Re: [phreeqpy-users] How to get the output of phreeqpy? Please help

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Parkhurst, David

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Dec 3, 2015, 11:36:04 AM12/3/15

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Not sure if your question got answered. The main way to extract results from PHREEQC runs in Python is through the GetSelectedOutput method. This returns essentially a table of data with rows and columns. The rows are each calculation in the last RunFile or RunString call, for example a row for a SOLUTION calculation and a row for a "reaction" calculation if the solution was equilibrated with minerals.

The columns of the table are defined in SELECTED_OUTPUT and USER_PUNCH definitions. These must be defined in the last input to RunFile or RunString, or in any previous RunFile or RunString. The definitions persist until they are changed or turned off. So to get the SI for hydroxyapatite you could include

SELECTED_OUTPUT

...

-SI Hydroxyapatite

in a definition for RunFile or RunString, and si_Hydroxyapatite should be one of the columns of the selected-output table that you can access with the IPhreeqc method GetSelectedOutput.

David Parkhurst
Hydrologist
dlp...@usgs.gov
Profile: https://profile.usgs.gov/dlpark
Project: http://wwwbrr.cr.usgs.gov/projects/GWC_coupled

On Thu, Nov 26, 2015 at 10:11 PM, charleywan2004 <charley...@gmail.com> wrote:

I am running a speciation program

#################################
import phreeqpy.iphreeqc.phreeqc_dll as phreeqc_mod

def make_initial_conditions ():
initial_conditions = """
TITLE Example 1.--water speciation.
SOLUTION 1 Water Speciation
units ppm
pH 8.22
pe 8.451
density 1.023
temp 25.0
redox O(0)/O(-2)
Ca 412.3
Mg 1291.8
Na 10768.0
K 399.1
Fe 0.002
Mn 0.0002 pe
Si 4.28
Cl 19353.0
Alkalinity 141.682 as HCO3
S(6) 2712.0
N(5) 0.29 gfw 62.0
N(-3) 0.03 as NH4
P 7 as PO4
O(0) 1.0 O2(g) -0.7
END
"""
return initial_conditions

phreeqc = phreeqc_mod.IPhreeqc()
phreeqc.load_database("phreeqc.dat")
initial_conditions = make_initial_conditions()
phreeqc.run_string(initial_conditions)

####################################

Running the same input in "PHREEQC interactive", I can get a set of output as follows. I want to get the "Saturation indices" section out into Python, how to do that? For example, I want to get the saturation index value for "Hydroxyapatite". How to do that? Please help!

######################################
------------------
Reading data base.
------------------

SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------

DATABASE C:\Program Files (x86)\USGS\Phreeqc Interactive 3.3.3-10424\database\phreeqc.dat
TITLE Example 1.--water speciate.
SOLUTION 1 Water Speciation
units ppm
pH 8.22
pe 8.451
density 1.023
temp 25.0
redox O(0)/O(-2)
Ca 412.3
Mg 1291.8
Na 10768.0
K 399.1
Fe 0.002
Mn 0.0002 pe
Si 4.28
Cl 19353.0
Alkalinity 141.682 as HCO3
S(6) 2712.0
N(5) 0.29 gfw 62.0
N(-3) 0.03 as NH4
P 7 as PO4
O(0) 1.0 O2(g) -0.7
END
-----
TITLE
-----

Example 1.--water speciate.

-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------

Initial solution 1. Water Speciation

-----------------------------Solution composition------------------------------

Elements Molality Moles

Alkalinity 2.406e-03 2.406e-03
Ca 1.066e-02 1.066e-02
Cl 5.657e-01 5.657e-01
Fe 3.711e-08 3.711e-08
K 1.058e-02 1.058e-02
Mg 5.507e-02 5.507e-02
Mn 3.773e-09 3.773e-09
N(-3) 1.724e-06 1.724e-06
N(5) 4.848e-06 4.848e-06
Na 4.854e-01 4.854e-01
O(0) 4.376e-04 4.376e-04 Equilibrium with O2(g)
P 7.638e-05 7.638e-05
S(6) 2.926e-02 2.926e-02
Si 7.382e-05 7.382e-05

----------------------------Description of solution----------------------------

pH = 8.220
pe = 8.451
Specific Conductance (µS/cm, 25°C) = 53274
Density (g/cm³) = 1.02324
Volume (L) = 1.01282
Activity of water = 0.981
Ionic strength = 6.747e-01
Mass of water (kg) = 1.000e+00
Total carbon (mol/kg) = 2.092e-03
Total CO2 (mol/kg) = 2.092e-03
Temperature (°C) = 25.00
Electrical balance (eq) = 7.172e-04
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 0.06
Iterations = 8
Total H = 1.110147e+02
Total O = 5.563058e+01

---------------------------------Redox couples---------------------------------

Redox couple pe Eh (volts)

N(-3)/N(5) 4.6750 0.2766
O(-2)/O(0) 12.4062 0.7339

----------------------------Distribution of species----------------------------

Log Log Log mole V
Species Molality Activity Molality Activity Gamma cm³/mol

OH- 2.705e-06 1.647e-06 -5.568 -5.783 -0.215 -2.63
H+ 7.984e-09 6.026e-09 -8.098 -8.220 -0.122 0.00
H2O 5.551e+01 9.806e-01 1.744 -0.009 0.000 18.07
C(4) 2.092e-03
HCO3- 1.424e-03 9.617e-04 -2.846 -3.017 -0.171 26.98
MgHCO3+ 2.454e-04 1.543e-04 -3.610 -3.812 -0.201 5.82
NaHCO3 1.590e-04 1.857e-04 -3.799 -3.731 0.067 1.80
MgCO3 8.385e-05 9.794e-05 -4.077 -4.009 0.067 -17.09
NaCO3- 6.409e-05 4.786e-05 -4.193 -4.320 -0.127 2.88
CaHCO3+ 4.270e-05 2.954e-05 -4.370 -4.530 -0.160 9.96
CO3-2 3.599e-05 7.485e-06 -4.444 -5.126 -0.682 -1.97
CaCO3 2.592e-05 3.028e-05 -4.586 -4.519 0.067 -14.60
CO2 1.137e-05 1.329e-05 -4.944 -4.877 0.067 34.43
MnCO3 2.454e-10 2.867e-10 -9.610 -9.543 0.067 (0)
MnHCO3+ 6.232e-11 4.133e-11 -10.205 -10.384 -0.178 (0)
(CO2)2 2.774e-12 3.240e-12 -11.557 -11.489 0.067 68.87
FeCO3 1.723e-20 2.013e-20 -19.764 -19.696 0.067 (0)
FeHCO3+ 1.443e-20 1.078e-20 -19.841 -19.967 -0.127 (0)
Ca 1.066e-02
Ca+2 9.631e-03 2.408e-03 -2.016 -2.618 -0.602 -16.69
CaSO4 9.547e-04 1.115e-03 -3.020 -2.953 0.067 7.50
CaHCO3+ 4.270e-05 2.954e-05 -4.370 -4.530 -0.160 9.96
CaCO3 2.592e-05 3.028e-05 -4.586 -4.519 0.067 -14.60
CaHPO4 3.771e-06 4.404e-06 -5.424 -5.356 0.067 (0)
CaPO4- 2.561e-06 1.729e-06 -5.592 -5.762 -0.171 (0)
CaOH+ 8.708e-08 6.503e-08 -7.060 -7.187 -0.127 (0)
CaH2PO4+ 2.954e-08 1.995e-08 -7.530 -7.700 -0.171 (0)
CaHSO4+ 5.914e-11 4.417e-11 -10.228 -10.355 -0.127 (0)
Cl 5.657e-01
Cl- 5.657e-01 3.568e-01 -0.247 -0.448 -0.200 18.79
MnCl+ 1.057e-09 7.010e-10 -8.976 -9.154 -0.178 -2.79
MnCl2 9.347e-11 1.092e-10 -10.029 -9.962 0.067 85.89
MnCl3- 1.618e-11 1.073e-11 -10.791 -10.969 -0.178 45.79
FeCl+2 1.519e-18 2.939e-19 -17.818 -18.532 -0.713 (0)
FeCl2+ 7.062e-19 4.684e-19 -18.151 -18.329 -0.178 (0)
FeCl+ 7.393e-20 5.521e-20 -19.131 -19.258 -0.127 (0)
FeCl3 1.431e-20 1.671e-20 -19.844 -19.777 0.067 (0)
Fe(2) 6.492e-19
Fe+2 4.891e-19 1.121e-19 -18.311 -18.950 -0.640 -20.71
FeCl+ 7.393e-20 5.521e-20 -19.131 -19.258 -0.127 (0)
FeSO4 4.444e-20 5.191e-20 -19.352 -19.285 0.067 18.97
FeCO3 1.723e-20 2.013e-20 -19.764 -19.696 0.067 (0)
FeHCO3+ 1.443e-20 1.078e-20 -19.841 -19.967 -0.127 (0)
FeOH+ 8.698e-21 5.768e-21 -20.061 -20.239 -0.178 (0)
FeHPO4 1.274e-21 1.489e-21 -20.895 -20.827 0.067 (0)
FeH2PO4+ 2.693e-23 1.819e-23 -22.570 -22.740 -0.171 (0)
Fe(OH)2 6.840e-24 7.990e-24 -23.165 -23.097 0.067 (0)
Fe(OH)3- 7.284e-26 4.831e-26 -25.138 -25.316 -0.178 (0)
FeHSO4+ 2.753e-27 2.056e-27 -26.560 -26.687 -0.127 (0)
Fe(3) 3.711e-08
Fe(OH)3 2.771e-08 3.237e-08 -7.557 -7.490 0.067 (0)
Fe(OH)4- 7.114e-09 4.804e-09 -8.148 -8.318 -0.171 (0)
Fe(OH)2+ 2.287e-09 1.544e-09 -8.641 -8.811 -0.171 (0)
FeOH+2 1.481e-13 2.866e-14 -12.829 -13.543 -0.713 (0)
FeCl+2 1.519e-18 2.939e-19 -17.818 -18.532 -0.713 (0)
FeSO4+ 1.174e-18 7.788e-19 -17.930 -18.109 -0.178 (0)
FeCl2+ 7.062e-19 4.684e-19 -18.151 -18.329 -0.178 (0)
Fe+3 3.432e-19 2.727e-20 -18.465 -19.564 -1.100 (0)
Fe(SO4)2- 5.941e-20 4.437e-20 -19.226 -19.353 -0.127 (0)
FeHPO4+ 3.692e-20 2.449e-20 -19.433 -19.611 -0.178 (0)
FeCl3 1.431e-20 1.671e-20 -19.844 -19.777 0.067 (0)
FeH2PO4+2 1.143e-20 2.377e-21 -19.942 -20.624 -0.682 (0)
Fe2(OH)2+4 2.359e-24 2.210e-26 -23.627 -25.656 -2.028 (0)
FeHSO4+2 4.039e-26 1.257e-26 -25.394 -25.901 -0.507 (0)
Fe3(OH)4+5 1.053e-29 7.130e-33 -28.978 -32.147 -3.169 (0)
H(0) 0.000e+00
H2 0.000e+00 0.000e+00 -44.470 -44.402 0.067 28.61
K 1.058e-02
K+ 1.040e-02 6.483e-03 -1.983 -2.188 -0.205 9.66
KSO4- 1.757e-04 1.186e-04 -3.755 -3.926 -0.171 34.85
KHPO4- 6.245e-08 4.217e-08 -7.204 -7.375 -0.171 39.62
Mg 5.507e-02
Mg+2 4.751e-02 1.371e-02 -1.323 -1.863 -0.540 -20.41
MgSO4 7.167e-03 8.371e-03 -2.145 -2.077 0.067 5.84
MgHCO3+ 2.454e-04 1.543e-04 -3.610 -3.812 -0.201 5.82
MgCO3 8.385e-05 9.794e-05 -4.077 -4.009 0.067 -17.09
MgHPO4 2.903e-05 3.391e-05 -4.537 -4.470 0.067 (0)
MgPO4- 1.967e-05 1.328e-05 -4.706 -4.877 -0.171 (0)
MgOH+ 1.150e-05 8.102e-06 -4.939 -5.091 -0.152 (0)
MgH2PO4+ 2.142e-07 1.447e-07 -6.669 -6.840 -0.171 (0)
Mn(2) 3.773e-09
Mn+2 2.104e-09 4.822e-10 -8.677 -9.317 -0.640 -16.36
MnCl+ 1.057e-09 7.010e-10 -8.976 -9.154 -0.178 -2.79
MnCO3 2.454e-10 2.867e-10 -9.610 -9.543 0.067 (0)
MnSO4 1.912e-10 2.233e-10 -9.719 -9.651 0.067 22.54
MnCl2 9.347e-11 1.092e-10 -10.029 -9.962 0.067 85.89
MnHCO3+ 6.232e-11 4.133e-11 -10.205 -10.384 -0.178 (0)
MnCl3- 1.618e-11 1.073e-11 -10.791 -10.969 -0.178 45.79
MnOH+ 3.041e-12 2.017e-12 -11.517 -11.695 -0.178 (0)
Mn(OH)3- 4.966e-20 3.294e-20 -19.304 -19.482 -0.178 (0)
Mn(NO3)2 1.330e-20 1.553e-20 -19.876 -19.809 0.067 41.04
Mn(3) 5.297e-26
Mn+3 5.297e-26 4.210e-27 -25.276 -26.376 -1.100 (0)
N(-3) 1.724e-06
NH4+ 1.610e-06 9.048e-07 -5.793 -6.043 -0.250 18.44
NH3 7.326e-08 8.557e-08 -7.135 -7.068 0.067 24.42
NH4SO4- 4.065e-08 3.036e-08 -7.391 -7.518 -0.127 39.98
N(5) 4.848e-06
NO3- 4.848e-06 2.844e-06 -5.314 -5.546 -0.232 30.29
Mn(NO3)2 1.330e-20 1.553e-20 -19.876 -19.809 0.067 41.04
Na 4.854e-01
Na+ 4.786e-01 3.434e-01 -0.320 -0.464 -0.144 -0.50
NaSO4- 6.638e-03 4.483e-03 -2.178 -2.348 -0.171 21.21
NaHCO3 1.590e-04 1.857e-04 -3.799 -3.731 0.067 1.80
NaCO3- 6.409e-05 4.786e-05 -4.193 -4.320 -0.127 2.88
NaHPO4- 3.308e-06 2.234e-06 -5.480 -5.651 -0.171 81.47
NaOH 4.843e-17 5.657e-17 -16.315 -16.247 0.067 (0)
O(0) 4.376e-04
O2 2.188e-04 2.556e-04 -3.660 -3.592 0.067 30.40
P 7.638e-05
MgHPO4 2.903e-05 3.391e-05 -4.537 -4.470 0.067 (0)
MgPO4- 1.967e-05 1.328e-05 -4.706 -4.877 -0.171 (0)
HPO4-2 1.724e-05 3.336e-06 -4.763 -5.477 -0.713 9.69
CaHPO4 3.771e-06 4.404e-06 -5.424 -5.356 0.067 (0)
NaHPO4- 3.308e-06 2.234e-06 -5.480 -5.651 -0.171 81.47
CaPO4- 2.561e-06 1.729e-06 -5.592 -5.762 -0.171 (0)
H2PO4- 4.794e-07 3.238e-07 -6.319 -6.490 -0.171 34.72
MgH2PO4+ 2.142e-07 1.447e-07 -6.669 -6.840 -0.171 (0)
KHPO4- 6.245e-08 4.217e-08 -7.204 -7.375 -0.171 39.62
CaH2PO4+ 2.954e-08 1.995e-08 -7.530 -7.700 -0.171 (0)
PO4-3 1.624e-08 2.496e-10 -7.789 -9.603 -1.813 -17.20
H3PO4 2.459e-13 2.872e-13 -12.609 -12.542 0.067 47.41
FeHPO4+ 3.692e-20 2.449e-20 -19.433 -19.611 -0.178 (0)
FeH2PO4+2 1.143e-20 2.377e-21 -19.942 -20.624 -0.682 (0)
FeHPO4 1.274e-21 1.489e-21 -20.895 -20.827 0.067 (0)
FeH2PO4+ 2.693e-23 1.819e-23 -22.570 -22.740 -0.171 (0)
S(6) 2.926e-02
SO4-2 1.432e-02 2.604e-03 -1.844 -2.584 -0.740 17.49
MgSO4 7.167e-03 8.371e-03 -2.145 -2.077 0.067 5.84
NaSO4- 6.638e-03 4.483e-03 -2.178 -2.348 -0.171 21.21
CaSO4 9.547e-04 1.115e-03 -3.020 -2.953 0.067 7.50
KSO4- 1.757e-04 1.186e-04 -3.755 -3.926 -0.171 34.85
NH4SO4- 4.065e-08 3.036e-08 -7.391 -7.518 -0.127 39.98
HSO4- 2.043e-09 1.526e-09 -8.690 -8.817 -0.127 40.96
MnSO4 1.912e-10 2.233e-10 -9.719 -9.651 0.067 22.54
CaHSO4+ 5.914e-11 4.417e-11 -10.228 -10.355 -0.127 (0)
FeSO4+ 1.174e-18 7.788e-19 -17.930 -18.109 -0.178 (0)
Fe(SO4)2- 5.941e-20 4.437e-20 -19.226 -19.353 -0.127 (0)
FeSO4 4.444e-20 5.191e-20 -19.352 -19.285 0.067 18.97
FeHSO4+2 4.039e-26 1.257e-26 -25.394 -25.901 -0.507 (0)
FeHSO4+ 2.753e-27 2.056e-27 -26.560 -26.687 -0.127 (0)
Si 7.382e-05
H4SiO4 7.061e-05 8.248e-05 -4.151 -4.084 0.067 52.08
H3SiO4- 3.210e-06 2.018e-06 -5.494 -5.695 -0.201 28.72
H2SiO4-2 1.096e-10 2.279e-11 -9.960 -10.642 -0.682 (0)

------------------------------Saturation indices-------------------------------

Phase SI** log IAP log K(298 K, 1 atm)

Anhydrite -0.93 -5.20 -4.28 CaSO4
Aragonite 0.59 -7.74 -8.34 CaCO3
Calcite 0.74 -7.74 -8.48 CaCO3
Chalcedony -0.52 -4.07 -3.55 SiO2
Chrysotile 3.35 35.56 32.20 Mg3Si2O5(OH)4
CO2(g) -3.41 -4.88 -1.47 CO2
Dolomite 2.36 -14.73 -17.09 CaMg(CO3)2
Fe(OH)3(a) 0.18 5.07 4.89 Fe(OH)3
Goethite 6.08 5.08 -1.00 FeOOH
Gypsum -0.64 -5.22 -4.58 CaSO4:2H2O
H2(g) -41.30 -44.40 -3.10 H2
H2O(g) -1.51 -0.01 1.50 H2O
Halite -2.48 -0.91 1.57 NaCl
Hausmannite 1.56 62.59 61.03 Mn3O4
Hematite 14.17 10.17 -4.01 Fe2O3
Hydroxyapatite 6.77 3.35 -3.42 Ca5(PO4)3OH
Jarosite-K -7.57 -16.78 -9.21 KFe3(SO4)2(OH)6
Manganite 2.39 27.73 25.34 MnOOH
Melanterite -19.39 -21.59 -2.21 FeSO4:7H2O
NH3(g) -8.86 -7.07 1.80 NH3
O2(g) -0.70 -3.59 -2.89 O2 Pressure 0.2 atm, phi 1.000
Pyrochroite -8.09 7.11 15.20 Mn(OH)2
Pyrolusite 6.97 48.35 41.38 MnO2:H2O
Quartz -0.09 -4.07 -3.98 SiO2
Rhodochrosite -3.31 -14.44 -11.13 MnCO3
Sepiolite 1.15 16.91 15.76 Mg2Si3O7.5OH:3H2O
Sepiolite(d) -1.75 16.91 18.66 Mg2Si3O7.5OH:3H2O
Siderite -13.19 -24.08 -10.89 FeCO3
SiO2(a) -1.35 -4.07 -2.71 SiO2
Sylvite -3.54 -2.64 0.90 KCl
Talc 6.03 27.43 21.40 Mg3Si4O10(OH)2
Vivianite -40.13 -76.13 -36.00 Fe3(PO4)2:8H2O

**For a gas, SI = log10(fugacity). Fugacity = pressure * phi / 1 atm.
For ideal gases, phi = 1.

------------------
End of simulation.
------------------

------------------------------------
Reading input data for simulation 2.
------------------------------------

-------------------------------
End of Run after 0.205 Seconds.
-------------------------------
############################################################################

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Oscar Branson

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Dec 4, 2015, 3:04:03 PM12/4/15

to phreeqpy-users

Dear Phreeqc users,

I'm new to phreeqc and phreeqpy, and am having a very similar problem with understanding how to get data out. I am performing some speciation calculations (phreeqc example 1), and would like to output the complete 'Distribution of Species' table. I'm having difficulties working out how to do this using either SELECTED_OUTPUT or USER_PUNCH... am I missing something? How can I get this information out of phreeqpy?

On a similar note, is it possible to get phreeqpy to print out the complete report, as generated by the interactive program in the example below?

Thanks very much in advance,

Oscar.

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Parkhurst, David

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Dec 4, 2015, 3:33:20 PM12/4/15

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First, to get the output from a RunFile or RunString command, you can either write a file or get a string. The methods that turn on these kinds of output are SetOutputStringOn and SetOutputFileOn, which must be called before a Run method ( RunString or RunFile)

The name of the output file is set with SetOutputFileName. If you perform two Run methods in sequence, I think the output file will be overwritten on the second run method, but I am not sure.

After a Run method, GetOutputString will retrieve the entire output as a string.

PHREEQC does not have an easy way to get all of the Distribution of Species. You could get all the molalities for instance by listing every species in the SELECTED_OUTPUT -molalities input, which you would have to repeat for activities, log activities, etc.

An alternative is to use the SYS function in USER_PUNCH. The following script

SOLUTION

Na 1

Cl 1

SELECTED_OUTPUT 2

USER_PUNCH 2

10 t = SYS("aq", count, name$, type$, moles)

20 FOR i = 1 TO count

30 PUNCH name$(i)

40 PUNCH LA(name$(i))

50 PUNCH LM(name$(i))

60 NEXT i

END

Generates a selected output table of log activities and log molalities that looks like this

Cl- -3.0155e+00 -3.0000e+00 Na+ -3.0154e+00 -3.0000e+00 OH- -6.9948e+00 ...

with additional species following OH-.

David Parkhurst
Hydrologist
dlp...@usgs.gov
Profile: https://profile.usgs.gov/dlpark
Project: http://wwwbrr.cr.usgs.gov/projects/GWC_coupled

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