH)2+2 1.780e-21 5.547e-22 -20.750 -21.256 -0.506
(UO2)3(OH)5+ 2.908e-23 2.173e-23 -22.536 -22.663 -0.127
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -0.84 -5.20 -4.36 CaSO4
Aragonite 0.61 -7.72 -8.34 CaCO3
Calcite 0.76 -7.72 -8.48 CaCO3
Chalcedony -0.51 -4.06 -3.55 SiO2
Chrysotile 3.36 35.56 32.20 Mg3Si2O5(OH)4
CO2(g) -3.38 -4.85 -1.47 CO2
Dolomite 2.41 -14.68 -17.09 CaMg(CO3)2
Fe(OH)3(a) 0.19 5.08 4.89 Fe(OH)3
Goethite 6.09 5.09 -1.00 FeOOH
Gypsum -0.63 -5.21 -4.58 CaSO4:2H2O
H2(g) -41.22 -44.37 -3.15 H2
H2O(g) -1.52 -0.01 1.51 H2O
Halite -2.50 -0.92 1.58 NaCl
Hausmannite 1.57 62.60 61.03 Mn3O4
Hematite 14.20 10.19 -4.01 Fe2O3
Jarosite-K -7.52 -16.73 -9.21 KFe3(SO4)2(OH)6
Manganite 2.39 27.73 25.34 MnOOH
Melanterite -19.35 -21.56 -2.21 FeSO4:7H2O
NH3(g) -8.84 -7.07 1.77 NH3
O2(g) -0.70 -3.66 -2.96 O2
Pyrochroite -8.08 7.12 15.20 Mn(OH)2
Pyrolusite 6.96 48.34 41.38 MnO2
Quartz -0.08 -4.06 -3.98 SiO2
Rhodochrosite -3.27 -14.40 -11.13 MnCO3
Sepiolite 1.16 16.92 15.76 Mg2Si3O7.5OH:3H2O
Sepiolite(d) -1.74 16.92 18.66 Mg2Si3O7.5OH:3H2O
Siderite -13.13 -24.02 -10.89 FeCO3
SiO2(a) -1.35 -4.06 -2.71 SiO2
Talc 6.04 27.44 21.40 Mg3Si4O10(OH)2
Uraninite -12.67 -16.16 -3.49 UO2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 2.
------------------------------------
-----------
End of run.
-----------
No memory leaks

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reaction lg_SigmaPi X_Arag X_Stront X_Ca_aq X_Sr_aq mol_Misc1 mol_Misc2 mol_Arag mol_Stront
1.0000e-05 -8.3356e+00 9.9996e-01 4.2096e-05 9.9905e-01 9.4867e-04 1.0000e-10 1.0000e-10 6.5428e-06 2.7544e-10
2.0000e-05 -8.3352e+00 9.9992e-01 8.4301e-05 9.9810e-01 1.8967e-03 1.0000e-10 1.0000e-10 1.3083e-05 1.1030e-09
3.0000e-05 -8.3348e+00 9.9987e-01 1.2662e-04 9.9716e-01 2.8440e-03 1.0000e-10 1.0000e-10 1.9622e-05 2.4848e-09
4.0000e-05 -8.3345e+00 9.9983e-01 1.6904e-04 9.9621e-01 3.7906e-03 1.0000e-10 1.0000e-10 2.6159e-05 4.4226e-09
5.0000e-05 -8.3341e+00 9.9979e-01 2.1158e-04 9.9526e-01 4.7366e-03 1.0000e-10 1.0000e-10 3.2693e-05 6.9185e-09
6.0000e-05 -8.3337e+00 9.9975e-01 2.5422e-04 9.9432e-01 5.6819e-03 1.0000e-10 1.0000e-10 3.9225e-05 9.9745e-09
7.0000e-05 -8.3333e+00 9.9970e-01 2.9698e-04 9.9337e-01 6.6265e-03 1.0000e-10 1.0000e-10 4.5755e-05 1.3593e-08
8.0000e-05 -8.3329e+00 9.9966e-01 3.3985e-04 9.9243e-01 7.5705e-03 1.0000e-10 1.0000e-10 5.2283e-05 1.7775e-08
9.0000e-05 -8.3325e+00 9.9962e-01 3.8284e-04 9.9149e-01 8.5137e-03 1.0000e-10 1.0000e-10 5.8809e-05 2.2523e-08
1.0000e-04 -8.3321e+00 9.9957e-01 4.2593e-04 9.9054e-01 9.4563e-03 1.0000e-10 1.0000e-10 6.5333e-05 2.7839e-08
1.1000e-04 -8.3318e+00 9.9953e-01 4.6914e-04 9.8960e-01 1.0398e-02 1.0000e-10 1.0000e-10 7.1855e-05 3.3726e-08
1.2000e-04 -8.3314e+00 9.9949e-01 5.1247e-04 9.8866e-01 1.1340e-02 1.0000e-10 1.0000e-10 7.8374e-05 4.0185e-08
1.3000e-04 -8.3310e+00 9.9944e-01 5.5591e-04 9.8772e-01 1.2280e-02 1.0000e-10 1.0000e-10 8.4891e-05 4.7218e-08
1.4000e-04 -8.3306e+00 9.9940e-01 5.9946e-04 9.8678e-01 1.3220e-02 1.0000e-10 1.0000e-10 9.1407e-05 5.4828e-08
1.5000e-04 -8.3302e+00 9.9936e-01 6.4313e-04 9.8584e-01 1.4159e-02 1.0000e-10 1.0000e-10 9.7920e-05 6.3016e-08
1.6000e-04 -8.3298e+00 9.9931e-01 6.8692e-04 9.8490e-01 1.5098e-02 1.0000e-10 1.0000e-10 1.0443e-04 7.1784e-08
1.7000e-04 -8.3294e+00 9.9927e-01 7.3082e-04 9.8396e-01 1.6036e-02 1.0000e-10 1.0000e-10 1.1094e-04 8.1136e-08
1.8000e-04 -8.3290e+00 9.9923e-01 7.7484e-04 9.8303e-01 1.6973e-02 1.0000e-10 1.0000e-10 1.1745e-04 9.1072e-08
1.9000e-04 -8.3287e+00 9.9918e-01 8.1897e-04 9.8209e-01 1.7909e-02 1.0000e-10 1.0000e-10 1.2395e-04 1.0160e-07
2.0000e-04 -8.3283e+00 9.9914e-01 8.6323e-04 9.8115e-01 1.8845e-02 1.0000e-10 1.0000e-10 1.3045e-04 1.1271e-07
2.1000e-04 -8.3279e+00 9.9909e-01 9.0760e-04 9.8022e-01 1.9780e-02 1.0000e-10 1.0000e-10 1.3695e-04 1.2441e-07
2.2000e-04 -8.3275e+00 9.9905e-01 9.5209e-04 9.7929e-01 2.0715e-02 1.0000e-10 1.0000e-10 1.4345e-04 1.3671e-07
2.3000e-04 -8.3271e+00 9.9900e-01 9.9670e-04 9.7835e-01 2.1649e-02 1.0000e-10 1.0000e-10 1.4995e-04 1.4960e-07
2.4000e-04 -8.3267e+00 9.9896e-01 1.0414e-03 9.7742e-01 2.2582e-02 1.0000e-10 1.0000e-10 1.5644e-04 1.6309e-07
2.5000e-04 -8.3263e+00 9.9891e-01 1.0863e-03 9.7649e-01 2.3514e-02 1.0000e-10 1.0000e-10 1.6293e-04 1.7719e-07
2.6000e-04 -8.3259e+00 9.9887e-01 1.1313e-03 9.7555e-01 2.4446e-02 1.0000e-10 1.0000e-10 1.6942e-04 1.9188e-07
2.7000e-04 -8.3256e+00 9.9882e-01 1.1764e-03 9.7462e-01 2.5377e-02 1.0000e-10 1.0000e-10 1.7591e-04 2.0718e-07
2.8000e-04 -8.3252e+00 9.9878e-01 1.2216e-03 9.7369e-01 2.6308e-02 1.0000e-10 1.0000e-10 1.8240e-04 2.2308e-07
2.9000e-04 -8.3248e+00 9.9873e-01 1.2669e-03 9.7276e-01 2.7238e-02 1.0000e-10 1.0000e-10 1.8888e-04 2.3960e-07
3.0000e-04 -8.3244e+00 9.9869e-01 1.3124e-03 9.7183e-01 2.8167e-02 1.0000e-10 1.0000e-10 1.9536e-04 2.5672e-07
3.1000e-04 -8.3240e+00 9.9864e-01 1.3580e-03 9.7090e-01 2.9095e-02 1.0000e-10 1.0000e-10 2.0184e-04 2.7446e-07
3.2000e-04 -8.3236e+00 9.9860e-01 1.4037e-03 9.6998e-01 3.0023e-02 1.0000e-10 1.0000e-10 2.0832e-04 2.9282e-07
3.3000e-04 -8.3232e+00 9.9855e-01 1.4495e-03 9.6905e-01 3.0950e-02 1.0000e-10 1.0000e-10 2.1479e-04 3.1179e-07
3.4000e-04 -8.3228e+00 9.9850e-01 1.4955e-03 9.6812e-01 3.1877e-02 1.0000e-10 1.0000e-10 2.2126e-04 3.3139e-07
3.5000e-04 -8.3225e+00 9.9846e-01 1.5416e-03 9.6720e-01 3.2802e-02 1.0000e-10 1.0000e-10 2.2773e-04 3.5161e-07
3.6000e-04 -8.3221e+00 9.9841e-01 1.5878e-03 9.6627e-01 3.3727e-02 1.0000e-10 1.0000e-10 2.3420e-04 3.7245e-07
3.7000e-04 -8.3217e+00 9.9837e-01 1.6341e-03 9.6535e-01 3.4652e-02 1.0000e-10 1.0000e-10 2.4067e-04 3.9392e-07
3.8000e-04 -8.3213e+00 9.9832e-01 1.6806e-03 9.6442e-01 3.5576e-02 1.0000e-10 1.0000e-10 2.4713e-04 4.1602e-07
3.9000e-04 -8.3209e+00 9.9827e-01 1.7272e-03 9.6350e-01 3.6499e-02 1.0000e-10 1.0000e-10 2.5359e-04 4.3876e-07
4.0000e-04 -8.3205e+00 9.9823e-01 1.7739e-03 9.6258e-01 3.7421e-02 1.0000e-10 1.0000e-10 2.6005e-04 4.6213e-07
4.1000e-04 -8.3201e+00 9.9818e-01 1.8208e-03 9.6166e-01 3.8343e-02 1.0000e-10 1.0000e-10 2.6651e-04 4.8614e-07
4.2000e-04 -8.3197e+00 9.9813e-01 1.8677e-03 9.6074e-01 3.9264e-02 1.0000e-10 1.0000e-10 2.7297e-04 5.1078e-07
4.3000e-04 -8.3193e+00 9.9809e-01 1.9149e-03 9.5982e-01 4.0184e-02 1.0000e-10 1.0000e-10 2.7942e-04 5.3607e-07
4.4000e-04 -8.3190e+00 9.9804e-01 1.9621e-03 9.5890e-01 4.1104e-02 1.0000e-10 1.0000e-10 2.8587e-04 5.6201e-07
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4.7000e-04 -8.3178e+00 9.9790e-01 2.1046e-03 9.5614e-01 4.3859e-02 1.0000e-10 1.0000e-10 3.0521e-04 6.4371e-07
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4.9000e-04 -8.3170e+00 9.9780e-01 2.2003e-03 9.5431e-01 4.5692e-02 1.0000e-10 1.0000e-10 3.1809e-04 7.0145e-07
5.0000e-04 -8.3166e+00 9.9775e-01 2.2484e-03 9.5339e-01 4.6608e-02 1.0000e-10 1.0000e-10 3.2453e-04 7.3131e-07
5.1000e-04 -8.3162e+00 9.9770e-01 2.2966e-03 9.5248e-01 4.7523e-02 1.0000e-10 1.0000e-10 3.3097e-04 7.6183e-07
5.2000e-04 -8.3159e+00 9.9766e-01 2.3449e-03 9.5156e-01 4.8437e-02 1.0000e-10 1.0000e-10 3.3740e-04 7.9302e-07
5.3000e-04 -8.3155e+00 9.9761e-01 2.3933e-03 9.5065e-01 4.9351e-02 1.0000e-10 1.0000e-10 3.4383e-04 8.2488e-07
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5.5000e-04 -8.3147e+00 9.9751e-01 2.4907e-03 9.4882e-01 5.1176e-02 1.0000e-10 1.0000e-10 3.5669e-04 8.9060e-07
5.6000e-04 -8.3143e+00 9.9746e-01 2.5395e-03 9.4791e-01 5.2088e-02 1.0000e-10 1.0000e-10 3.6311e-04 9.2448e-07
5.7000e-04 -8.3139e+00 9.9741e-01 2.5885e-03 9.4700e-01 5.2999e-02 1.0000e-10 1.0000e-10 3.6954e-04 9.5904e-07
5.8000e-04 -8.3135e+00 9.9736e-01 2.6377e-03 9.4609e-01 5.3909e-02 1.0000e-10 1.0000e-10 3.7596e-04 9.9428e-07
5.9000e-04 -8.3131e+00 9.9731e-01 2.6870e-03 9.4518e-01 5.4819e-02 1.0000e-10 1.0000e-10 3.8237e-04 1.0302e-06
6.0000e-04 -8.3127e+00 9.9726e-01 2.7364e-03 9.4427e-01 5.5728e-02 1.0000e-10 1.0000e-10 3.8879e-04 1.0668e-06
6.1000e-04 -8.3123e+00 9.9721e-01 2.7860e-03 9.4336e-01 5.6636e-02 1.0000e-10 1.0000e-10 3.9520e-04 1.1041e-06
6.2000e-04 -8.3120e+00 9.9716e-01 2.8357e-03 9.4246e-01 5.7544e-02 1.0000e-10 1.0000e-10 4.0162e-04 1.1421e-06
6.3000e-04 -8.3116e+00 9.9711e-01 2.8856e-03 9.4155e-01 5.8451e-02 1.0000e-10 1.0000e-10 4.0803e-04 1.1808e-06
6.4000e-04 -8.3112e+00 9.9706e-01 2.9356e-03 9.4064e-01 5.9357e-02 1.0000e-10 1.0000e-10 4.1443e-04 1.2202e-06
6.5000e-04 -8.3108e+00 9.9701e-01 2.9857e-03 9.3974e-01 6.0263e-02 1.0000e-10 1.0000e-10 4.2084e-04 1.2603e-06
6.6000e-04 -8.3104e+00 9.9696e-01 3.0360e-03 9.3883e-01 6.1167e-02 1.0000e-10 1.0000e-10 4.2724e-04 1.3011e-06
6.7000e-04 -8.3100e+00 9.9691e-01 3.0864e-03 9.3793e-01 6.2072e-02 1.0000e-10 1.0000e-10 4.3364e-04 1.3426e-06
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8.7000e-04 -8.3022e+00 9.9587e-01 4.1270e-03 9.1998e-01 8.0016e-02 1.0000e-10 1.0000e-10 5.6120e-04 2.3257e-06
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8.9000e-04 -8.3014e+00 9.9577e-01 4.2346e-03 9.1820e-01 8.1795e-02 1.0000e-10 1.0000e-10 5.7390e-04 2.4406e-06
9.0000e-04 -8.3010e+00 9.9571e-01 4.2886e-03 9.1732e-01 8.2684e-02 1.0000e-10 1.0000e-10 5.8025e-04 2.4992e-06
9.1000e-04 -8.3006e+00 9.9566e-01 4.3427e-03 9.1643e-01 8.3572e-02 1.0000e-10 1.0000e-10 5.8660e-04 2.5586e-06
9.2000e-04 -8.3002e+00 9.9560e-01 4.3971e-03 9.1554e-01 8.4460e-02 1.0000e-10 1.0000e-10 5.9295e-04 2.6187e-06
9.3000e-04 -8.2999e+00 9.9555e-01 4.4516e-03 9.1465e-01 8.5347e-02 1.0000e-10 1.0000e-10 5.9929e-04 2.6797e-06
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9.5000e-04 -8.2991e+00 9.9544e-01 4.5611e-03 9.1288e-01 8.7118e-02 1.0000e-10 1.0000e-10 6.1197e-04 2.8040e-06
9.6000e-04 -8.2987e+00 9.9538e-01 4.6161e-03 9.1200e-01 8.8003e-02 1.0000e-10 1.0000e-10 6.1831e-04 2.8674e-06
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9.9000e-04 -8.2975e+00 9.9522e-01 4.7821e-03 9.0935e-01 9.0653e-02 1.0000e-10 1.0000e-10 6.3730e-04 3.0623e-06
1.0000e-03 -8.2974e+00 9.8567e-01 1.4329e-02 9.0901e-01 9.0987e-02 6.4175e-04 7.2473e-06 6.3970e-04 9.2997e-06
1.0100e-03 -8.2974e+00 9.7071e-01 2.9286e-02 9.0901e-01 9.0987e-02 6.4009e-04 1.8914e-05 6.3970e-04 1.9300e-05
1.0200e-03 -8.2974e+00 9.5620e-01 4.3796e-02 9.0901e-01 9.0987e-02 6.3842e-04 3.0580e-05 6.3970e-04 2.9300e-05
1.0300e-03 -8.2974e+00 9.4212e-01 5.7879e-02 9.0901e-01 9.0987e-02 6.3675e-04 4.2246e-05 6.3970e-04 3.9300e-05
1.0400e-03 -8.2974e+00 9.2845e-01 7.1552e-02 9.0901e-01 9.0987e-02 6.3509e-04 5.3912e-05 6.3970e-04 4.9300e-05
1.0500e-03 -8.2974e+00 9.1516e-01 8.4835e-02 9.0901e-01 9.0987e-02 6.3342e-04 6.5578e-05 6.3970e-04 5.9300e-05
1.0600e-03 -8.2974e+00 9.0226e-01 9.7743e-02 9.0901e-01 9.0987e-02 6.3176e-04 7.7245e-05 6.3970e-04 6.9300e-05
1.0700e-03 -8.2974e+00 8.8971e-01 1.1029e-01 9.0901e-01 9.0987e-02 6.3009e-04 8.8911e-05 6.3970e-04 7.9300e-05
1.0800e-03 -8.2974e+00 8.7750e-01 1.2250e-01 9.0901e-01 9.0987e-02 6.2842e-04 1.0058e-04 6.3970e-04 8.9300e-05
1.0900e-03 -8.2974e+00 8.6563e-01 1.3437e-01 9.0901e-01 9.0987e-02 6.2676e-04 1.1224e-04 6.3970e-04 9.9300e-05
1.1000e-03 -8.2974e+00 8.5407e-01 1.4593e-01 9.0901e-01 9.0987e-02 6.2509e-04 1.2391e-04 6.3970e-04 1.0930e-04
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1.1300e-03 -8.2974e+00 8.2118e-01 1.7882e-01 9.0901e-01 9.0987e-02 6.2009e-04 1.5891e-04 6.3970e-04 1.3930e-04
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1.1500e-03 -8.2974e+00 8.0063e-01 1.9937e-01 9.0901e-01 9.0987e-02 6.1676e-04 1.8224e-04 6.3970e-04 1.5930e-04
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9.9000e+00 -9.2523e+00 1.0425e-03 9.9896e-01 4.2713e-02 9.5729e-01 1.0000e-10 1.0000e-10 1.0326e-02 9.8953e+00
1.0000e+01 -9.2525e+00 1.0323e-03 9.9897e-01 4.2310e-02 9.5769e-01 1.0000e-10 1.0000e-10 1.0328e-02 9.9953e+00

0
Sun/examples/ex11.log
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Sun/examples/ex11.out
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Sun/examples/ex11adv.sel
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step Na Cl K Ca Pore_vol
-99 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 1.2500e-02
-99 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.2500e-02
-99 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.2500e-02
1 5.2815e-04 1.2000e-03 4.5842e-04 1.0672e-04 3.7500e-02
1 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 3.7500e-02
2 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 6.2500e-02
3 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 8.7500e-02
4 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.1250e-01
5 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.3750e-01
6 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.6250e-01
7 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.8750e-01
8 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 2.1250e-01
9 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 2.3750e-01
10 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 2.6250e-01
11 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 2.8750e-01
12 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 3.1250e-01
13 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 3.3750e-01
14 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 3.6250e-01
15 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 3.8750e-01
16 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 4.1250e-01
17 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 4.3750e-01
18 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 4.6250e-01
19 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 4.8750e-01
20 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 5.1250e-01
21 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 5.3750e-01
22 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 5.6250e-01
23 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 5.8750e-01
24 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 6.1250e-01
25 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 6.3750e-01
26 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 6.6250e-01
27 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 6.8750e-01
28 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 7.1250e-01
29 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 7.3750e-01
30 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 7.6250e-01
31 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 7.8750e-01
32 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 8.1250e-01
33 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 8.3750e-01
34 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 8.6250e-01
35 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 8.8750e-01
36 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 9.1250e-01
37 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 9.3750e-01
38 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 9.6250e-01
39 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 9.8750e-01
40 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.0125e+00
41 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.0375e+00
42 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.0625e+00
43 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.0875e+00
44 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.1125e+00
45 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.1375e+00
46 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.1625e+00
47 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.1875e+00
48 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.2125e+00
49 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.2375e+00
50 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.2625e+00
51 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.2875e+00
52 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.3125e+00
53 1.0000e-03 1.2000e-03 2.0000e-04 0.0000e+00 1.3375e+00
54 9.9998e-04 1.2000e-03 2.0002e-04 0.0000e+00 1.3625e+00
55 9.9993e-04 1.2000e-03 2.0007e-04 0.0000e+00 1.3875e+00
56 9.9969e-04 1.2000e-03 2.0031e-04 0.0000e+00 1.4125e+00
57 9.9860e-04 1.2000e-03 2.0140e-04 0.0000e+00 1.4375e+00
58 9.9376e-04 1.2000e-03 2.0624e-04 0.0000e+00 1.4625e+00
59 9.7266e-04 1.2000e-03 2.2734e-04 0.0000e+00 1.4875e+00
60 8.8947e-04 1.2000e-03 3.1053e-04 0.0000e+00 1.5125e+00
61 6.5396e-04 1.2000e-03 5.4604e-04 0.0000e+00 1.5375e+00
62 3.1876e-04 1.2000e-03 8.8124e-04 0.0000e+00 1.5625e+00
63 1.0663e-04 1.2000e-03 1.0934e-03 0.0000e+00 1.5875e+00
64 2.9829e-05 1.2000e-03 1.1702e-03 0.0000e+00 1.6125e+00
65 7.8763e-06 1.2000e-03 1.1921e-03 1.2216e-27 1.6375e+00
66 2.0460e-06 1.2000e-03 1.1980e-03 1.8112e-25 1.6625e+00
67 5.2878e-07 1.2000e-03 1.1995e-03 2.6557e-23 1.6875e+00
68 1.3629e-07 1.2000e-03 1.1999e-03 3.9376e-21 1.7125e+00
69 3.5021e-08 1.2000e-03 1.2000e-03 5.8912e-19 1.7375e+00
70 8.9558e-09 1.2000e-03 1.2000e-03 8.8181e-17 1.7625e+00
71 2.2719e-09 1.2000e-03 1.2000e-03 1.3080e-14 1.7875e+00
72 5.6835e-10 1.2000e-03 1.2000e-03 1.9126e-12 1.8125e+00
73 1.3869e-10 1.2000e-03 1.2000e-03 2.7576e-10 1.8375e+00
74 3.2281e-11 1.2000e-03 1.1999e-03 3.9374e-08 1.8625e+00
75 6.7673e-12 1.2000e-03 1.1890e-03 5.4946e-06 1.8875e+00
76 8.0510e-13 1.2000e-03 7.0494e-04 2.4753e-04 1.9125e+00
77 2.1968e-14 1.2000e-03 9.6079e-05 5.5196e-04 1.9375e+00
78 4.1771e-16 1.2000e-03 9.1269e-06 5.9544e-04 1.9625e+00
79 7.6748e-18 1.2000e-03 8.3782e-07 5.9958e-04 1.9875e+00
80 1.4057e-19 1.2000e-03 7.6671e-08 5.9996e-04 2.0125e+00
81 2.5740e-21 1.2000e-03 7.0147e-09 6.0000e-04 2.0375e+00
82 4.7052e-23 1.2000e-03 6.4179e-10 6.0000e-04 2.0625e+00
83 8.2642e-25 1.2000e-03 5.8721e-11 6.0000e-04 2.0875e+00
84 0.0000e+00 1.2000e-03 5.3731e-12 6.0000e-04 2.1125e+00
85 0.0000e+00 1.2000e-03 4.9168e-13 6.0000e-04 2.1375e+00
86 0.0000e+00 1.2000e-03 4.4995e-14 6.0000e-04 2.1625e+00
87 0.0000e+00 1.2000e-03 4.1178e-15 6.0000e-04 2.1875e+00
88 0.0000e+00 1.2000e-03 3.7688e-16 6.0000e-04 2.2125e+00
89 0.0000e+00 1.2000e-03 3.4497e-17 6.0000e-04 2.2375e+00
90 0.0000e+00 1.2000e-03 3.1577e-18 6.0000e-04 2.2625e+00
91 0.0000e+00 1.2000e-03 2.8907e-19 6.0000e-04 2.2875e+00
92 0.0000e+00 1.2000e-03 2.6465e-20 6.0000e-04 2.3125e+00
93 0.0000e+00 1.2000e-03 2.4231e-21 6.0000e-04 2.3375e+00
94 0.0000e+00 1.2000e-03 2.2183e-22 6.0000e-04 2.3625e+00
95 0.0000e+00 1.2000e-03 2.0287e-23 6.0000e-04 2.3875e+00
96 0.0000e+00 1.2000e-03 1.8364e-24 6.0000e-04 2.4125e+00
97 0.0000e+00 1.2000e-03 1.5102e-25 6.0000e-04 2.4375e+00
98 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.4625e+00
99 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.4875e+00
100 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.5125e+00
101 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.5375e+00
102 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.5625e+00
103 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.5875e+00
104 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.6125e+00
105 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.6375e+00
106 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.6625e+00
107 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.6875e+00
108 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.7125e+00
109 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.7375e+00
110 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.7625e+00
111 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.7875e+00
112 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.8125e+00
113 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.8375e+00
114 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.8625e+00
115 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.8875e+00
116 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.9125e+00
117 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.9375e+00
118 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.9625e+00
119 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 2.9875e+00
120 0.0000e+00 1.2000e-03 0.0000e+00 6.0000e-04 3.0125e+00

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Sun/examples/ex11trn.sel
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@ -1,125 +0,0 @@
step Na Cl K Ca Pore_vol
-99 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.2500e-02
-99 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.2500e-02
1 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 3.7500e-02
0 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.2500e-02
1 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 3.7500e-02
2 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 6.2500e-02
3 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 8.7500e-02
4 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.1250e-01
5 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.3750e-01
6 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.6250e-01
7 1.0000e-03 0.0000e+00 2.0000e-04 0.0000e+00 1.8750e-01
8 1.0000e-03 3.0997e-22 2.0000e-04 0.0000e+00 2.1250e-01
9 1.0000e-03 1.5009e-17 2.0000e-04 0.0000e+00 2.3750e-01
10 1.0000e-03 6.3378e-15 2.0000e-04 0.0000e+00 2.6250e-01
11 1.0000e-03 4.4948e-13 2.0000e-04 0.0000e+00 2.8750e-01
12 1.0000e-03 1.1487e-11 2.0000e-04 0.0000e+00 3.1250e-01
13 1.0000e-03 1.5022e-10 2.0000e-04 0.0000e+00 3.3750e-01
14 1.0000e-03 1.2225e-09 2.0000e-04 0.0000e+00 3.6250e-01
15 1.0000e-03 6.9925e-09 2.0000e-04 0.0000e+00 3.8750e-01
16 1.0000e-03 3.0480e-08 2.0000e-04 0.0000e+00 4.1250e-01
17 1.0000e-03 1.0717e-07 2.0000e-04 0.0000e+00 4.3750e-01
18 1.0000e-03 3.1679e-07 2.0000e-04 0.0000e+00 4.6250e-01
19 1.0000e-03 8.1192e-07 2.0000e-04 0.0000e+00 4.8750e-01
20 1.0000e-03 1.8478e-06 2.0000e-04 0.0000e+00 5.1250e-01
21 1.0000e-03 3.8042e-06 2.0000e-04 0.0000e+00 5.3750e-01
22 1.0000e-03 7.1918e-06 2.0000e-04 0.0000e+00 5.6250e-01
23 1.0000e-03 1.2635e-05 2.0000e-04 0.0000e+00 5.8750e-01
24 1.0000e-03 2.0834e-05 2.0000e-04 0.0000e+00 6.1250e-01
25 1.0000e-03 3.2507e-05 2.0000e-04 0.0000e+00 6.3750e-01
26 1.0000e-03 4.8325e-05 2.0000e-04 0.0000e+00 6.6250e-01
27 1.0000e-03 6.8844e-05 2.0000e-04 0.0000e+00 6.8750e-01
28 1.0000e-03 9.4449e-05 2.0000e-04 0.0000e+00 7.1250e-01
29 1.0000e-03 1.2532e-04 2.0000e-04 0.0000e+00 7.3750e-01
30 1.0000e-03 1.6140e-04 2.0000e-04 0.0000e+00 7.6250e-01
31 1.0000e-03 2.0242e-04 2.0000e-04 0.0000e+00 7.8750e-01
32 1.0000e-03 2.4790e-04 2.0000e-04 0.0000e+00 8.1250e-01
33 9.9999e-04 2.9719e-04 2.0001e-04 0.0000e+00 8.3750e-01
34 9.9999e-04 3.4951e-04 2.0001e-04 0.0000e+00 8.6250e-01
35 9.9998e-04 4.0403e-04 2.0002e-04 0.0000e+00 8.8750e-01
36 9.9996e-04 4.5987e-04 2.0004e-04 0.0000e+00 9.1250e-01
37 9.9993e-04 5.1616e-04 2.0007e-04 0.0000e+00 9.3750e-01
38 9.9988e-04 5.7209e-04 2.0012e-04 0.0000e+00 9.6250e-01
39 9.9979e-04 6.2694e-04 2.0021e-04 0.0000e+00 9.8750e-01
40 9.9964e-04 6.8006e-04 2.0036e-04 0.0000e+00 1.0125e+00
41 9.9940e-04 7.3093e-04 2.0060e-04 0.0000e+00 1.0375e+00
42 9.9902e-04 7.7913e-04 2.0098e-04 0.0000e+00 1.0625e+00
43 9.9842e-04 8.2437e-04 2.0158e-04 0.0000e+00 1.0875e+00
44 9.9749e-04 8.6644e-04 2.0251e-04 0.0000e+00 1.1125e+00
45 9.9606e-04 9.0523e-04 2.0394e-04 0.0000e+00 1.1375e+00
46 9.9390e-04 9.4071e-04 2.0610e-04 0.0000e+00 1.1625e+00
47 9.9067e-04 9.7294e-04 2.0933e-04 0.0000e+00 1.1875e+00
48 9.8590e-04 1.0020e-03 2.1410e-04 0.0000e+00 1.2125e+00
49 9.7896e-04 1.0281e-03 2.2104e-04 0.0000e+00 1.2375e+00
50 9.6900e-04 1.0513e-03 2.3100e-04 0.0000e+00 1.2625e+00
51 9.5496e-04 1.0718e-03 2.4504e-04 0.0000e+00 1.2875e+00
52 9.3563e-04 1.0899e-03 2.6437e-04 0.0000e+00 1.3125e+00
53 9.0974e-04 1.1058e-03 2.9026e-04 0.0000e+00 1.3375e+00
54 8.7620e-04 1.1196e-03 3.2380e-04 0.0000e+00 1.3625e+00
55 8.3445e-04 1.1316e-03 3.6555e-04 0.0000e+00 1.3875e+00
56 7.8479e-04 1.1420e-03 4.1521e-04 0.0000e+00 1.4125e+00
57 7.2845e-04 1.1510e-03 4.7155e-04 3.5277e-28 1.4375e+00
58 6.6747e-04 1.1587e-03 5.3253e-04 4.2108e-26 1.4625e+00
59 6.0423e-04 1.1652e-03 5.9577e-04 2.1113e-24 1.4875e+00
60 5.4107e-04 1.1708e-03 6.5893e-04 9.1531e-23 1.5125e+00
61 4.7992e-04 1.1756e-03 7.2008e-04 3.5143e-21 1.5375e+00
62 4.2217e-04 1.1796e-03 7.7783e-04 1.2072e-19 1.5625e+00
63 3.6873e-04 1.1830e-03 8.3127e-04 3.6941e-18 1.5875e+00
64 3.2004e-04 1.1859e-03 8.7996e-04 1.0357e-16 1.6125e+00
65 2.7623e-04 1.1883e-03 9.2377e-04 2.6573e-15 1.6375e+00
66 2.3720e-04 1.1903e-03 9.6280e-04 6.2721e-14 1.6625e+00
67 2.0268e-04 1.1920e-03 9.9732e-04 1.4041e-12 1.6875e+00
68 1.7232e-04 1.1934e-03 1.0277e-03 2.9709e-11 1.7125e+00
69 1.4570e-04 1.1945e-03 1.0543e-03 5.8657e-10 1.7375e+00
70 1.2238e-04 1.1955e-03 1.0776e-03 1.1507e-08 1.7625e+00
71 1.0193e-04 1.1963e-03 1.0977e-03 2.0826e-07 1.7875e+00
72 8.3815e-05 1.1970e-03 1.1095e-03 3.3299e-06 1.8125e+00
73 6.6682e-05 1.1975e-03 1.0249e-03 5.4190e-05 1.8375e+00
74 5.0532e-05 1.1980e-03 7.3505e-04 2.0721e-04 1.8625e+00
75 3.8797e-05 1.1983e-03 5.3569e-04 3.1276e-04 1.8875e+00
76 3.0077e-05 1.1986e-03 4.0212e-04 3.8390e-04 1.9125e+00
77 2.3445e-05 1.1989e-03 3.0685e-04 4.3485e-04 1.9375e+00
78 1.8340e-05 1.1991e-03 2.3662e-04 4.7252e-04 1.9625e+00
79 1.4384e-05 1.1993e-03 1.8380e-04 5.0091e-04 1.9875e+00
80 1.1303e-05 1.1994e-03 1.4355e-04 5.2257e-04 2.0125e+00
81 8.8949e-06 1.1995e-03 1.1260e-04 5.3925e-04 2.0375e+00
82 7.0081e-06 1.1996e-03 8.8613e-05 5.5219e-04 2.0625e+00
83 5.5269e-06 1.1997e-03 6.9934e-05 5.6227e-04 2.0875e+00
84 4.3622e-06 1.1997e-03 5.5321e-05 5.7016e-04 2.1125e+00
85 3.4452e-06 1.1998e-03 4.3847e-05 5.7635e-04 2.1375e+00
86 2.7225e-06 1.1998e-03 3.4813e-05 5.8123e-04 2.1625e+00
87 2.1523e-06 1.1999e-03 2.7680e-05 5.8508e-04 2.1875e+00
88 1.7023e-06 1.1999e-03 2.2038e-05 5.8813e-04 2.2125e+00
89 1.3467e-06 1.1999e-03 1.7565e-05 5.9054e-04 2.2375e+00
90 1.0658e-06 1.1999e-03 1.4014e-05 5.9246e-04 2.2625e+00
91 8.4359e-07 1.1999e-03 1.1192e-05 5.9398e-04 2.2875e+00
92 6.6787e-07 1.2000e-03 8.9443e-06 5.9519e-04 2.3125e+00
93 5.2883e-07 1.2000e-03 7.1535e-06 5.9616e-04 2.3375e+00
94 4.1880e-07 1.2000e-03 5.7250e-06 5.9693e-04 2.3625e+00
95 3.3169e-07 1.2000e-03 4.5844e-06 5.9754e-04 2.3875e+00
96 2.6273e-07 1.2000e-03 3.6730e-06 5.9803e-04 2.4125e+00
97 2.0811e-07 1.2000e-03 2.9442e-06 5.9842e-04 2.4375e+00
98 1.6486e-07 1.2000e-03 2.3611e-06 5.9874e-04 2.4625e+00
99 1.3060e-07 1.2000e-03 1.8942e-06 5.9899e-04 2.4875e+00
100 1.0347e-07 1.2000e-03 1.5202e-06 5.9919e-04 2.5125e+00
101 8.1970e-08 1.2000e-03 1.2205e-06 5.9935e-04 2.5375e+00
102 6.4939e-08 1.2000e-03 9.8015e-07 5.9948e-04 2.5625e+00
103 5.1446e-08 1.2000e-03 7.8736e-07 5.9958e-04 2.5875e+00
104 4.0756e-08 1.2000e-03 6.3266e-07 5.9966e-04 2.6125e+00
105 3.2287e-08 1.2000e-03 5.0848e-07 5.9973e-04 2.6375e+00
106 2.5577e-08 1.2000e-03 4.0877e-07 5.9978e-04 2.6625e+00
107 2.0260e-08 1.2000e-03 3.2868e-07 5.9983e-04 2.6875e+00
108 1.6048e-08 1.2000e-03 2.6433e-07 5.9986e-04 2.7125e+00
109 1.2712e-08 1.2000e-03 2.1262e-07 5.9989e-04 2.7375e+00
110 1.0068e-08 1.2000e-03 1.7105e-07 5.9991e-04 2.7625e+00
111 7.9740e-09 1.2000e-03 1.3763e-07 5.9993e-04 2.7875e+00
112 6.3151e-09 1.2000e-03 1.1076e-07 5.9994e-04 2.8125e+00
113 5.0010e-09 1.2000e-03 8.9141e-08 5.9995e-04 2.8375e+00
114 3.9601e-09 1.2000e-03 7.1753e-08 5.9996e-04 2.8625e+00
115 3.1357e-09 1.2000e-03 5.7764e-08 5.9997e-04 2.8875e+00
116 2.4828e-09 1.2000e-03 4.6507e-08 5.9998e-04 2.9125e+00
117 1.9657e-09 1.2000e-03 3.7447e-08 5.9998e-04 2.9375e+00
118 1.5562e-09 1.2000e-03 3.0156e-08 5.9998e-04 2.9625e+00
119 1.2319e-09 1.2000e-03 2.4286e-08 5.9999e-04 2.9875e+00
120 9.7513e-10 1.2000e-03 1.9560e-08 5.9999e-04 3.0125e+00

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Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex12
Output file: ex12.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 12.--Advective and diffusive transport of heat and solutes.
Constant boundary condition at one end, closed at other.
The problem is designed so that temperature should equal Na-conc
(in mmol/kgw) after diffusion.
EXCHANGE_SPECIES
Na+ + X- = NaX
log_k 0.0
gamma 4.0 0.075
H+ + X- = HX
log_k -99.
gamma 9.0 0.0
K+ + X- = KX
log_k 0.0
gamma 3.5 0.015
SOLUTION 0 24.0 mM KNO3
units mol/kgw
temp 0 # Incoming solution 0C
pH 7.0
pe 12.0 O2(g) -0.67
K 24.e-3
N(5) 24.e-3
SOLUTION 1-20 0.001 mM KCl
units mol/kgw
temp 25 # Column is at 25C
pH 7.0
pe 12.0 O2(g) -0.67
K 1e-6
Cl 1e-6
EXCHANGE 1-20
KX 0.048
TRANSPORT # Make column temperature 0C, displace Cl
cells 20
shifts 19
flow_direction forward
bcond flux flux
length 1.0
disp 0.0 # No dispersion
diffc 0.0 # No diffusion
thermal_diffusion 1.0 # No retardation for heat
PRINT
WARNING: Cell-lengths were read for 1 cells. Last value is used till cell 20.
WARNING: Dispersivities were read for 1 cells. Last value is used till cell 20.
reset false
END
SOLUTION 0 Fixed temp 24C, and NaCl conc (first type boundary cond) at inlet
units mol/kgw
temp 24
pH 7.0
pe 12.0 O2(g) -0.67
Na 24.e-3
Cl 24.e-3
SOLUTION 20 Same as soln 0 in cell 20 at closed column end (second type boundary cond)
units mol/kgw
temp 24
pH 7.0
pe 12.0 O2(g) -0.67
Na 24.e-3
Cl 24.e-3
EXCHANGE 20
NaX 0.048
TRANSPORT # Diffuse 24C, NaCl solution from column end
shifts 1
flow_direction diffusion
bcond constant closed
thermal_diffusion 3.0 # heat is retarded equal to Na
diffc 0.3e-9 # m^2/s
timest 1.0e+10 # 317 years, 19 substeps will be used
SELECTED_OUTPUT
file ex12.sel
high_precision true
reset false
distance true
temperature true
USER_PUNCH
heading Na_mmol K_mmol Cl_mmol
10 PUNCH TOT("Na")*1000, TOT("K")*1000, TOT("Cl")*1000
END
No memory leaks

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dist_x temp Na_mmol K_mmol Cl_mmol
-99 2.400000000000e+01 2.400000000000e+01 0.000000000000e+00 2.400000000000e+01
-99 2.400000000000e+01 2.400000000000e+01 0.000000000000e+00 2.400000000000e+01
-99 2.400000000000e+01 2.400000000000e+01 0.000000000000e+00 2.400000000000e+01
0.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
1.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
2.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
3.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
4.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
5.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
6.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
7.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
8.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
9.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
10.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
11.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
12.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
13.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
14.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
15.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
16.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
17.5 0.000000000000e+00 0.000000000000e+00 2.400000000010e+01 0.000000000000e+00
18.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
19.5 2.400000000000e+01 2.400000000000e+01 0.000000000000e+00 2.400000000000e+01
0.5 1.686181418415e+01 1.686181416184e+01 7.138185829939e+00 2.011377529332e+01
1.5 6.421492325960e+00 6.421492342616e+00 1.757850764418e+01 1.294968671951e+01
2.5 1.759908541854e+00 1.759908557221e+00 2.224009143309e+01 7.342808261321e+00
3.5 3.571924631562e-01 3.571924666823e-01 2.364280752813e+01 3.623408283684e+00
4.5 5.490209781370e-02 5.490209803302e-02 2.394509789974e+01 1.538555967129e+00
5.5 6.484238380348e-03 6.484238322345e-03 2.399351576095e+01 5.556625533113e-01
6.5 5.926340095484e-04 5.926339925265e-04 2.399940736587e+01 1.684990632469e-01
7.5 4.190926756604e-05 4.190926525116e-05 2.399995809080e+01 4.224784404205e-02
8.5 2.276345750780e-06 2.276345548554e-06 2.399999772377e+01 8.664946370896e-03
9.5 1.396593677778e-07 1.396593266673e-07 2.399999986046e+01 2.055609847093e-03
10.5 1.138869021831e-06 1.138868368161e-06 2.399999886125e+01 4.374443607427e-03
11.5 2.090811414205e-05 2.090810331638e-05 2.399997909199e+01 2.044715368548e-02
12.5 2.951795282278e-04 2.951793938629e-04 2.399970482061e+01 7.995922685941e-02
13.5 3.221164570742e-03 3.221163321490e-03 2.399677883641e+01 2.567109777341e-01
14.5 2.715473190226e-02 2.715472330367e-02 2.397284527577e+01 6.850286499844e-01
15.5 1.753541123879e-01 1.753540697297e-01 2.382464592812e+01 1.533872870596e+00
16.5 8.525032220200e-01 8.525030769812e-01 2.314749691919e+01 2.902126148041e+00
17.5 3.032149931402e+00 3.032149625513e+00 2.096785036949e+01 4.663139220104e+00
18.5 7.550952821146e+00 7.550952502686e+00 1.644904749357e+01 6.385483516941e+00
19.5 1.235834674495e+01 1.235834658501e+01 1.164165341481e+01 7.468268986482e+00

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Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex12a
Output file: ex12a.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 12a.--Advective and diffusive transport of heat and solutes.
Constant boundary condition at one end, closed at other.
The problem is designed so that temperature should equal Na-conc
(in mmol/kgw) after diffusion. Compares with analytical solution
for 20-cell and 60-cell models.
EXCHANGE_SPECIES
Na+ + X- = NaX
log_k 0.0
gamma 4.0 0.075
H+ + X- = HX
log_k -99.
gamma 9.0 0.0
K+ + X- = KX
log_k 0.0
gamma 3.5 0.015
SOLUTION 0 Fixed temp 24C, and NaCl conc (first type boundary cond) at inlet
units mol/kgw
temp 24
pH 7.0
pe 12.0 O2(g) -0.67
Na 24.e-3
Cl 24.e-3
SOLUTION 1-19 24.0 mM KNO3
units mol/kgw
temp 0 # Incoming solution 0C
pH 7.0
pe 12.0 O2(g) -0.67
K 24.e-3
N(5) 24.e-3
EXCHANGE 1-19
KX 0.048
SOLUTION 20 Same as soln 0 in cell 20 at closed column end (second type boundary cond)
units mol/kgw
temp 24
pH 7.0
pe 12.0 O2(g) -0.67
Na 24.e-3
Cl 24.e-3
EXCHANGE 20
NaX 0.048
PRINT
reset false
END
TRANSPORT # Diffuse 24C, NaCl solution from column end
cells 20
shifts 1
flow_direction diffusion
bcond constant closed
length 1.0
thermal_diffusion 3.0 # Heat is retarded equal to Na
disp 0.0 # No dispersion
diffc 0.3e-9 # m^2/s
timest 1.0e+10 # 317 years, 19 substeps will be used
SELECTED_OUTPUT
WARNING: Cell-lengths were read for 1 cells. Last value is used till cell 20.
WARNING: Dispersivities were read for 1 cells. Last value is used till cell 20.
file ex12a.sel
high_precision true
reset false
distance true
temperature true
USER_PUNCH
heading Na_mmol K_mmol Cl_mmol Cl-analytic Na_analytic
10 PUNCH TOT("Na")*1000, TOT("K")*1000, TOT("Cl")*1000
20 DATA 0.254829592, -0.284496736, 1.421413741, -1.453152027, 1.061405429
30 x = DIST
40 if (x > 8.5 OR SIM_TIME <= 0) THEN END
50 IF (ABS(x MOD 0.5) > 1e-3) OR (TC <= 0) THEN END
60 READ a1, a2, a3, a4, a5
70 REM calculate error in Cl
80 Arg = x / (2*SQRT(3e-10 * SIM_TIME / 1.0))
90 e = 1/(1 + 0.3275911 * Arg)
100 erfc_Cl = (e*(a1+e*(a2+e*(a3+e*(a4+e*a5)))))*EXP(-Arg*Arg)
110 REM calculate error in Na
120 Arg = x / (2*SQRT(3e-10 * SIM_TIME / 3.0))
130 e = 1/(1 + 0.3275911 * Arg)
140 erfc_Na = (e*(a1+e*(a2+e*(a3+e*(a4+e*a5)))))*EXP(-Arg*Arg)
150 REM punch results
160 error_Cl = 0.024 * erfc_Cl - TOT("Cl")
170 error_Na = 0.024 * erfc_Na - TOT("Na")
180 PUNCH error_Cl, error_Na
190 REM store results
200 j = x - 0.5
210 PUT(error_Cl, SIM_NO, j, 1)
220 PUT(error_Na, SIM_NO, j, 2)
500 END
END
SELECTED_OUTPUT
user_punch false
SOLUTION 0 Fixed temp 24C, and NaCl conc (first type boundary cond) at inlet
units mol/kgw
temp 24
pH 7.0
pe 12.0 O2(g) -0.67
Na 24.e-3
Cl 24.e-3
SOLUTION 1-59 24.0 mM KNO3
units mol/kgw
temp 0 # Incoming solution 0C
pH 7.0
pe 12.0 O2(g) -0.67
K 24.e-3
N(5) 24.e-3
EXCHANGE 1-59
KX 0.048
SOLUTION 60 Same as soln 0 in cell 60 at closed column end (second type boundary cond)
units mol/kgw
temp 24
pH 7.0
pe 12.0 O2(g) -0.67
Na 24.e-3
Cl 24.e-3
EXCHANGE 60
NaX 0.048
END
TRANSPORT # Diffuse 24C, NaCl solution from column end
cells 60
shifts 1
flow_direction diffusion
bcond constant closed
thermal_diffusion 3.0 # Heat is retarded equal to Na
disp 0.0 # No dispersion
diffc 0.3e-9 # m^2/s
length .33333333333333333
timest 1.0e+10 # 317 years
punch_cells 1-60
SELECTED_OUTPUT
WARNING: Cell-lengths were read for 1 cells. Last value is used till cell 60.
WARNING: Dispersivities were read for 1 cells. Last value is used till cell 60.
high_precision true
user_punch true
reset false
distance true
temperature true
END
SOLUTION # Initial solution calculation for pure water
PRINT
reset false # Initial solution calculation not printed
user_print true
SELECTED_OUTPUT
high_precision false # Controls precision for USER_PRINT too.
USER_PRINT
10 PRINT " Error in Cl concentration Error in Na concentration"
20 PRINT " ------------------------- -------------------------"
30 PRINT " Distance 20-cell 60-cell 20-cell 60-cell"
40 PRINT " "
50 FOR j = 0 TO 8
60 PRINT j + 0.5, GET(2, j, 1), GET(4, j, 1), GET(2, j, 2), GET(4, j, 2)
70 NEXT j
END
----------------------------------User print-----------------------------------
Error in Cl concentration Error in Na concentration
------------------------- -------------------------
Distance 20-cell 60-cell 20-cell 60-cell
5.0000e-01 4.3817e-06 9.0009e-08 5.0636e-04 3.9397e-05
1.5000e+00 1.7304e-05 1.0407e-06 5.1077e-04 5.5286e-05
2.5000e+00 3.5613e-05 3.2028e-06 9.0486e-05 1.4725e-05
3.5000e+00 4.9599e-05 5.2170e-06 -3.7312e-05 -3.8884e-06
4.5000e+00 5.0063e-05 5.6394e-06 -1.9794e-05 -2.5770e-06
5.5000e+00 3.8208e-05 4.4562e-06 -4.0684e-06 -5.0254e-07
6.5000e+00 2.2627e-05 2.7007e-06 -4.8926e-07 -4.8938e-08
7.5000e+00 1.0547e-05 1.2850e-06 -3.9174e-08 -2.7009e-09
8.5000e+00 3.8231e-06 4.5302e-07 -2.2318e-09 -9.0081e-11
No memory leaks

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dist_x temp Na_mmol K_mmol Cl_mmol Cl-analytic Na_analytic
0.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
1.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
2.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
3.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
4.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
5.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
6.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
7.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
8.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
9.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
10.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
11.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
12.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
13.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
14.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
15.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
16.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
17.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
18.5 0.000000000000e+00 0.000000000000e+00 2.400000000009e+01 0.000000000000e+00
19.5 2.400000000000e+01 2.400000000000e+01 0.000000000000e+00 2.400000000000e+01
0.5 1.686181418415e+01 1.686181419284e+01 7.138185798940e+00 2.011377529332e+01 4.381717721817e-06 5.063555346726e-04
1.5 6.421492325960e+00 6.421492401967e+00 1.757850758482e+01 1.294968671951e+01 1.730376465525e-05 5.107739267532e-04
2.5 1.759908541854e+00 1.759908596887e+00 2.224009139342e+01 7.342808261321e+00 3.561257289983e-05 9.048612448212e-05
3.5 3.571924631562e-01 3.571924817826e-01 2.364280751302e+01 3.623408283684e+00 4.959925523712e-05 -3.731213350966e-05
4.5 5.490209781370e-02 5.490210180416e-02 2.394509789597e+01 1.538555967129e+00 5.006313596727e-05 -1.979378199416e-05
5.5 6.484238380348e-03 6.484238983030e-03 2.399351576028e+01 5.556625533113e-01 3.820767165714e-05 -4.068366980646e-06
6.5 5.926340095484e-04 5.926340766447e-04 2.399940736578e+01 1.684990632469e-01 2.262672987200e-05 -4.892608394194e-07
7.5 4.190926756604e-05 4.190927316640e-05 2.399995809078e+01 4.224784404205e-02 1.054699173423e-05 -3.917411153365e-08
8.5 2.276345750780e-06 2.276346101865e-06 2.399999772376e+01 8.664946370896e-03 3.823149392506e-06 -2.231772077916e-09
9.5 1.396593677778e-07 1.396593921606e-07 2.399999986046e+01 2.055609847093e-03
10.5 1.138869021831e-06 1.138869196840e-06 2.399999886124e+01 4.374443607427e-03
11.5 2.090811414205e-05 2.090811693112e-05 2.399997909197e+01 2.044715368548e-02
12.5 2.951795282278e-04 2.951795617161e-04 2.399970482043e+01 7.995922685941e-02
13.5 3.221164570742e-03 3.221164872772e-03 2.399677883485e+01 2.567109777341e-01
14.5 2.715473190226e-02 2.715473392142e-02 2.397284526515e+01 6.850286499844e-01
15.5 1.753541123879e-01 1.753541220807e-01 2.382464587576e+01 1.533872870596e+00
16.5 8.525032220200e-01 8.525032534626e-01 2.314749674271e+01 2.902126148041e+00
17.5 3.032149931402e+00 3.032149994216e+00 2.096785000078e+01 4.663139220104e+00
18.5 7.550952821146e+00 7.550952899109e+00 1.644904709714e+01 6.385483516941e+00
19.5 1.235834674495e+01 1.235834684370e+01 1.164165315611e+01 7.468268986482e+00
dist_x temp
-99 2.400000000000e+01
-99 0.000000000000e+00
-99 2.400000000000e+01
-99 2.400000000000e+01
dist_x temp Na_mmol K_mmol Cl_mmol Cl-analytic Na_analytic
0.166667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
0.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
0.833333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
1.16667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
1.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
1.83333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
2.16667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
2.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
2.83333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
3.16667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
3.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
3.83333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
4.16667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
4.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
4.83333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
5.16667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
5.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
5.83333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
6.16667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
6.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
6.83333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
7.16667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
7.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
7.83333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
8.16667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
8.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
8.83333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
9.16667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
9.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
9.83333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
10.1667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
10.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
10.8333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
11.1667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
11.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
11.8333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
12.1667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
12.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
12.8333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
13.1667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
13.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
13.8333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
14.1667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
14.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
14.8333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
15.1667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
15.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
15.8333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
16.1667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
16.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
16.8333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
17.1667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
17.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
17.8333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
18.1667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
18.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
18.8333 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
19.1667 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
19.5 0.000000000000e+00 0.000000000000e+00 2.400000000000e+01 0.000000000000e+00
19.8333 2.400000000000e+01 2.400000000000e+01 0.000000000000e+00 2.400000000000e+01
0.166667 2.173421305916e+01 2.173421306343e+01 2.265786933713e+00 2.269804666237e+01
0.5 1.732877230198e+01 1.732877231885e+01 6.671227673618e+00 2.011806700231e+01 9.000873062853e-08 3.939740866218e-05
0.833333 1.328083118787e+01 1.328083122259e+01 1.071916876673e+01 1.760855984610e+01
1.16667 9.764783869793e+00 9.764783923632e+00 1.423521606399e+01 1.521226338251e+01
1.5 6.876979954453e+00 6.876980022636e+00 1.712301996456e+01 1.296594983180e+01 1.040652364160e-06 5.528630608450e-05
1.83333 4.633445178532e+00 4.633445251920e+00 1.936655473578e+01 1.089878644688e+01
2.16667 2.983957613764e+00 2.983957682799e+00 2.101604230602e+01 9.031332911172e+00
2.5 1.835670035272e+00 1.835670093239e+00 2.216432989702e+01 7.375218041863e+00 3.202792358406e-06 1.472462813043e-05
2.83333 1.078309641703e+00 1.078309685856e+00 2.292169030595e+01 5.933464823536e+00
3.16667 6.047271172834e-01 6.047271481610e-01 2.339527284513e+01 4.701369002513e+00
3.5 3.237687663205e-01 3.237687863260e-01 2.367623120832e+01 3.667790505378e+00 5.217033543007e-06 -3.888438053093e-06
3.83333 1.655091653734e-01 1.655091774636e-01 2.383449081836e+01 2.816693047508e+00
4.16667 8.080184009388e-02 8.080184694439e-02 2.391919814987e+01 2.128765884991e+00
4.5 3.768529738011e-02 3.768530103391e-02 2.396231469660e+01 1.582979737206e+00 5.639365889894e-06 -2.576981223905e-06
4.83333 1.679748179371e-02 1.679748363383e-02 2.398320251464e+01 1.157961028529e+00
5.16667 7.158658672534e-03 7.158659549847e-03 2.399284133922e+01 8.331081560779e-01
5.5 2.918406916536e-03 2.918407313331e-03 2.399708159183e+01 5.894139758477e-01 4.456249120743e-06 -5.025353109470e-07
5.83333 1.138704483513e-03 1.138704654056e-03 2.399886129476e+01 4.099947290008e-01
6.16667 4.254614091980e-04 4.254614789566e-04 2.399957453813e+01 2.803535790356e-01
6.5 1.523110828875e-04 1.523111100786e-04 2.399984768864e+01 1.884251292313e-01 2.700663887612e-06 -4.893787285338e-08
6.83333 5.227158932778e-05 5.227159943954e-05 2.399994772825e+01 1.244558376472e-01
7.16667 1.720693829075e-05 1.720694188206e-05 2.399998279298e+01 8.077556918093e-02
7.5 5.436060808742e-06 5.436062028079e-06 2.399999456390e+01 5.150981286307e-02 1.285022913218e-06 -2.700900395322e-09
7.83333 1.649087567417e-06 1.649087963540e-06 2.399999835090e+01 3.227276557119e-02
8.16667 4.806328011003e-07 4.806329243359e-07 2.399999951938e+01 1.987075437176e-02
8.5 1.346545980534e-07 1.346546347973e-07 2.399999986537e+01 1.203507596490e-02 4.530197984976e-07 -9.008061084852e-11
8.83333 3.628418612942e-08 3.628419663780e-08 2.399999996375e+01 7.194421703709e-03
9.16667 9.420115605087e-09 9.420118494085e-09 2.399999999061e+01 4.290208467916e-03
9.5 2.409789753518e-09 2.409790536015e-09 2.399999999763e+01 2.633460429579e-03
9.83333 8.318493065839e-10 8.318495907164e-10 2.399999999921e+01 1.799170182453e-03
10.1667 1.239138622414e-09 1.239139029450e-09 2.399999999880e+01 1.552911248870e-03
10.5 4.450121249069e-09 4.450122620282e-09 2.399999999559e+01 1.804410616828e-03
10.8333 1.697307773631e-08 1.697308267056e-08 2.399999998306e+01 2.583364148394e-03
11.1667 6.262520065472e-08 6.262521780825e-08 2.399999993741e+01 4.033590225456e-03
11.5 2.221760110271e-07 2.221760682136e-07 2.399999977785e+01 6.422343300949e-03
11.8333 7.572168365738e-07 7.572170191795e-07 2.399999924281e+01 1.016200278611e-02
12.1667 2.477714073998e-06 2.477714631994e-06 2.399999752230e+01 1.584124624556e-02
12.5 7.778925375184e-06 7.778927005412e-06 2.399999222108e+01 2.426212581439e-02
12.8333 2.341776426203e-05 2.341776881132e-05 2.399997658222e+01 3.647820852624e-02
13.1667 6.755207229881e-05 6.755208441218e-05 2.399993244787e+01 5.382725013175e-02
13.5 1.865949099352e-04 1.865949406769e-04 2.399981340498e+01 7.795002257855e-02
13.8333 4.931967003130e-04 4.931967745830e-04 2.399950680310e+01 1.107853267574e-01
14.1667 1.246472753669e-03 1.246472924261e-03 2.399875352688e+01 1.545304347559e-01
14.5 3.009977094510e-03 3.009977466523e-03 2.399699002225e+01 2.115568175130e-01
14.8333 6.939537438586e-03 6.939538207639e-03 2.399306046140e+01 2.842735712027e-01
15.1667 1.526331935379e-02 1.526332085840e-02 2.398473667861e+01 3.749358095681e-01
15.5 3.200217915009e-02 3.200218193090e-02 2.396799781737e+01 4.854024361712e-01
15.8333 6.391193399667e-02 6.391193884267e-02 2.393608806026e+01 6.168566584837e-01
16.1667 1.214834631133e-01 1.214834710604e-01 2.387851652783e+01 7.695123116931e-01
16.5 2.196089759550e-01 2.196089881955e-01 2.378039101048e+01 9.423379783552e-01
16.8333 3.772704376914e-01 3.772704553669e-01 2.362272954311e+01 1.132837159798e+00
17.1667 6.154714589941e-01 6.154714828922e-01 2.338452851541e+01 1.336924520486e+00
17.5 9.528239860304e-01 9.528240162733e-01 2.304717598190e+01 1.548934044811e+00
17.8333 1.398887571630e+00 1.398887607499e+00 2.260111239061e+01 1.761784203671e+00
18.1667 1.946511170344e+00 1.946511210371e+00 2.205348878777e+01 1.967308461518e+00
18.5 2.565669345631e+00 2.565669387970e+00 2.143433061028e+01 2.156738468785e+00
18.8333 3.201925616708e+00 3.201925659659e+00 2.079807433877e+01 2.321305007457e+00
19.1667 3.781994216092e+00 3.781994258530e+00 2.021800574010e+01 2.452901809002e+00
19.5 4.226690935644e+00 4.226690977196e+00 1.977330902162e+01 2.544743405451e+00
19.8333 4.468507319433e+00 4.468507360365e+00 1.953149263856e+01 2.591943163049e+00
dist_x temp Na_mmol K_mmol Cl_mmol Cl-analytic Na_analytic
-99 25.000 0.0000e+00 0.0000e+00 0.0000e+00

0
Sun/examples/ex13a.log
View File

310
Sun/examples/ex13a.out
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@ -1,310 +0,0 @@
Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex13a
Output file: ex13a.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 13A.--1 mmol/l NaCl/NO3 enters column with stagnant zones.
Implicit definition of first-order exchange model.
SOLUTION 0 # 1 mmol/l NaCl
units mmol/l
pH 7.0
pe 13.0 O2(g) -0.7
Na 1.0 # Na has Retardation = 2
Cl 1.0 # Cl has Retardation = 1, stagnant exchange
N(5) 1.0 # NO3 is conservative
END
-----
TITLE
-----
Example 13A.--1 mmol/l NaCl/NO3 enters column with stagnant zones.
Implicit definition of first-order exchange model.
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 0.
-----------------------------Solution composition------------------------------
Elements Molality Moles
Cl 1.000e-03 1.000e-03
N(5) 1.000e-03 1.000e-03
Na 1.000e-03 1.000e-03
----------------------------Description of solution----------------------------
pH = 7.000
pe = 13.605 Equilibrium with O2(g)
Activity of water = 1.000
Ionic strength = 1.500e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 4.551e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.000e-03
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -33.33
Iterations = 3
Total H = 1.110124e+02
Total O = 5.550965e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.046e-07 1.001e-07 -6.981 -7.000 -0.019
H+ 1.042e-07 1.000e-07 -6.982 -7.000 -0.018
H2O 5.551e+01 9.999e-01 1.744 -0.000 0.000
Cl 1.000e-03
Cl- 1.000e-03 9.576e-04 -3.000 -3.019 -0.019
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.360 -44.360 0.000
N(5) 1.000e-03
NO3- 1.000e-03 9.573e-04 -3.000 -3.019 -0.019
Na 1.000e-03
Na+ 1.000e-03 9.580e-04 -3.000 -3.019 -0.019
NaOH 6.327e-11 6.329e-11 -10.199 -10.199 0.000
O(0) 4.374e-04
O2 2.187e-04 2.188e-04 -3.660 -3.660 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -41.21 -44.36 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
Halite -7.62 -6.04 1.58 NaCl
O2(g) -0.70 -3.66 -2.96 O2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 2.
------------------------------------
SOLUTION 1-41 # Column with KNO3
units mmol/l
pH 7.0
pe 13.0 O2(g) -0.7
K 1.0
N(5) 1.0
EXCHANGE 1-41
equilibrate 1
X 1.e-3
EXCHANGE_SPECIES # For linear exchange, make KX exch. coeff. equal to NaX
K+ + X- = KX
log_k 0.0
gamma 3.5 0.015
END
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1.
-----------------------------Solution composition------------------------------
Elements Molality Moles
K 1.000e-03 1.000e-03
N(5) 1.000e-03 1.000e-03
----------------------------Description of solution----------------------------
pH = 7.000
pe = 13.605 Equilibrium with O2(g)
Activity of water = 1.000
Ionic strength = 1.000e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 3.351e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -3.351e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 3
Total H = 1.110124e+02
Total O = 5.550965e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.038e-07 1.001e-07 -6.984 -7.000 -0.016
H+ 1.034e-07 1.000e-07 -6.985 -7.000 -0.015
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.360 -44.360 0.000
K 1.000e-03
K+ 1.000e-03 9.649e-04 -3.000 -3.016 -0.016
KOH 3.345e-11 3.346e-11 -10.476 -10.476 0.000
N(5) 1.000e-03
NO3- 1.000e-03 9.647e-04 -3.000 -3.016 -0.016
O(0) 4.375e-04
O2 2.187e-04 2.188e-04 -3.660 -3.660 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -41.21 -44.36 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
O2(g) -0.70 -3.66 -2.96 O2
-------------------------------------------------------
Beginning of initial exchange-composition calculations.
-------------------------------------------------------
Exchange 1.
X 1.000e-03 mol
Equiv- Equivalent Log
Species Moles alents Fraction Gamma
KX 1.000e-03 1.000e-03 1.000e+00 -0.016
-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------
Reaction step 1.
Using solution 1.
Using exchange 1. Exchange assemblage after simulation 2.
-----------------------------Exchange composition------------------------------
X 1.000e-03 mol
Equiv- Equivalent Log
Species Moles alents Fraction Gamma
KX 1.000e-03 1.000e-03 1.000e+00 -0.016
NH4X 6.872e-63 6.872e-63 6.872e-60 -0.016
-----------------------------Solution composition------------------------------
Elements Molality Moles
K 1.000e-03 1.000e-03
N 1.000e-03 1.000e-03
----------------------------Description of solution----------------------------
pH = 7.000 Charge balance
pe = 13.605 Adjusted to redox equilibrium
Activity of water = 1.000
Ionic strength = 1.000e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 3.351e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -3.351e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 0
Total H = 1.110124e+02
Total O = 5.550965e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.038e-07 1.001e-07 -6.984 -7.000 -0.016
H+ 1.034e-07 1.000e-07 -6.985 -7.000 -0.015
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.360 -44.360 0.000
K 1.000e-03
K+ 1.000e-03 9.649e-04 -3.000 -3.016 -0.016
KOH 3.345e-11 3.346e-11 -10.476 -10.476 0.000
N(-3) 0.000e+00
NH4+ 0.000e+00 0.000e+00 -62.763 -62.779 -0.016
NH3 0.000e+00 0.000e+00 -65.023 -65.023 0.000
N(0) 1.994e-19
N2 9.971e-20 9.973e-20 -19.001 -19.001 0.000
N(3) 2.291e-16
NO2- 2.291e-16 2.210e-16 -15.640 -15.656 -0.016
N(5) 1.000e-03
NO3- 1.000e-03 9.647e-04 -3.000 -3.016 -0.016
O(0) 4.375e-04
O2 2.187e-04 2.188e-04 -3.660 -3.660 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -41.21 -44.36 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
N2(g) -15.74 -19.00 -3.26 N2
NH3(g) -66.79 -65.02 1.77 NH3
O2(g) -0.70 -3.66 -2.96 O2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 3.
------------------------------------
TRANSPORT
cells 20
shifts 5
flow_direction forward
timest 3600
bcond flux flux
diffc 0.0
length 0.1
disp 0.015
stagnant 1 6.8e-6 0.3 0.1
PRINT
WARNING: Cell-lengths were read for 1 cells. Last value is used till cell 20.
WARNING: Dispersivities were read for 1 cells. Last value is used till cell 20.
reset false
END
SOLUTION 0 # Original solution reenters
units mmol/l
pH 7.0
pe 13.0 O2(g) -0.7
K 1.0
N(5) 1.0
TRANSPORT
shifts 10
punch_frequency 10
punch_cells 1-20
SELECTED_OUTPUT
file ex13a.sel
reset false
solution
distance true
USER_PUNCH
heading Cl_mmol Na_mmol
10 PUNCH TOT("Cl")*1000, TOT("Na")*1000
END
No memory leaks

42
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@ -1,42 +0,0 @@
soln dist_x Cl_mmol Na_mmol
0 -99 0.0000e+00 0.0000e+00
1 0.05 9.6495e-01 8.8504e-01
2 0.15 9.1812e-01 6.9360e-01
3 0.25 8.4451e-01 4.3288e-01
4 0.35 7.1652e-01 1.9734e-01
5 0.45 4.9952e-01 6.0705e-02
6 0.55 2.4048e-01 1.1785e-02
7 0.65 7.2812e-02 1.4039e-03
8 0.75 1.3132e-02 9.9324e-05
9 0.85 1.2882e-03 3.8318e-06
10 0.95 5.2940e-05 6.2140e-08
11 1.05 0.0000e+00 0.0000e+00
12 1.15 0.0000e+00 0.0000e+00
13 1.25 0.0000e+00 0.0000e+00
14 1.35 0.0000e+00 0.0000e+00
15 1.45 0.0000e+00 0.0000e+00
16 1.55 0.0000e+00 0.0000e+00
17 1.65 0.0000e+00 0.0000e+00
18 1.75 0.0000e+00 0.0000e+00
19 1.85 0.0000e+00 0.0000e+00
20 1.95 0.0000e+00 0.0000e+00
1 0.05 7.5889e-03 2.0250e-02
2 0.15 1.7993e-02 5.0943e-02
3 0.25 3.3135e-02 1.0209e-01
4 0.35 5.3591e-02 1.7480e-01
5 0.45 8.0158e-02 2.5484e-01
6 0.55 1.1396e-01 3.1308e-01
7 0.65 1.5767e-01 3.2277e-01
8 0.75 2.1666e-01 2.7968e-01
9 0.85 2.9573e-01 2.0468e-01
10 0.95 3.8769e-01 1.2726e-01
11 1.05 4.6467e-01 6.7581e-02
12 1.15 4.9243e-01 3.0745e-02
13 1.25 4.5811e-01 1.1988e-02
14 1.35 3.7620e-01 3.9981e-03
15 1.45 2.7323e-01 1.1366e-03
16 1.55 1.7416e-01 2.7440e-04
17 1.65 9.6074e-02 5.6038e-05
18 1.75 4.5211e-02 9.6477e-06
19 1.85 1.7934e-02 1.3954e-06
20 1.95 6.4869e-03 1.7678e-07

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Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex13b
Output file: ex13b.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 13B.--1 mmol/l NaCl/NO3 enters column with stagnant zones.
Explicit definition of first-order exchange factors.
SOLUTION 0 # 1 mmol/l NaCl
units mmol/l
pH 7.0
pe 13.0 O2(g) -0.7
Na 1.0 # Na has Retardation = 2
Cl 1.0 # Cl has Retardation = 1, stagnant exchange
N(5) 1.0 # NO3 is conservative
END
-----
TITLE
-----
Example 13B.--1 mmol/l NaCl/NO3 enters column with stagnant zones.
Explicit definition of first-order exchange factors.
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 0.
-----------------------------Solution composition------------------------------
Elements Molality Moles
Cl 1.000e-03 1.000e-03
N(5) 1.000e-03 1.000e-03
Na 1.000e-03 1.000e-03
----------------------------Description of solution----------------------------
pH = 7.000
pe = 13.605 Equilibrium with O2(g)
Activity of water = 1.000
Ionic strength = 1.500e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 4.551e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.000e-03
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -33.33
Iterations = 3
Total H = 1.110124e+02
Total O = 5.550965e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.046e-07 1.001e-07 -6.981 -7.000 -0.019
H+ 1.042e-07 1.000e-07 -6.982 -7.000 -0.018
H2O 5.551e+01 9.999e-01 1.744 -0.000 0.000
Cl 1.000e-03
Cl- 1.000e-03 9.576e-04 -3.000 -3.019 -0.019
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.360 -44.360 0.000
N(5) 1.000e-03
NO3- 1.000e-03 9.573e-04 -3.000 -3.019 -0.019
Na 1.000e-03
Na+ 1.000e-03 9.580e-04 -3.000 -3.019 -0.019
NaOH 6.327e-11 6.329e-11 -10.199 -10.199 0.000
O(0) 4.374e-04
O2 2.187e-04 2.188e-04 -3.660 -3.660 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -41.21 -44.36 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
Halite -7.62 -6.04 1.58 NaCl
O2(g) -0.70 -3.66 -2.96 O2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 2.
------------------------------------
SOLUTION 1-41 # Column with KNO3
units mmol/l
pH 7.0
pe 13.0 O2(g) -0.7
K 1.0
N(5) 1.0
EXCHANGE 1-41
equilibrate 1
X 1.e-3
EXCHANGE_SPECIES # For linear exchange, make KX exch. coeff. equal to NaX
K+ + X- = KX
log_k 0.0
gamma 3.5 0.015
END
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1.
-----------------------------Solution composition------------------------------
Elements Molality Moles
K 1.000e-03 1.000e-03
N(5) 1.000e-03 1.000e-03
----------------------------Description of solution----------------------------
pH = 7.000
pe = 13.605 Equilibrium with O2(g)
Activity of water = 1.000
Ionic strength = 1.000e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 3.351e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -3.351e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 3
Total H = 1.110124e+02
Total O = 5.550965e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.038e-07 1.001e-07 -6.984 -7.000 -0.016
H+ 1.034e-07 1.000e-07 -6.985 -7.000 -0.015
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.360 -44.360 0.000
K 1.000e-03
K+ 1.000e-03 9.649e-04 -3.000 -3.016 -0.016
KOH 3.345e-11 3.346e-11 -10.476 -10.476 0.000
N(5) 1.000e-03
NO3- 1.000e-03 9.647e-04 -3.000 -3.016 -0.016
O(0) 4.375e-04
O2 2.187e-04 2.188e-04 -3.660 -3.660 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -41.21 -44.36 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
O2(g) -0.70 -3.66 -2.96 O2
-------------------------------------------------------
Beginning of initial exchange-composition calculations.
-------------------------------------------------------
Exchange 1.
X 1.000e-03 mol
Equiv- Equivalent Log
Species Moles alents Fraction Gamma
KX 1.000e-03 1.000e-03 1.000e+00 -0.016
-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------
Reaction step 1.
Using solution 1.
Using exchange 1. Exchange assemblage after simulation 2.
-----------------------------Exchange composition------------------------------
X 1.000e-03 mol
Equiv- Equivalent Log
Species Moles alents Fraction Gamma
KX 1.000e-03 1.000e-03 1.000e+00 -0.016
NH4X 6.872e-63 6.872e-63 6.872e-60 -0.016
-----------------------------Solution composition------------------------------
Elements Molality Moles
K 1.000e-03 1.000e-03
N 1.000e-03 1.000e-03
----------------------------Description of solution----------------------------
pH = 7.000 Charge balance
pe = 13.605 Adjusted to redox equilibrium
Activity of water = 1.000
Ionic strength = 1.000e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 3.351e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -3.351e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 0
Total H = 1.110124e+02
Total O = 5.550965e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.038e-07 1.001e-07 -6.984 -7.000 -0.016
H+ 1.034e-07 1.000e-07 -6.985 -7.000 -0.015
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.360 -44.360 0.000
K 1.000e-03
K+ 1.000e-03 9.649e-04 -3.000 -3.016 -0.016
KOH 3.345e-11 3.346e-11 -10.476 -10.476 0.000
N(-3) 0.000e+00
NH4+ 0.000e+00 0.000e+00 -62.763 -62.779 -0.016
NH3 0.000e+00 0.000e+00 -65.023 -65.023 0.000
N(0) 1.994e-19
N2 9.971e-20 9.973e-20 -19.001 -19.001 0.000
N(3) 2.291e-16
NO2- 2.291e-16 2.210e-16 -15.640 -15.656 -0.016
N(5) 1.000e-03
NO3- 1.000e-03 9.647e-04 -3.000 -3.016 -0.016
O(0) 4.375e-04
O2 2.187e-04 2.188e-04 -3.660 -3.660 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -41.21 -44.36 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
N2(g) -15.74 -19.00 -3.26 N2
NH3(g) -66.79 -65.02 1.77 NH3
O2(g) -0.70 -3.66 -2.96 O2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 3.
------------------------------------
MIX 1
1 .93038
22 .06962
MIX 2
2 .93038
23 .06962
MIX 3
3 .93038
24 .06962
MIX 4
4 .93038
25 .06962
MIX 5
5 .93038
26 .06962
MIX 6
6 .93038
27 .06962
MIX 7
7 .93038
28 .06962
MIX 8
8 .93038
29 .06962
MIX 9
9 .93038
30 .06962
MIX 10
10 .93038
31 .06962
MIX 11
11 .93038
32 .06962
MIX 12
12 .93038
33 .06962
MIX 13
13 .93038
34 .06962
MIX 14
14 .93038
35 .06962
MIX 15
15 .93038
36 .06962
MIX 16
16 .93038
37 .06962
MIX 17
17 .93038
38 .06962
MIX 18
18 .93038
39 .06962
MIX 19
19 .93038
40 .06962
MIX 20
20 .93038
41 .06962
MIX 22
1 .20886
22 .79114
MIX 23
2 .20886
23 .79114
MIX 24
3 .20886
24 .79114
MIX 25
4 .20886
25 .79114
MIX 26
5 .20886
26 .79114
MIX 27
6 .20886
27 .79114
MIX 28
7 .20886
28 .79114
MIX 29
8 .20886
29 .79114
MIX 30
9 .20886
30 .79114
MIX 31
10 .20886
31 .79114
MIX 32
11 .20886
32 .79114
MIX 33
12 .20886
33 .79114
MIX 34
13 .20886
34 .79114
MIX 35
14 .20886
35 .79114
MIX 36
15 .20886
36 .79114
MIX 37
16 .20886
37 .79114
MIX 38
17 .20886
38 .79114
MIX 39
18 .20886
39 .79114
MIX 40
19 .20886
40 .79114
MIX 41
20 .20886
41 .79114
TRANSPORT
cells 20
shifts 5
flow_direction forward
timest 3600
bcond flux flux
diffc 0.0
length 0.1
disp 0.015
stagnant 1
PRINT
WARNING: Cell-lengths were read for 1 cells. Last value is used till cell 20.
WARNING: Dispersivities were read for 1 cells. Last value is used till cell 20.
reset false
END
SOLUTION 0 # Original solution reenters
units mmol/l
pH 7.0
pe 13.0 O2(g) -0.7
K 1.0
N(5) 1.0
TRANSPORT
shifts 10
punch_frequency 10
punch_cells 1-20
SELECTED_OUTPUT
file ex13b.sel
reset false
distance true
solution
USER_PUNCH
heading Cl_mmol Na_mmol
10 PUNCH TOT("Cl")*1000, TOT("Na")*1000
END
No memory leaks

42
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@ -1,42 +0,0 @@
soln dist_x Cl_mmol Na_mmol
0 -99 0.0000e+00 0.0000e+00
1 0.05 9.6495e-01 8.8504e-01
2 0.15 9.1812e-01 6.9360e-01
3 0.25 8.4451e-01 4.3288e-01
4 0.35 7.1652e-01 1.9734e-01
5 0.45 4.9952e-01 6.0705e-02
6 0.55 2.4048e-01 1.1785e-02
7 0.65 7.2813e-02 1.4039e-03
8 0.75 1.3132e-02 9.9324e-05
9 0.85 1.2882e-03 3.8318e-06
10 0.95 5.2941e-05 6.2140e-08
11 1.05 0.0000e+00 0.0000e+00
12 1.15 0.0000e+00 0.0000e+00
13 1.25 0.0000e+00 0.0000e+00
14 1.35 0.0000e+00 0.0000e+00
15 1.45 0.0000e+00 0.0000e+00
16 1.55 0.0000e+00 0.0000e+00
17 1.65 0.0000e+00 0.0000e+00
18 1.75 0.0000e+00 0.0000e+00
19 1.85 0.0000e+00 0.0000e+00
20 1.95 0.0000e+00 0.0000e+00
1 0.05 7.5889e-03 2.0249e-02
2 0.15 1.7993e-02 5.0943e-02
3 0.25 3.3135e-02 1.0209e-01
4 0.35 5.3590e-02 1.7480e-01
5 0.45 8.0158e-02 2.5484e-01
6 0.55 1.1395e-01 3.1308e-01
7 0.65 1.5766e-01 3.2277e-01
8 0.75 2.1666e-01 2.7969e-01
9 0.85 2.9573e-01 2.0468e-01
10 0.95 3.8768e-01 1.2727e-01
11 1.05 4.6467e-01 6.7581e-02
12 1.15 4.9243e-01 3.0745e-02
13 1.25 4.5811e-01 1.1988e-02
14 1.35 3.7620e-01 3.9981e-03
15 1.45 2.7323e-01 1.1366e-03
16 1.55 1.7416e-01 2.7440e-04
17 1.65 9.6075e-02 5.6039e-05
18 1.75 4.5211e-02 9.6477e-06
19 1.85 1.7934e-02 1.3954e-06
20 1.95 6.4870e-03 1.7678e-07

0
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Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex13c
Output file: ex13c.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 13C.--1 mmol/l NaCl/NO3 enters column with stagnant zones.
5 layer stagnant zone with finite differences.
SOLUTION 0 # 1 mmol/l NaCl
units mmol/l
pH 7.0
pe 13.0 O2(g) -0.7
Na 1.0 # Na has Retardation = 2
Cl 1.0 # Cl has Retardation = 1, stagnant exchange
N(5) 1.0 # NO3 is conservative
END
-----
TITLE
-----
Example 13C.--1 mmol/l NaCl/NO3 enters column with stagnant zones.
5 layer stagnant zone with finite differences.
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 0.
-----------------------------Solution composition------------------------------
Elements Molality Moles
Cl 1.000e-03 1.000e-03
N(5) 1.000e-03 1.000e-03
Na 1.000e-03 1.000e-03
----------------------------Description of solution----------------------------
pH = 7.000
pe = 13.605 Equilibrium with O2(g)
Activity of water = 1.000
Ionic strength = 1.500e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 4.551e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.000e-03
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -33.33
Iterations = 3
Total H = 1.110124e+02
Total O = 5.550965e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.046e-07 1.001e-07 -6.981 -7.000 -0.019
H+ 1.042e-07 1.000e-07 -6.982 -7.000 -0.018
H2O 5.551e+01 9.999e-01 1.744 -0.000 0.000
Cl 1.000e-03
Cl- 1.000e-03 9.576e-04 -3.000 -3.019 -0.019
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.360 -44.360 0.000
N(5) 1.000e-03
NO3- 1.000e-03 9.573e-04 -3.000 -3.019 -0.019
Na 1.000e-03
Na+ 1.000e-03 9.580e-04 -3.000 -3.019 -0.019
NaOH 6.327e-11 6.329e-11 -10.199 -10.199 0.000
O(0) 4.374e-04
O2 2.187e-04 2.188e-04 -3.660 -3.660 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -41.21 -44.36 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
Halite -7.62 -6.04 1.58 NaCl
O2(g) -0.70 -3.66 -2.96 O2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 2.
------------------------------------
SOLUTION 1-121 # Column with KNO3
units mmol/l
pH 7.0
pe 13.0 O2(g) -0.7
K 1.0
N(5) 1.0
EXCHANGE 1-121
equilibrate 1
X 1.e-3
EXCHANGE_SPECIES # For linear exchange, make KX exch. coeff. equal to NaX
K+ + X- = KX
log_k 0.0
gamma 3.5 0.015
END
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1.
-----------------------------Solution composition------------------------------
Elements Molality Moles
K 1.000e-03 1.000e-03
N(5) 1.000e-03 1.000e-03
----------------------------Description of solution----------------------------
pH = 7.000
pe = 13.605 Equilibrium with O2(g)
Activity of water = 1.000
Ionic strength = 1.000e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 3.351e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -3.351e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 3
Total H = 1.110124e+02
Total O = 5.550965e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.038e-07 1.001e-07 -6.984 -7.000 -0.016
H+ 1.034e-07 1.000e-07 -6.985 -7.000 -0.015
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.360 -44.360 0.000
K 1.000e-03
K+ 1.000e-03 9.649e-04 -3.000 -3.016 -0.016
KOH 3.345e-11 3.346e-11 -10.476 -10.476 0.000
N(5) 1.000e-03
NO3- 1.000e-03 9.647e-04 -3.000 -3.016 -0.016
O(0) 4.375e-04
O2 2.187e-04 2.188e-04 -3.660 -3.660 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -41.21 -44.36 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
O2(g) -0.70 -3.66 -2.96 O2
-------------------------------------------------------
Beginning of initial exchange-composition calculations.
-------------------------------------------------------
Exchange 1.
X 1.000e-03 mol
Equiv- Equivalent Log
Species Moles alents Fraction Gamma
KX 1.000e-03 1.000e-03 1.000e+00 -0.016
-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------
Reaction step 1.
Using solution 1.
Using exchange 1. Exchange assemblage after simulation 2.
-----------------------------Exchange composition------------------------------
X 1.000e-03 mol
Equiv- Equivalent Log
Species Moles alents Fraction Gamma
KX 1.000e-03 1.000e-03 1.000e+00 -0.016
NH4X 6.872e-63 6.872e-63 6.872e-60 -0.016
-----------------------------Solution composition------------------------------
Elements Molality Moles
K 1.000e-03 1.000e-03
N 1.000e-03 1.000e-03
----------------------------Description of solution----------------------------
pH = 7.000 Charge balance
pe = 13.605 Adjusted to redox equilibrium
Activity of water = 1.000
Ionic strength = 1.000e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 3.351e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -3.351e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 0
Total H = 1.110124e+02
Total O = 5.550965e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.038e-07 1.001e-07 -6.984 -7.000 -0.016
H+ 1.034e-07 1.000e-07 -6.985 -7.000 -0.015
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.360 -44.360 0.000
K 1.000e-03
K+ 1.000e-03 9.649e-04 -3.000 -3.016 -0.016
KOH 3.345e-11 3.346e-11 -10.476 -10.476 0.000
N(-3) 0.000e+00
NH4+ 0.000e+00 0.000e+00 -62.763 -62.779 -0.016
NH3 0.000e+00 0.000e+00 -65.023 -65.023 0.000
N(0) 1.994e-19
N2 9.971e-20 9.973e-20 -19.001 -19.001 0.000
N(3) 2.291e-16
NO2- 2.291e-16 2.210e-16 -15.640 -15.656 -0.016
N(5) 1.000e-03
NO3- 1.000e-03 9.647e-04 -3.000 -3.016 -0.016
O(0) 4.375e-04
O2 2.187e-04 2.188e-04 -3.660 -3.660 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -41.21 -44.36 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
N2(g) -15.74 -19.00 -3.26 N2
NH3(g) -66.79 -65.02 1.77 NH3
O2(g) -0.70 -3.66 -2.96 O2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 3.
------------------------------------
MIX 1
1 0.90712
22 0.09288
MIX 22
1 0.57098
22 0.21656
42 0.21246
MIX 42
22 0.35027
42 0.45270
62 0.19703
MIX 62
42 0.38368
62 0.44579
82 0.17053
MIX 82
62 0.46286
82 0.42143
102 0.11571
MIX 102
82 0.81000
102 0.19000
MIX 2
2 0.90712
23 0.09288
MIX 23
2 0.57098
23 0.21656
43 0.21246
MIX 43
23 0.35027
43 0.45270
63 0.19703
MIX 63
43 0.38368
63 0.44579
83 0.17053
MIX 83
63 0.46286
83 0.42143
103 0.11571
MIX 103
83 0.81000
103 0.19000
MIX 3
3 0.90712
24 0.09288
MIX 24
3 0.57098
24 0.21656
44 0.21246
MIX 44
24 0.35027
44 0.45270
64 0.19703
MIX 64
44 0.38368
64 0.44579
84 0.17053
MIX 84
64 0.46286
84 0.42143
104 0.11571
MIX 104
84 0.81000
104 0.19000
MIX 4
4 0.90712
25 0.09288
MIX 25
4 0.57098
25 0.21656
45 0.21246
MIX 45
25 0.35027
45 0.45270
65 0.19703
MIX 65
45 0.38368
65 0.44579
85 0.17053
MIX 85
65 0.46286
85 0.42143
105 0.11571
MIX 105
85 0.81000
105 0.19000
MIX 5
5 0.90712
26 0.09288
MIX 26
5 0.57098
26 0.21656
46 0.21246
MIX 46
26 0.35027
46 0.45270
66 0.19703
MIX 66
46 0.38368
66 0.44579
86 0.17053
MIX 86
66 0.46286
86 0.42143
106 0.11571
MIX 106
86 0.81000
106 0.19000
MIX 6
6 0.90712
27 0.09288
MIX 27
6 0.57098
27 0.21656
47 0.21246
MIX 47
27 0.35027
47 0.45270
67 0.19703
MIX 67
47 0.38368
67 0.44579
87 0.17053
MIX 87
67 0.46286
87 0.42143
107 0.11571
MIX 107
87 0.81000
107 0.19000
MIX 7
7 0.90712
28 0.09288
MIX 28
7 0.57098
28 0.21656
48 0.21246
MIX 48
28 0.35027
48 0.45270
68 0.19703
MIX 68
48 0.38368
68 0.44579
88 0.17053
MIX 88
68 0.46286
88 0.42143
108 0.11571
MIX 108
88 0.81000
108 0.19000
MIX 8
8 0.90712
29 0.09288
MIX 29
8 0.57098
29 0.21656
49 0.21246
MIX 49
29 0.35027
49 0.45270
69 0.19703
MIX 69
49 0.38368
69 0.44579
89 0.17053
MIX 89
69 0.46286
89 0.42143
109 0.11571
MIX 109
89 0.81000
109 0.19000
MIX 9
9 0.90712
30 0.09288
MIX 30
9 0.57098
30 0.21656
50 0.21246
MIX 50
30 0.35027
50 0.45270
70 0.19703
MIX 70
50 0.38368
70 0.44579
90 0.17053
MIX 90
70 0.46286
90 0.42143
110 0.11571
MIX 110
90 0.81000
110 0.19000
MIX 10
10 0.90712
31 0.09288
MIX 31
10 0.57098
31 0.21656
51 0.21246
MIX 51
31 0.35027
51 0.45270
71 0.19703
MIX 71
51 0.38368
71 0.44579
91 0.17053
MIX 91
71 0.46286
91 0.42143
111 0.11571
MIX 111
91 0.81000
111 0.19000
MIX 11
11 0.90712
32 0.09288
MIX 32
11 0.57098
32 0.21656
52 0.21246
MIX 52
32 0.35027
52 0.45270
72 0.19703
MIX 72
52 0.38368
72 0.44579
92 0.17053
MIX 92
72 0.46286
92 0.42143
112 0.11571
MIX 112
92 0.81000
112 0.19000
MIX 12
12 0.90712
33 0.09288
MIX 33
12 0.57098
33 0.21656
53 0.21246
MIX 53
33 0.35027
53 0.45270
73 0.19703
MIX 73
53 0.38368
73 0.44579
93 0.17053
MIX 93
73 0.46286
93 0.42143
113 0.11571
MIX 113
93 0.81000
113 0.19000
MIX 13
13 0.90712
34 0.09288
MIX 34
13 0.57098
34 0.21656
54 0.21246
MIX 54
34 0.35027
54 0.45270
74 0.19703
MIX 74
54 0.38368
74 0.44579
94 0.17053
MIX 94
74 0.46286
94 0.42143
114 0.11571
MIX 114
94 0.81000
114 0.19000
MIX 14
14 0.90712
35 0.09288
MIX 35
14 0.57098
35 0.21656
55 0.21246
MIX 55
35 0.35027
55 0.45270
75 0.19703
MIX 75
55 0.38368
75 0.44579
95 0.17053
MIX 95
75 0.46286
95 0.42143
115 0.11571
MIX 115
95 0.81000
115 0.19000
MIX 15
15 0.90712
36 0.09288
MIX 36
15 0.57098
36 0.21656
56 0.21246
MIX 56
36 0.35027
56 0.45270
76 0.19703
MIX 76
56 0.38368
76 0.44579
96 0.17053
MIX 96
76 0.46286
96 0.42143
116 0.11571
MIX 116
96 0.81000
116 0.19000
MIX 16
16 0.90712
37 0.09288
MIX 37
16 0.57098
37 0.21656
57 0.21246
MIX 57
37 0.35027
57 0.45270
77 0.19703
MIX 77
57 0.38368
77 0.44579
97 0.17053
MIX 97
77 0.46286
97 0.42143
117 0.11571
MIX 117
97 0.81000
117 0.19000
MIX 17
17 0.90712
38 0.09288
MIX 38
17 0.57098
38 0.21656
58 0.21246
MIX 58
38 0.35027
58 0.45270
78 0.19703
MIX 78
58 0.38368
78 0.44579
98 0.17053
MIX 98
78 0.46286
98 0.42143
118 0.11571
MIX 118
98 0.81000
118 0.19000
MIX 18
18 0.90712
39 0.09288
MIX 39
18 0.57098
39 0.21656
59 0.21246
MIX 59
39 0.35027
59 0.45270
79 0.19703
MIX 79
59 0.38368
79 0.44579
99 0.17053
MIX 99
79 0.46286
99 0.42143
119 0.11571
MIX 119
99 0.81000
119 0.19000
MIX 19
19 0.90712
40 0.09288
MIX 40
19 0.57098
40 0.21656
60 0.21246
MIX 60
40 0.35027
60 0.45270
80 0.19703
MIX 80
60 0.38368
80 0.44579
100 0.17053
MIX 100
80 0.46286
100 0.42143
120 0.11571
MIX 120
100 0.81000
120 0.19000
MIX 20
20 0.90712
41 0.09288
MIX 41
20 0.57098
41 0.21656
61 0.21246
MIX 61
41 0.35027
61 0.45270
81 0.19703
MIX 81
61 0.38368
81 0.44579
101 0.17053
MIX 101
81 0.46286
101 0.42143
121 0.11571
MIX 121
101 0.81000
121 0.19000
TRANSPORT
cells 20
shifts 5
flow_direction forward
timest 3600
tempr 3.0
bcond flux flux
diffc 0.0
length 0.10
disp 0.015
stagnant 5
PRINT
WARNING: Cell-lengths were read for 1 cells. Last value is used till cell 20.
WARNING: Dispersivities were read for 1 cells. Last value is used till cell 20.
reset false
END
SOLUTION 0 # Original solution reenters
units mmol/l
pH 7.0
pe 13.0 O2(g) -0.7
K 1.0
N(5) 1.0
TRANSPORT
shifts 10
punch_frequency 10
punch_cells 1-20
SELECTED_OUTPUT
file ex13c.sel
reset false
solution
distance true
USER_PUNCH
heading Cl_mmol Na_mmol
10 PUNCH TOT("Cl")*1000, TOT("Na")*1000
END
No memory leaks

42
Sun/examples/ex13c.sel
View File

@ -1,42 +0,0 @@
soln dist_x Cl_mmol Na_mmol
0 -99 0.0000e+00 0.0000e+00
1 0.05 9.7683e-01 8.8829e-01
2 0.15 9.4255e-01 6.9066e-01
3 0.25 8.7253e-01 4.2503e-01
4 0.35 7.2600e-01 1.9091e-01
5 0.45 4.8246e-01 5.8021e-02
6 0.55 2.2239e-01 1.1177e-02
7 0.65 6.5489e-02 1.3256e-03
8 0.75 1.1639e-02 9.3569e-05
9 0.85 1.1350e-03 3.6065e-06
10 0.95 4.6646e-05 5.8485e-08
11 1.05 0.0000e+00 0.0000e+00
12 1.15 0.0000e+00 0.0000e+00
13 1.25 0.0000e+00 0.0000e+00
14 1.35 0.0000e+00 0.0000e+00
15 1.45 0.0000e+00 0.0000e+00
16 1.55 0.0000e+00 0.0000e+00
17 1.65 0.0000e+00 0.0000e+00
18 1.75 0.0000e+00 0.0000e+00
19 1.85 0.0000e+00 0.0000e+00
20 1.95 0.0000e+00 0.0000e+00
1 0.05 4.7101e-03 1.6916e-02
2 0.15 1.0234e-02 4.9729e-02
3 0.25 1.8109e-02 1.0883e-01
4 0.35 2.9565e-02 1.9194e-01
5 0.45 4.7408e-02 2.7841e-01
6 0.55 7.7191e-02 3.3492e-01
7 0.65 1.2832e-01 3.3632e-01
8 0.75 2.1109e-01 2.8375e-01
9 0.85 3.2572e-01 2.0251e-01
10 0.95 4.4908e-01 1.2304e-01
11 1.05 5.3819e-01 6.3977e-02
12 1.15 5.5716e-01 2.8554e-02
13 1.25 5.0158e-01 1.0943e-02
14 1.35 3.9581e-01 3.5935e-03
15 1.45 2.7424e-01 1.0078e-03
16 1.55 1.6586e-01 2.4047e-04
17 1.65 8.6688e-02 4.8621e-05
18 1.75 3.8743e-02 8.3007e-06
19 1.85 1.4669e-02 1.1922e-06
20 1.95 5.0940e-03 1.5016e-07

0
Sun/examples/ex14.log
View File

3000
Sun/examples/ex14.out
View File

File diff suppressed because it is too large Load Diff

202
Sun/examples/ex14.sel
View File

@ -1,202 +0,0 @@
step m_Ca m_Mg m_Na umol_As pH
1 4.6428e-01 1.6167e-01 5.4020e+00 5.0000e-02 5.3496e+00
1 5.2071e-04 3.6797e-04 1.0345e-01 2.9703e-04 7.0358e+00
2 4.3418e-05 3.0073e-05 2.7681e-02 1.4274e-02 8.4251e+00
3 1.6723e-05 1.0553e-05 1.5102e-02 1.7369e-01 9.0861e+00
4 1.3810e-05 8.4300e-06 1.2580e-02 3.4749e-01 9.2687e+00
5 1.3241e-05 8.0170e-06 1.1705e-02 4.2057e-01 9.3189e+00
6 1.3253e-05 8.0279e-06 1.1293e-02 4.3148e-01 9.3249e+00
7 1.3481e-05 8.1962e-06 1.1055e-02 4.1548e-01 9.3142e+00
8 1.3805e-05 8.4346e-06 1.0889e-02 3.9004e-01 9.2967e+00
9 1.4178e-05 8.7091e-06 1.0758e-02 3.6247e-01 9.2767e+00
10 1.4581e-05 9.0053e-06 1.0645e-02 3.3557e-01 9.2558e+00
11 1.5006e-05 9.3176e-06 1.0542e-02 3.1029e-01 9.2348e+00
12 1.5449e-05 9.6438e-06 1.0447e-02 2.8686e-01 9.2138e+00
13 1.5911e-05 9.9834e-06 1.0358e-02 2.6525e-01 9.1929e+00
14 1.6392e-05 1.0337e-05 1.0274e-02 2.4534e-01 9.1722e+00
15 1.6892e-05 1.0704e-05 1.0195e-02 2.2698e-01 9.1517e+00
16 1.7412e-05 1.1087e-05 1.0119e-02 2.1004e-01 9.1314e+00
17 1.7954e-05 1.1485e-05 1.0047e-02 1.9440e-01 9.1111e+00
18 1.8519e-05 1.1901e-05 9.9787e-03 1.7994e-01 9.0910e+00
19 1.9109e-05 1.2335e-05 9.9131e-03 1.6656e-01 9.0710e+00
20 1.9725e-05 1.2787e-05 9.8504e-03 1.5418e-01 9.0510e+00
21 2.0368e-05 1.3260e-05 9.7904e-03 1.4270e-01 9.0311e+00
22 2.1041e-05 1.3755e-05 9.7328e-03 1.3206e-01 9.0112e+00
23 2.1745e-05 1.4273e-05 9.6775e-03 1.2220e-01 8.9913e+00
24 2.2482e-05 1.4815e-05 9.6243e-03 1.1304e-01 8.9714e+00
25 2.3254e-05 1.5383e-05 9.5731e-03 1.0454e-01 8.9515e+00
26 2.4064e-05 1.5978e-05 9.5238e-03 9.6657e-02 8.9316e+00
27 2.4914e-05 1.6603e-05 9.4761e-03 8.9334e-02 8.9116e+00
28 2.5807e-05 1.7260e-05 9.4301e-03 8.2534e-02 8.8916e+00
29 2.6745e-05 1.7950e-05 9.3855e-03 7.6219e-02 8.8715e+00
30 2.7732e-05 1.8675e-05 9.3423e-03 7.0356e-02 8.8514e+00
31 2.8770e-05 1.9439e-05 9.3004e-03 6.4912e-02 8.8312e+00
32 2.9863e-05 2.0243e-05 9.2597e-03 5.9857e-02 8.8109e+00
33 3.1015e-05 2.1090e-05 9.2200e-03 5.5166e-02 8.7905e+00
34 3.2230e-05 2.1983e-05 9.1814e-03 5.0812e-02 8.7699e+00
35 3.3513e-05 2.2926e-05 9.1436e-03 4.6773e-02 8.7493e+00
36 3.4867e-05 2.3922e-05 9.1067e-03 4.3028e-02 8.7285e+00
37 3.6299e-05 2.4975e-05 9.0705e-03 3.9555e-02 8.7076e+00
38 3.7813e-05 2.6089e-05 9.0350e-03 3.6337e-02 8.6865e+00
39 3.9416e-05 2.7267e-05 9.0000e-03 3.3356e-02 8.6653e+00
40 4.1113e-05 2.8516e-05 8.9656e-03 3.0597e-02 8.6439e+00
41 4.2913e-05 2.9840e-05 8.9315e-03 2.8043e-02 8.6224e+00
42 4.4823e-05 3.1244e-05 8.8978e-03 2.5682e-02 8.6006e+00
43 4.6851e-05 3.2736e-05 8.8643e-03 2.3500e-02 8.5787e+00
44 4.9006e-05 3.4321e-05 8.8310e-03 2.1485e-02 8.5565e+00
45 5.1298e-05 3.6006e-05 8.7977e-03 1.9626e-02 8.5342e+00
46 5.3738e-05 3.7800e-05 8.7644e-03 1.7911e-02 8.5116e+00
47 5.6337e-05 3.9712e-05 8.7309e-03 1.6331e-02 8.4889e+00
48 5.9107e-05 4.1749e-05 8.6973e-03 1.4877e-02 8.4658e+00
49 6.2064e-05 4.3924e-05 8.6633e-03 1.3539e-02 8.4426e+00
50 6.5221e-05 4.6246e-05 8.6288e-03 1.2309e-02 8.4191e+00
51 6.8596e-05 4.8728e-05 8.5938e-03 1.1181e-02 8.3954e+00
52 7.2206e-05 5.1383e-05 8.5581e-03 1.0146e-02 8.3714e+00
53 7.6071e-05 5.4225e-05 8.5216e-03 9.1972e-03 8.3471e+00
54 8.0212e-05 5.7271e-05 8.4840e-03 8.3294e-03 8.3226e+00
55 8.4653e-05 6.0537e-05 8.4454e-03 7.5361e-03 8.2978e+00
56 8.9419e-05 6.4042e-05 8.4055e-03 6.8118e-03 8.2727e+00
57 9.4538e-05 6.7807e-05 8.3641e-03 6.1514e-03 8.2473e+00
58 1.0004e-04 7.1853e-05 8.3211e-03 5.5498e-03 8.2217e+00
59 1.0596e-04 7.6206e-05 8.2762e-03 5.0027e-03 8.1958e+00
60 1.1233e-04 8.0892e-05 8.2293e-03 4.5057e-03 8.1696e+00
61 1.1919e-04 8.5939e-05 8.1800e-03 4.0548e-03 8.1431e+00
62 1.2659e-04 9.1378e-05 8.1283e-03 3.6464e-03 8.1164e+00
63 1.3456e-04 9.7244e-05 8.0737e-03 3.2769e-03 8.0893e+00
64 1.4317e-04 1.0357e-04 8.0161e-03 2.9432e-03 8.0621e+00
65 1.5246e-04 1.1040e-04 7.9550e-03 2.6421e-03 8.0345e+00
66 1.6249e-04 1.1778e-04 7.8904e-03 2.3710e-03 8.0067e+00
67 1.7301e-04 1.2608e-04 7.8205e-03 2.1257e-03 7.9786e+00
68 1.8432e-04 1.3516e-04 7.7465e-03 1.9049e-03 7.9501e+00
69 1.9654e-04 1.4497e-04 7.6681e-03 1.7071e-03 7.9214e+00
70 2.0974e-04 1.5559e-04 7.5847e-03 1.5302e-03 7.8925e+00
71 2.2397e-04 1.6707e-04 7.4960e-03 1.3724e-03 7.8636e+00
72 2.3933e-04 1.7947e-04 7.4015e-03 1.2317e-03 7.8345e+00
73 2.5587e-04 1.9285e-04 7.3009e-03 1.1064e-03 7.8054e+00
74 2.7370e-04 2.0729e-04 7.1938e-03 9.9507e-04 7.7763e+00
75 2.9288e-04 2.2286e-04 7.0799e-03 8.9618e-04 7.7472e+00
76 3.1349e-04 2.3961e-04 6.9590e-03 8.0843e-04 7.7182e+00
77 3.3561e-04 2.5763e-04 6.8306e-03 7.3066e-04 7.6893e+00
78 3.5933e-04 2.7696e-04 6.6948e-03 6.6179e-04 7.6606e+00
79 3.8469e-04 2.9767e-04 6.5512e-03 6.0086e-04 7.6321e+00
80 4.1177e-04 3.1980e-04 6.3998e-03 5.4698e-04 7.6039e+00
81 4.4060e-04 3.4340e-04 6.2406e-03 4.9938e-04 7.5760e+00
82 4.7122e-04 3.6849e-04 6.0737e-03 4.5735e-04 7.5485e+00
83 5.0365e-04 3.9509e-04 5.8993e-03 4.2027e-04 7.5215e+00
84 5.3788e-04 4.2320e-04 5.7176e-03 3.8756e-04 7.4950e+00
85 5.7386e-04 4.5277e-04 5.5290e-03 3.5874e-04 7.4691e+00
86 6.1156e-04 4.8377e-04 5.3342e-03 3.3335e-04 7.4438e+00
87 6.5087e-04 5.1613e-04 5.1337e-03 3.1101e-04 7.4193e+00
88 6.9168e-04 5.4973e-04 4.9284e-03 2.9135e-04 7.3955e+00
89 7.3384e-04 5.8447e-04 4.7190e-03 2.7407e-04 7.3726e+00
90 7.7716e-04 6.2017e-04 4.5066e-03 2.5890e-04 7.3505e+00
91 8.2146e-04 6.5669e-04 4.2923e-03 2.4559e-04 7.3293e+00
92 8.6649e-04 6.9381e-04 4.0771e-03 2.3392e-04 7.3090e+00
93 9.1201e-04 7.3133e-04 3.8623e-03 2.2372e-04 7.2897e+00
94 9.5775e-04 7.6903e-04 3.6490e-03 2.1480e-04 7.2714e+00
95 1.0035e-03 8.0669e-04 3.4384e-03 2.0702e-04 7.2541e+00
96 1.0489e-03 8.4407e-04 3.2315e-03 2.0024e-04 7.2377e+00
97 1.0937e-03 8.8096e-04 3.0295e-03 1.9436e-04 7.2223e+00
98 1.1377e-03 9.1715e-04 2.8333e-03 1.8926e-04 7.2079e+00
99 1.1807e-03 9.5246e-04 2.6436e-03 1.8485e-04 7.1945e+00
100 1.2224e-03 9.8670e-04 2.4613e-03 1.8105e-04 7.1819e+00
101 1.2628e-03 1.0197e-03 2.2869e-03 1.7780e-04 7.1703e+00
102 1.3015e-03 1.0514e-03 2.1208e-03 1.7501e-04 7.1595e+00
103 1.3386e-03 1.0817e-03 1.9634e-03 1.7264e-04 7.1495e+00
104 1.3740e-03 1.1105e-03 1.8148e-03 1.7063e-04 7.1403e+00
105 1.4074e-03 1.1377e-03 1.6752e-03 1.6893e-04 7.1318e+00
106 1.4391e-03 1.1633e-03 1.5444e-03 1.6752e-04 7.1239e+00
107 1.4689e-03 1.1874e-03 1.4225e-03 1.6634e-04 7.1168e+00
108 1.4968e-03 1.2099e-03 1.3090e-03 1.6537e-04 7.1102e+00
109 1.5229e-03 1.2309e-03 1.2038e-03 1.6458e-04 7.1042e+00
110 1.5472e-03 1.2503e-03 1.1066e-03 1.6394e-04 7.0987e+00
111 1.5699e-03 1.2683e-03 1.0170e-03 1.6344e-04 7.0937e+00
112 1.5909e-03 1.2849e-03 9.3458e-04 1.6305e-04 7.0891e+00
113 1.6103e-03 1.3002e-03 8.5895e-04 1.6275e-04 7.0850e+00
114 1.6282e-03 1.3143e-03 7.8970e-04 1.6254e-04 7.0812e+00
115 1.6448e-03 1.3271e-03 7.2642e-04 1.6239e-04 7.0777e+00
116 1.6600e-03 1.3389e-03 6.6867e-04 1.6229e-04 7.0746e+00
117 1.6740e-03 1.3496e-03 6.1608e-04 1.6225e-04 7.0718e+00
118 1.6868e-03 1.3594e-03 5.6824e-04 1.6224e-04 7.0692e+00
119 1.6986e-03 1.3682e-03 5.2478e-04 1.6226e-04 7.0669e+00
120 1.7093e-03 1.3763e-03 4.8535e-04 1.6230e-04 7.0648e+00
121 1.7192e-03 1.3836e-03 4.4962e-04 1.6236e-04 7.0629e+00
122 1.7282e-03 1.3901e-03 4.1726e-04 1.6244e-04 7.0612e+00
123 1.7365e-03 1.3960e-03 3.8800e-04 1.6252e-04 7.0596e+00
124 1.7441e-03 1.4014e-03 3.6155e-04 1.6262e-04 7.0582e+00
125 1.7509e-03 1.4062e-03 3.3765e-04 1.6272e-04 7.0569e+00
126 1.7572e-03 1.4105e-03 3.1609e-04 1.6282e-04 7.0558e+00
127 1.7630e-03 1.4143e-03 2.9664e-04 1.6292e-04 7.0547e+00
128 1.7683e-03 1.4178e-03 2.7910e-04 1.6302e-04 7.0538e+00
129 1.7731e-03 1.4208e-03 2.6330e-04 1.6312e-04 7.0529e+00
130 1.7774e-03 1.4236e-03 2.4907e-04 1.6321e-04 7.0522e+00
131 1.7815e-03 1.4260e-03 2.3626e-04 1.6331e-04 7.0515e+00
132 1.7851e-03 1.4281e-03 2.2472e-04 1.6339e-04 7.0509e+00
133 1.7885e-03 1.4300e-03 2.1435e-04 1.6348e-04 7.0503e+00
134 1.7916e-03 1.4317e-03 2.0502e-04 1.6356e-04 7.0498e+00
135 1.7944e-03 1.4331e-03 1.9662e-04 1.6364e-04 7.0494e+00
136 1.7970e-03 1.4344e-03 1.8908e-04 1.6371e-04 7.0490e+00
137 1.7994e-03 1.4355e-03 1.8230e-04 1.6377e-04 7.0486e+00
138 1.8016e-03 1.4364e-03 1.7621e-04 1.6384e-04 7.0483e+00
139 1.8036e-03 1.4372e-03 1.7073e-04 1.6390e-04 7.0480e+00
140 1.8055e-03 1.4379e-03 1.6582e-04 1.6395e-04 7.0477e+00
141 1.8072e-03 1.4385e-03 1.6140e-04 1.6400e-04 7.0475e+00
142 1.8088e-03 1.4390e-03 1.5743e-04 1.6405e-04 7.0473e+00
143 1.8103e-03 1.4394e-03 1.5387e-04 1.6409e-04 7.0471e+00
144 1.8117e-03 1.4397e-03 1.5068e-04 1.6413e-04 7.0469e+00
145 1.8130e-03 1.4399e-03 1.4780e-04 1.6417e-04 7.0467e+00
146 1.8142e-03 1.4401e-03 1.4523e-04 1.6421e-04 7.0466e+00
147 1.8153e-03 1.4402e-03 1.4291e-04 1.6424e-04 7.0465e+00
148 1.8164e-03 1.4402e-03 1.4084e-04 1.6427e-04 7.0464e+00
149 1.8174e-03 1.4402e-03 1.3897e-04 1.6429e-04 7.0463e+00
150 1.8183e-03 1.4402e-03 1.3730e-04 1.6432e-04 7.0462e+00
151 1.8192e-03 1.4401e-03 1.3580e-04 1.6434e-04 7.0461e+00
152 1.8200e-03 1.4400e-03 1.3445e-04 1.6436e-04 7.0461e+00
153 1.8208e-03 1.4399e-03 1.3325e-04 1.6438e-04 7.0460e+00
154 1.8216e-03 1.4397e-03 1.3216e-04 1.6440e-04 7.0459e+00
155 1.8223e-03 1.4396e-03 1.3119e-04 1.6441e-04 7.0459e+00
156 1.8230e-03 1.4394e-03 1.3032e-04 1.6443e-04 7.0459e+00
157 1.8236e-03 1.4391e-03 1.2953e-04 1.6444e-04 7.0458e+00
158 1.8243e-03 1.4389e-03 1.2883e-04 1.6446e-04 7.0458e+00
159 1.8249e-03 1.4386e-03 1.2820e-04 1.6447e-04 7.0458e+00
160 1.8255e-03 1.4384e-03 1.2763e-04 1.6448e-04 7.0457e+00
161 1.8260e-03 1.4381e-03 1.2713e-04 1.6449e-04 7.0457e+00
162 1.8266e-03 1.4378e-03 1.2667e-04 1.6450e-04 7.0457e+00
163 1.8271e-03 1.4375e-03 1.2626e-04 1.6451e-04 7.0457e+00
164 1.8276e-03 1.4372e-03 1.2590e-04 1.6451e-04 7.0457e+00
165 1.8281e-03 1.4369e-03 1.2557e-04 1.6452e-04 7.0457e+00
166 1.8286e-03 1.4366e-03 1.2527e-04 1.6453e-04 7.0457e+00
167 1.8291e-03 1.4363e-03 1.2501e-04 1.6453e-04 7.0456e+00
168 1.8296e-03 1.4360e-03 1.2477e-04 1.6454e-04 7.0456e+00
169 1.8300e-03 1.4356e-03 1.2456e-04 1.6454e-04 7.0456e+00
170 1.8305e-03 1.4353e-03 1.2437e-04 1.6455e-04 7.0456e+00
171 1.8309e-03 1.4350e-03 1.2420e-04 1.6455e-04 7.0456e+00
172 1.8313e-03 1.4347e-03 1.2404e-04 1.6456e-04 7.0456e+00
173 1.8318e-03 1.4343e-03 1.2390e-04 1.6456e-04 7.0456e+00
174 1.8322e-03 1.4340e-03 1.2378e-04 1.6456e-04 7.0456e+00
175 1.8326e-03 1.4337e-03 1.2367e-04 1.6457e-04 7.0456e+00
176 1.8330e-03 1.4333e-03 1.2357e-04 1.6457e-04 7.0456e+00
177 1.8334e-03 1.4330e-03 1.2348e-04 1.6457e-04 7.0456e+00
178 1.8338e-03 1.4327e-03 1.2340e-04 1.6458e-04 7.0456e+00
179 1.8342e-03 1.4323e-03 1.2333e-04 1.6458e-04 7.0457e+00
180 1.8346e-03 1.4320e-03 1.2326e-04 1.6458e-04 7.0457e+00
181 1.8349e-03 1.4317e-03 1.2321e-04 1.6458e-04 7.0457e+00
182 1.8353e-03 1.4313e-03 1.2315e-04 1.6459e-04 7.0457e+00
183 1.8357e-03 1.4310e-03 1.2311e-04 1.6459e-04 7.0457e+00
184 1.8360e-03 1.4307e-03 1.2306e-04 1.6459e-04 7.0457e+00
185 1.8364e-03 1.4304e-03 1.2303e-04 1.6459e-04 7.0457e+00
186 1.8368e-03 1.4300e-03 1.2299e-04 1.6460e-04 7.0457e+00
187 1.8371e-03 1.4297e-03 1.2296e-04 1.6460e-04 7.0457e+00
188 1.8375e-03 1.4294e-03 1.2294e-04 1.6460e-04 7.0457e+00
189 1.8378e-03 1.4291e-03 1.2291e-04 1.6460e-04 7.0457e+00
190 1.8382e-03 1.4287e-03 1.2289e-04 1.6460e-04 7.0457e+00
191 1.8385e-03 1.4284e-03 1.2287e-04 1.6460e-04 7.0457e+00
192 1.8388e-03 1.4281e-03 1.2285e-04 1.6461e-04 7.0457e+00
193 1.8392e-03 1.4278e-03 1.2284e-04 1.6461e-04 7.0457e+00
194 1.8395e-03 1.4275e-03 1.2282e-04 1.6461e-04 7.0457e+00
195 1.8398e-03 1.4272e-03 1.2281e-04 1.6461e-04 7.0457e+00
196 1.8402e-03 1.4269e-03 1.2280e-04 1.6461e-04 7.0458e+00
197 1.8405e-03 1.4266e-03 1.2279e-04 1.6461e-04 7.0458e+00
198 1.8408e-03 1.4263e-03 1.2278e-04 1.6462e-04 7.0458e+00
199 1.8411e-03 1.4260e-03 1.2277e-04 1.6462e-04 7.0458e+00
200 1.8415e-03 1.4257e-03 1.2276e-04 1.6462e-04 7.0458e+00

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sim state soln dist_x time step pH pe m_Nta-3 m_CoNta- m_HNta-2 m_Co+2 hours Co_sorb CoNta_sorb Biomass
1 transp 10 9.5 0 0 6 14.3937 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 5.0000e-01 0.0000e+00 0.0000e+00 0.0000e+00
1 transp 10 9.5 3600 1 6 14.3937 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 1.5000e+00 0.0000e+00 0.0000e+00 1.3572e-04
1 transp 10 9.5 7200 2 6 14.3937 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 2.5000e+00 0.0000e+00 0.0000e+00 1.3544e-04
1 transp 10 9.5 10800 3 6 14.3937 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 3.5000e+00 0.0000e+00 0.0000e+00 1.3515e-04
1 transp 10 9.5 14400 4 6 14.3937 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 4.5000e+00 0.0000e+00 0.0000e+00 1.3487e-04
1 transp 10 9.5 18000 5 6 14.3937 4.1637e-17 4.8355e-19 8.3076e-13 2.3172e-14 5.5000e+00 6.1781e-18 1.4377e-22 1.3459e-04
1 transp 10 9.5 21600 6 6.00019 14.3935 5.3587e-15 7.6672e-15 1.0687e-10 2.8548e-12 6.5000e+00 1.0994e-15 2.6066e-18 1.3431e-04
1 transp 10 9.5 25200 7 6.00441 14.3893 1.1039e-13 3.4338e-12 2.1803e-09 6.2065e-11 7.5000e+00 2.2731e-14 9.7754e-16 1.3406e-04
1 transp 10 9.5 28800 8 6.03587 14.3576 8.7248e-13 1.8088e-10 1.6028e-08 4.1366e-10 8.5000e+00 1.5703e-13 4.8045e-14 1.3399e-04
1 transp 10 9.5 32400 9 6.12883 14.264 3.7779e-12 1.9561e-09 5.6030e-08 1.0331e-09 9.5000e+00 4.8525e-13 5.5433e-13 1.3445e-04
1 transp 10 9.5 36000 10 6.2369 14.1549 9.6448e-12 8.0004e-09 1.1153e-07 1.6551e-09 1.0500e+01 9.8421e-13 2.4608e-12 1.3556e-04
1 transp 10 9.5 39600 11 6.30614 14.0851 1.5152e-11 2.0272e-08 1.4940e-07 2.6695e-09 1.1500e+01 1.7623e-12 6.7849e-12 1.3707e-04
1 transp 10 9.5 43200 12 6.35376 14.0371 1.9799e-11 4.1065e-08 1.7494e-07 4.1384e-09 1.2500e+01 2.9364e-12 1.4662e-11 1.3886e-04
1 transp 10 9.5 46800 13 6.3909 13.9998 2.3996e-11 7.2616e-08 1.9464e-07 6.0380e-09 1.3500e+01 4.6059e-12 2.7261e-11 1.4085e-04
1 transp 10 9.5 50400 14 6.4217 13.9688 2.7923e-11 1.1683e-07 2.1099e-07 8.3484e-09 1.4500e+01 6.8561e-12 4.5675e-11 1.4301e-04
1 transp 10 9.5 54000 15 6.44804 13.9423 3.1619e-11 1.7515e-07 2.2486e-07 1.1052e-08 1.5500e+01 9.7615e-12 7.0827e-11 1.4533e-04
1 transp 10 9.5 57600 16 6.47097 13.9193 3.5087e-11 2.4844e-07 2.3669e-07 1.4128e-08 1.6500e+01 1.3385e-11 1.0340e-10 1.4778e-04
1 transp 10 9.5 61200 17 6.49117 13.8989 3.8321e-11 3.3699e-07 2.4675e-07 1.7546e-08 1.7500e+01 1.7779e-11 1.4381e-10 1.5036e-04
1 transp 10 9.5 64800 18 6.50914 13.8808 4.1316e-11 4.4051e-07 2.5526e-07 2.1274e-08 1.8500e+01 2.2982e-11 1.9215e-10 1.5306e-04
1 transp 10 9.5 68400 19 6.52519 13.8647 4.4065e-11 5.5820e-07 2.6236e-07 2.5276e-08 1.9500e+01 2.9022e-11 2.4826e-10 1.5586e-04
1 transp 10 9.5 72000 20 6.53959 13.8502 4.6562e-11 6.8880e-07 2.6819e-07 2.9517e-08 2.0500e+01 3.5915e-11 3.1170e-10 1.5876e-04
2 transp 10 9.5 72000 0 6.53959 13.8502 4.6562e-11 6.8880e-07 2.6819e-07 2.9517e-08 2.0500e+01 0.0000e+00 0.0000e+00 0.0000e+00
2 transp 10 9.5 75600 1 6.55254 13.8371 4.8804e-11 8.3068e-07 2.7284e-07 3.3961e-08 2.1500e+01 4.3669e-11 3.8179e-10 1.6174e-04
2 transp 10 9.5 79200 2 6.56419 13.8254 5.0791e-11 9.8198e-07 2.7644e-07 3.8576e-08 2.2500e+01 5.2280e-11 4.5769e-10 1.6481e-04
2 transp 10 9.5 82800 3 6.57469 13.8148 5.2526e-11 1.1406e-06 2.7905e-07 4.3329e-08 2.3500e+01 6.1739e-11 5.3842e-10 1.6796e-04
2 transp 10 9.5 86400 4 6.58413 13.8053 5.4012e-11 1.3046e-06 2.8077e-07 4.8193e-08 2.4500e+01 7.2027e-11 6.2293e-10 1.7117e-04
2 transp 10 9.5 90000 5 6.59263 13.7967 5.5256e-11 1.4717e-06 2.8168e-07 5.3142e-08 2.5500e+01 8.3123e-11 7.1013e-10 1.7444e-04
2 transp 10 9.5 93600 6 6.60028 13.789 5.6269e-11 1.6400e-06 2.8183e-07 5.8153e-08 2.6500e+01 9.4998e-11 7.9893e-10 1.7778e-04
2 transp 10 9.5 97200 7 6.60754 13.7817 5.7056e-11 1.8075e-06 2.8103e-07 6.3208e-08 2.7500e+01 1.0762e-10 8.8826e-10 1.8116e-04
2 transp 10 9.5 100800 8 6.61795 13.7713 5.7637e-11 1.9718e-06 2.7717e-07 6.8258e-08 2.8500e+01 1.2096e-10 9.7697e-10 1.8457e-04
2 transp 10 9.5 104400 9 6.64212 13.7473 5.8212e-11 2.1299e-06 2.6478e-07 7.3002e-08 2.9500e+01 1.3490e-10 1.0636e-09 1.8791e-04
2 transp 10 9.5 108000 10 6.6795 13.7103 5.8949e-11 2.2783e-06 2.4602e-07 7.7114e-08 3.0500e+01 1.4924e-10 1.1465e-09 1.9109e-04
2 transp 10 9.5 111600 11 6.69156 13.6985 5.8746e-11 2.4117e-06 2.3846e-07 8.1911e-08 3.1500e+01 1.6415e-10 1.2236e-09 1.9424e-04
2 transp 10 9.5 115200 12 6.68638 13.7039 5.7684e-11 2.5260e-06 2.3696e-07 8.7374e-08 3.2500e+01 1.7978e-10 1.2925e-09 1.9741e-04
2 transp 10 9.5 118800 13 6.67462 13.7157 5.6097e-11 2.6183e-06 2.3676e-07 9.3127e-08 3.3500e+01 1.9616e-10 1.3514e-09 2.0062e-04
2 transp 10 9.5 122400 14 6.66009 13.7304 5.4144e-11 2.6860e-06 2.3630e-07 9.8982e-08 3.4500e+01 2.1330e-10 1.3987e-09 2.0387e-04
2 transp 10 9.5 126000 15 6.64373 13.7469 5.1900e-11 2.7276e-06 2.3520e-07 1.0486e-07 3.5500e+01 2.3114e-10 1.4332e-09 2.0716e-04
2 transp 10 9.5 129600 16 6.62579 13.7649 4.9419e-11 2.7424e-06 2.3341e-07 1.1072e-07 3.6500e+01 2.4964e-10 1.4540e-09 2.1047e-04
2 transp 10 9.5 133200 17 6.60638 13.7845 4.6754e-11 2.7304e-06 2.3091e-07 1.1652e-07 3.7500e+01 2.6875e-10 1.4608e-09 2.1379e-04
2 transp 10 9.5 136800 18 6.58562 13.8054 4.3956e-11 2.6927e-06 2.2772e-07 1.2223e-07 3.8500e+01 2.8841e-10 1.4537e-09 2.1712e-04
2 transp 10 9.5 140400 19 6.56361 13.8275 4.1075e-11 2.6309e-06 2.2386e-07 1.2780e-07 3.9500e+01 3.0854e-10 1.4333e-09 2.2044e-04
2 transp 10 9.5 144000 20 6.54047 13.8508 3.8158e-11 2.5474e-06 2.1934e-07 1.3320e-07 4.0500e+01 3.2906e-10 1.4004e-09 2.2375e-04
2 transp 10 9.5 147600 21 6.51631 13.8751 3.5247e-11 2.4449e-06 2.1419e-07 1.3841e-07 4.1500e+01 3.4990e-10 1.3562e-09 2.2702e-04
2 transp 10 9.5 151200 22 6.49127 13.9003 3.2379e-11 2.3266e-06 2.0845e-07 1.4337e-07 4.2500e+01 3.7097e-10 1.3021e-09 2.3026e-04
2 transp 10 9.5 154800 23 6.46547 13.9262 2.9588e-11 2.1956e-06 2.0213e-07 1.4806e-07 4.3500e+01 3.9217e-10 1.2398e-09 2.3344e-04
2 transp 10 9.5 158400 24 6.43907 13.9527 2.6899e-11 2.0552e-06 1.9529e-07 1.5245e-07 4.4500e+01 4.1340e-10 1.1710e-09 2.3656e-04
2 transp 10 9.5 162000 25 6.41223 13.9797 2.4336e-11 1.9087e-06 1.8794e-07 1.5649e-07 4.5500e+01 4.3456e-10 1.0972e-09 2.3959e-04
2 transp 10 9.5 165600 26 6.38512 14.0069 2.1913e-11 1.7589e-06 1.8013e-07 1.6016e-07 4.6500e+01 4.5554e-10 1.0202e-09 2.4253e-04
2 transp 10 9.5 169200 27 6.35794 14.0343 1.9643e-11 1.6088e-06 1.7189e-07 1.6342e-07 4.7500e+01 4.7623e-10 9.4150e-10 2.4537e-04
2 transp 10 9.5 172800 28 6.33089 14.0614 1.7532e-11 1.4607e-06 1.6329e-07 1.6624e-07 4.8500e+01 4.9652e-10 8.6254e-10 2.4809e-04
2 transp 10 9.5 176400 29 6.30416 14.0883 1.5584e-11 1.3168e-06 1.5436e-07 1.6859e-07 4.9500e+01 5.1630e-10 7.8460e-10 2.5068e-04
2 transp 10 9.5 180000 30 6.27797 14.1146 1.3798e-11 1.1788e-06 1.4516e-07 1.7047e-07 5.0500e+01 5.3545e-10 7.0877e-10 2.5312e-04
2 transp 10 9.5 183600 31 6.25252 14.1402 1.2170e-11 1.0482e-06 1.3576e-07 1.7185e-07 5.1500e+01 5.5388e-10 6.3597e-10 2.5541e-04
2 transp 10 9.5 187200 32 6.228 14.1648 1.0695e-11 9.2591e-07 1.2623e-07 1.7274e-07 5.2500e+01 5.7148e-10 5.6693e-10 2.5754e-04
2 transp 10 9.5 190800 33 6.20459 14.1883 9.3648e-12 8.1273e-07 1.1666e-07 1.7316e-07 5.3500e+01 5.8818e-10 5.0219e-10 2.5949e-04
2 transp 10 9.5 194400 34 6.18244 14.2105 8.1717e-12 7.0904e-07 1.0712e-07 1.7312e-07 5.4500e+01 6.0391e-10 4.4212e-10 2.6127e-04
2 transp 10 9.5 198000 35 6.16167 14.2314 7.1059e-12 6.1497e-07 9.7713e-08 1.7268e-07 5.5500e+01 6.1861e-10 3.8695e-10 2.6286e-04
2 transp 10 9.5 201600 36 6.14237 14.2508 6.1578e-12 5.3042e-07 8.8524e-08 1.7187e-07 5.6500e+01 6.3226e-10 3.3676e-10 2.6427e-04
2 transp 10 9.5 205200 37 6.12459 14.2686 5.3178e-12 4.5509e-07 7.9641e-08 1.7075e-07 5.7500e+01 6.4483e-10 2.9149e-10 2.6550e-04
2 transp 10 9.5 208800 38 6.10837 14.2849 4.5763e-12 3.8853e-07 7.1145e-08 1.6940e-07 5.8500e+01 6.5634e-10 2.5101e-10 2.6655e-04
2 transp 10 9.5 212400 39 6.09369 14.2996 3.9244e-12 3.3017e-07 6.3107e-08 1.6787e-07 5.9500e+01 6.6679e-10 2.1511e-10 2.6742e-04
2 transp 10 9.5 216000 40 6.08053 14.3129 3.3534e-12 2.7937e-07 5.5584e-08 1.6623e-07 6.0500e+01 6.7624e-10 1.8349e-10 2.6813e-04
2 transp 10 9.5 219600 41 6.06883 14.3246 2.8552e-12 2.3545e-07 4.8619e-08 1.6454e-07 6.1500e+01 6.8474e-10 1.5585e-10 2.6869e-04
2 transp 10 9.5 223200 42 6.05851 14.335 2.4224e-12 1.9772e-07 4.2241e-08 1.6286e-07 6.2500e+01 6.9233e-10 1.3184e-10 2.6910e-04
2 transp 10 9.5 226800 43 6.04948 14.3441 2.0479e-12 1.6548e-07 3.6461e-08 1.6123e-07 6.3500e+01 6.9911e-10 1.1112e-10 2.6938e-04
2 transp 10 9.5 230400 44 6.04163 14.3519 1.7253e-12 1.3809e-07 3.1277e-08 1.5969e-07 6.4500e+01 7.0513e-10 9.3326e-11 2.6955e-04
2 transp 10 9.5 234000 45 6.03487 14.3587 1.4485e-12 1.1491e-07 2.6672e-08 1.5827e-07 6.5500e+01 7.1047e-10 7.8132e-11 2.6960e-04
2 transp 10 9.5 237600 46 6.02908 14.3645 1.2122e-12 9.5378e-08 2.2620e-08 1.5699e-07 6.6500e+01 7.1521e-10 6.5220e-11 2.6957e-04
2 transp 10 9.5 241200 47 6.02415 14.3695 1.0113e-12 7.8988e-08 1.9086e-08 1.5585e-07 6.7500e+01 7.1941e-10 5.4292e-11 2.6945e-04
2 transp 10 9.5 244800 48 6.01999 14.3737 8.4110e-13 6.5277e-08 1.6027e-08 1.5485e-07 6.8500e+01 7.2315e-10 4.5082e-11 2.6926e-04
2 transp 10 9.5 248400 49 6.01648 14.3772 6.9760e-13 5.3842e-08 1.3400e-08 1.5400e-07 6.9500e+01 7.2648e-10 3.7348e-11 2.6901e-04
2 transp 10 9.5 252000 50 6.01355 14.3801 5.7705e-13 4.4330e-08 1.1160e-08 1.5328e-07 7.0500e+01 7.2947e-10 3.0873e-11 2.6870e-04
2 transp 10 9.5 255600 51 6.01111 14.3826 4.7615e-13 3.6437e-08 9.2604e-09 1.5268e-07 7.1500e+01 7.3215e-10 2.5469e-11 2.6836e-04
2 transp 10 9.5 259200 52 6.00908 14.3846 3.9198e-13 2.9901e-08 7.6592e-09 1.5220e-07 7.2500e+01 7.3458e-10 2.0972e-11 2.6798e-04
2 transp 10 9.5 262800 53 6.00741 14.3863 3.2200e-13 2.4501e-08 6.3161e-09 1.5182e-07 7.3500e+01 7.3678e-10 1.7238e-11 2.6756e-04
2 transp 10 9.5 266400 54 6.00603 14.3877 2.6398e-13 2.0046e-08 5.1944e-09 1.5152e-07 7.4500e+01 7.3880e-10 1.4145e-11 2.6713e-04
2 transp 10 9.5 270000 55 6.0049 14.3888 2.1600e-13 1.6379e-08 4.2615e-09 1.5130e-07 7.5500e+01 7.4066e-10 1.1589e-11 2.6667e-04

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435
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@ -1,435 +0,0 @@
Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex16
Output file: ex16.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 16.--Inverse modeling of Sierra springs
SOLUTION_SPREAD
units mmol/L
Number pH Si Ca Mg Na K Alkalinity S(6) Cl
1 6.2 0.273 0.078 0.029 0.134 0.028 0.328 0.01 0.014
2 6.8 0.41 0.26 0.071 0.259 0.04 0.895 0.025 0.03
INVERSE_MODELING 1
solutions 1 2
uncertainty 0.025
range
phases
Halite
Gypsum
Kaolinite precip
Ca-montmorillonite precip
CO2(g)
Calcite
Chalcedony precip
Biotite dissolve
Plagioclase dissolve
balances
Ca 0.05 0.025
PHASES
Biotite
KMg3AlSi3O10(OH)2 + 6H+ + 4H2O = K+ + 3Mg+2 + Al(OH)4- + 3H4SiO4
log_k 0.0 # No log_k, Inverse modeling only
Plagioclase
Na0.62Ca0.38Al1.38Si2.62O8 + 5.52 H+ + 2.48H2O = 0.62Na+ + 0.38Ca+2 + 1.38Al+3 + 2.62H4SiO4
log_k 0.0 # No log_k, inverse modeling only
END
-----
TITLE
-----
Example 16.--Inverse modeling of Sierra springs
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1.
-----------------------------Solution composition------------------------------
Elements Molality Moles
Alkalinity 3.280e-04 3.280e-04
Ca 7.800e-05 7.800e-05
Cl 1.400e-05 1.400e-05
K 2.800e-05 2.800e-05
Mg 2.900e-05 2.900e-05
Na 1.340e-04 1.340e-04
S(6) 1.000e-05 1.000e-05
Si 2.730e-04 2.730e-04
----------------------------Description of solution----------------------------
pH = 6.200
pe = 4.000
Activity of water = 1.000
Ionic strength = 4.851e-04
Mass of water (kg) = 1.000e+00
Total carbon (mol/kg) = 7.825e-04
Total CO2 (mol/kg) = 7.825e-04
Temperature (deg C) = 25.000
Electrical balance (eq) = 1.400e-05
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 1.90
Iterations = 7
Total H = 1.110139e+02
Total O = 5.550924e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
H+ 6.464e-07 6.310e-07 -6.189 -6.200 -0.011
OH- 1.627e-08 1.587e-08 -7.789 -7.800 -0.011
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
C(4) 7.825e-04
CO2 4.540e-04 4.540e-04 -3.343 -3.343 0.000
HCO3- 3.281e-04 3.200e-04 -3.484 -3.495 -0.011
CaHCO3+ 2.940e-07 2.868e-07 -6.532 -6.542 -0.011
MgHCO3+ 1.003e-07 9.783e-08 -6.999 -7.010 -0.011
CO3-2 2.628e-08 2.379e-08 -7.580 -7.624 -0.043
NaHCO3 2.351e-08 2.352e-08 -7.629 -7.629 0.000
CaCO3 2.806e-09 2.807e-09 -8.552 -8.552 0.000
MgCO3 5.929e-10 5.930e-10 -9.227 -9.227 0.000
NaCO3- 5.935e-11 5.788e-11 -10.227 -10.237 -0.011
Ca 7.800e-05
Ca+2 7.758e-05 7.023e-05 -4.110 -4.153 -0.043
CaHCO3+ 2.940e-07 2.868e-07 -6.532 -6.542 -0.011
CaSO4 1.244e-07 1.245e-07 -6.905 -6.905 0.000
CaCO3 2.806e-09 2.807e-09 -8.552 -8.552 0.000
CaOH+ 1.894e-11 1.847e-11 -10.723 -10.733 -0.011
CaHSO4+ 4.717e-13 4.600e-13 -12.326 -12.337 -0.011
Cl 1.400e-05
Cl- 1.400e-05 1.365e-05 -4.854 -4.865 -0.011
H(0) 5.636e-24
H2 2.818e-24 2.818e-24 -23.550 -23.550 0.000
K 2.800e-05
K+ 2.800e-05 2.730e-05 -4.553 -4.564 -0.011
KSO4- 1.747e-09 1.704e-09 -8.758 -8.769 -0.011
KOH 1.500e-13 1.500e-13 -12.824 -12.824 0.000
Mg 2.900e-05
Mg+2 2.885e-05 2.612e-05 -4.540 -4.583 -0.043
MgHCO3+ 1.003e-07 9.783e-08 -6.999 -7.010 -0.011
MgSO4 5.438e-08 5.439e-08 -7.265 -7.264 0.000
MgCO3 5.929e-10 5.930e-10 -9.227 -9.227 0.000
MgOH+ 1.541e-10 1.503e-10 -9.812 -9.823 -0.011
Na 1.340e-04
Na+ 1.340e-04 1.307e-04 -3.873 -3.884 -0.011
NaHCO3 2.351e-08 2.352e-08 -7.629 -7.629 0.000
NaSO4- 5.964e-09 5.816e-09 -8.224 -8.235 -0.011
NaCO3- 5.935e-11 5.788e-11 -10.227 -10.237 -0.011
NaOH 1.368e-12 1.368e-12 -11.864 -11.864 0.000
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -45.280 -45.280 0.000
S(6) 1.000e-05
SO4-2 9.813e-06 8.882e-06 -5.008 -5.052 -0.043
CaSO4 1.244e-07 1.245e-07 -6.905 -6.905 0.000
MgSO4 5.438e-08 5.439e-08 -7.265 -7.264 0.000
NaSO4- 5.964e-09 5.816e-09 -8.224 -8.235 -0.011
KSO4- 1.747e-09 1.704e-09 -8.758 -8.769 -0.011
HSO4- 5.587e-10 5.448e-10 -9.253 -9.264 -0.011
CaHSO4+ 4.717e-13 4.600e-13 -12.326 -12.337 -0.011
Si 2.730e-04
H4SiO4 2.729e-04 2.730e-04 -3.564 -3.564 0.000
H3SiO4- 6.541e-08 6.379e-08 -7.184 -7.195 -0.011
H2SiO4-2 7.604e-15 6.877e-15 -14.119 -14.163 -0.044
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -4.84 -9.20 -4.36 CaSO4
Aragonite -3.44 -11.78 -8.34 CaCO3
Calcite -3.30 -11.78 -8.48 CaCO3
Chalcedony -0.01 -3.56 -3.55 SiO2
Chrysotile -15.88 16.32 32.20 Mg3Si2O5(OH)4
CO2(g) -1.87 -3.34 -1.47 CO2
Dolomite -6.89 -23.98 -17.09 CaMg(CO3)2
Gypsum -4.62 -9.20 -4.58 CaSO4:2H2O
H2(g) -20.40 -23.55 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
Halite -10.33 -8.75 1.58 NaCl
O2(g) -42.32 -45.28 -2.96 O2
Quartz 0.42 -3.56 -3.98 SiO2
Sepiolite -10.82 4.94 15.76 Mg2Si3O7.5OH:3H2O
Sepiolite(d) -13.72 4.94 18.66 Mg2Si3O7.5OH:3H2O
SiO2(a) -0.85 -3.56 -2.71 SiO2
Talc -12.20 9.20 21.40 Mg3Si4O10(OH)2
Initial solution 2.
-----------------------------Solution composition------------------------------
Elements Molality Moles
Alkalinity 8.951e-04 8.951e-04
Ca 2.600e-04 2.600e-04
Cl 3.000e-05 3.000e-05
K 4.000e-05 4.000e-05
Mg 7.101e-05 7.101e-05
Na 2.590e-04 2.590e-04
S(6) 2.500e-05 2.500e-05
Si 4.100e-04 4.100e-04
----------------------------Description of solution----------------------------
pH = 6.800
pe = 4.000
Activity of water = 1.000
Ionic strength = 1.313e-03
Mass of water (kg) = 1.000e+00
Total carbon (mol/kg) = 1.199e-03
Total CO2 (mol/kg) = 1.199e-03
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.400e-05
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.73
Iterations = 6
Total H = 1.110150e+02
Total O = 5.551125e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
H+ 1.647e-07 1.585e-07 -6.783 -6.800 -0.017
OH- 6.579e-08 6.316e-08 -7.182 -7.200 -0.018
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
C(4) 1.199e-03
HCO3- 8.907e-04 8.559e-04 -3.050 -3.068 -0.017
CO2 3.049e-04 3.050e-04 -3.516 -3.516 0.000
CaHCO3+ 2.485e-06 2.387e-06 -5.605 -5.622 -0.017
MgHCO3+ 6.235e-07 5.987e-07 -6.205 -6.223 -0.018
CO3-2 2.971e-07 2.533e-07 -6.527 -6.596 -0.069
NaHCO3 1.196e-07 1.197e-07 -6.922 -6.922 0.000
CaCO3 9.299e-08 9.302e-08 -7.032 -7.031 0.000
MgCO3 1.444e-08 1.445e-08 -7.840 -7.840 0.000
NaCO3- 1.221e-09 1.173e-09 -8.913 -8.931 -0.018
Ca 2.600e-04
Ca+2 2.566e-04 2.186e-04 -3.591 -3.660 -0.069
CaHCO3+ 2.485e-06 2.387e-06 -5.605 -5.622 -0.017
CaSO4 8.841e-07 8.843e-07 -6.054 -6.053 0.000
CaCO3 9.299e-08 9.302e-08 -7.032 -7.031 0.000
CaOH+ 2.384e-10 2.289e-10 -9.623 -9.640 -0.018
CaHSO4+ 8.551e-13 8.211e-13 -12.068 -12.086 -0.018
Cl 3.000e-05
Cl- 3.000e-05 2.880e-05 -4.523 -4.541 -0.018
H(0) 3.555e-25
H2 1.778e-25 1.778e-25 -24.750 -24.750 0.000
K 4.000e-05
K+ 4.000e-05 3.840e-05 -4.398 -4.416 -0.018
KSO4- 5.696e-09 5.470e-09 -8.244 -8.262 -0.018
KOH 8.398e-13 8.401e-13 -12.076 -12.076 0.000
Mg 7.101e-05
Mg+2 7.008e-05 5.978e-05 -4.154 -4.223 -0.069
MgHCO3+ 6.235e-07 5.987e-07 -6.205 -6.223 -0.018
MgSO4 2.840e-07 2.841e-07 -6.547 -6.547 0.000
MgCO3 1.444e-08 1.445e-08 -7.840 -7.840 0.000
MgOH+ 1.426e-09 1.370e-09 -8.846 -8.863 -0.018
Na 2.590e-04
Na+ 2.589e-04 2.486e-04 -3.587 -3.604 -0.018
NaHCO3 1.196e-07 1.197e-07 -6.922 -6.922 0.000
NaSO4- 2.631e-08 2.526e-08 -7.580 -7.598 -0.018
NaCO3- 1.221e-09 1.173e-09 -8.913 -8.931 -0.018
NaOH 1.036e-11 1.036e-11 -10.985 -10.984 0.000
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -42.880 -42.880 0.000
S(6) 2.500e-05
SO4-2 2.380e-05 2.027e-05 -4.623 -4.693 -0.070
CaSO4 8.841e-07 8.843e-07 -6.054 -6.053 0.000
MgSO4 2.840e-07 2.841e-07 -6.547 -6.547 0.000
NaSO4- 2.631e-08 2.526e-08 -7.580 -7.598 -0.018
KSO4- 5.696e-09 5.470e-09 -8.244 -8.262 -0.018
HSO4- 3.253e-10 3.124e-10 -9.488 -9.505 -0.018
CaHSO4+ 8.551e-13 8.211e-13 -12.068 -12.086 -0.018
Si 4.100e-04
H4SiO4 4.096e-04 4.098e-04 -3.388 -3.387 0.000
H3SiO4- 3.970e-07 3.812e-07 -6.401 -6.419 -0.018
H2SiO4-2 1.924e-13 1.636e-13 -12.716 -12.786 -0.070
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -3.99 -8.35 -4.36 CaSO4
Aragonite -1.92 -10.26 -8.34 CaCO3
Calcite -1.78 -10.26 -8.48 CaCO3
Chalcedony 0.16 -3.39 -3.55 SiO2
Chrysotile -10.85 21.35 32.20 Mg3Si2O5(OH)4
CO2(g) -2.05 -3.52 -1.47 CO2
Dolomite -3.99 -21.08 -17.09 CaMg(CO3)2
Gypsum -3.77 -8.35 -4.58 CaSO4:2H2O
H2(g) -21.60 -24.75 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
Halite -9.73 -8.14 1.58 NaCl
O2(g) -39.92 -42.88 -2.96 O2
Quartz 0.59 -3.39 -3.98 SiO2
Sepiolite -7.17 8.59 15.76 Mg2Si3O7.5OH:3H2O
Sepiolite(d) -10.07 8.59 18.66 Mg2Si3O7.5OH:3H2O
SiO2(a) -0.68 -3.39 -2.71 SiO2
Talc -6.82 14.58 21.40 Mg3Si4O10(OH)2
-------------------------------------------
Beginning of inverse modeling calculations.
-------------------------------------------
Solution 1:
Input Delta Input+Delta
pH 6.200e+00 + 1.246e-02 = 6.212e+00
Al 0.000e+00 + 0.000e+00 = 0.000e+00
Alkalinity 3.280e-04 + 5.500e-06 = 3.335e-04
C(-4) 0.000e+00 + 0.000e+00 = 0.000e+00
C(4) 7.825e-04 + 0.000e+00 = 7.825e-04
Ca 7.800e-05 + -3.900e-06 = 7.410e-05
Cl 1.400e-05 + 0.000e+00 = 1.400e-05
H(0) 0.000e+00 + 0.000e+00 = 0.000e+00
K 2.800e-05 + -7.000e-07 = 2.730e-05
Mg 2.900e-05 + 0.000e+00 = 2.900e-05
Na 1.340e-04 + 0.000e+00 = 1.340e-04
O(0) 0.000e+00 + 0.000e+00 = 0.000e+00
S(-2) 0.000e+00 + 0.000e+00 = 0.000e+00
S(6) 1.000e-05 + 0.000e+00 = 1.000e-05
Si 2.730e-04 + 0.000e+00 = 2.730e-04
Solution 2:
Input Delta Input+Delta
pH 6.800e+00 + -3.407e-03 = 6.797e+00
Al 0.000e+00 + 0.000e+00 = 0.000e+00
Alkalinity 8.951e-04 + -1.796e-06 = 8.933e-04
C(-4) 0.000e+00 + 0.000e+00 = 0.000e+00
C(4) 1.199e-03 + 0.000e+00 = 1.199e-03
Ca 2.600e-04 + 6.501e-06 = 2.665e-04
Cl 3.000e-05 + 0.000e+00 = 3.000e-05
H(0) 0.000e+00 + 0.000e+00 = 0.000e+00
K 4.000e-05 + 1.000e-06 = 4.100e-05
Mg 7.101e-05 + -8.979e-07 = 7.011e-05
Na 2.590e-04 + 0.000e+00 = 2.590e-04
O(0) 0.000e+00 + 0.000e+00 = 0.000e+00
S(-2) 0.000e+00 + 0.000e+00 = 0.000e+00
S(6) 2.500e-05 + 0.000e+00 = 2.500e-05
Si 4.100e-04 + 0.000e+00 = 4.100e-04
Solution fractions: Minimum Maximum
Solution 1 1.000e+00 1.000e+00 1.000e+00
Solution 2 1.000e+00 1.000e+00 1.000e+00
Phase mole transfers: Minimum Maximum
Halite 1.600e-05 1.490e-05 1.710e-05 NaCl
Gypsum 1.500e-05 1.413e-05 1.588e-05 CaSO4:2H2O
Kaolinite -3.392e-05 -5.587e-05 -1.224e-05 Al2Si2O5(OH)4
Ca-Montmorillon -8.090e-05 -1.100e-04 -5.154e-05 Ca0.165Al2.33Si3.67O10(OH)2
CO2(g) 2.928e-04 2.363e-04 3.563e-04 CO2
Calcite 1.240e-04 1.007e-04 1.309e-04 CaCO3
Biotite 1.370e-05 1.317e-05 1.370e-05 KMg3AlSi3O10(OH)2
Plagioclase 1.758e-04 1.582e-04 1.935e-04 Na0.62Ca0.38Al1.38Si2.62O8
Redox mole transfers:
Sum of residuals (epsilons in documentation): 5.574e+00
Sum of delta/uncertainty limit: 5.574e+00
Maximum fractional error in element concentration: 5.000e-02
Model contains minimum number of phases.
===============================================================================
Solution 1:
Input Delta Input+Delta
pH 6.200e+00 + 1.246e-02 = 6.212e+00
Al 0.000e+00 + 0.000e+00 = 0.000e+00
Alkalinity 3.280e-04 + 5.500e-06 = 3.335e-04
C(-4) 0.000e+00 + 0.000e+00 = 0.000e+00
C(4) 7.825e-04 + 0.000e+00 = 7.825e-04
Ca 7.800e-05 + -3.900e-06 = 7.410e-05
Cl 1.400e-05 + 0.000e+00 = 1.400e-05
H(0) 0.000e+00 + 0.000e+00 = 0.000e+00
K 2.800e-05 + -7.000e-07 = 2.730e-05
Mg 2.900e-05 + 0.000e+00 = 2.900e-05
Na 1.340e-04 + 0.000e+00 = 1.340e-04
O(0) 0.000e+00 + 0.000e+00 = 0.000e+00
S(-2) 0.000e+00 + 0.000e+00 = 0.000e+00
S(6) 1.000e-05 + 0.000e+00 = 1.000e-05
Si 2.730e-04 + 0.000e+00 = 2.730e-04
Solution 2:
Input Delta Input+Delta
pH 6.800e+00 + -3.407e-03 = 6.797e+00
Al 0.000e+00 + 0.000e+00 = 0.000e+00
Alkalinity 8.951e-04 + -1.796e-06 = 8.933e-04
C(-4) 0.000e+00 + 0.000e+00 = 0.000e+00
C(4) 1.199e-03 + 0.000e+00 = 1.199e-03
Ca 2.600e-04 + 6.501e-06 = 2.665e-04
Cl 3.000e-05 + 0.000e+00 = 3.000e-05
H(0) 0.000e+00 + 0.000e+00 = 0.000e+00
K 4.000e-05 + 1.000e-06 = 4.100e-05
Mg 7.101e-05 + -8.980e-07 = 7.011e-05
Na 2.590e-04 + 0.000e+00 = 2.590e-04
O(0) 0.000e+00 + 0.000e+00 = 0.000e+00
S(-2) 0.000e+00 + 0.000e+00 = 0.000e+00
S(6) 2.500e-05 + 0.000e+00 = 2.500e-05
Si 4.100e-04 + 0.000e+00 = 4.100e-04
Solution fractions: Minimum Maximum
Solution 1 1.000e+00 1.000e+00 1.000e+00
Solution 2 1.000e+00 1.000e+00 1.000e+00
Phase mole transfers: Minimum Maximum
Halite 1.600e-05 1.490e-05 1.710e-05 NaCl
Gypsum 1.500e-05 1.413e-05 1.588e-05 CaSO4:2H2O
Kaolinite -1.282e-04 -1.403e-04 -1.159e-04 Al2Si2O5(OH)4
CO2(g) 3.061e-04 2.490e-04 3.703e-04 CO2
Calcite 1.106e-04 8.680e-05 1.182e-04 CaCO3
Chalcedony -1.084e-04 -1.473e-04 -6.906e-05 SiO2
Biotite 1.370e-05 1.317e-05 1.370e-05 KMg3AlSi3O10(OH)2
Plagioclase 1.758e-04 1.582e-04 1.935e-04 Na0.62Ca0.38Al1.38Si2.62O8
Redox mole transfers:
Sum of residuals (epsilons in documentation): 5.574e+00
Sum of delta/uncertainty limit: 5.574e+00
Maximum fractional error in element concentration: 5.000e-02
Model contains minimum number of phases.
===============================================================================
Summary of inverse modeling:
Number of models found: 2
Number of minimal models found: 2
Number of infeasible sets of phases saved: 20
Number of calls to cl1: 62
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 2.
------------------------------------
-----------
End of run.
-----------
No memory leaks

0
Sun/examples/ex17.log
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349
Sun/examples/ex17.out
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@ -1,349 +0,0 @@
Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex17
Output file: ex17.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 17.--Inverse modeling of Black Sea water evaporation
SOLUTION 1 Black Sea water
units mg/L
density 1.014
pH 8.0 # estimated
Ca 233
Mg 679
Na 5820
K 193
S(6) 1460
Cl 10340
Br 35
C 1 CO2(g) -3.5
SOLUTION 2 Composition during halite precipitation
units mg/L
density 1.271
pH 5.0 # estimated
Ca 0.0
Mg 50500
Na 55200
K 15800
S(6) 76200
Cl 187900
Br 2670
C 1 CO2(g) -3.5
INVERSE_MODELING
solutions 1 2
uncertainties .025
range
balances
Br
K
Mg
phases
H2O(g) pre
Calcite pre
CO2(g) pre
Gypsum pre
Halite pre
END
-----
TITLE
-----
Example 17.--Inverse modeling of Black Sea water evaporation
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1. Black Sea water
-----------------------------Solution composition------------------------------
Elements Molality Moles
Br 4.401e-04 4.401e-04
C 8.284e-04 8.284e-04 Equilibrium with CO2(g)
Ca 5.841e-03 5.841e-03
Cl 2.930e-01 2.930e-01
K 4.959e-03 4.959e-03
Mg 2.806e-02 2.806e-02
Na 2.544e-01 2.544e-01
S(6) 1.527e-02 1.527e-02
----------------------------Description of solution----------------------------
pH = 8.000
pe = 4.000
Activity of water = 0.990
Ionic strength = 3.540e-01
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 8.625e-04
Total CO2 (mol/kg) = 8.284e-04
Temperature (deg C) = 25.000
Electrical balance (eq) = 2.240e-03
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 0.36
Iterations = 5
Total H = 1.110132e+02
Total O = 5.556978e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.500e-06 9.909e-07 -5.824 -6.004 -0.180
H+ 1.288e-08 1.000e-08 -7.890 -8.000 -0.110
H2O 5.551e+01 9.899e-01 1.744 -0.004 0.000
Br 4.401e-04
Br- 4.401e-04 2.835e-04 -3.356 -3.547 -0.191
C(-4) 0.000e+00
CH4 0.000e+00 0.000e+00 -76.604 -76.569 0.035
C(4) 8.284e-04
HCO3- 6.657e-04 4.740e-04 -3.177 -3.324 -0.147
MgHCO3+ 5.725e-05 4.187e-05 -4.242 -4.378 -0.136
NaHCO3 4.444e-05 4.822e-05 -4.352 -4.317 0.035
MgCO3 1.476e-05 1.601e-05 -4.831 -4.796 0.035
CaHCO3+ 1.247e-05 8.879e-06 -4.904 -5.052 -0.147
NaCO3- 1.024e-05 7.488e-06 -4.990 -5.126 -0.136
CO2 9.923e-06 1.077e-05 -5.003 -4.968 0.035
CO3-2 8.646e-06 2.223e-06 -5.063 -5.653 -0.590
CaCO3 5.053e-06 5.483e-06 -5.296 -5.261 0.035
Ca 5.841e-03
Ca+2 5.267e-03 1.468e-03 -2.278 -2.833 -0.555
CaSO4 5.563e-04 6.035e-04 -3.255 -3.219 0.035
CaHCO3+ 1.247e-05 8.879e-06 -4.904 -5.052 -0.147
CaCO3 5.053e-06 5.483e-06 -5.296 -5.261 0.035
CaOH+ 3.298e-08 2.412e-08 -7.482 -7.618 -0.136
CaHSO4+ 4.835e-11 3.536e-11 -10.316 -10.452 -0.136
Cl 2.930e-01
Cl- 2.930e-01 1.960e-01 -0.533 -0.708 -0.175
H(0) 1.305e-27
H2 6.525e-28 7.079e-28 -27.185 -27.150 0.035
K 4.959e-03
K+ 4.895e-03 3.274e-03 -2.310 -2.485 -0.175
KSO4- 6.480e-05 4.739e-05 -4.188 -4.324 -0.136
KOH 1.036e-09 1.124e-09 -8.985 -8.949 0.035
Mg 2.806e-02
Mg+2 2.463e-02 7.549e-03 -1.609 -2.122 -0.514
MgSO4 3.360e-03 3.646e-03 -2.474 -2.438 0.035
MgHCO3+ 5.725e-05 4.187e-05 -4.242 -4.378 -0.136
MgCO3 1.476e-05 1.601e-05 -4.831 -4.796 0.035
MgOH+ 3.710e-06 2.713e-06 -5.431 -5.567 -0.136
Na 2.544e-01
Na+ 2.518e-01 1.809e-01 -0.599 -0.743 -0.144
NaSO4- 2.554e-03 1.868e-03 -2.593 -2.729 -0.136
NaHCO3 4.444e-05 4.822e-05 -4.352 -4.317 0.035
NaCO3- 1.024e-05 7.488e-06 -4.990 -5.126 -0.136
NaOH 1.090e-07 1.183e-07 -6.962 -6.927 0.035
O(0) 1.502e-38
O2 7.512e-39 8.150e-39 -38.124 -38.089 0.035
S(6) 1.527e-02
SO4-2 8.735e-03 2.060e-03 -2.059 -2.686 -0.627
MgSO4 3.360e-03 3.646e-03 -2.474 -2.438 0.035
NaSO4- 2.554e-03 1.868e-03 -2.593 -2.729 -0.136
CaSO4 5.563e-04 6.035e-04 -3.255 -3.219 0.035
KSO4- 6.480e-05 4.739e-05 -4.188 -4.324 -0.136
HSO4- 2.739e-09 2.003e-09 -8.562 -8.698 -0.136
CaHSO4+ 4.835e-11 3.536e-11 -10.316 -10.452 -0.136
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -1.16 -5.52 -4.36 CaSO4
Aragonite -0.15 -8.49 -8.34 CaCO3
Calcite -0.01 -8.49 -8.48 CaCO3
CH4(g) -73.71 -76.57 -2.86 CH4
CO2(g) -3.50 -4.97 -1.47 CO2
Dolomite 0.83 -16.26 -17.09 CaMg(CO3)2
Gypsum -0.95 -5.53 -4.58 CaSO4:2H2O
H2(g) -24.00 -27.15 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
Halite -3.03 -1.45 1.58 NaCl
O2(g) -35.13 -38.09 -2.96 O2
Initial solution 2. Composition during halite precipitation
-----------------------------Solution composition------------------------------
Elements Molality Moles
Br 3.785e-02 3.785e-02
C 7.019e-06 7.019e-06 Equilibrium with CO2(g)
Cl 6.004e+00 6.004e+00
K 4.578e-01 4.578e-01
Mg 2.353e+00 2.353e+00
Na 2.720e+00 2.720e+00
S(6) 8.986e-01 8.986e-01
----------------------------Description of solution----------------------------
pH = 5.000
pe = 4.000
Activity of water = 0.802
Ionic strength = 7.827e+00
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = -9.195e-06
Total CO2 (mol/kg) = 7.019e-06
Temperature (deg C) = 25.000
Electrical balance (eq) = 4.491e-02
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 0.36
Iterations = 10
Total H = 1.110125e+02
Total O = 5.910064e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
H+ 1.425e-05 1.000e-05 -4.846 -5.000 -0.154
OH- 1.749e-09 8.029e-10 -8.757 -9.095 -0.338
H2O 5.551e+01 8.021e-01 1.744 -0.096 0.000
Br 3.785e-02
Br- 3.785e-02 1.580e-02 -1.422 -1.801 -0.379
C(-4) 0.000e+00
CH4 0.000e+00 0.000e+00 -53.169 -52.386 0.783
C(4) 7.019e-06
MgHCO3+ 4.391e-06 2.905e-05 -5.357 -4.537 0.821
CO2 1.776e-06 1.077e-05 -5.751 -4.968 0.783
HCO3- 6.660e-07 3.841e-07 -6.177 -6.416 -0.239
NaHCO3 1.847e-07 1.120e-06 -6.734 -5.951 0.783
MgCO3 1.833e-09 1.111e-08 -8.737 -7.954 0.783
NaCO3- 2.628e-11 1.739e-10 -10.580 -9.760 0.821
CO3-2 1.629e-11 1.801e-12 -10.788 -11.744 -0.956
Cl 6.004e+00
Cl- 6.004e+00 3.612e+00 0.778 0.558 -0.221
H(0) 2.335e-22
H2 1.168e-22 7.079e-22 -21.933 -21.150 0.783
K 4.578e-01
K+ 4.568e-01 2.748e-01 -0.340 -0.561 -0.221
KSO4- 9.513e-04 6.294e-03 -3.022 -2.201 0.821
KOH 1.261e-11 7.643e-11 -10.899 -10.117 0.783
Mg 2.353e+00
Mg+2 1.538e+00 6.465e+00 0.187 0.811 0.624
MgSO4 8.148e-01 4.940e+00 -0.089 0.694 0.783
MgHCO3+ 4.391e-06 2.905e-05 -5.357 -4.537 0.821
MgOH+ 2.845e-07 1.883e-06 -6.546 -5.725 0.821
MgCO3 1.833e-09 1.111e-08 -8.737 -7.954 0.783
Na 2.720e+00
Na+ 2.707e+00 5.184e+00 0.433 0.715 0.282
NaSO4- 1.280e-02 8.469e-02 -1.893 -1.072 0.821
NaHCO3 1.847e-07 1.120e-06 -6.734 -5.951 0.783
NaOH 4.531e-10 2.747e-09 -9.344 -8.561 0.783
NaCO3- 2.628e-11 1.739e-10 -10.580 -9.760 0.821
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -51.054 -50.272 0.783
S(6) 8.986e-01
MgSO4 8.148e-01 4.940e+00 -0.089 0.694 0.783
SO4-2 7.004e-02 3.259e-03 -1.155 -2.487 -1.332
NaSO4- 1.280e-02 8.469e-02 -1.893 -1.072 0.821
KSO4- 9.513e-04 6.294e-03 -3.022 -2.201 0.821
HSO4- 4.789e-07 3.169e-06 -6.320 -5.499 0.821
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
CH4(g) -49.53 -52.39 -2.86 CH4
CO2(g) -3.50 -4.97 -1.47 CO2
H2(g) -18.00 -21.15 -3.15 H2
H2O(g) -1.61 -0.10 1.51 H2O
Halite -0.31 1.27 1.58 NaCl
O2(g) -47.31 -50.27 -2.96 O2
-------------------------------------------
Beginning of inverse modeling calculations.
-------------------------------------------
Solution 1: Black Sea water
Input Delta Input+Delta
pH 8.000e+00 + 0.000e+00 = 8.000e+00
Alkalinity 8.625e-04 + 0.000e+00 = 8.625e-04
Br 4.401e-04 + 0.000e+00 = 4.401e-04
C(-4) 0.000e+00 + 0.000e+00 = 0.000e+00
C(4) 8.284e-04 + 0.000e+00 = 8.284e-04
Ca 5.841e-03 + 0.000e+00 = 5.841e-03
Cl 2.930e-01 + 7.845e-04 = 2.938e-01
H(0) 0.000e+00 + 0.000e+00 = 0.000e+00
K 4.959e-03 + 1.034e-04 = 5.063e-03
Mg 2.806e-02 + -7.016e-04 = 2.736e-02
Na 2.544e-01 + 0.000e+00 = 2.544e-01
O(0) 0.000e+00 + 0.000e+00 = 0.000e+00
S(-2) 0.000e+00 + 0.000e+00 = 0.000e+00
S(6) 1.527e-02 + 7.768e-05 = 1.535e-02
Solution 2: Composition during halite precipitation
Input Delta Input+Delta
pH 5.000e+00 + 5.711e-14 = 5.000e+00
Alkalinity -9.195e-06 + 0.000e+00 = -9.195e-06
Br 3.785e-02 + 9.440e-04 = 3.880e-02
C(-4) 0.000e+00 + 0.000e+00 = 0.000e+00
C(4) 7.019e-06 + 0.000e+00 = 7.019e-06
Ca 0.000e+00 + 0.000e+00 = 0.000e+00
Cl 6.004e+00 + 1.501e-01 = 6.154e+00
H(0) 0.000e+00 + 0.000e+00 = 0.000e+00
K 4.578e-01 + -1.144e-02 = 4.463e-01
Mg 2.353e+00 + 5.883e-02 = 2.412e+00
Na 2.720e+00 + -4.500e-02 = 2.675e+00
O(0) 0.000e+00 + 0.000e+00 = 0.000e+00
S(-2) 0.000e+00 + 0.000e+00 = 0.000e+00
S(6) 8.986e-01 + -2.247e-02 = 8.761e-01
Solution fractions: Minimum Maximum
Solution 1 8.815e+01 8.780e+01 8.815e+01
Solution 2 1.000e+00 1.000e+00 1.000e+00
Phase mole transfers: Minimum Maximum
H2O(g) -4.837e+03 -4.817e+03 -4.817e+03 H2O
Calcite -3.802e-02 -3.897e-02 -3.692e-02 CaCO3
CO2(g) -3.500e-02 -3.615e-02 -3.371e-02 CO2
Gypsum -4.769e-01 -4.907e-01 -4.612e-01 CaSO4:2H2O
Halite -1.975e+01 -2.033e+01 -1.901e+01 NaCl
Redox mole transfers:
Sum of residuals (epsilons in documentation): 1.947e+02
Sum of delta/uncertainty limit: 7.804e+00
Maximum fractional error in element concentration: 2.500e-02
Model contains minimum number of phases.
===============================================================================
Summary of inverse modeling:
Number of models found: 1
Number of minimal models found: 1
Number of infeasible sets of phases saved: 6
Number of calls to cl1: 22
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 2.
------------------------------------
-----------
End of run.
-----------
No memory leaks

0
Sun/examples/ex18.log
View File

550
Sun/examples/ex18.out
View File

@ -1,550 +0,0 @@
Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex18
Output file: ex18.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 18.--Inverse modeling of Madison aquifer
SOLUTION 1 Recharge number 3
units mmol/kgw
temp 9.9
pe 0.
pH 7.55
Ca 1.2
Mg 1.01
Na 0.02
K 0.02
Fe(2) 0.001
Cl 0.02
S(6) 0.16
S(-2) 0
C(4) 4.30
isotope 13C -7.0 1.4
isotope 34S 9.7 0.9
SOLUTION 2 Mysse
units mmol/kgw
temp 63.
pH 6.61
pe 0.
redox S(6)/S(-2)
Ca 11.28
Mg 4.54
Na 31.89
K 2.54
Fe(2) 0.0004
Cl 17.85
S(6) 19.86
S(-2) 0.26
C(4) 6.87
isotope 13C -2.3 0.2
isotope 34S(6) 16.3 1.5
isotope 34S(-2) -22.1 7
INVERSE_MODELING 1
solutions 1 2
uncertainty 0.05
range
isotopes
13C
34S
balances
Fe(2) 1.0
ph 0.1
phases
Dolomite dis 13C 3.0 2
Calcite pre 13C -1.5 1
Anhydrite dis 34S 13.5 2
CH2O dis 13C -25.0 5
Goethite
Pyrite pre 34S -22. 2
CaX2 pre
Ca.75Mg.25X2 pre
MgX2 pre
NaX
Halite
Sylvite
PHASES
Sylvite
KCl = K+ + Cl-
log_k 0.0
CH2O
CH2O + H2O = CO2 + 4H+ + 4e-
log_k 0.0
EXCHANGE_SPECIES
0.75Ca+2 + 0.25Mg+2 + 2X- = Ca.75Mg.25X2
log_k 0.0
END
-----
TITLE
-----
Example 18.--Inverse modeling of Madison aquifer
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1. Recharge number 3
-----------------------------Solution composition------------------------------
Elements Molality Moles
C(4) 4.300e-03 4.300e-03
Ca 1.200e-03 1.200e-03
Cl 2.000e-05 2.000e-05
Fe(2) 1.000e-06 1.000e-06
K 2.000e-05 2.000e-05
Mg 1.010e-03 1.010e-03
Na 2.000e-05 2.000e-05
S(6) 1.600e-04 1.600e-04
----------------------------Description of solution----------------------------
pH = 7.550
pe = 0.000
Activity of water = 1.000
Ionic strength = 6.543e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 4.016e-03
Total CO2 (mol/kg) = 4.300e-03
Temperature (deg C) = 9.900
Electrical balance (eq) = 1.061e-04
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 1.24
Iterations = 8
Total H = 1.110164e+02
Total O = 5.551946e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.120e-07 1.029e-07 -6.951 -6.988 -0.037
H+ 3.038e-08 2.818e-08 -7.517 -7.550 -0.033
H2O 5.551e+01 9.999e-01 1.744 -0.000 0.000
C(4) 4.300e-03
HCO3- 3.929e-03 3.623e-03 -2.406 -2.441 -0.035
CO2 2.970e-04 2.974e-04 -3.527 -3.527 0.001
MgHCO3+ 3.098e-05 2.850e-05 -4.509 -4.545 -0.036
CaHCO3+ 3.027e-05 2.792e-05 -4.519 -4.554 -0.035
CO3-2 5.765e-06 4.168e-06 -5.239 -5.380 -0.141
CaCO3 4.727e-06 4.734e-06 -5.325 -5.325 0.001
MgCO3 2.208e-06 2.211e-06 -5.656 -5.655 0.001
FeHCO3+ 2.086e-07 1.919e-07 -6.681 -6.717 -0.036
FeCO3 5.289e-08 5.297e-08 -7.277 -7.276 0.001
NaHCO3 3.737e-08 3.742e-08 -7.428 -7.427 0.001
NaCO3- 6.948e-10 6.391e-10 -9.158 -9.194 -0.036
Ca 1.200e-03
Ca+2 1.151e-03 8.317e-04 -2.939 -3.080 -0.141
CaHCO3+ 3.027e-05 2.792e-05 -4.519 -4.554 -0.035
CaSO4 1.393e-05 1.395e-05 -4.856 -4.855 0.001
CaCO3 4.727e-06 4.734e-06 -5.325 -5.325 0.001
CaOH+ 5.323e-09 4.897e-09 -8.274 -8.310 -0.036
CaHSO4+ 2.136e-12 1.965e-12 -11.670 -11.707 -0.036
Cl 2.000e-05
Cl- 2.000e-05 1.838e-05 -4.699 -4.736 -0.037
FeCl+ 1.461e-11 1.344e-11 -10.835 -10.872 -0.036
Fe(2) 1.000e-06
Fe+2 7.296e-07 5.298e-07 -6.137 -6.276 -0.139
FeHCO3+ 2.086e-07 1.919e-07 -6.681 -6.717 -0.036
FeCO3 5.289e-08 5.297e-08 -7.277 -7.276 0.001
FeSO4 6.861e-09 6.871e-09 -8.164 -8.163 0.001
FeOH+ 1.969e-09 1.811e-09 -8.706 -8.742 -0.036
FeCl+ 1.461e-11 1.344e-11 -10.835 -10.872 -0.036
FeHSO4+ 1.361e-15 1.252e-15 -14.866 -14.903 -0.036
H(0) 1.316e-18
H2 6.579e-19 6.588e-19 -18.182 -18.181 0.001
K 2.000e-05
K+ 1.999e-05 1.837e-05 -4.699 -4.736 -0.037
KSO4- 1.037e-08 9.538e-09 -7.984 -8.021 -0.036
KOH 2.256e-12 2.260e-12 -11.647 -11.646 0.001
Mg 1.010e-03
Mg+2 9.662e-04 7.011e-04 -3.015 -3.154 -0.139
MgHCO3+ 3.098e-05 2.850e-05 -4.509 -4.545 -0.036
MgSO4 1.063e-05 1.064e-05 -4.974 -4.973 0.001
MgCO3 2.208e-06 2.211e-06 -5.656 -5.655 0.001
MgOH+ 2.335e-08 2.148e-08 -7.632 -7.668 -0.036
Na 2.000e-05
Na+ 1.995e-05 1.837e-05 -4.700 -4.736 -0.036
NaHCO3 3.737e-08 3.742e-08 -7.428 -7.427 0.001
NaSO4- 8.826e-09 8.119e-09 -8.054 -8.090 -0.036
NaCO3- 6.948e-10 6.391e-10 -9.158 -9.194 -0.036
NaOH 4.299e-12 4.306e-12 -11.367 -11.366 0.001
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -61.151 -61.151 0.001
S(6) 1.600e-04
SO4-2 1.354e-04 9.754e-05 -3.868 -4.011 -0.142
CaSO4 1.393e-05 1.395e-05 -4.856 -4.855 0.001
MgSO4 1.063e-05 1.064e-05 -4.974 -4.973 0.001
KSO4- 1.037e-08 9.538e-09 -7.984 -8.021 -0.036
NaSO4- 8.826e-09 8.119e-09 -8.054 -8.090 -0.036
FeSO4 6.861e-09 6.871e-09 -8.164 -8.163 0.001
HSO4- 2.136e-10 1.965e-10 -9.670 -9.707 -0.036
CaHSO4+ 2.136e-12 1.965e-12 -11.670 -11.707 -0.036
FeHSO4+ 1.361e-15 1.252e-15 -14.866 -14.903 -0.036
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -2.76 -7.09 -4.34 CaSO4
Aragonite -0.21 -8.46 -8.25 CaCO3
Calcite -0.05 -8.46 -8.41 CaCO3
CH2O -33.73 -33.73 0.00 CH2O
CO2(g) -2.26 -3.53 -1.27 CO2
Dolomite -0.27 -16.99 -16.72 CaMg(CO3)2
Gypsum -2.50 -7.09 -4.59 CaSO4:2H2O
H2(g) -15.10 -18.18 -3.08 H2
H2O(g) -1.92 -0.00 1.92 H2O
Halite -11.02 -9.47 1.55 NaCl
Melanterite -7.88 -10.29 -2.41 FeSO4:7H2O
O2(g) -58.26 -61.15 -2.89 O2
Siderite -0.86 -11.66 -10.79 FeCO3
Sylvite -9.47 -9.47 0.00 KCl
Initial solution 2. Mysse
-----------------------------Solution composition------------------------------
Elements Molality Moles
C(4) 6.870e-03 6.870e-03
Ca 1.128e-02 1.128e-02
Cl 1.785e-02 1.785e-02
Fe(2) 4.000e-07 4.000e-07
K 2.540e-03 2.540e-03
Mg 4.540e-03 4.540e-03
Na 3.189e-02 3.189e-02
S(-2) 2.600e-04 2.600e-04
S(6) 1.986e-02 1.986e-02
----------------------------Description of solution----------------------------
pH = 6.610
pe = 0.000
Activity of water = 0.999
Ionic strength = 7.256e-02
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 5.258e-03
Total CO2 (mol/kg) = 6.870e-03
Temperature (deg C) = 63.000
Electrical balance (eq) = 3.242e-03
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 3.20
Iterations = 8
Total H = 1.110179e+02
Total O = 5.560448e+01
---------------------------------Redox couples---------------------------------
Redox couple pe Eh (volts)
S(-2)/S(6) -3.6487 -0.2434
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 5.726e-07 4.419e-07 -6.242 -6.355 -0.112
H+ 2.963e-07 2.455e-07 -6.528 -6.610 -0.082
H2O 5.551e+01 9.985e-01 1.744 -0.001 0.000
C(4) 6.870e-03
HCO3- 4.711e-03 3.746e-03 -2.327 -2.426 -0.100
CO2 1.784e-03 1.814e-03 -2.749 -2.741 0.007
CaHCO3+ 2.347e-04 1.867e-04 -3.629 -3.729 -0.100
MgHCO3+ 6.578e-05 5.169e-05 -4.182 -4.287 -0.105
NaHCO3 5.046e-05 5.131e-05 -4.297 -4.290 0.007
CaCO3 1.560e-05 1.586e-05 -4.807 -4.800 0.007
NaCO3- 3.512e-06 2.760e-06 -5.454 -5.559 -0.105
CO3-2 2.780e-06 1.112e-06 -5.556 -5.954 -0.398
MgCO3 1.642e-06 1.670e-06 -5.784 -5.777 0.007
FeHCO3+ 1.177e-08 9.248e-09 -7.929 -8.034 -0.105
FeCO3 6.474e-10 6.583e-10 -9.189 -9.182 0.007
Ca 1.128e-02
Ca+2 7.217e-03 2.899e-03 -2.142 -2.538 -0.396
CaSO4 3.813e-03 3.877e-03 -2.419 -2.411 0.007
CaHCO3+ 2.347e-04 1.867e-04 -3.629 -3.729 -0.100
CaCO3 1.560e-05 1.586e-05 -4.807 -4.800 0.007
CaHSO4+ 1.322e-08 1.039e-08 -7.879 -7.983 -0.105
CaOH+ 2.491e-09 1.957e-09 -8.604 -8.708 -0.105
Cl 1.785e-02
Cl- 1.785e-02 1.381e-02 -1.748 -1.860 -0.111
FeCl+ 5.988e-10 4.706e-10 -9.223 -9.327 -0.105
Fe(2) 4.000e-07
Fe(HS)2 2.830e-07 2.878e-07 -6.548 -6.541 0.007
Fe+2 5.978e-08 2.468e-08 -7.223 -7.608 -0.384
FeSO4 3.911e-08 3.977e-08 -7.408 -7.400 0.007
FeHCO3+ 1.177e-08 9.248e-09 -7.929 -8.034 -0.105
Fe(HS)3- 4.561e-09 3.585e-09 -8.341 -8.446 -0.105
FeCO3 6.474e-10 6.583e-10 -9.189 -9.182 0.007
FeCl+ 5.988e-10 4.706e-10 -9.223 -9.327 -0.105
FeOH+ 5.014e-10 3.940e-10 -9.300 -9.404 -0.105
FeHSO4+ 1.125e-13 8.843e-14 -12.949 -13.053 -0.105
H(0) 1.190e-09
H2 5.948e-10 6.048e-10 -9.226 -9.218 0.007
K 2.540e-03
K+ 2.394e-03 1.852e-03 -2.621 -2.732 -0.111
KSO4- 1.459e-04 1.146e-04 -3.836 -3.941 -0.105
KOH 2.569e-11 2.613e-11 -10.590 -10.583 0.007
Mg 4.540e-03
MgSO4 2.360e-03 2.399e-03 -2.627 -2.620 0.007
Mg+2 2.113e-03 8.783e-04 -2.675 -3.056 -0.381
MgHCO3+ 6.578e-05 5.169e-05 -4.182 -4.287 -0.105
MgCO3 1.642e-06 1.670e-06 -5.784 -5.777 0.007
MgOH+ 3.463e-07 2.721e-07 -6.461 -6.565 -0.105
Na 3.189e-02
Na+ 3.090e-02 2.435e-02 -1.510 -1.613 -0.103
NaSO4- 9.408e-04 7.393e-04 -3.027 -3.131 -0.105
NaHCO3 5.046e-05 5.131e-05 -4.297 -4.290 0.007
NaCO3- 3.512e-06 2.760e-06 -5.454 -5.559 -0.105
NaOH 6.437e-10 6.545e-10 -9.191 -9.184 0.007
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -63.075 -63.067 0.007
S(-2) 2.600e-04
HS- 1.482e-04 1.144e-04 -3.829 -3.942 -0.112
H2S 1.112e-04 1.131e-04 -3.954 -3.947 0.007
Fe(HS)2 2.830e-07 2.878e-07 -6.548 -6.541 0.007
Fe(HS)3- 4.561e-09 3.585e-09 -8.341 -8.446 -0.105
S-2 1.449e-09 5.662e-10 -8.839 -9.247 -0.408
S(6) 1.986e-02
SO4-2 1.260e-02 4.892e-03 -1.900 -2.311 -0.411
CaSO4 3.813e-03 3.877e-03 -2.419 -2.411 0.007
MgSO4 2.360e-03 2.399e-03 -2.627 -2.620 0.007
NaSO4- 9.408e-04 7.393e-04 -3.027 -3.131 -0.105
KSO4- 1.459e-04 1.146e-04 -3.836 -3.941 -0.105
HSO4- 3.792e-07 2.980e-07 -6.421 -6.526 -0.105
FeSO4 3.911e-08 3.977e-08 -7.408 -7.400 0.007
CaHSO4+ 1.322e-08 1.039e-08 -7.879 -7.983 -0.105
FeHSO4+ 1.125e-13 8.843e-14 -12.949 -13.053 -0.105
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -0.14 -4.85 -4.71 CaSO4
Aragonite 0.18 -8.49 -8.67 CaCO3
Calcite 0.30 -8.49 -8.79 CaCO3
CH2O -14.59 -14.59 0.00 CH2O
CO2(g) -0.94 -2.74 -1.80 CO2
Dolomite 0.37 -17.50 -17.87 CaMg(CO3)2
FeS(ppt) -1.02 -4.94 -3.92 FeS
Gypsum -0.18 -4.85 -4.67 CaSO4:2H2O
H2(g) -5.92 -9.22 -3.30 H2
H2O(g) -0.64 -0.00 0.64 H2O
H2S(g) -2.57 -3.95 -1.38 H2S
Halite -5.13 -3.47 1.66 NaCl
Mackinawite -0.29 -4.94 -4.65 FeS
Melanterite -8.07 -9.92 -1.85 FeSO4:7H2O
O2(g) -59.95 -63.07 -3.11 O2
Pyrite 7.97 -9.57 -17.54 FeS2
Siderite -2.47 -13.56 -11.10 FeCO3
Sulfur -2.12 1.98 4.09 S
Sylvite -4.59 -4.59 0.00 KCl
-------------------------------------------
Beginning of inverse modeling calculations.
-------------------------------------------
Solution 1: Recharge number 3
Input Delta Input+Delta
pH 7.550e+00 + 0.000e+00 = 7.550e+00
Alkalinity 4.016e-03 + 0.000e+00 = 4.016e-03
C(-4) 0.000e+00 + 0.000e+00 = 0.000e+00
C(4) 4.300e-03 + 0.000e+00 = 4.300e-03
Ca 1.200e-03 + -5.306e-05 = 1.147e-03
Cl 2.000e-05 + 0.000e+00 = 2.000e-05
Fe(2) 1.000e-06 + 0.000e+00 = 1.000e-06
Fe(3) 0.000e+00 + 0.000e+00 = 0.000e+00
H(0) 0.000e+00 + 0.000e+00 = 0.000e+00
K 2.000e-05 + 0.000e+00 = 2.000e-05
Mg 1.010e-03 + 0.000e+00 = 1.010e-03
Na 2.000e-05 + 0.000e+00 = 2.000e-05
O(0) 0.000e+00 + 0.000e+00 = 0.000e+00
S(-2) 0.000e+00 + 0.000e+00 = 0.000e+00
S(6) 1.600e-04 + 0.000e+00 = 1.600e-04
X 0.000e+00 + 0.000e+00 = 0.000e+00
13C(-4) -7 + 0 = -7
13C(4) -7 + 0 = -7
34S(-2) 9.7 + 0 = 9.7
34S(6) 9.7 + 0 = 9.7
Solution 2: Mysse
Input Delta Input+Delta
pH 6.610e+00 + 0.000e+00 = 6.610e+00
Alkalinity 5.258e-03 + 0.000e+00 = 5.258e-03
C(-4) 0.000e+00 + 0.000e+00 = 0.000e+00
C(4) 6.870e-03 + 0.000e+00 = 6.870e-03
Ca 1.128e-02 + 0.000e+00 = 1.128e-02
Cl 1.785e-02 + 0.000e+00 = 1.785e-02
Fe(2) 4.000e-07 + 0.000e+00 = 4.000e-07
Fe(3) 0.000e+00 + 0.000e+00 = 0.000e+00
H(0) 1.190e-09 + 0.000e+00 = 1.190e-09
K 2.540e-03 + 0.000e+00 = 2.540e-03
Mg 4.540e-03 + 0.000e+00 = 4.540e-03
Na 3.189e-02 + -1.256e-03 = 3.063e-02
O(0) 0.000e+00 + 0.000e+00 = 0.000e+00
S(-2) 2.600e-04 + 0.000e+00 = 2.600e-04
S(6) 1.986e-02 + 9.930e-04 = 2.085e-02
X 0.000e+00 + 0.000e+00 = 0.000e+00
13C(-4) -2.3 + 0 = -2.3
13C(4) -2.3 + 0 = -2.3
34S(-2) -22.1 + 0 = -22.1
34S(6) 16.3 + 0 = 16.3
Isotopic composition of phases:
13C Dolomite 3 + 0 = 3
13C Calcite -1.5 + 0 = -1.5
34S Anhydrite 13.5 + -0.65116 = 12.8488
13C CH2O -25 + 3.56577 = -21.4342
34S Pyrite -22 + 2 = -20
Solution fractions: Minimum Maximum
Solution 1 1.000e+00 9.999e-01 1.000e+00
Solution 2 1.000e+00 1.000e+00 1.000e+00
Phase mole transfers: Minimum Maximum
Dolomite 1.118e-02 1.022e-02 1.193e-02 CaMg(CO3)2
Calcite -2.393e-02 -2.567e-02 -2.144e-02 CaCO3
Anhydrite 2.288e-02 2.076e-02 2.348e-02 CaSO4
CH2O 4.138e-03 3.003e-03 5.273e-03 CH2O
Goethite 9.642e-04 6.533e-04 1.275e-03 FeOOH
Pyrite -9.648e-04 -1.274e-03 -6.553e-04 FeS2
MgX2 -7.652e-03 -8.576e-03 -6.972e-03 MgX2
NaX 1.530e-02 1.394e-02 1.715e-02 NaX
Halite 1.531e-02 1.429e-02 1.633e-02 NaCl
Sylvite 2.520e-03 2.392e-03 2.648e-03 KCl
Redox mole transfers:
Fe(3) 9.642e-04
H(0) -1.190e-09
S(-2) -2.190e-03
Sum of residuals (epsilons in documentation): 2.684e+00
Sum of delta/uncertainty limit: 4.711e+00
Maximum fractional error in element concentration: 5.000e-02
Model contains minimum number of phases.
===============================================================================
Solution 1: Recharge number 3
Input Delta Input+Delta
pH 7.550e+00 + 0.000e+00 = 7.550e+00
Alkalinity 4.016e-03 + 1.061e-04 = 4.122e-03
C(-4) 0.000e+00 + 0.000e+00 = 0.000e+00
C(4) 4.300e-03 + 1.136e-04 = 4.414e-03
Ca 1.200e-03 + 0.000e+00 = 1.200e-03
Cl 2.000e-05 + 0.000e+00 = 2.000e-05
Fe(2) 1.000e-06 + 0.000e+00 = 1.000e-06
Fe(3) 0.000e+00 + 0.000e+00 = 0.000e+00
H(0) 0.000e+00 + 0.000e+00 = 0.000e+00
K 2.000e-05 + 0.000e+00 = 2.000e-05
Mg 1.010e-03 + 0.000e+00 = 1.010e-03
Na 2.000e-05 + 0.000e+00 = 2.000e-05
O(0) 0.000e+00 + 0.000e+00 = 0.000e+00
S(-2) 0.000e+00 + 0.000e+00 = 0.000e+00
S(6) 1.600e-04 + 0.000e+00 = 1.600e-04
X 0.000e+00 + 0.000e+00 = 0.000e+00
13C(-4) -7 + 0 = -7
13C(4) -7 + 0 = -7
34S(-2) 9.7 + 0 = 9.7
34S(6) 9.7 + 0 = 9.7
Solution 2: Mysse
Input Delta Input+Delta
pH 6.610e+00 + 5.872e-02 = 6.669e+00
Alkalinity 5.258e-03 + 0.000e+00 = 5.258e-03
C(-4) 0.000e+00 + 0.000e+00 = 0.000e+00
C(4) 6.870e-03 + -2.581e-04 = 6.612e-03
Ca 1.128e-02 + 0.000e+00 = 1.128e-02
Cl 1.785e-02 + 0.000e+00 = 1.785e-02
Fe(2) 4.000e-07 + 0.000e+00 = 4.000e-07
Fe(3) 0.000e+00 + 0.000e+00 = 0.000e+00
H(0) 1.190e-09 + 0.000e+00 = 1.190e-09
K 2.540e-03 + 0.000e+00 = 2.540e-03
Mg 4.540e-03 + 0.000e+00 = 4.540e-03
Na 3.189e-02 + -1.256e-03 = 3.063e-02
O(0) 0.000e+00 + 0.000e+00 = 0.000e+00
S(-2) 2.600e-04 + 0.000e+00 = 2.600e-04
S(6) 1.986e-02 + 9.930e-04 = 2.085e-02
X 0.000e+00 + 0.000e+00 = 0.000e+00
13C(-4) -2.3 + 0 = -2.3
13C(4) -2.3 + 0 = -2.3
34S(-2) -22.1 + 0 = -22.1
34S(6) 16.3 + 0 = 16.3
Isotopic composition of phases:
13C Dolomite 3 + 2 = 5
13C Calcite -1.5 + -1 = -2.5
34S Anhydrite 13.5 + -0.119926 = 13.3801
13C CH2O -25 + 5 = -20
34S Pyrite -22 + 2 = -20
Solution fractions: Minimum Maximum
Solution 1 1.000e+00 1.000e+00 1.000e+00
Solution 2 1.000e+00 1.000e+00 1.000e+00
Phase mole transfers: Minimum Maximum
Dolomite 5.443e-03 4.995e-03 5.838e-03 CaMg(CO3)2
Calcite -1.214e-02 -1.333e-02 -1.098e-02 CaCO3
Anhydrite 2.252e-02 2.076e-02 2.297e-02 CaSO4
CH2O 3.455e-03 3.003e-03 4.297e-03 CH2O
Goethite 7.821e-04 6.533e-04 1.015e-03 FeOOH
Pyrite -7.827e-04 -1.014e-03 -6.553e-04 FeS2
Ca.75Mg.25X2 -7.652e-03 -8.576e-03 -6.972e-03 Ca.75Mg.25X2
NaX 1.530e-02 1.394e-02 1.715e-02 NaX
Halite 1.531e-02 1.429e-02 1.633e-02 NaCl
Sylvite 2.520e-03 2.392e-03 2.648e-03 KCl
Redox mole transfers:
Fe(3) 7.821e-04
H(0) -1.190e-09
S(-2) -1.825e-03
Sum of residuals (epsilons in documentation): 4.207e+00
Sum of delta/uncertainty limit: 8.243e+00
Maximum fractional error in element concentration: 5.000e-02
Model contains minimum number of phases.
===============================================================================
Summary of inverse modeling:
Number of models found: 2
Number of minimal models found: 2
Number of infeasible sets of phases saved: 28
Number of calls to cl1: 80
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 2.
------------------------------------
-----------
End of run.
-----------
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sim state soln dist_x time step pH pe temp si_anhydrite si_gypsum
1 i_soln 1 -99 -99 -99 7 4 25.000 -999.9990 -999.9990
1 react 1 -99 0 1 7.06676 10.6862 25.000 -0.2197 0.0000
1 react 1 -99 0 2 7.05329 10.6168 26.000 -0.2157 0.0000
1 react 1 -99 0 3 7.03993 10.5719 27.000 -0.2115 0.0000
1 react 1 -99 0 4 7.02667 10.4793 28.000 -0.2071 0.0000
1 react 1 -99 0 5 7.01353 10.4109 29.000 -0.2025 0.0000
1 react 1 -99 0 6 7.00051 10.3439 30.000 -0.1977 0.0000
1 react 1 -99 0 7 6.9876 10.2766 31.000 -0.1928 0.0000
1 react 1 -99 0 8 6.97482 10.2099 32.000 -0.1877 0.0000
1 react 1 -99 0 9 6.96217 10.149 33.000 -0.1824 0.0000
1 react 1 -99 0 10 6.94965 10.0785 34.000 -0.1769 0.0000
1 react 1 -99 0 11 6.93726 10.0131 35.000 -0.1713 0.0000
1 react 1 -99 0 12 6.925 9.94603 36.000 -0.1655 0.0000
1 react 1 -99 0 13 6.91288 9.88397 37.000 -0.1595 0.0000
1 react 1 -99 0 14 6.90089 9.86516 38.000 -0.1533 0.0000
1 react 1 -99 0 15 6.88905 9.75536 39.000 -0.1470 0.0000
1 react 1 -99 0 16 6.87734 9.69233 40.000 -0.1406 0.0000
1 react 1 -99 0 17 6.86578 9.62865 41.000 -0.1340 0.0000
1 react 1 -99 0 18 6.85435 9.56448 42.000 -0.1272 0.0000
1 react 1 -99 0 19 6.84307 9.50323 43.000 -0.1203 0.0000
1 react 1 -99 0 20 6.83193 9.44484 44.000 -0.1132 0.0000
1 react 1 -99 0 21 6.82093 9.37869 45.000 -0.1060 0.0000
1 react 1 -99 0 22 6.81008 9.31598 46.000 -0.0986 0.0000
1 react 1 -99 0 23 6.79936 9.25548 47.000 -0.0911 0.0000
1 react 1 -99 0 24 6.78879 9.19236 48.000 -0.0835 0.0000
1 react 1 -99 0 25 6.77836 9.14193 49.000 -0.0757 0.0000
1 react 1 -99 0 26 6.76807 9.07059 50.000 -0.0678 0.0000
1 react 1 -99 0 27 6.75793 9.01241 51.000 -0.0597 0.0000
1 react 1 -99 0 28 6.74792 8.95269 52.000 -0.0515 0.0000
1 react 1 -99 0 29 6.73806 8.89104 53.000 -0.0432 0.0000
1 react 1 -99 0 30 6.72833 8.83437 54.000 -0.0347 0.0000
1 react 1 -99 0 31 6.71874 8.77256 55.000 -0.0261 0.0000
1 react 1 -99 0 32 6.7093 8.71589 56.000 -0.0174 0.0000
1 react 1 -99 0 33 6.69999 8.65867 57.000 -0.0085 0.0000
1 react 1 -99 0 34 6.69076 8.59025 58.000 0.0000 -0.0004
1 react 1 -99 0 35 6.68054 8.53312 59.000 0.0000 -0.0095
1 react 1 -99 0 36 6.67043 8.4773 60.000 0.0000 -0.0187
1 react 1 -99 0 37 6.66041 8.42236 61.000 0.0000 -0.0280
1 react 1 -99 0 38 6.65049 8.36458 62.000 0.0000 -0.0375
1 react 1 -99 0 39 6.64066 8.22145 63.000 0.0000 -0.0471
1 react 1 -99 0 40 6.63093 8.25388 64.000 0.0000 -0.0567
1 react 1 -99 0 41 6.62129 8.1986 65.000 0.0000 -0.0665
1 react 1 -99 0 42 6.61175 8.05474 66.000 0.0000 -0.0764
1 react 1 -99 0 43 6.6023 8.09202 67.000 0.0000 -0.0864
1 react 1 -99 0 44 6.59294 8.03836 68.000 0.0000 -0.0966
1 react 1 -99 0 45 6.58367 7.98491 69.000 0.0000 -0.1068
1 react 1 -99 0 46 6.57449 7.93039 70.000 0.0000 -0.1171
1 react 1 -99 0 47 6.5654 7.87729 71.000 0.0000 -0.1276
1 react 1 -99 0 48 6.55641 7.82446 72.000 0.0000 -0.1381
1 react 1 -99 0 49 6.5475 7.76904 73.000 0.0000 -0.1488
1 react 1 -99 0 50 6.53867 7.71679 74.000 0.0000 -0.1595
1 react 1 -99 0 51 6.52994 7.66434 75.000 0.0000 -0.1704

0
Sun/examples/ex3.log
View File

789
Sun/examples/ex3.out
View File

@ -1,789 +0,0 @@
Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex3
Output file: ex3.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 3, part A.--Calcite equilibrium at log Pco2 = -2.0 and 25C.
SOLUTION 1 Pure water
pH 7.0
temp 25.0
EQUILIBRIUM_PHASES
CO2(g) -2.0
Calcite 0.0
SAVE solution 1
END
-----
TITLE
-----
Example 3, part A.--Calcite equilibrium at log Pco2 = -2.0 and 25C.
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1. Pure water
-----------------------------Solution composition------------------------------
Elements Molality Moles
Pure water
----------------------------Description of solution----------------------------
pH = 7.000
pe = 4.000
Activity of water = 1.000
Ionic strength = 1.001e-07
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 1.082e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.082e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.05
Iterations = 0
Total H = 1.110124e+02
Total O = 5.550622e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.002e-07 1.001e-07 -6.999 -6.999 -0.000
H+ 1.001e-07 1.000e-07 -7.000 -7.000 -0.000
H2O 5.551e+01 1.000e+00 1.744 0.000 0.000
H(0) 1.416e-25
H2 7.079e-26 7.079e-26 -25.150 -25.150 0.000
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -42.080 -42.080 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -22.00 -25.15 -3.15 H2
H2O(g) -1.51 0.00 1.51 H2O
O2(g) -39.12 -42.08 -2.96 O2
-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------
Reaction step 1.
Using solution 1. Pure water
Using pure phase assemblage 1.
-------------------------------Phase assemblage--------------------------------
Moles in assemblage
Phase SI log IAP log KT Initial Final Delta
Calcite 0.00 -8.48 -8.48 1.000e+01 9.998e+00 -1.646e-03
CO2(g) -2.00 -20.15 -18.15 1.000e+01 9.998e+00 -1.976e-03
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 3.622e-03 3.622e-03
Ca 1.646e-03 1.646e-03
----------------------------Description of solution----------------------------
pH = 7.297 Charge balance
pe = -0.987 Adjusted to redox equilibrium
Activity of water = 1.000
Ionic strength = 4.826e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 3.291e-03
Total CO2 (mol/kg) = 3.622e-03
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.082e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 16
Total H = 1.110124e+02
Total O = 5.551511e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 2.137e-07 1.982e-07 -6.670 -6.703 -0.033
H+ 5.403e-08 5.050e-08 -7.267 -7.297 -0.029
H2O 5.551e+01 9.999e-01 1.744 -0.000 0.000
C(-4) 2.799e-30
CH4 2.799e-30 2.802e-30 -29.553 -29.552 0.000
C(4) 3.622e-03
HCO3- 3.224e-03 2.998e-03 -2.492 -2.523 -0.032
CO2 3.401e-04 3.405e-04 -3.468 -3.468 0.000
CaHCO3+ 4.894e-05 4.551e-05 -4.310 -4.342 -0.032
CaCO3 5.559e-06 5.565e-06 -5.255 -5.255 0.000
CO3-2 3.721e-06 2.784e-06 -5.429 -5.555 -0.126
Ca 1.646e-03
Ca+2 1.591e-03 1.190e-03 -2.798 -2.925 -0.126
CaHCO3+ 4.894e-05 4.551e-05 -4.310 -4.342 -0.032
CaCO3 5.559e-06 5.565e-06 -5.255 -5.255 0.000
CaOH+ 4.212e-09 3.910e-09 -8.376 -8.408 -0.032
H(0) 3.403e-16
H2 1.701e-16 1.703e-16 -15.769 -15.769 0.000
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -60.843 -60.843 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Aragonite -0.14 -8.48 -8.34 CaCO3
Calcite 0.00 -8.48 -8.48 CaCO3
CH4(g) -26.69 -29.55 -2.86 CH4
CO2(g) -2.00 -3.47 -1.47 CO2
H2(g) -12.62 -15.77 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
O2(g) -57.88 -60.84 -2.96 O2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 2.
------------------------------------
TITLE Example 3, part B.--Definition of seawater.
SOLUTION 2 Seawater
units ppm
pH 8.22
pe 8.451
density 1.023
temp 25.0
Ca 412.3
Mg 1291.8
Na 10768.0
K 399.1
Si 4.28
Cl 19353.0
Alkalinity 141.682 as HCO3
S(6) 2712.0
END
-----
TITLE
-----
Example 3, part B.--Definition of seawater.
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 2. Seawater
-----------------------------Solution composition------------------------------
Elements Molality Moles
Alkalinity 2.406e-03 2.406e-03
Ca 1.066e-02 1.066e-02
Cl 5.657e-01 5.657e-01
K 1.058e-02 1.058e-02
Mg 5.507e-02 5.507e-02
Na 4.854e-01 4.854e-01
S(6) 2.926e-02 2.926e-02
Si 7.382e-05 7.382e-05
----------------------------Description of solution----------------------------
pH = 8.220
pe = 8.451
Activity of water = 0.981
Ionic strength = 6.748e-01
Mass of water (kg) = 1.000e+00
Total carbon (mol/kg) = 2.180e-03
Total CO2 (mol/kg) = 2.180e-03
Temperature (deg C) = 25.000
Electrical balance (eq) = 7.967e-04
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 0.07
Iterations = 7
Total H = 1.110147e+02
Total O = 5.563008e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 2.674e-06 1.629e-06 -5.573 -5.788 -0.215
H+ 7.981e-09 6.026e-09 -8.098 -8.220 -0.122
H2O 5.551e+01 9.806e-01 1.744 -0.009 0.000
C(4) 2.180e-03
HCO3- 1.514e-03 1.023e-03 -2.820 -2.990 -0.170
MgHCO3+ 2.196e-04 1.640e-04 -3.658 -3.785 -0.127
NaHCO3 1.668e-04 1.948e-04 -3.778 -3.710 0.067
MgCO3 8.914e-05 1.041e-04 -4.050 -3.982 0.067
NaCO3- 6.719e-05 5.020e-05 -4.173 -4.299 -0.127
CaHCO3+ 4.598e-05 3.106e-05 -4.337 -4.508 -0.170
CO3-2 3.821e-05 7.960e-06 -4.418 -5.099 -0.681
CaCO3 2.725e-05 3.183e-05 -4.565 -4.497 0.067
CO2 1.210e-05 1.413e-05 -4.917 -4.850 0.067
Ca 1.066e-02
Ca+2 9.504e-03 2.380e-03 -2.022 -2.623 -0.601
CaSO4 1.083e-03 1.266e-03 -2.965 -2.898 0.067
CaHCO3+ 4.598e-05 3.106e-05 -4.337 -4.508 -0.170
CaCO3 2.725e-05 3.183e-05 -4.565 -4.497 0.067
CaOH+ 8.604e-08 6.429e-08 -7.065 -7.192 -0.127
CaHSO4+ 5.979e-11 4.467e-11 -10.223 -10.350 -0.127
Cl 5.657e-01
Cl- 5.657e-01 3.528e-01 -0.247 -0.452 -0.205
H(0) 5.515e-37
H2 2.757e-37 3.221e-37 -36.559 -36.492 0.067
K 1.058e-02
K+ 1.041e-02 6.495e-03 -1.982 -2.187 -0.205
KSO4- 1.627e-04 1.216e-04 -3.789 -3.915 -0.127
KOH 3.137e-09 3.665e-09 -8.503 -8.436 0.067
Mg 5.507e-02
Mg+2 4.742e-02 1.371e-02 -1.324 -1.863 -0.539
MgSO4 7.330e-03 8.562e-03 -2.135 -2.067 0.067
MgHCO3+ 2.196e-04 1.640e-04 -3.658 -3.785 -0.127
MgCO3 8.914e-05 1.041e-04 -4.050 -3.982 0.067
MgOH+ 1.084e-05 8.100e-06 -4.965 -5.092 -0.127
Na 4.854e-01
Na+ 4.791e-01 3.387e-01 -0.320 -0.470 -0.151
NaSO4- 6.053e-03 4.523e-03 -2.218 -2.345 -0.127
NaHCO3 1.668e-04 1.948e-04 -3.778 -3.710 0.067
NaCO3- 6.719e-05 5.020e-05 -4.173 -4.299 -0.127
NaOH 3.117e-07 3.641e-07 -6.506 -6.439 0.067
O(0) 6.614e-20
O2 3.307e-20 3.863e-20 -19.481 -19.413 0.067
S(6) 2.926e-02
SO4-2 1.463e-02 2.664e-03 -1.835 -2.574 -0.740
MgSO4 7.330e-03 8.562e-03 -2.135 -2.067 0.067
NaSO4- 6.053e-03 4.523e-03 -2.218 -2.345 -0.127
CaSO4 1.083e-03 1.266e-03 -2.965 -2.898 0.067
KSO4- 1.627e-04 1.216e-04 -3.789 -3.915 -0.127
HSO4- 2.089e-09 1.561e-09 -8.680 -8.807 -0.127
CaHSO4+ 5.979e-11 4.467e-11 -10.223 -10.350 -0.127
Si 7.382e-05
H4SiO4 7.110e-05 8.306e-05 -4.148 -4.081 0.067
H3SiO4- 2.720e-06 2.032e-06 -5.565 -5.692 -0.127
H2SiO4-2 7.362e-11 2.294e-11 -10.133 -10.639 -0.506
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -0.84 -5.20 -4.36 CaSO4
Aragonite 0.61 -7.72 -8.34 CaCO3
Calcite 0.76 -7.72 -8.48 CaCO3
Chalcedony -0.51 -4.06 -3.55 SiO2
Chrysotile 3.36 35.56 32.20 Mg3Si2O5(OH)4
CO2(g) -3.38 -4.85 -1.47 CO2
Dolomite 2.41 -14.68 -17.09 CaMg(CO3)2
Gypsum -0.63 -5.21 -4.58 CaSO4:2H2O
H2(g) -33.34 -36.49 -3.15 H2
H2O(g) -1.52 -0.01 1.51 H2O
Halite -2.50 -0.92 1.58 NaCl
O2(g) -16.45 -19.41 -2.96 O2
Quartz -0.08 -4.06 -3.98 SiO2
Sepiolite 1.16 16.92 15.76 Mg2Si3O7.5OH:3H2O
Sepiolite(d) -1.74 16.92 18.66 Mg2Si3O7.5OH:3H2O
SiO2(a) -1.35 -4.06 -2.71 SiO2
Talc 6.04 27.44 21.40 Mg3Si4O10(OH)2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 3.
------------------------------------
TITLE Example 3, part C.--Mix 70% ground water, 30% seawater.
MIX 1
1 0.7
2 0.3
SAVE solution 3
END
-----
TITLE
-----
Example 3, part C.--Mix 70% ground water, 30% seawater.
-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------
Reaction step 1.
Using mix 1.
Mixture 1.
7.000e-01 Solution 1 Solution after simulation 1.
3.000e-01 Solution 2 Seawater
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 3.189e-03 3.189e-03
Ca 4.350e-03 4.350e-03
Cl 1.697e-01 1.697e-01
K 3.173e-03 3.173e-03
Mg 1.652e-02 1.652e-02
Na 1.456e-01 1.456e-01
S 8.777e-03 8.777e-03
Si 2.215e-05 2.215e-05
----------------------------Description of solution----------------------------
pH = 7.351 Charge balance
pe = -1.717 Adjusted to redox equilibrium
Activity of water = 0.994
Ionic strength = 2.087e-01
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 3.026e-03
Total CO2 (mol/kg) = 3.189e-03
Temperature (deg C) = 25.000
Electrical balance (eq) = 2.390e-04
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 0.06
Iterations = 13
Total H = 1.110131e+02
Total O = 5.554960e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 3.170e-07 2.231e-07 -6.499 -6.651 -0.153
H+ 5.603e-08 4.460e-08 -7.252 -7.351 -0.099
H2O 5.551e+01 9.941e-01 1.744 -0.003 0.000
C(-4) 4.007e-25
CH4 4.007e-25 4.204e-25 -24.397 -24.376 0.021
C(4) 3.189e-03
HCO3- 2.662e-03 1.980e-03 -2.575 -2.703 -0.129
CO2 1.904e-04 1.998e-04 -3.720 -3.699 0.021
MgHCO3+ 1.545e-04 1.151e-04 -3.811 -3.939 -0.128
NaHCO3 1.137e-04 1.192e-04 -3.944 -3.924 0.021
CaHCO3+ 4.245e-05 3.158e-05 -4.372 -4.501 -0.129
MgCO3 9.408e-06 9.871e-06 -5.027 -5.006 0.021
CO3-2 6.803e-06 2.082e-06 -5.167 -5.682 -0.514
NaCO3- 5.572e-06 4.151e-06 -5.254 -5.382 -0.128
CaCO3 4.166e-06 4.371e-06 -5.380 -5.359 0.021
Ca 4.350e-03
Ca+2 3.928e-03 1.250e-03 -2.406 -2.903 -0.497
CaSO4 3.753e-04 3.938e-04 -3.426 -3.405 0.021
CaHCO3+ 4.245e-05 3.158e-05 -4.372 -4.501 -0.129
CaCO3 4.166e-06 4.371e-06 -5.380 -5.359 0.021
CaOH+ 6.204e-09 4.622e-09 -8.207 -8.335 -0.128
CaHSO4+ 1.381e-10 1.029e-10 -9.860 -9.988 -0.128
Cl 1.697e-01
Cl- 1.697e-01 1.203e-01 -0.770 -0.920 -0.149
H(0) 7.279e-15
H2 3.640e-15 3.819e-15 -14.439 -14.418 0.021
K 3.173e-03
K+ 3.140e-03 2.226e-03 -2.503 -2.652 -0.149
KSO4- 3.316e-05 2.470e-05 -4.479 -4.607 -0.128
KOH 1.639e-10 1.720e-10 -9.785 -9.764 0.021
Mg 1.652e-02
Mg+2 1.460e-02 4.968e-03 -1.836 -2.304 -0.468
MgSO4 1.753e-03 1.839e-03 -2.756 -2.735 0.021
MgHCO3+ 1.545e-04 1.151e-04 -3.811 -3.939 -0.128
MgCO3 9.408e-06 9.871e-06 -5.027 -5.006 0.021
MgOH+ 5.396e-07 4.020e-07 -6.268 -6.396 -0.128
Na 1.456e-01
Na+ 1.444e-01 1.071e-01 -0.841 -0.970 -0.130
NaSO4- 1.138e-03 8.476e-04 -2.944 -3.072 -0.128
NaHCO3 1.137e-04 1.192e-04 -3.944 -3.924 0.021
NaCO3- 5.572e-06 4.151e-06 -5.254 -5.382 -0.128
NaOH 1.503e-08 1.577e-08 -7.823 -7.802 0.021
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -63.570 -63.549 0.021
S(-2) 4.890e-22
HS- 3.876e-22 2.728e-22 -21.412 -21.564 -0.153
H2S 1.014e-22 1.064e-22 -21.994 -21.973 0.021
S-2 2.513e-27 7.386e-28 -26.600 -27.132 -0.532
S(6) 8.777e-03
SO4-2 5.478e-03 1.579e-03 -2.261 -2.802 -0.540
MgSO4 1.753e-03 1.839e-03 -2.756 -2.735 0.021
NaSO4- 1.138e-03 8.476e-04 -2.944 -3.072 -0.128
CaSO4 3.753e-04 3.938e-04 -3.426 -3.405 0.021
KSO4- 3.316e-05 2.470e-05 -4.479 -4.607 -0.128
HSO4- 9.193e-09 6.849e-09 -8.037 -8.164 -0.128
CaHSO4+ 1.381e-10 1.029e-10 -9.860 -9.988 -0.128
Si 2.215e-05
H4SiO4 2.204e-05 2.313e-05 -4.657 -4.636 0.021
H3SiO4- 1.026e-07 7.646e-08 -6.989 -7.117 -0.128
H2SiO4-2 3.784e-13 1.166e-13 -12.422 -12.933 -0.511
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -1.34 -5.70 -4.36 CaSO4
Aragonite -0.25 -8.58 -8.34 CaCO3
Calcite -0.10 -8.58 -8.48 CaCO3
CH4(g) -21.52 -24.38 -2.86 CH4
Chalcedony -1.08 -4.63 -3.55 SiO2
Chrysotile -4.28 27.92 32.20 Mg3Si2O5(OH)4
CO2(g) -2.23 -3.70 -1.47 CO2
Dolomite 0.52 -16.57 -17.09 CaMg(CO3)2
Gypsum -1.13 -5.71 -4.58 CaSO4:2H2O
H2(g) -11.27 -14.42 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
H2S(g) -20.98 -21.97 -1.00 H2S
Halite -3.47 -1.89 1.58 NaCl
O2(g) -60.59 -63.55 -2.96 O2
Quartz -0.65 -4.63 -3.98 SiO2
Sepiolite -4.87 10.89 15.76 Mg2Si3O7.5OH:3H2O
Sepiolite(d) -7.77 10.89 18.66 Mg2Si3O7.5OH:3H2O
SiO2(a) -1.92 -4.63 -2.71 SiO2
Sulfur -15.59 -10.71 4.88 S
Talc -2.74 18.66 21.40 Mg3Si4O10(OH)2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 4.
------------------------------------
TITLE Example 3, part D.--Equilibrate mixture with calcite and dolomite.
EQUILIBRIUM_PHASES 1
Calcite 0.0
Dolomite 0.0
USE solution 3
END
-----
TITLE
-----
Example 3, part D.--Equilibrate mixture with calcite and dolomite.
-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------
Reaction step 1.
Using solution 3. Solution after simulation 3.
Using pure phase assemblage 1.
-------------------------------Phase assemblage--------------------------------
Moles in assemblage
Phase SI log IAP log KT Initial Final Delta
Calcite 0.00 -8.48 -8.48 1.000e+01 9.984e+00 -1.571e-02
Dolomite 0.00 -17.09 -17.09 1.000e+01 1.001e+01 7.935e-03
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 3.029e-03 3.029e-03
Ca 1.213e-02 1.212e-02
Cl 1.697e-01 1.697e-01
K 3.173e-03 3.173e-03
Mg 8.585e-03 8.585e-03
Na 1.456e-01 1.456e-01
S 8.777e-03 8.777e-03
Si 2.215e-05 2.215e-05
----------------------------Description of solution----------------------------
pH = 7.056 Charge balance
pe = -1.421 Adjusted to redox equilibrium
Activity of water = 0.994
Ionic strength = 2.087e-01
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 2.704e-03
Total CO2 (mol/kg) = 3.029e-03
Temperature (deg C) = 25.000
Electrical balance (eq) = 2.390e-04
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 0.06
Iterations = 5
Total H = 1.110131e+02
Total O = 5.554912e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.609e-07 1.132e-07 -6.793 -6.946 -0.153
H+ 1.104e-07 8.788e-08 -6.957 -7.056 -0.099
H2O 5.551e+01 9.941e-01 1.744 -0.003 0.000
C(-4) 6.977e-25
CH4 6.977e-25 7.320e-25 -24.156 -24.135 0.021
C(4) 3.029e-03
HCO3- 2.397e-03 1.783e-03 -2.620 -2.749 -0.129
CO2 3.377e-04 3.543e-04 -3.471 -3.451 0.021
CaHCO3+ 1.065e-04 7.920e-05 -3.973 -4.101 -0.129
NaHCO3 1.023e-04 1.073e-04 -3.990 -3.969 0.021
MgHCO3+ 7.221e-05 5.380e-05 -4.141 -4.269 -0.128
CaCO3 5.304e-06 5.565e-06 -5.275 -5.255 0.021
CO3-2 3.109e-06 9.513e-07 -5.507 -6.022 -0.514
NaCO3- 2.546e-06 1.897e-06 -5.594 -5.722 -0.128
MgCO3 2.232e-06 2.341e-06 -5.651 -5.631 0.021
Ca 1.213e-02
Ca+2 1.095e-02 3.482e-03 -1.961 -2.458 -0.497
CaSO4 1.067e-03 1.119e-03 -2.972 -2.951 0.021
CaHCO3+ 1.065e-04 7.920e-05 -3.973 -4.101 -0.129
CaCO3 5.304e-06 5.565e-06 -5.275 -5.255 0.021
CaOH+ 8.774e-09 6.537e-09 -8.057 -8.185 -0.128
CaHSO4+ 7.734e-10 5.762e-10 -9.112 -9.239 -0.128
Cl 1.697e-01
Cl- 1.697e-01 1.203e-01 -0.770 -0.920 -0.149
H(0) 7.246e-15
H2 3.623e-15 3.801e-15 -14.441 -14.420 0.021
K 3.173e-03
K+ 3.140e-03 2.225e-03 -2.503 -2.653 -0.149
KSO4- 3.381e-05 2.519e-05 -4.471 -4.599 -0.128
KOH 8.319e-11 8.729e-11 -10.080 -10.059 0.021
Mg 8.585e-03
Mg+2 7.582e-03 2.579e-03 -2.120 -2.588 -0.468
MgSO4 9.283e-04 9.740e-04 -3.032 -3.011 0.021
MgHCO3+ 7.221e-05 5.380e-05 -4.141 -4.269 -0.128
MgCO3 2.232e-06 2.341e-06 -5.651 -5.631 0.021
MgOH+ 1.422e-07 1.059e-07 -6.847 -6.975 -0.128
Na 1.456e-01
Na+ 1.444e-01 1.071e-01 -0.841 -0.970 -0.130
NaSO4- 1.160e-03 8.644e-04 -2.935 -3.063 -0.128
NaHCO3 1.023e-04 1.073e-04 -3.990 -3.969 0.021
NaCO3- 2.546e-06 1.897e-06 -5.594 -5.722 -0.128
NaOH 7.627e-09 8.002e-09 -8.118 -8.097 0.021
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -63.566 -63.545 0.021
S(-2) 1.159e-21
HS- 7.648e-22 5.382e-22 -21.116 -21.269 -0.153
H2S 3.941e-22 4.136e-22 -21.404 -21.383 0.021
S-2 2.517e-27 7.397e-28 -26.599 -27.131 -0.532
S(6) 8.777e-03
SO4-2 5.588e-03 1.611e-03 -2.253 -2.793 -0.540
NaSO4- 1.160e-03 8.644e-04 -2.935 -3.063 -0.128
CaSO4 1.067e-03 1.119e-03 -2.972 -2.951 0.021
MgSO4 9.283e-04 9.740e-04 -3.032 -3.011 0.021
KSO4- 3.381e-05 2.519e-05 -4.471 -4.599 -0.128
HSO4- 1.847e-08 1.376e-08 -7.733 -7.861 -0.128
CaHSO4+ 7.734e-10 5.762e-10 -9.112 -9.239 -0.128
Si 2.215e-05
H4SiO4 2.210e-05 2.318e-05 -4.656 -4.635 0.021
H3SiO4- 5.221e-08 3.890e-08 -7.282 -7.410 -0.128
H2SiO4-2 9.772e-14 3.011e-14 -13.010 -13.521 -0.511
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -0.89 -5.25 -4.36 CaSO4
Aragonite -0.14 -8.48 -8.34 CaCO3
Calcite 0.00 -8.48 -8.48 CaCO3
CH4(g) -21.28 -24.14 -2.86 CH4
Chalcedony -1.08 -4.63 -3.55 SiO2
Chrysotile -6.90 25.30 32.20 Mg3Si2O5(OH)4
CO2(g) -1.98 -3.45 -1.47 CO2
Dolomite 0.00 -17.09 -17.09 CaMg(CO3)2
Gypsum -0.68 -5.26 -4.58 CaSO4:2H2O
H2(g) -11.27 -14.42 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
H2S(g) -20.39 -21.38 -1.00 H2S
Halite -3.47 -1.89 1.58 NaCl
O2(g) -60.58 -63.54 -2.96 O2
Quartz -0.65 -4.63 -3.98 SiO2
Sepiolite -6.62 9.14 15.76 Mg2Si3O7.5OH:3H2O
Sepiolite(d) -9.52 9.14 18.66 Mg2Si3O7.5OH:3H2O
SiO2(a) -1.92 -4.63 -2.71 SiO2
Sulfur -15.00 -10.11 4.88 S
Talc -5.36 16.04 21.40 Mg3Si4O10(OH)2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 5.
------------------------------------
TITLE Example 3, part E.--Equilibrate mixture with calcite only.
EQUILIBRIUM_PHASES 2
Calcite 0.0
USE solution 3
END
-----
TITLE
-----
Example 3, part E.--Equilibrate mixture with calcite only.
-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------
Reaction step 1.
Using solution 3. Solution after simulation 3.
Using pure phase assemblage 2.
-------------------------------Phase assemblage--------------------------------
Moles in assemblage
Phase SI log IAP log KT Initial Final Delta
Calcite 0.00 -8.48 -8.48 1.000e+01 1.000e+01 -3.992e-05
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 3.229e-03 3.229e-03
Ca 4.390e-03 4.390e-03
Cl 1.697e-01 1.697e-01
K 3.173e-03 3.173e-03
Mg 1.652e-02 1.652e-02
Na 1.456e-01 1.456e-01
S 8.777e-03 8.777e-03
Si 2.215e-05 2.215e-05
----------------------------Description of solution----------------------------
pH = 7.442 Charge balance
pe = -1.861 Adjusted to redox equilibrium
Activity of water = 0.994
Ionic strength = 2.088e-01
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 3.106e-03
Total CO2 (mol/kg) = 3.229e-03
Temperature (deg C) = 25.000
Electrical balance (eq) = 2.390e-04
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 0.06
Iterations = 6
Total H = 1.110131e+02
Total O = 5.554972e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 3.915e-07 2.755e-07 -6.407 -6.560 -0.153
H+ 4.537e-08 3.612e-08 -7.343 -7.442 -0.099
H2O 5.551e+01 9.941e-01 1.744 -0.003 0.000
C(-4) 8.842e-25
CH4 8.842e-25 9.278e-25 -24.053 -24.033 0.021
C(4) 3.229e-03
HCO3- 2.721e-03 2.024e-03 -2.565 -2.694 -0.129
MgHCO3+ 1.579e-04 1.176e-04 -3.802 -3.930 -0.128
CO2 1.576e-04 1.653e-04 -3.803 -3.782 0.021
NaHCO3 1.161e-04 1.219e-04 -3.935 -3.914 0.021
CaHCO3+ 4.376e-05 3.255e-05 -4.359 -4.487 -0.129
MgCO3 1.187e-05 1.245e-05 -4.926 -4.905 0.021
CO3-2 8.587e-06 2.628e-06 -5.066 -5.580 -0.514
NaCO3- 7.033e-06 5.240e-06 -5.153 -5.281 -0.128
CaCO3 5.304e-06 5.565e-06 -5.275 -5.255 0.021
Ca 4.390e-03
Ca+2 3.963e-03 1.261e-03 -2.402 -2.899 -0.497
CaSO4 3.784e-04 3.971e-04 -3.422 -3.401 0.021
CaHCO3+ 4.376e-05 3.255e-05 -4.359 -4.487 -0.129
CaCO3 5.304e-06 5.565e-06 -5.275 -5.255 0.021
CaOH+ 7.728e-09 5.758e-09 -8.112 -8.240 -0.128
CaHSO4+ 1.128e-10 8.402e-11 -9.948 -10.076 -0.128
Cl 1.697e-01
Cl- 1.697e-01 1.203e-01 -0.770 -0.920 -0.149
H(0) 9.302e-15
H2 4.651e-15 4.880e-15 -14.332 -14.312 0.021
K 3.173e-03
K+ 3.140e-03 2.226e-03 -2.503 -2.652 -0.149
KSO4- 3.314e-05 2.469e-05 -4.480 -4.607 -0.128
KOH 2.025e-10 2.124e-10 -9.694 -9.673 0.021
Mg 1.652e-02
Mg+2 1.460e-02 4.966e-03 -1.836 -2.304 -0.468
MgSO4 1.752e-03 1.838e-03 -2.757 -2.736 0.021
MgHCO3+ 1.579e-04 1.176e-04 -3.802 -3.930 -0.128
MgCO3 1.187e-05 1.245e-05 -4.926 -4.905 0.021
MgOH+ 6.661e-07 4.963e-07 -6.176 -6.304 -0.128
Na 1.456e-01
Na+ 1.444e-01 1.071e-01 -0.841 -0.970 -0.130
NaSO4- 1.137e-03 8.472e-04 -2.944 -3.072 -0.128
NaHCO3 1.161e-04 1.219e-04 -3.935 -3.914 0.021
NaCO3- 7.033e-06 5.240e-06 -5.153 -5.281 -0.128
NaOH 1.856e-08 1.947e-08 -7.731 -7.711 0.021
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -63.783 -63.762 0.021
S(-2) 1.014e-21
HS- 8.367e-22 5.888e-22 -21.077 -21.230 -0.153
H2S 1.772e-22 1.860e-22 -21.751 -21.731 0.021
S-2 6.701e-27 1.969e-27 -26.174 -26.706 -0.532
S(6) 8.777e-03
SO4-2 5.477e-03 1.579e-03 -2.261 -2.802 -0.540
MgSO4 1.752e-03 1.838e-03 -2.757 -2.736 0.021
NaSO4- 1.137e-03 8.472e-04 -2.944 -3.072 -0.128
CaSO4 3.784e-04 3.971e-04 -3.422 -3.401 0.021
KSO4- 3.314e-05 2.469e-05 -4.480 -4.607 -0.128
HSO4- 7.441e-09 5.544e-09 -8.128 -8.256 -0.128
CaHSO4+ 1.128e-10 8.402e-11 -9.948 -10.076 -0.128
Si 2.215e-05
H4SiO4 2.202e-05 2.311e-05 -4.657 -4.636 0.021
H3SiO4- 1.266e-07 9.432e-08 -6.898 -7.025 -0.128
H2SiO4-2 5.766e-13 1.776e-13 -12.239 -12.750 -0.511
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -1.34 -5.70 -4.36 CaSO4
Aragonite -0.14 -8.48 -8.34 CaCO3
Calcite 0.00 -8.48 -8.48 CaCO3
CH4(g) -21.17 -24.03 -2.86 CH4
Chalcedony -1.08 -4.63 -3.55 SiO2
Chrysotile -3.73 28.47 32.20 Mg3Si2O5(OH)4
CO2(g) -2.31 -3.78 -1.47 CO2
Dolomite 0.73 -16.36 -17.09 CaMg(CO3)2
Gypsum -1.13 -5.71 -4.58 CaSO4:2H2O
H2(g) -11.16 -14.31 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
H2S(g) -20.73 -21.73 -1.00 H2S
Halite -3.47 -1.89 1.58 NaCl
O2(g) -60.80 -63.76 -2.96 O2
Quartz -0.65 -4.63 -3.98 SiO2
Sepiolite -4.51 11.25 15.76 Mg2Si3O7.5OH:3H2O
Sepiolite(d) -7.41 11.25 18.66 Mg2Si3O7.5OH:3H2O
SiO2(a) -1.92 -4.63 -2.71 SiO2
Sulfur -15.45 -10.57 4.88 S
Talc -2.19 19.21 21.40 Mg3Si4O10(OH)2
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 6.
------------------------------------
-----------
End of run.
-----------
No memory leaks

0
Sun/examples/ex4.log
View File

478
Sun/examples/ex4.out
View File

@ -1,478 +0,0 @@
Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex4
Output file: ex4.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 4a.--Rain water evaporation
SOLUTION 1 Precipitation from Central Oklahoma
units mg/L
pH 4.5 # estimated
temp 25.0
Ca .384
Mg .043
Na .141
K .036
Cl .236
C(4) .1 CO2(g) -3.5
S(6) 1.3
N(-3) .208
N(5) .237
REACTION 1
H2O -1.0
52.73 moles
SAVE solution 2
END
-----
TITLE
-----
Example 4a.--Rain water evaporation
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1. Precipitation from Central Oklahoma
-----------------------------Solution composition------------------------------
Elements Molality Moles
C(4) 1.092e-05 1.092e-05 Equilibrium with CO2(g)
Ca 9.581e-06 9.581e-06
Cl 6.657e-06 6.657e-06
K 9.207e-07 9.207e-07
Mg 1.769e-06 1.769e-06
N(-3) 1.485e-05 1.485e-05
N(5) 1.692e-05 1.692e-05
Na 6.133e-06 6.133e-06
S(6) 1.353e-05 1.353e-05
----------------------------Description of solution----------------------------
pH = 4.500
pe = 4.000
Activity of water = 1.000
Ionic strength = 8.838e-05
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = -3.185e-05
Total CO2 (mol/kg) = 1.092e-05
Temperature (deg C) = 25.000
Electrical balance (eq) = 2.581e-05
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 20.29
Iterations = 3
Total H = 1.110125e+02
Total O = 5.550634e+01
---------------------------------Redox couples---------------------------------
Redox couple pe Eh (volts)
N(-3)/N(5) 9.2667 0.5482
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
H+ 3.196e-05 3.162e-05 -4.495 -4.500 -0.005
OH- 3.200e-10 3.166e-10 -9.495 -9.500 -0.005
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
C(4) 1.092e-05
CO2 1.077e-05 1.077e-05 -4.968 -4.968 0.000
HCO3- 1.531e-07 1.514e-07 -6.815 -6.820 -0.005
CaHCO3+ 1.787e-11 1.768e-11 -10.748 -10.753 -0.005
MgHCO3+ 3.025e-12 2.992e-12 -11.519 -11.524 -0.005
NaHCO3 5.166e-13 5.166e-13 -12.287 -12.287 0.000
CO3-2 2.345e-13 2.246e-13 -12.630 -12.649 -0.019
CaCO3 3.452e-15 3.452e-15 -14.462 -14.462 0.000
MgCO3 3.619e-16 3.619e-16 -15.441 -15.441 0.000
NaCO3- 2.565e-17 2.537e-17 -16.591 -16.596 -0.005
Ca 9.581e-06
Ca+2 9.557e-06 9.151e-06 -5.020 -5.039 -0.019
CaSO4 2.353e-08 2.353e-08 -7.628 -7.628 0.000
CaHCO3+ 1.787e-11 1.768e-11 -10.748 -10.753 -0.005
CaHSO4+ 4.408e-12 4.360e-12 -11.356 -11.361 -0.005
CaOH+ 4.855e-14 4.803e-14 -13.314 -13.319 -0.005
CaCO3 3.452e-15 3.452e-15 -14.462 -14.462 0.000
Cl 6.657e-06
Cl- 6.657e-06 6.585e-06 -5.177 -5.181 -0.005
H(0) 1.416e-20
H2 7.079e-21 7.079e-21 -20.150 -20.150 0.000
K 9.207e-07
K+ 9.206e-07 9.106e-07 -6.036 -6.041 -0.005
KSO4- 8.337e-11 8.247e-11 -10.079 -10.084 -0.005
KOH 9.984e-17 9.985e-17 -16.001 -16.001 0.000
Mg 1.769e-06
Mg+2 1.764e-06 1.689e-06 -5.754 -5.772 -0.019
MgSO4 5.103e-09 5.103e-09 -8.292 -8.292 0.000
MgHCO3+ 3.025e-12 2.992e-12 -11.519 -11.524 -0.005
MgOH+ 1.960e-13 1.939e-13 -12.708 -12.712 -0.005
MgCO3 3.619e-16 3.619e-16 -15.441 -15.441 0.000
N(-3) 1.485e-05
NH4+ 1.485e-05 1.469e-05 -4.828 -4.833 -0.005
NH4SO4- 2.465e-09 2.438e-09 -8.608 -8.613 -0.005
NH3 2.646e-10 2.647e-10 -9.577 -9.577 0.000
N(5) 1.692e-05
NO3- 1.692e-05 1.674e-05 -4.772 -4.776 -0.005
Na 6.133e-06
Na+ 6.133e-06 6.066e-06 -5.212 -5.217 -0.005
NaSO4- 3.962e-10 3.919e-10 -9.402 -9.407 -0.005
NaHCO3 5.166e-13 5.166e-13 -12.287 -12.287 0.000
NaOH 1.267e-15 1.267e-15 -14.897 -14.897 0.000
NaCO3- 2.565e-17 2.537e-17 -16.591 -16.596 -0.005
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -52.080 -52.080 0.000
S(6) 1.353e-05
SO4-2 1.346e-05 1.289e-05 -4.871 -4.890 -0.019
HSO4- 4.006e-08 3.963e-08 -7.397 -7.402 -0.005
CaSO4 2.353e-08 2.353e-08 -7.628 -7.628 0.000
MgSO4 5.103e-09 5.103e-09 -8.292 -8.292 0.000
NH4SO4- 2.465e-09 2.438e-09 -8.608 -8.613 -0.005
NaSO4- 3.962e-10 3.919e-10 -9.402 -9.407 -0.005
KSO4- 8.337e-11 8.247e-11 -10.079 -10.084 -0.005
CaHSO4+ 4.408e-12 4.360e-12 -11.356 -11.361 -0.005
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -5.57 -9.93 -4.36 CaSO4
Aragonite -9.35 -17.69 -8.34 CaCO3
Calcite -9.21 -17.69 -8.48 CaCO3
CO2(g) -3.50 -4.97 -1.47 CO2
Dolomite -19.02 -36.11 -17.09 CaMg(CO3)2
Gypsum -5.35 -9.93 -4.58 CaSO4:2H2O
H2(g) -17.00 -20.15 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
Halite -11.98 -10.40 1.58 NaCl
NH3(g) -11.35 -9.58 1.77 NH3
O2(g) -49.12 -52.08 -2.96 O2
-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------
Reaction step 1.
Using solution 1. Precipitation from Central Oklahoma
Using reaction 1.
Reaction 1. Irreversible reaction defined in simulation 1.
5.273e+01 moles of the following reaction have been added:
Relative
Reactant moles
H2O -1.00
Relative
Element moles
H -2.00
O -1.00
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 2.183e-04 1.092e-05
Ca 1.916e-04 9.581e-06
Cl 1.331e-04 6.657e-06
K 1.841e-05 9.207e-07
Mg 3.536e-05 1.769e-06
N 6.352e-04 3.177e-05
Na 1.226e-04 6.133e-06
S 2.706e-04 1.353e-05
----------------------------Description of solution----------------------------
pH = 3.148 Charge balance
pe = 16.530 Adjusted to redox equilibrium
Activity of water = 1.000
Ionic strength = 1.528e-03
Mass of water (kg) = 5.002e-02
Total alkalinity (eq/kg) = -7.555e-04
Total CO2 (mol/kg) = 2.183e-04
Temperature (deg C) = 25.000
Electrical balance (eq) = 2.581e-05
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 24.31
Iterations = 20
Total H = 5.552525e+00
Total O = 2.776344e+00
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
H+ 7.406e-04 7.108e-04 -3.130 -3.148 -0.018
OH- 1.472e-11 1.408e-11 -10.832 -10.851 -0.019
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
C(-4) 0.000e+00
CH4 0.000e+00 0.000e+00 -136.693 -136.693 0.000
C(4) 2.183e-04
CO2 2.182e-04 2.182e-04 -3.661 -3.661 0.000
HCO3- 1.425e-07 1.366e-07 -6.846 -6.865 -0.019
CaHCO3+ 2.834e-10 2.715e-10 -9.548 -9.566 -0.019
MgHCO3+ 4.780e-11 4.576e-11 -10.321 -10.340 -0.019
NaHCO3 9.005e-12 9.008e-12 -11.046 -11.045 0.000
CO3-2 1.070e-14 9.010e-15 -13.971 -14.045 -0.074
CaCO3 2.358e-15 2.359e-15 -14.627 -14.627 0.000
MgCO3 2.461e-16 2.462e-16 -15.609 -15.609 0.000
NaCO3- 2.056e-17 1.968e-17 -16.687 -16.706 -0.019
Ca 1.916e-04
Ca+2 1.851e-04 1.559e-04 -3.733 -3.807 -0.075
CaSO4 6.474e-06 6.477e-06 -5.189 -5.189 0.000
CaHSO4+ 2.817e-08 2.697e-08 -7.550 -7.569 -0.019
CaHCO3+ 2.834e-10 2.715e-10 -9.548 -9.566 -0.019
CaOH+ 3.801e-14 3.639e-14 -13.420 -13.439 -0.019
CaCO3 2.358e-15 2.359e-15 -14.627 -14.627 0.000
Cl 1.331e-04
Cl- 1.331e-04 1.274e-04 -3.876 -3.895 -0.019
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -42.506 -42.506 0.000
K 1.841e-05
K+ 1.838e-05 1.759e-05 -4.736 -4.755 -0.019
KSO4- 2.689e-08 2.575e-08 -7.570 -7.589 -0.019
KOH 8.579e-17 8.582e-17 -16.067 -16.066 0.000
Mg 3.536e-05
Mg+2 3.396e-05 2.864e-05 -4.469 -4.543 -0.074
MgSO4 1.398e-06 1.398e-06 -5.855 -5.854 0.000
MgHCO3+ 4.780e-11 4.576e-11 -10.321 -10.340 -0.019
MgOH+ 1.528e-13 1.463e-13 -12.816 -12.835 -0.019
MgCO3 2.461e-16 2.462e-16 -15.609 -15.609 0.000
N(-3) 0.000e+00
NH4+ 0.000e+00 0.000e+00 -48.438 -48.457 -0.019
NH4SO4- 0.000e+00 0.000e+00 -51.009 -51.028 -0.019
NH3 0.000e+00 0.000e+00 -54.553 -54.553 0.000
N(0) 4.751e-04
N2 2.375e-04 2.376e-04 -3.624 -3.624 0.000
N(3) 2.623e-15
NO2- 2.623e-15 2.510e-15 -14.581 -14.600 -0.019
N(5) 1.601e-04
NO3- 1.601e-04 1.532e-04 -3.796 -3.815 -0.019
Na 1.226e-04
Na+ 1.225e-04 1.173e-04 -3.912 -3.931 -0.019
NaSO4- 1.279e-07 1.224e-07 -6.893 -6.912 -0.019
NaHCO3 9.005e-12 9.008e-12 -11.046 -11.045 0.000
NaOH 1.090e-15 1.090e-15 -14.963 -14.962 0.000
NaCO3- 2.056e-17 1.968e-17 -16.687 -16.706 -0.019
O(0) 8.553e-08
O2 4.277e-08 4.278e-08 -7.369 -7.369 0.000
S(-2) 0.000e+00
H2S 0.000e+00 0.000e+00 -126.809 -126.809 0.000
HS- 0.000e+00 0.000e+00 -130.583 -130.602 -0.019
S-2 0.000e+00 0.000e+00 -140.297 -140.372 -0.075
S(6) 2.706e-04
SO4-2 2.475e-04 2.083e-04 -3.606 -3.681 -0.075
HSO4- 1.503e-05 1.439e-05 -4.823 -4.842 -0.019
CaSO4 6.474e-06 6.477e-06 -5.189 -5.189 0.000
MgSO4 1.398e-06 1.398e-06 -5.855 -5.854 0.000
NaSO4- 1.279e-07 1.224e-07 -6.893 -6.912 -0.019
CaHSO4+ 2.817e-08 2.697e-08 -7.550 -7.569 -0.019
KSO4- 2.689e-08 2.575e-08 -7.570 -7.589 -0.019
NH4SO4- 0.000e+00 0.000e+00 -51.009 -51.028 -0.019
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -3.13 -7.49 -4.36 CaSO4
Aragonite -9.52 -17.85 -8.34 CaCO3
Calcite -9.37 -17.85 -8.48 CaCO3
CH4(g) -133.83 -136.69 -2.86 CH4
CO2(g) -2.19 -3.66 -1.47 CO2
Dolomite -19.35 -36.44 -17.09 CaMg(CO3)2
Gypsum -2.91 -7.49 -4.58 CaSO4:2H2O
H2(g) -39.36 -42.51 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
H2S(g) -125.81 -126.81 -1.00 H2S
Halite -9.41 -7.83 1.58 NaCl
N2(g) -0.36 -3.62 -3.26 N2
NH3(g) -56.32 -54.55 1.77 NH3
O2(g) -4.41 -7.37 -2.96 O2
Sulfur -92.34 -87.45 4.88 S
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 2.
------------------------------------
TITLE Example 4b.--Factor of 20 more solution
MIX
2 20.
SAVE solution 3
END
-----
TITLE
-----
Example 4b.--Factor of 20 more solution
-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------
Reaction step 1.
Using mix 1.
Mixture 1.
2.000e+01 Solution 2 Solution after simulation 1.
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 2.183e-04 2.184e-04
Ca 1.916e-04 1.916e-04
Cl 1.331e-04 1.331e-04
K 1.841e-05 1.841e-05
Mg 3.536e-05 3.537e-05
N 6.352e-04 6.354e-04
Na 1.226e-04 1.227e-04
S 2.706e-04 2.707e-04
----------------------------Description of solution----------------------------
pH = 3.148 Charge balance
pe = 16.530 Adjusted to redox equilibrium
Activity of water = 1.000
Ionic strength = 1.528e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = -7.555e-04
Total CO2 (mol/kg) = 2.183e-04
Temperature (deg C) = 25.000
Electrical balance (eq) = 5.162e-04
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 24.31
Iterations = 0
Total H = 1.110505e+02
Total O = 5.552687e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
H+ 7.406e-04 7.108e-04 -3.130 -3.148 -0.018
OH- 1.472e-11 1.408e-11 -10.832 -10.851 -0.019
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
C(-4) 0.000e+00
CH4 0.000e+00 0.000e+00 -136.693 -136.693 0.000
C(4) 2.183e-04
CO2 2.182e-04 2.182e-04 -3.661 -3.661 0.000
HCO3- 1.425e-07 1.366e-07 -6.846 -6.865 -0.019
CaHCO3+ 2.834e-10 2.715e-10 -9.548 -9.566 -0.019
MgHCO3+ 4.780e-11 4.576e-11 -10.321 -10.340 -0.019
NaHCO3 9.005e-12 9.008e-12 -11.046 -11.045 0.000
CO3-2 1.070e-14 9.010e-15 -13.971 -14.045 -0.074
CaCO3 2.358e-15 2.359e-15 -14.627 -14.627 0.000
MgCO3 2.461e-16 2.462e-16 -15.609 -15.609 0.000
NaCO3- 2.056e-17 1.968e-17 -16.687 -16.706 -0.019
Ca 1.916e-04
Ca+2 1.851e-04 1.559e-04 -3.733 -3.807 -0.075
CaSO4 6.474e-06 6.477e-06 -5.189 -5.189 0.000
CaHSO4+ 2.817e-08 2.697e-08 -7.550 -7.569 -0.019
CaHCO3+ 2.834e-10 2.715e-10 -9.548 -9.566 -0.019
CaOH+ 3.801e-14 3.639e-14 -13.420 -13.439 -0.019
CaCO3 2.358e-15 2.359e-15 -14.627 -14.627 0.000
Cl 1.331e-04
Cl- 1.331e-04 1.274e-04 -3.876 -3.895 -0.019
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -42.506 -42.506 0.000
K 1.841e-05
K+ 1.838e-05 1.759e-05 -4.736 -4.755 -0.019
KSO4- 2.689e-08 2.575e-08 -7.570 -7.589 -0.019
KOH 8.579e-17 8.582e-17 -16.067 -16.066 0.000
Mg 3.536e-05
Mg+2 3.396e-05 2.864e-05 -4.469 -4.543 -0.074
MgSO4 1.398e-06 1.398e-06 -5.855 -5.854 0.000
MgHCO3+ 4.780e-11 4.576e-11 -10.321 -10.340 -0.019
MgOH+ 1.528e-13 1.463e-13 -12.816 -12.835 -0.019
MgCO3 2.461e-16 2.462e-16 -15.609 -15.609 0.000
N(-3) 0.000e+00
NH4+ 0.000e+00 0.000e+00 -48.438 -48.457 -0.019
NH4SO4- 0.000e+00 0.000e+00 -51.009 -51.028 -0.019
NH3 0.000e+00 0.000e+00 -54.553 -54.553 0.000
N(0) 4.751e-04
N2 2.375e-04 2.376e-04 -3.624 -3.624 0.000
N(3) 2.623e-15
NO2- 2.623e-15 2.510e-15 -14.581 -14.600 -0.019
N(5) 1.601e-04
NO3- 1.601e-04 1.532e-04 -3.796 -3.815 -0.019
Na 1.226e-04
Na+ 1.225e-04 1.173e-04 -3.912 -3.931 -0.019
NaSO4- 1.279e-07 1.224e-07 -6.893 -6.912 -0.019
NaHCO3 9.005e-12 9.008e-12 -11.046 -11.045 0.000
NaOH 1.090e-15 1.090e-15 -14.963 -14.962 0.000
NaCO3- 2.056e-17 1.968e-17 -16.687 -16.706 -0.019
O(0) 8.553e-08
O2 4.277e-08 4.278e-08 -7.369 -7.369 0.000
S(-2) 0.000e+00
H2S 0.000e+00 0.000e+00 -126.809 -126.809 0.000
HS- 0.000e+00 0.000e+00 -130.583 -130.602 -0.019
S-2 0.000e+00 0.000e+00 -140.297 -140.372 -0.075
S(6) 2.706e-04
SO4-2 2.475e-04 2.083e-04 -3.606 -3.681 -0.075
HSO4- 1.503e-05 1.439e-05 -4.823 -4.842 -0.019
CaSO4 6.474e-06 6.477e-06 -5.189 -5.189 0.000
MgSO4 1.398e-06 1.398e-06 -5.855 -5.854 0.000
NaSO4- 1.279e-07 1.224e-07 -6.893 -6.912 -0.019
CaHSO4+ 2.817e-08 2.697e-08 -7.550 -7.569 -0.019
KSO4- 2.689e-08 2.575e-08 -7.570 -7.589 -0.019
NH4SO4- 0.000e+00 0.000e+00 -51.009 -51.028 -0.019
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -3.13 -7.49 -4.36 CaSO4
Aragonite -9.52 -17.85 -8.34 CaCO3
Calcite -9.37 -17.85 -8.48 CaCO3
CH4(g) -133.83 -136.69 -2.86 CH4
CO2(g) -2.19 -3.66 -1.47 CO2
Dolomite -19.35 -36.44 -17.09 CaMg(CO3)2
Gypsum -2.91 -7.49 -4.58 CaSO4:2H2O
H2(g) -39.36 -42.51 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
H2S(g) -125.81 -126.81 -1.00 H2S
Halite -9.41 -7.83 1.58 NaCl
N2(g) -0.36 -3.62 -3.26 N2
NH3(g) -56.32 -54.55 1.77 NH3
O2(g) -4.41 -7.37 -2.96 O2
Sulfur -92.34 -87.45 4.88 S
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 3.
------------------------------------
-----------
End of run.
-----------
No memory leaks

0
Sun/examples/ex5.log
View File

942
Sun/examples/ex5.out
View File

@ -1,942 +0,0 @@
Input file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../examples/ex5
Output file: ex5.out
Database file: /z/parkplace/home/dlpark/../../home/dlpark/programs/phreeqc/src/../src/Sun/../../database/phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 5.--Add oxygen, equilibrate with pyrite, calcite, and goethite.
SOLUTION 1 PURE WATER
pH 7.0
temp 25.0
EQUILIBRIUM_PHASES 1
Pyrite 0.0
Goethite 0.0
Calcite 0.0
CO2(g) -3.5
Gypsum 0.0 0.0
REACTION 1
O2 1.0
NaCl 0.5
0.0 0.001 0.005 0.01 0.05
SELECTED_OUTPUT
file ex5.sel
totals Cl
si Gypsum
equilibrium_phases pyrite goethite calcite CO2(g) gypsum
END
-----
TITLE
-----
Example 5.--Add oxygen, equilibrate with pyrite, calcite, and goethite.
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1. PURE WATER
-----------------------------Solution composition------------------------------
Elements Molality Moles
Pure water
----------------------------Description of solution----------------------------
pH = 7.000
pe = 4.000
Activity of water = 1.000
Ionic strength = 1.001e-07
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 1.082e-10
Total carbon (mol/kg) = 0.000e+00
Total CO2 (mol/kg) = 0.000e+00
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.082e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.05
Iterations = 0
Total H = 1.110124e+02
Total O = 5.550622e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.002e-07 1.001e-07 -6.999 -6.999 -0.000
H+ 1.001e-07 1.000e-07 -7.000 -7.000 -0.000
H2O 5.551e+01 1.000e+00 1.744 0.000 0.000
H(0) 1.416e-25
H2 7.079e-26 7.079e-26 -25.150 -25.150 0.000
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -42.080 -42.080 0.000
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
H2(g) -22.00 -25.15 -3.15 H2
H2O(g) -1.51 0.00 1.51 H2O
O2(g) -39.12 -42.08 -2.96 O2
-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------
Reaction step 1.
Using solution 1. PURE WATER
Using pure phase assemblage 1.
Using reaction 1.
Reaction 1. Irreversible reaction defined in simulation 1.
0.000e+00 moles of the following reaction have been added:
Relative
Reactant moles
O2 1.00
NaCl 0.50
Relative
Element moles
Cl 0.50
Na 0.50
O 2.00
-------------------------------Phase assemblage--------------------------------
Moles in assemblage
Phase SI log IAP log KT Initial Final Delta
Calcite 0.00 -8.48 -8.48 1.000e+01 1.000e+01 -4.934e-04
CO2(g) -3.50 -21.65 -18.15 1.000e+01 1.000e+01 -4.870e-04
Goethite 0.00 12.02 12.02 1.000e+01 1.000e+01 1.105e-08
Gypsum -6.13 -10.71 -4.58 0.000e+00 0.000e+00
Pyrite 0.00 -85.78 -85.78 1.000e+01 1.000e+01 -3.154e-08
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 9.804e-04 9.804e-04
Ca 4.934e-04 4.934e-04
Fe 2.049e-08 2.049e-08
S 6.308e-08 6.308e-08
----------------------------Description of solution----------------------------
pH = 8.279 Charge balance
pe = -4.943 Adjusted to redox equilibrium
Activity of water = 1.000
Ionic strength = 1.463e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 9.867e-04
Total CO2 (mol/kg) = 9.803e-04
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.082e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 14
Total H = 1.110124e+02
Total O = 5.550867e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.987e-06 1.903e-06 -5.702 -5.720 -0.019
H+ 5.476e-09 5.260e-09 -8.262 -8.279 -0.018
H2O 5.551e+01 1.000e+00 1.744 -0.000 0.000
C(-4) 5.403e-08
CH4 5.403e-08 5.405e-08 -7.267 -7.267 0.000
C(4) 9.803e-04
HCO3- 9.494e-04 9.104e-04 -3.023 -3.041 -0.018
CO2 1.076e-05 1.077e-05 -4.968 -4.968 0.000
CO3-2 9.603e-06 8.117e-06 -5.018 -5.091 -0.073
CaCO3 5.563e-06 5.565e-06 -5.255 -5.255 0.000
CaHCO3+ 4.943e-06 4.740e-06 -5.306 -5.324 -0.018
FeCO3 2.600e-09 2.601e-09 -8.585 -8.585 0.000
FeHCO3+ 1.269e-09 1.216e-09 -8.896 -8.915 -0.019
Ca 4.934e-04
Ca+2 4.829e-04 4.081e-04 -3.316 -3.389 -0.073
CaCO3 5.563e-06 5.565e-06 -5.255 -5.255 0.000
CaHCO3+ 4.943e-06 4.740e-06 -5.306 -5.324 -0.018
CaOH+ 1.344e-08 1.288e-08 -7.872 -7.890 -0.019
CaSO4 3.896e-09 3.897e-09 -8.409 -8.409 0.000
CaHSO4+ 1.253e-16 1.201e-16 -15.902 -15.920 -0.019
Fe(2) 2.049e-08
Fe+2 1.578e-08 1.336e-08 -7.802 -7.874 -0.072
FeCO3 2.600e-09 2.601e-09 -8.585 -8.585 0.000
FeHCO3+ 1.269e-09 1.216e-09 -8.896 -8.915 -0.019
FeOH+ 8.381e-10 8.031e-10 -9.077 -9.095 -0.019
FeSO4 1.137e-13 1.137e-13 -12.944 -12.944 0.000
Fe(HS)2 6.287e-17 6.289e-17 -16.202 -16.201 0.000
FeHSO4+ 4.102e-21 3.931e-21 -20.387 -20.406 -0.019
Fe(HS)3- 1.643e-23 1.574e-23 -22.784 -22.803 -0.019
Fe(3) 3.369e-14
Fe(OH)3 2.753e-14 2.754e-14 -13.560 -13.560 0.000
Fe(OH)4- 4.984e-15 4.776e-15 -14.302 -14.321 -0.019
Fe(OH)2+ 1.174e-15 1.124e-15 -14.931 -14.949 -0.019
FeOH+2 2.119e-20 1.786e-20 -19.674 -19.748 -0.074
Fe+3 2.091e-26 1.455e-26 -25.680 -25.837 -0.158
FeSO4+ 7.970e-30 7.637e-30 -29.099 -29.117 -0.019
Fe(SO4)2- 8.346e-36 7.997e-36 -35.079 -35.097 -0.019
FeHSO4+2 1.276e-37 1.076e-37 -36.894 -36.968 -0.074
Fe2(OH)2+4 1.700e-38 8.587e-39 -37.769 -38.066 -0.297
Fe3(OH)4+5 0.000e+00 0.000e+00 -50.232 -50.695 -0.464
H(0) 3.009e-10
H2 1.505e-10 1.505e-10 -9.823 -9.822 0.000
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -72.735 -72.735 0.000
S(-2) 2.505e-09
HS- 2.399e-09 2.298e-09 -8.620 -8.639 -0.019
H2S 1.057e-10 1.057e-10 -9.976 -9.976 0.000
S-2 6.249e-14 5.278e-14 -13.204 -13.278 -0.073
Fe(HS)2 6.287e-17 6.289e-17 -16.202 -16.201 0.000
Fe(HS)3- 1.643e-23 1.574e-23 -22.784 -22.803 -0.019
S(6) 6.057e-08
SO4-2 5.668e-08 4.786e-08 -7.247 -7.320 -0.073
CaSO4 3.896e-09 3.897e-09 -8.409 -8.409 0.000
FeSO4 1.137e-13 1.137e-13 -12.944 -12.944 0.000
HSO4- 2.554e-14 2.448e-14 -13.593 -13.611 -0.019
CaHSO4+ 1.253e-16 1.201e-16 -15.902 -15.920 -0.019
FeHSO4+ 4.102e-21 3.931e-21 -20.387 -20.406 -0.019
FeSO4+ 7.970e-30 7.637e-30 -29.099 -29.117 -0.019
Fe(SO4)2- 8.346e-36 7.997e-36 -35.079 -35.097 -0.019
FeHSO4+2 1.276e-37 1.076e-37 -36.894 -36.968 -0.074
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -6.35 -10.71 -4.36 CaSO4
Aragonite -0.14 -8.48 -8.34 CaCO3
Calcite 0.00 -8.48 -8.48 CaCO3
CH4(g) -4.41 -7.27 -2.86 CH4
CO2(g) -3.50 -4.97 -1.47 CO2
Fe(OH)3(a) -5.89 -1.00 4.89 Fe(OH)3
FeS(ppt) -4.32 -8.23 -3.92 FeS
Goethite 0.00 -1.00 -1.00 FeOOH
Gypsum -6.13 -10.71 -4.58 CaSO4:2H2O
H2(g) -6.67 -9.82 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
H2S(g) -8.98 -9.98 -1.00 H2S
Hematite 2.01 -2.00 -4.01 Fe2O3
Mackinawite -3.59 -8.23 -4.65 FeS
Melanterite -12.99 -15.19 -2.21 FeSO4:7H2O
O2(g) -69.78 -72.74 -2.96 O2
Pyrite 0.00 -18.48 -18.48 FeS2
Siderite -2.07 -12.96 -10.89 FeCO3
Sulfur -8.19 -3.30 4.88 S
Reaction step 2.
Using solution 1. PURE WATER
Using pure phase assemblage 1.
Using reaction 1.
Reaction 1. Irreversible reaction defined in simulation 1.
1.000e-03 moles of the following reaction have been added:
Relative
Reactant moles
O2 1.00
NaCl 0.50
Relative
Element moles
Cl 0.50
Na 0.50
O 2.00
-------------------------------Phase assemblage--------------------------------
Moles in assemblage
Phase SI log IAP log KT Initial Final Delta
Calcite 0.00 -8.48 -8.48 1.000e+01 9.999e+00 -9.277e-04
CO2(g) -3.50 -21.65 -18.15 1.000e+01 1.000e+01 1.418e-04
Goethite 0.00 12.02 12.02 1.000e+01 1.000e+01 2.667e-04
Gypsum -2.02 -6.60 -4.58 0.000e+00 0.000e+00
Pyrite 0.00 -85.78 -85.78 1.000e+01 1.000e+01 -2.667e-04
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 7.859e-04 7.859e-04
Ca 9.277e-04 9.277e-04
Cl 5.000e-04 5.000e-04
Fe 9.939e-09 9.939e-09
Na 5.000e-04 5.000e-04
S 5.333e-04 5.333e-04
----------------------------Description of solution----------------------------
pH = 8.171 Charge balance
pe = -4.287 Adjusted to redox equilibrium
Activity of water = 1.000
Ionic strength = 3.591e-03
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 7.887e-04
Total CO2 (mol/kg) = 7.859e-04
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.082e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 24
Total H = 1.110122e+02
Total O = 5.551018e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.585e-06 1.484e-06 -5.800 -5.829 -0.029
H+ 7.160e-09 6.745e-09 -8.145 -8.171 -0.026
H2O 5.551e+01 9.999e-01 1.744 -0.000 0.000
C(-4) 2.240e-12
CH4 2.240e-12 2.242e-12 -11.650 -11.649 0.000
C(4) 7.859e-04
HCO3- 7.565e-04 7.099e-04 -3.121 -3.149 -0.028
CO2 1.076e-05 1.077e-05 -4.968 -4.968 0.000
CaHCO3+ 6.477e-06 6.078e-06 -5.189 -5.216 -0.028
CO3-2 6.364e-06 4.936e-06 -5.196 -5.307 -0.110
CaCO3 5.560e-06 5.565e-06 -5.255 -5.255 0.000
NaHCO3 1.865e-07 1.867e-07 -6.729 -6.729 0.000
NaCO3- 4.587e-08 4.298e-08 -7.338 -7.367 -0.028
FeCO3 7.363e-10 7.369e-10 -9.133 -9.133 0.000
FeHCO3+ 4.715e-10 4.418e-10 -9.327 -9.355 -0.028
Ca 9.277e-04
Ca+2 8.657e-04 6.711e-04 -3.063 -3.173 -0.111
CaSO4 4.996e-05 5.000e-05 -4.301 -4.301 0.000
CaHCO3+ 6.477e-06 6.078e-06 -5.189 -5.216 -0.028
CaCO3 5.560e-06 5.565e-06 -5.255 -5.255 0.000
CaOH+ 1.762e-08 1.651e-08 -7.754 -7.782 -0.028
CaHSO4+ 2.108e-12 1.976e-12 -11.676 -11.704 -0.028
Cl 5.000e-04
Cl- 5.000e-04 4.682e-04 -3.301 -3.330 -0.029
FeCl+ 4.293e-12 4.023e-12 -11.367 -11.396 -0.028
FeCl+2 5.629e-28 4.339e-28 -27.250 -27.363 -0.113
FeCl2+ 9.686e-31 9.076e-31 -30.014 -30.042 -0.028
FeCl3 4.246e-35 4.250e-35 -34.372 -34.372 0.000
Fe(2) 9.939e-09
Fe+2 8.002e-09 6.223e-09 -8.097 -8.206 -0.109
FeCO3 7.363e-10 7.369e-10 -9.133 -9.133 0.000
FeHCO3+ 4.715e-10 4.418e-10 -9.327 -9.355 -0.028
FeSO4 4.129e-10 4.132e-10 -9.384 -9.384 0.000
FeOH+ 3.114e-10 2.918e-10 -9.507 -9.535 -0.028
FeCl+ 4.293e-12 4.023e-12 -11.367 -11.396 -0.028
FeHSO4+ 1.955e-17 1.832e-17 -16.709 -16.737 -0.028
Fe(HS)2 5.043e-18 5.047e-18 -17.297 -17.297 0.000
Fe(HS)3- 5.596e-25 5.243e-25 -24.252 -24.280 -0.028
Fe(3) 3.303e-14
Fe(OH)3 2.752e-14 2.754e-14 -13.560 -13.560 0.000
Fe(OH)4- 3.974e-15 3.724e-15 -14.401 -14.429 -0.028
Fe(OH)2+ 1.539e-15 1.442e-15 -14.813 -14.841 -0.028
FeOH+2 3.810e-20 2.937e-20 -19.419 -19.532 -0.113
FeSO4+ 1.341e-25 1.256e-25 -24.873 -24.901 -0.028
Fe+3 5.252e-26 3.069e-26 -25.280 -25.513 -0.233
Fe(SO4)2- 1.095e-27 1.026e-27 -26.960 -26.989 -0.028
FeCl+2 5.629e-28 4.339e-28 -27.250 -27.363 -0.113
FeCl2+ 9.686e-31 9.076e-31 -30.014 -30.042 -0.028
FeHSO4+2 2.943e-33 2.269e-33 -32.531 -32.644 -0.113
FeCl3 4.246e-35 4.250e-35 -34.372 -34.372 0.000
Fe2(OH)2+4 6.575e-38 2.322e-38 -37.182 -37.634 -0.452
Fe3(OH)4+5 0.000e+00 0.000e+00 -49.449 -50.155 -0.706
H(0) 2.414e-11
H2 1.207e-11 1.208e-11 -10.918 -10.918 0.000
Na 5.000e-04
Na+ 4.988e-04 4.677e-04 -3.302 -3.330 -0.028
NaSO4- 9.340e-07 8.752e-07 -6.030 -6.058 -0.028
NaHCO3 1.865e-07 1.867e-07 -6.729 -6.729 0.000
NaCO3- 4.587e-08 4.298e-08 -7.338 -7.367 -0.028
NaOH 4.577e-10 4.581e-10 -9.339 -9.339 0.000
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -70.545 -70.544 0.000
S(-2) 1.075e-09
HS- 1.019e-09 9.540e-10 -8.992 -9.020 -0.029
H2S 5.621e-11 5.626e-11 -10.250 -10.250 0.000
S-2 2.207e-14 1.708e-14 -13.656 -13.767 -0.111
Fe(HS)2 5.043e-18 5.047e-18 -17.297 -17.297 0.000
Fe(HS)3- 5.596e-25 5.243e-25 -24.252 -24.280 -0.028
S(6) 5.333e-04
SO4-2 4.824e-04 3.734e-04 -3.317 -3.428 -0.111
CaSO4 4.996e-05 5.000e-05 -4.301 -4.301 0.000
NaSO4- 9.340e-07 8.752e-07 -6.030 -6.058 -0.028
FeSO4 4.129e-10 4.132e-10 -9.384 -9.384 0.000
HSO4- 2.613e-10 2.449e-10 -9.583 -9.611 -0.028
CaHSO4+ 2.108e-12 1.976e-12 -11.676 -11.704 -0.028
FeHSO4+ 1.955e-17 1.832e-17 -16.709 -16.737 -0.028
FeSO4+ 1.341e-25 1.256e-25 -24.873 -24.901 -0.028
Fe(SO4)2- 1.095e-27 1.026e-27 -26.960 -26.989 -0.028
FeHSO4+2 2.943e-33 2.269e-33 -32.531 -32.644 -0.113
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -2.24 -6.60 -4.36 CaSO4
Aragonite -0.14 -8.48 -8.34 CaCO3
Calcite 0.00 -8.48 -8.48 CaCO3
CH4(g) -8.79 -11.65 -2.86 CH4
CO2(g) -3.50 -4.97 -1.47 CO2
Fe(OH)3(a) -5.89 -1.00 4.89 Fe(OH)3
FeS(ppt) -5.14 -9.06 -3.92 FeS
Goethite -0.00 -1.00 -1.00 FeOOH
Gypsum -2.02 -6.60 -4.58 CaSO4:2H2O
H2(g) -7.77 -10.92 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
H2S(g) -9.25 -10.25 -1.00 H2S
Halite -8.24 -6.66 1.58 NaCl
Hematite 2.01 -2.00 -4.01 Fe2O3
Mackinawite -4.41 -9.06 -4.65 FeS
Melanterite -9.42 -11.63 -2.21 FeSO4:7H2O
O2(g) -67.58 -70.54 -2.96 O2
Pyrite -0.00 -18.48 -18.48 FeS2
Siderite -2.62 -13.51 -10.89 FeCO3
Sulfur -7.36 -2.48 4.88 S
Reaction step 3.
Using solution 1. PURE WATER
Using pure phase assemblage 1.
Using reaction 1.
Reaction 1. Irreversible reaction defined in simulation 1.
5.000e-03 moles of the following reaction have been added:
Relative
Reactant moles
O2 1.00
NaCl 0.50
Relative
Element moles
Cl 0.50
Na 0.50
O 2.00
-------------------------------Phase assemblage--------------------------------
Moles in assemblage
Phase SI log IAP log KT Initial Final Delta
Calcite 0.00 -8.48 -8.48 1.000e+01 9.997e+00 -2.937e-03
CO2(g) -3.50 -21.65 -18.15 1.000e+01 1.000e+01 2.395e-03
Goethite 0.00 12.02 12.02 1.000e+01 1.000e+01 1.333e-03
Gypsum -1.06 -5.64 -4.58 0.000e+00 0.000e+00
Pyrite 0.00 -85.78 -85.78 1.000e+01 9.999e+00 -1.333e-03
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 5.424e-04 5.424e-04
Ca 2.937e-03 2.937e-03
Cl 2.500e-03 2.500e-03
Fe 2.124e-08 2.124e-08
Na 2.500e-03 2.500e-03
S 2.667e-03 2.667e-03
----------------------------Description of solution----------------------------
pH = 7.982 Charge balance
pe = -3.970 Adjusted to redox equilibrium
Activity of water = 1.000
Ionic strength = 1.210e-02
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 5.415e-04
Total CO2 (mol/kg) = 5.424e-04
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.082e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 25
Total H = 1.110111e+02
Total O = 5.551757e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 1.077e-06 9.604e-07 -5.968 -6.018 -0.050
H+ 1.149e-08 1.042e-08 -7.940 -7.982 -0.042
H2O 5.551e+01 9.998e-01 1.744 -0.000 0.000
C(-4) 2.129e-13
CH4 2.129e-13 2.135e-13 -12.672 -12.671 0.001
C(4) 5.424e-04
HCO3- 5.118e-04 4.594e-04 -3.291 -3.338 -0.047
CO2 1.074e-05 1.077e-05 -4.969 -4.968 0.001
CaHCO3+ 1.046e-05 9.392e-06 -4.980 -5.027 -0.047
CaCO3 5.549e-06 5.565e-06 -5.256 -5.255 0.001
CO3-2 3.184e-06 2.067e-06 -5.497 -5.685 -0.188
NaHCO3 5.724e-07 5.740e-07 -6.242 -6.241 0.001
NaCO3- 9.566e-08 8.553e-08 -7.019 -7.068 -0.049
FeHCO3+ 5.691e-10 5.088e-10 -9.245 -9.293 -0.049
FeCO3 5.477e-10 5.493e-10 -9.261 -9.260 0.001
Ca 2.937e-03
Ca+2 2.469e-03 1.602e-03 -2.607 -2.795 -0.188
CaSO4 4.520e-04 4.532e-04 -3.345 -3.344 0.001
CaHCO3+ 1.046e-05 9.392e-06 -4.980 -5.027 -0.047
CaCO3 5.549e-06 5.565e-06 -5.256 -5.255 0.001
CaOH+ 2.854e-08 2.551e-08 -7.545 -7.593 -0.049
CaHSO4+ 3.095e-11 2.767e-11 -10.509 -10.558 -0.049
Cl 2.500e-03
Cl- 2.500e-03 2.230e-03 -2.602 -2.652 -0.050
FeCl+ 3.814e-11 3.410e-11 -10.419 -10.467 -0.049
FeCl+2 1.194e-26 7.627e-27 -25.923 -26.118 -0.194
FeCl2+ 8.499e-29 7.599e-29 -28.071 -28.119 -0.049
FeCl3 1.690e-32 1.695e-32 -31.772 -31.771 0.001
Fe(2) 2.124e-08
Fe+2 1.693e-08 1.108e-08 -7.771 -7.956 -0.184
FeSO4 2.784e-09 2.792e-09 -8.555 -8.554 0.001
FeHCO3+ 5.691e-10 5.088e-10 -9.245 -9.293 -0.049
FeCO3 5.477e-10 5.493e-10 -9.261 -9.260 0.001
FeOH+ 3.758e-10 3.360e-10 -9.425 -9.474 -0.049
FeCl+ 3.814e-11 3.410e-11 -10.419 -10.467 -0.049
FeHSO4+ 2.139e-16 1.913e-16 -15.670 -15.718 -0.049
Fe(HS)2 2.796e-18 2.804e-18 -17.553 -17.552 0.001
Fe(HS)3- 1.820e-25 1.627e-25 -24.740 -24.789 -0.049
Fe(3) 3.265e-14
Fe(OH)3 2.746e-14 2.754e-14 -13.561 -13.560 0.001
Fe(OH)4- 2.695e-15 2.409e-15 -14.569 -14.618 -0.049
Fe(OH)2+ 2.492e-15 2.228e-15 -14.603 -14.652 -0.049
FeOH+2 1.098e-19 7.014e-20 -18.960 -19.154 -0.194
FeSO4+ 1.968e-24 1.760e-24 -23.706 -23.755 -0.049
Fe+3 2.720e-25 1.132e-25 -24.566 -24.946 -0.381
Fe(SO4)2- 6.105e-26 5.458e-26 -25.214 -25.263 -0.049
FeCl+2 1.194e-26 7.627e-27 -25.923 -26.118 -0.194
FeCl2+ 8.499e-29 7.599e-29 -28.071 -28.119 -0.049
FeHSO4+2 7.686e-32 4.911e-32 -31.114 -31.309 -0.194
FeCl3 1.690e-32 1.695e-32 -31.772 -31.771 0.001
Fe2(OH)2+4 7.941e-37 1.324e-37 -36.100 -36.878 -0.778
Fe3(OH)4+5 0.000e+00 0.000e+00 -47.995 -49.210 -1.216
H(0) 1.338e-11
H2 6.691e-12 6.710e-12 -11.174 -11.173 0.001
Na 2.500e-03
Na+ 2.482e-03 2.222e-03 -2.605 -2.653 -0.048
NaSO4- 1.766e-05 1.579e-05 -4.753 -4.802 -0.049
NaHCO3 5.724e-07 5.740e-07 -6.242 -6.241 0.001
NaCO3- 9.566e-08 8.553e-08 -7.019 -7.068 -0.049
NaOH 1.404e-09 1.408e-09 -8.853 -8.851 0.001
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -70.035 -70.034 0.001
S(-2) 6.460e-10
HS- 5.976e-10 5.329e-10 -9.224 -9.273 -0.050
H2S 4.843e-11 4.856e-11 -10.315 -10.314 0.001
S-2 9.562e-15 6.176e-15 -14.019 -14.209 -0.190
Fe(HS)2 2.796e-18 2.804e-18 -17.553 -17.552 0.001
Fe(HS)3- 1.820e-25 1.627e-25 -24.740 -24.789 -0.049
S(6) 2.667e-03
SO4-2 2.197e-03 1.418e-03 -2.658 -2.848 -0.190
CaSO4 4.520e-04 4.532e-04 -3.345 -3.344 0.001
NaSO4- 1.766e-05 1.579e-05 -4.753 -4.802 -0.049
FeSO4 2.784e-09 2.792e-09 -8.555 -8.554 0.001
HSO4- 1.606e-09 1.436e-09 -8.794 -8.843 -0.049
CaHSO4+ 3.095e-11 2.767e-11 -10.509 -10.558 -0.049
FeHSO4+ 2.139e-16 1.913e-16 -15.670 -15.718 -0.049
FeSO4+ 1.968e-24 1.760e-24 -23.706 -23.755 -0.049
Fe(SO4)2- 6.105e-26 5.458e-26 -25.214 -25.263 -0.049
FeHSO4+2 7.686e-32 4.911e-32 -31.114 -31.309 -0.194
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -1.28 -5.64 -4.36 CaSO4
Aragonite -0.14 -8.48 -8.34 CaCO3
Calcite 0.00 -8.48 -8.48 CaCO3
CH4(g) -9.81 -12.67 -2.86 CH4
CO2(g) -3.50 -4.97 -1.47 CO2
Fe(OH)3(a) -5.89 -1.00 4.89 Fe(OH)3
FeS(ppt) -5.33 -9.25 -3.92 FeS
Goethite -0.00 -1.00 -1.00 FeOOH
Gypsum -1.06 -5.64 -4.58 CaSO4:2H2O
H2(g) -8.02 -11.17 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
H2S(g) -9.32 -10.31 -1.00 H2S
Halite -6.89 -5.30 1.58 NaCl
Hematite 2.01 -2.00 -4.01 Fe2O3
Mackinawite -4.60 -9.25 -4.65 FeS
Melanterite -8.60 -10.80 -2.21 FeSO4:7H2O
O2(g) -67.07 -70.03 -2.96 O2
Pyrite -0.00 -18.48 -18.48 FeS2
Siderite -2.75 -13.64 -10.89 FeCO3
Sulfur -7.17 -2.29 4.88 S
Reaction step 4.
Using solution 1. PURE WATER
Using pure phase assemblage 1.
Using reaction 1.
Reaction 1. Irreversible reaction defined in simulation 1.
1.000e-02 moles of the following reaction have been added:
Relative
Reactant moles
O2 1.00
NaCl 0.50
Relative
Element moles
Cl 0.50
Na 0.50
O 2.00
-------------------------------Phase assemblage--------------------------------
Moles in assemblage
Phase SI log IAP log KT Initial Final Delta
Calcite 0.00 -8.48 -8.48 1.000e+01 9.994e+00 -5.559e-03
CO2(g) -3.50 -21.65 -18.15 1.000e+01 1.001e+01 5.105e-03
Goethite 0.00 12.02 12.02 1.000e+01 1.000e+01 2.667e-03
Gypsum -0.65 -5.23 -4.58 0.000e+00 0.000e+00
Pyrite -0.00 -85.78 -85.78 1.000e+01 9.997e+00 -2.667e-03
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 4.540e-04 4.540e-04
Ca 5.560e-03 5.559e-03
Cl 5.000e-03 5.000e-03
Fe 3.429e-08 3.429e-08
Na 5.000e-03 5.000e-03
S 5.333e-03 5.333e-03
----------------------------Description of solution----------------------------
pH = 7.884 Charge balance
pe = -3.817 Adjusted to redox equilibrium
Activity of water = 1.000
Ionic strength = 2.218e-02
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 4.522e-04
Total CO2 (mol/kg) = 4.540e-04
Temperature (deg C) = 25.000
Electrical balance (eq) = -1.082e-10
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 25
Total H = 1.110098e+02
Total O = 5.552735e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 8.898e-07 7.665e-07 -6.051 -6.115 -0.065
H+ 1.474e-08 1.306e-08 -7.832 -7.884 -0.053
H2O 5.551e+01 9.997e-01 1.744 -0.000 0.000
C(-4) 7.696e-14
CH4 7.696e-14 7.735e-14 -13.114 -13.112 0.002
C(4) 4.540e-04
HCO3- 4.210e-04 3.666e-04 -3.376 -3.436 -0.060
CaHCO3+ 1.351e-05 1.177e-05 -4.869 -4.929 -0.060
CO2 1.071e-05 1.077e-05 -4.970 -4.968 0.002
CaCO3 5.536e-06 5.565e-06 -5.257 -5.255 0.002
CO3-2 2.289e-06 1.317e-06 -5.640 -5.880 -0.240
NaHCO3 8.791e-07 8.836e-07 -6.056 -6.054 0.002
NaCO3- 1.214e-07 1.051e-07 -6.916 -6.978 -0.063
FeHCO3+ 6.487e-10 5.616e-10 -9.188 -9.251 -0.063
FeCO3 4.814e-10 4.839e-10 -9.317 -9.315 0.002
Ca 5.560e-03
Ca+2 4.373e-03 2.515e-03 -2.359 -2.599 -0.240
CaSO4 1.168e-03 1.174e-03 -2.933 -2.930 0.002
CaHCO3+ 1.351e-05 1.177e-05 -4.869 -4.929 -0.060
CaCO3 5.536e-06 5.565e-06 -5.257 -5.255 0.002
CaOH+ 3.692e-08 3.196e-08 -7.433 -7.495 -0.063
CaHSO4+ 1.037e-10 8.977e-11 -9.984 -10.047 -0.063
Cl 5.000e-03
Cl- 5.000e-03 4.311e-03 -2.301 -2.365 -0.064
FeCl+ 1.053e-10 9.114e-11 -9.978 -10.040 -0.063
FeCl+2 5.162e-26 2.899e-26 -25.287 -25.538 -0.251
FeCl2+ 6.449e-28 5.583e-28 -27.191 -27.253 -0.063
FeCl3 2.394e-31 2.406e-31 -30.621 -30.619 0.002
Fe(2) 3.429e-08
Fe+2 2.629e-08 1.532e-08 -7.580 -7.815 -0.235
FeSO4 6.337e-09 6.369e-09 -8.198 -8.196 0.002
FeHCO3+ 6.487e-10 5.616e-10 -9.188 -9.251 -0.063
FeCO3 4.814e-10 4.839e-10 -9.317 -9.315 0.002
FeOH+ 4.284e-10 3.708e-10 -9.368 -9.431 -0.063
FeCl+ 1.053e-10 9.114e-11 -9.978 -10.040 -0.063
FeHSO4+ 6.314e-16 5.466e-16 -15.200 -15.262 -0.063
Fe(HS)2 2.164e-18 2.175e-18 -17.665 -17.663 0.002
Fe(HS)3- 1.092e-25 9.454e-26 -24.962 -25.024 -0.063
Fe(3) 3.284e-14
Fe(OH)3 2.739e-14 2.753e-14 -13.562 -13.560 0.002
Fe(OH)2+ 3.224e-15 2.791e-15 -14.492 -14.554 -0.063
Fe(OH)4- 2.221e-15 1.923e-15 -14.653 -14.716 -0.063
FeOH+2 1.960e-19 1.101e-19 -18.708 -18.958 -0.251
FeSO4+ 6.596e-24 5.710e-24 -23.181 -23.243 -0.063
Fe+3 6.635e-25 2.227e-25 -24.178 -24.652 -0.474
Fe(SO4)2- 3.374e-25 2.921e-25 -24.472 -24.534 -0.063
FeCl+2 5.162e-26 2.899e-26 -25.287 -25.538 -0.251
FeCl2+ 6.449e-28 5.583e-28 -27.191 -27.253 -0.063
FeHSO4+2 3.555e-31 1.996e-31 -30.449 -30.700 -0.251
FeCl3 2.394e-31 2.406e-31 -30.621 -30.619 0.002
Fe2(OH)2+4 3.279e-36 3.263e-37 -35.484 -36.486 -1.002
Fe3(OH)4+5 0.000e+00 0.000e+00 -47.155 -48.721 -1.566
H(0) 1.036e-11
H2 5.179e-12 5.205e-12 -11.286 -11.284 0.002
Na 5.000e-03
Na+ 4.941e-03 4.286e-03 -2.306 -2.368 -0.062
NaSO4- 5.802e-05 5.023e-05 -4.236 -4.299 -0.063
NaHCO3 8.791e-07 8.836e-07 -6.056 -6.054 0.002
NaCO3- 1.214e-07 1.051e-07 -6.916 -6.978 -0.063
NaOH 2.157e-09 2.168e-09 -8.666 -8.664 0.002
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -69.815 -69.813 0.002
S(-2) 5.087e-10
HS- 4.634e-10 3.992e-10 -9.334 -9.399 -0.065
H2S 4.533e-11 4.557e-11 -10.344 -10.341 0.002
S-2 6.474e-15 3.693e-15 -14.189 -14.433 -0.244
Fe(HS)2 2.164e-18 2.175e-18 -17.665 -17.663 0.002
Fe(HS)3- 1.092e-25 9.454e-26 -24.962 -25.024 -0.063
S(6) 5.333e-03
SO4-2 4.108e-03 2.338e-03 -2.386 -2.631 -0.245
CaSO4 1.168e-03 1.174e-03 -2.933 -2.930 0.002
NaSO4- 5.802e-05 5.023e-05 -4.236 -4.299 -0.063
FeSO4 6.337e-09 6.369e-09 -8.198 -8.196 0.002
HSO4- 3.429e-09 2.968e-09 -8.465 -8.527 -0.063
CaHSO4+ 1.037e-10 8.977e-11 -9.984 -10.047 -0.063
FeHSO4+ 6.314e-16 5.466e-16 -15.200 -15.262 -0.063
FeSO4+ 6.596e-24 5.710e-24 -23.181 -23.243 -0.063
Fe(SO4)2- 3.374e-25 2.921e-25 -24.472 -24.534 -0.063
FeHSO4+2 3.555e-31 1.996e-31 -30.449 -30.700 -0.251
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -0.87 -5.23 -4.36 CaSO4
Aragonite -0.14 -8.48 -8.34 CaCO3
Calcite 0.00 -8.48 -8.48 CaCO3
CH4(g) -10.25 -13.11 -2.86 CH4
CO2(g) -3.50 -4.97 -1.47 CO2
Fe(OH)3(a) -5.89 -1.00 4.89 Fe(OH)3
FeS(ppt) -5.41 -9.33 -3.92 FeS
Goethite -0.00 -1.00 -1.00 FeOOH
Gypsum -0.65 -5.23 -4.58 CaSO4:2H2O
H2(g) -8.13 -11.28 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
H2S(g) -9.34 -10.34 -1.00 H2S
Halite -6.32 -4.73 1.58 NaCl
Hematite 2.01 -2.00 -4.01 Fe2O3
Mackinawite -4.68 -9.33 -4.65 FeS
Melanterite -8.24 -10.45 -2.21 FeSO4:7H2O
O2(g) -66.85 -69.81 -2.96 O2
Pyrite -0.00 -18.48 -18.48 FeS2
Siderite -2.81 -13.70 -10.89 FeCO3
Sulfur -7.09 -2.21 4.88 S
Reaction step 5.
Using solution 1. PURE WATER
Using pure phase assemblage 1.
Using reaction 1.
Reaction 1. Irreversible reaction defined in simulation 1.
5.000e-02 moles of the following reaction have been added:
Relative
Reactant moles
O2 1.00
NaCl 0.50
Relative
Element moles
Cl 0.50
Na 0.50
O 2.00
-------------------------------Phase assemblage--------------------------------
Moles in assemblage
Phase SI log IAP log KT Initial Final Delta
Calcite 0.00 -8.48 -8.48 1.000e+01 9.973e+00 -2.684e-02
CO2(g) -3.50 -21.65 -18.15 1.000e+01 1.003e+01 2.649e-02
Goethite 0.00 12.02 12.02 1.000e+01 1.001e+01 1.333e-02
Gypsum 0.00 -4.58 -4.58 0.000e+00 9.002e-03 9.002e-03
Pyrite -0.00 -85.78 -85.78 1.000e+01 9.987e+00 -1.333e-02
-----------------------------Solution composition------------------------------
Elements Molality Moles
C 3.526e-04 3.524e-04
Ca 1.785e-02 1.784e-02
Cl 2.501e-02 2.500e-02
Fe 8.735e-08 8.732e-08
Na 2.501e-02 2.500e-02
S 1.767e-02 1.766e-02
----------------------------Description of solution----------------------------
pH = 7.719 Charge balance
pe = -3.565 Adjusted to redox equilibrium
Activity of water = 0.999
Ionic strength = 7.432e-02
Mass of water (kg) = 9.996e-01
Total alkalinity (eq/kg) = 3.499e-04
Total CO2 (mol/kg) = 3.526e-04
Temperature (deg C) = 25.000
Electrical balance (eq) = -4.778e-11
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.00
Iterations = 25
Total H = 1.109631e+02
Total O = 5.555309e+01
----------------------------Distribution of species----------------------------
Log Log Log
Species Molality Activity Molality Activity Gamma
OH- 6.681e-07 5.237e-07 -6.175 -6.281 -0.106
H+ 2.279e-08 1.909e-08 -7.642 -7.719 -0.077
H2O 5.551e+01 9.986e-01 1.744 -0.001 0.000
C(-4) 1.534e-14
CH4 1.534e-14 1.561e-14 -13.814 -13.807 0.007
C(4) 3.526e-04
HCO3- 3.108e-04 2.505e-04 -3.508 -3.601 -0.094
CaHCO3+ 2.134e-05 1.720e-05 -4.671 -4.764 -0.094
CO2 1.058e-05 1.077e-05 -4.975 -4.968 0.007
CaCO3 5.470e-06 5.565e-06 -5.262 -5.255 0.007
NaHCO3 2.706e-06 2.752e-06 -5.568 -5.560 0.007
CO3-2 1.458e-06 6.155e-07 -5.836 -6.211 -0.374
NaCO3- 2.804e-07 2.239e-07 -6.552 -6.650 -0.098
FeHCO3+ 8.424e-10 6.727e-10 -9.074 -9.172 -0.098
FeCO3 3.897e-10 3.964e-10 -9.409 -9.402 0.007
Ca 1.785e-02
Ca+2 1.266e-02 5.382e-03 -1.898 -2.269 -0.371
CaSO4 5.162e-03 5.251e-03 -2.287 -2.280 0.007
CaHCO3+ 2.134e-05 1.720e-05 -4.671 -4.764 -0.094
CaCO3 5.470e-06 5.565e-06 -5.262 -5.255 0.007
CaOH+ 5.853e-08 4.673e-08 -7.233 -7.330 -0.098
CaHSO4+ 7.355e-10 5.872e-10 -9.133 -9.231 -0.098
Cl 2.501e-02
Cl- 2.501e-02 1.966e-02 -1.602 -1.706 -0.105
FeCl+ 9.125e-10 7.286e-10 -9.040 -9.138 -0.098
FeCl+2 1.019e-24 4.140e-25 -23.992 -24.383 -0.391
FeCl2+ 4.553e-26 3.635e-26 -25.342 -25.439 -0.098
FeCl3 7.025e-29 7.146e-29 -28.153 -28.146 0.007
Fe(2) 8.735e-08
Fe+2 6.170e-08 2.685e-08 -7.210 -7.571 -0.361
FeSO4 2.295e-08 2.335e-08 -7.639 -7.632 0.007
FeCl+ 9.125e-10 7.286e-10 -9.040 -9.138 -0.098
FeHCO3+ 8.424e-10 6.727e-10 -9.074 -9.172 -0.098
FeOH+ 5.563e-10 4.442e-10 -9.255 -9.352 -0.098
FeCO3 3.897e-10 3.964e-10 -9.409 -9.402 0.007
FeHSO4+ 3.669e-15 2.930e-15 -14.435 -14.533 -0.098
Fe(HS)2 1.432e-18 1.457e-18 -17.844 -17.837 0.007
Fe(HS)3- 4.903e-26 3.915e-26 -25.310 -25.407 -0.098
Fe(3) 3.379e-14
Fe(OH)3 2.704e-14 2.750e-14 -13.568 -13.561 0.007
Fe(OH)2+ 5.111e-15 4.081e-15 -14.291 -14.389 -0.098
Fe(OH)4- 1.644e-15 1.312e-15 -14.784 -14.882 -0.098
FeOH+2 5.796e-19 2.356e-19 -18.237 -18.628 -0.391
FeSO4+ 4.683e-23 3.739e-23 -22.329 -22.427 -0.098
Fe(SO4)2- 5.010e-24 4.000e-24 -23.300 -23.398 -0.098
Fe+3 3.432e-24 6.974e-25 -23.464 -24.156 -0.692
FeCl+2 1.019e-24 4.140e-25 -23.992 -24.383 -0.391
FeCl2+ 4.553e-26 3.635e-26 -25.342 -25.439 -0.098
FeCl3 7.025e-29 7.146e-29 -28.153 -28.146 0.007
FeHSO4+2 4.703e-30 1.911e-30 -29.328 -29.719 -0.391
Fe2(OH)2+4 5.473e-35 1.494e-36 -34.262 -35.826 -1.564
Fe3(OH)4+5 0.000e+00 0.000e+00 -45.451 -47.895 -2.444
H(0) 6.856e-12
H2 3.428e-12 3.487e-12 -11.465 -11.458 0.007
Na 2.501e-02
Na+ 2.441e-02 1.954e-02 -1.612 -1.709 -0.097
NaSO4- 5.997e-04 4.788e-04 -3.222 -3.320 -0.098
NaHCO3 2.706e-06 2.752e-06 -5.568 -5.560 0.007
NaCO3- 2.804e-07 2.239e-07 -6.552 -6.650 -0.098
NaOH 6.639e-09 6.753e-09 -8.178 -8.170 0.007
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -69.474 -69.466 0.007
S(-2) 3.552e-10
HS- 3.148e-10 2.467e-10 -9.502 -9.608 -0.106
H2S 4.048e-11 4.118e-11 -10.393 -10.385 0.007
S-2 3.777e-15 1.561e-15 -14.423 -14.807 -0.384
Fe(HS)2 1.432e-18 1.457e-18 -17.844 -17.837 0.007
Fe(HS)3- 4.903e-26 3.915e-26 -25.310 -25.407 -0.098
S(6) 1.767e-02
SO4-2 1.191e-02 4.890e-03 -1.924 -2.311 -0.387
CaSO4 5.162e-03 5.251e-03 -2.287 -2.280 0.007
NaSO4- 5.997e-04 4.788e-04 -3.222 -3.320 -0.098
FeSO4 2.295e-08 2.335e-08 -7.639 -7.632 0.007
HSO4- 1.137e-08 9.075e-09 -7.944 -8.042 -0.098
CaHSO4+ 7.355e-10 5.872e-10 -9.133 -9.231 -0.098
FeHSO4+ 3.669e-15 2.930e-15 -14.435 -14.533 -0.098
FeSO4+ 4.683e-23 3.739e-23 -22.329 -22.427 -0.098
Fe(SO4)2- 5.010e-24 4.000e-24 -23.300 -23.398 -0.098
FeHSO4+2 4.703e-30 1.911e-30 -29.328 -29.719 -0.391
------------------------------Saturation indices-------------------------------
Phase SI log IAP log KT
Anhydrite -0.22 -4.58 -4.36 CaSO4
Aragonite -0.14 -8.48 -8.34 CaCO3
Calcite 0.00 -8.48 -8.48 CaCO3
CH4(g) -10.95 -13.81 -2.86 CH4
CO2(g) -3.50 -4.97 -1.47 CO2
Fe(OH)3(a) -5.89 -1.00 4.89 Fe(OH)3
FeS(ppt) -5.54 -9.46 -3.92 FeS
Goethite 0.00 -1.00 -1.00 FeOOH
Gypsum 0.00 -4.58 -4.58 CaSO4:2H2O
H2(g) -8.31 -11.46 -3.15 H2
H2O(g) -1.51 -0.00 1.51 H2O
H2S(g) -9.39 -10.39 -1.00 H2S
Halite -5.00 -3.42 1.58 NaCl
Hematite 2.01 -2.00 -4.01 Fe2O3
Mackinawite -4.81 -9.46 -4.65 FeS
Melanterite -7.68 -9.89 -2.21 FeSO4:7H2O
O2(g) -66.51 -69.47 -2.96 O2
Pyrite -0.00 -18.48 -18.48 FeS2
Siderite -2.89 -13.78 -10.89 FeCO3
Sulfur -6.96 -2.08 4.88 S
------------------
End of simulation.
------------------
------------------------------------
Reading input data for simulation 2.
------------------------------------
-----------
End of run.
-----------
No memory leaks

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sim state soln dist_x time step pH pe Cl pyrite d_pyrite goethite d_goethite calcite d_calcite CO2(g) d_CO2(g) gypsum d_gypsum si_Gypsum
1 i_soln 1 -99 -99 -99 7 4 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 -999.9990
1 react 1 -99 0 1 8.27904 -4.94284 0.0000e+00 1.0000e+01 -3.1538e-08 1.0000e+01 1.1047e-08 9.9995e+00 -4.9340e-04 9.9995e+00 -4.8697e-04 0.0000e+00 0.0000e+00 -6.1283
1 react 1 -99 0 2 8.17103 -4.28707 5.0000e-04 9.9997e+00 -2.6667e-04 1.0000e+01 2.6666e-04 9.9991e+00 -9.2766e-04 1.0000e+01 1.4180e-04 0.0000e+00 0.0000e+00 -2.0202
1 react 1 -99 0 3 7.98207 -3.97043 2.5000e-03 9.9987e+00 -1.3333e-03 1.0001e+01 1.3333e-03 9.9971e+00 -2.9374e-03 1.0002e+01 2.3951e-03 0.0000e+00 0.0000e+00 -1.0629
1 react 1 -99 0 4 7.88418 -3.81741 5.0001e-03 9.9973e+00 -2.6667e-03 1.0003e+01 2.6666e-03 9.9944e+00 -5.5594e-03 1.0005e+01 5.1054e-03 0.0000e+00 0.0000e+00 -0.6499
1 react 1 -99 0 5 7.71922 -3.56545 2.5011e-02 9.9867e+00 -1.3333e-02 1.0013e+01 1.3333e-02 9.9732e+00 -2.6841e-02 1.0026e+01 2.6489e-02 9.0018e-03 9.0018e-03 0.0000

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sim state soln dist_x time step pH pe la_K+ la_H+ la_H4SiO4 Gibbsite d_Gibbsite Kaolinite d_Kaolinite K-mica d_K-mica K-feldspar d_K-feldspar si_Gibbsite si_Kaolinite si_K-mica si_K-feldspar
1 i_soln 1 -99 -99 -99 6.99977 4 -1.0000e+03 -6.9998e+00 -1.0000e+03 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 -999.9990 -999.9990 -999.9990 -999.9990
2 react 1 -99 0 1 7.00609 11.4683 -7.5735e+00 -7.0061e+00 -7.0969e+00 1.0000e+01 -2.6709e-08 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000 -3.8037 -10.6810 -14.6840
3 react 1 -99 0 1 8.2125 9.89391 -5.6625e+00 -8.2125e+00 -5.1950e+00 1.7820e-06 1.7820e-06 1.0000e+01 -2.1788e-06 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 -0.0000 -0.0000 -1.8580 -5.8610
4 react 1 -99 0 1 9.10891 9.06313 -4.7009e+00 -9.1089e+00 -4.4670e+00 0.0000e+00 0.0000e+00 9.7149e-06 9.7149e-06 1.0000e+01 -2.0015e-05 0.0000e+00 0.0000e+00 -0.7280 0.0000 -0.0000 -2.5471
5 react 1 -99 0 1 9.3893 8.71926 -3.9009e+00 -9.3893e+00 -3.5536e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 6.3607e-05 6.3607e-05 9.9998e+00 -1.9088e-04 -2.0015 -0.7202 -0.0000 -0.0000
6 react 1 -99 0 1 8.35402 9.7856 -5.5204e+00 -8.3540e+00 -5.1950e+00 1.0000e+01 -3.0232e-06 1.0000e+00 1.2370e-06 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000 -0.0000 -1.5744 -5.5774
7 react 1 -99 0 1 9.06998 8.8364 -4.6620e+00 -9.0700e+00 -4.2522e+00 0.0000e+00 0.0000e+00 1.0000e+01 -3.2683e-05 1.0000e+00 1.0785e-05 0.0000e+00 0.0000e+00 -0.9428 0.0000 0.0000 -2.1175
8 react 1 -99 0 1 7.03143 11.4569 -7.3981e+00 -7.0314e+00 -6.9215e+00 1.1865e-08 1.1865e-08 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 -0.0000 -3.4530 -9.9542 -13.9572
8 react 1 -99 0 2 7.10578 11.2881 -7.0971e+00 -7.1058e+00 -6.6206e+00 4.7135e-08 4.7135e-08 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 -0.0000 -2.8512 -8.6762 -12.6792
8 react 1 -99 0 3 7.24112 11.2405 -6.7961e+00 -7.2411e+00 -6.3199e+00 1.1602e-07 1.1602e-07 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000 -2.2497 -7.3376 -11.3406
8 react 1 -99 0 4 7.45138 11.1879 -6.4952e+00 -7.4514e+00 -6.0195e+00 2.4993e-07 2.4993e-07 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 -0.0000 -1.6491 -5.9254 -9.9284
8 react 1 -99 0 5 7.71458 10.9939 -6.1942e+00 -7.7146e+00 -5.7200e+00 5.1299e-07 5.1299e-07 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000 -1.0500 -4.4627 -8.4657
8 react 1 -99 0 6 7.89551 10.7897 -6.0005e+00 -7.8955e+00 -5.5279e+00 8.0811e-07 8.0811e-07 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000 -0.6658 -3.5117 -7.5147
8 react 1 -99 0 7 8.17803 10.4976 -5.6997e+00 -8.1780e+00 -5.2314e+00 1.6334e-06 1.6334e-06 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000 -0.0728 -2.0389 -6.0419
8 react 1 -99 0 8 8.48402 9.39003 -5.3990e+00 -8.4840e+00 -5.0858e+00 0.0000e+00 0.0000e+00 1.7119e-06 1.7119e-06 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 -0.1092 -0.0000 -1.3229 -5.1076
8 react 1 -99 0 9 8.77878 9.50556 -5.0983e+00 -8.7788e+00 -4.8166e+00 0.0000e+00 0.0000e+00 3.6945e-06 3.6945e-06 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 -0.3784 -0.0000 -0.7276 -3.9737
8 react 1 -99 0 10 9.0347 8.80148 -4.7979e+00 -9.0347e+00 -4.5514e+00 0.0000e+00 0.0000e+00 7.7006e-06 7.7006e-06 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 -0.6436 0.0000 -0.1712 -2.8871
8 react 1 -99 0 11 9.07198 8.97748 -4.6640e+00 -9.0720e+00 -4.2616e+00 0.0000e+00 0.0000e+00 5.2701e-07 5.2701e-07 1.0204e-05 1.0204e-05 0.0000e+00 0.0000e+00 -0.9334 0.0000 -0.0000 -2.1362
8 react 1 -99 0 12 9.2252 8.68998 -4.3726e+00 -9.2252e+00 -3.9889e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 2.1273e-05 2.1273e-05 0.0000e+00 0.0000e+00 -1.3543 -0.2964 0.0000 -1.2945
8 react 1 -99 0 13 9.30457 8.57016 -4.1800e+00 -9.3046e+00 -3.8127e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 3.3294e-05 3.3294e-05 0.0000e+00 0.0000e+00 -1.6212 -0.4777 0.0000 -0.7607
8 react 1 -99 0 14 9.3893 8.9467 -3.9009e+00 -9.3893e+00 -3.5536e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 6.3607e-05 6.3607e-05 9.1200e-06 9.1200e-06 -2.0015 -0.7202 -0.0000 0.0000

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pH+log[K] log[H4SiO4]
-6.0002e+00 -1.2524e+01
-1.8975e+00 -8.4212e+00
-8.5316e-01 -7.3798e+00
3.5755e-01 -6.3763e+00
2.1823e+00 -5.3818e+00
4.1360e+00 -4.6005e+00
5.2614e+00 -3.7187e+00
5.4884e+00 -3.5536e+00

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sim state reaction si_CO2(g) si_CH4(g) si_N2(g) si_NH3(g) pressure total mol volume g_CO2(g) g_CH4(g) g_N2(g) g_NH3(g)
1 i_soln -99 -999.9990 -999.9990 -999.9990 -999.9990 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
1 react -99 -1.5000 -26.2591 -999.9990 -999.9990 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
2 react 1.0000e-03 -1.3544 -0.4402 -3.8961 -8.3809 1.1000e+00 1.0000e-25 2.2242e-24 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
2 react 2.0000e-03 -1.2453 -0.1392 -3.6436 -8.1826 1.1000e+00 1.0000e-25 2.2242e-24 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00
2 react 3.0000e-03 -1.1592 0.0130 -3.5015 -8.0869 1.1000e+00 8.5793e-05 1.9082e-03 5.4061e-06 8.0362e-05 2.4578e-08 6.3856e-13
2 react 4.0000e-03 -1.0929 0.0081 -3.3212 -8.0234 1.1000e+00 6.4416e-04 1.4327e-02 4.7279e-05 5.9660e-04 2.7953e-07 5.5492e-12
2 react 8.0000e-03 -0.9101 -0.0107 -2.9007 -7.8887 1.1000e+00 2.9972e-03 6.6664e-02 3.3511e-04 2.6587e-03 3.4247e-06 3.5204e-11
2 react 1.6000e-02 -0.7156 -0.0438 -2.4738 -7.7606 1.1000e+00 8.2421e-03 1.8332e-01 1.4423e-03 6.7746e-03 2.5169e-05 1.3002e-10
2 react 3.2000e-02 -0.5438 -0.0941 -2.0462 -7.6302 1.1000e+00 2.0521e-02 4.5644e-01 5.3332e-03 1.5021e-02 1.6775e-04 4.3718e-10
2 react 6.4000e-02 -0.4248 -0.1517 -1.7252 -7.5359 1.1000e+00 4.9404e-02 1.0988e+00 1.6888e-02 3.1671e-02 8.4558e-04 1.3075e-09
2 react 1.2500e-01 -0.3613 -0.1954 -1.5662 -7.4966 1.1000e+00 1.0982e-01 2.4427e+00 4.3447e-02 6.3666e-02 2.7111e-03 3.1820e-09
2 react 2.5000e-01 -0.3288 -0.2227 -1.4927 -7.4823 1.1000e+00 2.3770e-01 5.2868e+00 1.0135e-01 1.2940e-01 6.9491e-03 7.1171e-09
2 react 5.0000e-01 -0.3131 -0.2373 -1.4597 -7.4772 1.1000e+00 4.9570e-01 1.1025e+01 2.1912e-01 2.6094e-01 1.5635e-02 1.5019e-08
2 react 1.0000e+00 -0.3055 -0.2448 -1.4443 -7.4751 1.1000e+00 1.0128e+00 2.2527e+01 4.5565e-01 5.2406e-01 3.3103e-02 3.0832e-08
3 react 1.0000e-03 -2.7554 -3.2432 -4.4230 -9.1701 2.3652e-03 2.1751e-03 2.2500e+01 1.6151e-03 5.2527e-04 3.4720e-05 6.2162e-10
3 react 2.0000e-03 -2.6525 -2.9422 -4.1221 -8.9453 3.4435e-03 3.1668e-03 2.2500e+01 2.0468e-03 1.0505e-03 6.9421e-05 1.0430e-09
3 react 3.0000e-03 -2.5681 -2.7661 -3.9462 -8.8230 4.5301e-03 4.1661e-03 2.2500e+01 2.4862e-03 1.5758e-03 1.0409e-04 1.3823e-09
3 react 4.0000e-03 -2.4967 -2.6412 -3.8215 -8.7406 5.6217e-03 5.1699e-03 2.2500e+01 2.9303e-03 2.1010e-03 1.3872e-04 1.6713e-09
3 react 8.0000e-03 -2.2889 -2.3402 -3.5212 -8.5555 1.0011e-02 9.2068e-03 2.2500e+01 4.7283e-03 4.2016e-03 2.7697e-04 2.5595e-09
3 react 1.6000e-02 -2.0415 -2.0392 -3.2214 -8.3855 1.8825e-02 1.7312e-02 2.2500e+01 8.3576e-03 8.4019e-03 5.5233e-04 3.7856e-09
3 react 3.2000e-02 -1.7694 -1.7383 -2.9223 -8.2251 3.6471e-02 3.3540e-02 2.2500e+01 1.5640e-02 1.6800e-02 1.0998e-03 5.4762e-09
3 react 6.4000e-02 -1.4834 -1.4374 -2.6240 -8.0704 7.1755e-02 6.5989e-02 2.2500e+01 3.0213e-02 3.3590e-02 2.1859e-03 7.8205e-09
3 react 1.2500e-01 -1.2004 -1.1468 -2.3367 -7.9240 1.3896e-01 1.2779e-01 2.2500e+01 5.7976e-02 6.5580e-02 4.2353e-03 1.0956e-08
3 react 2.5000e-01 -0.9036 -0.8460 -2.0399 -7.7740 2.7653e-01 2.5431e-01 2.2500e+01 1.1482e-01 1.3110e-01 8.3897e-03 1.5474e-08
3 react 5.0000e-01 -0.6049 -0.5452 -1.7426 -7.6246 5.5147e-01 5.0716e-01 2.2500e+01 2.2843e-01 2.6209e-01 1.6634e-02 2.1827e-08
3 react 1.0000e+00 -0.3050 -0.2442 -1.4438 -7.4749 1.1013e+00 1.0128e+00 2.2500e+01 4.5563e-01 5.2406e-01 3.3101e-02 3.0813e-08

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sim state soln dist_x time step pH pe m_Zn+2 m_Hfo_wOZn+ m_Hfo_sOZn+
2 react 1 -99 0 1 5 15.0946 9.9667e-08 1.3194e-11 3.1498e-10
3 react 1 -99 0 1 5.25 14.8089 9.9093e-08 3.6118e-11 8.6216e-10
4 react 1 -99 0 1 5.5 14.5232 9.7567e-08 9.7221e-11 2.3200e-09
5 react 1 -99 0 1 5.75 14.2374 9.3657e-08 2.5418e-10 6.0611e-09
6 react 1 -99 0 1 6 13.9517 8.4476e-08 6.2406e-10 1.4855e-08
7 react 1 -99 0 1 6.25 13.666 6.6695e-08 1.3446e-09 3.1897e-08
8 react 1 -99 0 1 6.5 13.3803 4.2322e-08 2.3406e-09 5.5265e-08
9 react 1 -99 0 1 6.75 13.0946 2.1052e-08 3.2179e-09 7.5665e-08
10 react 1 -99 0 1 7 12.8089 8.7494e-09 3.7289e-09 8.7472e-08
11 react 1 -99 0 1 7.25 12.5232 3.3000e-09 3.9564e-09 9.2708e-08
12 react 1 -99 0 1 7.5 12.2374 1.1903e-09 4.0447e-09 9.4740e-08
13 react 1 -99 0 1 7.75 11.9517 4.2114e-10 4.0771e-09 9.5483e-08
14 react 1 -99 0 1 8 11.666 1.4799e-10 4.0887e-09 9.5749e-08
15 react 2 -99 0 1 5 15.0946 9.9686e-05 1.3187e-08 2.9620e-07
16 react 2 -99 0 1 5.25 14.8089 9.9220e-05 3.6081e-08 7.3494e-07
17 react 2 -99 0 1 5.5 14.5231 9.8300e-05 9.7297e-08 1.5866e-06
18 react 2 -99 0 1 5.75 14.2374 9.6947e-05 2.5891e-07 2.7658e-06
19 react 2 -99 0 1 6 13.9517 9.5437e-05 6.8302e-07 3.8297e-06
20 react 2 -99 0 1 6.25 13.666 9.3651e-05 1.7815e-06 4.4782e-06
21 react 2 -99 0 1 6.5 13.3803 9.0584e-05 4.4798e-06 4.7815e-06
22 react 2 -99 0 1 6.75 13.0946 8.4566e-05 1.0266e-05 4.9051e-06
23 react 2 -99 0 1 7 12.8088 7.4581e-05 2.0039e-05 4.9534e-06
24 react 2 -99 0 1 7.25 12.5229 6.1786e-05 3.2572e-05 4.9732e-06
25 react 2 -99 0 1 7.5 12.2374 4.8388e-05 4.5601e-05 4.9823e-06
26 react 2 -99 0 1 7.75 11.9517 3.5918e-05 5.7508e-05 4.9871e-06
27 react 2 -99 0 1 8 11.666 2.5127e-05 6.7404e-05 4.9897e-06

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Days Fe(2) Fe(3) pH si_goethite
0.0000e+00 1.0000e+02 0.0000e+00 7.0000e+00 -9.9990e+01
1.1574e-03 9.8942e+01 1.0578e+00 6.0476e+00 6.6424e+00
5.7870e-03 9.8206e+01 1.7942e+00 5.8097e+00 6.6543e+00
4.1667e-02 9.6592e+01 3.4082e+00 5.5247e+00 6.6602e+00
1.6667e-01 9.4639e+01 5.3610e+00 5.3268e+00 6.6620e+00
4.1667e-01 9.2764e+01 7.2360e+00 5.1975e+00 6.6627e+00
1.0000e+00 9.0358e+01 9.6422e+00 5.0750e+00 6.6632e+00
2.0000e+00 8.7896e+01 1.2104e+01 4.9790e+00 6.6635e+00
4.0000e+00 8.4808e+01 1.5192e+01 4.8840e+00 6.6638e+00
6.0000e+00 8.2651e+01 1.7349e+01 4.8290e+00 6.6639e+00
8.0000e+00 8.0939e+01 1.9061e+01 4.7903e+00 6.6640e+00
1.0000e+01 7.9498e+01 2.0502e+01 4.7605e+00 6.6640e+00

103
advection.cpp
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#define EXTERNAL extern
#include "global.h"
#include "phqalloc.h"
#include "output.h"
#include "phrqproto.h"
static char const svnid[] = "$Id: advection.c 78 2005-02-01 22:47:12Z dlpark $";
/* ---------------------------------------------------------------------- */
int advection(void)
/* ---------------------------------------------------------------------- */
{
int i, n;
LDBLE kin_time;
if (svnid == NULL) fprintf(stderr," ");
/*
* Calculate advection
*/
state = ADVECTION;
/* mass_water_switch = TRUE; */
/*
* Check existence of all solutions
*/
for (i = 0; i <= count_ad_cells; i++) {
if (solution_bsearch(i, &n, TRUE) == NULL) {
input_error++;
sprintf(error_string, "Solution %d is needed for advection, but is not defined.", i);
error_msg(error_string, CONTINUE);
}
}
/*
* Check kinetics logic
*/
kin_time = advection_kin_time;
if (kin_time <= 0.0) {
for (i = 1; i <= count_ad_cells; i++) {
if (kinetics_bsearch(i, &n) != NULL) {
input_error++;
sprintf(error_string, "KINETIC reaction(s) defined, but time_step is not defined in ADVECTION keyword.");
error_msg(error_string, CONTINUE);
break;
}
}
}
/*
* Quit on error
*/
if (input_error > 0) {
error_msg("Program terminating due to input errors.", STOP);
}
/*
* Equilibrate solutions with phases, exchangers, surfaces
*/
last_model.force_prep = TRUE;
rate_sim_time_start = 0;
for (advection_step = 1; advection_step <= count_ad_shifts; advection_step++) {
output_msg(OUTPUT_LOG, "\nBeginning of advection time step %d, cumulative pore volumes %f.\n", advection_step, (double) (((LDBLE) advection_step) / ((LDBLE) count_ad_cells)));
if (pr.use == TRUE && pr.all == TRUE) {
output_msg(OUTPUT_MESSAGE, "Beginning of advection time step %d, cumulative pore volumes %f.\n",
advection_step, (double) (((LDBLE) advection_step) / ((LDBLE) count_ad_cells)));
}
/*
* Advect
*/
for (i = count_ad_cells; i > 0; i--) {
solution_duplicate(i - 1, i);
}
/*
* Equilibrate and (or) mix
*/
for (i = 1; i <= count_ad_cells; i++) {
cell_no = i;
set_advection(i, TRUE, TRUE, i);
run_reactions(i, kin_time, TRUE, 1.0);
if (advection_kin_time_defined == TRUE) {
rate_sim_time = rate_sim_time_start + kin_time;
}
output_msg(OUTPUT_LOG, "\nCell %d.\n\n", i);
if (pr.use == TRUE && pr.all == TRUE &&
advection_step % print_ad_modulus == 0 &&
advection_print[i-1] == TRUE) {
output_msg(OUTPUT_MESSAGE, "\nCell %d.\n\n", i);
}
if (advection_step % punch_ad_modulus == 0 &&
advection_punch[i-1] == TRUE ) {
punch_all();
}
if (advection_step % print_ad_modulus == 0 &&
advection_print[i-1] == TRUE ) {
print_all();
}
if (i > 1) solution_duplicate(-2, i-1);
saver();
}
solution_duplicate(-2, count_ad_cells);
rate_sim_time_start += kin_time;
}
initial_total_time += rate_sim_time_start;
/* free_model_allocs(); */
mass_water_switch = FALSE;
return(OK);
}

4400
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#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdlib.h>
/* must be defined here and in global.h */
#if !defined(WIN32_MEMORY_DEBUG)
#define USE_PHRQ_ALLOC
#endif
#include "phqalloc.h"
#include "output.h"
#include "phrqtype.h"
int cl1(int k, int l, int m, int n,
int nklmd, int n2d,
LDBLE *q,
int *kode, LDBLE toler,
int *iter, LDBLE *x, LDBLE *res, LDBLE *error,
LDBLE *cu, int *iu, int *s,
int check);
static char const svnid[] = "$Id: cl1.c 248 2005-04-14 17:10:53Z dlpark $";
extern void *free_check_null(void *ptr);
extern void malloc_error(void);
/* debug
#define DEBUG_CL1
#define CHECK_ERRORS
*/
int cl1(int k, int l, int m, int n,
int nklmd, int n2d,
LDBLE *q,
int *kode, LDBLE toler,
int *iter, LDBLE *x, LDBLE *res, LDBLE *error,
LDBLE *cu, int *iu, int *s, int check)
{
/* System generated locals */
LDBLE *scratch;
union double_or_int {int ival; LDBLE dval;} *q2;
/* Local variables */
static int nklm;
static LDBLE xmin, xmax;
static int iout, i, j;
static LDBLE z;
static int maxit, n1, n2;
static LDBLE pivot;
static int ia, ii, kk, in, nk, js;
static LDBLE sn;
static int iphase, kforce;
static LDBLE zu, zv;
static LDBLE tpivot;
static int klm, jmn, nkl, jpn;
static LDBLE cuv, sum;
static int klm1;
int q_dim, cu_dim;
int kode_arg;
LDBLE *x_arg, *res_arg, check_toler;
#ifdef CHECK_ERRORS
extern char **col_name, **row_name;
extern int *row_back, *col_back;
#endif
/* THIS SUBROUTINE USES A MODIFICATION OF THE SIMPLEX */
/* METHOD OF LINEAR PROGRAMMING TO CALCULATE AN L1 SOLUTION */
/* TO A K BY N SYSTEM OF LINEAR EQUATIONS */
/* AX=B */
/* SUBJECT TO L LINEAR EQUALITY CONSTRAINTS */
/* CX=D */
/* AND M LINEAR INEQUALITY CONSTRAINTS */
/* EX.LE.F. */
/* DESCRIPTION OF PARAMETERS */
/* K NUMBER OF ROWS OF THE MATRIX A (K.GE.1). */
/* L NUMBER OF ROWS OF THE MATRIX C (L.GE.0). */
/* M NUMBER OF ROWS OF THE MATRIX E (M.GE.0). */
/* N NUMBER OF COLUMNS OF THE MATRICES A,C,E (N.GE.1). */
/* KLMD SET TO AT LEAST K+L+M FOR ADJUSTABLE DIMENSIONS. */
/* KLM2D SET TO AT LEAST K+L+M+2 FOR ADJUSTABLE DIMENSIONS. */
/* NKLMD SET TO AT LEAST N+K+L+M FOR ADJUSTABLE DIMENSIONS. */
/* N2D SET TO AT LEAST N+2 FOR ADJUSTABLE DIMENSIONS */
/* Q TWO DIMENSIONAL REAL ARRAY WITH KLM2D ROWS AND */
/* AT LEAST N2D COLUMNS. */
/* ON ENTRY THE MATRICES A,C AND E, AND THE VECTORS */
/* B,D AND F MUST BE STORED IN THE FIRST K+L+M ROWS */
/* AND N+1 COLUMNS OF Q AS FOLLOWS */
/* A B */
/* Q = C D */
/* E F */
/* THESE VALUES ARE DESTROYED BY THE SUBROUTINE. */
/* KODE A CODE USED ON ENTRY TO, AND EXIT */
/* FROM, THE SUBROUTINE. */
/* ON ENTRY, THIS SHOULD NORMALLY BE SET TO 0. */
/* HOWEVER, IF CERTAIN NONNEGATIVITY CONSTRAINTS */
/* ARE TO BE INCLUDED IMPLICITLY, RATHER THAN */
/* EXPLICITLY IN THE CONSTRAINTS EX.LE.F, THEN KODE */
/* SHOULD BE SET TO 1, AND THE NONNEGATIVITY */
/* CONSTRAINTS INCLUDED IN THE ARRAYS X AND */
/* RES (SEE BELOW). */
/* ON EXIT, KODE HAS ONE OF THE */
/* FOLLOWING VALUES */
/* 0- OPTIMAL SOLUTION FOUND, */
/* 1- NO FEASIBLE SOLUTION TO THE */
/* CONSTRAINTS, */
/* 2- CALCULATIONS TERMINATED */
/* PREMATURELY DUE TO ROUNDING ERRORS, */
/* 3- MAXIMUM NUMBER OF ITERATIONS REACHED. */
/* TOLER A SMALL POSITIVE TOLERANCE. EMPIRICAL */
/* EVIDENCE SUGGESTS TOLER = 10**(-D*2/3), */
/* WHERE D REPRESENTS THE NUMBER OF DECIMAL */
/* DIGITS OF ACCURACY AVAILABLE. ESSENTIALLY, */
/* THE SUBROUTINE CANNOT DISTINGUISH BETWEEN ZERO */
/* AND ANY QUANTITY WHOSE MAGNITUDE DOES NOT EXCEED */
/* TOLER. IN PARTICULAR, IT WILL NOT PIVOT ON ANY */
/* NUMBER WHOSE MAGNITUDE DOES NOT EXCEED TOLER. */
/* ITER ON ENTRY ITER MUST CONTAIN AN UPPER BOUND ON */
/* THE MAXIMUM NUMBER OF ITERATIONS ALLOWED. */
/* A SUGGESTED VALUE IS 10*(K+L+M). ON EXIT ITER */
/* GIVES THE NUMBER OF SIMPLEX ITERATIONS. */
/* X ONE DIMENSIONAL REAL ARRAY OF SIZE AT LEAST N2D. */
/* ON EXIT THIS ARRAY CONTAINS A */
/* SOLUTION TO THE L1 PROBLEM. IF KODE=1 */
/* ON ENTRY, THIS ARRAY IS ALSO USED TO INCLUDE */
/* SIMPLE NONNEGATIVITY CONSTRAINTS ON THE */
/* VARIABLES. THE VALUES -1, 0, OR 1 */
/* FOR X(J) INDICATE THAT THE J-TH VARIABLE */
/* IS RESTRICTED TO BE .LE.0, UNRESTRICTED, */
/* OR .GE.0 RESPECTIVELY. */
/* RES ONE DIMENSIONAL REAL ARRAY OF SIZE AT LEAST KLMD. */
/* ON EXIT THIS CONTAINS THE RESIDUALS B-AX */
/* IN THE FIRST K COMPONENTS, D-CX IN THE */
/* NEXT L COMPONENTS (THESE WILL BE =0),AND */
/* F-EX IN THE NEXT M COMPONENTS. IF KODE=1 ON */
/* ENTRY, THIS ARRAY IS ALSO USED TO INCLUDE SIMPLE */
/* NONNEGATIVITY CONSTRAINTS ON THE RESIDUALS */
/* B-AX. THE VALUES -1, 0, OR 1 FOR RES(I) */
/* INDICATE THAT THE I-TH RESIDUAL (1.LE.I.LE.K) IS */
/* RESTRICTED TO BE .LE.0, UNRESTRICTED, OR .GE.0 */
/* RESPECTIVELY. */
/* ERROR ON EXIT, THIS GIVES THE MINIMUM SUM OF */
/* ABSOLUTE VALUES OF THE RESIDUALS. */
/* CU A TWO DIMENSIONAL REAL ARRAY WITH TWO ROWS AND */
/* AT LEAST NKLMD COLUMNS USED FOR WORKSPACE. */
/* IU A TWO DIMENSIONAL INTEGER ARRAY WITH TWO ROWS AND */
/* AT LEAST NKLMD COLUMNS USED FOR WORKSPACE. */
/* S INTEGER ARRAY OF SIZE AT LEAST KLMD, USED FOR */
/* WORKSPACE. */
/* DOUBLE PRECISION DBLE */
/* REAL */
/* INITIALIZATION. */
if (svnid == NULL) fprintf(stderr," ");
zv = 0;
kode_arg = *kode;
x_arg = NULL;
res_arg = NULL;
if (check == 1) {
/*
q_arg = PHRQ_malloc((size_t) (max_row_count * max_column_count * sizeof(LDBLE)));
if (q_arg == NULL) malloc_error();
for (i = 0; i < max_row_count*max_column_count; i++) {
q_arg[i] = q[i];
}
*/
x_arg = (double *) PHRQ_malloc((size_t) (n2d * sizeof(LDBLE)));
if (x_arg == NULL) malloc_error();
for (i = 0; i < n2d; i++) {
x_arg[i] = x[i];
}
res_arg = (double *) PHRQ_malloc((size_t) ((k + l + m) * sizeof(LDBLE)));
if (res_arg == NULL) malloc_error();
for (i = 0; i < k + l + m; i++) {
res_arg[i] = res[i];
}
}
/* Parameter adjustments */
q_dim = n2d;
q2 = (union double_or_int *) q;
cu_dim = nklmd;
/* Function Body */
maxit = *iter;
n1 = n + 1;
n2 = n + 2;
nk = n + k;
nkl = nk + l;
klm = k + l + m;
klm1 = klm + 1;
nklm = n + klm;
kforce = 1;
*iter = 0;
js = 0;
ia = -1;
/* Make scratch space */
scratch = (LDBLE *) PHRQ_malloc( (size_t) nklmd * sizeof(LDBLE));
if (scratch == NULL) malloc_error();
for (i=0; i < nklmd; i++) {
scratch[i] = 0.0;
}
/* SET UP LABELS IN Q. */
for (j = 0; j < n; ++j) {
q2[ klm1 * q_dim + j ].ival = j + 1;
}
/* L10: */
for (i = 0; i < klm; ++i) {
q2[ i * q_dim + n1 ].ival = n + i + 1;
if (q2[ i * q_dim + n ].dval < 0.) {
for (j = 0; j < n1; ++j) {
q2[ i * q_dim + j ].dval = -q2[ i * q_dim + j ].dval;
}
q2[ i * q_dim + n1 ].ival = -q2[ i * q_dim + n1 ].ival;
/* L20: */
}
}
/* L30: */
/* SET UP PHASE 1 COSTS. */
iphase = 2;
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "Set up phase 1 costs\n");
#endif
/* Zero first row of cu and iu */
memcpy( (void *) &(cu[0]), (void *) &(scratch[0]),
(size_t) nklm * sizeof(LDBLE) );
for (j = 0; j < nklm; ++j) {
iu[ j ] = 0;
}
/* L40: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L40\n");
#endif
if (l != 0) {
for (j = nk; j < nkl; ++j) {
cu[ j ] = 1.;
iu[ j ] = 1;
}
/* L50: */
iphase = 1;
}
/* Copy first row of cu and iu to second row */
memcpy( (void *) &(cu[cu_dim]), (void *) &(cu[0]),
(size_t) nklm * sizeof(LDBLE) );
memcpy( (void *) &(iu[cu_dim]), (void *) &(iu[0]),
(size_t) nklm * sizeof(int) );
/* L60: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L60\n");
#endif
if (m != 0) {
for (j = nkl; j < nklm; ++j) {
cu[ cu_dim + j ] = 1.;
iu[ cu_dim + j ] = 1;
jmn = j - n;
if (q2[ jmn * q_dim + n1 ].ival < 0) {
iphase = 1;
}
}
/* L70: */
}
/* L80: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L80\n");
#endif
if (*kode != 0) {
for (j = 0; j < n; ++j) {
if ( x[j] < 0.) {
/* L90: */
cu[ j ] = 1.;
iu[ j ] = 1;
} else if (x[j] > 0.) {
cu[ cu_dim + j ] = 1.;
iu[ cu_dim + j ] = 1;
}
}
/* L110: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L110\n");
#endif
for (j = 0; j < k; ++j) {
jpn = j + n;
if ( res[j] < 0.) {
/* L120: */
cu[ jpn ] = 1.;
iu[ jpn ] = 1;
if (q2[ j * q_dim + n1 ].ival > 0) {
iphase = 1;
}
} else if (res[j] > 0.) {
/* L130: */
cu[ cu_dim + jpn ] = 1.;
iu[ cu_dim + jpn ] = 1;
if (q2[ j * q_dim + n1 ].ival < 0) {
iphase = 1;
}
}
}
/* L140: */
}
/* L150: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L150\n");
#endif
if (iphase == 2) {
goto L500;
}
/* COMPUTE THE MARGINAL COSTS. */
L160:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L160\n");
#endif
for (j = js; j < n1; ++j) {
sum = 0.;
for (i = 0; i < klm; ++i) {
ii = q2[ i * q_dim + n1 ].ival;
if (ii < 0) {
z = cu[ cu_dim - ii - 1 ];
} else {
z = cu[ ii - 1 ];
}
sum += q2[ i * q_dim + j ].dval * z;
}
q2[ klm * q_dim + j ].dval = sum;
}
for (j = js; j < n; ++j) {
ii = q2[ klm1 * q_dim + j].ival;
if (ii < 0) {
z = cu[ cu_dim - ii - 1 ];
} else {
z = cu[ ii - 1 ];
}
q2[ klm * q_dim + j ].dval -= z;
}
/* DETERMINE THE VECTOR TO ENTER THE BASIS. */
L240:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L240, xmax %e\n", xmax);
#endif
xmax = 0.;
if (js >= n) {
goto L490; /* test for optimality */
}
for (j = js; j < n; ++j) {
zu = q2[ klm * q_dim + j ].dval;
ii = q2[ klm1 * q_dim + j ].ival;
if (ii > 0) {
zv = -zu - cu[ ii - 1 ] - cu[ cu_dim + ii - 1 ];
} else {
ii = -ii;
zv = zu;
zu = -zu - cu[ ii - 1 ] - cu[ cu_dim + ii - 1 ];
}
/* L260 */
if (kforce == 1 && ii > n) {
continue;
}
if (iu[ ii - 1 ] != 1 && zu > xmax){
xmax = zu;
in = j;
}
/* L270 */
if (iu[ cu_dim + ii - 1 ] != 1 && zv > xmax ) {
xmax = zv;
in = j;
}
}
/* L280 */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L280 xmax %e, toler %e\n", xmax, toler);
#endif
if (xmax <= toler) {
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "xmax before optimality test %e\n",xmax);
#endif
goto L490; /* test for optimality */
}
if (q2[ klm * q_dim + in ].dval != xmax) {
for (i = 0; i < klm1; ++i) {
q2[ i * q_dim + in ].dval = -q2[ i * q_dim + in ].dval;
}
q2[ klm1 * q_dim + in ].ival = -q2[ klm1 * q_dim + in ].ival;
/* L290: */
q2[ klm * q_dim + in ].dval = xmax;
}
/* DETERMINE THE VECTOR TO LEAVE THE BASIS. */
if (iphase != 1 && ia != -1) {
xmax = 0.;
/* find maximum absolute value in column "in" */
for (i = 0; i <= ia; ++i) {
z = fabs(q2[ i * q_dim + in ].dval);
if (z > xmax) {
xmax = z;
iout = i;
}
}
/* L310: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L310, xmax %e\n", xmax);
#endif
/* switch row ia with row iout, use memcpy */
if (xmax > toler) {
memcpy( (void *) &(scratch[0]), (void *) &(q2[ ia * q_dim]),
(size_t) n2 * sizeof(LDBLE) );
memcpy( (void *) &(q2[ ia * q_dim ]), (void *) &(q2[ iout * q_dim]),
(size_t) n2 * sizeof(LDBLE) );
memcpy( (void *) &(q2[ iout * q_dim ]), (void *) &(scratch[ 0 ]),
(size_t) n2 * sizeof(LDBLE) );
/* L320: */
/* set pivot to row ia, column in */
iout = ia;
--ia;
pivot = q2[ iout * q_dim + in ].dval;
goto L420; /* Gauss Jordan */
}
}
/* L330: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L330, xmax %e\n", xmax);
#endif
kk = -1;
/* divide column n1 by positive value in column "in" greater than toler */
for (i = 0; i < klm; ++i) {
z = q2[ i * q_dim + in ].dval;
if (z > toler) {
++kk;
res[kk] = q2[ i * q_dim + n ].dval / z;
s[kk] = i;
}
}
/* L340: */
#ifdef DEBUG_CL1
if (kk < 0) {
output_msg(OUTPUT_MESSAGE, "kode = 2 in loop 340.\n");
}
#endif
L350:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L350, xmax %e\n", xmax);
#endif
if (kk < 0) {
/* no positive value found in L340 or bypass intermediate verticies */
*kode = 2;
goto L590;
}
/* L360: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L360, xmax %e\n", xmax);
#endif
/* find minimum residual */
xmin = res[ 0 ];
iout = s[ 0 ];
j = 0;
if (kk != 0) {
for (i = 1; i <= kk; ++i) {
if (res[i] < xmin) {
j = i;
xmin = res[i];
iout = s[i];
}
}
/* L370: */
/* put kk in position j */
res[j] = res[kk];
s[j] = s[kk];
}
/* L380: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L380 iout %d, xmin %e, xmax %e\n", iout, xmin, xmax);
#endif
--kk;
pivot = q2[ iout * q_dim + in ].dval;
ii = q2[ iout * q_dim + n1 ].ival;
if (iphase != 1) {
if (ii < 0) {
/* L390: */
if (iu[ - ii - 1 ] == 1) {
goto L420;
}
} else {
if (iu[ cu_dim + ii - 1 ] == 1) {
goto L420;
}
}
}
/* L400: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L400\n");
#endif
ii = abs(ii);
cuv = cu[ ii - 1 ] + cu[ cu_dim + ii - 1];
if (q2[ klm * q_dim + in ].dval - pivot * cuv > toler) {
/* BYPASS INTERMEDIATE VERTICES. */
for (j = js; j < n1; ++j) {
z = q2[ iout * q_dim + j ].dval;
q2[ klm * q_dim + j ].dval -= z * cuv;
q2[ iout * q_dim + j ].dval = -z;
}
/* L410: */
q2[ iout * q_dim + n1 ].ival = -q2[ iout * q_dim + n1 ].ival;
goto L350;
}
/* GAUSS-JORDAN ELIMINATION. */
L420:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "Gauss Jordon %d\n", *iter);
#endif
if (*iter >= maxit) {
*kode = 3;
goto L590;
}
/* L430: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L430\n");
#endif
++(*iter);
for (j = js; j < n1; ++j) {
if (j != in) {
q2[ iout * q_dim + j ].dval /= pivot;
}
}
/* L440: */
for (j = js; j < n1; ++j) {
if (j != in) {
z = -q2[ iout * q_dim + j ].dval;
for (i = 0; i < klm1; ++i) {
if (i != iout) {
q2[ i * q_dim + j ].dval += z * q2[ i * q_dim + in ].dval;
}
}
/* L450: */
}
}
/* L460: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L460\n");
#endif
tpivot = -pivot;
for (i = 0; i < klm1; ++i) {
if (i != iout) {
q2[ i * q_dim + in ].dval /= tpivot;
}
}
/* L470: */
q2[ iout * q_dim + in ].dval = 1. / pivot;
ii = q2[ iout * q_dim + n1 ].ival;
q2[ iout * q_dim + n1 ].ival = q2[ klm1 * q_dim + in ].ival;
q2[ klm1 * q_dim + in ].ival = ii;
ii = abs(ii);
if (iu[ ii - 1 ] == 0 || iu[ cu_dim + ii - 1 ] == 0) {
goto L240;
}
/* switch column */
for (i = 0; i < klm1; ++i) {
z = q2[ i * q_dim + in ].dval;
q2[ i * q_dim + in ].dval = q2[ i * q_dim + js ].dval;
q2[ i * q_dim + js ].dval = z;
}
i = q2[ klm1 * q_dim + in ].ival;
q2[ klm1 * q_dim + in ].ival = q2[ klm1 * q_dim + js ].ival;
q2[ klm1 * q_dim + js ].ival = i;
/* L480: */
++js;
goto L240;
/* TEST FOR OPTIMALITY. */
L490:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L490\n");
#endif
if (kforce == 0) {
if (iphase == 1) {
if (q2[ klm * q_dim + n ].dval <= toler) {
goto L500;
}
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE,"q2[klm1-1, n1-1] > *toler. %e\n",q2[ ( klm1 - 1 ) * q_dim + n1 - 1 ].dval);
#endif
*kode = 1;
goto L590;
}
*kode = 0;
goto L590;
}
if (iphase != 1 || q2[ klm * q_dim + n ].dval > toler) {
kforce = 0;
goto L240;
}
/* SET UP PHASE 2 COSTS. */
L500:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "Set up phase 2 costs %d\n", *iter);
#endif
iphase = 2;
for (j = 0; j < nklm; ++j) {
cu[ j ] = 0.;
}
/* L510: */
for (j = n; j < nk; ++j) {
cu[ j ] = 1.;
}
memcpy( (void *) &(cu[cu_dim]), (void *) &(cu[0]),
(size_t) nklm * sizeof(LDBLE) );
/* L520: */
for (i = 0; i < klm; ++i) {
ii = q2[ i * q_dim + n1 ].ival;
if (ii <= 0) {
if (iu[ cu_dim - ii - 1 ] == 0) {
continue;
}
cu[ cu_dim - ii - 1 ] = 0.;
} else {
/* L530: */
if (iu[ ii - 1 ] == 0) {
continue;
}
cu[ ii - 1 ] = 0.;
}
/* L540: */
++ia;
/* switch row */
memcpy( (void *) &(scratch[0]), (void *) &(q2[ ia * q_dim]),
(size_t) n2 * sizeof(LDBLE) );
memcpy( (void *) &(q2[ ia * q_dim ]), (void *) &(q2[ i * q_dim]),
(size_t) n2 * sizeof(LDBLE) );
memcpy( (void *) &(q2[ i * q_dim ]), (void *) &(scratch[ 0 ]),
(size_t) n2 * sizeof(LDBLE) );
/* L550: */
}
/* L560: */
goto L160;
/* PREPARE OUTPUT. */
L590:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L590\n");
#endif
sum = 0.;
for (j = 0; j < n; ++j) {
x[j] = 0.;
}
/* L600: */
for (i = 0; i < klm; ++i) {
res[i] = 0.;
}
/* L610: */
for (i = 0; i < klm; ++i) {
ii = q2[ i * q_dim + n1 ].ival;
sn = 1.;
if (ii < 0) {
ii = -ii;
sn = -1.;
}
if (ii <= n) {
/* L620: */
x[ii - 1] = sn * q2[ i * q_dim + n ].dval;
} else {
/* L630: */
res[ii - n - 1] = sn * q2[ i * q_dim + n ].dval;
if (ii >= n1 && ii <= nk ) {
/* * DBLE(Q(I,N1)) */
sum += q2[ i * q_dim + n ].dval;
}
}
}
/* L640: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L640\n");
#endif
*error = sum;
scratch = (double *) free_check_null (scratch);
/*
* Check calculation
*/
if ((check == 1) && (*kode == 0)) {
check_toler = 10.*toler;
/*
* Check optimization constraints
*/
if (kode_arg == 1) {
for (i = 0; i < k; i++) {
if (res_arg[i] < 0.0) {
if (res[i] > check_toler) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1: optimization constraint not satisfied row %d, res %s, constraint %f.\n", row_name[row_back[i]], res[i], res_arg[i]);
#endif
*kode = 1;
}
} else if (res_arg[i] > 0.0) {
if (res[i] < -check_toler) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1: optimization constraint not satisfied row %s, res %e, constraint %f.\n", row_name[row_back[i]], res[i], res_arg[i]);
#endif
*kode = 1;
}
}
}
}
/*
* Check equalities
*/
for (i = k; i < k + l; i++) {
if (fabs(res[i]) > check_toler) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1: equality constraint not satisfied row %s, res %e, tolerance %e.\n", row_name[row_back[i]], res[i], check_toler);
#endif
*kode = 1;
}
}
/*
* Check inequalities
*/
for (i = k + l; i < k + l + m; i++) {
if (res[i] < -check_toler) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1: inequality constraint not satisfied row %s, res %e, tolerance %e.\n", row_name[row_back[i]], res[i], check_toler);
#endif
*kode = 1;
}
}
/*
* Check dissolution/precipitation constraints
*/
if (kode_arg == 1) {
for (i = 0; i < n; i++) {
if (x_arg[i] < 0.0) {
if (x[i] > check_toler) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1: dis/pre constraint not satisfied column %s, x %e, constraint %f.\n", col_name[col_back[i]], x[i], x_arg[i]);
#endif
*kode = 1;
}
} else if (x_arg[i] > 0.0) {
if (x[i] < -check_toler) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1: dis/pre constraint not satisfied column %s, x %e, constraint %f.\n", col_name[col_back[i]], x[i], x_arg[i]);
#endif
*kode = 1;
}
}
}
}
if (*kode == 1) {
output_msg(OUTPUT_MESSAGE, "\n\tCL1: Roundoff errors in optimization.\n\t Try using -multiple_precision in INVERSE_MODELING\n");
}
}
if (check == 1) {
x_arg = (double *) free_check_null(x_arg);
res_arg = (double *) free_check_null(res_arg);
}
return 0;
}

974
cl1mp.cpp
View File

@ -1,974 +0,0 @@
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdlib.h>
#include <gmp.h>
/* must be defined here and in global.h */
#if !defined(WIN32_MEMORY_DEBUG)
#define USE_PHRQ_ALLOC
#endif
#include "phqalloc.h"
#include "output.h"
#include "phrqtype.h"
extern int max_row_count, max_column_count;
static char const svnid[] = "$Id: cl1mp.c 78 2005-02-01 22:47:12Z dlpark $";
int cl1mp(int k, int l, int m, int n,
int nklmd, int n2d,
LDBLE *q_arg,
int *kode, LDBLE toler,
int *iter, LDBLE *x_arg, LDBLE *res_arg, LDBLE *error,
LDBLE *cu_arg, int *iu, int *s, int check, LDBLE censor_arg);
extern void *free_check_null(void *ptr);
extern void malloc_error(void);
/* debug
#define DEBUG_CL1
#define CHECK_ERRORS
*/
int cl1mp(int k, int l, int m, int n,
int nklmd, int n2d,
LDBLE *q_arg,
int *kode_arg, LDBLE toler_arg,
int *iter, LDBLE *x_arg, LDBLE *res_arg, LDBLE *error_arg,
LDBLE *cu_arg, int *iu, int *s, int check, LDBLE censor_arg)
{
/* System generated locals */
union double_or_int {int ival; mpf_t dval;} *q2;
/* Local variables */
static int nklm;
static int iout, i, j;
static int maxit, n1, n2;
static int ia, ii, kk, in, nk, js;
static int iphase, kforce;
static int klm, jmn, nkl, jpn;
static int klm1;
static int *kode;
int q_dim, cu_dim;
int iswitch;
mpf_t *q;
mpf_t *x;
mpf_t *res;
mpf_t error;
mpf_t *cu;
mpf_t dummy, dummy1, sum, z, zu, zv, xmax, minus_one, toler, check_toler;
/*mpf_t *scratch;*/
mpf_t pivot, xmin, cuv, tpivot, sn;
mpf_t zero;
int censor;
mpf_t censor_tol;
/* THIS SUBROUTINE USES A MODIFICATION OF THE SIMPLEX */
/* METHOD OF LINEAR PROGRAMMING TO CALCULATE AN L1 SOLUTION */
/* TO A K BY N SYSTEM OF LINEAR EQUATIONS */
/* AX=B */
/* SUBJECT TO L LINEAR EQUALITY CONSTRAINTS */
/* CX=D */
/* AND M LINEAR INEQUALITY CONSTRAINTS */
/* EX.LE.F. */
/* DESCRIPTION OF PARAMETERS */
/* K NUMBER OF ROWS OF THE MATRIX A (K.GE.1). */
/* L NUMBER OF ROWS OF THE MATRIX C (L.GE.0). */
/* M NUMBER OF ROWS OF THE MATRIX E (M.GE.0). */
/* N NUMBER OF COLUMNS OF THE MATRICES A,C,E (N.GE.1). */
/* KLMD SET TO AT LEAST K+L+M FOR ADJUSTABLE DIMENSIONS. */
/* KLM2D SET TO AT LEAST K+L+M+2 FOR ADJUSTABLE DIMENSIONS. */
/* NKLMD SET TO AT LEAST N+K+L+M FOR ADJUSTABLE DIMENSIONS. */
/* N2D SET TO AT LEAST N+2 FOR ADJUSTABLE DIMENSIONS */
/* Q TWO DIMENSIONAL REAL ARRAY WITH KLM2D ROWS AND */
/* AT LEAST N2D COLUMNS. */
/* ON ENTRY THE MATRICES A,C AND E, AND THE VECTORS */
/* B,D AND F MUST BE STORED IN THE FIRST K+L+M ROWS */
/* AND N+1 COLUMNS OF Q AS FOLLOWS */
/* A B */
/* Q = C D */
/* E F */
/* THESE VALUES ARE DESTROYED BY THE SUBROUTINE. */
/* KODE A CODE USED ON ENTRY TO, AND EXIT */
/* FROM, THE SUBROUTINE. */
/* ON ENTRY, THIS SHOULD NORMALLY BE SET TO 0. */
/* HOWEVER, IF CERTAIN NONNEGATIVITY CONSTRAINTS */
/* ARE TO BE INCLUDED IMPLICITLY, RATHER THAN */
/* EXPLICITLY IN THE CONSTRAINTS EX.LE.F, THEN KODE */
/* SHOULD BE SET TO 1, AND THE NONNEGATIVITY */
/* CONSTRAINTS INCLUDED IN THE ARRAYS X AND */
/* RES (SEE BELOW). */
/* ON EXIT, KODE HAS ONE OF THE */
/* FOLLOWING VALUES */
/* 0- OPTIMAL SOLUTION FOUND, */
/* 1- NO FEASIBLE SOLUTION TO THE */
/* CONSTRAINTS, */
/* 2- CALCULATIONS TERMINATED */
/* PREMATURELY DUE TO ROUNDING ERRORS, */
/* 3- MAXIMUM NUMBER OF ITERATIONS REACHED. */
/* TOLER A SMALL POSITIVE TOLERANCE. EMPIRICAL */
/* EVIDENCE SUGGESTS TOLER = 10**(-D*2/3), */
/* WHERE D REPRESENTS THE NUMBER OF DECIMAL */
/* DIGITS OF ACCURACY AVAILABLE. ESSENTIALLY, */
/* THE SUBROUTINE CANNOT DISTINGUISH BETWEEN ZERO */
/* AND ANY QUANTITY WHOSE MAGNITUDE DOES NOT EXCEED */
/* TOLER. IN PARTICULAR, IT WILL NOT PIVOT ON ANY */
/* NUMBER WHOSE MAGNITUDE DOES NOT EXCEED TOLER. */
/* ITER ON ENTRY ITER MUST CONTAIN AN UPPER BOUND ON */
/* THE MAXIMUM NUMBER OF ITERATIONS ALLOWED. */
/* A SUGGESTED VALUE IS 10*(K+L+M). ON EXIT ITER */
/* GIVES THE NUMBER OF SIMPLEX ITERATIONS. */
/* X ONE DIMENSIONAL REAL ARRAY OF SIZE AT LEAST N2D. */
/* ON EXIT THIS ARRAY CONTAINS A */
/* SOLUTION TO THE L1 PROBLEM. IF KODE=1 */
/* ON ENTRY, THIS ARRAY IS ALSO USED TO INCLUDE */
/* SIMPLE NONNEGATIVITY CONSTRAINTS ON THE */
/* VARIABLES. THE VALUES -1, 0, OR 1 */
/* FOR X(J) INDICATE THAT THE J-TH VARIABLE */
/* IS RESTRICTED TO BE .LE.0, UNRESTRICTED, */
/* OR .GE.0 RESPECTIVELY. */
/* RES ONE DIMENSIONAL REAL ARRAY OF SIZE AT LEAST KLMD. */
/* ON EXIT THIS CONTAINS THE RESIDUALS B-AX */
/* IN THE FIRST K COMPONENTS, D-CX IN THE */
/* NEXT L COMPONENTS (THESE WILL BE =0),AND */
/* F-EX IN THE NEXT M COMPONENTS. IF KODE=1 ON */
/* ENTRY, THIS ARRAY IS ALSO USED TO INCLUDE SIMPLE */
/* NONNEGATIVITY CONSTRAINTS ON THE RESIDUALS */
/* B-AX. THE VALUES -1, 0, OR 1 FOR RES(I) */
/* INDICATE THAT THE I-TH RESIDUAL (1.LE.I.LE.K) IS */
/* RESTRICTED TO BE .LE.0, UNRESTRICTED, OR .GE.0 */
/* RESPECTIVELY. */
/* ERROR ON EXIT, THIS GIVES THE MINIMUM SUM OF */
/* ABSOLUTE VALUES OF THE RESIDUALS. */
/* CU A TWO DIMENSIONAL REAL ARRAY WITH TWO ROWS AND */
/* AT LEAST NKLMD COLUMNS USED FOR WORKSPACE. */
/* IU A TWO DIMENSIONAL INTEGER ARRAY WITH TWO ROWS AND */
/* AT LEAST NKLMD COLUMNS USED FOR WORKSPACE. */
/* S INTEGER ARRAY OF SIZE AT LEAST KLMD, USED FOR */
/* WORKSPACE. */
/* DOUBLE PRECISION DBLE */
/* REAL */
/* INITIALIZATION. */
if (svnid == NULL) fprintf(stderr," ");
/*
* mp variables
*/
censor = 1;
if (censor_arg == 0.0) censor = 0;
mpf_set_default_prec(96);
mpf_init(zero);
mpf_init(dummy);
mpf_init(dummy1);
mpf_init_set_d(censor_tol, censor_arg);
q = (mpf_t *) PHRQ_malloc((size_t) (max_row_count * max_column_count * sizeof(mpf_t)));
if (q == NULL) malloc_error();
for (i = 0; i < max_row_count*max_column_count; i++) {
mpf_init_set_d(q[i], q_arg[i]);
if (censor == 1) {
if (mpf_cmp(q[ i ], zero) != 0) {
mpf_abs(dummy1, q[ i ]);
if (mpf_cmp(dummy1, censor_tol) <= 0) {
mpf_set_si(q[ i ], 0);
}
}
}
}
x = (mpf_t *) PHRQ_malloc((size_t) (n2d * sizeof(mpf_t)));
if (x == NULL) malloc_error();
for (i = 0; i < n2d; i++) {
mpf_init_set_d (x[i], x_arg[i]);
}
res = (mpf_t *) PHRQ_malloc((size_t) ((k + l + m) * sizeof(mpf_t)));
if (res == NULL) malloc_error();
for (i = 0; i < k + l + m; i++) {
mpf_init_set_d (res[i], res_arg[i]);
}
cu = (mpf_t *) PHRQ_malloc((size_t) (2*nklmd * sizeof(mpf_t)));
if (cu == NULL) malloc_error();
for (i = 0; i < 2*nklmd; i++) {
mpf_init_set_d (cu[i], cu_arg[i]);
}
kode = (int *) PHRQ_malloc(sizeof(int));
if (kode == NULL) malloc_error();
*kode = *kode_arg;
mpf_init(sum);
mpf_init(error);
mpf_init(z);
mpf_init(zu);
mpf_init(zv);
mpf_init(xmax);
mpf_init_set_si(minus_one, -1);
mpf_init_set_d(toler, toler_arg);
mpf_init_set_d(check_toler, toler_arg);
mpf_init(pivot);
mpf_init(xmin);
mpf_init(cuv);
mpf_init(tpivot);
mpf_init(sn);
/* Parameter adjustments */
q_dim = n2d;
q2 = (union double_or_int *) q;
cu_dim = nklmd;
/* Function Body */
maxit = *iter;
n1 = n + 1;
n2 = n + 2;
nk = n + k;
nkl = nk + l;
klm = k + l + m;
klm1 = klm + 1;
nklm = n + klm;
kforce = 1;
*iter = 0;
js = 0;
ia = -1;
/* Make scratch space */
/*
scratch = (LDBLE *) PHRQ_malloc( (size_t) nklmd * sizeof(LDBLE));
if (scratch == NULL) malloc_error();
for (i=0; i < nklmd; i++) {
scratch[i] = 0.0;
}
*/
/*
scratch = (mpf_t *) PHRQ_malloc( (size_t) nklmd * sizeof(mpf_t));
if (scratch == NULL) malloc_error();
for (i=0; i < nklmd; i++) {
mpf_init(scratch[i]);
}
*/
/* SET UP LABELS IN Q. */
for (j = 0; j < n; ++j) {
q2[ klm1 * q_dim + j ].ival = j + 1;
}
/* L10: */
for (i = 0; i < klm; ++i) {
q2[ i * q_dim + n1 ].ival = n + i + 1;
if (mpf_cmp_d(q2[ i * q_dim + n ].dval, 0.0) < 0) {
for (j = 0; j < n1; ++j) {
/* q2[ i * q_dim + j ].dval = -q2[ i * q_dim + j ].dval; */
mpf_neg(q2[ i * q_dim + j ].dval, q2[ i * q_dim + j ].dval);
}
q2[ i * q_dim + n1 ].ival = -q2[ i * q_dim + n1 ].ival;
/* L20: */
}
}
/* L30: */
/* SET UP PHASE 1 COSTS. */
iphase = 2;
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "Set up phase 1 costs\n");
#endif
/* Zero first row of cu and iu */
/*memcpy( (void *) &(cu[0]), (void *) &(scratch[0]), (size_t) nklm * sizeof(mpf_t) );*/
for (j = 0; j < nklm; ++j) {
mpf_set_si(cu[j], 0);
iu[ j ] = 0;
}
/* L40: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L40\n");
#endif
if (l != 0) {
for (j = nk; j < nkl; ++j) {
mpf_set_si(cu[j], 1);
/*cu[ j ] = 1.;*/
iu[ j ] = 1;
}
/* L50: */
iphase = 1;
}
/* Copy first row of cu and iu to second row */
/*memcpy( (void *) &(cu[cu_dim]), (void *) &(cu[0]), (size_t) nklm * sizeof(mpf_t) );*/
for (i = 0; i < nklm; i++) {
mpf_set(cu[cu_dim + i], cu[i]);
}
memcpy( (void *) &(iu[cu_dim]), (void *) &(iu[0]), (size_t) nklm * sizeof(int) );
/* L60: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L60\n");
#endif
if (m != 0) {
for (j = nkl; j < nklm; ++j) {
/* cu[ cu_dim + j ] = 1.;*/
mpf_set_si(cu[cu_dim + j], 1);
iu[ cu_dim + j ] = 1;
jmn = j - n;
if (q2[ jmn * q_dim + n1 ].ival < 0) {
iphase = 1;
}
}
/* L70: */
}
/* L80: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L80\n");
#endif
if (*kode != 0) {
for (j = 0; j < n; ++j) {
/* if ( x[j] < 0.) { */
if (mpf_cmp_si(x[j], 0) < 0) {
/* L90: */
/* cu[ j ] = 1.;*/
mpf_set_si(cu[j], 1);
iu[ j ] = 1;
/* } else if (x[j] > 0.) {*/
} else if (mpf_cmp_si(x[j], 0) > 0) {
/* cu[ cu_dim + j ] = 1.; */
mpf_set_si(cu[cu_dim + j], 1);
iu[ cu_dim + j ] = 1;
}
}
/* L110: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L110\n");
#endif
for (j = 0; j < k; ++j) {
jpn = j + n;
/* if (res[j] < 0.) { */
if (mpf_cmp_si(res[j], 0) < 0) {
/* L120: */
/* cu[ jpn ] = 1.;*/
mpf_set_si(cu[jpn], 1);
iu[ jpn ] = 1;
if (q2[ j * q_dim + n1 ].ival > 0) {
iphase = 1;
}
/* } else if (res[j] > 0.) { */
} else if (mpf_cmp_si(res[j], 0) > 0) {
/* L130: */
/* cu[ cu_dim + jpn ] = 1.;*/
mpf_set_si(cu[cu_dim + jpn], 1);
iu[ cu_dim + jpn ] = 1;
if (q2[ j * q_dim + n1 ].ival < 0) {
iphase = 1;
}
}
}
/* L140: */
}
/* L150: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L150\n");
#endif
if (iphase == 2) {
goto L500;
}
/* COMPUTE THE MARGINAL COSTS. */
L160:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L160\n");
#endif
for (j = js; j < n1; ++j) {
mpf_set_si(sum, 0);
for (i = 0; i < klm; ++i) {
ii = q2[ i * q_dim + n1 ].ival;
if (ii < 0) {
/* z = cu[ cu_dim - ii - 1 ];*/
mpf_set(z, cu[ cu_dim - ii - 1 ]);
} else {
/*z = cu[ ii - 1 ];*/
mpf_set(z, cu[ ii - 1 ]);
}
/*sum += q2[ i * q_dim + j ].dval * z;*/
mpf_mul(dummy, q2[ i * q_dim + j ].dval, z);
mpf_add(sum, sum, dummy);
}
/*q2[ klm * q_dim + j ].dval = sum;*/
mpf_set(q2[ klm * q_dim + j ].dval, sum);
}
for (j = js; j < n; ++j) {
ii = q2[ klm1 * q_dim + j].ival;
if (ii < 0) {
/*z = cu[ cu_dim - ii - 1 ];*/
mpf_set(z, cu[ cu_dim - ii - 1 ]);
} else {
/*z = cu[ ii - 1 ];*/
mpf_set(z, cu[ ii - 1 ]);
}
/*q2[ klm * q_dim + j ].dval -= z;*/
mpf_sub(q2[ klm * q_dim + j ].dval, q2[ klm * q_dim + j ].dval, z);
}
/* DETERMINE THE VECTOR TO ENTER THE BASIS. */
L240:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L240, xmax %e\n", mpf_get_d(xmax));
#endif
/*xmax = 0.;*/
mpf_set_si(xmax, 0);
if (js >= n) {
goto L490; /* test for optimality */
}
for (j = js; j < n; ++j) {
/*zu = q2[ klm * q_dim + j ].dval;*/
mpf_set(zu, q2[ klm * q_dim + j ].dval);
ii = q2[ klm1 * q_dim + j ].ival;
if (ii > 0) {
/*zv = -zu - cu[ ii - 1 ] - cu[ cu_dim + ii - 1 ];*/
mpf_mul(dummy, cu[ cu_dim + ii - 1 ], minus_one);
mpf_sub(dummy, dummy, cu[ ii - 1 ]);
mpf_sub(zv, dummy, zu);
} else {
ii = -ii;
/* zv = zu; */
mpf_set(zv, zu);
/* zu = -zu - cu[ ii - 1 ] - cu[ cu_dim + ii - 1 ]; */
mpf_mul(dummy, cu[ cu_dim + ii - 1 ], minus_one);
mpf_sub(dummy, dummy, cu[ ii - 1 ]);
mpf_sub(zu, dummy, zu);
}
/* L260 */
if (kforce == 1 && ii > n) {
continue;
}
/*if (iu[ ii - 1 ] != 1 && zu > xmax){*/
if ((iu[ ii - 1 ] != 1) && (mpf_cmp(zu, xmax) > 0)) {
/*xmax = zu;*/
mpf_set(xmax, zu);
in = j;
}
/* L270 */
/*if (iu[ cu_dim + ii - 1 ] != 1 && zv > xmax ) {*/
if ((iu[ cu_dim + ii - 1 ] != 1) && (mpf_cmp(zv, xmax) > 0)) {
/*xmax = zv;*/
mpf_set(xmax, zv);
in = j;
}
}
/* L280 */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L280 xmax %e, toler %e\n", mpf_get_d(xmax), mpf_get_d(toler));
#endif
/*if (xmax <= toler) {*/
if (mpf_cmp(xmax, toler) <= 0) {
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "xmax before optimality test %e\n", mpf_get_d(xmax));
#endif
goto L490; /* test for optimality */
}
/*if (q2[ klm * q_dim + in ].dval != xmax) {*/
if (mpf_cmp(q2[ klm * q_dim + in ].dval,xmax) != 0) {
for (i = 0; i < klm1; ++i) {
/*q2[ i * q_dim + in ].dval = -q2[ i * q_dim + in ].dval;*/
mpf_neg(q2[ i * q_dim + in ].dval, q2[ i * q_dim + in ].dval);
}
q2[ klm1 * q_dim + in ].ival = -q2[ klm1 * q_dim + in ].ival;
/* L290: */
/*q2[ klm * q_dim + in ].dval = xmax;*/
mpf_set(q2[ klm * q_dim + in ].dval, xmax);
}
/* DETERMINE THE VECTOR TO LEAVE THE BASIS. */
if (iphase != 1 && ia != -1) {
/*xmax = 0.;*/
mpf_set_si(xmax, 0);
/* find maximum absolute value in column "in" */
for (i = 0; i <= ia; ++i) {
/*z = fabs(q2[ i * q_dim + in ].dval);*/
mpf_abs(z, q2[ i * q_dim + in ].dval);
/*if (z > xmax) {*/
if (mpf_cmp(z, xmax) > 0) {
/*xmax = z;*/
mpf_set(xmax, z);
iout = i;
}
}
/* L310: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L310, xmax %e\n", mpf_get_d(xmax));
#endif
/* switch row ia with row iout, use memcpy */
/*if (xmax > toler) {*/
if (mpf_cmp(xmax, toler) > 0) {
/*
memcpy( (void *) &(scratch[0]), (void *) &(q2[ ia * q_dim]),
(size_t) n2 * sizeof(mpf_t) );
memcpy( (void *) &(q2[ ia * q_dim ]), (void *) &(q2[ iout * q_dim]),
(size_t) n2 * sizeof(mpf_t) );
memcpy( (void *) &(q2[ iout * q_dim ]), (void *) &(scratch[ 0 ]),
(size_t) n2 * sizeof(mpf_t) );
*/
for (i = 0; i < n1; i++) {
mpf_set(dummy, q2[ ia * q_dim + i].dval);
mpf_set(q2[ ia * q_dim + i].dval, q2[ iout * q_dim + i].dval);
mpf_set(q2[ iout * q_dim + i].dval, dummy);
}
j = q2[ ia * q_dim + n1].ival;
q2[ ia * q_dim + n1].ival = q2[ iout * q_dim + n1].ival;
q2[ iout * q_dim + n1].ival = j;
/* L320: */
/* set pivot to row ia, column in */
iout = ia;
--ia;
/*pivot = q2[ iout * q_dim + in ].dval;*/
mpf_set(pivot, q2[ iout * q_dim + in ].dval);
goto L420; /* Gauss Jordan */
}
}
/* L330: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L330, xmax %e\n", mpf_get_d(xmax));
#endif
kk = -1;
/* divide column n1 by positive value in column "in" greater than toler */
for (i = 0; i < klm; ++i) {
/*z = q2[ i * q_dim + in ].dval;*/
mpf_set(z, q2[ i * q_dim + in ].dval);
/*if (z > toler) {*/
if (mpf_cmp(z, toler) > 0) {
++kk;
/*res[kk] = q2[ i * q_dim + n ].dval / z;*/
mpf_div(res[kk], q2[ i * q_dim + n ].dval, z);
s[kk] = i;
}
}
/* L340: */
if (kk < 0) {
output_msg(OUTPUT_MESSAGE, "kode = 2 in loop 340.\n");
}
L350:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L350, xmax %e\n", mpf_get_d(xmax));
#endif
if (kk < 0) {
/* no positive value found in L340 or bypass intermediate verticies */
*kode = 2;
goto L590;
}
/* L360: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L360, xmax %e\n", mpf_get_d(xmax));
#endif
/* find minimum residual */
/*xmin = res[ 0 ];*/
mpf_set(xmin, res[0]);
iout = s[ 0 ];
j = 0;
if (kk != 0) {
for (i = 1; i <= kk; ++i) {
/*if (res[i] < xmin) {*/
if (mpf_cmp(res[i], xmin) < 0) {
j = i;
/*xmin = res[i];*/
mpf_set(xmin, res[i]);
iout = s[i];
}
}
/* L370: */
/* put kk in position j */
/*res[j] = res[kk];*/
mpf_set(res[j], res[kk]);
s[j] = s[kk];
}
/* L380: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L380 iout %d, xmin %e, xmax %e\n", iout, mpf_get_d(xmin), mpf_get_d(xmax));
#endif
--kk;
/*pivot = q2[ iout * q_dim + in ].dval;*/
mpf_set(pivot, q2[ iout * q_dim + in ].dval);
ii = q2[ iout * q_dim + n1 ].ival;
if (iphase != 1) {
if (ii < 0) {
/* L390: */
if (iu[ - ii - 1 ] == 1) {
goto L420;
}
} else {
if (iu[ cu_dim + ii - 1 ] == 1) {
goto L420;
}
}
}
/* L400: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L400\n");
#endif
ii = abs(ii);
/*cuv = cu[ ii - 1 ] + cu[ cu_dim + ii - 1];*/
mpf_add(cuv, cu[ ii - 1 ], cu[ cu_dim + ii - 1]);
/*if (q2[ klm * q_dim + in ].dval - pivot * cuv > toler) {*/
mpf_mul(dummy, pivot, cuv);
mpf_sub(dummy, q2[ klm * q_dim + in ].dval, dummy);
if (mpf_cmp(dummy, toler) > 0) {
/* BYPASS INTERMEDIATE VERTICES. */
for (j = js; j < n1; ++j) {
/*z = q2[ iout * q_dim + j ].dval;*/
mpf_set(z, q2[ iout * q_dim + j ].dval);
/*q2[ klm * q_dim + j ].dval -= z * cuv;*/
mpf_mul(dummy1, z, cuv);
mpf_sub(q2[ klm * q_dim + j ].dval, q2[ klm * q_dim + j ].dval, dummy1);
if (censor == 1) {
if (mpf_cmp(q2[ klm * q_dim + j ].dval, zero) != 0) {
mpf_abs(dummy1, q2[ klm * q_dim + j ].dval);
if (mpf_cmp(dummy1, censor_tol) <= 0) {
mpf_set_si(q2[ klm * q_dim + j ].dval, 0);
}
}
}
/*q2[ iout * q_dim + j ].dval = -z;*/
mpf_neg(q2[ iout * q_dim + j ].dval, z);
}
/* L410: */
q2[ iout * q_dim + n1 ].ival = -q2[ iout * q_dim + n1 ].ival;
goto L350;
}
/* GAUSS-JORDAN ELIMINATION. */
L420:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "Gauss Jordon %d\n", *iter);
#endif
if (*iter >= maxit) {
*kode = 3;
goto L590;
}
/* L430: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L430\n");
#endif
++(*iter);
for (j = js; j < n1; ++j) {
if (j != in) {
/*q2[ iout * q_dim + j ].dval /= pivot;*/
mpf_div(q2[ iout * q_dim + j ].dval, q2[ iout * q_dim + j ].dval, pivot);
}
}
/* L440: */
for (j = js; j < n1; ++j) {
if (j != in) {
/*z = -q2[ iout * q_dim + j ].dval;*/
mpf_neg(z, q2[ iout * q_dim + j ].dval);
for (i = 0; i < klm1; ++i) {
if (i != iout) {
/*q2[ i * q_dim + j ].dval += z * q2[ i * q_dim + in ].dval;*/
mpf_mul(dummy, z, q2[ i * q_dim + in ].dval);
mpf_add(q2[ i * q_dim + j ].dval, q2[ i * q_dim + j ].dval, dummy);
if (censor == 1) {
if (mpf_cmp(q2[ i * q_dim + j ].dval, zero) != 0) {
mpf_abs(dummy1, q2[ i * q_dim + j ].dval);
if (mpf_cmp(dummy1, censor_tol) <= 0) {
mpf_set_si(q2[ i * q_dim + j ].dval, 0);
}
}
}
}
}
/* L450: */
}
}
/* L460: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L460\n");
#endif
/*tpivot = -pivot;*/
mpf_neg(tpivot, pivot);
for (i = 0; i < klm1; ++i) {
if (i != iout) {
/*q2[ i * q_dim + in ].dval /= tpivot;*/
mpf_div(q2[ i * q_dim + in ].dval, q2[ i * q_dim + in ].dval, tpivot);
}
}
/* L470: */
/*q2[ iout * q_dim + in ].dval = 1. / pivot;*/
mpf_set_si(dummy, 1);
mpf_div(q2[ iout * q_dim + in ].dval, dummy, pivot);
ii = q2[ iout * q_dim + n1 ].ival;
q2[ iout * q_dim + n1 ].ival = q2[ klm1 * q_dim + in ].ival;
q2[ klm1 * q_dim + in ].ival = ii;
ii = abs(ii);
if (iu[ ii - 1 ] == 0 || iu[ cu_dim + ii - 1 ] == 0) {
goto L240;
}
/* switch column */
for (i = 0; i < klm1; ++i) {
/*z = q2[ i * q_dim + in ].dval;*/
mpf_set(z, q2[ i * q_dim + in ].dval);
/*q2[ i * q_dim + in ].dval = q2[ i * q_dim + js ].dval;*/
mpf_set(q2[ i * q_dim + in ].dval, q2[ i * q_dim + js ].dval);
/*q2[ i * q_dim + js ].dval = z;*/
mpf_set(q2[ i * q_dim + js ].dval, z);
}
i = q2[ klm1 * q_dim + in ].ival;
q2[ klm1 * q_dim + in ].ival = q2[ klm1 * q_dim + js ].ival;
q2[ klm1 * q_dim + js ].ival = i;
/* L480: */
++js;
goto L240;
/* TEST FOR OPTIMALITY. */
L490:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L490\n");
#endif
if (kforce == 0) {
if (iphase == 1) {
/*if (q2[ klm * q_dim + n ].dval <= toler) {*/
if (mpf_cmp(q2[ klm * q_dim + n ].dval, toler) <= 0) {
goto L500;
}
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE,"q2[klm1-1, n1-1] > *toler. %e\n", mpf_get_d(q2[ ( klm1 - 1 ) * q_dim + n1 - 1 ].dval));
#endif
*kode = 1;
goto L590;
}
*kode = 0;
goto L590;
}
/*if (iphase != 1 || q2[ klm * q_dim + n ].dval > toler) {*/
if ((iphase != 1) || (mpf_cmp(q2[ klm * q_dim + n ].dval, toler) > 0)) {
kforce = 0;
goto L240;
}
/* SET UP PHASE 2 COSTS. */
L500:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "Set up phase 2 costs %d\n", *iter);
#endif
iphase = 2;
for (j = 0; j < nklm; ++j) {
/*cu[ j ] = 0.;*/
mpf_set_si(cu[j], 0);
}
/* L510: */
for (j = n; j < nk; ++j) {
/*cu[ j ] = 1.;*/
mpf_set_si(cu[j], 1);
}
/*
memcpy( (void *) &(cu[cu_dim]), (void *) &(cu[0]), (size_t) nklm * sizeof(LDBLE) );
*/
for (i = 0; i < nklm; i++) {
mpf_set(cu[cu_dim + i], cu[i]);
}
/* L520: */
for (i = 0; i < klm; ++i) {
ii = q2[ i * q_dim + n1 ].ival;
if (ii <= 0) {
if (iu[ cu_dim - ii - 1 ] == 0) {
continue;
}
/*cu[ cu_dim - ii - 1 ] = 0.;*/
mpf_set_si(cu[ cu_dim - ii - 1 ], 0);
} else {
/* L530: */
if (iu[ ii - 1 ] == 0) {
continue;
}
/*cu[ ii - 1 ] = 0.;*/
mpf_set_si(cu[ ii - 1 ], 0);
}
/* L540: */
++ia;
/* switch row */
/*
memcpy( (void *) &(scratch[0]), (void *) &(q2[ ia * q_dim]),
(size_t) n2 * sizeof(LDBLE) );
memcpy( (void *) &(q2[ ia * q_dim ]), (void *) &(q2[ i * q_dim]),
(size_t) n2 * sizeof(LDBLE) );
memcpy( (void *) &(q2[ i * q_dim ]), (void *) &(scratch[ 0 ]),
(size_t) n2 * sizeof(LDBLE) );
*/
for (iswitch = 0; iswitch < n1; iswitch++) {
mpf_set(dummy, q2[ ia * q_dim + iswitch].dval);
mpf_set(q2[ ia * q_dim + iswitch].dval, q2[ i * q_dim + iswitch].dval);
mpf_set(q2[ i * q_dim + iswitch].dval, dummy);
}
iswitch = q2[ ia * q_dim + n1].ival;
q2[ ia * q_dim + n1].ival = q2[ i * q_dim + n1].ival;
q2[ i * q_dim + n1].ival = iswitch;
/* L550: */
}
/* L560: */
goto L160;
/* PREPARE OUTPUT. */
L590:
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L590\n");
#endif
/*sum = 0.;*/
mpf_set_si(sum, 0);
for (j = 0; j < n; ++j) {
/*x[j] = 0.;*/
mpf_set_si(x[j], 0);
}
/* L600: */
for (i = 0; i < klm; ++i) {
/*res[i] = 0.;*/
mpf_set_si(res[i], 0);
}
/* L610: */
for (i = 0; i < klm; ++i) {
ii = q2[ i * q_dim + n1 ].ival;
/*sn = 1.;*/
mpf_set_si(sn, 1);
if (ii < 0) {
ii = -ii;
/*sn = -1.;*/
mpf_set_si(sn, -1);
}
if (ii <= n) {
/* L620: */
/*x[ii - 1] = sn * q2[ i * q_dim + n ].dval;*/
mpf_mul(x[ii - 1], sn, q2[ i * q_dim + n ].dval);
} else {
/* L630: */
/*res[ii - n - 1] = sn * q2[ i * q_dim + n ].dval;*/
mpf_mul(res[ii - n - 1], sn, q2[ i * q_dim + n ].dval);
if (ii >= n1 && ii <= nk ) {
/* * DBLE(Q(I,N1)) */
/*sum += q2[ i * q_dim + n ].dval;*/
mpf_add(sum, sum, q2[ i * q_dim + n ].dval);
}
}
}
/* L640: */
#ifdef DEBUG_CL1
output_msg(OUTPUT_MESSAGE, "L640\n");
#endif
/*
* Check calculation
*/
mpf_set_si(dummy, 100);
mpf_mul(check_toler, toler, dummy);
if (check && *kode == 0) {
/*
* Check optimization constraints
*/
if (*kode_arg == 1) {
for (i = 0; i < k; i++) {
if (res_arg[i] < 0.0) {
mpf_sub(dummy, res[i], check_toler);
mpf_set_si(dummy1, 0);
if (mpf_cmp(dummy,dummy1) > 0) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1MP: optimization constraint not satisfied row %d, res %e, constraint %f.\n", i, mpf_get_d(res[i]), res_arg[i]);
#endif
*kode = 1;
}
} else if (res_arg[i] > 0.0) {
mpf_add(dummy, res[i], check_toler);
mpf_set_si(dummy1, 0);
if (mpf_cmp(dummy,dummy1) < 0) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1MP: optimization constraint not satisfied row %d, res %e, constraint %f.\n", i, mpf_get_d(res[i]), res_arg[i]);
#endif
*kode = 1;
}
}
}
}
/*
* Check equalities
*/
for (i = k; i < k + l; i++) {
mpf_abs(dummy, res[i]);
if (mpf_cmp(dummy, check_toler) > 0) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1MP: equality constraint not satisfied row %d, res %e, tolerance %e.\n", i, mpf_get_d(res[i]), mpf_get_d(check_toler));
#endif
*kode = 1;
}
}
/*
* Check inequalities
*/
for (i = k + l; i < k + l + m; i++) {
mpf_neg(dummy, check_toler);
if (mpf_cmp(res[i], dummy) < 0) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1MP: inequality constraint not satisfied row %d, res %e, tolerance %e.\n", i, mpf_get_d(res[i]), mpf_get_d(check_toler));
#endif
*kode = 1;
}
}
/*
* Check dissolution/precipitation constraints
*/
if (*kode_arg == 1) {
for (i = 0; i < n; i++) {
if (x_arg[i] < 0.0) {
mpf_sub(dummy, x[i], check_toler);
mpf_set_si(dummy1, 0);
if (mpf_cmp(dummy,dummy1) > 0) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1MP: dis/pre constraint not satisfied column %d, x %e, constraint %f.\n", i, mpf_get_d(x[i]), x_arg[i]);
#endif
*kode = 1;
}
} else if (x_arg[i] > 0.0) {
mpf_add(dummy, x[i], check_toler);
mpf_set_si(dummy1, 0);
if (mpf_cmp(dummy,dummy1) < 0) {
#ifdef CHECK_ERRORS
output_msg(OUTPUT_MESSAGE, "\tCL1MP: dis/pre constraint not satisfied column %d, x %e, constraint %f.\n", i, mpf_get_d(x[i]), x_arg[i]);
#endif
*kode = 1;
}
}
}
}
if (*kode == 1) {
output_msg(OUTPUT_MESSAGE, "\n\tCL1MP: Roundoff errors in optimization.\n\t Deleting model.\n");
}
}
/*
* set return variables
*/
/**error = sum;*/
mpf_set(error, sum);
*error_arg = mpf_get_d(error);
*kode_arg = *kode;
for (i = 0; i < n2d; i++) {
x_arg[i] = mpf_get_d (x[i]);
}
for (i = 0; i < k + l + m; i++) {
res_arg[i] = mpf_get_d (res[i]);
}
/*scratch = free_check_null (scratch);*/
for (i = 0; i < max_row_count*max_column_count; i++) {
mpf_clear(q[i]);
}
q = (mpf_t *) free_check_null(q);
for (i = 0; i < n2d; i++) {
mpf_clear (x[i]);
}
x = (mpf_t *) free_check_null(x);
for (i = 0; i < k + l + m; i++) {
mpf_clear (res[i]);
}
res = (mpf_t *) free_check_null(res);
for (i = 0; i < 2*nklmd; i++) {
mpf_clear (cu[i]);
}
cu = (mpf_t *) free_check_null(cu);
mpf_clear(dummy);
mpf_clear(dummy1);
mpf_clear(sum);
mpf_clear(error);
mpf_clear(z);
mpf_clear(zu);
mpf_clear(zv);
mpf_clear(xmax);
mpf_clear(minus_one);
mpf_clear(toler);
mpf_clear(check_toler);
mpf_clear(pivot);
mpf_clear(xmin);
mpf_clear(cuv);
mpf_clear(tpivot);
mpf_clear(sn);
mpf_clear(censor_tol);
kode = (int *) free_check_null(kode);
return 0;
}

473
cvdense.cpp
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@ -1,473 +0,0 @@
/*******************************************************************
* *
* File : cvdense.c *
* Programmers : Scott D. Cohen, Alan C. Hindmarsh, and *
* Radu Serban @ LLNL *
* Version of : 26 June 2002 *
*-----------------------------------------------------------------*
* Copyright (c) 2002, The Regents of the University of California *
* Produced at the Lawrence Livermore National Laboratory *
* All rights reserved *
* For details, see sundials/cvode/LICENSE *
*-----------------------------------------------------------------*
* This is the implementation file for the CVODE dense linear *
* solver, CVDENSE. *
* *
*******************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "cvdense.h"
#include "cvode.h"
#include "dense.h"
#include "sundialstypes.h"
#include "nvector.h"
#include "sundialsmath.h"
#include "output.h"
#include "phqalloc.h"
/* WARNING don't include any headers below here */
#define malloc PHRQ_malloc
static char const svnid[] = "$Id: cvdense.c 78 2005-02-01 22:47:12Z dlpark $";
/* Error Messages */
#define CVDENSE "CVDense/CVReInitDense-- "
#define MSG_CVMEM_NULL CVDENSE "CVode Memory is NULL.\n\n"
#define MSG_MEM_FAIL CVDENSE "A memory request failed.\n\n"
#define MSG_WRONG_NVEC CVDENSE "Incompatible NVECTOR implementation.\n\n"
/* Other Constants */
#define MIN_INC_MULT RCONST(1000.0)
#define ZERO RCONST(0.0)
#define ONE RCONST(1.0)
#define TWO RCONST(2.0)
/******************************************************************
* *
* Types : CVDenseMemRec, CVDenseMem *
*----------------------------------------------------------------*
* The type CVDenseMem is pointer to a CVDenseMemRec. This *
* structure contains CVDense solver-specific data. *
* *
******************************************************************/
typedef struct {
CVDenseJacFn d_jac; /* jac = Jacobian routine to be called */
DenseMat d_M; /* M = I - gamma J, gamma = h / l1 */
integertype *d_pivots; /* pivots = pivot array for PM = LU */
DenseMat d_savedJ; /* savedJ = old Jacobian */
long int d_nstlj; /* nstlj = nst at last Jacobian eval. */
long int d_nje; /* nje = no. of calls to jac */
void *d_J_data; /* J_data is passed to jac */
} CVDenseMemRec, *CVDenseMem;
/* CVDENSE linit, lsetup, lsolve, lfree, and DQJac routines */
static int CVDenseInit(CVodeMem cv_mem);
static int CVDenseSetup(CVodeMem cv_mem, int convfail, N_Vector ypred,
N_Vector fpred, booleantype *jcurPtr, N_Vector vtemp1,
N_Vector vtemp2, N_Vector vtemp3);
static int CVDenseSolve(CVodeMem cv_mem, N_Vector b, N_Vector ycur,
N_Vector fcur);
static void CVDenseFree(CVodeMem cv_mem);
static void CVDenseDQJac(integertype N, DenseMat J, RhsFn f, void *f_data,
realtype t, N_Vector y, N_Vector fy, N_Vector ewt,
realtype h, realtype uround, void *jac_data,
long int *nfePtr, N_Vector vtemp1,
N_Vector vtemp2, N_Vector vtemp3);
/*************** CVDenseDQJac ****************************************
This routine generates a dense difference quotient approximation to
the Jacobian of f(t,y). It assumes that a dense matrix of type
DenseMat is stored column-wise, and that elements within each column
are contiguous. The address of the jth column of J is obtained via
the macro DENSE_COL and an N_Vector with the jth column as the
component array is created using N_VMake and N_VSetData. Finally, the
actual computation of the jth column of the Jacobian is done with a
call to N_VLinearSum.
**********************************************************************/
static void CVDenseDQJac(integertype N, DenseMat J, RhsFn f, void *f_data,
realtype tn, N_Vector y, N_Vector fy, N_Vector ewt,
realtype h, realtype uround, void *jac_data,
long int *nfePtr, N_Vector vtemp1,
N_Vector vtemp2, N_Vector vtemp3)
{
realtype fnorm, minInc, inc, inc_inv, yjsaved, srur;
realtype *y_data, *ewt_data;
N_Vector ftemp, jthCol;
M_Env machEnv;
integertype j;
if (svnid == NULL) fprintf(stderr," ");
machEnv = y->menv; /* Get machine environment */
ftemp = vtemp1; /* Rename work vector for use as f vector value */
/* Obtain pointers to the data for ewt, y */
ewt_data = N_VGetData(ewt);
y_data = N_VGetData(y);
/* Set minimum increment based on uround and norm of f */
srur = RSqrt(uround);
fnorm = N_VWrmsNorm(fy, ewt);
minInc = (fnorm != ZERO) ?
(MIN_INC_MULT * ABS(h) * uround * N * fnorm) : ONE;
jthCol = N_VMake(N, y_data, machEnv); /* j loop overwrites this data address */
/* This is the only for loop for 0..N-1 in CVODE */
for (j = 0; j < N; j++) {
/* Generate the jth col of J(tn,y) */
N_VSetData(DENSE_COL(J,j), jthCol);
yjsaved = y_data[j];
inc = MAX(srur*ABS(yjsaved), minInc/ewt_data[j]);
y_data[j] += inc;
f(N, tn, y, ftemp, f_data);
inc_inv = ONE/inc;
N_VLinearSum(inc_inv, ftemp, -inc_inv, fy, jthCol);
y_data[j] = yjsaved;
}
N_VDispose(jthCol);
/* Increment counter nfe = *nfePtr */
*nfePtr += N;
}
/* Readability Replacements */
#define N (cv_mem->cv_N)
#define lmm (cv_mem->cv_lmm)
#define f (cv_mem->cv_f)
#define f_data (cv_mem->cv_f_data)
#define uround (cv_mem->cv_uround)
#define nst (cv_mem->cv_nst)
#define tn (cv_mem->cv_tn)
#define h (cv_mem->cv_h)
#define gamma (cv_mem->cv_gamma)
#define gammap (cv_mem->cv_gammap)
#define gamrat (cv_mem->cv_gamrat)
#define ewt (cv_mem->cv_ewt)
#define nfe (cv_mem->cv_nfe)
#define errfp (cv_mem->cv_errfp)
#define iopt (cv_mem->cv_iopt)
#define linit (cv_mem->cv_linit)
#define lsetup (cv_mem->cv_lsetup)
#define lsolve (cv_mem->cv_lsolve)
#define lfree (cv_mem->cv_lfree)
#define lmem (cv_mem->cv_lmem)
#define setupNonNull (cv_mem->cv_setupNonNull)
#define machenv (cv_mem->cv_machenv)
#define jac (cvdense_mem->d_jac)
#define M (cvdense_mem->d_M)
#define pivots (cvdense_mem->d_pivots)
#define savedJ (cvdense_mem->d_savedJ)
#define nstlj (cvdense_mem->d_nstlj)
#define nje (cvdense_mem->d_nje)
#define J_data (cvdense_mem->d_J_data)
/*************** CVDense *********************************************
This routine initializes the memory record and sets various function
fields specific to the dense linear solver module. CVDense first
calls the existing lfree routine if this is not NULL. Then it sets
the cv_linit, cv_lsetup, cv_lsolve, cv_lfree fields in (*cvode_mem)
to be CVDenseInit, CVDenseSetup, CVDenseSolve, and CVDenseFree,
respectively. It allocates memory for a structure of type
CVDenseMemRec and sets the cv_lmem field in (*cvode_mem) to the
address of this structure. It sets setupNonNull in (*cvode_mem) to
TRUE, the d_J_data field in CVDenseMemRec to be the input
parameter jac_data, and the d_jac field to be:
(1) the input parameter djac if djac != NULL or
(2) CVDenseDQJac if djac == NULL.
Finally, it allocates memory for M, savedJ, and pivots.
The return value is SUCCESS = 0, or LMEM_FAIL = -1.
NOTE: The dense linear solver assumes a serial implementation
of the NVECTOR package. Therefore, CVDense will first
test for compatible a compatible N_Vector internal
representation by checking (1) the machine environment
ID tag and (2) that the functions N_VMake, N_VDispose,
N_VGetData, and N_VSetData are implemented.
**********************************************************************/
int CVDense(void *cvode_mem, CVDenseJacFn djac, void *jac_data)
{
CVodeMem cv_mem;
CVDenseMem cvdense_mem;
/* Return immediately if cvode_mem is NULL */
cv_mem = (CVodeMem) cvode_mem;
if (cv_mem == NULL) { /* CVode reports this error */
output_msg(OUTPUT_CVODE, MSG_CVMEM_NULL);
return(LMEM_FAIL);
}
/* Test if the NVECTOR package is compatible with the DENSE solver */
if ((strcmp(machenv->tag,"serial")) ||
machenv->ops->nvmake == NULL ||
machenv->ops->nvdispose == NULL ||
machenv->ops->nvgetdata == NULL ||
machenv->ops->nvsetdata == NULL) {
output_msg(OUTPUT_CVODE, MSG_WRONG_NVEC);
return(LMEM_FAIL);
}
if (lfree !=NULL) lfree(cv_mem);
/* Set four main function fields in cv_mem */
linit = CVDenseInit;
lsetup = CVDenseSetup;
lsolve = CVDenseSolve;
lfree = CVDenseFree;
/* Get memory for CVDenseMemRec */
lmem = cvdense_mem = (CVDenseMem) malloc(sizeof(CVDenseMemRec));
if (cvdense_mem == NULL) {
output_msg(OUTPUT_CVODE, MSG_MEM_FAIL);
return(LMEM_FAIL);
}
/* Set Jacobian routine field, J_data, and setupNonNull */
if (djac == NULL) {
jac = CVDenseDQJac;
} else {
jac = djac;
}
J_data = jac_data;
setupNonNull = TRUE;
/* Allocate memory for M, savedJ, and pivot array */
M = DenseAllocMat(N);
if (M == NULL) {
output_msg(OUTPUT_CVODE, MSG_MEM_FAIL);
return(LMEM_FAIL);
}
savedJ = DenseAllocMat(N);
if (savedJ == NULL) {
output_msg(OUTPUT_CVODE, MSG_MEM_FAIL);
DenseFreeMat(M);
return(LMEM_FAIL);
}
pivots = DenseAllocPiv(N);
if (pivots == NULL) {
output_msg(OUTPUT_CVODE, MSG_MEM_FAIL);
DenseFreeMat(M);
DenseFreeMat(savedJ);
return(LMEM_FAIL);
}
return(SUCCESS);
}
/*************** CVReInitDense****************************************
This routine resets the link between the main CVODE module and the
dense linear solver module CVDENSE. No memory freeing or allocation
operations are done, as the existing linear solver memory is assumed
sufficient. All other initializations are the same as in CVDense.
The return value is SUCCESS = 0, or LMEM_FAIL = -1.
**********************************************************************/
int CVReInitDense(void *cvode_mem, CVDenseJacFn djac, void *jac_data)
{
CVodeMem cv_mem;
CVDenseMem cvdense_mem;
/* Return immediately if cvode_mem is NULL */
cv_mem = (CVodeMem) cvode_mem;
if (cv_mem == NULL) { /* CVode reports this error */
output_msg(OUTPUT_CVODE, MSG_CVMEM_NULL);
return(LMEM_FAIL);
}
/* Test if the NVECTOR package is compatible with the DENSE solver */
if ((strcmp(machenv->tag,"serial")) ||
machenv->ops->nvmake == NULL ||
machenv->ops->nvdispose == NULL ||
machenv->ops->nvgetdata == NULL ||
machenv->ops->nvsetdata == NULL) {
output_msg(OUTPUT_CVODE, MSG_WRONG_NVEC);
return(LMEM_FAIL);
}
cvdense_mem = (CVDenseMem) lmem; /* Use existing linear solver memory pointer */
/* Set four main function fields in cv_mem */
linit = CVDenseInit;
lsetup = CVDenseSetup;
lsolve = CVDenseSolve;
lfree = CVDenseFree;
/* Set Jacobian routine field, J_data, and setupNonNull */
if (djac == NULL) {
jac = CVDenseDQJac;
} else {
jac = djac;
}
J_data = jac_data;
setupNonNull = TRUE;
return(SUCCESS);
}
/*************** CVDenseInit *****************************************
This routine does remaining initializations specific to the dense
linear solver.
**********************************************************************/
static int CVDenseInit(CVodeMem cv_mem)
{
CVDenseMem cvdense_mem;
cvdense_mem = (CVDenseMem) lmem;
/* Initialize nje and nstlj, and set workspace lengths */
nje = 0;
if (iopt != NULL) {
iopt[DENSE_NJE] = nje;
iopt[DENSE_LRW] = 2*N*N;
iopt[DENSE_LIW] = N;
}
nstlj = 0;
return(LINIT_OK);
}
/*************** CVDenseSetup ****************************************
This routine does the setup operations for the dense linear solver.
It makes a decision whether or not to call the Jacobian evaluation
routine based on various state variables, and if not it uses the
saved copy. In any case, it constructs the Newton matrix
M = I - gamma*J, updates counters, and calls the dense LU
factorization routine.
**********************************************************************/
static int CVDenseSetup(CVodeMem cv_mem, int convfail, N_Vector ypred,
N_Vector fpred, booleantype *jcurPtr,
N_Vector vtemp1, N_Vector vtemp2, N_Vector vtemp3)
{
booleantype jbad, jok;
realtype dgamma;
integertype ier;
CVDenseMem cvdense_mem;
cvdense_mem = (CVDenseMem) lmem;
/* Use nst, gamma/gammap, and convfail to set J eval. flag jok */
dgamma = ABS((gamma/gammap) - ONE);
jbad = (nst == 0) || (nst > nstlj + CVD_MSBJ) ||
((convfail == FAIL_BAD_J) && (dgamma < CVD_DGMAX)) ||
(convfail == FAIL_OTHER);
jok = !jbad;
if (jok) {
/* If jok = TRUE, use saved copy of J */
*jcurPtr = FALSE;
DenseCopy(savedJ, M);
} else {
/* If jok = FALSE, call jac routine for new J value */
nje++;
if (iopt != NULL) iopt[DENSE_NJE] = nje;
nstlj = nst;
*jcurPtr = TRUE;
DenseZero(M);
jac(N, M, f, f_data, tn, ypred, fpred, ewt, h,
uround, J_data, &nfe, vtemp1, vtemp2, vtemp3);
DenseCopy(M, savedJ);
}
/* Scale and add I to get M = I - gamma*J */
DenseScale(-gamma, M);
DenseAddI(M);
/* Do LU factorization of M */
ier = DenseFactor(M, pivots);
/* Return 0 if the LU was complete; otherwise return 1 */
if (ier > 0) return(1);
return(0);
}
/*************** CVDenseSolve ****************************************
This routine handles the solve operation for the dense linear solver
by calling the dense backsolve routine. The returned value is 0.
**********************************************************************/
static int CVDenseSolve(CVodeMem cv_mem, N_Vector b, N_Vector ycur,
N_Vector fcur)
{
CVDenseMem cvdense_mem;
realtype *bd;
cvdense_mem = (CVDenseMem) lmem;
bd = N_VGetData(b);
DenseBacksolve(M, pivots, bd);
N_VSetData(bd, b);
/* If BDF, scale the correction to account for change in gamma */
if ((lmm == BDF) && (gamrat != ONE)) {
N_VScale(TWO/(ONE + gamrat), b, b);
}
return(0);
}
/*************** CVDenseFree *****************************************
This routine frees memory specific to the dense linear solver.
**********************************************************************/
static void CVDenseFree(CVodeMem cv_mem)
{
CVDenseMem cvdense_mem;
cvdense_mem = (CVDenseMem) lmem;
DenseFreeMat(M);
DenseFreeMat(savedJ);
DenseFreePiv(pivots);
free(cvdense_mem);
}

3330
cvode.cpp
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File diff suppressed because it is too large Load Diff

114
dense.cpp
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@ -1,114 +0,0 @@
/*******************************************************************
* *
* File : dense.c *
* Programmers : Scott D. Cohen, Alan C. Hindmarsh, and *
* Radu Serban @ LLNL *
* Version of : 26 June 2002 *
*-----------------------------------------------------------------*
* Copyright (c) 2002, The Regents of the University of California *
* Produced at the Lawrence Livermore National Laboratory *
* All rights reserved *
* For details, see sundials/shared/LICENSE *
*-----------------------------------------------------------------*
* This is the implementation file for a generic DENSE linear *
* solver package. *
* *
*******************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include "sundialstypes.h"
#include "sundialsmath.h"
#include "dense.h"
#include "smalldense.h"
#include "output.h"
#include "phqalloc.h"
/* WARNING don't include any headers below here */
#define malloc PHRQ_malloc
static char const svnid[] = "$Id: dense.c 78 2005-02-01 22:47:12Z dlpark $";
#define ZERO RCONST(0.0)
#define ONE RCONST(1.0)
/* Implementation */
DenseMat DenseAllocMat(integertype N)
{
DenseMat A;
if (svnid == NULL) fprintf(stderr," ");
if (N <= 0) return(NULL);
A = (DenseMat) malloc(sizeof *A);
if (A==NULL) return (NULL);
A->data = denalloc(N);
if (A->data == NULL) {
free(A);
return(NULL);
}
A->size = N;
return(A);
}
integertype *DenseAllocPiv(integertype N)
{
if (N <= 0) return(NULL);
return((integertype *) malloc(N * sizeof(integertype)));
}
integertype DenseFactor(DenseMat A, integertype *p)
{
return(gefa(A->data, A->size, p));
}
void DenseBacksolve(DenseMat A, integertype *p, realtype *b)
{
gesl(A->data, A->size, p, b);
}
void DenseZero(DenseMat A)
{
denzero(A->data, A->size);
}
void DenseCopy(DenseMat A, DenseMat B)
{
dencopy(A->data, B->data, A->size);
}
void DenseScale(realtype c, DenseMat A)
{
denscale(c, A->data, A->size);
}
void DenseAddI(DenseMat A)
{
denaddI(A->data, A->size);
}
void DenseFreeMat(DenseMat A)
{
denfree(A->data);
free(A);
}
void DenseFreePiv(integertype *p)
{
free(p);
}
void DensePrint(DenseMat A)
{
denprint(A->data, A->size);
}

298
dense.h
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@ -1,298 +0,0 @@
/*******************************************************************
* *
* File : dense.h *
* Programmers : Scott D. Cohen, Alan C. Hindmarsh, and *
* Radu Serban @ LLNL *
* Version of : 26 June 2002 *
*-----------------------------------------------------------------*
* Copyright (c) 2002, The Regents of the University of California *
* Produced at the Lawrence Livermore National Laboratory *
* All rights reserved *
* For details, see sundials/shared/LICENSE *
*-----------------------------------------------------------------*
* This is the header file for a generic DENSE linear solver *
* package. The routines listed in this file all use type *
* DenseMat, defined below, for matrices. These routines in turn *
* call routines in the smalldense.h/smalldense.c module, which *
* use the type realtype** for matrices. This separation allows *
* for possible modifications in which matrices of type DenseMat *
* may not be stored contiguously, while small matrices can still *
* be treated with the routines in smalldense. *
* *
* Routines that work with the type DenseMat begin with "Dense". *
* The DenseAllocMat function allocates a dense matrix for use in *
* the other DenseMat routines listed in this file. Matrix *
* storage details are given in the documentation for the type *
* DenseMat. The DenseAllocPiv function allocates memory for *
* pivot information. The storage allocated by DenseAllocMat and *
* DenseAllocPiv is deallocated by the routines DenseFreeMat and *
* DenseFreePiv, respectively. The DenseFactor and DenseBacksolve *
* routines perform the actual solution of a dense linear system. *
* *
* Routines that work with realtype** begin with "den" (except for *
* the factor and solve routines which are called gefa and gesl, *
* respectively). The underlying matrix storage is described in *
* the documentation for denalloc in smalldense.h *
* *
*******************************************************************/
#ifdef PHREEQC_IDENT
static char const svniddense[] = "$Id$";
#endif
#ifdef __cplusplus /* wrapper to enable C++ usage */
extern "C" {
#endif
#ifndef _dense_h
#define _dense_h
#include "sundialstypes.h"
#include "smalldense.h"
/******************************************************************
* *
* Type: DenseMat *
*----------------------------------------------------------------*
* The type DenseMat is defined to be a pointer to a structure *
* with a size and a data field. The size field indicates the *
* number of columns (== number of rows) of a dense matrix, while *
* the data field is a two dimensional array used for component *
* storage. The elements of a dense matrix are stored columnwise *
* (i.e columns are stored one on top of the other in memory). If *
* A is of type DenseMat, then the (i,j)th element of A (with *
* 0 <= i,j <= size-1) is given by the expression (A->data)[j][i] *
* or by the expression (A->data)[0][j*n+i]. The macros below *
* allow a user to access efficiently individual matrix *
* elements without writing out explicit data structure *
* references and without knowing too much about the underlying *
* element storage. The only storage assumption needed is that *
* elements are stored columnwise and that a pointer to the jth *
* column of elements can be obtained via the DENSE_COL macro. *
* Users should use these macros whenever possible. *
* *
******************************************************************/
typedef struct _DenseMat {
integertype size;
realtype **data;
} *DenseMat;
/* DenseMat accessor macros */
/******************************************************************
* *
* Macro : DENSE_ELEM *
* Usage : DENSE_ELEM(A,i,j) = a_ij; OR *
* a_ij = DENSE_ELEM(A,i,j); *
*----------------------------------------------------------------*
* DENSE_ELEM(A,i,j) references the (i,j)th element of the N by N *
* DenseMat A, 0 <= i,j <= N-1. *
* *
******************************************************************/
#define DENSE_ELEM(A,i,j) ((A->data)[j][i])
/******************************************************************
* *
* Macro : DENSE_COL *
* Usage : col_j = DENSE_COL(A,j); *
*----------------------------------------------------------------*
* DENSE_COL(A,j) references the jth column of the N by N *
* DenseMat A, 0 <= j <= N-1. The type of the expression *
* DENSE_COL(A,j) is realtype *. After the assignment in the usage*
* above, col_j may be treated as an array indexed from 0 to N-1. *
* The (i,j)th element of A is referenced by col_j[i]. *
* *
******************************************************************/
#define DENSE_COL(A,j) ((A->data)[j])
/* Functions that use the DenseMat representation for a dense matrix */
/******************************************************************
* *
* Function : DenseAllocMat *
* Usage : A = DenseAllocMat(N); *
* if (A == NULL) ... memory request failed *
*----------------------------------------------------------------*
* DenseAllocMat allocates memory for an N by N dense matrix and *
* returns the storage allocated (type DenseMat). DenseAllocMat *
* returns NULL if the request for matrix storage cannot be *
* satisfied. See the above documentation for the type DenseMat *
* for matrix storage details. *
* *
******************************************************************/
DenseMat DenseAllocMat(integertype N);
/******************************************************************
* *
* Function : DenseAllocPiv *
* Usage : p = DenseAllocPiv(N); *
* if (p == NULL) ... memory request failed *
*----------------------------------------------------------------*
* DenseAllocPiv allocates memory for pivot information to be *
* filled in by the DenseFactor routine during the factorization *
* of an N by N dense matrix. The underlying type for pivot *
* information is an array of N integers and this routine returns *
* the pointer to the memory it allocates. If the request for *
* pivot storage cannot be satisfied, DenseAllocPiv returns NULL. *
* *
******************************************************************/
integertype *DenseAllocPiv(integertype N);
/******************************************************************
* *
* Function : DenseFactor *
* Usage : ier = DenseFactor(A, p); *
* if (ier != 0) ... A is singular *
*----------------------------------------------------------------*
* DenseFactor performs the LU factorization of the N by N dense *
* matrix A. This is done using standard Gaussian elimination *
* with partial pivoting. *
* *
* A successful LU factorization leaves the matrix A and the *
* pivot array p with the following information: *
* *
* (1) p[k] contains the row number of the pivot element chosen *
* at the beginning of elimination step k, k=0, 1, ..., N-1. *
* *
* (2) If the unique LU factorization of A is given by PA = LU, *
* where P is a permutation matrix, L is a lower triangular *
* matrix with all 1's on the diagonal, and U is an upper *
* triangular matrix, then the upper triangular part of A *
* (including its diagonal) contains U and the strictly lower *
* triangular part of A contains the multipliers, I-L. *
* *
* DenseFactor returns 0 if successful. Otherwise it encountered *
* a zero diagonal element during the factorization. In this case *
* it returns the column index (numbered from one) at which *
* it encountered the zero. *
* *
******************************************************************/
integertype DenseFactor(DenseMat A, integertype *p);
/******************************************************************
* *
* Function : DenseBacksolve *
* Usage : DenseBacksolve(A, p, b); *
*----------------------------------------------------------------*
* DenseBacksolve solves the N-dimensional system A x = b using *
* the LU factorization in A and the pivot information in p *
* computed in DenseFactor. The solution x is returned in b. This *
* routine cannot fail if the corresponding call to DenseFactor *
* did not fail. *
* *
******************************************************************/
void DenseBacksolve(DenseMat A, integertype *p, realtype *b);
/******************************************************************
* *
* Function : DenseZero *
* Usage : DenseZero(A); *
*----------------------------------------------------------------*
* DenseZero sets all the elements of the N by N matrix A to 0.0. *
* *
******************************************************************/
void DenseZero(DenseMat A);
/******************************************************************
* *
* Function : DenseCopy *
* Usage : DenseCopy(A, B); *
*----------------------------------------------------------------*
* DenseCopy copies the contents of the N by N matrix A into the *
* N by N matrix B. *
* *
******************************************************************/
void DenseCopy(DenseMat A, DenseMat B);
/******************************************************************
* *
* Function: DenseScale *
* Usage : DenseScale(c, A); *
*----------------------------------------------------------------*
* DenseScale scales the elements of the N by N matrix A by the *
* constant c and stores the result back in A. *
* *
******************************************************************/
void DenseScale(realtype c, DenseMat A);
/******************************************************************
* *
* Function : DenseAddI *
* Usage : DenseAddI(A); *
*----------------------------------------------------------------*
* DenseAddI adds the identity matrix to A and stores the result *
* back in A. *
* *
******************************************************************/
void DenseAddI(DenseMat A);
/******************************************************************
* *
* Function : DenseFreeMat *
* Usage : DenseFreeMat(A); *
*----------------------------------------------------------------*
* DenseFreeMat frees the memory allocated by DenseAllocMat for *
* the N by N matrix A. *
* *
******************************************************************/
void DenseFreeMat(DenseMat A);
/******************************************************************
* *
* Function : DenseFreePiv *
* Usage : DenseFreePiv(p); *
*----------------------------------------------------------------*
* DenseFreePiv frees the memory allocated by DenseAllocPiv for *
* the pivot information array p. *
* *
******************************************************************/
void DenseFreePiv(integertype *p);
/******************************************************************
* *
* Function : DensePrint *
* Usage : DensePrint(A); *
*----------------------------------------------------------------*
* This routine prints the N by N dense matrix A to standard *
* output as it would normally appear on paper. It is intended *
* as a debugging tool with small values of N. The elements are *
* printed using the %g option. A blank line is printed before *
* and after the matrix. *
* *
******************************************************************/
void DensePrint(DenseMat A);
#endif
#ifdef __cplusplus
}
#endif

349
dw.cpp
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@ -1,349 +0,0 @@
#define EXTERNAL extern
#include "global.h"
#include "phrqproto.h"
#include "output.h"
#define PITZER_EXTERNAL extern
#include "pitzer.h"
static int BB (double T);
static double PS (double T);
static double VLEST (double T);
static int DFIND (double *DOUT, double P, double D, double T);
static int QQ (double T, double D);
static double BASE (double D);
/* COMMON /QQQQ/ */
static double Q0,Q5;
/* COMMON /ACONST/ */
static double GASCON=0.461522e0, TZ=647.073e0, AA=1.e0;
static double Z, DZ, Y;
/* COMMON /ELLCON/ */
static double G1=11.e0,G2=44.333333333333e0,GF=3.5e0;
static double B1, B2, B1T, B2T, B1TT, B2TT;
/* ---------------------------------------------------------------------- */
int DW (double T)
/* ---------------------------------------------------------------------- */
/*
C
C SUBROUTINE TO CALCULATE THE DENSITY OF WATER AS A FUNCTION OF
C TEMPERATURE. T IS IN KELVIN, P IS IN PASCALS, DW0 IS IN G/CM^3
C
C FROM L. HAAR, J. S. GALLAGHER, AND G. S. KELL, (1984)
C
*/
{
double FP = 9.869232667e0, P, DGSS, D;
BB (T);
P=1.0e0/FP;
if (T > 373.149e0) P=PS(T);
DGSS=P/T/.4e0;
if (T < TZ) {
DGSS=1.0e0/(VLEST(T));
}
DFIND (&D,P,DGSS,T);
DW0=D;
VP=P*FP;
return OK;
}
/* ---------------------------------------------------------------------- */
static int BB (double T)
/* ---------------------------------------------------------------------- */
/*
C
C THIS SUBROUTINE CALCULATES THE B'S NEEDED FOR FUNCTION DW.
C THE B'S CALCULATED HERE ARE IN CM3/G.
C
C FROM L. HAAR, J. S. GALLAGHER, AND G. S. KELL, (1984)
C
*/
{
double V[11];
int I;
/* COMMON /BCONST/ */
double P[11]={0, 0.7478629e0, -.3540782e0, 0.e0, 0e0, .007159876e0, 0.e0,
-.003528426e0, 0., 0., 0.};
double Q[11]={0, 1.1278334e0,0.e0,-.5944001e0,-5.010996e0,0.e0,.63684256e0,
0., 0., 0., 0.};
V[1]=1.0;
for (I = 2; I <= 10; I++) {
V[I]=V[I-1]*TZ/T;
}
B1=P[1]+P[2]*log(1.e0/V[2]);
B2=Q[1];
B1T=P[2]*V[2]/TZ;
B2T=0.e0;
B1TT=0.e0;
B2TT=0.e0;
for (I = 3; I <= 10; I++) {
B1=B1+P[I]*V[I-1];
B2=B2+Q[I]*V[I-1];
B1T=B1T-(I-2)*P[I]*V[I-1]/T;
B2T=B2T-(I-2)*Q[I]*V[I-1]/T;
B1TT=B1TT+P[I]*(I-2)*(I-2)*V[I-1]/T/T;
B2TT=B2TT+Q[I]*(I-2)*(I-2)*V[I-1]/T/T;
}
B1TT=B1TT-B1T/T;
B2TT=B2TT-B2T/T;
return OK;
}
/* ---------------------------------------------------------------------- */
static double PS (double T)
/* ---------------------------------------------------------------------- */
/*
C
C THIS FUNCTION CALCULATES AN APPROXIMATION TO THE VAPOR PRESSURE, P
C AS A FUNCTION OF THE INPUT TEMPERATURE. THE VAPOR PRESSURE
C CALCULATED AGREES WITH THE VAPOR PRESSURE PREDICTED BY THE SURFACE
C TO WITHIN .02% TO WITHIN A DEGREE OR SO OF THE CRITICAL TEMPERATUR
C AND CAN SERVE AS AN INITIAL GUESS FOR FURTHER REFINEMENT BY
C IMPOSING THE CONDITION THAT GL=GV.
C
C FROM L. HAAR, J. S. GALLAGHER, AND G. S. KELL, (1984)
C
*/
{
double A[9]={0, -7.8889166e0,2.5514255e0,-6.716169e0,
33.239495e0,-105.38479e0,174.35319e0,-148.39348e0,
48.631602e0};
double PL, V, W, B, Z, Q;
int I;
if(T <= 314.e0) {
PL=6.3573118e0-8858.843e0/T+607.56335e0*pow(T,-.6e0);
return (.1e0*exp(PL));
}
V=T/647.25e0;
W=fabs(1.e0-V);
B=0.e0;
for (I = 1; I <= 8; I++) {
Z=I;
B=B+A[I]*pow(W,((Z+1.e0)/2.e0));
}
Q=B/V;
return (22.093e0*exp(Q));
}
/* ---------------------------------------------------------------------- */
static double VLEST (double T)
/* ---------------------------------------------------------------------- */
/*
C
C FROM L. HAAR, J. S. GALLAGHER, AND G. S. KELL, (1984)
C
*/
{
double A=-1.59259e1,B=6.57886e-2,C=-1.12666e-4,D=7.33191e-8,
E=1.60229e3,F=2.88572e0,G=650.0e0;
return (A+B*T+C*T*T+D*T*T*T+E/T+F/(G-T));
}
/* ---------------------------------------------------------------------- */
static int DFIND (double *DOUT, double P, double D, double T)
/* ---------------------------------------------------------------------- */
/*
C
C ROUTINE TO FIND DENSITY CORRESPONDING TO INPUT PRESSURE P(MPA), AN
C TEMPERATURE T(K), USING INITIAL GUESS DENSITY D(G/CM3). THE OUTPUT
C DENSITY IS IN G/CM3.
C
C FROM L. HAAR, J. S. GALLAGHER, AND G. S. KELL, (1984)
C
*/
{
int L;
double DD, RT, PP_dfind, DPD, DPDX, DP, X;
/* double DD, RT, PP, DPD, DPDX, DP, X; */
DD=D;
RT=GASCON*T;
if(DD <= 0.e0) DD=1.e-8;
if(DD > 1.9e0) DD=1.9e0;
L=0;
for (L=1; L <= 30; L++) {
if(DD <= 0.e0) DD=1.e-8;
if(DD > 1.9e0) DD=1.9e0;
QQ(T,DD);
PP_dfind = RT*DD*BASE(DD)+Q0;
DPD=RT*(Z+Y*DZ)+Q5;
/*
C
C THE FOLLOWING 3 LINES CHECK FOR NEGATIVE DP/DRHO, AND IF SO ASSUME
C GUESS TO BE IN 2-PHASE REGION, AND CORRECT GUESS ACCORDINGLY.
C
*/
if(DPD <= 0.e0) {
if(D >= .2967e0) DD=DD*1.02e0;
if(D < .2967e0) DD=DD*.98e0;
if(L <= 10) continue;
} else {
/* 13 */
DPDX=DPD*1.1e0;
if(DPDX < 0.1e0) DPDX=0.1e0;
DP=fabs(1.e0-PP_dfind/P);
if(DP < 1.e-8) break;
if(D > .3e0 && DP < 1.e-7) break;
if(D > .7e0 && DP < 1.e-6) break;
X=(P-PP_dfind)/DPDX;
if(fabs(X) > .1e0) X=X*.1e0/fabs(X);
DD=DD+X;
if(DD < 0.e0) DD=1.e-8;
}
}
if (L > 30) error_msg("In subroutine DFIND", STOP);
/* 20 CONTINUE */
*DOUT=DD;
return OK;
}
/* ---------------------------------------------------------------------- */
static int QQ (double T, double D)
/* ---------------------------------------------------------------------- */
/*
C
C THIS ROUTINE CALCULATES, FOR A GIVEN T(K) AND D(G/CM3), THE RESIDUL
C CONTRIBUTIONS TO: PRESSURE (Q), DP/DRHO (Q5)
C THIS SUBROUTINE IS USED IN DENSITY OF WATER CALCULATION.
C
C FROM L. HAAR, J. S. GALLAGHER, AND G. S. KELL, (1984)
C
*/
{
/* COMMON /NCONST/ */
double G[41]={0,-.53062968529023e3,.22744901424408e4,.78779333020687e3
,-.69830527374994e2,.17863832875422e5,-.39514731563338e5
,.33803884280753e5,-.13855050202703e5,-.25637436613260e6
,.48212575981415e6,-.34183016969660e6, .12223156417448e6
,.11797433655832e7,-.21734810110373e7, .10829952168620e7
,-.25441998064049e6,-.31377774947767e7,.52911910757704e7
,-.13802577177877e7,-.25109914369001e6, .46561826115608e7
,-.72752773275387e7,.41774246148294e6,.14016358244614e7
,-.31555231392127e7,.47929666384584e7,.40912664781209e6
,-.13626369388386e7, .69625220862664e6,-.10834900096447e7
,-.22722827401688e6,.38365486000660e6,.68833257944332e4
,.21757245522644e5,-.26627944829770e4,-.70730418082074e5
,-.225e0,-1.68e0,.055e0,-93.0e0};
/*int II[41]={0,4*0,4*1,4*2,4*3,4*4,4*5,4*6,4*8,2*2,0,4,3*2,4};*/
int II[41]={0, 0,0,0,0, 1,1,1,1, 2,2,2,2, 3,3,3,3, 4,4,4,4, 5,5,5,5, 6,6,6,6, 8,8,8,8, 2,2, 0,4, 2,2,2,4};
/*int JJ[41]={0,2,3,5,7,2,3,5,7,2,3,5,7,2,3,5,7,2,3,5,7,2,3,5,7,2,3,5,7,2,3,5,7,1,3*4,0,2,0,0};*/
int JJ[41]={0,2,3,5,7,2,3,5,7,2,3,5,7,2,3,5,7,2,3,5,7,2,3,5,7,2,3,5,7,2,3,5,7,1,4,4,4,0,2,0,0};
int NC=36;
/* COMMON /ADDCON/ */
double ATZ[5]={0,64.e1,64.e1,641.6e0,27.e1},ADZ[5]={0,.319e0,.319e0,.319e0,1.55e0},
AAT[5]={0,2.e4,2.e4,4.e4,25.e0}, AAD[5]={0,34.e0,4.e1,3.e1,1.05e3};
double *QZT;
double QR[12],QT[11] /*, QZT[10]*/;
/*EQUIVALENCE (QT(2),QZT(1))*/
double E, Q10, Q20, V, QP, DDZ, DEL, EX1, DEX, ATT, TX,
TAU, EX2, TEX, QM, FCT, Q5T;
int I, K, L, J, KM;
QZT = &(QT[1]);
QR[1]=0.e0;
Q5=0.e0;
Q0=0.e0;
E=exp(-AA*D);
Q10=D*D*E;
Q20=1.e0-E;
QR[2]=Q10;
V=TZ/T;
QT[1]=T/TZ;
/*DO 4 I=2,10*/
for (I = 2; I <= 10; I++) {
QR[I+1]=QR[I]*Q20;
/* 4 QT[I]=QT[I-1]*V*/
QT[I]=QT[I-1]*V;
}
/* DO 10 I=1,NC */
for (I = 1; I <= NC; I++) {
K=II[I]+1;
L=JJ[I];
QP=G[I]*AA*QR[K+1]*QZT[L];
Q0=Q0+QP;
/*10 Q5 = Q5 + AA*(2.e0/D-AA*(1.e0-E*(K-1)/Q20))*QP*/
Q5 = Q5 + AA*(2.e0/D-AA*(1.e0-E*(K-1)/Q20))*QP;
}
QP=0.e0;
/* DO 20 J=37,40 */
for (J=37; J <= 40; J++) {
if(fabs(G[J]) < 1.0e-20) continue;
K=II[J];
KM=JJ[J];
DDZ = ADZ[J-36];
DEL = D/DDZ - 1.e0;
if(fabs(DEL) < 1.e-10) DEL=1.e-10;
EX1 = -AAD[J-36]*pow(DEL,K);
if (EX1 <= -88.028e0) {
DEX=0.e0;
} else {
DEX=exp(EX1)*pow(DEL,KM);
}
ATT = AAT[J-36];
TX = ATZ[J-36];
TAU = T/TX-1.e0;
EX2 = -ATT*TAU*TAU;
if (EX2 <= -88.028e0) {
TEX=0.e0;
} else {
TEX = exp(EX2);
}
Q10 = DEX*TEX;
QM = KM/DEL - K*AAD[J-36]*pow(DEL,(K-1));
FCT=QM*D*D*Q10/DDZ;
Q5T = FCT*(2.e0/D+QM/DDZ)-pow((D/DDZ),2)*Q10*(KM/DEL/DEL+
K*(K-1)*AAD[J-36]*pow(DEL,(K-2)));
Q5 = Q5 + Q5T*G[J];
QP = QP + G[J]*FCT;
/* 20 CONTINUE */
}
Q0=Q0+QP;
return OK;
}
/* ---------------------------------------------------------------------- */
static double BASE (double D)
/* ---------------------------------------------------------------------- */
/*
C
C THIS FUNCTION CALCULATES THE Z (=PBASE/(DRT)) NEEDED FOR FUNCTION
C
C FROM L. HAAR, J. S. GALLAGHER, AND G. S. KELL, (1984)
C
*/
{
double X, Z0, DZ0;
/*
C
C G1,G2 AND GF ARE THE ALPHA, BETA AND GAMMA FOR DENSITY OF WATER
C CALCULATIONS. B1 AND B2 ARE THE 'EXCLUDED VOLUME' AND '2ND VIRIAL
C SUPPLIED BY THE SUBROUTINE BB(T), WHICH ALSO SUPPLIES THE 1ST AND
C 2ND DERIVATIVES WITH RESPECT TO T (B1T,B2T,B1TT,B2TT).
C
*/
Y=.25e0*B1*D;
X=1.e0-Y;
Z0=(1.e0+G1*Y+G2*Y*Y)/pow(X,3);
Z=Z0+4.e0*Y*(B2/B1-GF);
DZ0=(G1+2.e0*G2*Y)/pow(X,3) + 3.e0*(1.e0+G1*Y+G2*Y*Y)/pow(X,4);
DZ=DZ0+4.e0*(B2/B1-GF);
return(Z);
}
/* ---------------------------------------------------------------------- */
double DC (double T)
/* ---------------------------------------------------------------------- */
/*
C
C THIS FUNCTION CALCULATES THE RELATIVE DIELECTRIC CONSTANT AS A
C FUNCTION OF TEMPERATURE, ASSUMING ONE ATMOSPHERE PRESSURE
C ACCORDING TO D. J. BRADLEY AND K. S. PITZER, (1979)
C
*/
{
double D1000, C, B;
double U[10]={0, 3.4279e2, -5.0866e-3, 9.4690e-7, -2.0525e0, 3.1159e3,
-1.8289e2, -8.0325e3, 4.2142e6, 2.1417e0};
D1000=U[1]*exp(U[2]*T+U[3]*T*T);
C=U[4]+U[5]/(U[6]+T);
B=U[7]+U[8]/T+U[9]*T;
return (D1000+C*log((B+VP*1.01325e0)/(B+1000.0e0)));
}

1638
global.h
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249
input.cpp
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@ -1,249 +0,0 @@
#define EXTERNAL extern
#include <setjmp.h>
#include "global.h"
#include "input.h"
#include "output.h"
#include "phrqproto.h"
#include "phqalloc.h"
static char const svnid[] = "$Id: input.c 78 2005-02-01 22:47:12Z dlpark $";
int check_line_return;
static struct read_callback s_read_callback;
/* ---------------------------------------------------------------------- */
int set_read_callback(PFN_READ_CALLBACK pfn, void *cookie, int database)
/* ---------------------------------------------------------------------- */
{
if (svnid == NULL) fprintf(stderr," ");
s_read_callback.callback = pfn;
s_read_callback.cookie = cookie;
s_read_callback.database = database;
return OK;
}
/* ---------------------------------------------------------------------- */
int reading_database(void)
/* ---------------------------------------------------------------------- */
{
return s_read_callback.database;
}
/* ---------------------------------------------------------------------- */
int check_line(const char *string, int allow_empty, int allow_eof, int allow_keyword, int print)
/* ---------------------------------------------------------------------- */
{
assert(s_read_callback.callback != NULL);
if (s_read_callback.callback == NULL) return EOF;
if (reading_database()) print = FALSE;
return check_line_impl(s_read_callback.callback, s_read_callback.cookie, string, allow_empty, allow_eof, allow_keyword, print);
}
/* ---------------------------------------------------------------------- */
int check_line_impl(PFN_READ_CALLBACK pfn, void *cookie, const char *string, int allow_empty, int allow_eof, int allow_keyword, int print)
/* ---------------------------------------------------------------------- */
{
/*
* Function gets a new line and checks for empty, eof, and keywords.
*
* Arguments:
* string Input, character string used in printing error message
* allow_empty Input, True or false, if a blank line is accepable
* if false, another line is read
* allow_eof Input, True or false, if EOF is acceptable
* allow_keyword Input, True or false, if a keyword is acceptable
*
* Returns:
* EMPTY if empty line read and allow_empty == true
* KEYWORD if line begins with keyword
* EOF if eof and allow_eof == true
* OK otherwise
* OPTION if line begins with -[alpha]
*
* Terminates if EOF and allow_eof == false.
*/
int i;
/* Get line */
do {
i = get_line(pfn, cookie);
if ((print == TRUE && i != EOF) || i == KEYWORD) {
output_msg(OUTPUT_CHECKLINE,"\t%s\n",line_save);
}
} while ( i == EMPTY && allow_empty == FALSE );
/* Check eof */
if ( i == EOF && allow_eof == FALSE ) {
sprintf(error_string,"Unexpected eof while reading %s\nExecution terminated.\n",string);
error_msg(error_string, STOP);
}
/* Check keyword */
if (i == KEYWORD && allow_keyword == FALSE ) {
sprintf(error_string, "Expected data for %s, but got a keyword ending data block.", string);
error_msg(error_string, CONTINUE);
input_error++;
}
check_line_return = i;
return (i);
}
/* ---------------------------------------------------------------------- */
int get_line(PFN_READ_CALLBACK pfn, void *cookie)
/* ---------------------------------------------------------------------- */
{
/*
* Read a line from input file put in "line".
* Copy of input line is stored in "line_save".
* Characters after # are discarded in line but retained in "line_save"
*
* Arguments:
* fp is file name
* Returns:
* EMPTY,
* EOF,
* KEYWORD,
* OK,
* OPTION
*/
int i, j, return_value, empty, l;
char *ptr;
char token[MAX_LENGTH];
return_value = EMPTY;
while (return_value == EMPTY) {
/*
* Eliminate all characters after # sign as a comment
*/
i=-1;
empty=TRUE;
/*
* Get line, check for eof
*/
if (get_logical_line(pfn, cookie, &l) == EOF) {
next_keyword=0;
return (EOF);
}
/*
* Get long lines
*/
j = l;
ptr = strchr (line_save, '#');
if (ptr != NULL) {
j = ptr - line_save;
}
strncpy(line, line_save, (unsigned) j);
line[j] = '\0';
for (i = 0; i < j; i++) {
if (! isspace((int) line[i]) ) {
empty = FALSE;
break;
}
}
/*
* New line character encountered
*/
if (empty == TRUE) {
return_value=EMPTY;
} else {
return_value=OK;
}
}
/*
* Determine return_value
*/
if (return_value == OK) {
if ( check_key(line) == TRUE) {
return_value=KEYWORD;
} else {
ptr = line;
copy_token(token, &ptr, &i);
if (token[0] == '-' && isalpha((int) token[1])) {
return_value = OPTION;
}
}
}
return (return_value);
}
/* ---------------------------------------------------------------------- */
int get_logical_line(PFN_READ_CALLBACK pfn, void *cookie, int *l)
/* ---------------------------------------------------------------------- */
{
/*
* Reads file fp until end of line, ";", or eof
* stores characters in line_save
* reallocs line_save and line if more space is needed
*
* returns:
* EOF on empty line on end of file or
* OK otherwise
* *l returns length of line
*/
int i, j;
int pos;
char c;
i = 0;
if (!pfn) return EOF;
while ((j = pfn(cookie)) != EOF) {
c = (char) j;
if (c == '#') {
/* ignore all chars after # until newline */
do {
c = (char) j;
if (c == '\n') {
break;
}
add_char_to_line(&i, c);
} while ((j = pfn(cookie)) != EOF);
}
if (c == ';') break;
if (c == '\n') {
break;
}
if (c == '\\') {
pos = i;
add_char_to_line(&i, c);
while ((j = pfn(cookie)) != EOF) {
c = (char) j;
if (c == '\\') {
pos = i;
add_char_to_line(&i, c);
continue;
}
if (c == '\n') {
/* remove '\\' */
for (; pos < i; pos++) {
line_save[pos] = line_save[pos+1];
}
i--;
break;
}
add_char_to_line(&i, c);
if (!isspace(j)) break;
}
} else {
add_char_to_line(&i, c);
}
}
if (j == EOF && i == 0) {
*l = 0;
line_save[i] = '\0';
return(EOF);
}
line_save[i] = '\0';
*l = i;
return(OK);
}
/* ---------------------------------------------------------------------- */
int add_char_to_line(int *i, char c)
/* ---------------------------------------------------------------------- */
{
if ( *i + 20 >= max_line) {
max_line *= 2;
line_save = (char *) PHRQ_realloc(line_save, (size_t) max_line * sizeof(char));
if (line_save == NULL) malloc_error();
line = (char *) PHRQ_realloc(line, (size_t) max_line * sizeof(char));
if (line == NULL) malloc_error();
}
line_save[*i] = c;
*i += 1;
return(OK);
}

24
input.h
View File

@ -1,24 +0,0 @@
#ifndef _INC_INPUT_H
#define _INC_INPUT_H
#ifdef PHREEQC_IDENT
static char const svnidinput[] = "$Id$";
#endif
typedef int (*PFN_READ_CALLBACK)(void *cookie);
struct read_callback {
PFN_READ_CALLBACK callback;
void *cookie;
int database;
};
int add_char_to_line(int *i, char c);
int check_line_impl(PFN_READ_CALLBACK pfn, void *cookie, const char *string, int allow_empty, int allow_eof, int allow_keyword, int print);
int get_line(PFN_READ_CALLBACK pfn, void *cookie);
int get_logical_line(PFN_READ_CALLBACK pfn, void *cookie, int *l);
int read_database(PFN_READ_CALLBACK pfn, void *cookie);
int run_simulations(PFN_READ_CALLBACK pfn, void *cookie);
int set_read_callback(PFN_READ_CALLBACK pfn, void *cookie, int database);
#endif /* _INC_INPUT_H */

851
integrate.cpp
View File

@ -1,851 +0,0 @@
#define EXTERNAL extern
#include "global.h"
#include "phqalloc.h"
#include "output.h"
#include "phrqproto.h"
static char const svnid[] = "$Id: integrate.c 78 2005-02-01 22:47:12Z dlpark $";
#define MAX_QUAD 20
#define K_POLY 5
static LDBLE g_function(LDBLE x_value);
static LDBLE midpnt (LDBLE x1, LDBLE x2, int n);
static void polint(LDBLE *xa, LDBLE *ya, int n, LDBLE xv, LDBLE *yv, LDBLE *dy);
static LDBLE qromb_midpnt (LDBLE x1, LDBLE x2);
static LDBLE z, xd, alpha, G_TOL;
static struct surface_charge *surface_charge_ptr;
/*static LDBLE calc_psi_avg(char *name);*/
static LDBLE calc_psi_avg(LDBLE surf_chrg_eq);
/* ---------------------------------------------------------------------- */
int calc_all_g( void )
/* ---------------------------------------------------------------------- */
{
int i, j, k;
int converge, converge1;
int count_g, count_charge;
LDBLE new_g, xd1;
LDBLE epsilon;
if (svnid == NULL) fprintf(stderr," ");
if (use.surface_ptr == NULL) return(OK);
/*
* calculate g for each surface
*/
#ifdef SKIP
if (punch.high_precision == FALSE) {
epsilon = 1e-8;
G_TOL = 1e-9;
} else {
epsilon = 1.e-12;
G_TOL = 1e-10;
}
#endif
epsilon = convergence_tolerance;
if (convergence_tolerance >= 1e-8) {
G_TOL = 1e-9;
} else {
G_TOL = 1e-10;
}
converge = TRUE;
count_charge = 0;
for (j = 0; j < count_unknowns; j++) {
if (x[j]->type != SURFACE_CB) continue;
if (debug_diffuse_layer == TRUE) output_msg(OUTPUT_MESSAGE, "Calc_all_g, X[%d]\n", j);
surface_charge_ptr = x[j]->surface_charge;
count_g = 1;
x[j]->surface_charge->g[0].charge = 0.0;
x[j]->surface_charge->g[0].g = 0.0;
x[j]->surface_charge->g[0].dg = 0.0;
xd = exp(-2 * x[j]->master[0]->s->la * LOG_10);
/* alpha = 0.02935 @ 25; (ee0RT/2)**1/2, (L/mol)**1/2 C / m**2 */
/* 1000 J/kJ and 1000 L/m**3 */
alpha = sqrt( EPSILON * EPSILON_ZERO * (R_KJ_DEG_MOL * 1000.0) * 1000.0 * tk_x * 0.5);
/*
* calculate g for given surface for each species
*/
for (i = 0; i < count_s_x; i++) {
if (s_x[i]->type > HPLUS) continue;
for (k=0; k < count_g; k++) {
if (equal(x[j]->surface_charge->g[k].charge, s_x[i]->z, G_TOL) == TRUE) {
s_x[i]->diff_layer[count_charge].charge = x[j]->surface_charge;
s_x[i]->diff_layer[count_charge].count_g = k;
break;
}
}
if (k < count_g) continue;
if (x[j]->surface_charge->grams > 0.0) {
z = s_x[i]->z;
if ((use.surface_ptr->only_counter_ions == FALSE) ||
(((x[j]->master[0]->s->la > 0) && (z < 0)) || ((x[j]->master[0]->s->la < 0) && (z > 0)))) {
if (xd > 0.1) {
new_g = qromb_midpnt( 1.0, xd);
} else if (xd > 0.01) {
new_g = qromb_midpnt( 1.0, 0.1);
new_g += qromb_midpnt( 0.1, xd);
} else if (xd > 0.001) {
new_g = qromb_midpnt( 1.0, 0.1);
new_g += qromb_midpnt( 0.1, 0.01);
new_g += qromb_midpnt( 0.01, xd);
} else if (xd > 0.0001) {
new_g = qromb_midpnt( 1.0, 0.1);
new_g += qromb_midpnt( 0.1, 0.01);
new_g += qromb_midpnt( 0.01, .001);
new_g += qromb_midpnt( 0.001, xd);
} else if (xd > 0.00001) {
new_g = qromb_midpnt( 1.0, 0.1);
new_g += qromb_midpnt( 0.1, 0.01);
new_g += qromb_midpnt( 0.01, .001);
new_g += qromb_midpnt( 0.001, .0001);
new_g += qromb_midpnt( 0.0001, xd);
} else if (xd > 0.000001) {
new_g = qromb_midpnt( 1.0, 0.1);
new_g += qromb_midpnt( 0.1, 0.01);
new_g += qromb_midpnt( 0.01, .001);
new_g += qromb_midpnt( 0.001, .0001);
new_g += qromb_midpnt( 0.0001, .00001);
new_g += qromb_midpnt( 0.00001, xd);
} else if (xd > 0.0000001) {
new_g = qromb_midpnt( 1.0, 0.1);
new_g += qromb_midpnt( 0.1, 0.01);
new_g += qromb_midpnt( 0.01, .001);
new_g += qromb_midpnt( 0.001, .0001);
new_g += qromb_midpnt( 0.0001, .00001);
new_g += qromb_midpnt( 0.00001, .000001);
new_g += qromb_midpnt( 0.000001, xd);
} else if (xd > 0.00000001) {
new_g = qromb_midpnt( 1.0, 0.1);
new_g += qromb_midpnt( 0.1, 0.01);
new_g += qromb_midpnt( 0.01, .001);
new_g += qromb_midpnt( 0.001, .0001);
new_g += qromb_midpnt( 0.0001, .00001);
new_g += qromb_midpnt( 0.00001, .000001);
new_g += qromb_midpnt( 0.000001, .0000001);
new_g += qromb_midpnt( 0.0000001, xd);
} else {
new_g = qromb_midpnt( 1.0, 0.1);
new_g += qromb_midpnt( 0.1, 0.01);
new_g += qromb_midpnt( 0.01, .001);
new_g += qromb_midpnt( 0.001, .0001);
new_g += qromb_midpnt( 0.0001, .00001);
new_g += qromb_midpnt( 0.00001, .000001);
new_g += qromb_midpnt( 0.000001, .0000001);
new_g += qromb_midpnt( 0.0000001, .00000001);
new_g += qromb_midpnt( 0.00000001, xd);
}
} else {
new_g = 0;
}
} else {
new_g = 0.0;
}
if ((use.surface_ptr->only_counter_ions == TRUE) && new_g < 0) new_g = 0;
x[j]->surface_charge->g[count_g].charge = s_x[i]->z;
converge1 = TRUE;
if (fabs(new_g) >= 1.) {
if (fabs((new_g - x[j]->surface_charge->g[count_g].g)/new_g) > epsilon) {
converge1 = FALSE;
}
} else {
if (fabs(new_g - x[j]->surface_charge->g[count_g].g) > epsilon) {
converge1 = FALSE;
}
}
if (converge1 == FALSE) {
converge = FALSE;
if (debug_diffuse_layer == TRUE) {
output_msg(OUTPUT_MESSAGE, "\t%12f\t%12.4e\t%12.4e\t%12.4e\n",
(double) x[j]->surface_charge->g[count_g].charge,
(double) x[j]->surface_charge->g[count_g].g,
(double) new_g,
(double) (new_g - x[j]->surface_charge->g[count_g].g) );
}
}
x[j]->surface_charge->g[count_g].g = new_g;
if (new_g == 0) {
x[j]->surface_charge->g[count_g].dg = 0;
} else {
if (x[j]->surface_charge->grams > 0.0) {
x[j]->surface_charge->g[count_g].dg = surface_charge_ptr->grams * surface_charge_ptr->specific_area * alpha * g_function(xd) / F_C_MOL;
x[j]->surface_charge->g[count_g].dg *= -2. /
(exp(x[j]->master[0]->s->la * LOG_10) *
exp(x[j]->master[0]->s->la * LOG_10));
if ((xd - 1) < 0.0) {
x[j]->surface_charge->g[count_g].dg *= -1.0;
}
if (fabs(x[j]->surface_charge->g[count_g].dg) < 1e-8) {
xd1 = exp(-2 * 1e-3 * LOG_10);
new_g = qromb_midpnt( 1.0, xd1);
x[j]->surface_charge->g[count_g].dg = new_g/.001;
}
} else {
x[j]->surface_charge->g[count_g].dg = 0.0;
}
}
s_x[i]->diff_layer[count_charge].charge = x[j]->surface_charge;
s_x[i]->diff_layer[count_charge].count_g = count_g;
count_g++;
}
if (debug_diffuse_layer == TRUE) {
output_msg(OUTPUT_MESSAGE, "\nSurface component %d: charge,\tg,\tdg/dlny,\txd\n", count_charge);
for (i = 0; i < count_g; i++) {
output_msg(OUTPUT_MESSAGE, "\t%12f\t%12.4e\t%12.4e\t%12.4e\n",
(double) x[j]->surface_charge->g[i].charge,
(double) x[j]->surface_charge->g[i].g,
(double) x[j]->surface_charge->g[i].dg,
(double) xd);
}
}
count_charge++;
}
return (converge);
}
/* ---------------------------------------------------------------------- */
LDBLE g_function(LDBLE x_value)
/* ---------------------------------------------------------------------- */
{
LDBLE sum, return_value, sum1;
int i, j;
LDBLE ln_x_value;
if (equal(x_value, 1.0, G_TOL*100) == TRUE) return(0.0);
sum = 0.0;
ln_x_value = log(x_value);
for (j = 0; j < use.surface_ptr->charge[0].count_g; j++) {
use.surface_ptr->charge[0].g[j].psi_to_z =
exp(ln_x_value * use.surface_ptr->charge[0].g[j].charge) - 1.0;
}
for (i = 0; i < count_s_x; i++) {
if (s_x[i]->type < H2O && s_x[i]->z != 0.0) {
for(j = 0; j < use.surface_ptr->charge[0].count_g; j++) {
if(use.surface_ptr->charge[0].g[j].charge == s_x[i]->z) {
sum += s_x[i]->moles * use.surface_ptr->charge[0].g[j].psi_to_z;
break;
}
}
}
}
if (sum < 0.0) {
sum = 0.0;
sum1 = 0.0;
output_msg(OUTPUT_MESSAGE, "Species\tmoles\tX**z-1\tsum\tsum charge\n");
for (i = 0; i < count_s_x; i++) {
if (s_x[i]->type < H2O && s_x[i]->z != 0.0) {
sum += s_x[i]->moles * (pow(x_value, s_x[i]->z) - 1.0);
sum1 += s_x[i]->moles * s_x[i]->z;
output_msg(OUTPUT_MESSAGE, "%s\t%e\t%e\t%e\t%e\n", s_x[i]->name, (double) s_x[i]->moles, (double) (pow(x_value, (double) s_x[i]->z) - 1.0), (double) sum, (double) sum1);
}
}
sprintf(error_string, "Negative sum in g_function, %e\t%e.", (double) sum, (double) x_value);
error_msg(error_string, CONTINUE);
sprintf(error_string, "Solutions must be charge balanced, charge imbalance is %e\n", (double) sum1);
error_msg(error_string, STOP);
}
return_value = ( exp (ln_x_value * z) - 1) / sqrt((x_value * x_value * mass_water_aq_x * sum ));
return(return_value);
}
/* ---------------------------------------------------------------------- */
void polint(LDBLE *xa, LDBLE *ya, int n, LDBLE xv, LDBLE *yv, LDBLE *dy)
/* ---------------------------------------------------------------------- */
{
int i, m, ns;
LDBLE den, dif, dift, ho, hp, w;
LDBLE *c, *d;
ns = 1;
dif = fabs(xv-xa[1]);
/*
* Malloc work space
*/
c = (double *) PHRQ_malloc((size_t) (n + 1) * sizeof (LDBLE) );
if (c == NULL) malloc_error();
d = (double *) PHRQ_malloc((size_t) (n + 1) * sizeof (LDBLE) );
if (d == NULL) malloc_error();
for (i=1; i <= n; i++) {
dift = fabs(xv-xa[i]);
if ( dift < dif ) {
ns = i;
dif = dift;
}
c[i] = ya[i];
d[i] = ya[i];
}
*yv = ya[ns--];
for (m = 1; m < n; m++) {
for (i=1; i <= n - m; i++) {
ho = xa[i] - xv;
hp = xa[i+m] - xv;
w = c[i+1] - d[i];
if ( (den=ho-hp) == 0.0) {
error_msg("In subroutine polint.", STOP);
}
den = w/den;
d[i] = hp*den;
c[i] = ho*den;
}
if (2 * ns < (n-m) ) {
*dy = c[ns+1];
} else {
*dy = d[ns--];
}
*yv += *dy;
/* *yv += (*dy = (2 * ns < (n-m) ? c[ns+1] : d[ns--])); */
}
c = (double *) free_check_null(c);
d = (double *) free_check_null(d);
return;
}
/* ---------------------------------------------------------------------- */
LDBLE midpnt (LDBLE x1, LDBLE x2, int n)
/* ---------------------------------------------------------------------- */
{
LDBLE xv, tnm, sum, del, ddel;
static LDBLE sv;
int it, j;
if (n == 1) {
sv = (x2-x1) * g_function(0.5 * (x1 + x2));
return(sv);
} else {
for (it=1, j=1; j<n-1; j++) it *=3;
tnm = (LDBLE) it;
del = (x2 - x1) / (3*tnm);
ddel = del + del;
xv = x1 + 0.5 * del;
sum = 0.0;
for (j=1; j <= it; j++) {
#if defined(PHREEQCI_GUI)
if (WaitForSingleObject(g_hKill /*g_eventKill*/, 0) == WAIT_OBJECT_0)
{
error_msg("Execution canceled by user.", CONTINUE);
RaiseException(USER_CANCELED_RUN, 0, 0, NULL);
}
#endif
sum += g_function(xv);
xv += ddel;
sum += g_function(xv);
xv += del;
}
sv = (sv + (x2 - x1) * sum / tnm) / 3.0;
return sv;
}
}
/* ---------------------------------------------------------------------- */
LDBLE qromb_midpnt (LDBLE x1, LDBLE x2)
/* ---------------------------------------------------------------------- */
{
LDBLE ss, dss;
LDBLE sv[MAX_QUAD + 2], h[MAX_QUAD + 2];
int j;
h[0] = 1.0;
sv[0] = midpnt( x1, x2, 1);
for (j = 1; j < MAX_QUAD; j++) {
sv[j] = midpnt( x1, x2, j + 1);
h[j] = h[j-1] / 9.0;
if (fabs(sv[j]-sv[j-1]) <= G_TOL * fabs(sv[j]) ) {
sv[j] *= surface_charge_ptr->grams * surface_charge_ptr->specific_area *
alpha / F_C_MOL; /* (ee0RT/2)**1/2, (L/mol)**1/2 C / m**2 */
if ((x2 - 1) < 0.0) sv[j] *= -1.0;
if (debug_diffuse_layer == TRUE) {
output_msg(OUTPUT_MESSAGE, "Iterations in qromb_midpnt: %d\n", j);
}
return(sv[j]);
}
if (j >= K_POLY - 1) {
polint( &h[j - K_POLY], &sv[j - K_POLY], K_POLY, 0.0, &ss, &dss);
if (fabs(dss) <= G_TOL * fabs(ss) || fabs(dss) < G_TOL) {
ss *= surface_charge_ptr->grams * surface_charge_ptr->specific_area *
alpha / F_C_MOL; /* (ee0RT/2)**1/2, (L/mol)**1/2 C / m**2 */
if ((x2 - 1) < 0.0) ss *= -1.0;
if (debug_diffuse_layer == TRUE) {
output_msg(OUTPUT_MESSAGE, "Iterations in qromb_midpnt: %d\n", j);
}
return(ss);
}
}
}
sprintf(error_string, "\nToo many iterations integrating diffuse layer.\n");
error_msg(error_string, STOP);
return(-999.9);
}
/* ---------------------------------------------------------------------- */
int calc_init_g(void)
/* ---------------------------------------------------------------------- */
{
int i, j, k;
int count_g, count_charge;
if (use.surface_ptr == NULL) return(OK);
/*
* calculate g for each surface
*/
count_charge = 0;
for (j = 0; j < count_unknowns; j++) {
if (x[j]->type != SURFACE_CB) continue;
surface_charge_ptr = x[j]->surface_charge;
count_g = 0;
if (x[j]->surface_charge->g != NULL) {
count_g = x[j]->surface_charge->count_g;
}
if( count_g == 0 ) {
x[j]->surface_charge->g = (struct surface_diff_layer *) PHRQ_malloc((size_t) sizeof(struct surface_diff_layer));
if (x[j]->surface_charge->g == NULL) malloc_error();
x[j]->surface_charge->g[0].charge = 0.0;
x[j]->surface_charge->g[0].g = 0.0;
x[j]->surface_charge->g[0].dg = 0.0;
xd = exp(-2 * x[j]->master[0]->s->la * LOG_10);
/* alpha = 0.02935 @ 25; (ee0RT/2)**1/2, (L/mol)**1/2 C / m**2 */
/* second 1000 is liters/m**3 */
alpha = sqrt( EPSILON * EPSILON_ZERO * (R_KJ_DEG_MOL * 1000.0) * 1000.0 * tk_x * 0.5);
}
/*
* calculate g for given surface for each species
*/
count_g = 1;
for (i = 0; i < count_s_x; i++) {
if (s_x[i]->type > HPLUS) continue;
for (k=0; k < count_g; k++) {
if (equal(x[j]->surface_charge->g[k].charge, s_x[i]->z, G_TOL) == TRUE) {
s_x[i]->diff_layer[count_charge].charge = x[j]->surface_charge;
s_x[i]->diff_layer[count_charge].count_g = k;
s_x[i]->diff_layer[count_charge].g_moles = 0.0;
s_x[i]->diff_layer[count_charge].dg_g_moles = 0.0;
break;
}
}
if (k >= count_g) {
/* malloc space to save g for charge */
x[j]->surface_charge->g = (struct surface_diff_layer *) PHRQ_realloc(x[j]->surface_charge->g,
(size_t) (count_g + 1) *
sizeof(struct surface_diff_layer));
if (x[j]->surface_charge->g == NULL) malloc_error();
/* save g for charge */
x[j]->surface_charge->g[count_g].charge = s_x[i]->z;
if (x[j]->surface_charge->grams > 0.0) {
x[j]->surface_charge->g[count_g].g = 2 * alpha * sqrt(mu_x) * (pow(xd, s_x[i]->z / 2.0) - 1) *surface_charge_ptr->grams * surface_charge_ptr->specific_area / F_C_MOL;
x[j]->surface_charge->g[count_g].dg = -s_x[i]->z;
if ((use.surface_ptr->only_counter_ions == TRUE) &&
x[j]->surface_charge->g[count_g].g < 0) {
x[j]->surface_charge->g[count_g].g = 0;
x[j]->surface_charge->g[count_g].dg = 0;
}
} else {
x[j]->surface_charge->g[count_g].g = 0.0;
x[j]->surface_charge->g[count_g].dg = -s_x[i]->z;
}
/* save g for species */
s_x[i]->diff_layer[count_charge].charge = x[j]->surface_charge;
s_x[i]->diff_layer[count_charge].count_g = count_g;
s_x[i]->diff_layer[count_charge].g_moles = 0.0;
s_x[i]->diff_layer[count_charge].dg_g_moles = 0.0;
count_g++;
}
}
if (debug_diffuse_layer == TRUE) {
output_msg(OUTPUT_MESSAGE, "\nSurface component %d: charge,\tg,\tdg\n", count_charge);
for (i = 0; i < count_g; i++) {
output_msg(OUTPUT_MESSAGE, "\t%12f\t%12.4e\t%12.4e\n",
(double) x[j]->surface_charge->g[i].charge, (double) x[j]->surface_charge->g[i].g, (double) x[j]->surface_charge->g[i].dg );
}
}
count_charge++;
x[j]->surface_charge->count_g = count_g;
}
return (OK);
}
/* ---------------------------------------------------------------------- */
int initial_surface_water(void)
/* ---------------------------------------------------------------------- */
{
/*
* In initial surface calculation, need to calculate
* mass of water in diffuse layer.
* diffuse layer water + aqueous solution water = bulk water.
* Ionic strength is fixed, so diffuse-layer water will not change
*/
int i;
/*#define DEBYE*/
#ifdef DEBYE
LDBLE debye_length;
LDBLE volume_diffuse_layer;
#endif
LDBLE mass_water_surface;
/*
* Debye length = 1/k = sqrt[eta*eta_zero*R*T/(2*F**2*mu_x*1000)], Dzombak and Morel, p 36
*
* 1000 converts kJ to J; 1000 converts Liters to meter**3; debye_length is in meters.
*/
#ifdef DEBYE
debye_length = (EPSILON * EPSILON_ZERO * R_KJ_DEG_MOL * 1000.0 * tk_x)
/ (2. * F_C_MOL * F_C_MOL * mu_x * 1000.);
debye_length = sqrt(debye_length);
#endif
/*
* Loop through all surface components, calculate each H2O surface (diffuse layer),
* H2O aq, and H2O bulk (diffuse layers plus aqueous).
*/
mass_water_surfaces_x = 0.0;
for (i = 0; i < count_unknowns; i++) {
if (x[i]->type != SURFACE_CB) continue;
#ifdef DEBYE
/* 1000 converts volume from m**3 to Liters */
volume_diffuse_layer = x[i]->surface_charge->specific_area *
x[i]->surface_charge->grams * debye_length * 1000;
/* Assume mol/L = mol/kgw */
mass_water_surface = volume_diffuse_layer;
#else
/* make constant thickness of, default 1e-8 m (100 Angstroms) */
mass_water_surface = x[i]->surface_charge->specific_area *
x[i]->surface_charge->grams * use.surface_ptr->thickness * 1000;
#endif
x[i]->surface_charge->mass_water = mass_water_surface;
mass_water_surfaces_x += mass_water_surface;
}
mass_water_bulk_x = mass_water_aq_x + mass_water_surfaces_x;
return(OK);
}
/* ---------------------------------------------------------------------- */
int sum_diffuse_layer(struct surface_charge *surface_charge_ptr1)
/* ---------------------------------------------------------------------- */
{
int i, j, count_g;
LDBLE mass_water_surface;
LDBLE molality, moles_excess, moles_surface;
if (use.surface_ptr == NULL) return(OK);
/*
* Find position of component in list of components
*/
i = 0;
for (j =0; j < use.surface_ptr->count_charge; j++) {
if (&(use.surface_ptr->charge[j]) == surface_charge_ptr1) {
i = j;
break;
}
}
if (j >= use.surface_ptr->count_charge) {
sprintf(error_string, "In sum_diffuse_layer, component not found, %s.", surface_charge_ptr1->name);
error_msg(error_string, STOP);
}
/*
* Loop through all surface components, calculate each H2O surface (diffuse layer),
* H2O aq, and H2O bulk (diffuse layers plus aqueous).
*/
count_elts = 0;
paren_count = 0;
mass_water_surface = surface_charge_ptr1->mass_water;
for (j = 0; j < count_s_x; j++) {
if (s_x[j]->type > HPLUS) continue;
molality = under(s_x[j]->lm);
count_g = s_x[j]->diff_layer[i].count_g;
#ifdef SKIP
moles_excess = mass_water_bulk_x *
/* s_x[j]->diff_layer[i].charge->g[count_g].g * molality; */
surface_charge_ptr1->g[count_g].g * molality;
#endif
moles_excess = mass_water_aq_x * molality * surface_charge_ptr1->g[count_g].g;
moles_surface = mass_water_surface * molality + moles_excess;
/*
* Accumulate elements in diffuse layer
*/
add_elt_list(s_x[j]->next_elt, moles_surface);
}
add_elt_list(s_h2o->next_elt, mass_water_surface / gfw_water);
if (count_elts > 0 ) {
qsort (elt_list, (size_t) count_elts,
(size_t) sizeof(struct elt_list), elt_list_compare);
elt_list_combine();
}
return(OK);
}
/* ---------------------------------------------------------------------- */
int calc_all_donnan(void)
/* ---------------------------------------------------------------------- */
{
int i, j, k;
int count_g, count_charge, converge;
char name[MAX_LENGTH];
LDBLE new_g, f_psi, surf_chrg_eq, psi_avg, f_sinh, A_surf, ratio_aq;
LDBLE new_g2, f_psi2, surf_chrg_eq2, psi_avg2, dif;
if (use.surface_ptr == NULL) return(OK);
f_sinh = sqrt(8000.0 * EPSILON * EPSILON_ZERO * (R_KJ_DEG_MOL * 1000.0) * tk_x * mu_x);
/*
* calculate g for each surface...
*/
converge = TRUE;
count_charge = 0;
for (j = 0; j < count_unknowns; j++) {
if (x[j]->type != SURFACE_CB) continue;
surface_charge_ptr = x[j]->surface_charge;
if (debug_diffuse_layer == TRUE) output_msg(OUTPUT_MESSAGE, "Calc_all_g, X[%d]\n", j);
/*
* sum eq of each charge number in solution...
*/
count_g = x[j]->surface_charge->count_g;
for (i = 0; i < count_g; i++) {
charge_group[i].eq = 0.0;
}
for (i = 0; i < count_s_x; i++) {
if (s_x[i]->type > HPLUS) continue;
for (k = 0; k < count_g; k++) {
if (equal(charge_group[k].z, s_x[i]->z, G_TOL) == TRUE) {
charge_group[k].eq += s_x[i]->z * s_x[i]->moles;
break;
}
}
}
/* find surface charge from potential... */
A_surf = x[j]->surface_charge->specific_area * x[j]->surface_charge->grams;
f_psi = x[j]->master[0]->s->la * LOG_10;
surf_chrg_eq = A_surf * f_sinh * sinh(f_psi) / F_C_MOL;
/* also for the derivative... */
dif = 1e-5;
f_psi2 = f_psi + dif;
surf_chrg_eq2 = A_surf * f_sinh * sinh(f_psi2) / F_C_MOL;
/* find psi_avg that matches surface charge... */
psi_avg = calc_psi_avg(surf_chrg_eq);
psi_avg2 = calc_psi_avg(surf_chrg_eq2);
/* fill in g's */
ratio_aq = surface_charge_ptr->mass_water / mass_water_aq_x;
for (k = 0; k < count_g; k++) {
x[j]->surface_charge->g[k].charge = charge_group[k].z;
new_g = exp(-charge_group[k].z * psi_avg) - 1;
if (new_g <= - ratio_aq) new_g = G_TOL;
new_g2 = exp(-charge_group[k].z * psi_avg2) - 1;
if (new_g2 <= - ratio_aq) new_g2 = G_TOL;
if (fabs(new_g) >= 1) {
if (fabs((new_g - x[j]->surface_charge->g[k].g) / new_g) > convergence_tolerance) {
converge = FALSE;
}
} else {
if (fabs(new_g - x[j]->surface_charge->g[k].g) > convergence_tolerance) {
converge = FALSE;
}
}
x[j]->surface_charge->g[k].g = new_g;
if (new_g != 0) {
x[j]->surface_charge->g[k].dg = (new_g2 - new_g) / dif;
} else {
x[j]->surface_charge->g[k].dg = -charge_group[k].z;
}
/* save g for species */
for (i = 0; i < count_s_x; i++) {
if (equal(charge_group[k].z, s_x[i]->z, G_TOL) == TRUE) {
s_x[i]->diff_layer[count_charge].charge = x[j]->surface_charge;
s_x[i]->diff_layer[count_charge].count_g = k;
}
}
}
if (debug_diffuse_layer == TRUE) {
strcpy(name, x[j]->master[0]->elt->name);
replace ("_psi", "", name);
/* surf_chrg_eq = calc_surface_charge(name);
*/
output_msg(OUTPUT_MESSAGE, "\nDonnan all on %s (%d): charge, \tg, \tdg, Psi_surface = %8f V. \n", name, count_charge,
x[j]->master[0]->s->la * 2 * LOG_10 * R_KJ_DEG_MOL * tk_x / F_KJ_V_EQ);
for (i = 0; i < count_g; i++) {
output_msg(OUTPUT_MESSAGE, "\t%12f\t%12.4e\t%12.4e\n",
(double) x[j]->surface_charge->g[i].charge,
(double) x[j]->surface_charge->g[i].g,
(double) x[j]->surface_charge->g[i].dg);
}
}
count_charge++;
}
return (converge);
}
/* ---------------------------------------------------------------------- */
int calc_init_donnan(void)
/* ---------------------------------------------------------------------- */
{
int i, j, k;
int count_g, count_charge;
char name[MAX_LENGTH];
LDBLE f_psi, surf_chrg_eq, psi_avg, f_sinh, A_surf, ratio_aq;
if (use.surface_ptr == NULL) return(OK);
f_sinh = sqrt(8000.0 * EPSILON * EPSILON_ZERO * (R_KJ_DEG_MOL * 1000.0) * tk_x * mu_x);
/*
* sum eq of each charge number in solution...
*/
charge_group = (struct charge_group *) free_check_null(charge_group);
charge_group = (struct charge_group *) PHRQ_malloc((size_t) sizeof(struct charge_group));
if (charge_group == NULL) malloc_error();
charge_group[0].z = 0.0;
charge_group[0].eq = 0.0;
count_g = 1;
for (i = 0; i < count_s_x; i++) {
if (s_x[i]->type > HPLUS) continue;
for (k = 0; k < count_g; k++) {
if (equal(charge_group[k].z, s_x[i]->z, G_TOL) == TRUE) {
charge_group[k].eq += s_x[i]->z * s_x[i]->moles;
break;
}
}
if (k >= count_g) {
charge_group = (struct charge_group *) PHRQ_realloc(charge_group, (size_t) (count_g + 1) *
sizeof(struct charge_group));
if (charge_group == NULL) malloc_error();
charge_group[count_g].z = s_x[i]->z;
charge_group[count_g].eq = s_x[i]->z * s_x[i]->moles;
count_g++;
}
}
/*
* calculate g for each surface...
*/
count_charge = 0;
for (j = 0; j < count_unknowns; j++) {
if (x[j]->type != SURFACE_CB) continue;
surface_charge_ptr = x[j]->surface_charge;
x[j]->surface_charge->g = (struct surface_diff_layer *) PHRQ_malloc((size_t) count_g * sizeof(struct surface_diff_layer));
if (x[j]->surface_charge->g == NULL) malloc_error();
x[j]->surface_charge->count_g = count_g;
/* find surface charge from potential... */
A_surf = x[j]->surface_charge->specific_area * x[j]->surface_charge->grams;
f_psi = x[j]->master[0]->s->la * LOG_10;
surf_chrg_eq = A_surf * f_sinh * sinh(f_psi) / F_C_MOL;
/* find psi_avg that matches surface charge... */
psi_avg = calc_psi_avg(surf_chrg_eq);
/* fill in g's */
ratio_aq = surface_charge_ptr->mass_water / mass_water_aq_x;
for (k = 0; k < count_g; k++) {
x[j]->surface_charge->g[k].charge = charge_group[k].z;
x[j]->surface_charge->g[k].g = exp(-charge_group[k].z * psi_avg) - 1;
if (x[j]->surface_charge->g[k].g != 0) {
x[j]->surface_charge->g[k].dg = - A_surf * f_sinh * cosh(f_psi) /
(charge_group[k].eq * F_C_MOL);
} else {
x[j]->surface_charge->g[k].dg = -charge_group[k].z;
}
/* save g for species */
for (i = 0; i < count_s_x; i++) {
if (equal(charge_group[k].z, s_x[i]->z, G_TOL) == TRUE) {
s_x[i]->diff_layer[count_charge].charge = x[j]->surface_charge;
s_x[i]->diff_layer[count_charge].count_g = k;
s_x[i]->diff_layer[count_charge].g_moles = 0.0;
s_x[i]->diff_layer[count_charge].dg_g_moles = 0.0;
}
}
}
if (debug_diffuse_layer == TRUE) {
strcpy(name, x[j]->master[0]->elt->name);
replace ("_psi", "", name);
/* surf_chrg_eq = calc_surface_charge(name);
*/
output_msg(OUTPUT_MESSAGE, "\nDonnan init on %s : charge, \tg, \tdg, Psi_surface = %8f V. \n", name,
x[j]->master[0]->s->la * 2 * LOG_10 * R_KJ_DEG_MOL * tk_x / F_KJ_V_EQ);
for (i = 0; i < count_g; i++) {
output_msg(OUTPUT_MESSAGE, "\t%12f\t%12.4e\t%12.4e\n",
(double) x[j]->surface_charge->g[i].charge, (double) x[j]->surface_charge->g[i].g, (double) x[j]->surface_charge->g[i].dg );
}
}
count_charge++;
}
return (OK);
}
/* ---------------------------------------------------------------------- */
LDBLE calc_psi_avg(LDBLE surf_chrg_eq)
/* ---------------------------------------------------------------------- */
{
/*
* calculate the average (F * Psi / RT) that lets the DL charge counter the surface charge
*/
int i, iter, count_g;
LDBLE fd, fd1, p, temp, ratio_aq;
/* LDBLE dif;
*/
count_g = surface_charge_ptr->count_g;
if (convergence_tolerance >= 1e-8) {
G_TOL = 1e-9;
} else {
G_TOL = 1e-10;
}
ratio_aq = surface_charge_ptr->mass_water / mass_water_aq_x;
p = 0;
if (surf_chrg_eq == 0) {
return(0.0);
} else if (surf_chrg_eq < 0) {
p = -0.5 * log(-surf_chrg_eq * ratio_aq / mu_x + 1);
} else if (surf_chrg_eq > 0) {
p = 0.5 * log(surf_chrg_eq * ratio_aq / mu_x + 1);
}
/*
* Optimize p in SS{s_x[i]->moles * z_i * g(p)} = -surf_chrg_eq
* g(p) = exp(-p * z_i) - 1
*/
iter = 0;
do {
fd = surf_chrg_eq;
fd1 = 0.0;
for (i = 1; i < count_g; i++) {
temp = exp(-charge_group[i].z * p);
if (temp > 1 - ratio_aq) {
fd += charge_group[i].eq * (temp - 1);
fd1 -= charge_group[i].z * charge_group[i].eq * temp;
}
}
/* fd1 = surf_chrg_eq * ratio_aq;
dif = 1e-5;
p += dif;
for (i = 1; i < count_g; i++) {
temp = exp(-charge_group[i].z * p);
fd1 += charge_group[i].eq * temp;
}
fd /= -(fd1 - fd) / dif;
p -= dif;
p += (fd > 1) ? 1 : ((fd < -1) ? -1 : fd);
*/
fd /= -fd1;
p += (fd > 1) ? 1 : ((fd < -1) ? -1 : fd);
if (fabs(p) < G_TOL) p = 0.0;
iter++;
if (iter > 50) {
sprintf(error_string, "\nToo many iterations for surface in subroutine calc_psi_avg.\n");
error_msg(error_string, STOP);
}
} while (fabs(fd) > G_TOL && p != 0.0);
if (debug_diffuse_layer == TRUE)
output_msg(OUTPUT_MESSAGE, "iter in calc_psi_avg = %d. g(+1) = %8f. surface charge = %8f.\n",
iter, (double) (exp(-p) - 1), (double) surf_chrg_eq);
return(p);
}

3014
inverse.cpp
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1540
isotopes.cpp
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2288
kinetics.cpp
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140
main.cpp
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@ -1,140 +0,0 @@
#define EXTERNAL
#include "global.h"
#include "output.h"
#include "phrqproto.h"
#include "input.h"
/*#define PHREEQC_XML*/
#ifdef PHREEQC_XML
#include "SAXPhreeqc.h"
extern void SAX_cleanup(void);
#endif
static char const svnid[] = "$Id: main.c 715 2006-01-18 01:26:29Z dlpark $";
#ifdef DOS
static int write_banner(void);
#endif
/* ----------------------------------------------------------------------
* MAIN
* ---------------------------------------------------------------------- */
int main(int argc, char *argv[])
/*
* Main program for PHREEQC
*/
{
int errors;
void *db_cookie = NULL;
void *input_cookie = NULL;
if (svnid == NULL) fprintf(stderr," ");
phast = FALSE;
/*
* Add callbacks for error_msg and warning_msg
*/
if (add_output_callback(phreeqc_handler, NULL) != OK) {
fprintf(stderr, "ERROR: %s\n", "NULL pointer returned from malloc or realloc.");
fprintf(stderr, "ERROR: %s\n", "Program terminating.");
return -1;
}
/*
* Open input/output files
*/
errors = process_file_names(argc, argv, &db_cookie, &input_cookie, TRUE);
if (errors != 0) {
clean_up();
return errors;
}
#ifdef DOS
write_banner();
#endif
/*
* Initialize arrays
*/
errors = do_initialize();
if (errors != 0) {
clean_up();
return errors;
}
/*
* Load database into memory
*/
errors = read_database(getc_callback, db_cookie);
if (errors != 0) {
clean_up();
return errors;
}
/*
* Read input data for simulation
*/
errors = run_simulations(getc_callback, input_cookie);
if (errors != 0) {
clean_up();
return errors;
}
/*
* Display successful status
*/
errors = do_status();
if (errors != 0) {
clean_up();
return errors;
}
#ifdef PHREEQC_XML
{
int n;
SAX_StartSystem();
for (n = 0; n < count_solution; ++n)
{
SAX_AddSolution(solution[n]);
}
SAX_EndSystem();
SAX_UnpackSolutions(SAX_GetXMLStr(), SAX_GetXMLLength());
}
#endif
clean_up();
close_input_files();
close_output_files();
#ifdef PHREEQC_XML
SAX_cleanup();
#endif
return 0;
}
/* ---------------------------------------------------------------------- */
int write_banner(void)
/* ---------------------------------------------------------------------- */
{
char buffer[80];
int len, indent;
output_msg(OUTPUT_SCREEN, " ÛßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßßÛ\n");
output_msg(OUTPUT_SCREEN, " º º\n");
/* version */
len = sprintf(buffer, "* PHREEQC-%s *", "@VERSION@");
indent = (44 - len) / 2;
output_msg(OUTPUT_SCREEN, "%14cº%*c%s%*cº\n", ' ', indent, ' ', buffer, 44 - indent - len, ' ');
output_msg(OUTPUT_SCREEN, " º º\n");
output_msg(OUTPUT_SCREEN, " º A hydrogeochemical transport model º\n");
output_msg(OUTPUT_SCREEN, " º º\n");
output_msg(OUTPUT_SCREEN, " º by º\n");
output_msg(OUTPUT_SCREEN, " º D.L. Parkhurst and C.A.J. Appelo º\n");
output_msg(OUTPUT_SCREEN, " º º\n");
/* date */
len = sprintf(buffer, "%s", "@VER_DATE@");
indent = (44 - len) / 2;
output_msg(OUTPUT_SCREEN, "%14cº%*c%s%*cº\n", ' ', indent, ' ', buffer, 44 - indent - len, ' ');
output_msg(OUTPUT_SCREEN, " ÛÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÜÛ\n\n");
return 0;
}

2486
mainsubs.cpp
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3102
model.cpp
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193
nvector.cpp
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@ -1,193 +0,0 @@
/*******************************************************************
* *
* File : nvector.c *
* Programmers : Radu Serban, LLNL *
* Version of : 26 June 2002 *
*-----------------------------------------------------------------*
* Copyright (c) 2002, The Regents of the University of California *
* Produced at the Lawrence Livermore National Laboratory *
* All rights reserved *
* For details, see sundials/shared/LICENSE *
*-----------------------------------------------------------------*
* This is the implementation file for a generic NVECTOR *
* package. It contains the implementation of the N_Vector *
* kernels listed in nvector.h. *
* *
*******************************************************************/
#include "nvector.h" /* generic M_Env and N_Vector */
#include "output.h"
static char const svnid[] = "$Id: nvector.c 78 2005-02-01 22:47:12Z dlpark $";
N_Vector N_VNew(integertype n, M_Env machEnv)
{
N_Vector v_new;
v_new = machEnv->ops->nvnew(n, machEnv);
return(v_new);
}
N_Vector_S N_VNew_S(integertype ns, integertype n, M_Env machEnv)
{
N_Vector_S vs_new;
vs_new = machEnv->ops->nvnewS(ns, n, machEnv);
return(vs_new);
}
void N_VFree(N_Vector v)
{
v->menv->ops->nvfree(v);
}
void N_VFree_S(integertype ns, N_Vector_S vs)
{
(*vs)->menv->ops->nvfreeS(ns, vs);
}
N_Vector N_VMake(integertype n, realtype *v_data, M_Env machEnv)
{
N_Vector v_new;
v_new = machEnv->ops->nvmake(n, v_data, machEnv);
return(v_new);
}
void N_VDispose(N_Vector v)
{
v->menv->ops->nvdispose(v);
}
realtype *N_VGetData(N_Vector v)
{
realtype *data;
data = v->menv->ops->nvgetdata(v);
return(data);
}
void N_VSetData(realtype *v_data, N_Vector v)
{
v->menv->ops->nvsetdata(v_data, v);
}
void N_VLinearSum(realtype a, N_Vector x, realtype b, N_Vector y, N_Vector z)
{
z->menv->ops->nvlinearsum(a, x, b, y, z);
}
void N_VConst(realtype c, N_Vector z)
{
z->menv->ops->nvconst(c, z);
}
void N_VProd(N_Vector x, N_Vector y, N_Vector z)
{
z->menv->ops->nvprod(x, y, z);
}
void N_VDiv(N_Vector x, N_Vector y, N_Vector z)
{
z->menv->ops->nvdiv(x, y, z);
}
void N_VScale(realtype c, N_Vector x, N_Vector z)
{
z->menv->ops->nvscale(c, x, z);
}
void N_VAbs(N_Vector x, N_Vector z)
{
z->menv->ops->nvabs(x, z);
}
void N_VInv(N_Vector x, N_Vector z)
{
z->menv->ops->nvinv(x, z);
}
void N_VAddConst(N_Vector x, realtype b, N_Vector z)
{
z->menv->ops->nvaddconst(x, b, z);
}
realtype N_VDotProd(N_Vector x, N_Vector y)
{
realtype prod;
prod = y->menv->ops->nvdotprod(x, y);
return(prod);
}
realtype N_VMaxNorm(N_Vector x)
{
realtype norm;
norm = x->menv->ops->nvmaxnorm(x);
return(norm);
}
realtype N_VWrmsNorm(N_Vector x, N_Vector w)
{
realtype norm;
norm = x->menv->ops->nvwrmsnorm(x, w);
return(norm);
}
realtype N_VMin(N_Vector x)
{
realtype minval;
minval = x->menv->ops->nvmin(x);
return(minval);
}
realtype N_VWL2Norm(N_Vector x, N_Vector w)
{
realtype norm;
norm = x->menv->ops->nvwl2norm(x, w);
return(norm);
}
realtype N_VL1Norm(N_Vector x)
{
realtype norm;
norm = x->menv->ops->nvl1norm(x);
return(norm);
}
void N_VOneMask(N_Vector x)
{
x->menv->ops->nvonemask(x);
}
void N_VCompare(realtype c, N_Vector x, N_Vector z)
{
z->menv->ops->nvcompare(c, x, z);
}
booleantype N_VInvTest(N_Vector x, N_Vector z)
{
booleantype flag;
flag = z->menv->ops->nvinvtest(x, z);
return(flag);
}
booleantype N_VConstrProdPos(N_Vector c, N_Vector x)
{
booleantype flag;
flag = x->menv->ops->nvconstrprodpos(c, x);
return(flag);
}
booleantype N_VConstrMask(N_Vector c, N_Vector x, N_Vector m)
{
booleantype flag;
flag = x->menv->ops->nvconstrmask(c, x, m);
return(flag);
}
realtype N_VMinQuotient(N_Vector num, N_Vector denom)
{
realtype quotient;
quotient = num->menv->ops->nvminquotient(num, denom);
return(quotient);
}
void N_VPrint(N_Vector x)
{
x->menv->ops->nvprint(x);
}

441
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@ -1,441 +0,0 @@
/*******************************************************************
* *
* File : nvector.h *
* Programmers : Radu Serban, LLNL *
* Version of : 26 June 2002 *
*-----------------------------------------------------------------*
* Copyright (c) 2002, The Regents of the University of California *
* Produced at the Lawrence Livermore National Laboratory *
* All rights reserved *
* For details, see sundials/shared/LICENSE *
*-----------------------------------------------------------------*
* This is the header file for a generic NVECTOR package. *
* It defines the N_Vector and M_Env structures: *
* M_Env has an implementation-dependent 'content' field *
* which contains the data needed to generate a new *
* nvector in that implementation and an 'ops' filed *
* which is a structure listing operations acting on *
* such nvectors. *
* N_Vector has an implementation-dependent 'content' field *
* which contains the description and actual data of *
* the nvector and a 'menv' field which points to the *
* M_Env structure used in creating the nvector. *
* *
* Part I of this file contains type declarations for the *
* the following structures: _generic_M_Env, _generic_N_Vector, *
* and _generic_N_Vector_Ops, as well as references to pointers *
* to such structures (M_Env and N_Vector). *
* *
* Part II of this file contains the prototypes for the vector *
* kernels which operate on N_Vector. *
* *
* A particular implementation of an NVECTOR package must then *
* specify the 'content' fields of M_Env and N_Vector, define *
* the propotypes for kernel operations on those N_Vectors *
* (NOTE: kernel routine names must be unique to that *
* implementation), and finally provide an initialization *
* routine (which generates an M_Env with that particular *
* 'content' field and links the defined vector kernel routines *
* into the 'ops' field). *
* *
*******************************************************************/
#ifdef PHREEQC_IDENT
static char const svnidnvector[] = "$Id$";
#endif
#ifdef __cplusplus /* wrapper to enable C++ usage */
extern "C" {
#endif
#ifndef included_nvector_h
#define included_nvector_h
#include "sundialstypes.h" /* definition of types */
/****************************************************************
* Generic definitions of machine environment and N_Vector *
****************************************************************/
/* Forward reference for pointer to N_Vector_Ops object */
typedef struct _generic_N_Vector_Ops *N_Vector_Ops;
/* Forward reference for pointer to M_Env object */
typedef struct _generic_M_Env *M_Env;
/* Forward reference for pointer to N_Vector object */
typedef struct _generic_N_Vector *N_Vector;
/* Define array of N_Vectors */
typedef N_Vector *N_Vector_S;
/* Structure containing function pointers to vector operations */
struct _generic_N_Vector_Ops {
N_Vector (*nvnew)(integertype, M_Env);
N_Vector_S (*nvnewS)(integertype, integertype, M_Env);
void (*nvfree)(N_Vector);
void (*nvfreeS)(integertype, N_Vector_S);
N_Vector (*nvmake)(integertype, realtype *, M_Env);
void (*nvdispose)(N_Vector);
realtype* (*nvgetdata)(N_Vector);
void (*nvsetdata)(realtype *, N_Vector);
void (*nvlinearsum)(realtype, N_Vector, realtype, N_Vector, N_Vector);
void (*nvconst)(realtype, N_Vector);
void (*nvprod)(N_Vector, N_Vector, N_Vector);
void (*nvdiv)(N_Vector, N_Vector, N_Vector);
void (*nvscale)(realtype, N_Vector, N_Vector);
void (*nvabs)(N_Vector, N_Vector);
void (*nvinv)(N_Vector, N_Vector);
void (*nvaddconst)(N_Vector, realtype, N_Vector);
realtype (*nvdotprod)(N_Vector, N_Vector);
realtype (*nvmaxnorm)(N_Vector);
realtype (*nvwrmsnorm)(N_Vector, N_Vector);
realtype (*nvmin)(N_Vector);
realtype (*nvwl2norm)(N_Vector, N_Vector);
realtype (*nvl1norm)(N_Vector);
void (*nvonemask)(N_Vector);
void (*nvcompare)(realtype, N_Vector, N_Vector);
booleantype (*nvinvtest)(N_Vector, N_Vector);
booleantype (*nvconstrprodpos)(N_Vector, N_Vector);
booleantype (*nvconstrmask)(N_Vector, N_Vector, N_Vector);
realtype (*nvminquotient)(N_Vector, N_Vector);
void (*nvprint)(N_Vector);
};
/* A machine environment is a structure with an implementation
dependent 'content' representation (used to generate a new vector
in that implementation), a set of operations defined in the above
structure, and an ID tag */
struct _generic_M_Env {
void *content;
struct _generic_N_Vector_Ops *ops;
char tag[8];
};
/* A vector is a structure with an implementation dependent content
representation and a pointer to the machine environment
corresponding to that implementation */
struct _generic_N_Vector {
void *content;
struct _generic_M_Env *menv;
};
/****************************************************************
* Functions exported by nvector *
****************************************************************/
/*--------------------------------------------------------------*
* Function : N_VNew *
* Usage : v = N_VNew(n, machEnv); *
*--------------------------------------------------------------*
* Returns a new N_Vector of length n. The parameter machEnv *
* is a pointer to machine environment-specific information. *
* If there is not enough memory for a new N_Vector, then *
* N_VNew returns NULL. *
*--------------------------------------------------------------*/
N_Vector N_VNew(integertype n, M_Env machEnv);
/*--------------------------------------------------------------*
* Function : N_VNew_S *
* Usage : v = N_VNew_S(ns, n, machEnv); *
*--------------------------------------------------------------*
* Returns an array of ns new N_Vectors of length n. The *
* parameter machEnv is a pointer to machine environment *
* specific information. *
* If there is not enough memory for a new array of N_Vectors *
* or for one of the components, then N_VNew_S returns NULL. *
*--------------------------------------------------------------*/
N_Vector_S N_VNew_S(integertype ns, integertype n, M_Env machEnv);
/*--------------------------------------------------------------*
* Function : N_VFree *
* Usage : N_VFree(v); *
*--------------------------------------------------------------*
* Frees the N_Vector v. It is illegal to use v after the call *
* N_VFree(v). *
*--------------------------------------------------------------*/
void N_VFree(N_Vector v);
/*--------------------------------------------------------------*
* Function : N_VFree_S *
* Usage : N_VFree_S(ns, vs); *
*--------------------------------------------------------------*
* Frees the array of ns N_Vectors vs. *
* It is illegal to use vs after the call N_VFree_S(Ns,vs). *
*--------------------------------------------------------------*/
void N_VFree_S(integertype ns, N_Vector_S vs);
/*--------------------------------------------------------------*
* Function : N_VMake *
* Usage : v = N_VMake(n, v_data, machEnv); *
*--------------------------------------------------------------*
* Creates an N_Vector with component array data allocated by *
* the user. *
*--------------------------------------------------------------*/
N_Vector N_VMake(integertype n, realtype *v_data, M_Env machEnv);
/*--------------------------------------------------------------*
* Function : N_VDispose *
* Usage : N_VDispose(v); *
*--------------------------------------------------------------*
* Destroys an N_Vector with component array data allocated by *
* the user. *
*--------------------------------------------------------------*/
void N_VDispose(N_Vector v);
/*--------------------------------------------------------------*
* Function : N_VGetData *
* Usage : v_data = N_VGetData(v); *
*--------------------------------------------------------------*
* Extracts the data component array from the N_Vector v. *
* Note: this routine is used in the solver-specific interfaces *
* to the dense and banded linear solvers, as well as the *
* interfaces to the banded preconditioners provided with *
* SUNDIALS. It needs not be implemented by a user *
* defined NVECTOR module, if these linear solvers are not*
* used. *
*--------------------------------------------------------------*/
realtype *N_VGetData(N_Vector v);
/*--------------------------------------------------------------*
* Function : N_VSetData *
* Usage : N_VSetData(v_data, v); *
*--------------------------------------------------------------*
* Attaches the data component array v_data to the N_Vector v. *
* Note: this routine is used in the solver-specific interfaces *
* to the dense and banded linear solvers, as well as the *
* interfaces to the banded preconditioners provided with *
* SUNDIALS. It needs not be implemented by a user *
* defined NVECTOR module, if these linear solvers are not*
* used. *
*--------------------------------------------------------------*/
void N_VSetData(realtype *v_data, N_Vector v);
/*--------------------------------------------------------------*
* Function : N_VLinearSum *
* Operation : z = a x + b y *
*--------------------------------------------------------------*/
void N_VLinearSum(realtype a, N_Vector x, realtype b, N_Vector y,
N_Vector z);
/*--------------------------------------------------------------*
* Function : N_VConst *
* Operation : z[i] = c for i=0, 1, ..., N-1 *
*--------------------------------------------------------------*/
void N_VConst(realtype c, N_Vector z);
/*--------------------------------------------------------------*
* Function : N_VProd *
* Operation : z[i] = x[i] * y[i] for i=0, 1, ..., N-1 *
*--------------------------------------------------------------*/
void N_VProd(N_Vector x, N_Vector y, N_Vector z);
/*--------------------------------------------------------------*
* Function : N_VDiv *
* Operation : z[i] = x[i] / y[i] for i=0, 1, ..., N-1 *
*--------------------------------------------------------------*/
void N_VDiv(N_Vector x, N_Vector y, N_Vector z);
/*--------------------------------------------------------------*
* Function : N_VScale *
* Operation : z = c x *
*--------------------------------------------------------------*/
void N_VScale(realtype c, N_Vector x, N_Vector z);
/*--------------------------------------------------------------*
* Function : N_VAbs *
* Operation : z[i] = |x[i]|, for i=0, 1, ..., N-1 *
*--------------------------------------------------------------*/
void N_VAbs(N_Vector x, N_Vector z);
/*--------------------------------------------------------------*
* Function : N_VInv *
* Operation : z[i] = 1.0 / x[i] for i = 0, 1, ..., N-1 *
*--------------------------------------------------------------*
* This routine does not check for division by 0. It should be *
* called only with an N_Vector x which is guaranteed to have *
* all non-zero components. *
*--------------------------------------------------------------*/
void N_VInv(N_Vector x, N_Vector z);
/*--------------------------------------------------------------*
* Function : N_VAddConst *
* Operation : z[i] = x[i] + b for i = 0, 1, ..., N-1 *
*--------------------------------------------------------------*/
void N_VAddConst(N_Vector x, realtype b, N_Vector z);
/*--------------------------------------------------------------*
* Function : N_VDotProd *
* Usage : dotprod = N_VDotProd(x, y); *
*--------------------------------------------------------------*
* Returns the value of the ordinary dot product of x and y: *
* -> sum (i=0 to N-1) {x[i] * y[i]} *
* Returns 0.0 if N <= 0. *
*--------------------------------------------------------------*/
realtype N_VDotProd(N_Vector x, N_Vector y);
/*--------------------------------------------------------------*
* Function : N_VMaxNorm *
* Usage : maxnorm = N_VMaxNorm(x); *
*--------------------------------------------------------------*
* Returns the maximum norm of x: *
* -> max (i=0 to N-1) |x[i]| *
* Returns 0.0 if N <= 0. *
*--------------------------------------------------------------*/
realtype N_VMaxNorm(N_Vector x);
/*--------------------------------------------------------------*
* Function : N_VWrmsNorm *
* Usage : wrmsnorm = N_VWrmsNorm(x, w); *
*--------------------------------------------------------------*
* Returns the weighted root mean square norm of x with *
* weight vector w: *
* -> sqrt [(sum (i=0 to N-1) {(x[i] * w[i])^2}) / N] *
* Returns 0.0 if N <= 0. *
*--------------------------------------------------------------*/
realtype N_VWrmsNorm(N_Vector x, N_Vector w);
/*--------------------------------------------------------------*
* Function : N_VMin *
* Usage : min = N_VMin(x); *
*--------------------------------------------------------------*
* Returns the smallest element of x: *
* -> min (i=0 to N-1) x[i] *
* Returns 0.0 if N <= 0. *
*--------------------------------------------------------------*/
realtype N_VMin(N_Vector x);
/*--------------------------------------------------------------*
* Function : N_VWL2Norm *
* Usage : wl2norm = N_VWL2Norm(x, w); *
*--------------------------------------------------------------*
* Returns the weighted Euclidean L2 norm of x with *
* weight vector w: *
* -> sqrt [(sum (i=0 to N-1) {(x[i] * w[i])^2}) ] *
* Returns 0.0 if N <= 0. *
*--------------------------------------------------------------*/
realtype N_VWL2Norm(N_Vector x, N_Vector w);
/*--------------------------------------------------------------*
* Function : N_VL1Norm *
* Usage : l1norm = N_VL1Norm(x); *
*--------------------------------------------------------------*
* Returns the L1 norm of x: *
* -> sum (i=0 to N-1) {ABS(x[i])} *
* Returns 0.0 if N <= 0. *
*--------------------------------------------------------------*/
realtype N_VL1Norm(N_Vector x);
/*--------------------------------------------------------------*
* Function : N_VOneMask *
* Operation : x[i] = 1.0 if |x[i]| != 0. i = 0, 1, ..., N-1 *
* 0.0 otherwise *
*--------------------------------------------------------------*/
void N_VOneMask(N_Vector x);
/*--------------------------------------------------------------*
* Function : N_VCompare *
* Operation : z[i] = 1.0 if |x[i]| >= c i = 0, 1, ..., N-1 *
* 0.0 otherwise *
*--------------------------------------------------------------*/
void N_VCompare(realtype c, N_Vector x, N_Vector z);
/*--------------------------------------------------------------*
* Function : N_VInvTest *
* Operation : z[i] = 1.0 / x[i] with a test for x[i]==0.0 *
* before inverting x[i]. *
*--------------------------------------------------------------*
* This routine returns TRUE if all components of x are *
* non-zero (successful inversion) and returns FALSE *
* otherwise. *
*--------------------------------------------------------------*/
booleantype N_VInvTest(N_Vector x, N_Vector z);
/*--------------------------------------------------------------*
* Function : N_VConstrProdPos *
* Usage : booltest = N_VConstrProdPos(c,x); *
*--------------------------------------------------------------*
* Returns a boolean equal to *
* FALSE if some c[i] != 0.0 and x[i]*c[i] <= 0.0, or *
* TRUE otherwise. *
* *
* This routine is used for constraint checking. *
*--------------------------------------------------------------*/
booleantype N_VConstrProdPos(N_Vector c, N_Vector x);
/*--------------------------------------------------------------*
* Function : N_VConstrMask *
* Operation : m[i] = 1.0 if constraint test fails for x[i] *
* m[i] = 0.0 if constraint test passes for x[i] *
* where the constraint tests are as follows: *
* If c[i] = 2.0, then x[i] must be > 0.0. *
* If c[i] = 1.0, then x[i] must be >= 0.0. *
* If c[i] = -1.0, then x[i] must be <= 0.0. *
* If c[i] = -2.0, then x[i] must be < 0.0. *
*--------------------------------------------------------------*
* This routine returns a boolean FALSE if any element failed *
* the constraint test, TRUE if all passed. It also sets a *
* mask vector m, with elements equal to 1.0 where the *
* corresponding constraint test failed, and equal to 0.0 *
* where the constraint test passed. *
* This routine is specialized in that it is used only for *
* constraint checking. *
*--------------------------------------------------------------*/
booleantype N_VConstrMask(N_Vector c, N_Vector x, N_Vector m);
/*--------------------------------------------------------------*
* Function : N_VMinQuotient *
* Operation : minq = min ( num[i]/denom[i]) over all i such *
* that denom[i] != 0. *
*--------------------------------------------------------------*
* This routine returns the minimum of the quotients obtained *
* by term-wise dividing num[i] by denom[i]. A zero element *
* in denom will be skipped. If no such quotients are found, *
* then the large value 1.e99 is returned. *
*--------------------------------------------------------------*/
realtype N_VMinQuotient(N_Vector num, N_Vector denom);
/*--------------------------------------------------------------*
* Function : N_VPrint *
* Usage : N_VPrint(x); *
*--------------------------------------------------------------*
* Prints the N_Vector x to stdout. *
* This routine is provided as an aid in debugging code which *
* uses this vector package. *
*--------------------------------------------------------------*/
void N_VPrint(N_Vector x);
#endif
#ifdef __cplusplus
}
#endif

869
nvector_serial.cpp
View File

@ -1,869 +0,0 @@
/*******************************************************************
* *
* File : nvector_serial.c *
* Programmers : Scott D. Cohen, Alan C. Hindmarsh, *
* Radu Serban, and Allan G. Taylor, LLNL *
* Version of : 26 June 2002 *
*-----------------------------------------------------------------*
* Copyright (c) 2002, The Regents of the University of California *
* Produced at the Lawrence Livermore National Laboratory *
* All rights reserved *
* For details, see sundials/shared/LICENSE *
*-----------------------------------------------------------------*
* This is the implementation file for a serial implementation *
* of the NVECTOR package. It contains the implementation of *
* the serial machine environment intialization and free *
* routines (and of the Fortran callable interfaces to them) *
* and of the N_Vector kernels listed in nvector_serial.h. *
* *
*******************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "nvector_serial.h"
#include "sundialstypes.h"
#include "sundialsmath.h"
#include "output.h"
#include "phqalloc.h"
/* WARNING don't include any headers below here */
#define malloc PHRQ_malloc
static char const svnid[] = "$Id: nvector_serial.c 663 2005-11-16 00:46:04Z dlpark $";
#define ZERO RCONST(0.0)
#define HALF RCONST(0.5)
#define ONE RCONST(1.0)
#define ONEPT5 RCONST(1.5)
/* Private Helper Prototypes */
/* z=x */
static void VCopy_Serial(N_Vector x, N_Vector z);
/* z=x+y */
static void VSum_Serial(N_Vector x, N_Vector y, N_Vector z);
/* z=x-y */
static void VDiff_Serial(N_Vector x, N_Vector y, N_Vector z);
/* z=-x */
static void VNeg_Serial(N_Vector x, N_Vector z);
/* z=c(x+y) */
static void VScaleSum_Serial(realtype c, N_Vector x, N_Vector y, N_Vector z);
/* z=c(x-y) */
static void VScaleDiff_Serial(realtype c, N_Vector x, N_Vector y, N_Vector z);
/* z=ax+y */
static void VLin1_Serial(realtype a, N_Vector x, N_Vector y, N_Vector z);
/* z=ax-y */
static void VLin2_Serial(realtype a, N_Vector x, N_Vector y, N_Vector z);
/* y <- ax+y */
static void Vaxpy_Serial(realtype a, N_Vector x, N_Vector y);
/* x <- ax */
static void VScaleBy_Serial(realtype a, N_Vector x);
/********************* Exported Functions ************************/
/* Serial implementation of the machine environment
initialization routine */
M_Env M_EnvInit_Serial(integertype vec_length)
{
M_Env me;
if (svnid == NULL) fprintf(stderr," ");
/* Create machine environment structure */
me = (M_Env) malloc(sizeof *me);
if (me == NULL) return(NULL);
/* Create serial content of machine environment structure */
me->content = (M_EnvSerialContent) malloc(sizeof(struct _M_EnvSerialContent));
if (me->content == NULL) {
free(me);
return(NULL);
}
/* Load serial content of machine environment structure */
ME_CONTENT_S(me)->length = vec_length;
/* Attach vector operations */
me->ops = (N_Vector_Ops) malloc(sizeof(struct _generic_N_Vector_Ops));
if (me->ops == NULL) {
free(me->content);
free(me);
return(NULL);
}
me->ops->nvnew = N_VNew_Serial;
me->ops->nvnewS = N_VNew_S_Serial;
me->ops->nvfree = N_VFree_Serial;
me->ops->nvfreeS = N_VFree_S_Serial;
me->ops->nvmake = N_VMake_Serial;
me->ops->nvdispose = N_VDispose_Serial;
me->ops->nvgetdata = N_VGetData_Serial;
me->ops->nvsetdata = N_VSetData_Serial;
me->ops->nvlinearsum = N_VLinearSum_Serial;
me->ops->nvconst = N_VConst_Serial;
me->ops->nvprod = N_VProd_Serial;
me->ops->nvdiv = N_VDiv_Serial;
me->ops->nvscale = N_VScale_Serial;
me->ops->nvabs = N_VAbs_Serial;
me->ops->nvinv = N_VInv_Serial;
me->ops->nvaddconst = N_VAddConst_Serial;
me->ops->nvdotprod = N_VDotProd_Serial;
me->ops->nvmaxnorm = N_VMaxNorm_Serial;
me->ops->nvwrmsnorm = N_VWrmsNorm_Serial;
me->ops->nvmin = N_VMin_Serial;
me->ops->nvwl2norm = N_VWL2Norm_Serial;
me->ops->nvl1norm = N_VL1Norm_Serial;
me->ops->nvonemask = N_VOneMask_Serial;
me->ops->nvcompare = N_VCompare_Serial;
me->ops->nvinvtest = N_VInvTest_Serial;
me->ops->nvconstrprodpos = N_VConstrProdPos_Serial;
me->ops->nvconstrmask = N_VConstrMask_Serial;
me->ops->nvminquotient = N_VMinQuotient_Serial;
me->ops->nvprint = N_VPrint_Serial;
/* Attach ID tag */
strcpy(me->tag, ID_TAG_S);
return(me);
}
/* Serial implementation of the machine environment
free routine */
void M_EnvFree_Serial(M_Env machEnv)
{
if (machEnv == NULL) return;
free(machEnv->content);
free(machEnv->ops);
free(machEnv);
}
/***************************************************************************/
/* BEGIN implementation of vector operations */
N_Vector N_VNew_Serial(integertype n, M_Env machEnv)
{
N_Vector v;
integertype length;
if (n <= 0) return(NULL);
if (machEnv == NULL) return(NULL);
v = (N_Vector) malloc(sizeof *v);
if (v == NULL) return(NULL);
v->content = (N_VectorSerialContent) malloc(sizeof(struct _N_VectorSerialContent));
if (v->content == NULL) {
free(v);
return(NULL);
}
length = ME_CONTENT_S(machEnv)->length;
NV_CONTENT_S(v)->data = (realtype *) malloc(length * sizeof(realtype));
if(NV_CONTENT_S(v)->data == NULL) {
free(v->content);
free(v);
return(NULL);
}
NV_CONTENT_S(v)->length = length;
v->menv = machEnv;
return(v);
}
N_Vector_S N_VNew_S_Serial(integertype ns, integertype n, M_Env machEnv)
{
N_Vector_S vs;
integertype is, j;
if (ns <= 0 || n <= 0) return(NULL);
if (machEnv == NULL) return(NULL);
vs = (N_Vector_S) malloc(ns * sizeof(N_Vector *));
if (vs == NULL) return(NULL);
for (is=0; is<ns; is++) {
vs[is] = N_VNew_Serial(n, machEnv);
if (vs[is] == NULL) {
for (j=0; j<is; j++) N_VFree_Serial(vs[j]);
free(vs);
return(NULL);
}
}
return(vs);
}
void N_VFree_Serial(N_Vector v)
{
free(NV_DATA_S(v));
free(NV_CONTENT_S(v));
free(v);
}
void N_VFree_S_Serial(integertype ns, N_Vector_S vs)
{
integertype is;
for (is=0; is<ns; is++) N_VFree_Serial(vs[is]);
free(vs);
}
N_Vector N_VMake_Serial(integertype n, realtype *v_data, M_Env machEnv)
{
N_Vector v;
integertype length;
if (n <= 0) return(NULL);
if (machEnv == NULL) return(NULL);
v = (N_Vector) malloc(sizeof *v);
if (v == NULL) return(NULL);
v->content = (N_VectorSerialContent) malloc(sizeof(struct _N_VectorSerialContent));
if (v->content == NULL) {
free(v);
return(NULL);
}
length = ME_CONTENT_S(machEnv)->length;
NV_CONTENT_S(v)->data = v_data;
NV_CONTENT_S(v)->length = length;
v->menv = machEnv;
return(v);
}
void N_VDispose_Serial(N_Vector v)
{
free(NV_CONTENT_S(v));
free(v);
}
realtype *N_VGetData_Serial(N_Vector v)
{
realtype *v_data;
v_data = NV_CONTENT_S(v)->data;
return(v_data);
}
void N_VSetData_Serial(realtype *v_data, N_Vector v)
{
NV_CONTENT_S(v)->data = v_data;
}
void N_VLinearSum_Serial(realtype a, N_Vector x, realtype b, N_Vector y, N_Vector z)
{
integertype i, N;
realtype c, *xd, *yd, *zd;
N_Vector v1, v2;
booleantype test;
if ((b == ONE) && (z == y)) { /* BLAS usage: axpy y <- ax+y */
Vaxpy_Serial(a,x,y);
return;
}
if ((a == ONE) && (z == x)) { /* BLAS usage: axpy x <- by+x */
Vaxpy_Serial(b,y,x);
return;
}
/* Case: a == b == 1.0 */
if ((a == ONE) && (b == ONE)) {
VSum_Serial(x, y, z);
return;
}
/* Cases: (1) a == 1.0, b = -1.0, (2) a == -1.0, b == 1.0 */
/*if ((test = ((a == ONE) && (b == -ONE))) || ((a == -ONE) && (b == ONE))) {*/
test = ((a == ONE) && (b == -ONE));
if (test || ((a == -ONE) && (b == ONE))) {
v1 = test ? y : x;
v2 = test ? x : y;
VDiff_Serial(v2, v1, z);
return;
}
/* Cases: (1) a == 1.0, b == other or 0.0, (2) a == other or 0.0, b == 1.0 */
/* if a or b is 0.0, then user should have called N_VScale */
/*if ((test = (a == ONE)) || (b == ONE)) {*/
test = (a == ONE);
if (test || (b == ONE)) {
c = test ? b : a;
v1 = test ? y : x;
v2 = test ? x : y;
VLin1_Serial(c, v1, v2, z);
return;
}
/* Cases: (1) a == -1.0, b != 1.0, (2) a != 1.0, b == -1.0 */
/*if ((test = (a == -ONE)) || (b == -ONE)) {*/
test = (a == -ONE);
if (test || (b == -ONE)) {
c = test ? b : a;
v1 = test ? y : x;
v2 = test ? x : y;
VLin2_Serial(c, v1, v2, z);
return;
}
/* Case: a == b */
/* catches case both a and b are 0.0 - user should have called N_VConst */
if (a == b) {
VScaleSum_Serial(a, x, y, z);
return;
}
/* Case: a == -b */
if (a == -b) {
VScaleDiff_Serial(a, x, y, z);
return;
}
/* Do all cases not handled above:
(1) a == other, b == 0.0 - user should have called N_VScale
(2) a == 0.0, b == other - user should have called N_VScale
(3) a,b == other, a !=b, a != -b */
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = a * (*xd++) + b * (*yd++);
}
void N_VConst_Serial(realtype c, N_Vector z)
{
integertype i, N;
realtype *zd;
N = NV_LENGTH_S(z);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = c;
}
void N_VProd_Serial(N_Vector x, N_Vector y, N_Vector z)
{
integertype i, N;
realtype *xd, *yd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = (*xd++) * (*yd++);
}
void N_VDiv_Serial(N_Vector x, N_Vector y, N_Vector z)
{
integertype i, N;
realtype *xd, *yd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = (*xd++) / (*yd++);
}
void N_VScale_Serial(realtype c, N_Vector x, N_Vector z)
{
integertype i, N;
realtype *xd, *zd;
if (z == x) { /* BLAS usage: scale x <- cx */
VScaleBy_Serial(c, x);
return;
}
if (c == ONE) {
VCopy_Serial(x, z);
} else if (c == -ONE) {
VNeg_Serial(x, z);
} else {
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = c * (*xd++);
}
}
void N_VAbs_Serial(N_Vector x, N_Vector z)
{
integertype i, N;
realtype *xd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
zd = NV_DATA_S(z);
for (i=0; i < N; i++, xd++, zd++)
*zd = ABS(*xd);
}
void N_VInv_Serial(N_Vector x, N_Vector z)
{
integertype i, N;
realtype *xd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = ONE / (*xd++);
}
void N_VAddConst_Serial(N_Vector x, realtype b, N_Vector z)
{
integertype i, N;
realtype *xd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = (*xd++) + b;
}
realtype N_VDotProd_Serial(N_Vector x, N_Vector y)
{
integertype i, N;
realtype sum = ZERO, *xd, *yd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
for (i=0; i < N; i++)
sum += (*xd++) * (*yd++);
return(sum);
}
realtype N_VMaxNorm_Serial(N_Vector x)
{
integertype i, N;
realtype max = ZERO, *xd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
for (i=0; i < N; i++, xd++) {
if (ABS(*xd) > max) max = ABS(*xd);
}
return(max);
}
realtype N_VWrmsNorm_Serial(N_Vector x, N_Vector w)
{
integertype i, N;
realtype sum = ZERO, prodi, *xd, *wd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
wd = NV_DATA_S(w);
for (i=0; i < N; i++) {
prodi = (*xd++) * (*wd++);
sum += prodi * prodi;
}
return(RSqrt(sum / N));
}
realtype N_VMin_Serial(N_Vector x)
{
integertype i, N;
realtype min, *xd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
min = xd[0];
xd++;
for (i=1; i < N; i++, xd++) {
if ((*xd) < min) min = *xd;
}
return(min);
}
realtype N_VWL2Norm_Serial(N_Vector x, N_Vector w)
{
integertype i, N;
realtype sum = ZERO, prodi, *xd, *wd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
wd = NV_DATA_S(w);
for (i=0; i < N; i++) {
prodi = (*xd++) * (*wd++);
sum += prodi * prodi;
}
return(RSqrt(sum));
}
realtype N_VL1Norm_Serial(N_Vector x)
{
integertype i, N;
realtype sum = ZERO, *xd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
for (i=0; i<N; i++)
sum += ABS(xd[i]);
return(sum);
}
void N_VOneMask_Serial(N_Vector x)
{
integertype i, N;
realtype *xd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
for (i=0; i<N; i++,xd++) {
if (*xd != ZERO) *xd = ONE;
}
}
void N_VCompare_Serial(realtype c, N_Vector x, N_Vector z)
{
integertype i, N;
realtype *xd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
zd = NV_DATA_S(z);
for (i=0; i < N; i++, xd++, zd++) {
*zd = (ABS(*xd) >= c) ? ONE : ZERO;
}
}
booleantype N_VInvTest_Serial(N_Vector x, N_Vector z)
{
integertype i, N;
realtype *xd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
zd = NV_DATA_S(z);
for (i=0; i < N; i++) {
if (*xd == ZERO) return(FALSE);
*zd++ = ONE / (*xd++);
}
return(TRUE);
}
booleantype N_VConstrProdPos_Serial(N_Vector c, N_Vector x)
{
integertype i, N;
realtype *xd, *cd;
booleantype test;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
cd = NV_DATA_S(c);
test = TRUE;
for (i=0; i < N; i++, xd++,cd++) {
if (*cd != ZERO) {
if ((*xd)*(*cd) <= ZERO) {
test = FALSE;
break;
}
}
}
return(test);
}
booleantype N_VConstrMask_Serial(N_Vector c, N_Vector x, N_Vector m)
{
integertype i, N;
booleantype test;
realtype *cd, *xd, *md;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
cd = NV_DATA_S(c);
md = NV_DATA_S(m);
test = TRUE;
for (i=0; i<N; i++, cd++, xd++, md++) {
*md = ZERO;
if (*cd == ZERO) continue;
if (*cd > ONEPT5 || (*cd) < -ONEPT5) {
if ( (*xd)*(*cd) <= ZERO) {test = FALSE; *md = ONE; }
continue;
}
if ( (*cd) > HALF || (*cd) < -HALF) {
if ( (*xd)*(*cd) < ZERO ) {test = FALSE; *md = ONE; }
}
}
return(test);
}
realtype N_VMinQuotient_Serial(N_Vector num, N_Vector denom)
{
booleantype notEvenOnce;
integertype i, N;
realtype *nd, *dd, min;
N = NV_LENGTH_S(num);
nd = NV_DATA_S(num);
dd = NV_DATA_S(denom);
min = 0;
notEvenOnce = TRUE;
for (i=0; i<N; i++, nd++, dd++) {
if (*dd == ZERO) continue;
else {
if (notEvenOnce) {
min = *nd / *dd ;
notEvenOnce = FALSE;
}
else
min = MIN(min, (*nd)/(*dd));
}
}
if (notEvenOnce) min = 1.e99;
return(min);
}
void N_VPrint_Serial(N_Vector x)
{
integertype i, N;
realtype *xd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
for (i=0; i < N; i++) printf("%11.8g\n", (double) (*xd++));
printf("\n");
}
/***************** Private Helper Functions **********************/
static void VCopy_Serial(N_Vector x, N_Vector z)
{
integertype i, N;
realtype *xd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = *xd++;
}
static void VSum_Serial(N_Vector x, N_Vector y, N_Vector z)
{
integertype i, N;
realtype *xd, *yd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = (*xd++) + (*yd++);
}
static void VDiff_Serial(N_Vector x, N_Vector y, N_Vector z)
{
integertype i, N;
realtype *xd, *yd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = (*xd++) - (*yd++);
}
static void VNeg_Serial(N_Vector x, N_Vector z)
{
integertype i, N;
realtype *xd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = -(*xd++);
}
static void VScaleSum_Serial(realtype c, N_Vector x, N_Vector y, N_Vector z)
{
integertype i, N;
realtype *xd, *yd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = c * ((*xd++) + (*yd++));
}
static void VScaleDiff_Serial(realtype c, N_Vector x, N_Vector y, N_Vector z)
{
integertype i, N;
realtype *xd, *yd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = c * ((*xd++) - (*yd++));
}
static void VLin1_Serial(realtype a, N_Vector x, N_Vector y, N_Vector z)
{
integertype i, N;
realtype *xd, *yd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = a * (*xd++) + (*yd++);
}
static void VLin2_Serial(realtype a, N_Vector x, N_Vector y, N_Vector z)
{
integertype i, N;
realtype *xd, *yd, *zd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
zd = NV_DATA_S(z);
for (i=0; i < N; i++)
*zd++ = a * (*xd++) - (*yd++);
}
static void Vaxpy_Serial(realtype a, N_Vector x, N_Vector y)
{
integertype i, N;
realtype *xd, *yd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
yd = NV_DATA_S(y);
if (a == ONE) {
for (i=0; i < N; i++)
*yd++ += (*xd++);
return;
}
if (a == -ONE) {
for (i=0; i < N; i++)
*yd++ -= (*xd++);
return;
}
for (i=0; i < N; i++)
*yd++ += a * (*xd++);
}
static void VScaleBy_Serial(realtype a, N_Vector x)
{
integertype i, N;
realtype *xd;
N = NV_LENGTH_S(x);
xd = NV_DATA_S(x);
for (i=0; i < N; i++)
*xd++ *= a;
}

325
nvector_serial.h
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@ -1,325 +0,0 @@
/*******************************************************************
* *
* File : nvector_serial.h *
* Programmers : Scott D. Cohen, Alan C. Hindmarsh, *
* : Radu Serban, and Allan G. Taylor, LLNL *
* Version of : 26 June 2002 *
*-----------------------------------------------------------------*
* Copyright (c) 2002, The Regents of the University of California *
* Produced at the Lawrence Livermore National Laboratory *
* All rights reserved *
* For details, see sundials/shared/LICENSE *
*-----------------------------------------------------------------*
* This is the header file for a serial implementation of the *
* NVECTOR package. *
* *
* Part I of this file contains declarations which are specific *
* to the particular machine environment in which this version *
* of the vector package is to be used. This includes the *
* typedef for the 'content' fields of the structures M_Env and *
* N_Vector (M_EnvSerialContent and N_VectorSerialContent, *
* respectively). *
* *
* Part II of this file defines accessor macros that allow the *
* user to use efficiently the type N_Vector without making *
* explicit references to its underlying representation. *
* *
* Part III of this file contains the prototype for the *
* initialization routine specific to this implementation *
* (M_EnvInit_Serial) as well as prototypes for the vector *
* kernels which operate on the serial N_Vector. These *
* prototypes are unique to this particular implementation of *
* the vector package. *
* *
* NOTES: *
* *
* The definitions of the generic M_Env and N_Vector structures *
* are in the header file nvector.h. *
* *
* The definitions of the types realtype and integertype are in *
* the header file sundialstypes.h and these may be changed *
* according to the user's needs. The sundialstypes.h file also *
* contains the definition for the type booleantype. *
* *
* N_Vector arguments to arithmetic kernels need not be *
* distinct. Thus, for example, the call *
* N_VLinearSum_Serial(a,x,b,y,y); y <- ax+by *
* is legal. *
* *
* This version of nvector is for the ordinary sequential *
* machine environment. In the documentation given below, N is *
* the length of all N_Vector parameters and x[i] denotes the *
* ith component of the N_Vector x, where 0 <= i <= N-1. *
* *
*******************************************************************/
#ifdef PHREEQC_IDENT
static char const svnidnvector_serial[] = "$Id$";
#endif
#ifdef __cplusplus /* wrapper to enable C++ usage */
extern "C" {
#endif
#ifndef included_nvector_serial_h
#define included_nvector_serial_h
#include "nvector.h" /* Generic M_Env and N_Vector type definitions */
#include "sundialstypes.h"
/****************************************************************
* PART I: *
* Serial implementaion of M_Env and N_Vector *
****************************************************************/
/* The serial implementation of the machine environment has
ID tag 'serial' */
#define ID_TAG_S "serial"
/* The serial implementation of the machine environment 'content'
structure contains the length of vectors */
struct _M_EnvSerialContent {
integertype length;
};
typedef struct _M_EnvSerialContent *M_EnvSerialContent;
/* The serial implementation of the N_Vector 'content'
structure contains the length of the vector and a pointer
to an array of realtype components */
struct _N_VectorSerialContent {
integertype length;
realtype *data;
};
typedef struct _N_VectorSerialContent *N_VectorSerialContent;
/****************************************************************
* *
* PART II: Macros *
* NV_MAKE_S, NV_DISPOSE_S, NVS_MAKE_S, NVS_DISPOSE_S *
* ME_CONTENT_S, NV_CONTENT_S *
* NV_DATA_S, NV_LENGTH_S, NV_Ith_S *
*--------------------------------------------------------------*
* In the descriptions below, the following user declarations *
* are assumed: *
* *
* M_Env machenv; *
* N_Vector v, *vs; *
* realtype *v_data, **vs_data, r; *
* integertype v_len, s_len, i; *
* *
* (1) NV_MAKE_S, NV_DISPOSE_S *
* *
* These companion routines are used to create and *
* destroy an N_Vector with a component array v_data *
* allocated by the user. *
* *
* The call NV_MAKE_S(v, v_data, machenv) makes v an *
* N_Vector with component array v_data. The length of the *
* array is taken from machenv. *
* NV_MAKE_S stores the pointer v_data so that changes *
* made by the user to the elements of v_data are *
* simultaneously reflected in v. There is no copying of *
* elements. *
* *
* The call NV_DISPOSE_S(v) frees all memory associated *
* with v except for its component array. This memory was *
* allocated by the user and, therefore, should be *
* deallocated by the user. *
* *
* (2) NVS_MAKE_S, NVS_DISPOSE_S *
* *
* These companion routines are used to create and destroy *
* an array of N_Vectors with component vs_data allocated *
* by the user. *
* *
* The call NVS_MAKE_S(vs, vs_data, s_len, machenv) makes *
* vs an array of s_len N_Vectors, each with component *
* array vs_data[i] and array length taken from machenv. *
* NVS_MAKE_S stores the pointers vs_data[i] so that *
* changes made by the user to the elements of vs_data are *
* simultaneously reflected in vs. There is no copying of *
* elements. *
* *
* The call NVS_DISPOSE_S(vs) frees all memory associated *
* with vs except for its components' component array. *
* This memory was allocated by the user and, therefore, *
* should be deallocated by the user. *
* *
* (3) ME_CONTENT_S, NV_CONTENT_S *
* *
* These routines give access to the contents of the serial *
* machine environment and N_Vector, respectively. *
* *
* The assignment m_cont = ME_CONTENT_S(machenv) sets *
* m_cont to be a pointer to the serial machine *
* environment content structure. *
* *
* The assignment v_cont = NV_CONTENT_S(v) sets *
* v_cont to be a pointer to the serial N_Vector content *
* structure. *
* *
* (4) NV_DATA_S, NV_LENGTH_S *
* *
* These routines give individual access to the parts of *
* the content of a serial N_Vector. *
* *
* The assignment v_data=NV_DATA_S(v) sets v_data to be *
* a pointer to the first component of v. The assignment *
* NV_DATA_S(v)=v_data sets the component array of v to *
* be v_data by storing the pointer v_data. *
* *
* The assignment v_len=NV_LENGTH_S(v) sets v_len to be *
* the length of v. The call NV_LENGTH_S(v)=len_v sets *
* the length of v to be len_v. *
* *
* (5) NV_Ith_S *
* *
* In the following description, the components of an *
* N_Vector are numbered 0..N-1, where N is the length of *
* v. *
* *
* The assignment r=NV_Ith_S(v,i) sets r to be the value of *
* the ith component of v. The assignment NV_Ith_S(v,i)=r *
* sets the value of the ith component of v to be r. *
* *
* Notes.. *
* *
* Users who use the macros (1) and/or (2) must *
* #include<stdlib.h> since these macros expand to calls to *
* malloc and free. *
* *
* When looping over the components of an N_Vector v, it is *
* more efficient to first obtain the component array via *
* v_data=NV_DATA_S(v) and then access v_data[i] within the *
* loop than it is to use NV_Ith_S(v,i) within the loop. *
* *
* NV_MAKE_S and NV_DISPOSE_S are similar to N_VNew_Serial and *
* N_VFree_Serial, while NVS_MAKE_S and NVS_DISPOSE_S are *
* similar to N_VNew_S_Serial and N_VFree_S_Serial. The *
* difference is one of responsibility for component memory *
* allocation and deallocation. N_VNew_Serial allocates memory *
* for the N_Vector components and N_VFree_Serial frees the *
* component memory allocated by N_VNew_Serial. For NV_MAKE_S *
* and NV_DISPOSE_S, the component memory is allocated and *
* freed by the user of this package. Similar remarks hold for *
* NVS_MAKE_S, NVS_DISPOSE_S and N_VNew_S_Serial, *
* N_VFree_S_Serial. *
* *
****************************************************************/
#define NV_MAKE_S(v, v_data, machenv) \
v = (N_Vector) malloc(sizeof(*v)); \
v->content = (N_VectorSerialContent) malloc(sizeof(struct _N_VectorSerialContent)); \
v->content->data = v_data; \
v->content->length = machenv->content->v_len; \
v->menv = machenv
#define NV_DISPOSE_S(v) \
free((N_VectorSerialContent)(v->content)); \
free(v)
#define NVS_MAKE_S(vs, vs_data, s_len, machenv) \
vs = (N_Vector_S) malloc(s_len*sizeof(N_Vector *)); \
for ((int)is=0; is<s_len; is++) { \
NV_MAKE_S(vs[is], vs_data[is], machenv); \
}
#define NVS_DISPOSE_S(vs, s_len) \
for ((int)is=0; is<s_len; is++) NV_DISPOSE_S(vs[i]); \
free(vs);
#define ME_CONTENT_S(m) ( (M_EnvSerialContent)(m->content) )
#define NV_CONTENT_S(v) ( (N_VectorSerialContent)(v->content) )
#define NV_LENGTH_S(v) ( NV_CONTENT_S(v)->length )
#define NV_DATA_S(v) ( NV_CONTENT_S(v)->data )
#define NV_Ith_S(v,i) ( NV_DATA_S(v)[i] )
/****************************************************************
* PART III: *
* Functions exported by nvector_serial *
****************************************************************/
/*--------------------------------------------------------------*
* Routine : M_EnvInit_Serial *
*--------------------------------------------------------------*
* This function sets the content field of the machine *
* environment for the serial implementation to a structure of *
* type _MEnvSerialContent and attaches the vector operations *
* defined for this implementation. *
* *
* If successful, M_EnvInit_Serial returns a pointer of type *
* M_Env. This pointer should in turn be passed in any user *
* calls to N_VNew, or uses of the macros NV_MAKE_S and *
* NVS_MAKE_S. *
* *
*--------------------------------------------------------------*
* *
* vec_length is the length of the vector. *
* *
*--------------------------------------------------------------*/
M_Env M_EnvInit_Serial(integertype vec_length);
/*--------------------------------------------------------------*
* Function M_EnvFree_Serial *
*--------------------------------------------------------------*
* Function to free the block of machine-dependent environment *
* information created by M_EnvInit_Serial. *
* Its only argument is the pointer machenv returned by *
* M_EnvInit_Serial. *
* *
*--------------------------------------------------------------*/
void M_EnvFree_Serial(M_Env machenv);
/*--------------------------------------------------------------*
* Serial implementations of the vector operations *
* *
* For a complete description of each of the following routines *
* see the header file nvector.h *
*--------------------------------------------------------------*/
N_Vector N_VNew_Serial(integertype n, M_Env machEnv);
N_Vector_S N_VNew_S_Serial(integertype ns, integertype n, M_Env machEnv);
void N_VFree_Serial(N_Vector v);
void N_VFree_S_Serial(integertype ns, N_Vector_S vs);
N_Vector N_VMake_Serial(integertype n, realtype *v_data, M_Env machEnv);
void N_VDispose_Serial(N_Vector v);
realtype *N_VGetData_Serial(N_Vector v);
void N_VSetData_Serial(realtype *v_data, N_Vector v);
void N_VLinearSum_Serial(realtype a, N_Vector x, realtype b, N_Vector y, N_Vector z);
void N_VConst_Serial(realtype c, N_Vector z);
void N_VProd_Serial(N_Vector x, N_Vector y, N_Vector z);
void N_VDiv_Serial(N_Vector x, N_Vector y, N_Vector z);
void N_VScale_Serial(realtype c, N_Vector x, N_Vector z);
void N_VAbs_Serial(N_Vector x, N_Vector z);
void N_VInv_Serial(N_Vector x, N_Vector z);
void N_VAddConst_Serial(N_Vector x, realtype b, N_Vector z);
realtype N_VDotProd_Serial(N_Vector x, N_Vector y);
realtype N_VMaxNorm_Serial(N_Vector x);
realtype N_VWrmsNorm_Serial(N_Vector x, N_Vector w);
realtype N_VMin_Serial(N_Vector x);
realtype N_VWL2Norm_Serial(N_Vector x, N_Vector w);
realtype N_VL1Norm_Serial(N_Vector x);
void N_VOneMask_Serial(N_Vector x);
void N_VCompare_Serial(realtype c, N_Vector x, N_Vector z);
booleantype N_VInvTest_Serial(N_Vector x, N_Vector z);
booleantype N_VConstrProdPos_Serial(N_Vector c, N_Vector x);
booleantype N_VConstrMask_Serial(N_Vector c, N_Vector x, N_Vector m);
realtype N_VMinQuotient_Serial(N_Vector num, N_Vector denom);
void N_VPrint_Serial(N_Vector x);
#endif
#ifdef __cplusplus
}
#endif

182
output.cpp
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@ -1,182 +0,0 @@
#define EXTERNAL extern
#include <setjmp.h>
#include "global.h"
#include "output.h"
#include "phrqproto.h"
#include "phqalloc.h"
static char const svnid[] = "$Id: output.c 663 2005-11-16 00:46:04Z dlpark $";
#define MAX_CALLBACKS 10
static struct output_callback output_callbacks[MAX_CALLBACKS];
static size_t count_output_callback = 0;
static int forward_output_to_log = 0;
/* ---------------------------------------------------------------------- */
int add_output_callback(PFN_OUTPUT_CALLBACK pfn, void *cookie)
/* ---------------------------------------------------------------------- */
{
if (svnid == NULL) fprintf(stderr," ");
if (pfn) {
if (count_output_callback >= MAX_CALLBACKS - 1) {
sprintf(error_string, "Too many callbacks.\nSee %s\n", __FILE__);
fprintf(stderr, "%s", error_string);
error_msg(error_string, STOP);
return ERROR;
}
output_callbacks[count_output_callback].callback = pfn;
output_callbacks[count_output_callback].cookie = cookie;
++count_output_callback;
}
return OK;
}
/* ---------------------------------------------------------------------- */
int output_message(const int type, const char *err_str, const int stop, const char *format, va_list args)
/* ---------------------------------------------------------------------- */
{
extern jmp_buf mark;
size_t i;
for (i = 0; i < count_output_callback; ++i) {
(output_callbacks[i].callback)(ACTION_OUTPUT, type, err_str, stop, output_callbacks[i].cookie, format, args);
}
if (stop == STOP) {
longjmp(mark, input_error);
}
return OK;
}
/* ---------------------------------------------------------------------- */
int clean_up_output_callbacks(void)
/* ---------------------------------------------------------------------- */
{
count_output_callback = 0;
return OK;
}
/* ---------------------------------------------------------------------- */
int error_msg (const char *err_str, const int stop, ...)
/* ---------------------------------------------------------------------- */
{
va_list args;
int return_value;
if (input_error <= 0) input_error = 1;
va_start(args, stop);
return_value = output_message(OUTPUT_ERROR, err_str, stop, "", args);
va_end(args);
return(return_value);
}
/* ---------------------------------------------------------------------- */
int warning_msg (const char *err_str, ...)
/* ---------------------------------------------------------------------- */
{
va_list args;
int return_value;
va_start(args, err_str);
return_value = output_message(OUTPUT_WARNING, err_str, CONTINUE, "", args);
count_warnings++;
va_end(args);
return (return_value);
}
/* ---------------------------------------------------------------------- */
int output_msg (const int type, const char* format, ...)
/* ---------------------------------------------------------------------- */
{
int return_value;
va_list args;
va_start(args, format);
return_value = output_message(type, NULL, CONTINUE, format, args);
va_end(args);
return(return_value);
}
/* ---------------------------------------------------------------------- */
void set_forward_output_to_log(int value)
/* ---------------------------------------------------------------------- */
{
forward_output_to_log = value;
}
/* ---------------------------------------------------------------------- */
int get_forward_output_to_log(void)
/* ---------------------------------------------------------------------- */
{
return forward_output_to_log;
}
/* ---------------------------------------------------------------------- */
int output_fflush(const int type, ...)
/* ---------------------------------------------------------------------- */
{
size_t i;
int check;
va_list args;
check = OK;
va_start(args, type);
for (i = 0; i < count_output_callback; ++i) {
check = (output_callbacks[i].callback)(ACTION_FLUSH, type, NULL, CONTINUE, output_callbacks[i].cookie, NULL, args);
if (check != OK) break;
}
va_end(args);
if (check != OK) return(ERROR);
return(OK);
}
/* ---------------------------------------------------------------------- */
int output_rewind(const int type, ...)
/* ---------------------------------------------------------------------- */
{
size_t i;
int check;
va_list args;
check = OK;
va_start(args, type);
for (i = 0; i < count_output_callback; ++i) {
check = (output_callbacks[i].callback)(ACTION_REWIND, type, NULL, CONTINUE, output_callbacks[i].cookie, NULL, args);
if (check != OK) break;
}
va_end(args);
if (check != OK) return(ERROR);
return(OK);
}
/* ---------------------------------------------------------------------- */
int output_close(const int type, ...)
/* ---------------------------------------------------------------------- */
{
size_t i;
int check;
va_list args;
check = OK;
va_start(args, type);
for (i = 0; i < count_output_callback; ++i) {
check = (output_callbacks[i].callback)(ACTION_CLOSE, type, NULL, CONTINUE, output_callbacks[i].cookie, NULL, args);
if (check != OK) break;
}
va_end(args);
if (check != OK) return(ERROR);
return(OK);
}
/* ---------------------------------------------------------------------- */
int output_open(const int type, const char *file_name, ...)
/* ---------------------------------------------------------------------- */
{
size_t i;
int check;
va_list args;
assert(file_name && strlen(file_name));
check = OK;
va_start(args, file_name);
for (i = 0; i < count_output_callback; ++i) {
check = (output_callbacks[i].callback)(ACTION_OPEN, type, file_name, CONTINUE, output_callbacks[i].cookie, NULL, args);
if (check != OK) break;
}
va_end(args);
if (check != OK) return(ERROR);
return(OK);
}

57
output.h
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@ -1,57 +0,0 @@
#ifndef _INC_MESSAGE_H
#define _INC_MESSAGE_H
#include <stdarg.h>
#ifdef PHREEQC_IDENT
static char const svnidoutput[] = "$Id$";
#endif
typedef int (*PFN_OUTPUT_CALLBACK)(const int action, const int type, const char *err_str, const int stop, void *cookie, const char *, va_list args);
struct output_callback {
PFN_OUTPUT_CALLBACK callback;
void *cookie;
};
int add_output_callback(PFN_OUTPUT_CALLBACK pfn, void *cookie);
int clean_up_output_callbacks(void);
int output_msg (const int type, const char* format, ...);
int warning_msg (const char *err_str, ...);
int error_msg (const char *err_str, const int stop, ...);
int phreeqc_handler(const int action, const int type, const char *err_str, const int stop, void *cookie, const char *, va_list args);
void set_forward_output_to_log(int value);
int get_forward_output_to_log(void);
/*
* Functions for output callbacks
*/
int output_open(const int type, const char *file_name, ...);
int output_fflush(const int type, ...);
int output_rewind(const int type, ...);
int output_close(const int type, ...);
typedef enum {
OUTPUT_ERROR,
OUTPUT_WARNING,
OUTPUT_MESSAGE,
OUTPUT_PUNCH,
OUTPUT_SCREEN,
OUTPUT_LOG,
OUTPUT_CHECKLINE,
OUTPUT_GUI_ERROR,
OUTPUT_BASIC,
OUTPUT_CVODE,
OUTPUT_DUMP,
OUTPUT_STDERR,
OUTPUT_SEND_MESSAGE
} output_type;
typedef enum {
ACTION_OPEN,
ACTION_OUTPUT,
ACTION_CLOSE,
ACTION_REWIND,
ACTION_FLUSH
} action_type;
#endif /* _INC_MESSAGE_H */

543
p2c.h
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@ -1,543 +0,0 @@
#ifndef P2C_H
#define P2C_H
#ifdef PHREEQC_IDENT
static char const svnidp2c[] = "$Id$";
#endif
/* Header file for code generated by "p2c", the Pascal-to-C translator */
/* "p2c" Copyright (C) 1989, 1990, 1991 Free Software Foundation.
* By Dave Gillespie, daveg@csvax.cs.caltech.edu. Version 1.20.
* This file may be copied, modified, etc. in any way. It is not restricted
* by the licence agreement accompanying p2c itself.
*/
#include <stdio.h>
/* If the following heuristic fails, compile -DBSD=0 for non-BSD systems,
or -DBSD=1 for BSD systems. */
#ifdef M_XENIX
# define BSD 0
#endif
#ifdef vms
# define BSD 0
# ifndef __STDC__
# define __STDC__ 1
# endif
#endif
#ifdef __TURBOC__
# define MSDOS 1
#endif
#ifdef MSDOS
# define BSD 0
#endif
#ifdef FILE /* a #define in BSD, a typedef in SYSV (hp-ux, at least) */
# ifndef BSD /* (a convenient, but horrible kludge!) */
# define BSD 1
# endif
#endif
#ifdef BSD
# if !BSD
# undef BSD
# endif
#endif
#if (defined(__STDC__) && !defined(M_XENIX)) || defined(__TURBOC__)
# include <stddef.h>
# include <stdlib.h>
# define HAS_STDLIB
# if defined(vms) || defined(__TURBOC__)
# define __ID__(a)a
# endif
#else
# ifndef BSD
# ifndef __TURBOC__
# include <memory.h>
# endif
# endif
# ifdef hpux
# ifdef _INCLUDE__STDC__
# include <stddef.h>
# include <stdlib.h>
# endif
# endif
# include <sys/types.h>
# if !defined(MSDOS) || defined(__TURBOC__)
# define __ID__(a)a
# endif
#endif
#ifdef __ID__
# define __CAT__(a,b)__ID__(a)b
#else
# define __CAT__(a,b)a##b
#endif
#ifdef BSD
# include <strings.h>
# define memcpy(a,b,n) (bcopy(b,a,n),a)
# define memcmp(a,b,n) bcmp(a,b,n)
# define strchr(s,c) index(s,c)
# define strrchr(s,c) rindex(s,c)
#else
# include <string.h>
#endif
#include <ctype.h>
#include <math.h>
#include <setjmp.h>
#include <assert.h>
#ifndef NO_LACK
#ifdef vms
#define LACK_LABS
#define LACK_MEMMOVE
#define LACK_MEMCPY
#else
#define LACK_LABS /* Undefine these if your library has these */
#ifdef SKIP
#define LACK_MEMMOVE
#endif
#endif
#endif
typedef struct __p2c_jmp_buf {
struct __p2c_jmp_buf *next;
jmp_buf jbuf;
} __p2c_jmp_buf;
/* Warning: The following will not work if setjmp is used simultaneously.
This also violates the ANSI restriction about using vars after longjmp,
but a typical implementation of longjmp will get it right anyway. */
#ifndef FAKE_TRY
# define TRY(x) do { __p2c_jmp_buf __try_jb; \
__try_jb.next = __top_jb; \
if (!setjmp((__top_jb = &__try_jb)->jbuf)) {
# define RECOVER(x) __top_jb = __try_jb.next; } else {
#ifdef SKIP
# define RECOVER2(x,L) __top_jb = __try_jb.next; } else { \
if (0) { L: __top_jb = __try_jb.next; }
#endif
# define RECOVER2(x,L) __top_jb = __try_jb.next; } else { \
{ L: __top_jb = __try_jb.next; }
# define ENDTRY(x) } } while (0)
#else
# define TRY(x) if (1) {
# define RECOVER(x) } else do {
# define RECOVER2(x,L) } else do { L: ;
# define ENDTRY(x) } while (0)
#endif
#ifdef M_XENIX /* avoid compiler bug */
# define INT_MAX (32767)
# define INT_MIN (-32768)
#endif
/* The following definitions work only on twos-complement machines */
#ifndef INT_MAX
# define INT_MAX ((int)(((unsigned int) -1) >> 1))
# define INT_MIN (~INT_MAX)
#endif
#ifndef INT_MAX
# define INT_MAX ((int)(((unsigned int) -1) >> 1))
# define INT_MIN (~INT_MAX)
#endif
#ifndef LONG_MAX
# define LONG_MAX ((long)(((unsigned long) -1) >> 1))
# define LONG_MIN (~LONG_MAX)
#endif
#ifndef SEEK_SET
# define SEEK_SET 0
# define SEEK_CUR 1
# define SEEK_END 2
#endif
#ifndef EXIT_SUCCESS
# ifdef vms
# define EXIT_SUCCESS 1
# define EXIT_FAILURE (02000000000L)
# else
# define EXIT_SUCCESS 0
# define EXIT_FAILURE 1
# endif
#endif
#define SETBITS 32
#ifdef SKIP
#if defined(__STDC__) || defined(__TURBOC__)
# if !defined(vms) && !defined(M_LINT)
# define Signed signed
# else
# define Signed
# endif
# define Void void /* Void f() = procedure */
# ifndef Const
# define Const const
# endif
# ifndef Volatile
# define Volatile volatile
# endif
# ifdef M_LINT
# define P2PP(x) ()
# define PV() ()
typedef char *Anyptr;
# else
# define P2PP(x) x /* function prototype */
# define PV() (void) /* null function prototype */
typedef void *Anyptr;
# endif
#else
# define Signed
# define Void void
# ifndef Const
# define Const
# endif
# ifndef Volatile
# define Volatile
# endif
# define P2PP(x) ()
# define PV() ()
typedef char *Anyptr;
#endif
#endif
#define Signed
#define Void void
#ifndef Const
# define Const
#endif
#ifndef Volatile
# define Volatile
#endif
#define P2PP(x) ()
#define PV() ()
typedef char *Anyptr;
#ifdef __GNUC__
# define Inline inline
#else
# define Inline
#endif
#define Register register /* Register variables */
#define Char char /* Characters (not bytes) */
#ifndef Static
# define Static static /* Private global funcs and vars */
#endif
#ifndef Local
# define Local static /* Nested functions */
#endif
typedef Signed char schar;
/*typedef unsigned char uchar;*/
typedef unsigned char boolean;
#ifndef true
# define true 1
# define false 0
#endif
#ifndef TRUE
# define TRUE 1
# define FALSE 0
#endif
typedef struct {
Anyptr proc, link;
} _PROCEDURE;
#ifndef _FNSIZE
# define _FNSIZE 120
#endif
/*extern Void PASCAL_MAIN P2PP( (int, Char **) );*/
extern Void PASCAL_MAIN (int, Char **) ;
/*
extern Char **P_argv;
extern int P_argc;
*/
extern int P_escapecode;
extern int P_ioresult;
extern __p2c_jmp_buf *__top_jb;
#ifdef P2C_H_PROTO /* if you have Ansi C but non-prototyped header files */
extern Char *strcat P2PP( (Char *, Const Char *) );
extern Char *strchr P2PP( (Const Char *, int) );
extern int strcmp P2PP( (Const Char *, Const Char *) );
extern Char *strcpy P2PP( (Char *, Const Char *) );
extern size_t strlen P2PP( (Const Char *) );
extern Char *strncat P2PP( (Char *, Const Char *, size_t) );
extern int strncmp P2PP( (Const Char *, Const Char *, size_t) );
extern Char *strncpy P2PP( (Char *, Const Char *, size_t) );
extern Char *strrchr P2PP( (Const Char *, int) );
extern Anyptr memchr P2PP( (Const Anyptr, int, size_t) );
extern Anyptr memmove P2PP( (Anyptr, Const Anyptr, size_t) );
extern Anyptr memset P2PP( (Anyptr, int, size_t) );
#ifndef memcpy
extern Anyptr memcpy P2PP( (Anyptr, Const Anyptr, size_t) );
extern int memcmp P2PP( (Const Anyptr, Const Anyptr, size_t) );
#endif
extern int atoi P2PP( (Const Char *) );
extern LDBLE atof P2PP( (Const Char *) );
extern long atol P2PP( (Const Char *) );
extern LDBLE strtod P2PP( (Const Char *, Char **) );
extern long strtol P2PP( (Const Char *, Char **, int) );
#endif /*P2C_H_PROTO*/
/* force stdlib for DEC */
#define HAS_STDLIB
#ifndef HAS_STDLIB
extern Anyptr malloc P2PP( (size_t) );
extern Void free P2PP( (Anyptr) );
#endif
extern int _OutMem PV();
extern int _CaseCheck PV();
extern int _NilCheck PV();
/*extern int _Escape P2PP( (int) );*/
extern int _Escape(int);
/*extern int _EscIO P2PP( (int) );*/
extern int _EscIO (int);
extern long ipow P2PP( (long, long) );
extern Char *strsub P2PP( (Char *, Char *, int, int) );
extern Char *strltrim P2PP( (Char *) );
extern Char *strrtrim P2PP( (Char *) );
extern Char *strrpt P2PP( (Char *, Char *, int) );
extern Char *strpad P2PP( (Char *, Char *, int, int) );
extern int strpos2 P2PP( (Char *, Char *, int) );
extern long memavail PV();
extern int P_peek P2PP( (FILE *) );
extern int P_eof P2PP( (FILE *) );
extern int P_eoln P2PP( (FILE *) );
extern Void P_readpaoc P2PP( (FILE *, Char *, int) );
extern Void P_readlnpaoc P2PP( (FILE *, Char *, int) );
extern long P_maxpos P2PP( (FILE *) );
extern Char *P_trimname P2PP( (Char *, int) );
extern long *P_setunion P2PP( (long *, long *, long *) );
extern long *P_setint P2PP( (long *, long *, long *) );
extern long *P_setdiff P2PP( (long *, long *, long *) );
extern long *P_setxor P2PP( (long *, long *, long *) );
extern int P_inset P2PP( (unsigned, long *) );
extern int P_setequal P2PP( (long *, long *) );
extern int P_subset P2PP( (long *, long *) );
extern long *P_addset P2PP( (long *, unsigned) );
extern long *P_addsetr P2PP( (long *, unsigned, unsigned) );
extern long *P_remset P2PP( (long *, unsigned) );
extern long *P_setcpy P2PP( (long *, long *) );
extern long *P_expset P2PP( (long *, long) );
extern long P_packset P2PP( (long *) );
extern int P_getcmdline P2PP( (int, int, Char *) );
extern Void TimeStamp P2PP( (int *, int *, int *,
int *, int *, int *) );
extern Void P_sun_argv P2PP( (char *, int, int) );
/* I/O error handling */
#define _CHKIO(cond,ior,val,def) ((cond) ? P_ioresult=0,(val) \
: P_ioresult=(ior),(def))
#define _SETIO(cond,ior) (P_ioresult = (cond) ? 0 : (ior))
/* Following defines are suitable for the HP Pascal operating system */
#define FileNotFound 10
#define FileNotOpen 13
#define FileWriteError 38
#define BadInputFormat 14
#define EndOfFile 30
#define FILENOTFOUND 10
#define FILENOTOPEN 13
#define FILEWRITEERROR 38
#define BADINPUTFORMAT 14
#define ENDOFFILE 30
/* Creating temporary files */
#if (defined(BSD) || defined(NO_TMPFILE)) && !defined(HAVE_TMPFILE)
# define tmpfile() (fopen(tmpnam(NULL), "w+"))
#endif
/* File buffers */
#define FILEBUF(f,sc,type) sc int __CAT__(f,_BFLAGS); \
sc type __CAT__(f,_BUFFER)
#define FILEBUFNC(f,type) int __CAT__(f,_BFLAGS); \
type __CAT__(f,_BUFFER)
#define RESETBUF(f,type) (__CAT__(f,_BFLAGS) = 1)
#define SETUPBUF(f,type) (__CAT__(f,_BFLAGS) = 0)
#define GETFBUF(f,type) (*((__CAT__(f,_BFLAGS) == 1 && \
((__CAT__(f,_BFLAGS) = 2), \
fread(&__CAT__(f,_BUFFER), \
sizeof(type),1,(f)))),\
&__CAT__(f,_BUFFER)))
#define AGETFBUF(f,type) ((__CAT__(f,_BFLAGS) == 1 && \
((__CAT__(f,_BFLAGS) = 2), \
fread(__CAT__(f,_BUFFER), \
sizeof(type),1,(f)))),\
__CAT__(f,_BUFFER))
#define PUTFBUF(f,type,v) (GETFBUF(f,type) = (v))
#define CPUTFBUF(f,v) (PUTFBUF(f,char,v))
#define APUTFBUF(f,type,v) (memcpy(AGETFBUF(f,type), (v), \
sizeof(__CAT__(f,_BUFFER))))
#define GET(f,type) (__CAT__(f,_BFLAGS) == 1 ? \
fread(&__CAT__(f,_BUFFER),sizeof(type),1,(f)) : \
(__CAT__(f,_BFLAGS) = 1))
#define PUT(f,type) (fwrite(&__CAT__(f,_BUFFER),sizeof(type),1,(f)), \
(__CAT__(f,_BFLAGS) = 0))
#define CPUT(f) (PUT(f,char))
#define BUFEOF(f) (__CAT__(f,_BFLAGS) != 2 && P_eof(f))
#define BUFFPOS(f) (ftell(f) - (__CAT__(f,_BFLAGS) == 2))
#ifdef SKIP
typedef struct {
FILE *f;
FILEBUFNC(f,Char);
Char name[_FNSIZE];
} _TEXT;
#endif
/* Memory allocation */
#ifdef __GCC__
# define Malloc(n) (PHRQ_malloc(n) ?: (Anyptr)_OutMem())
#else
extern Anyptr __MallocTemp__;
# define Malloc(n) ((__MallocTemp__ = PHRQ_malloc(n)) ? __MallocTemp__ : (Anyptr)_OutMem())
#endif
#define FreeR(p) (free((Anyptr)(p))) /* used if arg is an rvalue */
#define Free(p) (free((Anyptr)(p)), (p)=NULL)
/* sign extension */
#define SEXT(x,n) ((x) | -(((x) & (1L<<((n)-1))) << 1))
/* packed arrays */ /* BEWARE: these are untested! */
#define P_getbits_UB(a,i,n,L) ((int)((a)[(i)>>(L)-(n)] >> \
(((~(i))&((1<<(L)-(n))-1)) << (n)) & \
(1<<(1<<(n)))-1))
#define P_getbits_SB(a,i,n,L) ((int)((a)[(i)>>(L)-(n)] << \
(16 - ((((~(i))&((1<<(L)-(n))-1))+1) <<\
(n)) >> (16-(1<<(n))))))
#define P_putbits_UB(a,i,x,n,L) ((a)[(i)>>(L)-(n)] |= \
(x) << (((~(i))&((1<<(L)-(n))-1)) << (n)))
#define P_putbits_SB(a,i,x,n,L) ((a)[(i)>>(L)-(n)] |= \
((x) & (1<<(1<<(n)))-1) << \
(((~(i))&((1<<(L)-(n))-1)) << (n)))
#define P_clrbits_B(a,i,n,L) ((a)[(i)>>(L)-(n)] &= \
~( ((1<<(1<<(n)))-1) << \
(((~(i))&((1<<(L)-(n))-1)) << (n))) )
/* small packed arrays */
#define P_getbits_US(v,i,n) ((int)((v) >> ((i)<<(n)) & (1<<(1<<(n)))-1))
#define P_getbits_SS(v,i,n) ((int)((long)(v) << (SETBITS - (((i)+1) << (n))) >> (SETBITS-(1<<(n)))))
#define P_putbits_US(v,i,x,n) ((v) |= (x) << ((i) << (n)))
#define P_putbits_SS(v,i,x,n) ((v) |= ((x) & (1<<(1<<(n)))-1) << ((i)<<(n)))
#define P_clrbits_S(v,i,n) ((v) &= ~( ((1<<(1<<(n)))-1) << ((i)<<(n)) ))
#define P_max(a,b) ((a) > (b) ? (a) : (b))
#define P_min(a,b) ((a) < (b) ? (a) : (b))
/* Fix ANSI-isms */
#ifdef LACK_LABS
# ifndef labs
# define labs my_labs
extern long my_labs P2PP( (long) );
# endif
#endif
#ifdef LACK_MEMMOVE
# ifndef memmove
# define memmove my_memmove
extern Anyptr my_memmove P2PP( (Anyptr, Const Anyptr, size_t) );
# endif
#endif
#ifdef LACK_MEMCPY
# ifndef memcpy
# define memcpy my_memcpy
extern Anyptr my_memcpy P2PP( (Anyptr, Const Anyptr, size_t) );
# endif
# ifndef memcmp
# define memcmp my_memcmp
extern int my_memcmp P2PP( (Const Anyptr, Const Anyptr, size_t) );
# endif
# ifndef memset
# define memset my_memset
extern Anyptr my_memset P2PP( (Anyptr, int, size_t) );
# endif
#endif
/* Fix toupper/tolower on Suns and other stupid BSD systems */
#ifdef toupper
# undef toupper
# undef tolower
# define toupper(c) my_toupper(c)
# define tolower(c) my_tolower(c)
#endif
#ifndef _toupper
# if 'A' == 65 && 'a' == 97
# define _toupper(c) ((c)-'a'+'A')
# define _tolower(c) ((c)-'A'+'a')
# else
# ifdef toupper
# undef toupper /* hope these are shadowing real functions, */
# undef tolower /* because my_toupper calls _toupper! */
# endif
# define _toupper(c) toupper(c)
# define _tolower(c) tolower(c)
# endif
#endif
#endif /* P2C_H */
/* End. */

936
p2clib.cpp
View File

@ -1,936 +0,0 @@
/* Run-time library for use with "p2c", the Pascal to C translator */
/* "p2c" Copyright (C) 1989, 1990, 1991 Free Software Foundation.
* By Dave Gillespie, daveg@csvax.cs.caltech.edu. Version --VERSION--.
* This file may be copied, modified, etc. in any way. It is not restricted
* by the licence agreement accompanying p2c itself.
*/
static char const svnid[] = "$Id: p2clib.c 663 2005-11-16 00:46:04Z dlpark $";
#include "p2c.h"
#include "output.h"
#define STOP 1
#define CONTINUE 0
#define NO_TIME
#ifndef NO_TIME
# include <time.h>
#endif
#include <stdlib.h>
#define Isspace(c) isspace(c) /* or "((c) == ' ')" if preferred */
static int P_argc;
static char **P_argv;
static char *_ShowEscape(char *buf, int code, int ior, char *prefix);
int P_escapecode;
int P_ioresult;
long EXCP_LINE; /* Used by Pascal workstation system */
Anyptr __MallocTemp__;
__p2c_jmp_buf *__top_jb;
void PASCAL_MAIN(int argc, char **argv)
{
if (svnid == NULL) fprintf(stderr," ");
P_argc = argc;
P_argv = argv;
__top_jb = NULL;
P_escapecode = 0;
P_ioresult = 0;
#ifdef LOCAL_INIT
LOCAL_INIT();
#endif
}
/* In case your system lacks these... */
long my_labs(long x)
{
return((x > 0) ? x : -x);
}
/* #define __STDC__ */ /* PHREEQ98 */
Anyptr my_memmove(Anyptr d, Const Anyptr s, size_t n)
{
register char *dd = (char *)d, *ss = (char *)s;
if (dd < ss || (unsigned int) (dd - ss) >= n) {
memcpy(dd, ss, n);
} else if (n > 0) {
dd += n;
ss += n;
while (n-- > 0)
*--dd = *--ss;
}
return d;
}
Anyptr my_memcpy(Anyptr d, Const Anyptr s, size_t n)
{
register char *ss = (char *)s, *dd = (char *)d;
while (n-- > 0)
*dd++ = *ss++;
return d;
}
int my_memcmp(Const Anyptr s1, Const Anyptr s2, size_t n)
{
register char *a = (char *)s1, *b = (char *)s2;
register int i;
while (n-- > 0)
if ((i = (*a++) - (*b++)) != 0)
return i;
return 0;
}
Anyptr my_memset(Anyptr d, int c, size_t n)
{
register char *dd = (char *)d;
while (n-- > 0)
*dd++ = (char) c;
return d;
}
int my_toupper(int c)
{
if (islower(c))
return _toupper(c);
else
return c;
}
int my_tolower(int c)
{
if (isupper(c))
return _tolower(c);
else
return c;
}
long ipow(long a, long b)
{
long v;
if (a == 0 || a == 1)
return a;
if (a == -1)
return (b & 1) ? -1 : 1;
if (b < 0)
return 0;
if (a == 2)
return 1L << b;
v = (b & 1) ? a : 1;
while ((b >>= 1) > 0) {
a *= a;
if (b & 1)
v *= a;
}
return v;
}
/* Common string functions: */
/* Store in "ret" the substring of length "len" starting from "pos" (1-based).
Store a shorter or null string if out-of-range. Return "ret". */
char *strsub(register char *ret, register char *s, register int pos, register int len)
{
register char *s2;
if (--pos < 0 || len <= 0) {
*ret = 0;
return ret;
}
while (pos > 0) {
if (!*s++) {
*ret = 0;
return ret;
}
pos--;
}
s2 = ret;
while (--len >= 0) {
if (!(*s2++ = *s++))
return ret;
}
*s2 = 0;
return ret;
}
/* Return the index of the first occurrence of "pat" as a substring of "s",
starting at index "pos" (1-based). Result is 1-based, 0 if not found. */
int strpos2(char *s, register char *pat, register int pos)
{
register char *cp, ch;
register int slen;
if (--pos < 0)
return 0;
slen = strlen(s) - pos;
cp = s + pos;
if (!(ch = *pat++))
return 0;
pos = strlen(pat);
slen -= pos;
while (--slen >= 0) {
if (*cp++ == ch && !strncmp(cp, pat, pos))
return cp - s;
}
return 0;
}
/* Case-insensitive version of strcmp. */
int strcicmp(register char *s1, register char *s2)
{
register unsigned char c1, c2;
while (*s1) {
if (*s1++ != *s2++) {
if (!s2[-1])
return 1;
c1 = (unsigned char) toupper(s1[-1]);
c2 = (unsigned char) toupper(s2[-1]);
if (c1 != c2)
return c1 - c2;
}
}
if (*s2)
return -1;
return 0;
}
/* HP and Turbo Pascal string functions: */
/* Trim blanks at left end of string. */
char *strltrim(register char *s)
{
while (Isspace((int) *s++)) ;
return s - 1;
}
/* Trim blanks at right end of string. */
char *strrtrim(register char *s)
{
register char *s2 = s;
if (!*s)
return s;
while (*++s2) ;
while (s2 > s && Isspace((int) *--s2))
*s2 = 0;
return s;
}
/* Store in "ret" "num" copies of string "s". Return "ret". */
#ifdef SKIP
char *strrpt(ret, s, num)
char *ret;
register char *s;
register int num;
{
register char *s2 = ret;
register char *s1;
while (--num >= 0) {
s1 = s;
while ((*s2++ = *s1++)) ;
s2--;
}
return ret;
}
#endif
/* Store in "ret" string "s" with enough pad chars added to reach "size". */
#ifdef SKIP
char *strpad
(ret, s, padchar, num)
char *ret;
register char *s;
register int padchar, num;
{
register char *d = ret;
if (s == d) {
while (*d++) ;
} else {
while ((*d++ = *s++)) ;
}
num -= (--d - ret);
while (--num >= 0)
*d++ = (char) padchar;
*d = 0;
return ret;
}
#endif
/* Copy the substring of length "len" from index "spos" of "s" (1-based)
to index "dpos" of "d", lengthening "d" if necessary. Length and
indices must be in-range. */
void strmove(register int len, register char *s, register int spos, register char *d, register int dpos)
{
s += spos - 1;
d += dpos - 1;
while (*d && --len >= 0)
*d++ = *s++;
if (len > 0) {
while (--len >= 0)
*d++ = *s++;
*d = 0;
}
}
/* Delete the substring of length "len" at index "pos" from "s".
Delete less if out-of-range. */
#ifdef SKIP
void strdelete(s, pos, len)
register char *s;
register int pos, len;
{
register int slen;
if (--pos < 0)
return;
slen = strlen(s) - pos;
if (slen <= 0)
return;
s += pos;
if (slen <= len) {
*s = 0;
return;
}
while ((*s = s[len])) s++;
}
#endif
/* Insert string "src" at index "pos" of "dst". */
void strinsert(register char *src, register char *dst, register int pos)
{
register int slen, dlen;
if (--pos < 0)
return;
dlen = strlen(dst);
dst += dlen;
dlen -= pos;
if (dlen <= 0) {
strcpy(dst, src);
return;
}
slen = strlen(src);
do {
dst[slen] = *dst;
--dst;
} while (--dlen >= 0);
dst++;
while (--slen >= 0)
*dst++ = *src++;
}
/* File functions */
/* Peek at next character of input stream; return EOF at end-of-file. */
int P_peek(FILE *f)
{
int ch;
ch = getc(f);
if (ch == EOF)
return EOF;
ungetc(ch, f);
return (ch == '\n') ? ' ' : ch;
}
/* Check if at end of file, using Pascal "eof" semantics. End-of-file for
stdin is broken; remove the special case for it to be broken in a
different way. */
/*int P_eof(FILE *f)*/
int P_eof(void)
{
#ifdef SKIP
register int ch;
if (feof(f))
return 1;
if (f == stdin)
return 0; /* not safe to look-ahead on the keyboard! */
ch = getc(f);
if (ch == EOF)
return 1;
ungetc(ch, f);
#endif
return 0;
}
/* Check if at end of line (or end of entire file). */
int P_eoln(FILE *f)
{
register int ch;
ch = getc(f);
if (ch == EOF)
return 1;
ungetc(ch, f);
return (ch == '\n');
}
/* Read a packed array of characters from a file. */
Void P_readpaoc(FILE *f, char *s, int len)
{
int ch;
for (;;) {
if (len <= 0)
return;
ch = getc(f);
if (ch == EOF || ch == '\n')
break;
*s++ = (char) ch;
--len;
}
while (--len >= 0)
*s++ = ' ';
if (ch != EOF)
ungetc(ch, f);
}
Void P_readlnpaoc(FILE *f, char *s, int len)
{
int ch;
for (;;) {
ch = getc(f);
if (ch == EOF || ch == '\n')
break;
if (len > 0) {
*s++ = (char) ch;
--len;
}
}
while (--len >= 0)
*s++ = ' ';
}
/* Compute maximum legal "seek" index in file (0-based). */
long P_maxpos(FILE *f)
{
long savepos = ftell(f);
long val;
if (fseek(f, 0L, SEEK_END))
return -1;
val = ftell(f);
if (fseek(f, savepos, SEEK_SET))
return -1;
return val;
}
/* Use packed array of char for a file name. */
Char *P_trimname(register Char *fn, register int len)
{
static Char fnbuf[256];
register Char *cp = fnbuf;
while (--len >= 0 && *fn && !isspace((int) *fn))
*cp++ = *fn++;
*cp = 0;
return fnbuf;
}
/* Pascal's "memavail" doesn't make much sense in Unix with virtual memory.
We fix memory size as 10Meg as a reasonable compromise. */
long memavail(void)
{
return 10000000; /* worry about this later! */
}
long maxavail(void)
{
return memavail();
}
/* Sets are stored as an array of longs. S[0] is the size of the set;
S[N] is the N'th 32-bit chunk of the set. S[0] equals the maximum
I such that S[I] is nonzero. S[0] is zero for an empty set. Within
each long, bits are packed from lsb to msb. The first bit of the
set is the element with ordinal value 0. (Thus, for a "set of 5..99",
the lowest five bits of the first long are unused and always zero.) */
/* (Sets with 32 or fewer elements are normally stored as plain longs.) */
long *P_setunion(register long *d, register long *s1, register long *s2) /* d := s1 + s2 */
{
long *dbase = d++;
register int sz1 = *s1++, sz2 = *s2++;
while (sz1 > 0 && sz2 > 0) {
*d++ = *s1++ | *s2++;
sz1--, sz2--;
}
while (--sz1 >= 0)
*d++ = *s1++;
while (--sz2 >= 0)
*d++ = *s2++;
*dbase = d - dbase - 1;
return dbase;
}
long *P_setint(register long *d, register long *s1, register long *s2) /* d := s1 * s2 */
{
long *dbase = d++;
register int sz1 = *s1++, sz2 = *s2++;
while (--sz1 >= 0 && --sz2 >= 0)
*d++ = *s1++ & *s2++;
while (--d > dbase && !*d) ;
*dbase = d - dbase;
return dbase;
}
long *P_setdiff(register long *d, register long *s1, register long *s2) /* d := s1 - s2 */
{
long *dbase = d++;
register int sz1 = *s1++, sz2 = *s2++;
while (--sz1 >= 0 && --sz2 >= 0)
*d++ = *s1++ & ~*s2++;
if (sz1 >= 0) {
while (sz1-- >= 0)
*d++ = *s1++;
}
while (--d > dbase && !*d) ;
*dbase = d - dbase;
return dbase;
}
long *P_setxor(register long *d, register long *s1, register long *s2) /* d := s1 / s2 */
{
long *dbase = d++;
register int sz1 = *s1++, sz2 = *s2++;
while (sz1 > 0 && sz2 > 0) {
*d++ = *s1++ ^ *s2++;
sz1--, sz2--;
}
while (--sz1 >= 0)
*d++ = *s1++;
while (--sz2 >= 0)
*d++ = *s2++;
while (--d > dbase && !*d) ;
*dbase = d - dbase;
return dbase;
}
int P_inset(register unsigned val, register long *s) /* val IN s */
{
register int bit;
bit = val % SETBITS;
val /= SETBITS;
if ((long) val < (*s++ && ((1L<<bit) & s[val])))
return 1;
return 0;
}
long *P_addset(register long *s, register unsigned val) /* s := s + [val] */
{
register long *sbase = s;
register int bit, size;
bit = val % SETBITS;
val /= SETBITS;
size = *s;
if ((long) ++val > size) {
s += size;
while ((long) val > size)
*++s = 0, size++;
*sbase = size;
} else
s += val;
*s |= 1L<<bit;
return sbase;
}
long *P_addsetr(register long *s, register unsigned v1, register unsigned v2) /* s := s + [v1..v2] */
{
register long *sbase = s;
register int b1, b2, size;
if ((int)v1 > (int)v2)
return sbase;
b1 = v1 % SETBITS;
v1 /= SETBITS;
b2 = v2 % SETBITS;
v2 /= SETBITS;
size = *s;
v1++;
if ((int) ++v2 > size) {
while ((int) v2 > size)
s[++size] = 0;
s[v2] = 0;
*s = v2;
}
s += v1;
if (v1 == v2) {
*s |= (~((-2L)<<(b2-b1))) << b1;
} else {
*s++ |= (-1L) << b1;
while (++v1 < v2)
*s++ = -1;
*s |= ~((-2L) << b2);
}
return sbase;
}
long *P_remset(register long *s, register unsigned val) /* s := s - [val] */
{
register int bit;
bit = val % SETBITS;
val /= SETBITS;
if ((long) ++val <= *s) {
if (!(s[val] &= ~(1L<<bit)))
while (*s && !s[*s])
(*s)--;
}
return s;
}
int P_setequal(register long *s1, register long *s2) /* s1 = s2 */
{
register int size = *s1++;
if (*s2++ != size)
return 0;
while (--size >= 0) {
if (*s1++ != *s2++)
return 0;
}
return 1;
}
int P_subset(register long *s1, register long *s2) /* s1 <= s2 */
{
register int sz1 = *s1++, sz2 = *s2++;
if (sz1 > sz2)
return 0;
while (--sz1 >= 0) {
if (*s1++ & ~*s2++)
return 0;
}
return 1;
}
long *P_setcpy(register long *d, register long *s) /* d := s */
{
register long *save_d = d;
#ifdef SETCPY_MEMCPY
memcpy(d, s, (*s + 1) * sizeof(long));
#else
register int i = *s + 1;
while (--i >= 0)
*d++ = *s++;
#endif
return save_d;
}
/* s is a "smallset", i.e., a 32-bit or less set stored
directly in a long. */
long *P_expset(register long *d, register long s) /* d := s */
{
if (s) {
d[1] = s;
*d = 1;
} else
*d = 0;
return d;
}
long P_packset(register long *s) /* convert s to a small-set */
{
if (*s++)
return *s;
else
return 0;
}
/* Oregon Software Pascal extensions, courtesy of William Bader */
int P_getcmdline(int l, int h, Char *line)
{
int i, len;
char *s;
h = h - l + 1;
len = 0;
for(i = 1; i < P_argc; i++) {
s = P_argv[i];
while (*s) {
if (len >= h) return len;
line[len++] = *s++;
}
if (len >= h) return len;
line[len++] = ' ';
}
return len;
}
#ifndef NO_TIME
Void TimeStamp(Day, Month, Year, Hour, Min, Sec)
int *Day, *Month, *Year, *Hour, *Min, *Sec;
{
struct tm *tm;
long clock;
time(&clock);
tm = localtime(&clock);
*Day = tm->tm_mday;
*Month = tm->tm_mon + 1; /* Jan = 0 */
*Year = tm->tm_year;
if (*Year < 1900)
*Year += 1900; /* year since 1900 */
*Hour = tm->tm_hour;
*Min = tm->tm_min;
*Sec = tm->tm_sec;
}
Void VAXdate(s)
char *s;
{
long clock;
char *c;
int i;
static int where[] = {8, 9, 0, 4, 5, 6, 0, 20, 21, 22, 23};
time(&clock);
c = ctime(&clock);
for (i = 0; i < 11; i++)
s[i] = my_toupper(c[where[i]]);
s[2] = '-';
s[6] = '-';
}
Void VAXtime(s)
char *s;
{
long clock;
char *c;
int i;
time(&clock);
c = ctime(&clock);
for (i = 0; i < 8; i++)
s[i] = c[i+11];
s[8] = '.';
s[9] = '0';
s[10] = '0';
}
#endif
/* SUN Berkeley Pascal extensions */
Void P_sun_argv(register char *s, register int len, register int n)
{
register char *cp;
if (n < P_argc)
cp = P_argv[n];
else
cp = "";
while (*cp && --len >= 0)
*s++ = *cp++;
while (--len >= 0)
*s++ = ' ';
}
int _OutMem(void)
{
return _Escape(-2);
}
int _CaseCheck(void)
{
return _Escape(-9);
}
int _NilCheck(void)
{
return _Escape(-3);
}
/* The following is suitable for the HP Pascal operating system.
It might want to be revised when emulating another system. */
#ifdef SKIP
static char *_ShowEscape(buf, code, ior, prefix)
char *buf, *prefix;
int code, ior;
#endif
static char *_ShowEscape(char *buf, int code, int ior, char *prefix)
{
char *bufp;
if (prefix && *prefix) {
strcpy(buf, prefix);
strcat(buf, ": ");
bufp = buf + strlen(buf);
} else {
bufp = buf;
}
if (code == -10) {
sprintf(bufp, "Pascal system I/O error %d", ior);
switch (ior) {
case 3:
strcat(buf, " (illegal I/O request)");
break;
case 7:
strcat(buf, " (bad file name)");
break;
case FileNotFound: /*10*/
strcat(buf, " (file not found)");
break;
case FileNotOpen: /*13*/
strcat(buf, " (file not open)");
break;
case BadInputFormat: /*14*/
strcat(buf, " (bad input format)");
break;
case 24:
strcat(buf, " (not open for reading)");
break;
case 25:
strcat(buf, " (not open for writing)");
break;
case 26:
strcat(buf, " (not open for direct access)");
break;
case 28:
strcat(buf, " (string subscript out of range)");
break;
case EndOfFile: /*30*/
strcat(buf, " (end-of-file)");
break;
case FileWriteError: /*38*/
strcat(buf, " (file write error)");
break;
}
} else {
sprintf(bufp, "Pascal system error %d", code);
switch (code) {
case -2:
strcat(buf, " (out of memory)");
break;
case -3:
strcat(buf, " (reference to NIL pointer)");
break;
case -4:
strcat(buf, " (integer overflow)");
break;
case -5:
strcat(buf, " (divide by zero)");
break;
case -6:
strcat(buf, " (real math overflow)");
break;
case -8:
strcat(buf, " (value range error)");
break;
case -9:
strcat(buf, " (CASE value range error)");
break;
case -12:
strcat(buf, " (bus error)");
break;
case -20:
strcat(buf, " (stopped by user)");
break;
}
}
return buf;
}
int _Escape(int code)
{
char buf[100];
char token[200];
P_escapecode = code;
if (__top_jb) {
__p2c_jmp_buf *jb = __top_jb;
__top_jb = jb->next;
longjmp(jb->jbuf, 1);
}
if (code == 0)
/* exit(EXIT_SUCCESS); */
error_msg("Exit success in Basic", STOP);
if (code == -1) {
error_msg("Fatal error in Basic interpreter.", CONTINUE);
sprintf(token, "%s", _ShowEscape(buf, P_escapecode, P_ioresult, ""));
error_msg(token, STOP);
exit(EXIT_FAILURE);
}
/* fprintf(stderr, "%s\n", _ShowEscape(buf, P_escapecode, P_ioresult, "")); */
/* exit(EXIT_FAILURE); */
error_msg("Fatal error in Basic interpreter.", CONTINUE);
sprintf(token, "%s", _ShowEscape(buf, P_escapecode, P_ioresult, ""));
error_msg(token, STOP);
return(1);
}
int _EscIO(int code)
{
P_ioresult = code;
return _Escape(-10);
}
/* End. */

904
parse.cpp
View File

@ -1,904 +0,0 @@
#define EXTERNAL extern
#include "global.h"
#include "phqalloc.h"
#include "output.h"
#include "phrqproto.h"
static char const svnid[] = "$Id: parse.c 392 2005-07-19 16:05:07Z dlpark $";
static int get_coef(LDBLE *coef, char **eqnaddr);
static int get_secondary (char **t_ptr, char *element, int *i);
static int get_species (char **ptr);
/* ---------------------------------------------------------------------- */
int parse_eq(char *eqn, struct elt_list **elt_ptr, int association)
/* ---------------------------------------------------------------------- */
/*
* function to break equation up into component species
* returns species name, coefficient, and charge in global variable "rxn_list".
* Also returns pointer to elt_list structure array with list of elements
* and coefficients in species.
* rxn_list global variable, output with contiguous rxn_list structures,
* which is the reaction. Target species is first in
* list, coefficient is -1.0.
*
* Argurments:
* *eqn input, pointer to equation to be parsed.
* **elt_ptr output, pointer to contiguous elt_list structures,
* which is list of elements and coefficients in the
* target species.
* association input, TRUE or FALSE if reaction is an association reaction
*/
{
int i;
LDBLE coef, z;
char c;
char *ptr, *char_ptr;
if (svnid == NULL) fprintf(stderr," ");
paren_count = 0;
/*
* Remove white space
*/
squeeze_white(eqn);
/*
* Check for illegal characters
*/
for (i = 0; (c=eqn[i]) != '\0'; i++) {
if( islegit(c) == FALSE ){
sprintf(error_string,"Character is not allowed,\
%c (octal: %o).",c,c);
error_msg(error_string, CONTINUE);
return(ERROR);
}
}
/*
* Find coefficients, name, and charge for each species for lhs
*/
count_trxn=0;
ptr=eqn;
c = ptr[0];
for (;;) {
if (c == '=') break;
if (c == '\0'){
sprintf(error_string,"Equation has no equal sign.\n\t%s",eqn);
error_msg(error_string, CONTINUE);
return(ERROR);
}
if ( get_species (&ptr) == ERROR ){
return(ERROR);
}
c = ptr[0];
if ( association == FALSE ) {
trxn.token[count_trxn].coef *= -1.0;
}
count_trxn++;
}
/*
* Get coefficient, name, and charge of species for dissociation reaction
*/
ptr++;
if ( association == TRUE ) {
if ( get_species (&ptr) == ERROR ){
return(ERROR);
}
trxn.token[count_trxn].coef *= -1.0;
/* Swap species into first structure position */
char_ptr=trxn.token[0].name;
coef=trxn.token[0].coef;
z=trxn.token[0].z;
trxn.token[0].name=trxn.token[count_trxn].name;
trxn.token[0].coef=trxn.token[count_trxn].coef;
trxn.token[0].z=trxn.token[count_trxn].z;
trxn.token[count_trxn].name=char_ptr;
trxn.token[count_trxn].coef=coef;
trxn.token[count_trxn].z=z;
count_trxn++;
}
/*
* Get reaction species from rhs of equation
*/
c = ptr[0];
for (;;) {
if (c == '\0') break;
if ( get_species (&ptr) == ERROR ){
return(ERROR);
}
c = ptr[0];
if ( association == TRUE ) {
trxn.token[count_trxn].coef *= -1.0;
}
count_trxn++;
}
/*
* Sort list of reaction species
*/
trxn_sort();
/*
* Get elements in species or mineral formula
*/
count_elts=0;
char_ptr=trxn.token[0].name;
if ( get_elts_in_species( &char_ptr , trxn.token[0].coef ) == ERROR ) {
return(ERROR);
}
/*
* Sort elements in reaction and combine
*/
qsort (elt_list, (size_t) count_elts, (size_t) sizeof(struct elt_list), elt_list_compare);
if (elt_list_combine () == ERROR) return(ERROR);
/*
* Malloc space and store element data for return
*/
*elt_ptr=(struct elt_list *) PHRQ_malloc((size_t) (count_elts + 1)*sizeof(struct elt_list));
if (*elt_ptr == NULL ) malloc_error();
for ( i=0; i < count_elts; i++ ) {
(*elt_ptr)[i].elt=elt_list[i].elt;
(*elt_ptr)[i].coef=-elt_list[i].coef;
}
(*elt_ptr)[count_elts].elt=NULL;
/*
* Debugging print of parsed equation
trxn_print();
*/
return(OK);
}
/* ---------------------------------------------------------------------- */
int check_eqn ( int association )
/* ---------------------------------------------------------------------- */
/*
* Check that equation is balanced reaction. Uses array "trxn.token" and
* assumes "count_trxn" is set to number of species in reaction.
* Charge and elements are checked.
*
* Arguments:
*
* association input, TRUE or FALSE if reaction is an association reaction.
*/
{
int i;
int oops=0;
char *t_ptr;
LDBLE sumcharge;
paren_count=0;
count_elts=0;
/*
* Check that coefficient of first species is -1.0
*/
if ( equal(trxn.token[0].coef,-1.0,TOL) == FALSE ) {
if (association == TRUE) {
sprintf(error_string, "Coefficient of first species on rhs is not equal to 1.0.");
error_msg(error_string, CONTINUE);
} else {
sprintf(error_string, "Coefficient of mineral (first on lhs) is not equal to 1.0.");
error_msg(error_string, CONTINUE);
}
return(ERROR);
}
/*
* Go through all species in the reaction; sum the charge and store elements
*/
sumcharge=0.0;
for (i=0; i < count_trxn; i++) {
sumcharge += ( trxn.token[i].coef)*(trxn.token[i].z);
t_ptr=trxn.token[i].name;
if ( get_elts_in_species(&t_ptr, trxn.token[i].coef ) == ERROR ) {
return(ERROR);
}
}
/*
* Sort elements in reaction and combine
*/
qsort (elt_list, (size_t) count_elts, (size_t) sizeof(struct elt_list), elt_list_compare);
if (elt_list_combine() == ERROR) return(ERROR);
/*
* Check charge
*/
if ( equal(sumcharge, 0.0, TOL) == FALSE) {
sprintf(error_string, "Equation is not charge balanced.");
error_msg(error_string, CONTINUE);
oops++;
}
/*
* Check mass balance
*/
for ( i=0; i < count_elts; i++) {
if ( (equal(elt_list[i].coef,0.0,TOL) == FALSE) &&
strncmp( (elt_list[i].elt)->name , "e" , MAX_LENGTH) != 0) {
sprintf(error_string, "Equation does not balance for element, %s.", (elt_list[i].elt)->name);
error_msg(error_string, CONTINUE);
oops++;
}
}
if (oops == 0) {
return(OK);
} else {
return(ERROR);
}
}
/* ---------------------------------------------------------------------- */
int get_charge(char *charge, LDBLE *z)
/* ---------------------------------------------------------------------- */
/*
* Function takes character string and calculates the charge on
* the species. Charge can be in two forms: (1) string of "+" or "-"
* or (2) + or - followed by an integer. Charge is reduced to form (2)
* and stored in the pointer location *charge.
*
* Arguments:
* *charge input, string containing charge
* output, string containing charge of the form + or -
* followed by an integer, if integer greater than 1.
* *z output, value of charge.
*
* Returns:
* ERROR,
* OK.
*/
{
int i;
char *ptr;
char c,c1;
/*
* Charge is zero
*/
if((c=charge[0]) == '\0'){
*z=0.0;
return(OK);
}
/*
* Error check for + or - at start of string
*/
if(c != '+' && c != '-'){
sprintf(error_string,"Character string for charge does not start with + or -,\t%s.", charge);
error_msg(error_string, CONTINUE);
return(ERROR);
}
/*
* Count string of +'s or -'s
*/
i=0;
while (c == (c1=charge[i++]) );
i--;
if (c1 == '\0') {
if (c == '-') i=-i;
} else {
/*
* + or - followed by a number
*/
errno=0;
i=strtol(charge,&ptr,0);
#ifdef SKIP
if (errno == ERANGE) {
sprintf(error_string, "Error in character string for charge, %s.", charge);
error_msg(error_string, CONTINUE);
return(ERROR);
}
#endif
/*
* Truncate fractional part of charge if all zeros
*/
if (*ptr != '\0') {
if ( *ptr == '.') {
while (*(++ptr) != '\0') {
if (*ptr != '0') {
*z = strtod(charge, &ptr);
return(OK);
#ifdef SKIP
sprintf(error_string, "Charge must be an integer, %s.", charge);
error_msg(error_string, CONTINUE);
return(ERROR);
#endif
}
}
/*
* Non-numeric characters
*/
} else {
sprintf(error_string, "Error in character string for charge, %s.", charge);
error_msg(error_string, CONTINUE);
return(ERROR);
}
}
}
/*
* Charge is zero, must have had +0 or -0 in eqn
*/
if (i == 0) {
charge[0]='\0';
}
/*
* Charge is +1 or -1, single + or -
*/
if (abs(i) == 1) {
charge[0]=c;
charge[1]='\0';
}
/*
* Abs(z)>1, set charge to + or - plus integer
*/
if (abs(i)>1) {
if (sprintf(charge,"%-+d",i) == EOF){
sprintf(error_string, "Error converting charge to character string, %s.", charge);
error_msg(error_string, CONTINUE);
return(ERROR);
}
}
*z=i;
return(OK);
}
/* ---------------------------------------------------------------------- */
int get_coef(LDBLE *coef, char **eqnaddr)
/* ---------------------------------------------------------------------- */
/*
* Function reads through eqn and determines the coefficient of the next
* species.
*
* Arguments:
* *coef output, coefficient of next species.
*
* **eqnaddr input, pointer to a position in eqn to start parsing
* output, pointer to next position after coefficient
*
* Returns:
* ERROR,
* OK.
*/
{
int i;
char c,c1;
char *ptr, *ptr1, *rest;
char token[MAX_LENGTH];;
rest=*eqnaddr;
ptr=*eqnaddr; /* address of a position in eqn */
c=*ptr; /* character in eqn */
*coef=0.0;
/*
* No leading sign or number
*/
if (isalpha((int) c) ||
(c == '(') ||
(c == ')') ||
(c == '[') ||
(c == ']')
) {
*coef=1.0;
return(OK);
}
/*
* Leading +, no digits
*/
c1=*(ptr+1);
if (c == '+' &&
( isalpha((int) c1) ||
(c1 == '(') ||
(c1 == ')') ||
(c1 == '[') ||
(c1 == ']') ) ) {
*eqnaddr=++ptr;
*coef=1.0;
return(OK);
}
/*
* Leading -, no digits
*/
if (c == '-' &&
( isalpha((int) c1) ||
(c1 == '(') ||
(c1 == ')') ||
(c1 == '[') ||
(c1 == ']')
) ) {
*eqnaddr=++ptr;
*coef=-1.0;
return(OK);
}
i=0;
/*
* Has number coefficient
*/
if (isdigit((int) c) || c == '+' || c == '-' || c =='.') {
while (isdigit((int) c) || c == '+' || c == '-' || c =='.') {
token[i++]=c;
if (i >= MAX_LENGTH) {
sprintf(error_string, "Coefficient has more than MAX_LENGTH characters.");
error_msg(error_string, CONTINUE);
return(ERROR);
}
c=*(++ptr);
}
token[i]='\0';
*eqnaddr=ptr;
errno = 0;
*coef=strtod(token,&ptr1);
if ((errno == ERANGE) ||
(*ptr1 != '\0') ) {
sprintf(error_string, "Error converting coefficient in get_coef, %s.", token);
error_msg(error_string, CONTINUE);
return(ERROR);
}
return(OK);
}
/*
* None of the above, unknown construct
*/
sprintf(error_string, "Illegal equation construct detected in get_coef.\n\t%s.", rest);
error_msg(error_string, CONTINUE);
return(ERROR);
}
/* ---------------------------------------------------------------------- */
int get_elt (char **t_ptr, char *element, int *i)
/* ---------------------------------------------------------------------- */
/*
* Function reads an element name out of the equation string.
* An element name is composed of a capital letter followed by any number
* of lower case characters.
*
* Arguments:
* **t_ptr input, points to position in the equation to begin
* output, points to next character of equation after
* element name.
* *element input pointer to place to return element character string
*/
{
char c;
c=*(*t_ptr)++;
if (c == '\0') {
sprintf(error_string, "Empty string in get_elt. Expected an element name.");
error_msg(error_string, CONTINUE);
return(ERROR);
}
/*
* Load name into char array element
*/
element[0]=c;
*i=1;
if (c == '[') {
while ((c=(**t_ptr)) != ']') {
element[*i]=c;
(*i)++;
(*t_ptr)++;
if ((c=(**t_ptr)) == ']') {
element[*i]=c;
(*i)++;
(*t_ptr)++;
break;
} else if (**t_ptr == '\0') {
error_msg("No ending bracket (]) for element name", CONTINUE);
input_error++;
break;
}
}
while (islower((int) (c=(**t_ptr))) || c == '_') {
element[*i]=c;
(*i)++;
(*t_ptr)++;
}
} else {
while (islower((int) (c=(**t_ptr))) || c == '_') {
element[*i]=c;
(*i)++;
(*t_ptr)++;
}
}
element[*i]='\0';
return(OK);
}
/* ---------------------------------------------------------------------- */
int get_elts_in_species (char **t_ptr, LDBLE coef)
/* ---------------------------------------------------------------------- */
{
/*
* Makes a list of elements with their coefficients, stores elements
* in elt_list at position count_elts. Global variable count_elts is
* updated with each stored element. Also uses static global variable
* paren_count.
*
* Arguments:
* **t_ptr input, point in token string to start looking
* output, is next position to start looking
* coef input, coefficient to multiply subscripts by
*/
int i, count, l;
char c, c1;
LDBLE d;
char element[MAX_LENGTH];
while ( ( (c=**t_ptr) != '+') &&
(c != '-') && (c != '\0') ) {
/* close parenthesis */
if (c == ')') {
paren_count--;
if (paren_count < 0) {
sprintf(error_string,"Too many right parentheses.");
error_msg(error_string, CONTINUE);
return(ERROR);
}
(*t_ptr)++;
return(OK);
}
c1=*((*t_ptr)+1);
/* beginning of element name */
if (isupper((int) c) ||
(c == 'e' && c1 == '-')
|| (c == '[')
) {
/*
* Get new element and subscript
*/
if ( get_elt( t_ptr, element, &l) == ERROR) {
return(ERROR);
}
if (count_elts >= max_elts) {
space ((void **) ((void *) &elt_list), count_elts, &max_elts,
sizeof(struct elt_list));
}
elt_list[count_elts].elt = element_store ( element );
if ( get_num( t_ptr , &d ) == ERROR) {
return(ERROR);
}
elt_list[count_elts].coef = d*coef;
count_elts++;
/*
* Expand working space for elements if necessary
*/
if (count_elts >= max_elts) {
space ((void **) ((void *) &elt_list), count_elts, &max_elts,
sizeof(struct elt_list));
}
continue;
}
/*
* Open parentheses
*/
if (c=='(') {
count=count_elts;
if (c1 == ')') {
sprintf(error_string, "Empty parentheses.");
warning_msg(error_string);
}
paren_count++;
(*t_ptr)++;
if ( get_elts_in_species(t_ptr, coef ) == ERROR ) {
return(ERROR);
}
if (get_num (t_ptr, &d) == ERROR ) {
return(ERROR);
}
for (i=count; i < count_elts; i++) {
elt_list[i].coef *= d;
}
continue;
}
/*
* Colon
*/
if (c==':') {
count=count_elts;
(*t_ptr)++;
if (get_num (t_ptr, &d) == ERROR ) {
return(ERROR);
}
if ( get_elts_in_species(t_ptr, coef ) == ERROR ) {
return(ERROR);
}
for (i=count; i < count_elts; i++) {
elt_list[i].coef *= d;
}
continue;
}
/*
* Not beginning of element and not opening paren
*/
sprintf(error_string, "Parsing error in get_elts_in_species, unexpected character, %c.", c);
error_msg(error_string, CONTINUE);
input_error++;
return (ERROR);
}
if (paren_count != 0) {
sprintf(error_string,"Unbalanced parentheses.");
error_msg(error_string, CONTINUE);
input_error++;
return(ERROR);
}
return (OK);
}
/* ---------------------------------------------------------------------- */
static int get_secondary (char **t_ptr, char *element, int *i)
/* ---------------------------------------------------------------------- */
/*
* Function reads an element name out of the equation string.
* An element name is composed of a capital letter followed by any number
* of lower case characters.
*
* Arguments:
* **t_ptr input, points to position in the equation to begin
* output, points to next character of equation after
* element name.
* *element input pointer to place to return element character string
*/
{
int j;
char c;
char *ptr;
c=*(*t_ptr)++;
if (c == '\0') {
sprintf(error_string, "Empty string in get_elt. Expected an element name.");
error_msg(error_string, CONTINUE);
input_error++;
return(ERROR);
}
/*
* Load name into char array element
*/
element[0]=c;
*i=1;
if (c == '[') {
while ((c=(**t_ptr)) != ']') {
element[*i]=c;
(*i)++;
(*t_ptr)++;
if ((c=(**t_ptr)) == ']') {
element[*i]=c;
(*i)++;
(*t_ptr)++;
c=(**t_ptr);
break;
} else if ((c=(**t_ptr)) == '\0') {
error_msg("Did not find ending bracket (])", CONTINUE);
input_error++;
return(ERROR);
}
}
while (islower((int) (c=(**t_ptr))) || c == '_') {
element[*i]=c;
(*i)++;
(*t_ptr)++;
}
} else {
while (islower((int) (c=(**t_ptr))) || c == '_') {
element[*i]=c;
(*i)++;
(*t_ptr)++;
}
}
/*
* Check if secondary master species element
*/
j = *i;
ptr = *t_ptr;
if (c == '(') {
/* copy parenthesis */
element[*i]=c;
(*i)++;
(*t_ptr)++;
/* copy number */
for (;;) {
c = **t_ptr;
if (isdigit((int) c) || c == '-' || c == '.') {
element[*i]=c;
(*i)++;
(*t_ptr)++;
} else if (c == '+') {
(*t_ptr)++;
} else {
break;
}
}
/* go back to before parenthesis */
if (c != ')' ) {
*i = j;
*t_ptr = ptr;
/* put in closing parenthesis */
} else {
element[*i]=c;
(*i)++;
(*t_ptr)++;
}
}
element[*i]='\0';
return(OK);
}
/* ---------------------------------------------------------------------- */
int get_secondary_in_species (char **t_ptr, LDBLE coef)
/* ---------------------------------------------------------------------- */
{
/*
* Makes a list of elements with their coefficients, stores elements
* in elt_list at position count_elts. Global variable count_elts is
* updated with each stored element. Also uses static global variable
* paren_count.
*
* Arguments:
* **t_ptr input, point in token string to start looking
* output, is next position to start looking
* coef input, coefficient to multiply subscripts by
*/
int i, count, l;
char c, c1;
LDBLE d;
char element[MAX_LENGTH];
while ( ( (c=**t_ptr) != '+') &&
(c != '-') && (c != '\0') ) {
/* close parenthesis */
if (c == ')') {
paren_count--;
if (paren_count < 0) {
sprintf(error_string,"Too many right parentheses.");
error_msg(error_string, CONTINUE);
input_error++;
return(ERROR);
}
(*t_ptr)++;
return(OK);
}
c1=*((*t_ptr)+1);
/* beginning of element name */
if (isupper((int) c) ||
c == '[' ||
(c == 'e' && c1 == '-') ) {
/*
* Get new element and subscript
*/
if ( get_secondary( t_ptr, element, &l) == ERROR) {
return(ERROR);
}
elt_list[count_elts].elt = element_store ( element );
if ( get_num( t_ptr , &d ) == ERROR) {
return(ERROR);
}
elt_list[count_elts].coef = d*coef;
count_elts++;
/*
* Expand working space for elements if necessary
*/
if (count_elts >= max_elts) {
space ((void **) ((void *) &elt_list), count_elts, &max_elts,
sizeof(struct elt_list));
}
continue;
}
/*
* Open parentheses
*/
if (c=='(') {
count=count_elts;
if (c1 == ')') {
sprintf(error_string, "Empty parentheses.");
warning_msg(error_string);
}
paren_count++;
(*t_ptr)++;
if ( get_secondary_in_species(t_ptr, coef ) == ERROR ) {
return(ERROR);
}
if (get_num (t_ptr, &d) == ERROR ) {
return(ERROR);
}
for (i=count; i < count_elts; i++) {
elt_list[i].coef *= d;
}
continue;
}
/*
* Colon
*/
if (c==':') {
count=count_elts;
(*t_ptr)++;
if (get_num (t_ptr, &d) == ERROR ) {
return(ERROR);
}
if ( get_secondary_in_species(t_ptr, coef ) == ERROR ) {
return(ERROR);
}
for (i=count; i < count_elts; i++) {
elt_list[i].coef *= d;
}
continue;
}
/*
* Not beginning of element and not opening paren
*/
sprintf(error_string, "Parsing error in get_secondary_in_species, unexpected character, %c.", c);
error_msg(error_string, CONTINUE);
return (ERROR);
}
if (paren_count != 0) {
sprintf(error_string,"Unbalanced parentheses.");
error_msg(error_string, CONTINUE);
return(ERROR);
}
return (OK);
}
/* ---------------------------------------------------------------------- */
int get_num (char **t_ptr, LDBLE *num)
/* ---------------------------------------------------------------------- */
/*
* Function reads through a string looking for leading numeric field
* if no numeric field is found, the number is set to 1.0.
*
* Arguments:
*
* **t_ptr input, points to a position in a character string from which
* a number is to be extracted.
* output, points to next position to be parsed.
* *num address where the number is to be stored.
*
* Returns:
* ERROR,
* OK.
*/
{
int i, decimal;
char c;
char *ptr1;
char token[MAX_LENGTH];
*num=1.0;
i=0;
c=**t_ptr;
decimal=0;
if (isdigit((int) c) || (c == '.') ){
while (isdigit((int) c) || (c == '.') ) {
if (c == '.') decimal++;
if (decimal > 1) break;
token[i++]=c;
/* check number length */
if (i >= MAX_LENGTH ) {
sprintf(error_string, "Number was greater than MAX_LENGTH characters.");
error_msg(error_string, CONTINUE);
input_error++;
return(ERROR);
}
c=*(++(*t_ptr));
}
token[i]='\0';
errno=0;
*num=strtod(token,&ptr1);
if ( errno == ERANGE ) {
sprintf(error_string,"Converting number in get_num, %s.", token);
input_error++;
error_msg(error_string, CONTINUE);
return(ERROR);
}
}
return(OK);
}
/* ---------------------------------------------------------------------- */
int get_species (char **ptr)
/* ---------------------------------------------------------------------- */
{
/* Function reads next species out of the equation, including optional
* preceding coefficient and optional trailing charge. Data are
* store in trxn.token[count].
*
* Arguments:
* **ptr input, points to the position in the equation to pick up the species.
* output, points to the next character after the species charge.
*
*/
char string[MAX_LENGTH];
int l;
if (count_trxn + 1 >= max_trxn) {
space ((void **) &(trxn.token), count_trxn+1, &max_trxn,
sizeof(struct rxn_token_temp));
}
/* coefficient */
if ( get_coef(&(trxn.token[count_trxn].coef), ptr) == ERROR ) {
return(ERROR);
}
/* name and charge */
if ( get_token( ptr, string, &trxn.token[count_trxn].z, &l) == ERROR ) {
return(ERROR);
}
trxn.token[count_trxn].name = string_hsave ( string );
return(OK);
}

246
phqalloc.cpp
View File

@ -1,246 +0,0 @@
#define EXTERNAL extern
#include "global.h"
#include "output.h"
/*#include <malloc.h>*/
#include <stdlib.h>
#include <string.h>
#include <assert.h>
static char const svnid[] = "$Id: phqalloc.c 78 2005-02-01 22:47:12Z dlpark $";
#if defined(PHREEQCI_GUI)
#define _CRTDBG_MAP_ALLOC
#include <crtdbg.h>
#endif
typedef struct PHRQMemHeader {
struct PHRQMemHeader *pNext; /* memory allocated just after this one */
struct PHRQMemHeader *pPrev; /* memory allocated just prior to this one */
#if !defined(NDEBUG)
size_t size; /* memory request + sizeof(PHRQMemHeader) */
char *szFileName; /* file name */
int nLine; /* line number */
int dummy; /* alignment */
#endif
} PHRQMemHeader;
/*
* This pointer points to the last allocated block
* Note: s_pTail->pNext should always be NULL
*/
static PHRQMemHeader *s_pTail = NULL;
/* ---------------------------------------------------------------------- */
#if !defined(NDEBUG)
void *PHRQ_malloc( size_t size, const char *szFileName, int nLine)
#else
void *PHRQ_malloc( size_t size)
#endif
/* ---------------------------------------------------------------------- */
{
PHRQMemHeader *p;
if (svnid == NULL) fprintf(stderr," ");
assert((s_pTail == NULL) || (s_pTail->pNext == NULL));
p = (PHRQMemHeader*)malloc(sizeof(PHRQMemHeader) + size);
if (p == NULL) return NULL;
#if !defined(NDEBUG)
memset(p, 0, sizeof(PHRQMemHeader) + size);
#endif
p->pNext = NULL;
if ( (p->pPrev = s_pTail) != NULL ) {
s_pTail->pNext = p;
}
#if !defined(NDEBUG)
p->size = sizeof(PHRQMemHeader) + size;
p->szFileName = (char *) malloc(strlen(szFileName) + 1);
if (p->szFileName) strcpy(p->szFileName, szFileName);
p->nLine = nLine;
#endif
s_pTail = p;
p++;
return ((void *)(p));
}
/* ---------------------------------------------------------------------- */
void PHRQ_free( void *ptr )
/* ---------------------------------------------------------------------- */
{
PHRQMemHeader *p;
assert((s_pTail == NULL) || (s_pTail->pNext == NULL));
if (ptr == NULL) return;
p = (PHRQMemHeader *)ptr - 1;
if (p->pNext != NULL) {
p->pNext->pPrev = p->pPrev;
} else {
/* Handle special case when (p == s_pTail) */
assert(s_pTail != NULL);
assert(p == s_pTail);
s_pTail = p->pPrev;
}
if (p->pPrev) {
p->pPrev->pNext = p->pNext;
}
#if !defined(NDEBUG)
free(p->szFileName);
#endif
free(p);
}
/* ---------------------------------------------------------------------- */
void PHRQ_free_all( void )
/* ---------------------------------------------------------------------- */
{
assert((s_pTail == NULL) || (s_pTail->pNext == NULL));
if (s_pTail == NULL) {
#if !defined(NDEBUG)
output_msg(OUTPUT_MESSAGE, "No memory leaks\n");
#endif
return;
}
while (s_pTail->pPrev != NULL)
{
s_pTail = s_pTail->pPrev;
#if !defined(NDEBUG)
output_msg(OUTPUT_MESSAGE, "%s(%d) %p: freed in PHRQ_free_all\n",
s_pTail->pNext->szFileName, s_pTail->pNext->nLine, (void *) (s_pTail->pNext + 1));
free(s_pTail->pNext->szFileName);
#endif
free(s_pTail->pNext);
}
#if !defined(NDEBUG)
output_msg(OUTPUT_MESSAGE, "%s(%d) %p: freed in PHRQ_free_all\n",
s_pTail->szFileName, s_pTail->nLine, (void *) (s_pTail+1));
if (phast == TRUE) {
output_msg(OUTPUT_STDERR, "%s(%d) %p: freed in PHRQ_free_all, %d\n",
s_pTail->szFileName, s_pTail->nLine, (void *) (s_pTail+1), phreeqc_mpi_myself);
}
free(s_pTail->szFileName);
#endif
free(s_pTail);
s_pTail = NULL;
}
/* ---------------------------------------------------------------------- */
void *PHRQ_calloc( size_t num,
size_t size
#if !defined(NDEBUG)
,
const char *szFileName,
int nLine
#endif
)
/* ---------------------------------------------------------------------- */
{
PHRQMemHeader *p;
assert((s_pTail == NULL) || (s_pTail->pNext == NULL));
p = (PHRQMemHeader*)malloc(sizeof(PHRQMemHeader) + size * num);
if (p == NULL) return NULL;
p->pNext = NULL;
if ( (p->pPrev = s_pTail) != NULL ) {
s_pTail->pNext = p;
}
#if !defined(NDEBUG)
p->size = sizeof(PHRQMemHeader) + size * num;
p->szFileName = (char *) malloc(strlen(szFileName) + 1);
if (p->szFileName) strcpy(p->szFileName, szFileName);
p->nLine = nLine;
#endif
s_pTail = p;
p++;
return memset(p, 0, size * num);
}
/* ---------------------------------------------------------------------- */
void *PHRQ_realloc( void *ptr,
size_t size
#if !defined(NDEBUG)
,
const char *szFileName,
int nLine
#endif
)
/* ---------------------------------------------------------------------- */
{
PHRQMemHeader *p;
size_t new_size;
#if !defined(NDEBUG)
size_t old_size;
#endif
if (ptr == NULL)
{
return PHRQ_malloc(size
#if !defined(NDEBUG)
,
szFileName,
nLine
#endif
);
}
assert((s_pTail == NULL) || (s_pTail->pNext == NULL));
p = (PHRQMemHeader*)ptr - 1;
new_size = sizeof(PHRQMemHeader) + size;
#if defined(NDEBUG)
p = (PHRQMemHeader*)realloc(p, new_size);
#else
old_size = p->size;
p = (PHRQMemHeader*)realloc(p, new_size);
if (p != NULL) {
p->size = new_size;
if (new_size > old_size) {
memset((char*)p + old_size, 0, new_size - old_size);
}
}
#endif
if (p == NULL) return NULL;
if (p->pPrev != NULL) {
p->pPrev->pNext = p;
}
if (p->pNext != NULL) {
p->pNext->pPrev = p;
} else {
s_pTail = p;
}
#if !defined(NDEBUG)
free(p->szFileName);
p->szFileName = (char *) malloc(strlen(szFileName) + 1);
if (p->szFileName) strcpy(p->szFileName, szFileName);
p->nLine = nLine;
#endif
p++;
return ((void *)(p));
}

524
phreeqc_files.cpp
View File

@ -1,524 +0,0 @@
#define EXTERNAL extern
#include "global.h"
#include "phqalloc.h"
#include "output.h"
#include "phrqproto.h"
#include "input.h"
/* following line defines path for default data base file */
const char *default_data_base = "phreeqc.dat";
static FILE *input_file = NULL;
static FILE *database_file = NULL;
static FILE *output = NULL; /* OUTPUT_MESSAGE */
static FILE *log_file = NULL; /* OUTPUT_LOG */
static FILE *punch_file = NULL; /* OUTPUT_PUNCH */
static FILE *error_file = NULL; /* OUTPUT_ERROR */
static FILE *dump_file = NULL; /* OUTPUT_DUMP */
static int fileop_handler(const int type, int (*PFN)(FILE*));
static int open_handler(const int type, const char *file_name);
static int output_handler(const int type, const char *err_str, const int stop, void *cookie, const char *format, va_list args);
static int rewind_wrapper(FILE* file_ptr);
static char const svnid[] = "$Id: phreeqc_files.c 78 2005-02-01 22:47:12Z dlpark $";
/* ---------------------------------------------------------------------- */
int phreeqc_handler(const int action, const int type, const char *err_str, const int stop, void *cookie, const char *format, va_list args)
/* ---------------------------------------------------------------------- */
{
int i;
switch (action) {
case ACTION_OPEN:
return open_handler(type, err_str);
break;
case ACTION_OUTPUT:
return output_handler(type, err_str, stop, cookie, format, args);
break;
case ACTION_FLUSH:
return fileop_handler(type, fflush);
break;
case ACTION_REWIND:
return fileop_handler(type, rewind_wrapper);
break;
case ACTION_CLOSE:
i = fileop_handler(type, fclose);
switch (type) {
case OUTPUT_ERROR:
error_file = NULL;
break;
case OUTPUT_WARNING:
break;
case OUTPUT_MESSAGE:
output = NULL;
break;
case OUTPUT_PUNCH:
punch_file = NULL;
break;
case OUTPUT_SCREEN:
break;
case OUTPUT_LOG:
log_file = NULL;
break;
case OUTPUT_STDERR:
break;
case OUTPUT_DUMP:
dump_file = NULL;
break;
}
return(i);
break;
}
return ERROR;
}
/* ---------------------------------------------------------------------- */
int close_input_files(void)
/* ---------------------------------------------------------------------- */
{
int i = 0;
i |= fclose(database_file);
i |= fclose(input_file);
input_file = database_file = NULL;
return (i);
}
/* ---------------------------------------------------------------------- */
int process_file_names(int argc, char *argv[], void **db_cookie, void **input_cookie, int log)
/* ---------------------------------------------------------------------- */
{
int l;
char token[2*MAX_LENGTH], default_name[2*MAX_LENGTH];
char query[2*MAX_LENGTH];
char in_file[2*MAX_LENGTH], out_file[2*MAX_LENGTH];
char *env_ptr;
char *ptr;
int errors;
ENTRY item, *found_item;
/*
* Prepare error handling
*/
errors = setjmp(mark);
if (errors != 0) {
return errors;
}
/*
* Prep for get_line
*/
max_line = MAX_LINE;
space ((void **) ((void *) &line), INIT, &max_line, sizeof(char));
space ((void **) ((void *) &line_save), INIT, &max_line, sizeof(char));
hcreate_multi(5, &strings_hash_table);
hcreate_multi(2, &keyword_hash_table);
/*
* Initialize hash table
*/
keyword_hash = (struct key *) PHRQ_malloc(sizeof(struct key));
if (keyword_hash == NULL) {
malloc_error();
} else {
keyword_hash->name = string_hsave("database");
keyword_hash->keycount = 0;
item.key = keyword_hash->name;
item.data = keyword_hash;
found_item = hsearch_multi(keyword_hash_table, item, ENTER);
if (found_item == NULL) {
sprintf(error_string, "Hash table error in keyword initialization.");
error_msg(error_string, STOP);
}
}
/*
* Open file for screen output
*/
if (argc > 4) {
error_file = fopen(argv[4], "w");
if (error_file == NULL) {
error_file = stderr;
sprintf(error_string, "Error opening file, %s.", argv[4]);
warning_msg(error_string);
}
} else {
error_file = stderr;
}
/*
* Open user-input file
*/
strcpy(query,"Name of input file?");
if (argc <= 1) {
default_name[0]='\0';
input_file = file_open(query, default_name, "r", FALSE);
} else {
strcpy(default_name, argv[1]);
input_file = file_open(query, default_name, "r", TRUE);
}
output_msg(OUTPUT_SCREEN, "Input file: %s\n\n", default_name);
output_msg(OUTPUT_SEND_MESSAGE, "Input file: %s\r\n\r\n", default_name);
strcpy(in_file, default_name);
/*
* Open file for output
*/
strcpy(query,"Name of output file?");
#ifdef DOS
replace("."," ",default_name);
#endif
ptr = default_name;
copy_token(token, &ptr, &l);
strcat(token,".out");
if (argc <= 1) {
output = file_open(query, token, "w", FALSE);
} else if (argc == 2) {
output = file_open(query, token, "w", TRUE);
} else if (argc >= 3) {
strcpy(token, argv[2]);
output = file_open(query, token, "w", TRUE);
}
output_msg(OUTPUT_SCREEN, "Output file: %s\n\n", token);
output_msg(OUTPUT_SEND_MESSAGE, "Output file: %s\r\n\r\n", token);
strcpy(out_file, token);
/*
* Open file for errors
*/
if (log == TRUE) {
if ((log_file = fopen("phreeqc.log","w")) == NULL) {
error_msg ("Can't open log file, phreeqc.log.", STOP);
}
}
/*
* Read input file for DATABASE keyword
*/
if (get_line(getc_callback, input_file) == KEYWORD) {
ptr = line;
copy_token(token, &ptr, &l);
if (strcmp_nocase(token, "database") == 0) {
user_database = string_duplicate(ptr);
if (string_trim(user_database) == EMPTY) {
warning_msg("DATABASE file name is missing; default database will be used.");
user_database = (char *) free_check_null(user_database);
}
}
}
fclose(input_file);
if ((input_file = fopen(in_file,"r")) == NULL) {;
error_msg ("Can't reopen input file.", STOP);
}
/*
* Open data base
*/
strcpy(query,"Name of database file?");
env_ptr = getenv("PHREEQC_DATABASE");
if (user_database != NULL) {
strcpy(token, user_database);
} else if (env_ptr != NULL) {
strcpy(token, env_ptr);
} else {
strcpy(token, default_data_base);
}
if (argc <= 1) {
database_file = file_open(query, token, "r", FALSE);
} else if (argc < 4) {
database_file = file_open(query, token, "r", TRUE);
} else if (argc >= 4) {
if (user_database == NULL) {
strcpy(token, argv[3]);
} else {
#ifndef PHREEQCI_GUI
warning_msg("Database file from DATABASE keyword is used; command line argument ignored.");
#endif
}
database_file = file_open(query, token, "r", TRUE);
}
output_msg(OUTPUT_SCREEN, "Database file: %s\n\n", token);
output_msg(OUTPUT_SEND_MESSAGE, "Database file: %s\r\n\r\n", token);
output_msg(OUTPUT_MESSAGE, " Input file: %s\n", in_file);
output_msg(OUTPUT_MESSAGE, " Output file: %s\n", out_file);
output_msg(OUTPUT_MESSAGE, "Database file: %s\n\n", token);
/*
* local cleanup
*/
user_database = (char *) free_check_null(user_database);
line = (char *) free_check_null(line);
line_save = (char *) free_check_null(line_save);
hdestroy_multi(keyword_hash_table);
keyword_hash = (struct key *) free_check_null(keyword_hash);
keyword_hash_table = NULL;
free_hash_strings(strings_hash_table);
hdestroy_multi(strings_hash_table);
strings_hash_table = NULL;
*db_cookie = database_file;
*input_cookie = input_file;
return 0;
}
/* ---------------------------------------------------------------------- */
int getc_callback(void* cookie)
/* ---------------------------------------------------------------------- */
{
int i;
assert(cookie);
i = getc((FILE*)cookie);
#ifdef PHREEQ98
if (i == '\n') ++inputlinenr;
#endif
return i;
}
/* ---------------------------------------------------------------------- */
static int output_handler(const int type, const char *err_str, const int stop, void *cookie, const char *format, va_list args)
/* ---------------------------------------------------------------------- */
{
int flush;
FILE *save_output = NULL;
flush = TRUE;
if (get_forward_output_to_log()) {
save_output = output;
output = log_file;
}
switch (type) {
case OUTPUT_ERROR:
if (status_on == TRUE) {
if (error_file != NULL) {
fprintf(error_file, "\n");
}
#ifndef DOS
status_on = FALSE;
#endif
}
if (error_file != NULL) {
fprintf(error_file, "ERROR: %s\n", err_str);
if (flush) fflush(error_file);
}
if (output != NULL) {
fprintf(output, "ERROR: %s\n", err_str);
if (flush) fflush(output);
}
if (stop == STOP) {
if (error_file != NULL) {
fprintf(error_file, "Stopping.\n");
fflush(error_file);
}
if (output != NULL) {
fprintf(output, "Stopping.\n");
fflush(output);
}
}
break;
case OUTPUT_WARNING:
if (pr.logfile == TRUE && log_file != NULL) {
fprintf(log_file,"WARNING: %s\n", err_str);
if (flush) fflush(log_file);
}
if (state == TRANSPORT && transport_warnings == FALSE) return(OK);
if (state == ADVECTION && advection_warnings == FALSE) return(OK);
if (pr.warnings >= 0) {
if (count_warnings > pr.warnings) return(OK);
}
if (status_on == TRUE) {
if (error_file != NULL) {
fprintf(error_file,"\n");
}
#ifndef DOS
status_on = FALSE;
#endif
}
if (error_file != NULL) {
fprintf(error_file,"WARNING: %s\n", err_str);
if (flush) fflush(error_file);
}
if (output != NULL) {
fprintf(output,"WARNING: %s\n", err_str);
if (flush) fflush(output);
}
break;
case OUTPUT_CHECKLINE:
if (pr.echo_input == TRUE) {
if (output != NULL) {
vfprintf(output, format, args);
if (flush) fflush(output);
}
}
break;
case OUTPUT_MESSAGE:
case OUTPUT_BASIC:
if (output != NULL) {
vfprintf(output, format, args);
if (flush) fflush(output);
}
break;
case OUTPUT_PUNCH:
if (punch_file != NULL) {
if (pr.punch == TRUE && punch.in == TRUE) {
vfprintf(punch_file, format, args);
if (flush) fflush(punch_file);
}
}
break;
case OUTPUT_LOG:
if (pr.logfile == TRUE && log_file != NULL) {
vfprintf(log_file, format, args);
if (flush) fflush(log_file);
}
break;
case OUTPUT_SCREEN:
if (error_file != NULL) {
vfprintf(error_file, format, args);
if (flush) fflush(error_file);
}
break;
case OUTPUT_STDERR:
case OUTPUT_CVODE:
if (stderr != NULL) {
vfprintf(stderr, format, args);
fflush(stderr);
}
break;
case OUTPUT_DUMP:
if (dump_file != NULL) {
vfprintf(dump_file, format, args);
if (flush) fflush(dump_file);
}
break;
}
if (get_forward_output_to_log()) {
output = save_output;
}
return(OK);
}
/* ---------------------------------------------------------------------- */
int close_output_files(void)
/* ---------------------------------------------------------------------- */
{
int ret = 0;
if (output != NULL) ret |= fclose(output);
if (log_file != NULL) ret |= fclose(log_file);
if (punch_file != NULL) ret |= fclose(punch_file);
if (dump_file != NULL) ret |= fclose(dump_file);
if (error_file != NULL) ret |= fclose(error_file);
error_file = NULL;
output = log_file = punch_file = dump_file = NULL;
return ret;
}
/* ---------------------------------------------------------------------- */
static int open_handler(const int type, const char *file_name)
/* ---------------------------------------------------------------------- */
{
switch (type) {
case OUTPUT_PUNCH:
if (punch_file != NULL) {
fclose(punch_file);
punch_file = NULL;
}
if( (punch_file = fopen(file_name, "w")) == NULL) {
return ERROR;
} else {
free_check_null(selected_output_file_name);
selected_output_file_name = string_duplicate(file_name);
}
break;
case OUTPUT_DUMP:
if (dump_file != NULL) {
fclose(dump_file);
dump_file = NULL;
}
if( (dump_file = fopen(file_name, "w")) == NULL) {
return ERROR;
} else {
free_check_null(dump_file_name);
dump_file_name = string_duplicate(file_name);
}
break;
}
return(OK);
}
/* ---------------------------------------------------------------------- */
static int fileop_handler(const int type, int (*PFN)(FILE*))
/* ---------------------------------------------------------------------- */
{
FILE *save_output = NULL;
int forward = get_forward_output_to_log();
if (forward) {
save_output = output;
output = log_file;
}
switch (type) {
case OUTPUT_ERROR:
if (error_file) PFN(error_file);
break;
case OUTPUT_WARNING:
if (error_file) PFN(error_file);
if (output) PFN(output);
break;
case OUTPUT_MESSAGE:
case OUTPUT_CHECKLINE:
case OUTPUT_BASIC:
if (output) PFN(output);
break;
case OUTPUT_PUNCH:
if (punch_file) PFN(punch_file);
break;
case OUTPUT_SCREEN:
if (error_file) PFN(error_file);
break;
case OUTPUT_LOG:
if (log_file) PFN(log_file);
break;
case OUTPUT_CVODE:
case OUTPUT_STDERR:
if (stderr) PFN(stderr);
break;
case OUTPUT_DUMP:
if (dump_file) PFN(dump_file);
break;
}
if (forward) {
output = save_output;
}
return(OK);
}
/* ---------------------------------------------------------------------- */
static int rewind_wrapper(FILE* file_ptr)
/* ---------------------------------------------------------------------- */
{
rewind(file_ptr);
return(OK);
}

515
phrqproto.h
View File

@ -1,515 +0,0 @@
#ifdef PHREEQC_IDENT
static char const svnidphrqproto[] = "$Id$";
#endif
/* advection.c */
int advection(void);
/* basic.c */
LDBLE system_total(char *total_name, LDBLE *count, char ***names, char ***types, LDBLE **moles);
int basic_main(char *commands);
void cmd_initialize(void);
void cmd_free(void);
int basic_compile(char *commands, void **lnbase, void **vbase, void **lpbase);
int basic_run(char *commands, void *lnbase, void *vbase, void *lpbase);
/* basicsubs.c */
LDBLE activity (char *species_name);
LDBLE calc_logk_n(char *name);
LDBLE calc_logk_p(char *name);
LDBLE calc_logk_s(char *name);
LDBLE calc_surface_charge(char *surface_name);
LDBLE diff_layer_total(char *total_name, char *surface_name);
LDBLE equi_phase (char *phase_name);
LDBLE find_gas_comp (char *gas_comp_name);
LDBLE find_misc1 (char *s_s_name);
LDBLE find_misc2 (char *s_s_name);
LDBLE find_s_s_comp (char *s_s_comp_name);
LDBLE get_calculate_value(char *name);
LDBLE kinetics_moles (char *kinetics_name);
LDBLE log_activity (char *species_name);
LDBLE log_molality (char *species_name);
LDBLE molality (char *species_name);
LDBLE saturation_ratio (char *phase_name);
int saturation_index (char *phase_name, LDBLE *iap, LDBLE *si);
LDBLE solution_sum_secondary(char *total_name);
LDBLE sum_match_gases (char *stemplate, char *name);
LDBLE sum_match_species (char *stemplate, char *name);
LDBLE sum_match_s_s (char *stemplate, char *name);
int match_elts_in_species (char *name, char *stemplate);
int extract_bracket(char **string, char *bracket_string);
LDBLE surf_total(char *total_name, char *surface_name);
int system_species_compare(const void *ptr1, const void *ptr2);
LDBLE system_total(char *total_name, LDBLE *count, char ***names, char ***types, LDBLE **moles);
int system_total_elements(void);
int system_total_si(void);
int system_total_aq(void);
int system_total_ex(void);
int system_total_surf(void);
int system_total_gas(void);
int system_total_s_s(void);
int system_total_elt(char *total_name);
int system_total_elt_secondary(char *total_name);
LDBLE total (char *total_name);
/* cl1.c */
int cl1(int k, int l, int m, int n,
int nklmd, int n2d,
LDBLE *q,
int *kode, LDBLE toler,
int *iter, LDBLE *x, LDBLE *res, LDBLE *error,
LDBLE *cu, int *iu, int *s,
int check);
/* default.c */
int close_input_files(void);
int close_output_files(void);
int getc_callback(void* cookie);
int process_file_names(int argc, char *argv[], void **db_cookie, void **input_cookie, int log);
/* integrate.c */
int calc_all_g(void);
int calc_init_g(void);
int initial_surface_water(void);
int sum_diffuse_layer(struct surface_charge *surface_charge_ptr1);
int calc_all_donnan(void);
int calc_init_donnan(void);
/* inverse.c */
int inverse_models(void);
/* isotopes.c */
int add_isotopes(struct solution *solution_ptr);
int calculate_values(void);
int calculate_isotope_moles(struct element *elt_ptr, struct solution *solution_ptr, LDBLE total_moles);
LDBLE convert_isotope(struct master_isotope *master_isotope_ptr, LDBLE ratio);
int from_pcil(struct master_isotope *master_isotope_ptr);
int from_permil(struct master_isotope *master_isotope_ptr, LDBLE major_total);
int from_pct(struct master_isotope *master_isotope_ptr, LDBLE major_total);
int from_tu(struct master_isotope *master_isotope_ptr);
struct calculate_value *calculate_value_alloc(void);
int calculate_value_free(struct calculate_value *calculate_value_ptr);
struct calculate_value *calculate_value_search (char *name);
struct calculate_value *calculate_value_store (char *name, int replace_if_found);
struct isotope_alpha *isotope_alpha_alloc(void);
struct isotope_alpha *isotope_alpha_search (char *name);
struct isotope_alpha *isotope_alpha_store (char *name, int replace_if_found);
struct isotope_ratio *isotope_ratio_alloc(void);
struct isotope_ratio *isotope_ratio_search (char *name);
struct isotope_ratio *isotope_ratio_store (char *name, int replace_if_found);
struct master_isotope *master_isotope_store (char *name, int replace_if_found);
struct master_isotope *master_isotope_alloc(void);
struct master_isotope *master_isotope_search (char *name);
int print_initial_solution_isotopes(void);
int print_isotope_ratios(void);
int print_isotope_alphas(void);
int punch_isotopes(void);
int punch_calculate_values(void);
int read_calculate_values (void);
int read_isotopes(void);
int read_isotope_ratios (void);
int read_isotope_alphas (void);
/* kinetics.c */
void cvode_init(void);
int run_reactions(int i, LDBLE kin_time, int use_mix, LDBLE step_fraction);
int set_and_run(int i, int use_mix, int use_kinetics, int nsaver, LDBLE step_fraction);
int set_and_run_wrapper(int i, int use_mix, int use_kinetics, int nsaver, LDBLE step_fraction);
int set_advection(int i, int use_mix, int use_kinetics, int nsaver);
int free_cvode(void);
/* main.c */
int main(int argc, char *argv[]);
/* mainsubs.c */
FILE *file_open (char *query, char *default_name, const char *status, int batch);
int copy_entities(void);
void initialize(void);
int initial_exchangers(int print);
int initial_gas_phases(int print);
int initial_solutions(int print);
int step_save_exch(int n_user);
int step_save_surf(int n_user);
int initial_surfaces(int print);
int k_temp(LDBLE tempc);
int reactions(void);
int saver(void);
int xsolution_save(int k_user);
int do_initialize(void);
int do_status(void);
/* model.c */
int check_residuals(void);
int free_model_allocs(void);
int ineq(int kode);
int model(void);
int jacobian_sums (void);
int mb_gases(void);
int mb_s_s(void);
int mb_sums (void);
int molalities (int allow_overflow);
int reset(void);
int residuals(void);
int set(int initial);
int sum_species(void);
int surface_model(void);
/* p2clib.c */
/* parse.c */
int check_eqn ( int association );
int get_charge(char *charge, LDBLE *z);
int get_elt (char **t_ptr, char *element, int *i);
int get_elts_in_species (char **t_ptr, LDBLE coef);
int get_num (char **t_ptr, LDBLE *num);
int get_secondary_in_species (char **t_ptr, LDBLE coef);
int parse_eq(char *eqn, struct elt_list **elt_ptr, int association);
/* pitzer.c */
int gammas_pz(void);
int model_pz(void);
int pitzer (void);
int pitzer_clean_up(void);
int pitzer_init (void);
int pitzer_tidy (void);
int read_pitzer (void);
int set_pz(int initial);
/* prep.c */
int check_same_model(void);
int k_temp(LDBLE tc);
LDBLE k_calc(LDBLE *logk, LDBLE tempk);
int prep(void);
int reprep (void);
int rewrite_master_to_secondary(struct master *master_ptr1, struct master *master_ptr2);
int switch_bases(void);
int write_phase_sys_total (int n);
/* print.c */
int fpunchf(const char* name, const char* format, ...);
int fpunchf_user(int user_index, const char* format, ...);
char *sformatf(const char* format, ...);
int array_print(LDBLE *array_l, int row_count, int column_count, int max_column_count);
int print_all(void);
int print_exchange(void);
int print_gas_phase(void);
int print_master_reactions(void);
int print_reaction(struct reaction *rxn_ptr);
int print_species(void);
int print_surface(void);
int punch_all(void);
/* read.c */
int read_input(void);
int read_conc(int n, int count_mass_balance, char *str);
int *read_list_ints_range (char **ptr, int *count_ints, int positive, int *int_list );
int read_log_k_only (char *ptr, LDBLE *log_k);
int read_number_description (char *ptr, int *n_user, int *n_user_end,
char **description);
int check_key (char *str);
int check_units (char *tot_units, int alkalinity, int check_compatibility,
const char *default_units, int print);
int find_option(char *item, int *n, const char **list, int count_list, int exact);
int get_option (const char **opt_list, int count_opt_list, char **next_char);
int get_true_false(char *string, int default_value);
/* readtr.c */
int read_transport (void);
int dump(void);
int dump_exchange(int k);
int dump_gas_phase(int k);
int dump_kinetics (int k);
int dump_mix (int k);
int dump_pp_assemblage(int k);
int dump_reaction (int k);
int dump_s_s_assemblage (int k);
int dump_solution (int k);
int dump_surface(int k);
/* spread.c */
int read_solution_spread(void);
/* step.c */
int step(LDBLE step_fraction);
int xsolution_zero (void);
int add_exchange (struct exchange *exchange_ptr);
int add_gas_phase (struct gas_phase *gas_phase_ptr);
int add_kinetics (struct kinetics *kinetics_ptr);
int add_mix (struct mix *mix_ptr);
int add_pp_assemblage (struct pp_assemblage *pp_assemblage_ptr);
int add_reaction (struct irrev *irrev_ptr, int step_number, LDBLE step_fraction);
int add_s_s_assemblage (struct s_s_assemblage *s_s_assemblage_ptr);
int add_solution (struct solution *solution_ptr, LDBLE extensive,
LDBLE intensive);
int add_surface (struct surface *surface_ptr);
int add_temperature(struct temperature *temperature_ptr, int step_number);
/* structures.c */
int clean_up(void);
int copier_add(struct copier *copier_ptr, int n_user, int start, int end);
int copier_free(struct copier *copier_ptr);
int copier_init(struct copier *copier_ptr);
int copy_entities(void);
int element_compare(const void *ptr1, const void *ptr2);
struct element *element_store (char *element);
int elt_list_combine(void);
int elt_list_compare(const void *ptr1, const void *ptr2);
struct elt_list *elt_list_dup(struct elt_list *elt_list_ptr_old);
int elt_list_print(struct elt_list *elt_list_ptr);
struct elt_list *elt_list_save(void);
struct exchange *exchange_alloc (void);
struct exchange *exchange_bsearch (int k, int *n);
int exchange_comp_compare(const void *ptr1, const void *ptr2);
int exchange_copy(struct exchange *exchange_old_ptr, struct exchange *exchange_new_ptr, int n_user_new);
int exchange_compare (const void *ptr1, const void *ptr2);
int exchange_copy_to_last(int n, int n_user);
int exchange_delete(int n_user_old);
int exchange_duplicate(int n_user_old, int n_user_new);
int exchange_init (struct exchange *exchange_ptr, int n_user, int n_user_end, char *description);
int exchange_free (struct exchange *exchange_ptr);
int exchange_ptr_to_user(struct exchange *exchange_old_ptr, int n_user_new);
struct exchange *exchange_replicate(struct exchange *exchange_old_ptr, int n_user_new);
struct exchange *exchange_search(int n_user, int *n, int print);
int exchange_sort(void);
int gas_comp_compare(const void *ptr1, const void *ptr2);
struct gas_phase *gas_phase_alloc (void);
struct gas_phase *gas_phase_bsearch (int k, int *n);
int gas_phase_compare (const void *ptr1, const void *ptr2);
int gas_phase_copy(struct gas_phase *gas_phase_old_ptr,
struct gas_phase *gas_phase_new_ptr, int n_user_new);
int gas_phase_copy_to_last(int n, int n_user);
int gas_phase_delete(int n_user_old);
int gas_phase_duplicate(int n_user_old, int n_user_new);
int gas_phase_init (struct gas_phase *gas_phase_ptr, int n_user, int n_user_end, char *description);
int gas_phase_free (struct gas_phase *gas_phase_ptr);
int gas_phase_ptr_to_user(struct gas_phase *gas_phase_ptr_old, int n_user_new);
struct gas_phase *gas_phase_replicate(struct gas_phase *gas_phase_old_ptr, int n_user_new);
struct gas_phase *gas_phase_search (int n_user, int *n);
int gas_phase_sort(void);
enum entity_type get_entity_enum (char *name);
struct inverse *inverse_alloc(void);
int inverse_delete (int i);
int inverse_isotope_compare (const void *ptr1, const void *ptr2);
struct inverse *inverse_search (int n_user, int *n);
int inverse_sort(void);
struct irrev *irrev_bsearch (int k, int *n);
int irrev_copy(struct irrev *irrev_old_ptr, struct irrev *irrev_new_ptr, int n_user_new);
int irrev_duplicate(int n_user_old, int n_user_new);
int irrev_free (struct irrev *irrev_ptr);
struct irrev *irrev_search(int n_user, int *n);
struct kinetics *kinetics_alloc (void);
struct kinetics *kinetics_bsearch (int k, int *n);
int kinetics_delete(int n_user_old);
int kinetics_comp_duplicate(struct kinetics_comp *kinetics_comp_new_ptr, struct kinetics_comp *kinetics_comp_old_ptr);
int kinetics_compare (const void *ptr1, const void *ptr2);
int kinetics_copy(struct kinetics *kinetics_old_ptr,
struct kinetics *kinetics_new_ptr, int n_user_new);
int kinetics_copy_to_last(int n, int n_user);
int kinetics_duplicate(int n_user_old, int n_user_new);
int kinetics_init (struct kinetics *kinetics_ptr, int n_user, int n_user_end, char *description);
int kinetics_free (struct kinetics *kinetics_ptr);
int kinetics_ptr_to_user(struct kinetics *kinetics_ptr_old, int n_user_new);
struct kinetics *kinetics_replicate(struct kinetics *kinetics_old_ptr, int n_user_new);
struct kinetics *kinetics_search(int n_user, int *n, int print);
int kinetics_sort(void);
struct logk *logk_alloc(void);
struct logk *logk_store (char *name, int replace_if_found);
struct logk *logk_search (char *name);
struct master *master_alloc(void);
int master_compare (const void *ptr1, const void *ptr2);
int master_delete(char *ptr);
struct master *master_bsearch (const char *ptr);
struct master *master_bsearch_primary (char *ptr);
struct master *master_search (char *ptr, int *n);
struct mix *mix_bsearch (int k, int *n);
int mix_copy(struct mix *mix_old_ptr,
struct mix *mix_new_ptr, int n_user_new);
int mix_duplicate(int n_user_old, int n_user_new);
int mix_free (struct mix *mix_ptr);
struct mix *mix_search(int n_user, int *n, int print);
int mix_sort(void);
struct pe_data *pe_data_alloc(void);
struct pe_data *pe_data_dup (struct pe_data *pe_ptr_old);
int pe_data_free (struct pe_data *pe_data_ptr);
int pe_data_store (struct pe_data **pe, const char *token);
struct phase *phase_bsearch (char *ptr, int *j, int print);
int phase_compare(const void *ptr1, const void *ptr2);
int phase_delete(int i);
struct phase *phase_store (char *name);
struct pp_assemblage *pp_assemblage_alloc (void);
struct pp_assemblage *pp_assemblage_bsearch (int k, int *n);
int pp_assemblage_compare(const void *ptr1, const void *ptr2);
int pp_assemblage_copy(struct pp_assemblage *pp_assemblage_old_ptr, struct pp_assemblage *pp_assemblage_new_ptr, int n_user_new);
int pp_assemblage_copy_to_last(int n, int n_user);
int pp_assemblage_delete(int n_user_old);
int pp_assemblage_duplicate(int n_user_old, int n_user_new);
int pp_assemblage_free (struct pp_assemblage *pp_assemblage_ptr);
int pp_assemblage_init (struct pp_assemblage *pp_assemblage_ptr, int n_user, int n_user_end, char *description);
int pp_assemblage_ptr_to_user(struct pp_assemblage *pp_assemblage_ptr_old, int n_user_new);
struct pp_assemblage *pp_assemblage_replicate(struct pp_assemblage *pp_assemblage_old_ptr, int n_user_new);
struct pp_assemblage *pp_assemblage_search (int n_user, int *n);
int pp_assemblage_sort(void);
int pure_phase_compare (const void *ptr1, const void *ptr2);
struct rate *rate_bsearch (char *ptr, int *j);
int rate_free(struct rate *rate_ptr);
struct rate *rate_search (char *name, int *n);
int rate_sort(void);
struct reaction *rxn_alloc(int ntokens);
struct reaction *rxn_dup(struct reaction *rxn_ptr_old);
LDBLE rxn_find_coef(struct reaction *r_ptr, const char *str);
int rxn_free(struct reaction *rxn_ptr);
int s_compare (const void *ptr1, const void *ptr2);
int s_delete (int i);
struct species *s_search (char *name);
struct species *s_store (char *name, LDBLE z, int replace_if_found);
struct s_s_assemblage *s_s_assemblage_alloc (void);
struct s_s_assemblage *s_s_assemblage_bsearch (int k, int *n);
int s_s_assemblage_compare (const void *ptr1, const void *ptr2);
int s_s_assemblage_copy(struct s_s_assemblage *s_s_assemblage_old_ptr,
struct s_s_assemblage *s_s_assemblage_new_ptr, int n_user_new);
int s_s_assemblage_copy_to_last(int n, int n_user);
int s_s_assemblage_duplicate(int n_user_old, int n_user_new);
int s_s_assemblage_delete(int n_user_old);
int s_s_assemblage_free (struct s_s_assemblage *s_s_assemblage_ptr);
int s_s_assemblage_init (struct s_s_assemblage *s_s_assemblage_ptr, int n_user, int n_user_end, char *description);
int s_s_assemblage_ptr_to_user(struct s_s_assemblage *s_s_assemblage_ptr_old, int n_user_new);
struct s_s_assemblage *s_s_assemblage_replicate(struct s_s_assemblage *s_s_assemblage_old_ptr, int n_user_new);
struct s_s_assemblage *s_s_assemblage_search (int n_user, int *n);
int s_s_assemblage_sort(void);
int s_s_compare (const void *ptr1, const void *ptr2);
struct save_values *save_values_bsearch (struct save_values *k, int *n);
int save_values_compare(const void *ptr1, const void *ptr2);
int save_values_sort(void);
int save_values_store(struct save_values *s_v);
int conc_compare(const void *ptr1, const void *ptr2);
int conc_init (struct conc *conc_ptr);
int isotope_compare (const void *ptr1, const void *ptr2);
struct solution *solution_alloc(void);
struct solution *solution_bsearch (int k, int *n, int print);
int solution_copy_to_last(int n, int n_user_new);
int solution_duplicate(int n_user_old, int n_user_new);
int solution_delete(int n_user_old);
int solution_free (struct solution *solution_ptr);
int solution_ptr_to_user(struct solution *solution_old_ptr, int n_user_new);
struct solution *solution_replicate(struct solution *solution_old_ptr, int n_user_new);
int solution_sort(void);
int species_list_compare_alk (const void *ptr1, const void *ptr2);
int species_list_compare_master (const void *ptr1, const void *ptr2);
int species_list_sort(void);
struct surface *surface_alloc (void);
struct surface *surface_bsearch (int k, int *n);
int surface_comp_compare(const void *ptr1, const void *ptr2);
int surface_compare (const void *ptr1, const void *ptr2);
int surface_copy(struct surface *surface_old_ptr, struct surface *surface_new_ptr, int n_user_new);
int surface_copy_to_last(int n, int n_user);
int surface_delete(int n_user_old);
int surface_duplicate(int n_user_old, int n_user_new);
int surface_free(struct surface *surface_ptr);
int surface_init(struct surface *surface_ptr, int n_user, int n_user_end, char *description);
int surface_ptr_to_user(struct surface *surface_ptr_old, int n_user_new);
struct surface *surface_replicate(struct surface *surface_old_ptr, int n_user_new);
struct surface *surface_search(int n_user, int *n, int print);
int surface_sort(void);
int system_duplicate (int i, int save_old);
struct temperature *temperature_bsearch (int k, int *n);
int temperature_copy(struct temperature *temperature_old_ptr,
struct temperature *temperature_new_ptr, int n_user_new);
int temperature_duplicate(int n_user_old, int n_user_new);
int temperature_free (struct temperature *temperature_ptr);
struct temperature *temperature_search(int n_user, int *n);
int temperature_sort(void);
int trxn_add (struct reaction *r_ptr, LDBLE coef, int combine);
int trxn_combine (void);
int trxn_copy (struct reaction *rxn_ptr);
LDBLE trxn_find_coef(const char *str, int start);
int trxn_print (void);
int trxn_reverse_k (void);
int trxn_sort( void );
int trxn_swap (const char *token);
struct unknown *unknown_alloc(void);
int unknown_delete(int i);
int unknown_free(struct unknown *unknown_ptr);
/* tally.c */
void add_all_components_tally(void);
int build_tally_table(void);
int calc_dummy_kinetic_reaction_tally(struct kinetics *kinetics_ptr);
int diff_tally_table(void);
int extend_tally_table(void);
int free_tally_table(void);
int fill_tally_table(int *n_user, int index_conservative, int n_buffer);
int get_tally_table_rows_columns(int *rows, int *columns);
int get_tally_table_column_heading(int column, int *type, char *string);
int get_tally_table_row_heading(int column, char *string);
int store_tally_table(double *array, int row_dim, int col_dim, double fill_factor);
int zero_tally_table(void);
/* tidy.c */
int add_other_logk(LDBLE *source_k, int count_add_logk, struct name_coef *add_logk);
int select_log_k_expression(LDBLE *source_k, LDBLE *target_k);
int s_s_prep(LDBLE t, struct s_s *s_s_ptr, int print);
int tidy_punch(void);
int tidy_model(void);
/* transport.c */
int transport(void);
int set_initial_moles(int i);
/* utilities.c */
int add_elt_list(struct elt_list *elt_list_ptr, LDBLE coef);
int backspace_screen (int spaces);
LDBLE calc_alk(struct reaction *rxn_ptr);
int compute_gfw(const char *string, LDBLE *gfw);
int copy_token (char *token_ptr, char **ptr, int *length);
int dup_print(const char *ptr, int emphasis);
int equal (LDBLE a, LDBLE b, LDBLE eps);
void *free_check_null(void *ptr);
void free_hash_strings(HashTable *Table);
int get_token(char **eqnaddr, char *string, LDBLE *z, int *l);
int hcreate_multi(unsigned Count, HashTable **HashTable_ptr);
void hdestroy_multi(HashTable *HashTable_ptr);
ENTRY * hsearch_multi(HashTable *Table, ENTRY item, ACTION action);
int islegit(const char c);
void malloc_error (void);
int parse_couple(char *token);
int print_centered(const char *string);
int replace(const char *str1, const char *str2, char *str);
void space (void **ptr, int i, int *max, int struct_size);
void squeeze_white(char *s_l);
int status (int count, const char *str);
void str_tolower(char *str);
void str_toupper(char *str);
int strcmp_nocase(const char *str1, const char *str2);
int strcmp_nocase_arg1(const char *str1, const char *str2);
char * string_duplicate (const char *token);
char *string_hsave (const char *str);
char *string_pad (char *str, int i);
int string_trim (char *str);
int string_trim_right (char *str);
int string_trim_left (char *str);
LDBLE under (LDBLE xval);
int get_elts_in_species (char **t_ptr, LDBLE coef);

19
phrqtype.h
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@ -1,19 +0,0 @@
/*
* The following implements long double
* Many machines long double = double so there is no advantage
* Check float.h include file for number of digits (LDBL_DIG)
* Need to define here and in cl1.c
*/
#ifdef PHREEQC_IDENT
static char const svnidphrqtype[] = "$Id$";
#endif
/*#define USE_LONG_DOUBLE*/
#ifdef USE_LONG_DOUBLE
#define LDBLE long double
#define SCANFORMAT "%Lf"
#else
#define LDBLE double
#define SCANFORMAT "%lf"
#endif

1587
pitzer.cpp
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File diff suppressed because it is too large Load Diff

50
pitzer.h
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@ -1,50 +0,0 @@
typedef enum { TYPE_B0, TYPE_B1, TYPE_B2, TYPE_C0, TYPE_THETA, TYPE_LAMDA, TYPE_ZETA, TYPE_PSI, TYPE_ETHETA, TYPE_Other } pitz_param_type;
PITZER_EXTERNAL double VP, DW0;
struct pitz_param {
char * species[3];
int ispec[3];
pitz_param_type type;
double p;
union {double b0;
double b1;
double b2;
double c0;
double theta;
double lamda;
double zeta;
double psi;} U;
double a[5];
double alpha;
struct theta_param *thetas;
};
PITZER_EXTERNAL struct pitz_param **pitz_params;
PITZER_EXTERNAL int count_pitz_param, max_pitz_param;
/* routines define in pitzer_structures.c */
PITZER_EXTERNAL struct pitz_param *pitz_param_read (char *string, int n);
PITZER_EXTERNAL int pitz_param_search(struct pitz_param *pzp_ptr);
PITZER_EXTERNAL struct theta_param *theta_param_search(double zj, double zk);
PITZER_EXTERNAL struct theta_param *theta_param_alloc (void);
PITZER_EXTERNAL int theta_param_init (struct theta_param *theta_param_ptr);
/* defined in DW */
PITZER_EXTERNAL int DW (double T);
PITZER_EXTERNAL double DC (double T);
struct theta_param {
double zj;
double zk;
double etheta;
double ethetap;
};
PITZER_EXTERNAL struct theta_param **theta_params;
PITZER_EXTERNAL int count_theta_param, max_theta_param;
PITZER_EXTERNAL double OTEMP;

195
pitzer_structures.cpp
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@ -1,195 +0,0 @@
#define EXTERNAL extern
#include "global.h"
#include "phqalloc.h"
#include "output.h"
#include "phrqproto.h"
#define PITZER_EXTERNAL extern
#include "pitzer.h"
static char const svnid[] = "$Id: structures.c 269 2005-04-27 19:54:25Z dlpark $";
static struct pitz_param *pitz_param_alloc (void);
static int pitz_param_init (struct pitz_param *pitz_param_ptr);
static struct pitz_param *pitz_param_duplicate(struct pitz_param *old_ptr);
static int pitz_param_copy(struct pitz_param *old_ptr, struct pitz_param *new_ptr);
/* **********************************************************************
*
* Routines related to structure "pitz_param"
*
* ********************************************************************** */
/* ---------------------------------------------------------------------- */
struct pitz_param *pitz_param_alloc (void)
/* ---------------------------------------------------------------------- */
{
struct pitz_param *pitz_param_ptr;
pitz_param_ptr = (struct pitz_param *) PHRQ_malloc(sizeof (struct pitz_param));
if (pitz_param_ptr == NULL) malloc_error();
return ( pitz_param_ptr );
}
/* ---------------------------------------------------------------------- */
int pitz_param_init (struct pitz_param *pitz_param_ptr)
/* ---------------------------------------------------------------------- */
{
int i;
/*
* Frees all data associated with pitz_param structure.
*/
if (pitz_param_ptr == NULL) return(ERROR);
pitz_param_ptr->species[0] = NULL;
pitz_param_ptr->species[1] = NULL;
pitz_param_ptr->species[2] = NULL;
pitz_param_ptr->ispec[0] = -1;
pitz_param_ptr->ispec[1] = -1;
pitz_param_ptr->ispec[2] = -1;
pitz_param_ptr->type = TYPE_Other;
pitz_param_ptr->p = 0.0;
pitz_param_ptr->U.b0 = 0.0;
for (i = 0; i < 5; i++) {
pitz_param_ptr->a[i] = 0.0;
}
pitz_param_ptr->alpha = 0.0;
pitz_param_ptr->thetas = NULL;
return(OK);
}
/* ---------------------------------------------------------------------- */
struct pitz_param *pitz_param_read (char *string, int n)
/* ---------------------------------------------------------------------- */
{
/*
* Read pitzer parameter info from string
* n is number of species (character values)
*
*/
int l, i, j, k;
char *ptr;
char token[2*MAX_LENGTH];
struct pitz_param pzp, *pzp_ptr;
if (n != 2 && n != 3) return (NULL);
if (string == NULL) return (NULL);
pitz_param_init(&pzp);
ptr = string;
if (copy_token(token, &ptr, &l) == EMPTY) return(NULL);
ptr = string;
for (i = 0; i < n; i++) {
if (copy_token(token, &ptr, &l) == EMPTY) return(NULL);
pzp.species[i] = string_hsave(token);
}
k = 0;
for (i = 0; i < 5; i++) {
if (copy_token(token, &ptr, &l) == EMPTY) break;
j=sscanf(token,"%le", &pzp.a[i]);
if (j <= 0) break;
k++;
}
if (k <= 0) return(NULL);
pzp_ptr = pitz_param_duplicate(&pzp);
return ( pzp_ptr);
}
/* ---------------------------------------------------------------------- */
struct pitz_param *pitz_param_duplicate(struct pitz_param *old_ptr)
/* ---------------------------------------------------------------------- */
{
/*
* Allocates space and makes duplicate copy of pitz_param structure
*/
struct pitz_param *new_ptr;
new_ptr = pitz_param_alloc();
pitz_param_init(new_ptr);
/*
* Copy data
*/
pitz_param_copy(old_ptr, new_ptr);
return(new_ptr);
}
/* ---------------------------------------------------------------------- */
int pitz_param_copy(struct pitz_param *old_ptr,
struct pitz_param *new_ptr)
/* ---------------------------------------------------------------------- */
{
/*
* Copies pitz_param data from old_ptr to new location, new_ptr.
* Space for the new_ptr structure must already be malloced.
*/
/*
* Store data for structure pitz_param
*/
memcpy(new_ptr, old_ptr, sizeof(struct pitz_param));
return(OK);
}
/* ---------------------------------------------------------------------- */
int pitz_param_search(struct pitz_param *pzp_ptr)
/* ---------------------------------------------------------------------- */
{
/*
* Does linear search of pitz_params for same type and species
* Returns -1 if not found, index number in pitz_params if found
*/
int i;
if (pzp_ptr == NULL) return -1;
if (pzp_ptr->type == TYPE_Other) return -1;
for (i = 0; i < count_pitz_param; i++) {
if (pitz_params[i]->type == pzp_ptr->type &&
pitz_params[i]->species[0] == pzp_ptr->species[0] &&
pitz_params[i]->species[1] == pzp_ptr->species[1] &&
pitz_params[i]->species[2] == pzp_ptr->species[2] ) {
break;
}
}
if (i >= count_pitz_param) {
return -1;
}
return i;
}
/* **********************************************************************
*
* Routines related to structure "theta_parm"
*
* ********************************************************************** */
/* ---------------------------------------------------------------------- */
struct theta_param *theta_param_alloc (void)
/* ---------------------------------------------------------------------- */
{
struct theta_param *theta_param_ptr;
theta_param_ptr = (struct theta_param *) PHRQ_malloc(sizeof (struct theta_param));
if (theta_param_ptr == NULL) malloc_error();
return ( theta_param_ptr );
}
/* ---------------------------------------------------------------------- */
int theta_param_init (struct theta_param *theta_param_ptr)
/* ---------------------------------------------------------------------- */
{
/*
* Frees all data associated with theta_param structure.
*/
if (theta_param_ptr == NULL) return(ERROR);
theta_param_ptr->zj = 0;
theta_param_ptr->zk = 0;
theta_param_ptr->etheta = 0;
theta_param_ptr->ethetap = 0;
return(OK);
}
/* ---------------------------------------------------------------------- */
struct theta_param *theta_param_search(double zj, double zk)
/* ---------------------------------------------------------------------- */
{
/*
* Does linear search of theta_params for same charge
* Returns NULL if not found, index number in theta_params if found
*/
int i;
for (i = 0; i < count_theta_param; i++) {
if ((theta_params[i]->zj == zj && theta_params[i]->zk == zk) ||
(theta_params[i]->zj == zk && theta_params[i]->zk == zj)) {
return theta_params[i];
}
}
return NULL;
}

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prep.cpp
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2259
print.cpp
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7904
read.cpp
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