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add_subdirectory(excel)
add_subdirectory(python)
SET(COM_Files
README.txt
)
SET(COM_Dir ${EXAMPLES_DIR}/com)
install(FILES ${COM_Files} DESTINATION ${COM_Dir})

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These examples require that IPhreeqcCOM-X.X.X-XXXX-(win32,x64).msi be installed.
64-bit operating systems should install both the win32 and x64 bit versions. Both are
available at http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html.

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SET(Excel_Files
phreeqc.dat
runphreeqc.xls
withcallback.xls
)
SET(Excel_Dir ${EXAMPLES_DIR}/com/excel)
install(FILES ${Excel_Files} DESTINATION ${Excel_Dir})

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Enhanced versions of the run_phreeqc.xls example have been contributed by
Peter de Moel and coworkers at the Technical University, Delft Netherlands.
They have an extensive Excel interface for PHREEQC that can be found at
http://www.omnisys.nl/, Aquatic Chemistry.
runphreeqc_1.xls : original example file with modified VBA to enable
decimal commas
runphreeqc_2.xls : original example file with original VBA, with additional
sheet Example for in- and output (decimal commas are handled by Excel at
sheet Input, Sheet1 renamed to Input, Sheet2 renamed to Output)
runphreeqc_3.xls : original example within the TU Delft PhreeqXcel
framework

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SET(Python_Files
Gypsum.py
parallel_advect.py
phreeqc.dat
pitzer.dat
wateq4f.dat
)
SET(Python_Dir ${EXAMPLES_DIR}/com/python)
install(FILES ${Python_Files} DESTINATION ${Python_Dir})

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"""Compares gypsum solubility for WATEQ4F and Pitzer databases.
"""
# Import standard library modules first.
import os
# Then get third party modules.
from win32com.client import Dispatch
import matplotlib.pyplot as plt
def selected_array(db_path, input_string):
"""Load database via COM and run input string.
"""
dbase = Dispatch('IPhreeqcCOM.Object')
dbase.LoadDatabase(db_path)
dbase.RunString(input_string)
return dbase.GetSelectedOutputArray()
def show_results(input_string):
"""Get results for different databases
"""
wateq4f_result = selected_array('wateq4f.dat', input_string)
pitzer_result = selected_array('pitzer.dat', input_string)
# Get data from the arrays.
nacl_conc = [entry[0] for entry in wateq4f_result][1:]
wateq4f_values = [entry[1] for entry in wateq4f_result][1:]
pitzer_values = [entry[1] for entry in pitzer_result][1:]
# Plot
plt.plot(nacl_conc, pitzer_values, 'k', nacl_conc, wateq4f_values,'k--')
plt.axis([0, 6, 0, .06])
plt.legend(('PITZER','WATEQ4F'), loc = (0.4, 0.4))
plt.ylabel('GYPSUM SOLUBILITY, MOLES PER KILOGRAM WATER')
plt.xlabel('NaCl, MOLES PER KILOGRAM WATER')
plt.savefig("Figure2.png")
plt.show()
if __name__ == '__main__':
# This will only run when called as script from the command line
# and not when imported from another script.
INPUT_STRING = """
SOLUTION 1
END
INCREMENTAL_REACTIONS
REACTION
NaCl 1.0
0 60*0.1 moles
EQUILIBRIUM_PHASES
Gypsum
USE solution 1
SELECTED_OUTPUT
-reset false
-total Na S(6)
END"""
show_results(INPUT_STRING)

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# -*- coding: utf-8 -*-
"""A coupled advection-reaction model using the COM server.
The sketch below. shows the setup. The coupled model contains a advection and a
reaction model. The reaction model can have one or more Phreeqc calculators.
The calculators can work in parallel using the module `multiprocessing`.
+--------------------------------------------------------------------------+
| CoupledModel |
| +--------------------------------------------------------------------+ |
| | AdvectionModel | |
| | | |
| +--------------------------------------------------------------------+ |
| | ReactionModel | |
| | +--------------------+--------------------+--------------------+ | |
| | | PhreeqcCalculator1 | PhreeqcCalculator2 | PhreeqcCalculator3 | | |
+--------------------------------------------------------------------------+
Author: Mike Müller, mmueller@hydrocomputing.com
"""
import multiprocessing
import os
import time
import matplotlib.pyplot as plt
from win32com.client import Dispatch
class CoupledModel(object):
"""This is a coupled advection model.
Since it is just a simple example, we use a 1D model.
The same approach can be applied to a 2d or 3D model
as long as the advection model supports it.
The PHREEQC part is the same.
Furthermore, instead of a simple advection model,
we can have a more sophisticated transport model.
"""
def __init__(self, ncells, nshifts, initial_conditions, processes):
self.nshifts = nshifts
self.reaction_model = ReactionModel(ncells, initial_conditions,
processes)
self.reaction_model.make_initial_state()
init_conc = dict([(name, [value] * ncells) for name, value in
self.reaction_model.init_conc.items()])
self.advection_model = AdvectionModel(init_conc,
self.reaction_model.inflow_conc)
self.component_names = self.reaction_model.component_names
self.results = {}
for name in self.component_names:
self.results[name] = []
def run(self):
"""Go over all time steps (shifts).
"""
for shift in xrange(self.nshifts):
self.advection_model.advect()
self.advection_model.save_results(self.results)
self.reaction_model.modify(self.advection_model.conc)
self.advection_model.update_conc(self.reaction_model.conc)
self.reaction_model.finish()
class AdvectionModel(object):
"""Very simple 1D advection model.
This model can be replaced by a more sophisticated transport
model with two or three dimensions.
This could be an external code such as MT3D or anything
else that is moving concentrations through the subsurface.
"""
def __init__(self, init_conc, inflow_conc):
"""Set the initial and inflow concentrations.
Both concentrations are dictionaries with the specie names as keys.
Values are 1D arrays for `init_conc` and scalars for `inflow_conc`.
"""
self.conc = init_conc
self.inflow_conc = inflow_conc
self.outflow = {}
def update_conc(self, new_conc):
"""Update the concentrations after the reactions step.
This is very simple but could be more involved
if the transport model is more complex.
"""
self.conc = new_conc
def advect(self):
"""Shift one cell.
"""
for name in self.conc:
self.outflow[name] = self.conc[name][-1]
self.conc[name][1:] = self.conc[name][:-1]
self.conc[name][0] = self.inflow_conc[name]
def save_results(self, results):
"""Save the calculation results.
Typically, we would write our results into a file.
For simplicity we just add the current outflow that
we stored in `self.outflow` and add it to `results`,
which is a dictionary with all specie names as keys
and lists as values.
"""
for name in self.conc:
results[name].append(self.outflow[name])
class ReactionModel(object):
"""Calculate reactions using PHREEQC as computational engine.
We have no direct contact with IPhreeqc here.
We make one or more instances of `PhreeqcCalculator`
that are actually using IPhreeqc.
We can use more than one processor with `multiprocessing`.
"""
def __init__(self, ncells, initial_conditions, processes):
if processes > ncells:
raise ValueError('Number of processes needs to be less or equal '
'than number of cells. %d processes %d cells.'
% (processes, ncells))
if processes < 1:
raise ValueError('Need at least one process got %d' % processes)
self.parallel = False
if processes > 1:
self.parallel = True
self.ncells = ncells
self.initial_conditions = initial_conditions
self.processes = processes
self.inflow_conc = {}
self.init_conc = {}
self.conc = {}
self.component_names = []
self.calculators = []
self.cell_ranges = []
self._init_calculators()
self.make_initial_state()
def _init_calculators(self):
"""If we are going parallel we need several calculators.
"""
if self.parallel:
# Domain decomposition.
slave_ncells, reminder = divmod(self.ncells, self.processes)
root_ncells = slave_ncells + reminder
current_cell = root_ncells
root_calculator = PhreeqcCalculator(root_ncells,
self.initial_conditions)
self.calculators = [root_calculator]
self.cell_ranges = [(0, root_ncells)]
for process in xrange(self.processes - 1):
self.calculators.append(PhreeqcCalculatorProxy(slave_ncells,
self.initial_conditions))
self.cell_ranges.append((current_cell,
current_cell + slave_ncells))
current_cell += slave_ncells
assert current_cell == self.ncells
self.calculators.reverse()
self.cell_ranges.reverse()
else:
root_calculator = PhreeqcCalculator(self.ncells,
self.initial_conditions)
# Just one calculator and the entire range but still use a list
# to provide the same interface as the parallel case.
self.calculators = [root_calculator]
self.cell_ranges = [(0, self.ncells)]
def make_initial_state(self):
"""Get the initial values from the calculator(s).
"""
self.inflow_conc = self.calculators[0].inflow_conc
self.init_conc = self.calculators[0].init_conc
self.component_names = self.calculators[0].component_names
if self.parallel:
# Make sure all calculators are initialized the same.
for calculator in self.calculators[1:]:
assert self.inflow_conc == calculator.inflow_conc
assert self.init_conc == calculator.init_conc
assert self.component_names == calculator.component_names
def modify(self, new_conc):
"""Pass new conc after advection to the calculator.
"""
self.conc = {}
for name in self.component_names:
self.conc[name] = []
for cell_range, calculator in zip(self.cell_ranges, self.calculators):
current_conc = dict([(name, value[cell_range[0]:cell_range[1]]) for
name, value in new_conc.items()])
calculator.modify(current_conc)
for calculator in self.calculators:
conc = calculator.get_modified()
for name in self.component_names:
self.conc[name].extend(conc[name])
def finish(self):
"""This is necessary for multiprocessing.
Multiprocessing uses external processes. These need to be
explicitly closed to avoid hanging of the program at
the end.
"""
for calculator in self.calculators:
calculator.finish()
class PhreeqcCalculator(object):
"""All PHREEQC calculations happen here.
This is the only place where we interact wit IPhreeqc.
Each instance of this class might run in a different
process using `multiprocessing`.
"""
def __init__(self, ncells, initial_conditions):
"""
ncells - number of cells
initial_conditions - string containing PHREEQC input for
solution and exchange, see example below
"""
self.ncells = ncells
self.initial_conditions = initial_conditions
self.inflow_conc = {}
self.init_conc = {}
self.conc = {}
self.phreeqc = Dispatch('IPhreeqcCOM.Object')
self.phreeqc.LoadDatabase(r"phreeqc.dat")
self.components = []
self.component_names = []
self._make_initial_state()
def _make_initial_state(self):
"""Copy solution to all cells and calculate initial conditions.
"""
self.phreeqc.RunString(self.initial_conditions)
self.components = self.phreeqc.GetComponentList()
start = 1
end = self.ncells
code = ''
code += "COPY solution 1 %d-%d\n" % (start, end)
code += "COPY exchange 1 %d-%d\n" % (start, end)
code += "END\n"
code += "RUN_CELLS; -cells %d-%d\n" % (start, end)
code += self.make_selected_output(self.components)
self.phreeqc.RunString(code)
self.conc = self.get_selected_output()
all_names = self.conc.keys()
self.component_names = [name for name in all_names if name not in
('cb', 'H', 'O')]
code = ''
code += self.make_selected_output(self.components)
code += "RUN_CELLS; -cells 0-1\n"
self.phreeqc.RunString(code)
start_conc = self.get_selected_output()
for name in self.component_names:
self.inflow_conc[name] = start_conc[name][0]
self.init_conc[name] = start_conc[name][1]
def modify(self, new_conc):
"""Set new concentration after advection and re-calculate.
"""
conc = self.conc
end = self.ncells + 1
conc.update(new_conc)
modify = []
for index, cell in enumerate(xrange(1, end)):
modify.append("SOLUTION_MODIFY %d" % cell)
modify.append("\t-cb %e" % conc['cb'][index])
modify.append("\t-total_h %s" % conc['H'][index])
modify.append("\t-total_o %s" % conc['O'][index])
modify.append("\t-totals")
for name in self.component_names:
modify.append("\t\t%s\t%s" % (name, conc[name][index]))
modify.append("RUN_CELLS; -cells %d-%d\n" % (1, self.ncells))
code = '\n'.join(modify)
self.phreeqc.RunString(code)
self.conc = self.get_selected_output()
def get_modified(self):
"""Return calculated conc.
"""
return self.conc
@ staticmethod # this is just a function but belongs here
def make_selected_output(components):
"""
Build SELECTED_OUTPUT data block.
"""
headings = "-headings cb H O "
headings += '\t'.join(components)
selected_output = """
SELECTED_OUTPUT
-reset false
USER_PUNCH
"""
selected_output += headings + "\n"
# charge balance, H, and O
code = '10 w = TOT("water")\n'
code += '20 PUNCH CHARGE_BALANCE, TOTMOLE("H"), TOTMOLE("O")\n'
# All other elements
lino = 30
for component in components:
code += '%d PUNCH w*TOT(\"%s\")\n' % (lino, component)
lino += 10
selected_output += code
return selected_output
def get_selected_output(self):
"""Return calculation result as dict.
Header entries are the keys and the columns
are the values as lists of numbers.
"""
output = self.phreeqc.GetSelectedOutputArray()
header = output[0]
conc = {}
for head in header:
conc[head] = []
for row in output[1:]:
for col, head in enumerate(header):
conc[head].append(row[col])
return conc
def finish(self):
"""Placeholder to give same interface as the multiprocessing version.
"""
pass
class PhreeqcCalculatorProxy(object):
"""Proxy that communicates with other processes.
We uses this proxy for parallel computations.
All code that is specific for parallel computing is located
in here.
"""
def __init__(self, ncells, initial_conditions):
"""Go parallel.
"""
self.in_queue = multiprocessing.JoinableQueue()
self.out_queue = multiprocessing.JoinableQueue()
self.process = multiprocessing.Process(
target=process_worker,
args=(ncells, initial_conditions, self.in_queue, self.out_queue))
self.process.start()
(self.inflow_conc,
self.init_conc,
self.component_names) = self.out_queue.get()
def modify(self, new_conc):
"""Run PHREEQC in another process.
"""
self.in_queue.put(new_conc)
def get_modified(self):
"""Return calculated conc.
"""
return self.out_queue.get()
def finish(self):
"""Terminate the process.
"""
self.in_queue.put(None)
self.process.join()
def process_worker(ncells, initial_conditions, in_queue, out_queue):
"""This runs in another process.
"""
print 'Started process with ID', os.getpid()
calculator = PhreeqcCalculator(ncells, initial_conditions)
out_queue.put((calculator.inflow_conc, calculator.init_conc,
calculator.component_names))
while True:
new_conc = in_queue.get()
# None is the sentinel. We are done
if new_conc is None:
break
calculator.modify(new_conc)
out_queue.put(calculator.conc)
def plot(ncells, outflow, specie_names):
"""Plot the results.
"""
colors = {'Ca': 'r', 'Cl': 'b', 'K': 'g', 'N': 'y', 'Na': 'm'}
x = [i / float(ncells) for i in
xrange(1, len(outflow[specie_names[0]]) + 1)]
args = []
for name in specie_names:
args.extend([x, outflow[name], colors[name]])
# pylint: disable-msg=W0142
# we do want *
plt.plot(*args)
plt.legend(specie_names, loc=(0.8, 0.5))
plt.ylabel('MILLIMOLES PER KILOGRAM WATER')
plt.xlabel('PORE VOLUME')
plt.show()
def measure_time(func, *args, **kwargs):
"""Convenience function to measure run times.
"""
import sys
if sys.platform == 'win32':
# time.clock is more accurate on Windows
timer_func = time.clock
else:
# but behaves differently on other platforms
timer_func = time.time
start = timer_func()
result = func(*args, **kwargs)
return result, time.clock() - start
if __name__ == '__main__':
def main(ncells, nshifts, processes=2):
"""
Specify initial conditions data blocks.
Uniform initial conditions are assumed.
"""
initial_conditions = """
TITLE Example 11.--Transport and ion exchange.
SOLUTION 0 CaCl2
units mmol/kgw
temp 25.0
pH 7.0 charge
pe 12.5 O2(g) -0.68
Ca 0.6
Cl 1.2
SOLUTION 1 Initial solution for column
units mmol/kgw
temp 25.0
pH 7.0 charge
pe 12.5 O2(g) -0.68
Na 1.0
K 0.2
N(5) 1.2
END
EXCHANGE 1
equilibrate 1
X 0.0011
END
"""
def run():
"""Do the work.
"""
model = CoupledModel(ncells, nshifts, initial_conditions,
processes)
model.run()
return model, model.results
(model, outflow), run_time = measure_time(run)
print 'Statistics'
print '=========='
print 'number of cells: ', ncells
print 'number of shifts: ', nshifts
print 'number of processes:', processes
print 'run_time: ', run_time
plot(ncells, outflow, model.component_names)
main(ncells=400, nshifts=1200, processes=2)

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SOLUTION_MASTER_SPECIES
H H+ -1. H 1.008
H(1) H+ -1. 0.0
E e- 0.0 0.0 0.0
O H2O 0.0 O 16.00
O(-2) H2O 0.0 0.0
Ca Ca+2 0.0 Ca 40.08
Mg Mg+2 0.0 Mg 24.305
Na Na+ 0.0 Na 22.9898
K K+ 0.0 K 39.0983
Fe Fe+2 0.0 Fe 55.847
Mn Mn+2 0.0 Mn 54.938
Ba Ba+2 0.0 Ba 137.33
Sr Sr+2 0.0 Sr 87.62
Cl Cl- 0.0 Cl 35.453
C CO3-2 2.0 HCO3 12.0111
C(4) CO3-2 2.0 HCO3 12.0111
Alkalinity CO3-2 1.0 Ca0.5(CO3)0.5 50.05
S SO4-2 0.0 SO4 32.064
S(6) SO4-2 0.0 SO4
B B(OH)3 0.0 B 10.81
Li Li+ 0.0 Li 6.941
Br Br- 0.0 Br 79.904
SOLUTION_SPECIES
H+ = H+
log_k 0.000
-dw 9.31e-9
e- = e-
log_k 0.000
H2O = H2O
log_k 0.000
Ca+2 = Ca+2
log_k 0.000
-dw 0.793e-9
-millero -19.69 0.1058 -0.001256 1.617 -0.075 0.0008262
Mg+2 = Mg+2
log_k 0.000
-dw 0.705e-9
-millero -22.32 0.0868 -0.0016 2.017 -0.125 0.001457
Na+ = Na+
log_k 0.000
-dw 1.33e-9
-millero -3.46 0.1092 -0.000768 2.698 -0.106 0.001651
K+ = K+
log_k 0.000
-dw 1.96e-9
-millero 7.26 0.0892 -0.000736 2.722 -0.101 0.00151
Fe+2 = Fe+2
log_k 0.000
-dw 0.719e-9
Mn+2 = Mn+2
log_k 0.000
-dw 0.688e-9
Ba+2 = Ba+2
log_k 0.000
-dw 0.848e-9
Sr+2 = Sr+2
log_k 0.000
-dw 0.794e-9
-millero -18.44 0.0082 -0.0006 1.727 -0.067 0.00084
Cl- = Cl-
log_k 0.000
-dw 2.03e-9
-millero 16.37 0.0896 -0.001264 -1.494 0.034 -0.000621
CO3-2 = CO3-2
log_k 0.000
-dw 0.955e-9
-millero -8.74 0.300 -0.004064 5.65; # d is value for 25 oC, e and f not reported by Millero, 2000
SO4-2 = SO4-2
log_k 0.000
-dw 1.07e-9
-millero 9.26 0.284 -0.003808 0.4348 -0.0099143 -8.4762e-05
B(OH)3 = B(OH)3
log_k 0.000
-dw 1.1e-9
-millero 36.56 0.130 -0.00081 # d, e and f not reported by Millero, 2000
Li+ = Li+
log_k 0.000
-dw 1.03e-9
Br- = Br-
log_k 0.000
-dw 2.01e-9
-millero 22.98 0.0934 -0.000968 -1.675 0.05 -0.001105
H2O = OH- + H+
log_k -13.998
delta_h 13.345 kcal
# -analytic -283.971 -0.05069842 13323.0 102.24447 -1119669.0
-dw 5.27e-9
CO3-2 + H+ = HCO3-
log_k 10.3393
delta_h -3.561 kcal
-analytic 107.8975 0.03252849 -5151.79 -38.92561 563713.9
-dw 1.18e-9
-millero 21.07 0.185 -0.002248 2.29 -0.006644 -3.667E-06
CO3-2 + 2 H+ = CO2 + H2O
log_k 16.6767
delta_h -5.738 kcal
-analytic 464.1925 0.09344813 -26986.16 -165.75951 2248628.9
-dw 1.92e-9
#CO3-2 + 2 H+ = CO2 + H2O
# log_k 16.681
# delta_h -5.738 kcal
# -analytic 464.1965 0.09344813 -26986.16 -165.75951 2248628.9
SO4-2 + H+ = HSO4-
log_k 1.979
delta_h 4.91 kcal
-analytic -5.3585 0.0183412 557.2461
-dw 1.33e-9
B(OH)3 + H2O = B(OH)4- + H+
log_k -9.239
delta_h 0 kcal
3B(OH)3 = B3O3(OH)4- + 2H2O + H+
log_k -7.528
delta_h 0 kcal
4B(OH)3 = B4O5(OH)4-2 + 3H2O + 2H+
log_k -16.134
delta_h 0 kcal
Ca+2 + B(OH)3 + H2O = CaB(OH)4+ + H+
log_k -7.589
delta_h 0 kcal
Mg+2 + B(OH)3 + H2O = MgB(OH)4+ + H+
log_k -7.840
delta_h 0 kcal
Ca+2 + CO3-2 = CaCO3
log_k 3.151
delta_h 3.547 kcal
-analytic -1228.806 -0.299440 35512.75 485.818
-dw 4.46e-10 # complexes: calc'd with the Pikal formula
Mg+2 + H2O = MgOH+ + H+
log_k -11.809
delta_h 15.419 kcal
Mg+2 + CO3-2 = MgCO3
log_k 2.928
delta_h 2.535 kcal
-analytic -32.225 0.0 1093.486 12.72433
-dw 4.21e-10
PHASES
Anhydrite
CaSO4 = Ca+2 + SO4-2
log_k -4.362
-analytic 422.950 0.0 -18431. -147.708
Aragonite
CaCO3 = CO3-2 + Ca+2
log_k -8.336
delta_h -2.589 kcal
-analytic -171.8607 -.077993 2903.293 71.595
Arcanite
K2SO4 = + 1.0000 SO4-- + 2.0000 K+
log_k -1.776
-analytic 2.823 0.0 -1371.2
Bischofite
MgCl2:6H2O = + 1.0000 Mg++ + 2.0000 Cl- + 6.0000 H2O
log_k 4.455
-analytic 3.524 0.0 277.6
Bloedite
Na2Mg(SO4)2:4H2O = + 1.0000 Mg++ + 2.0000 Na+ + 2.0000 SO4-- + 4.0000 H2O
log_k -2.347
-delta_H 0 # Not possible to calculate enthalpy of reaction Bloedite
Brucite
Mg(OH)2 = + 1.0000 Mg++ + 2.0000 OH-
log_k -10.88
-delta_H 4.85 kcal/mol
# -analytic -1.0280e+002 -1.9759e-002 9.0180e+003 3.8282e+001 1.4075e+002
# -Range: 0-300
Burkeite
Na6CO3(SO4)2 = + 1.0000 CO3-2 + 2.0000 SO4-- + 6.0000 Na+
log_k -0.772
Calcite
CaCO3 = CO3-2 + Ca+2
log_k -8.406
delta_h -2.297 kcal
-analytic -171.8329 -0.077993 2839.319 71.595
Carnallite
KMgCl3:6H2O = K+ + Mg++ + 3Cl- + 6H2O
log_k 4.330
Celestite
SrSO4 = Sr+2 + SO4-2
log_k -6.630
-analytic 35.3106 -0.00422837 0. -14.99586 -318312.
Dolomite
CaMg(CO3)2 = Ca+2 + Mg+2 + 2 CO3-2
log_k -17.083
delta_h -9.436 kcal
Epsomite
MgSO4:7H2O = Mg+2 + SO4-2 + 7 H2O
log_k -1.881
-analytical 1.718 0.0 -1073.
Gaylussite
CaNa2(CO3)2:5H2O = Ca+2 + 2 CO3-2 + 2 Na+ + 5 H2O
log_k -9.421
Glaserite
NaK3(SO4)2 = Na+ + 3K+ + 2SO4-2
log_k -3.803
Glauberite
Na2Ca(SO4)2 = Ca+2 + 2 Na+ + 2 SO4-2
log_k -5.245
Gypsum
CaSO4:2H2O = Ca+2 + SO4-2 + 2 H2O
log_k -4.581
delta_h -0.109 kcal
-analytic 90.318 0.0 -4213. -32.641
Halite
NaCl = Cl- + Na+
log_k 1.570
-analytic -713.4616 -.1201241 37302.21 262.4583 -2106915.
Hexahydrite
MgSO4:6H2O = Mg+2 + SO4-2 + 6 H2O
log_k -1.635
-analytic -62.666 0.0 1828. 22.187
Kainite
KMgClSO4:3H2O = Cl- + K+ + Mg+2 + SO4-2 + 3 H2O
log_k -0.193
Kalicinite
KHCO3 = K+ + H+ + CO3-2
log_k -10.058
Kieserite
MgSO4:H2O = Mg+2 + SO4-2 + H2O
log_k -0.123
Labile_S
Na4Ca(SO4)3:2H2O = 4Na+ + Ca+2 + 3SO4-2 + 2H2O
log_k -5.672
Leonhardite
MgSO4:4H2O = Mg+2 + SO4-2 + 4H2O
log_k -0.887
Leonite
K2Mg(SO4)2:4H2O = Mg+2 + 2 K+ + 2 SO4-2 + 4 H2O
log_k -3.979
Magnesite
MgCO3 = CO3-2 + Mg+2
log_k -7.834
delta_h -6.169
Mirabilite
Na2SO4:10H2O = SO4-2 + 2 Na+ + 10 H2O
log_k -1.214
-analytic -3862.234 -1.19856 93713.54 1577.756 0.
Misenite
K8H6(SO4)7 = 6 H+ + 7 SO4-2 + 8 K+
log_k -10.806
Nahcolite
NaHCO3 = CO3-2 + H+ + Na+
log_k -10.742
Natron
Na2CO3:10H2O = CO3-2 + 2 Na+ + 10.0000 H2O
log_k -0.825
Nesquehonite
MgCO3:3H2O = CO3-2 + Mg+2 + 3 H2O
log_k -5.167
CO2(g)
CO2 = CO2
log_k -1.468
-analytic 108.3865 0.01985076 -6919.53 -40.45154 669365.0
Pentahydrite
MgSO4:5H2O = Mg+2 + SO4-2 + 5 H2O
log_k -1.285
Pirssonite
Na2Ca(CO3)2:2H2O = 2Na+ + Ca+2 + 2CO3-2 + 2 H2O
log_k -9.234
Polyhalite
K2MgCa2(SO4)4:2H2O = 2K+ + Mg+2 + 2 Ca+2 + 4SO4-2 + 2 H2O
log_k -13.744
Portlandite
Ca(OH)2 = Ca+2 + 2 OH-
log_k -5.190
Schoenite
K2Mg(SO4)2:6H2O = 2K+ + Mg+2 + 2 SO4-2 + 6H2O
log_k -4.328
Sylvite
KCl = K+ + Cl-
log_k 0.900
-analytic 3.984 0.0 -919.55
Syngenite
K2Ca(SO4)2:H2O = 2K+ + Ca+2 + 2SO4-2 + H2O
log_k -7.448
Trona
Na3H(CO3)2:2H2O = 3 Na+ + H+ + 2CO3-2 + 2H2O
log_k -11.384
Borax
Na2(B4O5(OH)4):8H2O + 2 H+ = 4 B(OH)3 + 2 Na+ + 5 H2O
log_k 12.464
Boric_acid,s
B(OH)3 = B(OH)3
log_k -0.030
KB5O8:4H2O
KB5O8:4H2O + 3H2O + H+ = 5B(OH)3 + K+
log_k 4.671
K2B4O7:4H2O
K2B4O7:4H2O + H2O + 2H+ = 4B(OH)3 + 2K+
log_k 13.906
NaBO2:4H2O
NaBO2:4H2O + H+ = B(OH)3 + Na+ + 3H2O
log_k 9.568
NaB5O8:5H2O
NaB5O8:5H2O + 2H2O + H+ = 5B(OH)3 + Na+
log_k 5.895
Teepleite
Na2B(OH)4Cl + H+ = B(OH)3 + 2Na+ + Cl- + H2O
log_k 10.840
H2O(g)
H2O = H2O
log_k 1.51
delta_h -44.03 kJ
# Stumm and Morgan, from NBS and Robie, Hemmingway, and Fischer (1978)
PITZER
-B0
Na+ Cl- 0.0765 -777.03 -4.4706 0.008946 -3.3158E-6
K+ Cl- 0.04835 0 0 5.794E-4
Mg+2 Cl- 0.35235 0 0 -1.943E-4
Ca+2 Cl- 0.3159 0 0 -1.725E-4
MgOH+ Cl- -0.1
H+ Cl- 0.1775 0 0 -3.081E-4
Li+ Cl- 0.1494 0 0 -1.685E-4
Sr+2 Cl- 0.2858 0 0 0.717E-3
Fe+2 Cl- 0.335925
Mn+2 Cl- 0.327225
Ba+2 Cl- 0.2628 0 0 0.6405E-3
CaB(OH)4+ Cl- 0.12
MgB(OH)4+ Cl- 0.16
Na+ Br- 0.0973 0 0 7.692E-4
K+ Br- 0.0569 0 0 7.39E-4
H+ Br- 0.1960 0 0 -2.049E-4
Mg+2 Br- 0.4327 0 0 -5.625E-5
Ca+2 Br- 0.3816 0 0 -5.2275E-4
Li+ Br- 0.1748 0 0 -1.819E-4
Sr+2 Br- 0.331125 0 0 -0.32775E-3
Ba+2 Br- 0.31455 0 0 -0.33825E-3
Na+ SO4-2 0.01958 0 0 2.367E-3
K+ SO4-2 0.04995 0 0 1.44E-3
Mg+2 SO4-2 0.221 0 0 -0.69E-3
Ca+2 SO4-2 0.2
H+ SO4-2 0.0298
Li+ SO4-2 0.136275 0 0 0.5055E-3
Sr+2 SO4-2 0.200 0 0 -2.9E-3
Fe+2 SO4-2 0.2568
Mn+2 SO4-2 0.2065
Na+ HSO4- 0.0454
K+ HSO4- -0.0003
Mg+2 HSO4- 0.4746
Ca+2 HSO4- 0.2145
H+ HSO4- 0.2065
Fe+2 HSO4- 0.4273
Na+ OH- 0.0864 0 0 7.00E-4
K+ OH- 0.1298
Ca+2 OH- -0.1747
Li+ OH- 0.015
Ba+2 OH- 0.17175
Na+ HCO3- 0.0277 0 0 1.00E-3
K+ HCO3- 0.0296 0 0 0.996E-3
Mg+2 HCO3- 0.329
Ca+2 HCO3- 0.4
Sr+2 HCO3- 0.12
Na+ CO3-2 0.0399 0 0 1.79E-3
K+ CO3-2 0.1488 0 0 1.788E-3
Na+ B(OH)4- -0.0427
Na+ B3O3(OH)4- -0.056
Na+ B4O5(OH)4-2 -0.11
K+ B(OH)4- 0.035
K+ B3O3(OH)4- -0.13
K+ B4O5(OH)4-2 -0.022
-B1
Na+ Cl- 0.2664 0 0 6.1608E-5 1.0715E-6
K+ Cl- 0.2122 0 0 10.71E-4
Mg+2 Cl- 1.6815 0 0 3.6525E-3
Ca+2 Cl- 1.614 0 0 3.9E-3
MgOH+ Cl- 1.658
H+ Cl- 0.2945 0 0 1.419E-4
Li+ Cl- 0.3074 0 0 5.366E-4
Sr+2 Cl- 1.667 0 0 2.8425E-3
Fe+2 Cl- 1.53225
Mn+2 Cl- 1.55025
Ba+2 Cl- 1.49625 0 0 3.2325E-3
Na+ Br- 0.2791 0 0 10.79E-4
K+ Br- 0.2212 0 0 17.40E-4
H+ Br- 0.3564 0 0 4.467E-4
Mg+2 Br- 1.753 0 0 3.8625E-3
Ca+2 Br- 1.613 0 0 6.0375E-3
Li+ Br- 0.2547 0 0 6.636E-4
Sr+2 Br- 1.7115 0 0 6.5325E-3
Ba+2 Br- 1.56975 0 0 6.78E-3
Na+ SO4-2 1.113 0 0 5.6325E-3
K+ SO4-2 0.7793 0 0 6.6975E-3
Mg+2 SO4-2 3.343 0 0 1.53E-2
Ca+2 SO4-2 3.1973 0 0 5.46E-2
Li+ SO4-2 1.2705 0 0 1.41E-3
Sr+2 SO4-2 3.1973 0 0 27.0E-3
Fe+2 SO4-2 3.063
Mn+2 SO4-2 2.9511
Na+ HSO4- 0.398
K+ HSO4- 0.1735
Mg+2 HSO4- 1.729
Ca+2 HSO4- 2.53
H+ HSO4- 0.5556
Fe+2 HSO4- 3.48
Na+ OH- 0.253 0 0 1.34E-4
K+ OH- 0.32
Ca+2 OH- -0.2303
Li+ OH- 0.14
Ba+2 OH- 1.2
Na+ HCO3- 0.0411 0 0 1.10E-3
K+ HCO3- -0.013 0 0 1.104E-3
Mg+2 HCO3- 0.6072
Ca+2 HCO3- 2.977
Na+ CO3-2 1.389 0 0 2.05E-3
K+ CO3-2 1.43 0 0 2.051E-3
Na+ B(OH)4- 0.089
Na+ B3O3(OH)4- -0.910
Na+ B4O5(OH)4-2 -0.40
K+ B(OH)4- 0.14
-B2
Mg+2 SO4-2 -37.23 0 0 -0.253
Ca+2 SO4-2 -54.24 0 0 -0.516
Sr+2 SO4-2 -54.24 0 0 -0.42
Fe+2 SO4-2 -42.0
Mn+2 SO4-2 -40.0
Ca+2 OH- -5.72
-C0
Na+ Cl- 0.00127 33.317 0.09421 -4.655E-5
K+ Cl- -0.00084 0 0 -5.095E-5
Mg+2 Cl- 0.00519 0 0 -1.64933E-4
Ca+2 Cl- -0.00034
H+ Cl- 0.0008 0 0 6.213E-5
Li+ Cl- 0.00359 0 0 -4.520E-5
Sr+2 Cl- -0.00130
Fe+2 Cl- -0.00860725
Mn+2 Cl- -0.0204972
Ba+2 Cl- -0.0193782 0 0 -1.53796E-4
Na+ Br- 0.00116 0 0 -9.30E-5
K+ Br- -0.00180 0 0 -7.004E-5
H+ Br- 0.00827 0 0 -5.685E-5
Mg+2 Br- 0.00312
Ca+2 Br- -0.00257
Li+ Br- 0.0053 0 0 -2.813E-5
Sr+2 Br- 0.00122506
Ba+2 Br- -0.0159576
Na+ SO4-2 0.00497 0 0 -4.87904E-4
Mg+2 SO4-2 0.025 0 0 0.523E-3
H+ SO4-2 0.0438
Li+ SO4-2 -0.00399338 0 0 -2.33345E-4
Fe+2 SO4-2 0.0209
Mn+2 SO4-2 0.01636
Na+ OH- 0.0044 0 0 -18.94E-5
K+ OH- 0.0041
K+ HCO3- -0.008
Na+ CO3-2 0.0044
K+ CO3-2 -0.0015
Na+ B(OH)4- 0.0114
-THETA
K+ Na+ -0.012
Mg+2 Na+ 0.07
Ca+2 Na+ 0.07
Sr+2 Na+ 0.051
H+ Na+ 0.036
Ca+2 K+ 0.032
H+ K+ 0.005
Ca+2 Mg+2 0.007
H+ Mg+2 0.1
H+ Ca+2 0.092
SO4-2 Cl- 0.02
HSO4- Cl- -0.006
OH- Cl- -0.05
HCO3- Cl- 0.03
CO3-2 Cl- -0.02
B(OH)4- Cl- -0.065
B3O3(OH)4- Cl- 0.12
B4O5(OH)4-2 Cl- 0.074
OH- Br- -0.065
OH- SO4-2 -0.013
HCO3- SO4-2 0.01
CO3-2 SO4-2 0.02
B(OH)4- SO4-2 -0.012
B3O3(OH)4- SO4-2 0.10
B4O5(OH)4-2 SO4-2 0.12
CO3-2 OH- 0.1
CO3-2 HCO3- -0.04
B3O3(OH)4- HCO3- -0.10
B4O5(OH)4-2 HCO3- -0.087
-LAMBDA
Na+ CO2 0.1
K+ CO2 0.051
Mg+2 CO2 0.183
Ca+2 CO2 0.183
Cl- CO2 -0.005
SO4-2 CO2 0.097
HSO4- CO2 -0.003
Na+ B(OH)3 -0.097
K+ B(OH)3 -0.14
Cl- B(OH)3 0.091
SO4-2 B(OH)3 0.018
B3O3(OH)4- B(OH)3 -0.20
-ZETA
H+ Cl- B(OH)3 -0.0102
Na+ SO4-2 B(OH)3 0.046
-PSI
Na+ K+ Cl- -0.0018
Na+ K+ Br- -0.0022
Na+ K+ SO4-2 -0.010
Na+ K+ HCO3- -0.003
Na+ K+ CO3-2 0.003
Na+ Ca+2 Cl- -0.007
Na+ Sr+2 Cl- -0.0021
Na+ Ca+2 SO4-2 -0.055
Na+ Mg+2 Cl- -0.012
Na+ Mg+2 SO4-2 -0.015
Na+ H+ Cl- -0.004
Na+ H+ Br- -0.012
Na+ H+ HSO4- -0.0129
K+ Ca+2 Cl- -0.025
K+ Mg+2 Cl- -0.022
K+ Mg+2 SO4-2 -0.048
K+ H+ Cl- -0.011
K+ H+ Br- -0.021
K+ H+ SO4-2 0.197
K+ H+ HSO4- -0.0265
Ca+2 Mg+2 Cl- -0.012
Ca+2 Mg+2 SO4-2 0.024
Ca+2 H+ Cl- -0.015
Mg+2 MgOH+ Cl- 0.028
Mg+2 H+ Cl- -0.011
Mg+2 H+ HSO4- -0.0178
Cl- Br- K+ 0.0000
Cl- SO4-2 Na+ 0.0014
Cl- SO4-2 Ca+2 -0.018
Cl- SO4-2 Mg+2 -0.004
Cl- HSO4- Na+ -0.006
Cl- HSO4- H+ 0.013
Cl- OH- Na+ -0.006
Cl- OH- K+ -0.006
Cl- OH- Ca+2 -0.025
Cl- HCO3- Na+ -0.015
Cl- HCO3- Mg+2 -0.096
Cl- CO3-2 Na+ 0.0085
Cl- CO3-2 K+ 0.004
Cl- B(OH)4- Na+ -0.0073
Cl- B3O3(OH)4- Na+ -0.024
Cl- B4O5(OH)4-2 Na+ 0.026
SO4-2 HSO4- Na+ -0.0094
SO4-2 HSO4- K+ -0.0677
SO4-2 HSO4- Mg+2 -0.0425
SO4-2 OH- Na+ -0.009
SO4-2 OH- K+ -0.050
SO4-2 HCO3- Na+ -0.005
SO4-2 HCO3- Mg+2 -0.161
SO4-2 CO3-2 Na+ -0.005
SO4-2 CO3-2 K+ -0.009
OH- CO3-2 Na+ -0.017
OH- CO3-2 K+ -0.01
OH- Br- Na+ -0.018
OH- Br- K+ -0.014
HCO3- CO3-2 Na+ 0.002
HCO3- CO3-2 K+ 0.012
EXCHANGE_MASTER_SPECIES
X X-
EXCHANGE_SPECIES
X- = X-
log_k 0.0
Na+ + X- = NaX
log_k 0.0
K+ + X- = KX
log_k 0.7
delta_h -4.3 # Jardine & Sparks, 1984
Li+ + X- = LiX
log_k -0.08
delta_h 1.4 # Merriam & Thomas, 1956
Ca+2 + 2X- = CaX2
log_k 0.8
delta_h 7.2 # Van Bladel & Gheyl, 1980
Mg+2 + 2X- = MgX2
log_k 0.6
delta_h 7.4 # Laudelout et al., 1968
Sr+2 + 2X- = SrX2
log_k 0.91
delta_h 5.5 # Laudelout et al., 1968
Ba+2 + 2X- = BaX2
log_k 0.91
delta_h 4.5 # Laudelout et al., 1968
Mn+2 + 2X- = MnX2
log_k 0.52
Fe+2 + 2X- = FeX2
log_k 0.44
SURFACE_MASTER_SPECIES
Hfo_s Hfo_sOH
Hfo_w Hfo_wOH
SURFACE_SPECIES
# All surface data from
# Dzombak and Morel, 1990
#
#
# Acid-base data from table 5.7
#
# strong binding site--Hfo_s,
Hfo_sOH = Hfo_sOH
log_k 0.0
Hfo_sOH + H+ = Hfo_sOH2+
log_k 7.29 # = pKa1,int
Hfo_sOH = Hfo_sO- + H+
log_k -8.93 # = -pKa2,int
# weak binding site--Hfo_w
Hfo_wOH = Hfo_wOH
log_k 0.0
Hfo_wOH + H+ = Hfo_wOH2+
log_k 7.29 # = pKa1,int
Hfo_wOH = Hfo_wO- + H+
log_k -8.93 # = -pKa2,int
###############################################
# CATIONS #
###############################################
#
# Cations from table 10.1 or 10.5
#
# Calcium
Hfo_sOH + Ca+2 = Hfo_sOHCa+2
log_k 4.97
Hfo_wOH + Ca+2 = Hfo_wOCa+ + H+
log_k -5.85
# Strontium
Hfo_sOH + Sr+2 = Hfo_sOHSr+2
log_k 5.01
Hfo_wOH + Sr+2 = Hfo_wOSr+ + H+
log_k -6.58
Hfo_wOH + Sr+2 + H2O = Hfo_wOSrOH + 2H+
log_k -17.60
# Barium
Hfo_sOH + Ba+2 = Hfo_sOHBa+2
log_k 5.46
Hfo_wOH + Ba+2 = Hfo_wOBa+ + H+
log_k -7.2 # table 10.5
#
# Derived constants table 10.5
#
# Magnesium
Hfo_wOH + Mg+2 = Hfo_wOMg+ + H+
log_k -4.6
# Manganese
Hfo_sOH + Mn+2 = Hfo_sOMn+ + H+
log_k -0.4 # table 10.5
Hfo_wOH + Mn+2 = Hfo_wOMn+ + H+
log_k -3.5 # table 10.5
# Iron
# Hfo_sOH + Fe+2 = Hfo_sOFe+ + H+
# log_k 0.7 # LFER using table 10.5
# Hfo_wOH + Fe+2 = Hfo_wOFe+ + H+
# log_k -2.5 # LFER using table 10.5
# Iron, strong site: Appelo, Van der Weiden, Tournassat & Charlet, subm.
Hfo_sOH + Fe+2 = Hfo_sOFe+ + H+
log_k -0.95
# Iron, weak site: Liger et al., GCA 63, 2939, re-optimized for D&M
Hfo_wOH + Fe+2 = Hfo_wOFe+ + H+
log_k -2.98
Hfo_wOH + Fe+2 + H2O = Hfo_wOFeOH + 2H+
log_k -11.55
###############################################
# ANIONS #
###############################################
#
# Anions from table 10.6
#
#
# Anions from table 10.7
#
# Borate
Hfo_wOH + B(OH)3 = Hfo_wH2BO3 + H2O
log_k 0.62
#
# Anions from table 10.8
#
# Sulfate
Hfo_wOH + SO4-2 + H+ = Hfo_wSO4- + H2O
log_k 7.78
Hfo_wOH + SO4-2 = Hfo_wOHSO4-2
log_k 0.79
#
# Carbonate: Van Geen et al., 1994 reoptimized for HFO
# 0.15 g HFO/L has 0.344 mM sites == 2 g of Van Geen's Goethite/L
#
# Hfo_wOH + CO3-2 + H+ = Hfo_wCO3- + H2O
# log_k 12.56
#
# Hfo_wOH + CO3-2 + 2H+= Hfo_wHCO3 + H2O
# log_k 20.62
END
MEAN GAM
CaCl2
CaSO4
CaCO3
Ca(OH)2
MgCl2
MgSO4
MgCO3
Mg(OH)2
NaCl
Na2SO4
NaHCO3
Na2CO3
NaOH
KCl
K2SO4
KHCO3
K2CO3
KOH
HCl
H2SO4
HBr
END

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