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iphreeqc/RELEASE.TXT
Scott R Charlton fe86acddc5 added post-build to create backup manifest file 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@11251 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2016-06-09 03:58:23 +00:00

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Version 3.3.8: June 8, 2016
---------
svn 11152
---------
Added two new Basic functions related to KINETICS.
n$ = KINETICS_FORMULA$("Albite", count, elt$, coef)
This function searches for a kinetic reaction definition (Albite, in the example). If found, n$
is set equal to the first argument (Albite), otherwise an empty string is returned. The
function returns these values: count is the number of items in the arrays elt$ and coef; elt$
is a list of element names in the formula for the kinetic reaction; and coef is a numeric
array containing the number of atoms of each element in the kinetic-reaction formula, in the
order defined by elt$, which is alphabetical by element.
m = SYS("kin", count , name$ , type$ , moles)
This function identifies all of the kinetic reactants in the current KINETICS definition
and returns the sum of moles of all kinetic reactants. Count is number of kinetic
reactants. Name$ contains the kinetic reactant names. Type$ is “kin”. Moles contains the
moles of each kinetic reactant. The chemical formula used in the kinetic reaction can be
determined by using a reaction name from Name$ as the first argument of the
KINETICS_FORMULA$ Basic function.
---------
svn 11106
---------
Updated the online manual
(http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/phreeqc3-html/phreeqc3.htm)
to have revisions noted in italic text and better graphics for figures.
Version 3.3.7 (11094): April 21, 2016
---------
svn 11091
---------
Cerussite misspelled in 5 databases (Amm, minteq, minteq.v4, phreeqc, and wateq4f.
Modified Calcite RATES to handle M0=0. Added rate for quartz to wateq4f.dat.
---------
svn 11073
---------
PhreeqcI: The selected-output file was missing headers under some conditions, for example
: SOLUTION;SELECTED_OUTPUT;END.
---------
svn 11072
---------
PhreeqcI: Fixed bug that overwrote selected output files when (re-)opening a .pqi file
Version 3.3.6 (11064): April 18, 2016
---------
svn 10952
---------
PhreeqcRM: InitialPhreeqcCell2Module method had incorrect indexing when using a mapping of model
cells to chemistry cells that was not 1-to-1. The result was incorrect values for porosity, rv, and
saturation.
---------
svn 10932
---------
PHREEQC: Additional error checking. In SOLUTION_MASTER_SPECIES the master species must contain the
element name.
---------
svn 10929
---------
PHREEQC: If an aqueous species lacked a molar volume parameter (Vm), then the change in molar volume
for reactions involving that species were not calculated correctly. Now summations of molar volumes,
including zero for the species, are calculated.
---------
svn 10892
---------
PHREEQC: Added Vm values for Gibbsite, Kaolinite, Albite, Anorthite, K-feldspar, Ca-Montmorillonite,
Talc, Illite, Chrysotile, Sepiolite, Hematite, Goethite, Pyrite, and Mackinawite for the phreeqc.dat
and Amm.dat databases.
---------
svn 10877
---------
PHREEQC and PhreeqcI: PhreeqcI has updated documentation through the Help menu. All entries in green
font are modifications, corrections, or new features.
Corrected description of "EQUI" option of the SYS function.
-porosities is now an option in TRANSPORT for defining a heterogeneous distribution of porosity for
-multi_d calculations.
RHO_0 is a new Basic function that gives the density of pure water at the current temperature.
EDL_SPECIES(surf$, count, name$, moles, area, thickness)
Returns the total number of moles of species in the diffuse layer. The arguments to the function are
as follows: surf$ is the name of a surface, such as "Hfo", excluding the site type (such as "_s");
count is the number of species in the diffuse layer; name$ is an array of size count that contains
the names of aqueous species in the diffuse layer of surface surf$; moles is an array of size count
that contains the number of moles of each aqueous species in the diffuse layer of surface surf$;
area is the area of the surface in m^2; thickness is the thickness of the diffuse layer in m. The
function applies when -donnan or -diffuse_layer is defined in SURFACE calculations.
Corrected description of "EQUI" option of the SYS function.
---------
svn 10874
---------
PHREEQC: Corrected description of "EQUI" option of the SYS function. PhreeqcI has updated
documentation through the help. All entries in green font are modifications, corrections, or new
features.
---------
svn 10844
---------
PhreeqcI: Changed the way the current working directory is set. Now, the current working directory
is not changed when browsing for and changing the database.
---------
svn 10843
---------
PhreeqcI: SOLUTION_SPREAD did not import correctly when using the P4W tab of PhreeqcI to generate
the an example problem.
---------
svn 10834
---------
PHREEQC: In converting units of mass to moles per kilogram of water, it is possible to calculate a negative
mass of water. This problem is now trapped, and an error message is issued.
Version 3.3.5 (10806): February 3, 2016
---------
svn 10804
---------
PHREEQC: Created an option to enter cell porosities in keyword TRANSPORT, which was
motivated by the need to define porosities for a variable-porosity multicomponent diffusion
problem. Previously the Basic function CHANGE_POR had to be used to allow variable porosity.
-porosities 0.3 0.29 0.28 # porosities of cells 1, 2, 3-n, used for calculating
# tortuosity in multicomponent diffusion calculations. The
# numbers entered here take precedence over the value given
# with -multi_D. If one stagnant layer is defined together with
# an exchange-factor > 0 ('-stagnant 1 4e-6 0.3 0.1'), the
# mobile (here = 0.3) and immobile (here = 0.1) porosities
# defined with -stagnant are used.
---------
svn 10770
---------
IPhreeqc: Added optional argument sl to GetSelectedOutputValue in Fortran. The revised method
is as follows, where sl is a new optional argument.
CHARACTER(LEN=40) :: sv
status = GetSelectedOutputValue(id, i, j, vt, dv, sv, sl)
In the example, if the character string generated in IPhreeqc and stored in sv is 40 characters or
less, the value of sl will be 0. If the character string generated in IPhreeqc was greater than
40 characters, the truncated string is stored in sv, but the value of sl will contain the length
of the string before truncation.
---------
svn 10668
---------
All programs: Now using Jenkins for continuous integration.
---------
svn 10664
---------
PHREEQC: Erroneous input could cause a segmentation fault for surfaces
related to minerals or kinetics.
---------
svn 10644
---------
PHREEQC: Minor format change for specific conductance.
---------
svn 10640
---------
PhreeqcRM: Advection example in C and C++ had wrong MPI type for integer transfers.
Example code in documentation also had wrong MPI type for some integer transfers.
Integer transfers in Fortran should use MPI_INTEGER, while integer transfers in
C and C++ should use MPI_INT.
---------
svn 10632
---------
PhreeqcRM: Revised transfer of data for MPI when rebalancing. Serializes lists of
characters, integers, and doubles, instead of writing full "dump" version of each
reaction. Is much faster for cell transfers when rebalancing among processes.
---------
svn 10630
---------
PhreeqcRM: Fixed bug when transferring data for MPI. Surface related to kinetics lost
concentrations of sorbed elements.
---------
svn 10585
---------
Phreeqc: New set of convergence parameters that delay the removal of an unstable
phase by 1 iteration. Also new KNOBS identifier, -equi_delay n, where n is the
number of iterations to retain an unstable phase.
---------
svn 10537
---------
Phreeqc: Comments for K-spar and Albite RATEs were incorrect for phreeqc.dat and
wateq4f.dat
---------
svn 10521
---------
PhreeqcRM: Provided better error message for CreateMapping errors.
Version 3.3.3 (10424): October 23, 2015
---------
svn 10409
---------
PhreeqcRM: C function clock() does not provide sufficient resolution. Efficiency calculation
generated NaN, and rebalancing was poor. Revised to use MPI and OpenMP timers when available.
---------
svn 10393
---------
PhreeqcRM: Efficiency calculation generated NaN for OpenMP calculations.
---------
svn 10385
---------
PHREEQC: Fixed formula for pressure dependence of B1, B2, F1, F2 in the Pitzer formulation.
Previously had a limit of -10C; temperatures less than -10 produced a floating point exception
and convergence failure.
---------
svn 10364
---------
IPhreeqc and PhreeqcRM: Debug version asserted when trying to write an error message to std::cerr.
---------
svn 10359
---------
PhreeqcRM: Added methods and documentation for RM_GetEndCell and RM_GetStartCell for C and Fortran.
C++ methods already existed. The methods give the range of chemistry cell numbers that are assigned
by each worker (OpenMP) or process (MPI). If rebalancing is enabled, these numbers may change as
cells are shifted among workers or processes.
Version 3.3.2 (10335): October 2, 2015
---------
svn 10332
---------
PhreeqcRM: Bug in configure scripts required developer zlib to be installed. Now
zlib is only needed if the --with-zlib option is given in order to write compressed
dump files (USE_GZ).
---------
svn 10327
---------
PHREEQC: Fixed bug with SOLUTION_SPREAD. Element names starting with "[" were
not handled correctly.
---------
svn 10317
---------
PHREEQC: Handled case where GAS_PHASE components were not defined in PHASES.
---------
svn 10311
---------
New R version submitted.
---------
svn 10255
---------
PhreeqcRM: Added new method SetScreenOn (RM_SetScreenOn) to control messages
about rebalancing and any messages written with ScreenMessage (RM_ScreenMessage).
Version 3.3.0: September 15, 2015
---------------
svn 10160-10244
---------------
PhreeqcRM: Revised code to minimize memory footprint for MPI. Revised the logic
so that some variables, like porosity and saturation, have only the values
related to the cells that are defined to each worker. Previously, each worker
had lists of these variables for all nxyz cells in the model. The changes
should decrease the total amount of memory needed for MPI runs using PhreeqcRM.
---------------
svn 10231&10237
---------------
IPhreeqc: Fixed a bug in the Fortran module, where logical variables (such as
print control) could be set to true, but not back to false.
---------
svn 10177
---------
PHREEQC: Additional print for Donnan layer.
---------
svn 10176
---------
Pitzer.dat: Updates to CO2 and CH4 in pitzer.dat affecting gas solubilities.
Version 3.2.2: August 24, 2015
---------
svn 10118
---------
PhreeqcRM: Fixed same "feature" in C RM_GetBackwardMapping that
resulted in very slow callback function response.
---------
svn 10112
---------
Modified exceptions IPhreeqcStop and PhreeqcRMStop to
compile on Linux.
---------
svn 10107
---------
Modified exceptions IPhreeqcStop and PhreeqcRMStop to
allow them to be caught with other std::exceptions.
---------
svn 10089
---------
Modified open_output_files and close_output_files so that
stderr, stdout, and stdlog cannot be closed.
---------
svn 10072
---------
PhreeqcRM: Fixed a "feature" in Fortran RM_GetBackwardMapping that
resulted in very slow callback function response.
---------
svn 10053
---------
Moved files to /common directory for files that are used in both
phreeqc and phastinput.
---------
svn 10047
---------
In PhreeqcRM, made default rebalance fraction 0.0.
---------
svn 10040
---------
Bug in solution constructor caused PhreeqcRM debug tests to fail.
---------
svn 10030
---------
Null pointer if K-Cl interaction parameters (b0, b1, c0) were not defined.
---------
svn 10013
---------
The enrichment factor for diffusion in the diffuse layer was incorrectly
implemented.
---------
svn 10006
---------
Fix rare instance where mu = 0 caused a divide by zero.
--------
svn 9998
--------
Pitzer.dat was adjusted to fit CO2 pressure and density by changing
Vm, analytical expression, and adding a CO2-CO2 iteraction parameter.
--------
svn 9995
--------
Pressure of a gas phase mixture was calculated incorrectly in some
elevated T,P cases.
--------
svn 9915
--------
New Basic function EDL_SPECIES returns the moles of
species in the electrical double layer. Applies when -DONNAN or
-DIFFUSE_LAYER are defined in SURFACE calculations.
EDL_SPECIES(surf$, count, name$, moles, area, thickness)
The function returns the total number of moles of species in the
diffuse layer. The arguments to the function are as follows:
surf$ is the name of a surface, such as "Hfo", excluding
the site type (such as "_s").
count is the number of species in the diffuse layer.
name$ is an array of size count that contains the
names of aqueous species in the diffuse layer
of surface surf$.
moles is an array of size count that contains the number
of moles of each aqueous species in the diffuse layer
of surface surf$.
area is the area of the surface in m^2.
thickness is the thickness of the diffuse layer in m.
The volume of the diffuse layer is area * thickness, and
the concentrations of the species in the diffuse layer are
the number of moles divided by the volume.
Example:
10 t = EDL_SPECIES("Hfo", count, name$, moles, area, thickness)
20 PRINT "Surface: Hfo"
30 PRINT "Area: ", area
40 PRINT "Thickness: ", thickness
45 PRINT "Volume: ", area * thickness
50 for i = 1 to count
60 PRINT PAD(name$(i),20), moles(i)
70 next i
Version 3.2.1: July 7, 2015
--------
svn 9930
--------
PhreeqcRM had a serious error in the convertion of units from transport
to themodule. The error occurred when using H2O as a component and mg/L
as the transport unit.
Version 3.2.0: June 10, 2015
--------
svn 9809
--------
Pitzer calculations were optimized. The etheta calculation was improved
thans to Wouter Falkena and the MoReS team. Inefficient loops were also
rewritten.
--------
svn 9665
--------
See README.IPhreeqc.TXT for additional information about the IPhreeqc Module.
The IPhreeqc module has been updated to use CMake (build process manager)
for Visual Studio builds. CMake can be downloaded from http://www.cmake.org.
Fortran, you will need to include the source file IPhreeqc_interface.F90
in your project files. This file defines the IPhreeqc Fortran module.
For example:
USE IPhreeqc
INTEGER(KIND=4) id
id = CreateIPhreeqc()
This replaces the need to use the include files IPhreeqc.f.inc/IPhreeqc.f90.inc.
You will need to link to the IPhreeqc(d).lib/libiphreeqc.a that is created
during the build process.
--------
svn 9639
--------
After reading a dumped surface (SURFACE_RAW), it was later processed
incorrectly, resulting in a mass loss of the elements that were attached
to the surface.
--------
svn 9639
--------
Revised SIT database from www.thermochimie-tdb.com (sit.dat). Version 9a,
released 7/28/2014.
--------
svn 9639
--------
Revised numerical method for SIT aqueous model. Optimized processing of lists
of SIT parameters, revised method to obtain initial values of master variables,
added basis switching.
--------
svn 9462
--------
RATES definitions were revised in all databases. The area parameter
was changed to specific area (area per mole of reactant). Also, for aqueous kinetic
reactions, the solution volume was added explicitly. The changes
were made to facilitate a new version of PHAST that uses a representative
volume that does not have one liter of water.
--------
svn 9434
--------
Basic function lk_phase did not account for pressure properly.
--------
svn 9424
--------
IPhreeqc Basic callback was modified to use ISO_C_BINDING. IPhreeqc
will ultimately be a Fortran module.
--------
svn 9386
--------
Basic function SYS was missing the "equi" option to return
the equilibrium phases in the current system.
USER_PRINT
10 t = SYS("equi", count, name$, type$, moles)
15 PRINT "Number of equilibrium phases: ", count
20 for i = 1 to count
30 PRINT PAD(name$(i),20), moles(i)
40 next i
END
t is the total number of moles of equilibrium phases
count is the number of equilibrium phases
name$ is an array with the names of the equilibrium phases
type$ is an array with "equi" for each equilibrium phase
moles is an array with the number of moles of each equilibrium phase
--------
svn 9386
--------
New frezchem.dat database from Jonathon Toner and the
developers of the frezchem code (Toner and Sletten (2013),
Marion and coworkers). Frezchem is a Pitzer model for temperatures
of 0 C and below.
--------
svn 9345
--------
Initial solution number for a reaction calculation is now assigned
for SOLUTION_SPREAD in all cases.
--------
svn 9345
--------
Adjustment to the Peng-Robinson calculation for example with SO2.
--------
svn 9324
--------
Fixed divide by zero if gas phase components had all zero partial
pressures.
--------
svn 9309
--------
The function SURF gave incorrect results for O and H if O and H
were in the master species (SurfOH, for example).
--------
svn 9308
--------
Bug with case dependence of mineral names when running transport. If
case differed in adjacent cells for an EQUILIBRIUM_PHASE name, it could
lead to a program failure. Revised to remove case dependence.
--------
svn 9302
--------
Fixed Visual Studio static checker warnings.
--------
svn 9250
--------
Revised parameters for pitzer.dat. Additional temperature dependence,
element Si was added, calcite parameters adjusted for higher temperature.
Version 3.1.7: February 10, 2015
--------
svn 9203
--------
Fixed IPhreeqc. An error occurred when an empty string was sent to
IPhreeqc from Fortran.
Version 3.1.6: January 21, 2015
--------
svn 9191
--------
IPhreeqc "any" distribution was missing file fimpl.h for Windows builds.
--------
svn 9084
--------
Fixed initialization of cxxPPassemblage.
--------
svn 9165
--------
Fixed initialization of NameDouble.
Version 3.1.5: December 18, 2014
--------
svn 9084
--------
Fixed warnings identified by CRAN.
--------
svn 9073
--------
Aqueous species H+ was missing from the list of species returned by
SYS("aq", count, name$, type$, moles).
--------
svn 9072
--------
Added Basic function diff_c, which returns the diffusion coefficient
for a species at 25 C.
For example,
d = DIFF_C("CO3-2")
--------
svn 9029
--------
In inverse modeling, the writing of input files for NetpathXL was
incorrect. Revisions to the program had eliminated a speciation
calculation necessary to provide the correct values.
--------
svn 9000
--------
Kinetic names were not saved correctly to allow unique retrival by name.
The error could have lead to misidentification of kinetic reactions for a
cell.
--------
svn 8957
--------
Uninitialized variable for commands of USER_PUNCH.
Version 3.1.4: August 20, 2014
--------
svn 8925
--------
Molar volume was not calculated correctly in mixing a gas.
--------
svn 8923
--------
Acentric factor for H2(g) had positive sign. Corrected to
negative for H2(g) and Hdg(g) in phreeqc.dat, Amm.dat, and pitzer.dat.
--------
svn 8919
--------
When a batch kinetic reaction was simulated, followed by a transport
simulation with kinetics, the time was not reset between the
two simulations.
Version 3.1.3: August 6, 2014
--------
svn 8895
--------
Missing initializations in class_main.
--------
svn 8879
--------
Pressure was incorrect in mix of GAS_PHASE. Also fixed
a NULL pointer when the element in a gas phase was missing
from the system.
--------
svn 8875
--------
Error reading dump of SURFACE when using no_edl option.
--------
svn 8847
--------
Series of changes to correct memory leaks, uninitialized
variables, variables set but not used, and other warnings
detected by Valgrind and Visual Studio.
--------
svn 8756
--------
Relative dielectric constant was not calculated correctly.
--------
svn 8755
--------
Basic function LK_SPECIES was changed to use the
the log K as found in the SOLUTION_SPECIES
definition. Previously, the log K was for the
equations rewritten to the current master species.
--------
svn 8741
--------
Handling of isotopes uncertainty was inconsistent with
documentation in INVERSE_MODELING. Also missing
defaults for O and H redox states.
--------
svn 8628
--------
Entities with negative user numbers are not dumped.
--------
svn 8622
--------
Modifications to meet R requirements.
--------
svn 8576
--------
Fixed error when Pitzer or SIT parameter was redefined.
Version 3.1.2: March 1, 2014
--------
svn 8532
--------
Changed the way the pressure is assigned to a fixed-pressure
gas phase in a reaction calculation. Previously, pressure
of the gas phase did not change (unless GAS_PHASE_MODIFY
was used). Now, if REACTION_PRESSURE is defined, it is
used for the fixed pressure of the gas.
--------
svn 8520
--------
Changes in MCD to accomodate unequal cell lengths.
--------
svn 8502
--------
Modified not to DUMP temporary entities with negative user numbers.
--------
svn 8484
--------
Modified to allow diffusion calculations in TRANSPORT with unequal
cell lengths.
--------
svn 8469
--------
Logic for connecting points in USER_GRAPH was revised.
--------
svn 8453
--------
Error where punch file was deleted twice if there was a Basic error.
No longer an error if you try to modify a non-existing entity (SOLUTION,
EXCHANGE, etc), only a warning.
--------
svn 8378
--------
Removed yellow from colors for graphing; it was sometimes hard to see.
Changed Li molar volume in pitzer.dat, Amm.dat, and phreeqc.dat.
-------------
svn 8371-8375
-------------
Multiple bug fixes pointed out by Marco De-Vroed. Set basic_interpreter
to NULL after deleting. Revised handling of initial data for initial-solution
calculations. Revised logic for switching to numerical derivatives for
high-pressure calculations, the variable switch_numerical was removed.
--------
svn 8356
--------
Fixed bug with solution volume in initial solutions
containing Alkalinity.
--------
svn 8301
--------
Density was not stored with the solution after a calculation.
--------
svn 8293
--------
Solution volume was not initialized in zero(), and pressure was not set correctly
when mixing solutions.
Version 3.1.1: December 6, 2013
--------
svn 8203
--------
Updated more molar volumes in phreeqc.dat, Amm.dat, and
pitzer.dat. Mn+2, Al+3, PO4-3, F-, Li+, Br-, Zn+2, Cd+2,
Cu+2, NH4+, HPO4-2, H2PO4-, and H3PO4, and other related
ion pairs or complexes. Also estimated more ion size parameters
for pairs and complexes. Molar volume approach is published
in Appelo, Parkhurst, and Post, 2013, Geochimica et Cosmochimica
Acta, v. 125, p. 49-67.
--------
svn 7997
--------
Modified chart handling for PhreeqcI to allow charts from
multiple runs to remain open for comparison. Charts will
remain visible until closed.
--------
svn 7992
--------
Identifier -high_precision was added to the PRINT data
block to allow higher precision for the PRINT Basic
command, which is generally used in USER_PRINT
definitions.
--------
svn 7987
--------
Now can have multiple SELECTED_OUTPUT n and USER_PUNCH n.
SELECTED_OUTPUT 1 has the same functionality as previous
versions of SELECTED_OUTPUT, with a set of default print
definitions. SELECTED_OUTPUT n, where n is not equal to 1,
has no fields initially defined; it is equivalent to an
automatic -reset false.
A file may be defined for each SELECTED_OUTPUT n that will
recieve the output from the data block. Using i to
represent a specific integer, USER_PUNCH i will write to
the file defined for SELECTED_OUTPUT i. If USER_PUNCH i is
defined, but SELECTED_OUTPUT i is not, then no data will
be written from USER_PUNCH i.
Printing to the selected-output files is controlled
by three identifiers. PRINT; -selected_output true/false
will enable/disable printing of all selected-output
files. For an individual SELECTED_OUTPUT i definition,
-active true/false will enable/disable both
SELECTED_OUTPUT i and USER_PUNCH i. Again for
SELECTED_OUTPUT i, -user_punch true/false will enable/
disable the USER_PUNCH i data (rarely used).
If SELECTED_OUTPUT i has been defined, a new data block
of SELECTED_OUTPUT i will retain the previous definition
if only -active and (or) -user_punch are defined. Defining
any other identifier will cause the old definiton
to be removed and its file closed; the data for
SELECTED_OUTPUT i will be defined entirely by the new
data block.
--------
svn 7962
--------
Database modifications:
pitzer.dat: Parameters have been reordered to alphabetical order.
phreeqc.dat and Amm.dat: Vm refit for aqueous species Na+, CO3-2, SO4-2, NO3-,
HCO3-, NaCO3-, NaHCO3, NaSO4, KSO4. Analytical expression adjusted for gypsum,
anhydrite, and sylvite (delta H).
--------
svn 7916
--------
Addition of a temperature-dependent pressure correction for the Debye-Hueckel term
for the Pitzer formulation. An empirical, temperature-dependent pressure correction
has been introduced in the Debye-Hueckel part of Pitzer's equation for gamma
(activity coefficient), which lets the factor B vary from 1.2 to 1. Pitzer defined
this number to be 1.2 for all pressures and temperatures.
For monovalent species the correction is:
pap = (7e-5 + 1.93e-9 * (TK - 250)^ 2.0) * patm_x
For divalent species the correction is:
pap = (9.65e-10 * (TK - 263)^ 2.773) * (patm_x^0.623)
In both cases, pap is limited to less than 0.2.
The factor B in the Debye-Hueckel factor is
B = 1.2 - pap
The Debye-Hueckel factor is
F = = -A0 * (DI / (1.0 + B * DI) + 2.0 * log(1.0 + B * DI) / B)
where DI is the square root of the ionic strength.
--------
svn 7972
--------
A revised version of the manual is now distributed as a
compiled HTML file (phreeqc3.chm). It has corrections and
new features highlighted in forest green.
--------
svn 7920
--------
GAS_PHASE processing was incorrect for fixe-volume gas with
multiple components. The wrong number of moles of gas
some gas components was calculated.
--------
svn 7896
--------
The manual wording was wrong or confusing in some places
regarding the difference between fugacity (F) and
(partial) pressure (P) of a gas. For ideal gases, P = F.
However for Peng-Robinson gases F = P * phi / 1 atm
(unitless).
In EQUILIBRIUM_PHASES, the target saturation index for a
gas is log10(P). In SELECTED_OUTPUT -saturation_index, for
gases, the value printed will be the fugacity. For Basic
functions SI and SR, the values are based on the fugacity.
P and phi can be obtained with the Basic functions
PR_P and PR_PHI.
For the Saturation Index block of the output file,
the SI for a gas is its fugacity. However, for
Peng-Robinson gases, P and phi are appended to the
output line.
--------
svn 7884
--------
IPHREEQC: added a Basic function, CALLBACK, which
allows data be passed to and from the calling
program. The new IPhreeqc method is
for C,
iresult = SetBasicCallback(ID, function name, cookie)
and for Fortran,
iresult = SetBasicFortranCallback(ID, function name)
The two methods are necessary because arguments
are handled differenctly between C and Fortran.
The void pointer cookie in the C callback can be
used to allow the user-defined callback function
to find necessary data.
The user-defined function for C must be of the form
double my_callback(double, double, const char *, void *)
For Fortran the function must be of the form
double precision my_callback(double precision,
double precision, character(*))
As an example, to get the current time for
a calculation, the callback could be used as follows:
Basic:
10 date = CALLBACK(dummy, dummy, "Year")
Fortran after registering my_callback by using
SetBasicFortranCallback
double precision function my_callback(x1, x2, string)
USE date_module, only: year
double precision x1, x2, my_callback
character(*) string
if (string .eq. "Year") then
return dble(year)
endif
end
A usage of the callback feature has been added to the
IPhreeqc example advect for Fortran, C, and C++.
Additional documentation is in the .chm documentation
files for IPhreeqc.
--------
svn 7867
--------
SOLUTION_MODIFY and SOLUTION_RAW were missing the
-pressure identifier. It has now been added.
--------
svn 7857
--------
Trapped error when solid-solution components were
not defined correctly.
--------
svn 7855
--------
Error in pressure dependence when Pitzer or SIT
aqueous model was used. The pressure dependence
was not calculated if the pressure was changed,
but the temperature was not.
--------
svn 7829
--------
Added Basic fuction EQUIV_FRAC that returns the
equivalent fraction of a surface or exchange
species. The three arguments are
(1) Species name (input),
(2) Equivalents of exchange or surface sites
per mole of the species (output),
(3) The name of the surface or exchange site
(output).
For example,
10 f = EQUIV_FRAC("AlX3", eq, x$)
f = equivlalent fraction of AlX3 relative to
total equivalents of X sites.
eq = 3.0
x$ = "X"
If the species name is not found to be a surface
or exchange species, the return value is 0,
the second argument is set to 0, and the third
argument is set to an empty string.
Also added synonyms for Basic functions
PHASE_FORMULA and SPECIES_FORMULA with trailing
$ signs--PHASE_FORMULA$ and SPECIES_FORMULA$.
To be consistent with Basic, the functions should
have $ signs because they return strings.
--------
svn 7828
--------
Added Basic fuction SPECIES_FORMULA that returns the
stoichiometry of an aqueous, exchange, or surface
species. The function returns a string: "aq" for
aqueous, "ex" for exchange, "surf" for surface,
and "none" if there is no species of that name.
The four arguments are
(1) the name of the species (input),
(2) the number of elements, including charge (output),
(3) an string array of element names (output),
(4) a number array of coefficients corresponding to the elements (output).
The following example:
10 name$ = "AlX3"
20 ty$ = SPECIES_FORMULA(name$, count_s, elt$, coef)
20 print pad(name$, 15), ty$
30 for j = 1 to count_s
40 print pad(blank$, 5), pad(elt$(j),5), str_f$(coef(j), 5, 0)
50 next j
Produces the following output:
AlX3 ex
Al 1
X 3
charge 0
--------
svn 7781
--------
Basic function SYS("phases",...) returned 0.0, rather
than the maximum saturation index if the maximum
saturation index was less than zero. Now returns the
maximum saturation index even if it is less than zero.
Added new Basic function STR_E$(x, w, d) that produces
a string with exponential format from a number with a
given width (w) and number of decimal places (d). w is
the minimum width of the string. The string is padded
with spaces to the left to produce a string of the
specified width (w); however, the string will be wider
than w characters, if the number does not fit in the
specified width. If x = 123456.789, then STR_E$(x,15,5)
produces the following on a Windows computer:
1.23457e+005
--------
svn 7766
--------
Added new Basic function STR_F$(x, w, d) that produces
a string from a number with a given width (w) and
number of decimal places (d). w is the minimum width of
the string. The string is padded with spaces to the
left to produce a string of the specified width (w);
however, the string will be wider than w characters, if
the number does not fit in the specified width. If x =
123456.789, then STR_F$(x,15,5) produces the following
on a Windows computer:
123456.78900
--------
svn 7763
--------
Fixed bug with isotopes. Moles and molalities were
incorrect if the mass of water in the SOLUTION was not
1.0.
Version 3.0.6: June 4, 2013
--------
svn 7757
--------
Fixed bug introduced in version 3.0.5 if two DELETE
keywords were used in a run. Fixed a bug with fixed-
pressure gas, where the volume was 1.0 even when no
moles of gas were present in the gas phase. Minor
optimizations for initialization of Peng-Robinson gas
data.
Version 3.0.5: May 31, 2013
--------
svn 7748
--------
Optimizations for equilibrium phases, using pointers
instead of lookup function. Other optimizations for
SURFACE calculations to limit uses of std::map find,
eliminate strcmps, and skip inverse setup when not
needed. Minor fix to Peng Robinson. Fixed bug with
SOLUTION_MODIFY when a concentration was set to zero.
Removed lower limit on ionic strength.
Version 3.0.4: May 14, 2013
--------
svn 7703
--------
Fixed bug in PhreeqcI that caused no warnings to be
included in the output file.
--------
svn 7677
--------
Gas-phase volume was not correct in SELECTED_OUTPUT
-gas printout for Peng-Robinson calculations.
--------
svn 7677
--------
Added KIN_TIME Basic function, which gives the
time interval in seconds of the last kinetic
integration. KIN_DELTA("xxx")/KIN_TIME will give
the average rate over the time interval for
reaction xxx.
For example,
KINETICS
Calcite
-m 1
-step 864 8640
KIN_TIME will return 864 after the first
step and 8640 after the second. The result of
KIN_TIME will be the same whether INCREMENTAL_
REACTIONS is true or false (although TOTAL_
TIME will differ).
Version 3.0.3: April 30, 2013
Fixed errors in GAS_PHASE, -fixed_pressure used the
sum of the input pressures instead of the defined
total pressure in some cases, set upper limits in PR
calculations; revised Basic function LK_SPECIES;
logic for printing status line revised; fixed bug in
SOLUTION_SPREAD, mass of water was not read properly;
fixed problem with spaces in output file name;
revised logic for checking if opening files was
successful, old C-style check was incorrect; revised
molar volume definitions and selected parameters in
databases phreeqc.dat, Amm.dat, and pitzer.dat
Version 3.0.2: April 4, 2013
Fixed an initialization error for activity of water
that caused slow convergence. Dump wrote a file that
caused read errors when some names exceeded 21
characters. Gas_phase_modify did not work correctly.
Version 3.0.1: March 21, 2013
Fixed bug in printing of solid solutions that caused
a crash. The pressure dependence of log K in the
printout of the equilibrium phases assemblage in the
saturation index list was incorrect.
Version 3.0.0: February 1, 2013
PHREEQC Version 3 is finally released. Major new
features include pressure dependence for geochemical
reactions, the nonideal gas formulation of Peng and
Robinson, and charting. All features of PHREEQC
Version 3 are documented in U.S. Geological Survey
Techniques and Methods 6-A43, “Description of input
and examples for PHREEQC Version 3--A computer
program for speciation, batch-reaction, one-
dimensional transport, and inverse geochemical
calculations”, available at
http://pubs.usgs.gov/tm/06/a43/. Features not
previously documented include Pitzer and SIT aqueous
models, CD-MUSIC surface complexation, isotopic
capabilities, and new keyword data blocks to
manipulate reactants, such as RUN_CELLS, DELETE,
COPY, _MODIFY, _RAW, and DUMP.
************************************************************
************************************************************
* All features of PHREEQC Version 3 are *
* documented in Techniques and Methods 6-A43. *
************************************************************
************************************************************
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!PREVIOUS RELEASE NOTES!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!PREVIOUS RELEASE NOTES!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!PREVIOUS RELEASE NOTES!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!PREVIOUS RELEASE NOTES!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!PREVIOUS RELEASE NOTES!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
************************************************************
* Features in PHREEQC++ Not in PHREEQC version 2 *
* PHREEQC++ is used only in IPhreeqc Modules *
* Revisions and Bug Fixes *
************************************************************
------------------------------------------------------------
Version 2.18.2: April 9, 2011
------------------------------------------------------------
--------
svn 5471
--------
Added PHASE_FORMULA and LIST_S_S Basic functions.
PHASE_FORMULA returns a string value with the
chemical formula for the phase as defined in
PHASES data. If 4 arguments are provide, a list
of the elements and stoichiometric coefficients for
elements are returned.
USER_PRINT
10 min$ = "Calcite"
20 form$ = PHASE_FORMULA(min$)
30 print min$, form$
40 form$ = PHASE_FORMULA(min$, count, elts$, coefs)
50 for i = 1 to count
60 print " ", PAD(elts$[i], 20), coefs[i]
70 next i
This example produces the following output:
Calcite CaCO3
C 1
Ca 1
O 3
LIST_S_S returns the sum of moles of all components
in a specified solid solution. Lists of the components
and the number of moles of each component are also
returned.
SOLID_SOLUTIONS 1
Calcite_s_s
-comp Calcite 0.01
-comp Smithsonite 0.001
-comp Strontianite 0.02
USER_PRINT
10 name$ = "Calcite_s_s"
20 total = LIST_S_S(name$, count, comp$, moles)
30 print PAD(name$, 20), total
40 for i = 1 to count
50 print " ", PAD(comp$[i], 20), moles[i], moles[i]/total
60 next i
This example produces the following output:
Calcite_s_s 3.0876e-002
Calcite 9.9316e-003 3.2166e-001
Smithsonite 9.6666e-004 3.1308e-002
Strontianite 1.9978e-002 6.4704e-001
--------
svn 5455
--------
REACTION_MODIFY keyword was added to the modules. Previously,
REACTION_MODIFY was not recognized as a keyword.
--------
svn 5453
--------
Fixed bug with in READ_SOLUTION_RAW. A read error occurred
when -isotopes was encountered.
--------
svn 5448
--------
Reading of default user number, but specified description
was in error under some conditions.
--------
svn 5431
--------
RUN_CELLS was rewritten to perform multiple calculations
if multiple steps are defined in REACTION, REACTION_TEMPERATURE,
or KINETICS. It now operates in the same way that a
series of USE and SAVES would operate. Previously, only
one step of a series of reaction steps was taken. If a
time step is provided in RUN_CELLS for kinetic reactions and
nmax is the maximum number of steps defined for REACTION,
REACTION_TEMPERATURE, and KINETICS, the time step is divided
into nmax equal increments. It is equivalent to the following
definition in kinetics: -step time_step in nmax steps.
--------
svn 5324
--------
Modified solution method for solid solutions so that
mole transfers were limited to the total amount
available in the system.
------------------------------------------------------------
Version 2.18.0: April 9, 2011
------------------------------------------------------------
--------
svn 5281
--------
If SOLUTION_MODIFY is used to change a total for an element,
the activities for the master species of the element are
automatically updated by the ratio of the new total to the
old total, unless activities are specifically set for the
element with -activities. All valence states of redox elements
are adjusted.
--------
svn 5270
--------
Added logic to update estimates of log activity when
modifying totals in SOLUTION_MODIFY. The initial
guesses for activities are adjusted proportionally
to the change in total moles of elements (as defined
by SOLUTION_MODIFY; -totals).
This automatic adjustment is suggested rather than
explicit definition of the initial guesses through
SOLUTION_MODIFY; -activities. However, the -activities
identifier may be used and will supercede the automatic
adjustment.
The adjustment of the initial guesses for activities
should reduce the number of iterations needed to solve
a given set of equations and, consequently, should
lessen the total CPU time for a simulation.
--------
svn 4897
--------
Added capability to include files within the input
file. Files included in include files are also
included. Files are included verbatim and need not
contain complete keyword datablocks; however, the
combination of included files must result in a
legal PHREEQC input file. Files are included as
simulations are proceeding, so it is possible to
write a file at one point of a run that is included
later in the same run. Included files can contain
INCLUDE$ directives.
SOLUTION
INCLUDE$ file_name
END
where "file_name" contains:
EQUILIBRIUM_PHASES
Calcite 0 10
is the same as a single file with
SOLUTION
EQUILIBRIUM_PHASES
Calcite 0 10
END
--------
svn 4856
--------
Revised logic of searching pitzer parameters so that
order of ions in a parameter definition does not
matter.
--------
svn 4823
--------
Added -cells to DUMP and DELETE; cell option to COPY.
Example:
COPY cell 1 4
COPY cell 1 5-10
DUMP
-cell 1 2-3 10
DELETE
-cell 1-3 4 8-10
COPY cell n range
The cell option of the COPY keyword causes all reactants
defined with identifying number n to be copied to a single
range of numbers. The range of numbers can be a single
number or a range of numbers given by an integer, a
hyphen, and an integer, with no intervening spaces.
DUMP
-cell list
The -cell option writes _RAW formatted output to a
specified file(see below for more details) for each
reactant that is defined in the list.
DUMP
-cell list
The -cell deletes from memory all reactants that are
defined with identifying numbers in the list.
The list of numbers for DUMP and DELETE are
more flexible than for COPY. A list of ranges can be
given for DUMP and DELETE, where each element of
the list can be a single number or a range of numbers
defined by an integer, a hyphen, and an ingeger, with
no intervening spaces.
--------
svn 4816
--------
Added compile capability to use #include file_name
in input and database files. PHREEQCPP process the
files at the start of the run, possibly following
multiple layers of include files, to produce a stream
that is then used as input. Compile define is
MERGE_INCLUDE_FILES; PHREEQC_CLASS also must be defined.
Input file:
SOLUTION 1
#INCLUDE t2
#include t4
END
File t2:
REACTION
NaCl
1 mmol
#include t3
File t3:
REACTION_TEMPERATURE
10 20 30
File t4:
SAVE solution 1
When compiled with the include file #defines, the above
set of files produces the following input for PHREEQC:
SOLUTION 1
REACTION
NaCl
1 mmol
REACTION_TEMPERATURE
10 20 30
SAVE solution 1
END
--------
svn 4800
--------
Added capability to dump REACTIONs, REACTION_TEMPERATUREs,
and MIXes.
DUMP
-mix 1 4 6
-reaction 1-5
-reaction_temperature 1 3-9
List of numbers may be formatted as described for DUMP.
Data are written in a format suitable for an input file
to PHREEQCPP.
Example of dumped keywords:
MIX 1
1 0.33
2 0.33
3 0.34
REACTION_RAW 1
-units Mol
-reactant_list
Ba 1
Br 2
-element_list
-steps
0.01
-equal_increments 1
-count_steps 2
REACTION_TEMPERATURE_RAW 1
-count_temps 3
-equal_increments 1
-temps
25 45
--------
Added -cells option to DUMP.
DUMP
-cells 1-19 20
This -cells option will dump any reactant with numbers
between 1 and 20, including SOLUTIONs, EXCHANGERs,
GAS_PHASEs, KINETICS, SOLID_SOLUTIONs, SURFACEs, REACTIONs,
REACTION_TEMPERATUREs, and MIXes.
--------
svn 3730
--------
Added keyword RUN_CELLS.
RUN_CELLS
-cells 1 2
5-6
7
-time_step 10000
-start_time 100
For each i listed in -cells
it is the equivalent of the following:
USE solution i
USE equilibrium_phases i
USE exchange i
USE surface i
USE solid_solution i
USE gas_phase i
USE kinetics i
USE reaction i
USE reaction_temperature i
SAVE solution i
SAVE equilibrium_phases i
SAVE exchange i
SAVE surface i
SAVE solid_solution i
SAVE gas_phase i
If MIX i is defined, it is used in place of USE solution i.
A MIX i or SOLUTION i must be defined to use RUN_CELLS; -cells i.
All other entities are used only if they are defined.
-start_time and -time_step are needed if any kinetic reactions
are calculated. -start_time is the time at the start of the
calculation, and -time_step is the length of time over which
to integrate the kinetic reactions.
--------
svn 3727
--------
Added keywords to allow modification of each reactant.
A reactant must have been defined previously, but then
each data item of the reactant can be changed and new
components added. Data items read are changed, all
other data items remain the same. Input format is the
same as the RAW formats produced by DUMP.
New keywords are as follows:
SOLUTION_MODIFY
EQUILIBRIUM_PHASES_MODIFY
EXCHANGE_MODIFY
SURFACE_MODIFY
SOLID_SOLUTIONS_MODIFY
GAS_PHASE_MODIFY
KINETICS_MODIFY
The example below is indented to indicate which
information is necessary to change a data item.
Working back through the indention levels for
and item, each heading of a lower order is
necessary to define the data item. In the example
below, to change the number of moles of barite from
10 to 5 in the equilibrium phase assemblage, it
is necessary to define EQUILIBRIUM_PHASES_MODIFY 1;
-component; -name Barite; -moles 5.
Items identified by an asterisk are most likely to
consider for redefinition. Items with (*) are
marked to indicate that care is needed to maintain
charge balance relations. Unwanted redox and pH
reactions may result from incorrect redefinition
of these quantities. Items not marked are either
initial estimates of variables calculated in the
simulation, or are parameters thought not likely
to be changed.
The MODIFY data blocks change the data in the
PHREEQC storage structures. They do not cause
any initial composition calculations. Neither
do they generate default reactions to be simulated.
USE statements are needed to specify explicitly
the desired reactions.
SOLUTION_MODIFY 1
-temp 25 *
-total_h 111.01243359981 (*)
-total_o 55.506216800086 (*)
-cb -3.6579285790756e-010 (*)
-totals
Cl 0.0010000000000003 (*)
H(0) 1.4155655514601e-025 (*)
Na 0.0010000000000003 (*)
-Isotopes
-pH 7
-pe 4
-mu 0.0010001035690258
-ah2o 0.99996599647757
-mass_water 1
-total_alkalinity 3.6579283856577e-010
-activities
Cl -3.0155266404974
E -4
H(0) -25.15
Na -3.0153891985103
O(0) -42.080029535586
-gammas
EQUILIBRIUM_PHASES_MODIFY 1
-eltList
Ba 1
O 4
S 1
-component *
-name Barite
-si 0 *
-moles 10 *
-delta 0
-initial_moles 0
-force_equality 0
-dissolve_only 0
-precipitate_only 0
EXCHANGE_MODIFY 1
-pitzer_exchange_gammas 1
-component
-formula X
-totals
Na 1.0000000058717 (*)
X 1.0000000058717 (*)
-charge_balance 0
-moles 0
-la 3.0000000302372
-phase_proportion 0
-formula_z 0
-formula_totals
X 1
SURFACE_MODIFY 1 .
-type 2
-dl_type 0
-sites_units 0
-only_counter_ions 0
-thickness 1e-008
-debye_lengths 0
-DDL_viscosity 1
-DDL_limit 0.8
-transport 0
-component
-formula Hfo_s
-formula_z 0
-moles 0
-la -0.11486188676541
-charge_balance 3.7853465372651e-005
-phase_proportion 0
-Dw 0
-formula_totals
Hfo_s 0.01
-totals
H 0.01003785346547 (*)
Hfo_s 0.010000000000097 (*)
O 0.010000000000097 (*)
-charge_component
-name Hfo
-specific_area 600
-grams 1
-charge_balance 3.7853465372651e-005 (*)
-mass_water 0
-la_psi 0.55146269389617
-la_psi1 0
-la_psi2 0
-capacitance0 1
-capacitance1 5
-diffuse_layer_totals
SOLID_SOLUTIONS_MODIFY 1
-solid_solution
-name Calcite
-a0 0
-a1 0
-ag0 0
-ag1 0
-miscibility 0
-xb1 0.0
-xb2 0.0
-component
calcite 0.1 *
siderite 0.001 *
GAS_PHASE_MODIFY 1
-type 0
-total_p 1
-volume 1
-component
CO2(g) 1.4305508698401e-005 *
KINETICS_MODIFY 1
-step_divide 1
-rk 1
-bad_step_max 500
-use_cvode 0
-cvode_steps 100
-cvode_order 5
-component
-rate_name Calcite
-tol 1e-008
-m 0.9999999999991 *
-m0 1
-moles 8.9805940461929e-013
-namecoef
CaCO3 1
-d_params
1 1 1 1 *
-totals
C 8.9801193858101e-013
Ca 8.9801193858101e-013
O 2.694035815743e-012
-steps
--------
svn 3719
--------
Added DELETE keyword to delete any numbered reactant, as
listed in the example below. A list of single numbers and
number ranges are used to define the reactants to delete
from PHREEQC memory. Lists may continue on subsequent
lines. Deletion occurs as the last step of simulation
calculations, after all other calculations (initial
compositions, reactions, transport, inverse modeling) and
COPYing have occurred.
DELETE
-solution 2 3
-equilibrium_phases 2-3
-exchange 2
3
-surface
2-3
-solid_solution
2 3
-gas_phase 2-3
-kinetics 3 2
-mix 2
-mix 3
-reaction 2-3
-temperature
2
3
--------
svn 3704
--------
Added DUMP keyword. Writes complete data for solution,
equilibrium_phases, exchange, surface, solid solution,
gas phase, and kinetics classes. The format of the
output is suitable for data input to the C++ version
of PHREEQC. This feature allows the chemical state
of a simulation to be saved and read back in as
initial conditions for subsequent model runs.
Examples:
DUMP
-all
-file myfile.dmp
END
DUMP
-file myfile.dmp
-append true
-solution 1-2 3
-equi 3 1-2
-exch 1 2 3
-surf 1
2
3
-s_s 1
2-3
-gas 1
-gas 2
-gas 3
-kin 1-3
END
Explanation:
The first DUMP datablock will write the compositions at
the end of the simulation (after all simulation calculations,
TRANSPORTs, SAVEs, and COPYs are complete) for
every solution, equilibrium_phases, exchange, surface,
solid solution, gas phase, and kinetics entities that have
been defined or produced in the run. This write includes
internally saved entities (usually assigned negative numbers).
The second DUMP data appends the compositions of items
numbered 1-3 to myfile.dmp, if they exist. The second example
shows multiple ways to define the entities to be dumped to
file.
------
Begin
------
PHREEQC++ has classes that are equivalent to the PHREEQC C
structures. Each class has a method to "dump_raw" the
entire set of class data. The lines generated by dump_raw
can be read as keyword data blocks in an input file. The following
keywords are available in PHREEQC++: SOLUTION_RAW,
EQUILIBRIUM_PHASES_RAW, EXCHANGE_RAW, SURFACE_RAW,
SOLID_SOLUTIONS_RAW, GAS_PHASE_RAW, and KINETICS_RAW.
PHAST uses these classes and data blocks to dump the chemical
state of a simulation and read it back in as a starting
point for subsequent simulations.
Examples of raw output are given below. Some of the fields
are required and some are not.
SOLUTION_RAW 1
-temp 25
-pH 7
-pe 4
-mu 0.0010001035690258
-ah2o 0.99996599647757
-total_h 111.01243359981
-total_o 55.506216800086
-cb -3.6579285790756e-010
-mass_water 1
-total_alkalinity 3.6579283856577e-010
-totals
Cl 0.0010000000000003
H(0) 1.4155655514601e-025
Na 0.0010000000000003
-activities
Cl -3.0155266404974
E -4
H(0) -25.15
Na -3.0153891985103
O(0) -42.080029535586
-gammas
-Isotopes
EQUILIBRIUM_PHASES_RAW 1
-eltList
Ba 1
O 4
S 1
-component
-name Barite
-si 0
-moles 10
-delta 0
-initial_moles 0
-force_equality 0
-dissolve_only 0
-precipitate_only 0
EXCHANGE_RAW 1 Exchange assemblage after simulation 3.
-pitzer_exchange_gammas 1
-component
-formula X
-moles 0
-la 3.0000000302372
-charge_balance 0
-phase_proportion 0
-formula_z 0
-totals
Na 1.0000000058717
X 1.0000000058717
-formula_totals
X 1
SURFACE_RAW 1 Surface assemblage after simulation 4.
-type 2
-dl_type 0
-sites_units 0
-only_counter_ions 0
-thickness 1e-008
-debye_lengths 0
-DDL_viscosity 1
-DDL_limit 0.8
-transport 0
-component
-formula Hfo_s
-formula_z 0
-moles 0
-la -0.11486188676541
-charge_balance 3.7853465372651e-005
-phase_proportion 0
-Dw 0
-formula_totals
Hfo_s 0.01
-totals
H 0.01003785346547
Hfo_s 0.010000000000097
O 0.010000000000097
-charge_component
-name Hfo
-specific_area 600
-grams 1
-charge_balance 3.7853465372651e-005
-mass_water 0
-la_psi 0.55146269389617
-la_psi1 0
-la_psi2 0
-capacitance0 1
-capacitance1 5
-diffuse_layer_totals
SOLID_SOLUTIONS_RAW 1
-solid_solution
-name Calcite
-a0 0
-a1 0
-ag0 0
-ag1 0
-miscibility 0
-xb1 -6.2774385622042e+066
-xb2 -6.2774385622042e+066
-component
calcite 0.1
siderite 0.001
GAS_PHASE_RAW 1
-type 0
-total_p 1
-volume 1
-component
CO2(g) 1.4305508698401e-005
KINETICS_RAW 1
-step_divide 1
-rk 3
-bad_step_max 500
-use_cvode 0
-cvode_steps 100
-cvode_order 5
-component
-rate_name Calcite
-tol 1e-008
-m 1
-m0 1
-moles 0
-namecoef
CaCO3 1
-d_params
1 1 1 1
-totals
-steps
************************************************************
* Features in PHREEQC version 2 not *
* documented in WRIR 99-4259. *
************************************************************
------------------------------------------------------------
Version 2.18.3: April 10, 2011
------------------------------------------------------------
--------
svn 5570
--------
If -high_precision is set to true in SELECTED_OUTPUT,
convergence tolerance is set to 1e-12. If
-high_precision is set to false, convergence tolerance
is not changed. KNOBS; -convergence_tolerance sets the
convergence tolerance to a specified number. The last
definition (-high_precision true or
-convergence_tolerance) takes precedence for a
calculation.
------------------------------------------------------------
Version 2.18.0: April 9, 2011
------------------------------------------------------------
--------
svn 5212
--------
Added gfm (gram formula mass) as a synonym to gfw in
reading concentration data for SOLUTION.
S(6) 1 gfm 96
is equivalent to
S(6) 1 gfw 96.
--------
svn 5170
--------
Added ceil and floor Basic functions. Ceil(x) is the
smallest integer greater than or equal to x. Floor(x)
is the largest integer less than or equal to x. Note
that all numbers in Basic are of type double in C.
USER_PRINT
10 print ceil(2.8), floor(2.8), ceil(-2.8), floor(-2.8)
This USER_PRINT Basic program has the following output:
3 2 -2 -3
--------
svn 4988
--------
Added EOL$ Basic function. EOL$ is the end of line
character for whatever operating system you are
running.
USER_PRINT
10 PRINT "line 1"+EOL$+"line 2"+EOL$
The result of this USER_PRINT is
line 1
line 2
--------
svn 4942
--------
Added additional parameter in PRINT for status. Writing
the status line to the screen can slow calculations
substantially under some conditions.
PRINT
-status (t|f|n)
t--Print status line.
f--Do not print status line.
n--Print status line every n milliseconds.
-status 1000 would print the status line every
second.
--------
svn 4830
--------
Changed default for exchange species activty
coefficients to be equal to the Pitzer
aqueous activity coefficients when using Pitzer
aqueous model. Default is
-pitzer_exchange_gammas true.
------------------------------------------------------------
Version 2.17.5: September 7, 2010
------------------------------------------------------------
------------------------------------------------------------
Version 2.17.4: September 2, 2010
------------------------------------------------------------
--------
svn 4771
--------
Added synonyms to TOTMOLE: TOTMOL, TOTMOLES
------------------------------------------------------------
Version 2.17.3: August 12, 2010
------------------------------------------------------------
--------
svn 4191
--------
Added new Basic functions:
10 total_Ca_in_moles = TOTMOLE("Ca")
TOTMOLE provides the total number of moles of an element
or element valence state in solution. Special values are
"water", which gives number of moles of water, and
"charge", which gives total equivalents of charge
imbalance in solution (same as Basic function
CHARGE_BALANCE). In contrast, the Basic function TOT
returns moles per kilogram of water, or equivalents per
kilogram of water for TOT("charge").
10 O18_permil = ISO("[18O]")
ISO gives an isotopic composition in the input units for
an isotope--permil, pmc, or TU in current version of
iso.dat. The string argument can be an isotope name, or
any item defined in the ISOTOPE_RATIOS data block, For
example, ISO("R(13C)_Calcite") will return the carbon-13
composition of the calcite solid solution in permil
because of the definitions in iso.dat.
10 D_units$ = ISO_UNITS("D")
ISO_UNITS gives the input units for the isotope, D_units$ =
"permil" in the example. The string argument can be an
isotope name or an item defined in the ISOTOPE_RATIOS data
block as explained for the Basic function ISO.
------------------------------------------------------------
Version 2.17.0: February 25, 2010
------------------------------------------------------------
--------
svn 4006
--------
Changed the calculation of Specific Conductance (SC, uS/cm)
to be for the actual temperature of the SOLUTION (in output
and in BASIC function SC).
Previous versions calculated SC for 25 oC, whereas the
complexation model is done at the actual temperature.
To obtain SC at 25 oC, use keyword REACTION_TEMPERATURE,
for example:
SOLUTION 1; K 1; Cl 1; -temp 99
REACTION_TEMPERATURE; 25
END
The following example prints to the selected output
file the equivalent conductance in (mmho/cm / eq/L) at
20 degrees C for a 1:1 chloride salt solution:
USER_PUNCH
-head conc eq_EC_20
-start
10 punch tot("Cl"), SC / tot("Cl") * 1e-3
-end
where 1e-3 converts from microSiemens/cm to mmho/cm.
(The example given with svn 2448 multiplies SC's incorrectly
with the ratio of the temperatures.)
--------
svn 3986
--------
Added an option for time-substepping in multicomponent
diffusion (-multi_D true), keyword TRANSPORT:
-time_step 3600 3.0 # 3 time-substeps of 1200 seconds
This option is useful to avoid a warning about negative
concentrations that may occur in MCD simulations.
--------
svn 3902
--------
Added four basic functions for use only with PHAST. The
functions are related to the volume, porosity, and
water saturation of a PHAST finite-difference cell:
CELL_VOLUME--The total volume of the cell in liters.
CELL_PORE_VOLUME--The void volume of the cell in liters.
CELL_SATURATION--The fraction of the void volume filled
with water, unitless.
CELL_POROSITY--The porosity of the cell, equal to
CELL_PORE_VOLUME / CELL_VOLUME, unitless.
For example, in a USER_PUNCH program for a PHAST run,
the number of moles of dissolved chloride in a cell is
TOT("Cl")*CELL_PORE_VOLUME for confined flow simulations.
More generally, the number of moles of dissolved chloride
is TOT("Cl")*CELL_SATURATION*CELL_PORE_VOLUME, for confined
or unconfined flow.
For solids, the number of moles of calcite in the
saturated part of a cell is
EQUI("Calcite")*CELL_SATURATION*CELL_PORE_VOLUME. For
unconfined flow, the solid reactants are distributed
between the saturated and unsaturated part of a water-
table cell. It is a limitation of PHAST that it is not
possible to determine the amounts of solid reactants
in the unsaturated part of a cell. Note that for
steady-state, unconfined flow, the saturation of cells is
constant and the unsaturated part of a water-table cell
is never part of the active domain.
--------
svn 3600
--------
A new 1/T^2 term (A5 coefficient) was added for all Pitzer-parameter
temperature expressions.
P = A0 + A1*(1/TK - 1/TR) + A2log(TK/TR) + A3*(TK-TR) +
A4*(TK*TK - TR*TR) + A5*(1/(TK*TK) - 1/(TR*TR))
where TK is temperature in Kelvin. The optional A5 parameter
is read following A4.
--------
svn 3591
--------
Added T^2 term to analytical expressions for log k. A T^2 term
can now be used in the analytical expressions for any log K.
The analytical expression is as follows:
log10(K) = A1 + A2*TK + A3/TK + A4*log10(TK) + A5/TK^2 + A6*TK^2,
where TK is in Kelvin. The A6 term is the new addition. The optional
A6 parameter is read following A5.
--------
svn 3485
--------
Added the active fraction model for calculating exchanger
compositions described by Appelo (1994), Water Resour. Res. 30,
2793-2805. The active fraction model is useful for calculating
the decrease of selectivity when concentrations increase (more
specific sites being filled first). In the active fraction model,
log(K) of an exchange-half reaction depends on the equivalent
fraction on the exchanger:
log(K) = log_k + a_f * (1 - ß_i)
where log_k is the log of the equilibrium constant when all the
sites are occupied by ion i,
a_f is an empirical coefficient, and
ß_i is the equivalent fraction of i.
a_f can be defined in EXCHANGE_SPECIES with -gamma after the WATEQ
Debye-Hueckel parameters.
Example:
EXCHANGE_SPECIES
Na+ + X- = NaX; log_k -0.5
-gamma 4.0 0.075 0.50
The association constant for NaX becomes:
log(K) = -0.5 + 0.50 * (1 - ß_Na)
--------
svn 3453
--------
Added Specific ion Interaction Theory (SIT) activity coefficient
model as described in Grenthe, Ingmar, Plyasunov, A.V., and
Spahiu, Kastriot, 1997, Estimations of medium effects on
thermodynamic data, in Modelling in Aquatic Chemistry,
Grenthe, Ingmar, and Puigdomenech, Inasi, eds, OECD
Publications, ISBN 92-64-15569-4, 724 p.
Implementation is similar to the PITZER implementation, a
database with the SIT keyword invokes the SIT activity
coefficient model. Currently, No database is provided.
The SIT keyword has two identifiers,
-epsilon and -epsilon1, where -epsilon gives the pairwise
interaction parameters and -epsilon1 gives the linear ionic
strength dependency of epsilon, if available. Both parameters
allow for temperature dependence with the same expression used
in PITZER. The five-term expression for temperature dependence is
as follows:
P = A0 + A1*(1/TK - 1/TR) + A2log(TK/TR) + A3*(TK-TR) +
A4*(TK*TK - TR*TR),
where TK is Kelvin and TR is 298.15.
Example:
SIT
-epsilon
Na+ Br- 0.05 # 0.01
Na+ Cl- 0.03 # 0.01
-epsilon1 # not currently used
--------
svn 3288
--------
Additional arguments for the EDL function for the CD_MUSIC
surface complexation model. The values of charge, sigma, and psi
for the 0, 1, and 2 planes can be obtained from the EDL function.
EDL("element", "surface") gives the amount of
element in the diffuse layer for "surface".
not including sorbed species. "surface" should
be the surface name, not the surface-site name
(that is, no underscore).
Special values for "element" include:
"charge" - surface charge, equivalents.
For CD_MUSIC "charge" refers to plane 0.
"charge1"- surface charge on plane 1, equivalents
(CD_MUSIC only).
"charge2"- surface charge on plane 2, equivalents
(CD_MUSIC only).
"sigma" - surface charge density, C/m**2.
For CD_MUSIC "sigma" refers to plane 0.
"sigma1" - surface charge density on plane 1,
equivalents (CD_MUSIC only).
"sigma2" - surface charge density on plane 2,
equivalents (CD_MUSIC only).
"psi" - potential at the surface, Volts.
For CD_MUSIC "psi" refers to plane 0.
"psi1" - surface charge density on plane 1,
equivalents (CD_MUSIC only).
"psi2" - surface charge density on plane 2,
equivalents (CD_MUSIC only).
"water" - mass of water in the diffuse layer, kg.
--------
svn 3189
--------
Density of solutions is now calculated from the concentrations
of dissolved species. The algorithm has been described by Millero
(1974), Millero (2000), Millero (2001) and has been used
successfully by Millero and Lepple (1973), Millero et al (1976),
Fernendez et al. (1982) and Millero (2000) to calculate the
density of seawater, estuaries, lagoons and lakes.
The calculation relies on apparent molar volumes phi(i),
for individual aqueous species according to the following formula:
phi(i) = phi(i,inf) + s(t)I^0.5 + beta(i)I
where phi(i,inf) is the apparent molar volume of species i at
infinite dilution, s(t) is the Debije-Huckel limiting slope, beta(i)
is an empirical constant, and I is the ionic strength.
s(t) is calculated as a function of temperature. Parameterizations of
phi(i,inf) and beta(i) use the following formulas:
phi(i,inf) = a + bt +ct^2
beta(i) = d + et + ft^2
where a, b, c, d, e, and f are empirical constants and t in Celcius.
Data input of the constants are in the keyword data block SOLUTION_SPECIES
using the new identifier -millero.
Example:
SOLUTION_SPECIES
Na+ = Na+
log k 0.0
-gamma 4.0 0.075
-dw 1.33e-9
-millero -3.46 0.1092 -0.000768 2.698 -0.106 0.001651
Apparent molar volume parameters have been included in the database
phreeqd.dat. Calculations made with this database will include
the calculated density in the "Description of solution".
A new basic function, RHO, can be used to obtain the density in
USER_PRINT, USER_PUNCH, and RATES data blocks.
Example:
USER_PUNCH
-heading density
10 PUNCH RHO
--------
svn 3183
--------
Added option for an equilibrium-phase to precipitate only,
parallel to dissolve_only option.
"pre" is added at the end of a line defining an equilibrium-
phase. No data fields may be omitted. Should not
be used when adding an alternative reaction.
Example:
EQUILIBRIUM_PHASES
Dolomite 0 0.1 dissolve_only
Quartz 0 1.5 precipitate_only
--------
svn 3160
--------
Surface charge must be higher than -3000 equivalents,
when the diffuse double layer composition is
calculated with option -donnan.
--------
svn 3149
--------
Diffusion through DDL water is multiplied with c_DDL,i / c_i
with option -only_counter false. c_DDL,i is the concentration in
DDL water, c_i is the concentration in free porewater. (Previous
versions used a multiplier of 1).
Added -erm_ddl as parameter for aqueous species, to be defined
with keyword SOLUTION_SPECIES. erm_ddl (> 0) is an
enrichment factor in DDL water calculated with option -donnan:
c_DDL,i = c_i * Boltzmann_factor * erm_ddl
Example:
SOLUTION_SPECIES; Cs+ = Cs+; log_k 0; -erm_ddl 2.1
Default: erm_ddl = 1.0.
Added optional multicomponent diffusion of cations in interlayer
space of montmorillonite to keyword TRANSPORT.
In the example,
interlayer diffusion is true (default = false),
interlayer porosity is 0.09 (default = 0.1),
the porosity where interlayer diffusion stops is 0.01
(default is 0),
the tortuosity factor is 150 (default = 100).
TRANSPORT
-interlayer_D true 0.09 0.01 150
With interlayer_D true, also -multi_D true (and other
parameters) must be set, for example:
-multi_d true 1e-9 0.3 0.05 1.0
Interlayer diffusion is calculated for the cations associated with X-,
defined with keyword EXCHANGE.
Mass_transfer = -A * (Dw' / t_f) * c_CEC * grad(beta)
A is surface area, A_porewater * (interlayer porosity / free
porewater porosity),
Dw' is the temperature corrected diffusion coefficient of the
aqueous species (defined in SOLUTION_SPECIES),
corrected to zero charge transfer,
t_f is the interlayer tortuosity factor (-),
c_CEC is concentration of total X-, mol(X-) / (L interlayer
water). L interlayer water = (L porewater + L DDL-
water) * (interlayer porosity / free porewater porosity),
grad(beta) is the gradient of the equivalent fraction.
--------
svn 2969
--------
Added basic functions that return the activity coefficient of
an aqueous species (gamma) and the log base 10 of the activity
coefficient of an aqueous species (lg).
USER_PUNCH
-start
10 punch gamma("H+") # activity coefficient
20 punch lg("H+") # log base 10 activity coefficient
-end
The functions return zero if the species is not defined for
the aqueous model or if the species is an exchange or surface
species.
------------------------------------------------------------
Version 2.15.0: February 5, 2008
------------------------------------------------------------
--------
svn 2680
--------
Identifiers for paramaters controlling the integration by
CVODE have been added in the KINETICS data block.
-bad_step_max bad_steps
-cvode_steps steps
-cvode_order order
-bad_step_max bad_steps--This option was used only in the
Runge-Kutta method. Now, the value of this option is used for
CVODE as well. The value entered is the number of times that
PHREEQC will invoke CVODE to try to integrate a set of
rates over a time interval. Default is 500.
-cvode_steps steps--The value given is the maximum number of
steps that will taken during one invocation of CVODE.
Default is 100.
-cvode_order order--CVODE uses a specified number of terms in
an extrapolation of rates using the BFD method. Legal values
are 1 through 5. A smaller value (2) may be needed if the rate
equations are poorly behaved. The default is 5.
--------
svn 2457
--------
Added options to inverse modeling to translate current
solution definitions in PHREEQC to a Netpath .lon file and
(or) to .pat and model files.
INVERSE_MODELING
-lon_netpath prefix
At the beginning of the inverse modeling calculation, each
solution that has been defined (or saved) to PHREEQC, is
written to the file prefix.lon in a format readable by
DBXL (NetpathXL distribution).
INVERSE_MODELING
-pat_netpath prefix
A NETPATH model file is written for each inverse model that is
found. The model files are named prefix-n.mod, where n refers
to the sequence number of the model. In addition, a file named
prefix.pat is written that contains the solutions associated
with each model. The solutions are adjusted in accordance with
the deltas calculated for the inverse model. Thus, a solution
could be used for model 1 and model 2, but the concentrations
could be slightly different for the two models. The solutions
are identified by an initial integer corresponding to the
sequence number of the model, followed by the solution description.
--------
svn 2448
--------
Added calculation of specific conductance. Requires the
use of phreeqd.dat, which contains the diffusion coefficients
of aqueous species. If phreeqd.dat is used, the specific
conductance (uS/cm at 25 C) is printed in the
"Description of solution".
The Basic function SC returns the value of the specific
conductance for the solution at 25 C. The following example
would print to the selected output file the equivalent conductance
in (mmho/cm / eq/L) at 20 degrees C for a 1:1 chloride salt
solution:
USER_PUNCH
-head conc eq_EC_20
-start
10 punch tot("Cl"), SC / tot("Cl") / 1e3 * .89 * 298 / 293
-end
where 1e-3 converts from microSiemens/cm to mmho/cm, .89
accounts for the viscosity at 20 C, and 298/293
accounts for the temperature of 20 C.
------------------------------------------------------------
Version 2.14.3: November 17, 2007
------------------------------------------------------------
--------
svn 2312
--------
Added new option to PITZER datablock, use_etheta t/f.
If true, the nonsymmetric mixing terms--cation/cation and
anion/anion of different charge--are included; if false
these terms are excluded from all equations. Default is true.
PITZER
-use_etheta true
--------
svn 2270
--------
Added additional parameters Pitzer activity formulation for
neutral species, MU and ETA. MU applies to nnn, nnn', nn'n'',
nna, nn'a, nnc, nn'c interactions, where n, n', and n'' are
neutral species, a is an anion and c is a cation. ETA applies
to ncc' and naa' interactions. Also modified LAMDA for the
special case of nn interactions (coefficients in osmotic and
ln equations are different than other interaction types).
Source of equations is Clegg and Whitfield, 1991, Activity
coefficients in natural waters, Chapter 6, in Pitzer, K.S.
(Ed.) Activity Coefficients in Electrolyte Solutions, 2nd
Ed. CRC Press, Boca Raton. Removal of the 6 coefficient in
last two terms of eq 35 and 36 (p. 2404) per Cleg and
Whitfield, 1995, Geochimica et Cosmochemica Acta, v. 59,
no. 12, pp 2403-2421. Order of species in definitions should
not matter.
PITZER
-MU
CO2 CO2 CO2 ? # nnn
CO2 CO2 NH3 ? # nnn'
CO2 B(OH)3 NH3 ? # nn'n''
CO2 CO2 Ca+2 ? # nnc
CO2 CO2 Cl- ? # nna
CO2 NH3 Ca+2 ? # nn'c
CO2 NH3 Cl- ? # nn'a
-ETA
CO2 Ca+2 Mg+2 ? # ncc'
CO2 Cl- SO4-2 ? # naa'
As with all other Pitzer parameters, a five-term expression
for temperature dependence is available:
P = A0 + A1*(1/TK - 1/TR) + A2log(TK/TR) + A3*(TK-TR) +
A4*(TK*TK - TR*TR),
where TK is Kelvin and TR is 298.15. A0 through A4 are
defined in order. Any undefined values are assumed to
be zero.
-MU
CO2 CO2 CO2 ? ? ? ? ? # nnn
------------------------------------------------------------
Version 2.14.2: September 17, 2007
------------------------------------------------------------
Fixed logic of memory checking for PhreeqcI. This serious
bug makes versions 2.14.0 and 2.14.1 unusable.
------------------------------------------------------------
Version 2.14.1: September 5, 2007
------------------------------------------------------------
No new features.
------------------------------------------------------------
Version 2.14.0: August 30, 2007
------------------------------------------------------------
No new features.
------------------------------------------------------------
Version 2.13.3: February 15, 2007
------------------------------------------------------------
No new features.
------------------------------------------------------------
Version 2.13.2: February 1, 2007
------------------------------------------------------------
No new features.
------------------------------------------------------------
Version 2.13.1: January 16, 2007
------------------------------------------------------------
No new features.
------------------------------------------------------------
Version 2.13.0: November 3, 2006
------------------------------------------------------------
--------
svn 1368
--------
(1) Added multicomponent diffusion (MCD) to transport
capabilities. MCD allows different tracer diffusion
coefficients for species, but calculates charge balanced
transport. In the example, MCD is specified to be true,
default tracer diffusion coefficient for species (Dw) is 1e-9,
porosity is set to 0.3, porosity limit is set to 0.05, and an
exponent of porosity (n) is set to 1.0. Effective diffusion
coefficient is defined by the equation: De = Dw * porosity^n.
Diffusion stops when the porosity falls below the porosity
limit.
TRANSPORT
-multi_d true 1e-9 0.3 0.05 1.0
Added tracer diffusion coefficient to SOLUTION_SPECIES
definitions, -dw identifier.
SOLUTION_SPECIES
H+ = H+
log_k 0.0
-gamma 9.0 0.0
-dw 9.31e-9
(2) Added phreeqd.dat database with diffusion coefficients (-dw)
defined for aqueous species in database directory.
(3) Added BASIC functions to obtain and modify the porosity
in a cell. The functions can be used in BASIC programs
defined with keyword RATES, USER_PRINT, USER_PUNCH and
USER_GRAPH.
get_por(cell_no) # returns the porosity in cell
# 'cell_no'
change_por(0.21, cell_no) # porosity of cell 'cell_no'
# becomes 0.21
(4) Mobile surface and Donnan option in SURFACE. Mobile surfaces
are meant for modeling transport of colloids. Only surfaces with
a diffuse double layer can be transported (the ensemble must be
electrically neutral). Surfaces related to equilibrium-phases
and kinetics cannot be transported.
Example 1: Use donnan assumption to calculate the explicit
composition of the diffuse layer of surfaces. Thickness of the
diffuse layer is defined to be 1e-7 meters. (Default thickness
is 1e-8 meters.) Hfo (both sites Hfo_w and Hfo_s) is a surface
that is transported with advection and dispersion. The diffusion
coefficient of 1e-13 m^2/s is used with option -multi_d true in
TRANSPORT. Sfo is an immobile surface (Dw = 0).
SURFACE
-donnan 1e-7
Hfo_w 97.5e-5 600 88e-3 Dw 1e-13
Hfo_s 2.5e-5
Sfo_w 97.5e-5 600 88e-3 Dw 0
Sfo_s 2.5e-5
Example 2: Define Donnan calculation information. Thickness
of the diffuse layer is 1e-8 meters, and relative viscosity is
0.5. Relative viscosity only applies to multicomponent diffusion
of solutes in the diffuse layer. (Default viscosity is 1.0.)
SURFACE
-donnan 1e-8 viscosity 0.5
Example 3: Define Donnan calculation information. Thickness
of the diffuse layer is 1.5 Debye lengths, maximum fraction of
water that can be in the diffuse layer is 0.9. (Default
thickness in Debye lengths is 1, default limit is 0.8.)
SURFACE
-donnan debye_lengths 1.5 limit_ddl 0.9
When option '-only_counter_ions' is used in conjunction with
with '-donnan', all the co-ions (with the same sign of charge as
the surface) will be excluded from the DDL, and will be given a
concentration of (near) zero in the DDL.
(5) Added special BASIC function to change the diffusion
coefficient of (part of) a SURFACE, and hence to change the
status from mobile to immobile or immobile to mobile.
Example 1: take a fraction 0.2 of 'Hfo', rename it to
'Sorbedhfo', with a diffusion coefficient of 0, in cell 'cell_no'
USER_PRINT
10 print 'Changing surface in cell ', cell_no
20 change_surf("Hfo", 0.2, "Sorbedhfo", 0, cell_no)
Example 2: change the diffusion coefficient of 'Hfo' to 1e-12
m2/s in cell 'cell_no'
10 change_surf("Hfo", 1, "Hfo", 1e-12, cell_no)
This function can be used in BASIC programs defined with keywords
RATES, USER_PRINT, USER_PUNCH and USER_GRAPH. For correct
operation of 'change_surf', the surface components must have
been defined with the same surface species (the association
constants may differ) and the same diffuse layer thickness or
Debye length. The surfaces will be adapted at the end of a
calculation step. The result of change_surf does not show up in
print or punch results of that step, but the reformatting is
effective in the next timestep calculations.
--------
svn 1337
--------
Added -add_logk to NAMED_EXPRESSIONS keyword.
NAMED_EXPRESSIONS
Log_alpha_14C_CO3-2/CO2(aq)
-add_logk Log_alpha_14C_CO3-2/CO2(g) 1
-add_logk Log_alpha_14C_CO2(aq)/CO2(g) -1
--------
svn 1281
--------
Added new option to PITZER data block to allow definition of
alpha1 and alpha2 for specific electrolytes. Entries are
following -ALPHAS are Ion1, Ion2, alpha1, alpha2. Both
alpha1 and alpha2 should be defined. Default is 0.0 for
undefined values following Ion1 and Ion2.
Example:
PITZER
-ALPHAS
#
# Defaults for ion valences in salts
#
# 1-N (only B1): alpha1 = 2
# 2-2: alpha1 = 1.4 alpha2 = 12.0
# 3-2, 4-2: alpha1 = 2 alpha2 = 50
#
#Ion1 Ion2 Alpha1 Alpha2
Fe+2 Cl- 2 1
Fe+2 SO4-2 1.559 5.268
--------
svn 1279
--------
Added new Basic function OSMOTIC that returns the
osmotic coefficient if the Pitzer model (PITZER keyword data
block) is used or 0.0 if the ion-association model is used.
Example:
USER_PRINT
10 PRINT "Osmotic coefficient: ", OSMOTIC
--------
svn 1245
--------
Enabled redox in Pitzer model with option in
PITZER keyword. Typically, the option will be included
in the pitzer database file.
Example:
PITZER
-redox TRUE
The default database for the Pitzer model does not contain
any redox definitions and the default value for the option
is FALSE. At a minimum, species O2 and H2 must be defined
in the database or input file to allow redox calculations.
--------
svn 1207
--------
Added option to force an equilibrium phase to be
included in the equality constraints. Normally, the SIs of
equilibrium phases are optimized to be negative and the
sum of SIs is minimized. If -force_equality is used, then
the phase must reach its target SI or the calculation fails
with an error.
Example:
EQUILIBRIUM_PHASES
Fix_pH -7 NaOH
-force_equality
Calcite 0
Dolomite 0
CO2 -3.5
One example of using the new option would be to ensure that
a target pH is attained, as in the example above.
--------
svn 1179
--------
New option (-sites_units or -sites) allows alternative
units (sites/nm^2) for definition of number of sites for a
surface. This approach requires better consistency among the
parameters as both the number of sites and the surface area
are based on the mass. It makes more sense than the default,
which requires the number of sites (first numeric item in a
line) to be defined in units of moles, independently of the
number of grams of sorbent. Units descriptor is either DENSITY,
for defining number sites/nm^2, or ABSOLUTE, for defining
number of sites in moles. Optionally, sites, sites_units, or
-s[ites_units]. ABSOLUTE is the default for backward
compatibility with input files.
Example:
SURFACE 1
-sites_units DENSITY
SurfOH 2.6 600. 1.0
SurfaOH 2.6 30. 2.0
Explanation:
In this example, Surf has a site density of 2.6 sites per
nanometer squared, a specific area of 600 meters squared per
gram, and a mass of 1 gram. Surfa has a site density of 2.6
sites per nanometer squared, a specific area of 30 meters
squared per gram, and mass of 2 grams.
--------
svn 1096
--------
Allows solids and gases in the equations for PHASES. This
capability simplifies the definitions for gas and solid
isotopic components. Solids must be identified with "(s)" and
gases with "(g)". The first entity on the left- hand-side of
the equation must be the stoichiometric formula of the solid
or gas component being defined, optionally with (g) or (s). In
turn gases and solids included in the equation must be defined
with reactions that ultimately allow the defined species
(C[18O]2(g) in this case) in terms of aqueous species.
Example:
PHASES
C[18O]2(g)
C[18O]2(g) + CO2(g) = 2CO[18O](g)
log_k 0.602059991327962396 # log10(4)
--------
svn 1092
--------
CD_MUSIC sorption model has been implemented.
Still missing logic for surfaces related to equilibrium-
phases and kinetics. Has explicit calculation of diffuse
layer composition with Donnan assumption. Old diffuse-layer
calculation will not be implemented.
Example:
SURFACE
Goe_uniOH .000552 96.387 1
-capacitance 1.1 5
Goe_triO .000432
-cd_music
-donnan
Explanation:
1.1 5 are capacitances for the cd-music model for 0-1 and 1-2
planes, respectively.
-cd_music specifies that the surface is a cd-music surface.
-donnan optionally calculates the diffuse layer composition
with the Donnan model.
Example:
SURFACE_SPECIES
Goe_uniOH-0.5 + H+ + AsO4-3 = Goe_uniOAsO3-2.5 + H2O
log_k 20.1 # eq 7 K1, Kin1
-cd_music -1 -6 0 0.25 5
Explanation:
-cd_music--this option is used to specify the change in charge
by the reaction for three planes, 0 (specific sorption at the
surface), 1 (Stern layer), and 2 (or d, the diffuse layer).
The five numbers in the form above are (1) the change
in charge for plane 0 due to loss or gain of hydrogen and
oxygen at plane 0, (2) the change in charge for plane 1 due to
the hydrogen and oxygen in the ligand that are located at
plane 1, (3) the change in charge in diffuse layer, plane 2,
(4) the fraction of the central ion charge that is
associated with plane 0, and (5) the charge on the central
ion.
In this example the change in charge at plane 0 is (delta z0) =
-1 (loss of one hydrogen) + 0.25*5 (contribution from As+5) =
0.25. The charge at plane 0 becomes -0.5 + 0.25 = -0.25.
The change in charge at plane 1 is (delta z1) = -6 (3 oxygens of
the ligand are located at plane 1) + (1-0.25)*5 (contribution
from As+5) = -2.25. The charge at plane 1 becomes 0 + (-2.25) =
-2.25. There is no change in charge associated with plane 2.
The total charge of the species is -0.25 (plane 0) + -2.25
(plane 1) + 0 (plane 2) = -2.5.
Alternatively to the form above, the changes in charge
on the three planes can be entered directly as the first
three numbers in the option, followed by two zeros. Thus, the
following is equivalent to the -cd_music definition above, and
consistent with more recent papers which would list
delta z0 = 0.25, delta z1 = -2.25 and delta z2 = 0:
SURFACE_SPECIES
Goe_uniOH-0.5 + H+ + AsO4-3 = Goe_uniOAsO3-2.5 + H2O
log_k 20.1 # eq 7 K1, Kin1
-cd_music 0.25 -2.25 0 0 0
--------
svn 675:
--------
Added PRINT option to print the species that contribute
to alkalinity. Alkalinity distribution is printed in
the output file following the distribution of species.
Default at program startup is false.
Example:
PRINT
-alkalinity true
------------------------------------------------------------
Version 2.12:
------------------------------------------------------------
* Made aqueous activity coefficients the default activity
coefficients for exchange species when using the
Pitzer formulation. New option in EXCHANGE is
-pitzer_exchange_gammas T/F, default is true;
defining "false" sets exchange activity coefficients
to 1.0. Option has no effect for ion-association
model (non-Pitzer).
* Added multiplier format to REACTION steps and KINETICS steps,
which simplifies definition of multiple equal reaction increments.
This definition:
INCREMENTAL_REACTIONS true
REACTION
H2O 1
-36 3*-4 2*-.25 -0.19 4*-0.1 3*-0.05 moles
is equivalent to this definition:
INCREMENTAL_REACTIONS true
REACTION
H2O 1
-36 -4 -4 -4 -.25 -.25 -0.19 -0.1 -0.1 -0.1
-0.1 -0.05 -0.05 -0.05 moles
* Added Pitzer activity formulation. Use pitzer.dat database
to invoke the Pitzer model. Should have same capabilities
as ion-association model except explicit diffuse layer
calculation is not implemented with the Pitzer model.
New keyword is PITZER with following options:
PITZER
-MacInnes T/F # uses MacInnes assumption or unscaled for
# individual activities and activity coefficients
-B0
Na+ Cl- 0.0765 -777.03 -4.4706 0.008946 -3.3158E-6
-B1
Na+ Cl- 0.2664 0 0 6.1608E-5 1.0715E-6
-B2
Mg+2 SO4-2 -37.23 0 0 -0.253
-C0
Na+ Cl- 0.00127 33.317 0.09421 -4.655E-5
-THETA
K+ Na+ -0.012
-LAMDA
Na+ CO2 0.1
-ZETA
H+ Cl- B(OH)3 -0.0102
-PSI
Na+ K+ Cl- -0.0018
A five-term expression for temperature dependence is available
for all Pitzer parameter values:
P = A0 + A1*(1/TK - 1/TR) + A2log(TK/TR) + A3*(TK-TR) +
A4*(TK*TK - TR*TR),
where TK is Kelvin and TR is 298.15.
* Cl1mp is a new multiple precision version of routine cl1,
a simplex-based optimization routine. Cl1mp was develeped
by using the Gnu Multiple Precision package (gmp).
Calculations are carried out to about 30 significant
digits. Cl1mp may help in some situations where roundoff
errors are a problem, but it is still possible that roundoff
errors will cause cl1mp to fail to find a solution to an
optimization problem. The mp version has the following
options in INVERSE_MODELING:
-multiple_precision T/F--causes the mp version
to be used in inverse modeling calculations.
-mp_tolerance 1e-12--tolerance for mp version of
cl1. As in cl1, numbers less than the
tolerance are considered to be zero.
1e-12 is the default.
-censor_mp 1e-20--as calculations occur in the
linear equation array, elements less
than this value are set to zero. Default
is 1e-20. A value of 0.0 causes no
censoring to occur.
------------------------------------------------------------
Version 2.11:
------------------------------------------------------------
* A new database, minteq.v4.dat, has been translated from
version 4.02 of MINTEQA2 and is included in all
distributions. The database minteq.dat from earlier
version of MINTEQA2 has been slightly revised and is
also included.
------------------------------------------------------------
Version 2.10:
------------------------------------------------------------
No new features.
------------------------------------------------------------
Version 2.9:
------------------------------------------------------------
* Added new keyword COPY that allows a data entity
to be copied from one index to a new index
or to a range of indicies. Format is
COPY keyword index index_start[-index_end]
where keyword may be SOLUTION
EQUILIBRIUM_PHASES
EXCHANGE
GAS_PHASE
KINETICS
MIX
REACTION
REACTION_TEMPERATURE
SOLID_SOLUTION
SURFACE
* Added new Basic functions
b$ = PAD(a$, 20) pads a$ to a total of 20 characters
with spaces and stores result in b$. PAD returns
a copy of a$ if a$ is more than 20 characters.
i = INSTR(a$, b$) sets i to the character position of
string b$ in a$, 0 in not found.
b$ = LTRIM(a$) trims white space from beginning of
string a$ and stores result in b$.
b$ = RTRIM(a$) trims white space from end of string
a$ and stores result in b$.
b$ = TRIM(a$) trims white space from beginning and
end of string a$ and stores result in b$.
* Added new Basic function SYS that calculates the
total amount of an element in all phases (solution,
equilibrium_phases, surfaces, exchangers, solid solutions,
and gas phase). KINETIC reactions are not included.
The function has two forms: (1) one element name as an
argument (variable names are user specified)
10 t = SYS("As")
the function will return the total arsenic in the system.
(2) 5 argumens
10 t = SYS("As", count_species, names$, types$, moles)
will return the total arsenic in the system to t; count_species--
the number of species that contain arsenic, including
solution, equilibrium_phases, surfaces, exchangers, solid solutions,
and gas phase species; names$--a character array that has the
name of each species; type$--a character array that specifies the
type of phase for the species, aq, equi, surf, ex, s_s, gas, diff.
Diff refers to the amount of the element in the diffuse layer of
a surface when the explicit diffuse layer calculation is used;
moles--an array containing the number of moles of the element in
the species. The sum of moles(i) is equal to tot.
SYS has several special arguments for the form
SYS("arg", count, names$, types$, values)
arg is one of the options listed below.
count is a single numeric value and is the number of elements
in the following arrays.
name$ is an array of string values.
type$ is an array of string values.
values is an array of numeric values.
Values of arg:
elt_name returns total number of moles of element in system.
count is the number of species for the element in
the system, including aqueous, exchange, surface,
equilibrium_phase, solid solution component, and
gas phase "species".
Arrays are filled for each "species"; values are moles.
"elements" returns total number of moles of dissolved elements other
than H and O.
count is number of elements, valence states,
exchangers, and surfaces.
Arrays are filled for each element and valence state,
type is "dis"; exchanger, type is "ex",
and surface, type is "surf". Values are moles.
"phases" returns maximum saturation index of all phases.
count is number of phases in system.
Arrays are filled for each phase; values are
saturation indexes.
"aq" returns sum of moles of all aqueous species.
count is number of aqueous species in system.
Arrays are filled with each aqueous species;
values are moles.
"ex" returns sum of moles of all exchange species.
count is number of exchange species in system.
Arrays are filled with each exchange species;
values are moles.
"surf" returns sum of moles of all surface species.
count is number of surface species in system.
Arrays are filled with each surface species;
values are moles.
"s_s" returns sum of moles of all solid solution components.
count is number of solid solution components in system.
Arrays are filled with each solid solution component;
values are moles.
"gas" returns sum of moles of all gas components.
count is number of gas components in system.
Arrays are filled with each gas component;
values are moles.
* Added new Basic function, DESCRIPTION, that has the value
defined for the description field of the SOLUTION keyword line.
* Added alternative ordinary differential equation solver
called CVODE, a set of C routines from the Lawrence
Livermore National Labs. CVODE is part of the SUNDIALS
package. CVODE is used in place of the Runge Kutta method
when "-cvode true" is used within a KINETICS data block.
KINETICS
-cvode true
------------------------------------------------------------
Version 2.8:
------------------------------------------------------------
No new features.
------------------------------------------------------------
Version 2.7:
------------------------------------------------------------
Changed format of selected output file:
Removed quotations surrounding strings in headings.
Removed quotations surrounding strings in state variable.
All fields are 12 or 20 places depending on
-high_precision.
Headings are not truncated even if longer than
specified precision.
For isotopes, missing value is -9999.9
Selected output is updated each simulation.
If a species or phase is defined
subsequent to the simulation where SELECTED_OUTPUT
was defined it will appear in the selected output
file in the simulation in which it is defined and
in subsequent simulations.
Added strings for each file, which can be extracted from the
executable file with the "ident" command.
Fixed null pointer for isotope_ratios if Basic routine
was undefined.
Fixed problem in C++ if structure name is same as member name.
logk member of logk structure was renamed to log_k.
Added identifier -add_constant to PHASES, EXCHANGE_SPECIES,
SOLUTION_SPECIES, and SURFACE_SPECIES.
-add_constant -0.301
log K is augmented by the specified constant.
Theory and implementation of isotopes in PHREEQC is documented in:
Thorstenson, D.C., and Parkhurst, D.L., 2002, Calculation of
individual isotope equilibrium constants for implementation in
geochemical models: U.S. Geological Survey Water-Resources
Investigations Report 02-4172, 129 p.
Added KEYWORDS:
ISOTOPES
Element
-isotope isotope_name units standard_ratio
-total_is_major T/F (OPTION IS DISABLED!!)
CALCULATE_VALUES
Name
-start
Basic statements, must have SAVE
-end
ISOTOPE_RATIOS (for printing)
Name=Calculate_values_name Isotope_name
ISOTOPE_ALPHAS (for printing)
Name=Calculate_values_name Named_logk=named_expression_name
Basic functions:
calc_value("calc_value_name") evaluates a definition of CALCULATE_VALUES
lk_named("name") log10(K) of definition in NAMED_EXPRESSIONS
lk_phase("name") log10(K) of definition in PHASES
lk_species("name") log10(K) of definition in (SOLUTION, EXCHANGE, SURFACE)_SPECIES
sum_gas("template","element") Sum of element in gases with specified template, moles.
Example:
template="{C,[13C],[14C]}{O,[18O]}2" includes all CO2 gases
sum_species("template","element") Sum of element in aqueous, exchange, and surface species with
specified template (moles)
sum_s_s("s_s_name","element") Sum of element in a specified solid solution (moles)
PRINT keyword:
-initial_isotopes T/F
-isotope_ratios T/F
-isotope_alphas T/F
-censor_species 1e-8 # omit species from Distribution of Species if less than
# relative minimum of an element or element redox state
# total concentration
SELECTED_OUTPUT keyword:
-calculate_values name1 name2 ...
-isotopes minor_isotope1 minor_isotope2 ....
Added functions LK_SPECIES, LK_NAMED, LK_PHASE for Basic
interpreter. LK_SPECIES("CaHCO3+") returns the
log k for the association reaction for the ion pair
CaHCO3+ at the current temperature. The log K is
for the reaction as defined in the database or
input file. Similarly,
LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)") returns the
value for the log K at the current temperature using
expressions defined in NAMED_LOG_K data block;
LK_PHASE("Calcite") returns the value of log K
for calcite at the current temperature for the
dissociation reaction defined in the database or
input file. Values are "log10" values.
Example for Basic program:
10 PRINT "Log10 KCalcite: ", LK_PHASE("Calcite")
20 PRINT "Log10 KCaHCO3+: ", LK_SPECIES("CaHCO3+")
30 PRINT " 1000ln(alpha): ", LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)")*LOG(10)*1000
NAMED_EXPRESSION--New keyword data block.
This data block was implemented to facilitate isotopic
calculations. It allows analytical expressions that
are functions of temperature to be defined. The purpose
is to separate the fractionation factors from the log
K, so that the fractionation factor or its temperature
dependence can be easily modified. The named expression
can be added to a log K for a species or phase by the
-add_logk identifier in SOLUTION_SPECIES
EXCHANGE_SPECIES, SURFACE_SPECIES, or PHASES data
block. Log K, Delta H, and analytical expressions for a
log K can be defined with identifiers -log_k, -delta_h,
and -analytical_expression as described in SOLUTION_SPECIES
in WRIR 99-4259. Fractionation factors are often defined
as 1000*ln(alpha). The identifier -ln_alpha1000 can be used
to enter data in this form. The analytical expression is the
same as defined in SOLUTION_SPECIES, but the result of the
expression is converted to log10(alpha) by dividing by
1000*ln(10) before it is summed into log K values.
NAMED_EXPRESSIONS
Log_K_calcite # CaCO3 + 2H3O+ = Ca+2 + 3H2O + CO2
log_k 8.201
delta_h -8.035 kcal
-analytic 292.29 0.015455 -24146.841 -94.16451 2248628.9
Log_alpha_18O_CO2(aq)/Calcite
-ln_alpha1000 3.8498 0.0 10.611e3 0.0 -1.8034e6
Log_alpha_13C_CO2(aq)/Calcite
-ln_alpha1000 2.72 0.0 0.0 0.0 -1.1877e6
------------------------------------------------------------
Added identifier -add_logk to SOLUTION_SPECIES
EXCHANGE_SPECIES, SURFACE_SPECIES, and PHASES data
block.
Allows a named expression to be added to the definition
of the log K for a species or phase. In the following
example, the log K for the phase Ca[14C][18O]3 is summed from
four parts, one defined with the log_k identifier and the
other three parts from expressions defined in NAMED_EXPRESSIONS.
The named expression is multiplied by the coefficient at the
end of the line before it is summed into the log K. A missing
coefficient is 1.0 by default.
PHASES
Ca[13C][18O]3
Ca[13C][18O]3 + 3CO2 + 2H3O+ = Ca+2 + 3H2O + 3CO[18O] + [13C]O2
log_k 0.903089986991 # 3*log10(2)
-add_logk Log_K_calcite 1.0
-add_logk Log_alpha_13C_CO2(aq)/Calcite 1.0
-add_logk Log_alpha_18O_CO2(aq)/Calcite 3.0
SOLUTION keyword:
At present, can only define isotopes in the units defined in ISOTOPES.
------------------------------------------------------------
Version 2.6:
------------------------------------------------------------
No new features.
------------------------------------------------------------
Version 2.5:
------------------------------------------------------------
Added the capability to use square brackets to define an
"element" name. The brackets act like quotation marks
in that any character string can be used within the
brackets as an element name. For example, [Fe3], [13C],
and [N5] are now legal "element" names. All element
names without brackets must begin with a capital letter,
followed by zero or more lower case letters and underscores.
Added identifier -activity_water for a species in SOLUTION_SPECIES
data block. This identifier has been added for future updates
that will allow isotopic calculations. It is intended to be
used only for isotopic variations of H2O, like D2O or
H2[O18]. It forces the activity coefficient for the
species to be activity(water)/55.5. This effectively sets
the activity of the species to the mole fraction in
solution.
Added identifier -bad_step_max to KINETICS data block.
An integer following -bad_step_max gives the maximum number
of times a rate integration may fail before execution of the
program is terminated. Default is 500.
------------------------------------------------------------
Version 2.4:
------------------------------------------------------------
------------------------------------------------------------
Added identifier -warnings to PRINT keyword.
An integer following -warnings gives the maximum number
of warnings to print into the output file. A negative
number allows all warnings to be printed.
Example: -warnings 20
------------------------------------------------------------
Changed the results of the function CELL_NO in Basic programs.
Function cell_no in Basic now prints a number equivalent
to -solution in SELECTED_OUTPUT data block. It gives the
solution number for initial solution calculations and the
solution being used in batch reaction calculations.
Result is the same as previous versions for ADVECTION or
TRANSPORT calculations.
------------------------------------------------------------
Version 2.3:
------------------------------------------------------------
DATABASE--New keyword data block
It must be the first keyword in the input file.
The character string following the keyword is
the pathname for the database file to be used
in the calculation. The file that is specified
takes precedence over any default database
name, including environmental variable
PHREEQC_DATABASE and command line arguments.
LLNL_AQUEOUS_MODEL_PARAMETERS--New keyword data block
Added new keyword to make aqueous model similar to
EQ3/6 and Geochemists Workbench when using
llnl.dat as the database file. Values
of Debye-Huckel a and b and bdot (ionic strength
coefficient) are read at fixed temperatures.
Linear interpolation occurs between temperatures.
New options for SOLUTION_SPECIES are
-llnl_gamma a , where a is the ion-size parameter.
-co2_llnl_gamma , indicates the temperature dependent
function for the bdot term given in
-co2_coefs of LLNL_AQUEOUS_MODEL_PARAMETERS
will be used. Applies to uncharged
species only.
LLNL_AQUEOUS_MODEL_PARAMETERS
-temperatures
0.0100 25.0000 60.0000 100.0000
150.0000 200.0000 250.0000 300.0000
#debye huckel a (adh)
-dh_a
0.4939 0.5114 0.5465 0.5995
0.6855 0.7994 0.9593 1.2180
#debye huckel b (bdh)
-dh_b
0.3253 0.3288 0.3346 0.3421
0.3525 0.3639 0.3766 0.3925
-bdot
0.0394 0.0410 0.0438 0.0460
0.0470 0.0470 0.0340 0.0000
#cco2 (coefficients for the Drummond (1981) polynomial)
-co2_coefs
-1.0312 0.0012806
255.9 0.4445
-0.001606
------------------------------------------------------------
Added function SURF to Basic.
SURF("element", "surface") gives the amount of element
sorbed on "surface". "surface" should be the surface
name, not the surface-site name (that is, no underscore).
------------------------------------------------------------
Allow decimals in definition of secondary master species.
Some redox states do not average to integers,
for convenience in identifying them, decimal numbers
may be used within the parentheses that define the
redox state, example S(0.3) could be used in the
MASTER_SPECIES data block for the valence state of
aqueous species S6-2.
------------------------------------------------------------
Eliminate echo of input file in PRINT data block.
-echo_input T/F turns echoing on and off.
Default is true, initial value is true.
------------------------------------------------------------
Added option for an equilibrium-phase to dissolve only.
"dis" is added at the end of a line defining an equilibrium-
phase. No data fields may be omitted. Should not
be used when adding an alternative reaction.
Example:
EQUILIBRIUM_PHASES
Dolomite 0.0 0.001 dis
------------------------------------------------------------
Version 2.2:
------------------------------------------------------------
Added function EDL to Basic.
EDL("element", "surface") gives the amount of
element in the diffuse layer for "surface", not
including sorbed species. "surface" should be
the surface name, not the surface-site name
(that is, no underscore).
Special values for "element" include:
"charge" - gives surface charge, equivalents.
"sigma" - surface charge density, C/m**2.
"psi" - potential at the surface, Volts.
"water" - mass of water in the diffuse layer, kg.
------------------------------------------------------------
End of Features not documented in WRIR 99-4259.
------------------------------------------------------------
************************************************************
************************************************************
* Revisions and Bug Fixes *
************************************************************
************************************************************
------------------------------------------------------------
Version 3.3.8: June 8, 2016
------------------------------------------------------------
--------
svn 5570
--------
In SELECTED_OUTPUT; -totals, a redox state defined
with a "+" sign, such as Fe(+3), was not recognized
("Fe(3)" worked correctly). Now Fe(+3) is
synonymous with Fe(3).
------------------------------------------------------------
Version 2.18.0: April 9, 2011
------------------------------------------------------------
--------
svn 5212
--------
Subscript error in solver (ineq) when reseting deltas
after optimization failed.
--------
svn 4996
--------
Had conversion conversion to Kelvin as 273.16 in Basic
function TK, should be 273.15.
--------
svn 4955
--------
Changed O2(g) constant in Amm.dat and iso.dat to
definition from llnl.dat.
--------
svn 4954
--------
Added two more parameter sets in series of attempts
to converge: tolerance/100 and tolerance/1000.
--------
svn 4943
--------
Added separate As(3) in sit.dat.
--------
svn 4854
--------
Added two additional convergence parameter sets:
ineq_tol/100 and ineq_tol/1000.
--------
svn 4840
--------
Added missing -dw parameters to MgCO3, MgHCO3, and
MgSO4 aqueous species in phreeqc.dat.
------------------------------------------------------------
Version 2.17.5: September 7, 2010
------------------------------------------------------------
--------
svn 4793
--------
Revised fix for exponential of negative number
in Basic. Error message for negative number raised
to a fractional power.
------------------------------------------------------------
Version 2.17.4: September 2, 2010
------------------------------------------------------------
--------
svn 4771
--------
Added synonyms to TOTMOLE: TOTMOL, TOTMOLES
Fixed bug with negative exponential in basic,
for example -0.006^0.9
------------------------------------------------------------
Version 2.17.3: August 12, 2010
------------------------------------------------------------
--------
svn 4727
--------
Increased maximum iterations in cl1 solver. One test
case failed after new compiler was installed.
--------
svn 4700
--------
Initialized (nearly) all variables in class.
--------
svn 4697
--------
Fixed bug with second PITZER data block, parameters
were not updated if temperature was not changed.
--------
svn 4698
--------
Modified PHRQ_malloc and PHRQ_free logic. These routines
are used in almost all cases.
--------
svn 4694
--------
Initialized variables for V_M structure, rxn->dz (for CD_MUSIC),
Fixed problem where definitions in second SIT data block were
not added to model.
--------
svn 4677
--------
Renamed all variables that "shadowed" class variables.
--------
svn 4643
--------
Made isfinite a macro.
--------
svn 4539
--------
Fixed bug with long file names in inverse modeling files
netpath.fil or model.fil.
--------
svn 4490
--------
Redox had never been enabled for the SIT formulation.
Added the switch to include the hydrogen balance
equation for SIT.
--------
svn 4458
--------
Tweaked the convergence parameters for Pitzer log
gamma unknowns. Set a maximum step size for these
unknowns. Also changed usage of internal flags
for Pitzer calculations related to initial solution
calculations. Corrected print of Gamma iterations.
--------
svn 4399
--------
Error in PHRQ_calloc. Size of allocated block was
not set. Under some situations, could cause serious
errors and a crash.
--------
svn 4376
--------
Error in logic for removing unstable phases for Pitzer
and SIT.
--------
svn 4233
--------
Removed duplicate parameter for Na+ -- Cl- in sit.dat.
Value of 0.03 was entered erroneously for both Na/Cl and Cl/Na.
------------------------------------------------------------
Version 2.17.0: February 25, 2010
------------------------------------------------------------
--------
svn 4115
--------
Fixed bugs with unititialized strings in Basic, which
caused an error in renumbering with PhreeqcI. Tested
most Basic functions. Fixed bugs with LG and GAMMA
functions, which did not return the correct values
for H+. GET_POR now returns 0 if it is not a TRANSPORT
calculation.
--------
svn 4066
--------
Fixed bug with SIT calculations (and Pitzer). The
number of solver iterations was too few (200). With
SIT and Pitzer, each species has an unknown, so the
number of unknowns is large for a system with many
elements. Now set the maximum iterations to be
equal to the number of unknows plus the number of
equations/inequalities.
--------
svn 4023
--------
Trapped error when -mole_balance option was used in
SOLUTION_SPECIES and one of the stated elements was
not defined.
--------
svn 4022
--------
Redefined CN- and SCN- to be new elements Cyanide and
thiocyanate in llnl.dat. Former definitions were not
useful because cyanide and thiocyanate were never
stable and defining a master species as CN- caused
problems with mole balances, appearing in solutions
without any carbon.
--------
svn 3901
--------
Error with equations that included (s) or (g). The
equation and log K were correct only for the simulation
when initially read. Now equations an log Ks are correct
for all simulations. Calculates saturation index from
the equation after (s) and (g) are eliminated.
--------
svn 3695
--------
For transport calculations, fixed step_fraction when
nmix == 1 and ishift == 0.
--------
svn 3684
--------
Added more precision in writing dump file fields.
Multiple REACTIONS were not sorted correctly. Added sort
routine to tidy.c.
--------
svn 3640
--------
Print correct temperature for gas phase dump.
Correct total moles of exchanger for function sys("X").
--------
svn 3568
--------
minteq.dat: Changing log K of gypsum to minteq version
4 value (-4.61). Old value (-4.848) is too stable.
--------
svn 3483
--------
Alkalinity is now printed to the selected output file
when the Alkalinity is used with -totals.
SELECTED_OUTPUT; -totals Alkalinity
Modified numerical method to attempt to produce a numerical
solution when complexes are extremely strong. llnl.dat As and F
complexes caused PHREEQC to fail on an initial solution
calculation. The terms of the As and F mass balance equations
were identical to machine precision. One unknown log activity
was adjusted but the other was not. Now attempts an adjustment
for the unadjusted log activity.
--------
svn 3463
--------
Modified handling of not-a-number in places that
affected the adjustment of log activities (reset and
revise guesses). Uses isfinite function that is available
on Linux and is ifdef'd in global.h for Visual Studio.
The NaN problem occurred rarely and was related to
bad results from the solver and when poor estimates were
available in revise_guesses. Also insured that log activity
for new master species was well defined in switch_bases.
--------
svn 3446
--------
Fixed errors in casting for long double version.
--------
svn 3440
--------
Adjusted numerical calculation to avoid extremely large
calculated specific conductances in high ionic strength
waters.
--------
svn 3433
--------
-dw and -millero added to phreeqc.dat, which allows
calculation of specific conductance and density.
phreeqd.dat is now redundant and removed from distribution.
--------
svn 3425
--------
Added error message to require -multi_d for transport of
surfaces.
--------
svn 3424
--------
Checked for misspellings in EXCHANGE definitions, which
previously caused crash.
--------
svn 3423
--------
-dw and -millero added to pitzer.dat, which allows
calculation of specific conductance and density.
--------
svn 3292
--------
Removed redundant warnings related to transport of exchanger
and surface.
--------
svn 3287
--------
Fixed error in CD_MUSIC surface complexation model.
If reaction equation for a surface species was not
written with the primary surface species, the calculation
was incorrect. The logic to accumulate the change in
charges on the planes was erroneously not included when
rewriting the equations to the master species.
--------
svn 3247
--------
Revised donnan layer calculation with CD_MUSIC. Fixed
a bug related to moles versus concentration and stream
lined calculation. Minor differences in relevant test
cases.
--------
svn 3207
--------
Modifications to convergence criteria for surfaces
related to minerals, when moles of mineral is near
zero (<= 1e-14).
--------
svn 3100
--------
Error when multiple surfaces were used. Sometimes the
surface area from one surface was used for another.
Results were probably incorrect if the surfaces were
not in alphabetical order in their definition in
SURFACE.
--------
svn 2711
--------
Cleaned up compiler warnings for functions called
with constant strings.
------------------------------------------------------------
Version 2.15.0: February 5, 2008
------------------------------------------------------------
--------
svn 2386
--------
Fixed bug for SELECTED_OUTPUT; -activities H2O. The
resulting value was -30; now produces the correct
result.
------------------------------------------------------------
Version 2.14.3: November 17, 2007
------------------------------------------------------------
--------
svn 2386
--------
Fixed bug in routine find_Jstag. Incorrect index (cell_no)
caused segmentation violation in rare instances.
--------
svn 2312
--------
Added new option to PITZER datablock, use_etheta t/f.
--------
svn 2279
--------
Error lost 200 moles of mineral. Should only be a problem
in some cases where moles of mineral is greater than 200.
--------
svn 2270
--------
Added additional parameters Pitzer activity formulation for
neutral species, MU and ETA.
--------
svn 2269
--------
Fixed buffer overrun in SOLUTION_SPREAD when pasting.
--------
svn 2268
--------
Fixed error in prep.c where realloc was called instead
of PHRQ_realloc, which eliminated a memory leak.
------------------------------------------------------------
Version 2.14.2: September 17, 2007
------------------------------------------------------------
--------
svn 2267
--------
Fixed logic of memory checking for PhreeqcI. This serious
bug makes versions 2.14.0 and 2.14.1 unusable.
------------------------------------------------------------
Version 2.14.1: September 5, 2007
------------------------------------------------------------
--------
svn 2219
--------
Updated transport.c to adjust transport in diffuse
layer to be charge balanced for MCD calculation.
------------------------------------------------------------
Version 2.14.0: August 30, 2007
------------------------------------------------------------
-------------
svn 2203-2204
-------------
Revised logic for using phqalloc memory checker. Compiler
option USE_PHRQ_ALLOC now turns on memory checker. If
USE_PHRQ_ALLOC is defined and NDEBUG is not defined, file name
and line number are also used in memory checking. Model.c
now uses same compile options as all other files.
--------
svn 2199
--------
Initialized variables that caused problems when rerunning
simulations in PfW and PhreeqcI.
--------
svn 2138
--------
Fixed bugs in MCD calculation related to saving solutions
after initialization.
--------
svn 2055
--------
Profiled and optimized of code. Automatic string in Basic
factor saves many mallocs. Reordered to minimize call to
strcmp_nocase in basicsubs.c and xsolution_save. Minimized
mallocs for solver.
--------
svn 2051
--------
Fixed bugs in MCD calculation.
--------
svn 2040
--------
Fixed warnings for type-punned with new gcc.
Reverted to 2.12 for infilling solutions for transport.
Only solutions are used, not additional reactants for solution
0 and n+1.
Added digits to printout of REACTION stoichiometry.
--------
svn 1852
--------
Fixed error in CDMUSIC surface related to a phase.
Stoichiometry of H was calculated incorrectly.
--------
svn 1837
--------
Initialize flag for MCD calculation. PhreeqcI would
do MCD calculation after TRANSPORT was redefined not
to do MCD calculation.
------------------------------------------------------------
Version 2.13.2: February 1, 2007
------------------------------------------------------------
--------
svn 1700
--------
Fixed bug with redox elements in multi_diffusion
stagnant zones.
--------
svn 1683
--------
Worked on convergence problems when optimizer fails to
find a solution. Censored values greater than 1e8.
--------
svn 1637
--------
Fixed bug with dissolve only in ADVECTION calculations.
--------
svn 1629
--------
Fixed bug with redox elements in multi_diffusions. Added
Phreeqc For Windows changes from 2.13.1.
------------------------------------------------------------
Version 2.13.1: January 16, 2007
------------------------------------------------------------
--------
svn 1600
--------
Fixed logic error that required rebuilding aqueous model
when not necessary. Now runs faster (sometimes 3X) than
version 2.13.0.
--------
svn 1590
--------
Removed porosity from one statement to eliminate oscillations
in multicomponent diffusion calculation.
--------
svn 1558
--------
Dissolve-only option did not work correctly for stagnant cells
in TRANSPORT calculations. The moles of equilibrium phases,
kinetics, gas_phase, and solid solutions were not initialized
at the beginning of each transport step. Thus, the printed values
for delta moles for the step in the output and punch file were
incorrect for stagnant-zone cells. "Dissolve only" was
always tested relative to the number of moles initially in the
cells, not the amount remaining at a given time step.
--------
svn 1485
--------
Pitzer version with gas_phase did not work. Added
gas_phase and cd_music to numerical derivative routine.
svn 1368: (1) Added multicomponent diffusion in transport and
SOLUTION_SPECIES. (2) Added BASIC functions to obtain and
modify the porosity in a cell. (3) Aded mobile surface and Donnan
option in SURFACE. (4) Added special BASIC function to change
the diffusion coefficient of a SURFACE, and hence to
change the status from mobile to immobile or immobile to
mobile.
svn 1337: Added -add_logk to NAMED_EXPRESSIONS keyword.
svn 1306: Revised printing of distribution of species,
pure phase assemblages, and solid solutions to use
longer fields for names. More revisions to logic
for using gases and solids in equations for phases.
Revised logic for solid solutions with small (1e-25) amounts
of component.
svn 1282: Fixed bug when gas phase had no gas components.
Looked the same as not having a gas phase at all.
svn 1245: Enabled redox in Pitzer model with option in
PITZER keyword. Typically, the option will be included
in the pitzer database file.
PITZER
-redox TRUE
The default database for the Pitzer model does not contain
any redox definitions and the default value for the option
is FALSE. At a minimum, species O2 and H2 must be defined
in the database or input file to allow redox calculations.
svn 1179: New option (-sites_units density) allows alternative
units (sites/nm^2) for definition of number of sites for a
surface. This approach requires better consistency among the
parameters as both the number of sites and the surface area
are based on the mass. It makes more sense than the default,
which requires the number of sites (first numeric item in a
line) to be defined in units of moles, independently of the
number of grams of sorbent.
SURFACE 1
-sites DENSITY
SurfOH 2.6 600. 1.0
SurfaOH 2.6 30. 2.0
In this example, Surf has a site density of 2.6 sites per
nanometer squared, a specific area of 600 meters squared per
gram, and a mass of 1 gram. Surfa has a site density of 2.6
sites per nanometer squared, a specific area of 30 meters
squared per gram, and mass of 2 grams.
svn 1128: Fixed bug with value of time printed to selected
output file when using cvode. Value printed was an
intermediate integration time step, not time at end
of integration.
svn 1096: Allows solids and gases in the equations for
PHASES. This capability simplifies the definitions for
gas and solid isotopic components. Solids must be identified
with "(s)" and gases with "(g)". The first entity on the left-
hand-side of the equation must be the stoichiometric formula
of the solid of gas component being defined, optionally with
(g) or (s). In turn gases and solids included in the equation
must be defined with reactions that ultimately allow the
defined species (C[18O]2(g) in this case) in terms of aqueous
species.
C[18O]2(g)
C[18O]2(g) + CO2(g) = 2CO[18O](g)
log_k 0.602059991327962396 # log10(4)
svn 1092: CD_MUSIC sorption model has been implemented.
Still missing logic for surfaces related to equilibrium-
phases and kinetics. Has explicit calculation of diffuse
layer composition with Donnan assumption. Old diffuse-layer
calculation will not be implemented.
Example:
SURFACE
Goe_uniOH .000552 96.387 1
-capacitance 1.1 5
Goe_triO .000432
-cd_music
-donnan
1.1 5 are capacitances for the cd-music model for 0-1 and 1-2
planes, respectively.
-cd_music specifies that the surface is a cd-music surface.
-donnan optionally calculates the diffuse layer composition
with the Donnan model.
SURFACE_SPECIES
Goe_uniOH-0.5 + H+ + AsO4-3 = Goe_uniOAsO3-2.5 + H2O
log_k 20.1 # eq 7 K1, Kin1
-cd_music -1 -6 0 0.25 5
-cd_music gives the charge contribution of the surface
species to the three planes. Plane 0 is
-1 + 0.25*5; Plane 1 is -6 + (1-0.25)*5;
Plane 2 (or d) is 0.
svn 1030: Fixed bug in tranport. Mixing was not printed
when using -cvode in kinetics.
svn 984: Fixed bug in transport when cell without a
surface followed a cell with a diffuse-layer surface.
Fixed bug in TOTAL function; code ran of the end of
the list of master species; changed logic to recognize
the end of the list.
svn 874: Fixed bug in check_same_model. Thought surface
calculation was the same even though -edl switch was
different, which gave irratic results and possible
crash. Now checks more carefully to make sure calculation
for surfaces is really the same and reinitializes if
not.
svn 847: Fixed bug with DESCRIPTION function. Did not
give correct solution description for reactions.
svn 826: Update tally.c to avoid conflicts in C++
version of phast.
svn 801: Wrote around underflow in fabs in subroutine
reset.
svn 794: Errors in minteq.v4.dat database. Several redox
reactions had delta H listed as kcal instead of kJ. kcal
is correct only for the following species H2, NO2-, and
NH4+.
svn 675:
Added PRINT option to print the species that contribute
to alkalinity. Alkalinity distribution is printed in
the output file following the distribution of species.
Default at program startup is false.
PRINT
-alkalinity true
svn 655:
IAP and log K printed in Phase assemblage data
block were calculated from reactions rewritten to
new master species. Now the original data base
reaction is used to calculate IAP and log K.
Also fixed check that ensured all elements of
phase in are in solution before SI is calculated.
svn 631:
Fixed bug with alternate formula for equilibrium phase,
nothing happened if all other equations were satisfied
at beginning of reaction calculation.
svn 603:
Link gmp library statically.
svn 601:
Fixed statement on multiprecision.
svn 581:
Fixed bug in PhreeqcI that did not reinitialize
Chebyschev parameters leading to incorrect results
with Pitzer activity coefficients. Results were
correct on first run, but erroneous on subsequent
runs.
Added statement to identify multiprecision or
standard solver for inverse modeling.
svn 578:
Distribution changes. Fixed names in README file.
Modified Makefile to use specified version. Split
Linux and source distribution procedure.
------------------------------------------------------------
Version 2.12 Date: Wed September 28, 2005
------------------------------------------------------------
Executables and output files for Sun operating systems
are no longer provided.
Limited log activities of master species to be greater
than the smallest machine precision exponential number.
Avoids a matherr exception and allows trial of additional
parameter sets to attempt to solve the system of
equations.
Made aqueous activity coefficients the default activity
coefficients for exchange species when using the
Pitzer formulation. New option in EXCHANGE is
-pitzer_exchange_gammas T/F, default is true;
defining "false" sets exchange activity coefficients
to 1.0. Option has no effect for ion-association
model (non-Pitzer).
Edited phreeqc.dat to add -gamma expression for
CdX2 and PbX2.
Replaced O2(g) log K in phreeqc.dat and wateq4f.dat
with data from llnl.dat, which appears to be better.
Added multiplier format to REACTION increments, which
simplifies definition of multiple equal reaction increments.
REACTION
H2O 1
-36 3*-4 2*-.25 -0.19 4*-0.1 3*-0.05 moles
Added Pitzer activity formulation. Use pizer.dat database
to invoke the Pitzer model. Should have same capabilities
as ion-association model except explicit diffuse layer
calculation is not implemented with the Pitzer model.
Fixed bug in surface sites related to mineral and exchange
sites related to mineral. Did not have complete logic to
handle redox valence states in formula for species.
Modified to remove non standard usage of va_list.
Removed exchange master species from SYS("ex",..)
list of species. This species is fictive and should
not be included in the list.
Changed -redox in SOLUTION so that if one of the
redox states of a couple is not defined, then
redox defaults to pe.
Fixed buffer overrun in PhreeqcI with SOLUTION_SPREAD,
caused segmenatation fault with lines greater than
500 characters.
Added bigger string for some error messages to avoid
access violation in cvode.
Changed output_msg to warning_msg for combinations
of convergence parameters so that message would
be controlled by -warnings identifier.
Carriage returns are now stripped from Basic program
statements. Switching files from Windows to Unix sometimes
leaves extra carriage returns at the ends of lines, which
caused a syntax error for some Basic commands.
Two bugs were fixed in inverse modeling. (1) Potential
models are now checked for all equality and inequality
constraints. Previously some constraints were not checked.
(2) One loop of cl1 did not include the last row when
checking for the pivot element. Also printing of headers
was slightly modified for inverse modeling.
A new multiple precision version of cl1 was develeped by
using the Gnu Multiple Precision package (gmp). Calculations
are carried out to about 30 significant digits. The mp
version may help in some situations where roundoff errors are
a problem, but it is still possible that roundoff errors will
cause cl1mp to fail to find a solution to the optimization
problem. The mp version has the following options in
INVERSE_MODELING:
-multiple_precision T/F--causes the mp version
to be used in inverse modeling calculations.
-mp_tolerance 1e-12--tolerance for mp version of
cl1. As in cl1, numbers less than the
tolerance are considered to be zero.
1e-12 is the default.
-censor_mp 1e-20--as calculations occur in the
linear equation array, elements less
than this value are set to zero. Default
is 1e-20. A value of 0.0 causes no
censoring to occur.
------------------------------------------------------------
Version 2.11 Date: Mon February 7, 2005
------------------------------------------------------------
Fixed error in selected output file with mixing reaction.
MIX number was written to two columns, should be one.
Fixed memory leak with PAD function.
New database minteq.v4.dat has been translated from version
4.02 of MINTEQA2. An older version of the MINTEQA2 database is
retained in file minteq.dat.
Switched version control to subversion. Simplified,
reorganized makefiles.
Fixed bug with PRINT; -warnings n. Use of this option
generally eliminated all warning messages instead of
all messages after the nth. Default number of warning
messages printed in now 100 per simulation.
Fixed memory leaks in cvode that caused phreeqci to crash.
Now uses PHRQ_malloc in case of other memory leaks. Also
fixed potential memory error with PAD Basic function.
Saturation index phases that included water had wrong
value if distribution of species, exchange, or surface
not written also.
Fixed error message in cvode, if max iterations exceeded
the error caused a segmentation fault.
Made printing of parameter combination message a warning
message so that it could be turned off.
------------------------------------------------------------
Version 2.10 Date: Tue November 2, 2004
------------------------------------------------------------
Rearranged i/o for PHREEQC and reorganized driver
subroutine. The object of these changes is to make
the program more functional as a module for other
programs (PHAST) and eventually to produce a callable
C and Fortran module.
Fixed a problem with surface related to a phase, when
phase was not part of system (for example, Fe(OH)3a when
there is no iron in system.
Added convergence parameter set that requires mineral
transfers to produce positive concentrations in the
event that negative concentrations have been produced in
the prior Newton-Raphson iteration. (Fluorite example).
Fixed bug with kinetics formulas; did not account for
stoichiometric coefficient correctly when using
phase names. Generalized to allow multiple phase
names in the -formula definition.
------------------------------------------------------------
Version 2.9 Date: Wed September 15, 2004
------------------------------------------------------------
In inverse modeling, program terminates if sum of initial
solutions and phases is > 32.
Fixed bug with isotopes. Log activity estimate after initial
solution calculation was inf under some conditions. An initial
surface calculation failed when using D.
Changed saturation index print out to use reaction and log K
defined in PHASES definition. Previously, reaction could be
rewritten to predominant redox species.
Fixed incorrect print of elapsed time for kinetics in advection.
Added phrqproto.h prototype file and phrqtype.h for
switching compilation to long double.
Fixed incorrect printout of kinetics delta moles with
advection.
Added convergence parameter set that skips mineral
equations for first 5 iterations.
Added entity_exists for module.
Tried to fix bug with mix index incorrect (-2) for
mixing with kinetics.
Added new keyword COPY that allows a data entity
to be copied from one index to a new index
or to a range of indicies. Format is
COPY keyword index index_start[-index_end]
where keyword is one of the following:
SOLUTION
EQUILIBRIUM_PHASES
EXCHANGE
GAS_PHASE
KINETICS
MIX
REACTION
REACTION_TEMPERATURE
SOLID_SOLUTION
SURFACE
Numerical method had a bug with ionic strength, if
mass of water was not approximately 1. Routine
revise_guesses did not divide by the mass of
water. Also changed check in routine molalities
to check by molality, not moles.
Fixed a null pointer when surface was related to a
mineral and mineral was not in database.
Added new Basic functions
i = INSTR(a$, b$) sets i to the character position of
string b$ in a$, 0 in not found.
b$ = LTRIM(a$) trims white space from beginning of
string a$ and stores result in b$.
b$ = RTRIM(a$) trims white space from end of string
a$ and stores result in b$.
b$ = LTRIM(a$) trims white space from beginning and
end of string a$ and stores result in b$.
Added new Basic function SYS that calculates the to
total amount of an element in all phases (solution,
equilibrium_phases, surfaces, exchangers, solid solutions,
and gas phase). KINETIC reactions are not included.
The function has two forms: (1) one element name as an
argument (variable names are user specified)
10 t = SYS("As")
the function will return the total arsenic in the system.
(2) 5 argumens
10 t = SYS("As", count_species, names$, types$, moles)
will return the total arsenic in the system to tot; count_species--
the number of species that contain arsenic, including
solution, equilibrium_phases, surfaces, exchangers, solid solutions,
and gas phase species; names$--a character array that has the
name of each species; type$--a character array that specifies the
type of phase for the species, aq, equi, surf, ex, s_s, gas, diff.
Diff refers to the amount of the element in the diffuse layer of
a surface when the explicit diffuse layer calculation is used;
moles--an array containing the number of moles of the element in
the species. The sum of moles(i) is equal to tot.
SYS has several special arguments for the form
SYS("arg", count, names$, types$, values)
arg is one of the options listed below.
count is a single numeric value and is the number of elements
in the following arrays.
name$ is an array of string values.
type$ is an array of string values.
values is an array of numeric values.
Values of arg:
elt_name returns total number of moles of element in system.
count is the number of species for the element in
the system, including aqueous, exchange, surface,
equilibrium_phase, solid solution component, and
gas phase "species".
Arrays are filled for each "species"; values are moles.
"elements" returns total number of moles of all elements,
valence states, exchangers, and surfaces.
count is number of elements, valence states,
exchangers, and surfaces.
Arrays are filled for each element, valence state,
exchanger, and surface; values are moles.
"phases" returns maximum saturation index of all phases.
count is number of phases in system.
Arrays are filled for each phase; values are
saturation indexes.
"aq" returns sum of moles of all aqueous species.
count is number of aqueous species in system.
Arrays are filled with each aqueous species;
values are moles.
"ex" returns sum of moles of all exchange species.
count is number of exchange species in system.
Arrays are filled with each exchange species;
values are moles.
"surf" returns sum of moles of all surface species.
count is number of surface species in system.
Arrays are filled with each surface species;
values are moles.
"s_s" returns sum of moles of all solid solution components.
count is number of solid solution components in system.
Arrays are filled with each solid solution component;
values are moles.
"gas" returns sum of moles of all gas components.
count is number of gas components in system.
Arrays are filled with each gas component;
values are moles.
Added new Basic function, DESCRIPTION, that has the value
defined for the description field of the SOLUTION keyword line.
Added alternative ordinary differential equation solver
called CVODE, a set of C routines from the Lawrence
Livermore National Labs. CVODE is part of the SUNDIALS
package. CVODE is used in place of the Runge Kutta method
when "-cvode true" is used within a KINETICS data block.
KINETICS
-cvode true
Fixed error in SOLUTION_SPREAD, defining -redox
did not set the default redox for the solutions
that were defined; pe was always used as default.
Modified code to allocate space differently for
pp_assemblage, exchange, surface, gas_phase,
kinetics, and s_s_assemblage. Enough space is allocated
at beginning of distribute_initial_conditions.
May speed up phast initialization and make better
use of available memory.
Changed gfw of water to 18 if isotopes of water are
included. Solvent is [1H]2[16O].
Fixed a bug in surface integration where order of ions
in the list of g's was incorrect.
Pyrite rate was not 0 if supersaturated in phreeqc.dat
and wateq4f.dat
Segmentation error if a surface species was not
defined with an equation that contained another surface
species. In this case, the surface master species
had been redefined to be an aqueous species (SOLUTION_SPECIES).
------------------------------------------------------------
Version 2.8 Date: Tue April 15, 2003
------------------------------------------------------------
Updated arsenic data in wateq4f.dat to be consistent with
Archer and Nordstrom (2002).
Revised Basic interpreter to allow lines of any length
and character strings of any length.
Renumbering basic statement that included the function
SURF in PhreeqcI caused SURF to be omitted and generated
a syntax error. SURF and other functions had not been
implemented in PhreeqcI.
Fixed a bug in the Basic Interpreter. If elements of
a dimensioned variable (character or number) were used on
both sides of an equation, the result was erroneously
stored in the last element of the variable used on the
right-hand side instead of the element specified on the
left-hand side.
Using comma in some fields caused an infinite loop.
Fixed bug with SOLUTION_SPREAD, Phreeqc was not
calculating solution numbers for solution_spread
solutions without solution numbers.
Fixed bug with stagnant zone calculations. If solutions
not defined for stagnant cells, PhreeqcI crashed.
Added new state for calculations, PHAST. Previously
phast used the state TRANSPORT, which caused some
erroneous results with temperature when TRANSPORT was
used in the PHREEQC part of the calculation.
Trying to define dump file in TRANSPORT caused a file
opening error. Fixed logic so now can open a file
and the name can include blanks.
------------------------------------------------------------
Version 2.7 Date: Fri February 14, 2003
------------------------------------------------------------
Initialized gfw in elements structure.
Fixed bug where "time" would be wrong for initial
solution calculation. Needed to initialize
rate variables for PhreeqcI.
Added print of simulation number to error file for
phreeqci
Limited printing of cell numbers to output file in advection
calculations. Cell numbers only printed if results
for cell are going to be printed.
PhreeqcI captured status messages for kinetics, which
made a very large error file in some cases and
a long wait to view the output file in PhreeqcI.
Now PhreeqcI does not capture these intermediate
status messages.
Removed old code related to redirecting error file
Corrected error in transport where wrong time step was used
for integration.
Changes to speed up transport algorithm.
Allow file names with spaces in selected_output file name and
dump_file name.
Modifications to work with RC1 phast log file.
Allow any characters in square brackets for element name.
- and + and perhaps others caused problems before.
Fixed log molality of water in species printout, was
equal to log activity of water. Also fixed
basic function for LM.
Changed solid solution prints to print 0 if solid solution
is not present.
Fixed bug if no rate name was defined before options
in RATES.
Fixed warning on Mac compilation in fpunchf.
Fixed bug if isotopes were used but H and O isotopes
were not defined.
Fixed bug where special initial solution calculations
were done at later calculation stages.
Needed to set initial_solution_isotopes = FALSE;
Fixed problem in C++ if structure name is same as member name.
logk member of logk structure was renamed to log_k.
Added identifier -add_constant to PHASES, EXCHANGE_SPECIES,
SOLUTION_SPECIES, and SURFACE_SPECIES.
-add_constant -0.301
log K is augmented by the specified constant.
Added punch_isotopes and punch_calculate_values to allow
printing isotope ratios and any CALCULATE_VALUES result.
Added KEYWORDS:
ISOTOPES
Element
-isotope isotope_name units standard_ratio
-total_is_major T/F (OPTION IS DISABLED!!)
CALCULATE_VALUES
Name
-start
Basic statements, must have SAVE
-end
ISOTOPE_RATIOS (for printing)
Name=Calculate_values_name Isotope_name
ISOTOPE_ALPHAS (for printing)
Name=Calculate_values_name Named_logk=named_expression_name
Basic functions:
calc_value("calc_value_name") evaluates a definition of CALCULATE_VALUES
lk_named("name") log10(K) of definition in NAMED_EXPRESSIONS
lk_phase("name") log10(K) of definition in PHASES
lk_species("name") log10(K) of definition in (SOLUTION, EXCHANGE, SURFACE)_SPECIES
sum_gas("template","element") Sum of element in gases with specified template
template="{C,[13C],[14C]}{O,[18O]}2" includes all CO2 gases
sum_species("template","element") Sum of element in aqueous, exchange, and surface species with
specified template
sum_s_s("s_s_name","element") Sum of element in a specified solid solution
PRINT keyword:
-initial_isotopes T/F
-isotope_ratios T/F
-isotope_alphas T/F
-censor_species 1e-8 # Omits print of species if less than relative criterion
SELECTED_OUTPUT keyword:
-calculate_values name1 name2 ...
-isotopes minor_isotope1 minor_isotope2 ....
Added functions LK_SPECIES, LK_NAMED, LK_PHASE for Basic
interpreter. LK_SPECIES("CaHCO3+") returns the
log k for the association reaction for the ion pair
CaHCO3+ at the current temperature. The log K is
for the reaction as defined in the database or
input file. Similarly,
LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)") returns the
value for the log K at the current temperature using
expressions defined in NAMED_LOG_K data block;
LK_PHASE("Calcite") returns the value of log K
for calcite at the current temperature for the
dissociation reaction defined in the database or
input file. Values are "log10" values.
Example for Basic program:
10 PRINT "Log10 KCalcite: ", LK_PHASE("Calcite")
20 PRINT "Log10 KCaHCO3+: ", LK_SPECIES("CaHCO3+")
30 PRINT " 1000ln(alpha): ", LK_NAMED("Log_alpha_18O_CO2(aq)/CO2(g)")*LOG(10)*1000
Added NAMED_EXPRESSIONS data block. This data block was
implemented to facilitate isotopic calculations.
It allows analytical expressions that are functions
of temperature to be defined. The purpose is to
separate the fractionation factors from the log K,
so that the fractionation factor or its temperature
dependence can be easily modified. The named
expression can be added to a log K for a species
or phase by the -add_logk identifier in SOLUTION_SPECIES
EXCHANGE_SPECIES, SURFACE_SPECIES, or PHASES data
block.
------------------------------------------------------------
Version 2.6 Date: Mon April 22, 2002
------------------------------------------------------------
PhreeqcI released.
All selected_output is routed through a single routine.
Allow "_" inside square brackets, [A_bcd].
Fixed bug match_elts_in_species, check for "e-" was wrong.
Modified minteq.dat to put CuS4S5-3, Cu(S4)2-3 in
in Cu(1) mole balance equations instead of
Cu(2). Before the change, the program would
not converge if Cu(2) were defined in an
initial solution.
Made revisions hopefully to improve SOLID_SOLUTIONS
convergence with small numbers of moles of
solids.
Made changes related to dump file and PhreeqcI.
Iterations now sums iterations in all kinetics calculations
Fixed bug with LA("H2O"), which was returning natural log
of activity of water.
------------------------------------------------------------
Version 2.5 Date: Mon October 1, 2001
------------------------------------------------------------
In llnl.dat, fixed sign errors in RRE (rare earth elements)
for some redox reactions and removed some redundant
species, generally ReeO2- was retained and Ree(OH)4-
was removed.
Added the capability to use square brackets to define an
"element" name. The brackets act like quotation marks
in that any character string can be used within the
brackets as an element name. This was introduced to
simplify expansion of the model to isotopic species.
[13C], [14C], and [18O] are legal element names.
Added identifier -activity_water for a species in
SOLUTION_SPECIES data block. This identifier has been
added for future updates that will allow isotopic
calculations. It is intended to be used only for
isotopic variations of H2O, like D2O or H2[O18]. It
forces the activity coefficient for the species to be
activity(water)/55.5. This effectively sets the activity
of the species to the mole fraction in solution.
Fixed bug in checking solid solutions for presence or
absence of elements in the system. Programming
error caused segmentation fault if an error
was detected under certain conditions.
Changed return value of MOL to be molality of water
if argument is "H2O". Also changed return value
of LA to be activity of water if argument is
"H2O".
Diffuse layer calculation was incorrect if aqueous phase did not
have 1 kilogram of water. Eq. 74 of manual has molality,
but code used moles. The code was corrected by adding
the mass of water to the formulation.
Stagnant zones with first-order exchange approximation (1 stagnant
cell, exchange factor, and porosities defined) did not work
correctly if mobile and immobile cells did not have equal
volumes of water. The mixing factors were revised to account
for the masses of water in the stagnant and mobile zones.
A fatal error was erroneously detected if the database file
had a DATABASE data block. DATABASE data block is
now ignored while reading the database file.
Added identifier -bad_step_max to KINETICS data block.
An integer following -bad_step_max gives the maximum number
of times a rate integration may fail before execution of the
program is terminated. Default is 500.
------------------------------------------------------------
Version 2.4.2: Date: Fri June 15, 2001
------------------------------------------------------------
Fixed spreadsheet bug. Program was not ignoring columns
that could not be identified as either element
names or allowed data (ph, pe, number, description,
etc). Also, the program failed if a spreadsheet solution
number was negative.
------------------------------------------------------------
Version 2.4.1: Date: Mon June 4, 2001
------------------------------------------------------------
Fixed spreadsheet bugs with isotopes.
------------------------------------------------------------
Version 2.4: Date: Fri June 1, 2001
------------------------------------------------------------
Added structure for spreadsheet for use by PhreeqcI.
Isotope value initialized incorrectly if only an -uncertainty was
defined in SOLUTION_SPREAD.
Fixed segmentation violation when primary and secondary master
species were defined improperly.
Corrected enthalpies of reaction in llnl.dat. Previous release had
erroneously had enthalpies of formation in -delta_H
parameter; the values should be enthalpies of reaction.
Enthalpies of reaction were calculated from the
enthalpies of formation and these values are now included
in the -delta_H parameter. This change will have very
little impact on calculations because the analytical
expression has precedence over -delta_H in calculating
temperature dependence of log K, and nearly all species
and minerals have an analytical expression or lack both
an analytical expression and an enthalpy of reaction.
Corrected bugs in punch of solid solution components that caused
both selected output and output file errors: moles
were incorrect in selected output, and total moles and
mole fraction were incorrect in output file.
Added surface complexation constants for Fe+2; two complexes for
weak sites and one complex for strong sites. phreeqc.dat
and wateq4f.dat modified.
Comment for units of parameters for calcite rate equation was
wrong. Rate equation now uses cm^2/L for area parameter.
Previously the correct units would have been 1/decimeter.
phreeqc.dat and wateq4f.dat modified.
Fixed a bug when rates were equal within tolerance, but negative
concentrations occurred because of small initial
concentrations.
Added -warnings to PRINT keyword for specification of maximum
number of warnings to print. Negative number allows
all warnings to be printed.
Function CELL_NO in Basic now prints a number equivalent to
-solution in SELECTED_OUTPUT data block. This does not
change printing for ADVECTION or TRANSPORT calculations.
Kinetics time is halved for advective part of reaction in
transport; time incorrectly accounted for before.
-punch_ identifiers printed -1 instead of the correct solution
number for batch-reaction calculations.
-high_precision is no longer reset to false with every
SELECTED_OUTPUT data block.
SELECTED_OUTPUT file name stored for use by PhreeqcI.
Alkalinity for NH3 corrected to 1.0 in llnl.dat.
Fixed bug with USER_PRINT of kinetics. Did not find correct
kinetics information in some cases.
Fixed bug in default values for SOLUTION_SPREAD. Cannot use phase
name and SI for pH or pe, and bug did not allow PHREEQC
to run. Now PHREEQC runs, but warns that this is not
allowed.
------------------------------------------------------------
Version 2.3: Date: Tue January 2, 2001
------------------------------------------------------------
Added new keyword DATABASE. It must be the first keyword in
the input file. The character string following the
keyword is the pathname for the database file to
be used in the calculation. The file that is
specified takes precedence over any default
database name, including environmental variable
PHREEQC_DATABASE and command line arguments.
Fixed bug in SOLUTION_SPREAD. If first heading in
the spread-sheet input was an identifier--pH,
pe, units, etc--then the headings were interpreted
as an identifier and bad things happened.
Added new keyword to make aqueous model similar to
LLNL and Geochemists Workbench when using
llnl.dat as the database file. Values
of Debye-Huckel a and b and bdot (ionic strength
coefficient) are read at fixed temperatures.
Linear interpolation occurs between temperatures.
New options for SOLUTION_SPECIES are
-llnl_gamma a , where a is the ion-size parameter.
-co2_llnl_gamma , indicates the temperature dependent
function for the bdot term given in
-co2_coefs of LLNL_AQUEOUS_MODEL_PARAMETERS
will be used. Applies to uncharged
species only.
LLNL_AQUEOUS_MODEL_PARAMETERS
-temperatures
0.0100 25.0000 60.0000 100.0000
150.0000 200.0000 250.0000 300.0000
#debye huckel a (adh)
-dh_a
0.4939 0.5114 0.5465 0.5995
0.6855 0.7994 0.9593 1.2180
#debye huckel b (bdh)
-dh_b
0.3253 0.3288 0.3346 0.3421
0.3525 0.3639 0.3766 0.3925
-bdot
0.0394 0.0410 0.0438 0.0460
0.0470 0.0470 0.0340 0.0000
#cco2 (coefficients for the Drummond (1981) polynomial)
-co2_coefs
-1.0312 0.0012806
255.9 0.4445
-0.001606
Fixed bug in basic interpreter. A number like "..524" would
cause an infinite loop.
Added function SURF to Basic.
SURF("element", "surface") gives the amount of
element sorbed on "surface". "surface"
should be the surface name, not the
surface-site name (that is, no underscore).
Fixed option to "runge_kutta" from "runge-kutta" to match
documentation for KINETICS.
Fixed UO2+2 and Mn+2 reaction stoichiometry for Hfo surface complexation
in wateq4f.dat.
Added option for an equilibrium-phase to dissolve only.
"dis" is added at the end of a line defining an equilibrium-
phase. No data fields may be omitted. Should not
be used when adding an alternative reaction.
Example:
EQUILIBRIUM_PHASES
Dolomite 0.0 0.001 dis
R-K integration failed when only the final rate generated
negative concentrations.
Allow decimals in definition of secondary master species, for
example S(0.3).
Fixed bug if description was more than about 85 characters;
now allows about 400 characters.
Fixed bug for surface/exchange sites related to phases. Was
checking internal copies of surfaces/exchange with negative
numbers.
Fixed bug in quick prep that did not set the correct pointer
for gas phases.
Fixed segmentation fault that occurred if all elements for
phase-boundary mineral were not in the solution.
Only applied to a phase used to define concentration
in an initial solution calculation.
Added option to eliminate echo of input file in PRINT
data block. -echo_input T/F turns echoing on
and off. Default is on.
------------------------------------------------------------
Release 2.2: Date: Wed March 1, 2000
------------------------------------------------------------
Fixed bug in MIX if no solutions are defined.
Changed printout for surface.
Only gives net surface charge for diffuse layer
calculation.
Prints correct value for the surface charge and
surface charge density for diffuse-layer
calculation.
Added function EDL to Basic.
EDL("element", "surface") gives the amount of
element in the diffuse layer for "surface".
not including sorbed species. "surface" should
be the surface name, not the surface-site name
(that is, no underscore).
Special values for "element" include:
"charge" - gives surface charge, equivalents.
"sigma" - surface charge density, C/m**2.
"psi" - potential at the surface, Volts.
"water" - mass of water in the diffuse layer, kg.
Changed distribution to be more consistent with other USGS
water-resources applications.
------------------------------------------------------------
Release 2.1: Date: Wed January 19, 2000
------------------------------------------------------------
Added additional #ifdef's for PhreeqcI.
Fixed problem with formats for USER_PUNCH and
others with Microsoft C++ 3 digit
exponents.
Initial Release 2.0: Date: Wed December 15, 1999
Version: C_54 = Version 2.0
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