PHREEQC is a useful tool for hydrochemical modeling. However, I hear more and more complains from people using MacOS or Linux who don’t know how to install (compile it). Here is what we’ll have to do:
First, we have to download it. Unlike for Windows, there exists no GUI for Linux and MacOS. For Linux and MacOS we get the batch version of PHREEQC.
$ mkdir PHREEQC
$ cd PHREEQC
$ curl -OLC - https://water.usgs.gov/water-resources/software/PHREEQC/phreeqc-3.4.0-12927.zip
$ unzip phreeqc-3.4.0-12927.zip
$ cd phreeqc-3.4.0-12927
$ ./configure
$ make
$ sudo make install
Now we can run it on an example and figure out if it works correctly. First, we have to copy the thermodynamic database we want to use into the folder of our files. Afterwards, we can run phreeqc and view our results:
$ cd examples
$ less ex1
TITLE Example 1.--Add uranium and speciate seawater.
SOLUTION 1 SEAWATER FROM NORDSTROM AND OTHERS (1979)
units ppm
pH 8.22
pe 8.451
density 1.023
temp 25.0
redox O(0)/O(-2)
Ca 412.3
Mg 1291.8
Na 10768.0
K 399.1
Fe 0.002
Mn 0.0002 pe
Si 4.28
Cl 19353.0
Alkalinity 141.682 as HCO3
S(6) 2712.0
N(5) 0.29 gfw 62.0
N(-3) 0.03 as NH4
U 3.3 ppb N(5)/N(-3)
O(0) 1.0 O2(g) -0.7
SOLUTION_MASTER_SPECIES
U U+4 0.0 238.0290 238.0290
U(4) U+4 0.0 238.0290
U(5) UO2+ 0.0 238.0290
U(6) UO2+2 0.0 238.0290
SOLUTION_SPECIES
#primary master species for U
#is also secondary master species for U(4)
U+4 = U+4
log_k 0.0
U+4 + 4 H2O = U(OH)4 + 4 H+
log_k -8.538
delta_h 24.760 kcal
U+4 + 5 H2O = U(OH)5- + 5 H+
log_k -13.147
delta_h 27.580 kcal
#secondary master species for U(5)
U+4 + 2 H2O = UO2+ + 4 H+ + e-
log_k -6.432
delta_h 31.130 kcal
#secondary master species for U(6)
U+4 + 2 H2O = UO2+2 + 4 H+ + 2 e-
log_k -9.217
delta_h 34.430 kcal
UO2+2 + H2O = UO2OH+ + H+
log_k -5.782
delta_h 11.015 kcal
2UO2+2 + 2H2O = (UO2)2(OH)2+2 + 2H+
log_k -5.626
delta_h -36.04 kcal
3UO2+2 + 5H2O = (UO2)3(OH)5+ + 5H+
log_k -15.641
delta_h -44.27 kcal
UO2+2 + CO3-2 = UO2CO3
log_k 10.064
delta_h 0.84 kcal
UO2+2 + 2CO3-2 = UO2(CO3)2-2
log_k 16.977
delta_h 3.48 kcal
UO2+2 + 3CO3-2 = UO2(CO3)3-4
log_k 21.397
delta_h -8.78 kcal
PHASES
Uraninite
UO2 + 4 H+ = U+4 + 2 H2O
log_k -3.490
delta_h -18.630 kcal
END
$ cp /usr/local/share/doc/phreeqc/database/phreeqc.dat ./
$ phreeqc ex1
$ less ex1.out
Input file: ex1
Output file: ex1.out
Database file: phreeqc.dat
------------------
Reading data base.
------------------
SOLUTION_MASTER_SPECIES
SOLUTION_SPECIES
PHASES
EXCHANGE_MASTER_SPECIES
EXCHANGE_SPECIES
SURFACE_MASTER_SPECIES
SURFACE_SPECIES
RATES
END
------------------------------------
Reading input data for simulation 1.
------------------------------------
TITLE Example 1.--Add uranium and speciate seawater.
SOLUTION 1 SEAWATER FROM NORDSTROM AND OTHERS (1979)
units ppm
pH 8.22
pe 8.451
density 1.023
temp 25.0
redox O(0)/O(-2)
Ca 412.3
Mg 1291.8
Na 10768.0
K 399.1
Fe 0.002
Mn 0.0002 pe
Si 4.28
Cl 19353.0
Alkalinity 141.682 as HCO3
S(6) 2712.0
N(5) 0.29 gfw 62.0
N(-3) 0.03 as NH4
U 3.3 ppb N(5)/N(-3)
O(0) 1.0 O2(g) -0.7
SOLUTION_MASTER_SPECIES
U U+4 0.0 238.0290 238.0290
U(4) U+4 0.0 238.0290
U(5) UO2+ 0.0 238.0290
U(6) UO2+2 0.0 238.0290
SOLUTION_SPECIES
U+4 = U+4
log_k 0.0
U+4 + 4 H2O = U(OH)4 + 4 H+
log_k -8.538
delta_h 24.760 kcal
U+4 + 5 H2O = U(OH)5- + 5 H+
log_k -13.147
delta_h 27.580 kcal
U+4 + 2 H2O = UO2+ + 4 H+ + e-
log_k -6.432
delta_h 31.130 kcal
U+4 + 2 H2O = UO2+2 + 4 H+ + 2 e-
log_k -9.217
delta_h 34.430 kcal
UO2+2 + H2O = UO2OH+ + H+
log_k -5.782
delta_h 11.015 kcal
2UO2+2 + 2H2O = (UO2)2(OH)2+2 + 2H+
log_k -5.626
delta_h -36.04 kcal
3UO2+2 + 5H2O = (UO2)3(OH)5+ + 5H+
log_k -15.641
delta_h -44.27 kcal
UO2+2 + CO3-2 = UO2CO3
log_k 10.064
delta_h 0.84 kcal
UO2+2 + 2CO3-2 = UO2(CO3)2-2
log_k 16.977
delta_h 3.48 kcal
UO2+2 + 3CO3-2 = UO2(CO3)3-4
log_k 21.397
delta_h -8.78 kcal
PHASES
Uraninite
UO2 + 4 H+ = U+4 + 2 H2O
log_k -3.490
delta_h -18.630 kcal
END
-----
TITLE
-----
Example 1.--Add uranium and speciate seawater.
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------
Initial solution 1. SEAWATER FROM NORDSTROM AND OTHERS (1979)
-----------------------------Solution composition------------------------------
Elements Molality Moles
Alkalinity 2.406e-03 2.406e-03
Ca 1.066e-02 1.066e-02
Cl 5.657e-01 5.657e-01
Fe 3.711e-08 3.711e-08
K 1.058e-02 1.058e-02
Mg 5.507e-02 5.507e-02
Mn 3.773e-09 3.773e-09
N(-3) 1.724e-06 1.724e-06
N(5) 4.847e-06 4.847e-06
Na 4.854e-01 4.854e-01
O(0) 4.376e-04 4.376e-04 Equilibrium with O2(g)
S(6) 2.926e-02 2.926e-02
Si 7.382e-05 7.382e-05
U 1.437e-08 1.437e-08
----------------------------Description of solution----------------------------
pH = 8.220
pe = 8.451
Specific Conductance (µS/cm, 25°C) = 52630
Density (g/cm³) = 1.02323
Volume (L) = 1.01282
Activity of water = 0.981
Ionic strength (mol/kgw) = 6.747e-01
Mass of water (kg) = 1.000e+00
Total carbon (mol/kg) = 2.182e-03
Total CO2 (mol/kg) = 2.182e-03
Temperature (°C) = 25.00
Electrical balance (eq) = 7.936e-04
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 0.07
Iterations = 7
Total H = 1.110147e+02
Total O = 5.563054e+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) 2.182e-03
HCO3- 1.485e-03 1.003e-03 -2.828 -2.999 -0.171 26.98
MgHCO3+ 2.560e-04 1.610e-04 -3.592 -3.793 -0.201 5.82
NaHCO3 1.658e-04 1.936e-04 -3.781 -3.713 0.067 1.80
MgCO3 8.747e-05 1.022e-04 -4.058 -3.991 0.067 -17.09
NaCO3- 6.682e-05 4.990e-05 -4.175 -4.302 -0.127 2.88
CaHCO3+ 4.453e-05 3.081e-05 -4.351 -4.511 -0.160 9.96
CO3-2 3.752e-05 7.803e-06 -4.426 -5.108 -0.682 -1.97
CaCO3 2.703e-05 3.158e-05 -4.568 -4.501 0.067 -14.60
CO2 1.186e-05 1.385e-05 -4.926 -4.858 0.067 34.43
UO2(CO3)3-4 1.252e-08 1.173e-10 -7.902 -9.931 -2.028 (0)
UO2(CO3)2-2 1.837e-09 5.716e-10 -8.736 -9.243 -0.507 (0)
MnCO3 2.550e-10 2.979e-10 -9.593 -9.526 0.067 (0)
MnHCO3+ 6.475e-11 4.294e-11 -10.189 -10.367 -0.178 (0)
UO2CO3 7.662e-12 8.950e-12 -11.116 -11.048 0.067 (0)
(CO2)2 3.015e-12 3.522e-12 -11.521 -11.453 0.067 68.87
FeCO3 1.796e-20 2.098e-20 -19.746 -19.678 0.067 (0)
FeHCO3+ 1.505e-20 1.124e-20 -19.823 -19.949 -0.127 (0)
Ca 1.066e-02
Ca+2 9.634e-03 2.409e-03 -2.016 -2.618 -0.602 -16.69
CaSO4 9.548e-04 1.115e-03 -3.020 -2.953 0.067 7.50
CaHCO3+ 4.453e-05 3.081e-05 -4.351 -4.511 -0.160 9.96
CaCO3 2.703e-05 3.158e-05 -4.568 -4.501 0.067 -14.60
CaOH+ 8.711e-08 6.505e-08 -7.060 -7.187 -0.127 (0)
CaHSO4+ 5.915e-11 4.418e-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+ 1.053e-09 6.985e-10 -8.977 -9.156 -0.178 -2.79
MnCl2 9.314e-11 1.088e-10 -10.031 -9.963 0.067 85.89
MnCl3- 1.612e-11 1.069e-11 -10.793 -10.971 -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+ 7.392e-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 4.892e-19 1.121e-19 -18.311 -18.950 -0.640 -20.71
FeCl+ 7.392e-20 5.521e-20 -19.131 -19.258 -0.127 (0)
FeSO4 4.443e-20 5.190e-20 -19.352 -19.285 0.067 18.97
FeCO3 1.796e-20 2.098e-20 -19.746 -19.678 0.067 (0)
FeHCO3+ 1.505e-20 1.124e-20 -19.823 -19.949 -0.127 (0)
FeOH+ 8.698e-21 5.768e-21 -20.061 -20.239 -0.178 (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 7.786e-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 -18.464 -19.564 -1.100 (0)
Fe(SO4)2- 5.939e-20 4.436e-20 -19.226 -19.353 -0.127 (0)
FeCl3 1.431e-20 1.671e-20 -19.844 -19.777 0.067 (0)
Fe2(OH)2+4 2.359e-24 2.210e-26 -23.627 -25.656 -2.028 (0)
FeHSO4+2 4.038e-26 1.256e-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- 1.756e-04 1.186e-04 -3.755 -3.926 -0.171 34.85
Mg 5.507e-02
Mg+2 4.754e-02 1.372e-02 -1.323 -1.863 -0.540 -20.41
MgSO4 7.170e-03 8.375e-03 -2.144 -2.077 0.067 5.84
MgHCO3+ 2.560e-04 1.610e-04 -3.592 -3.793 -0.201 5.82
MgCO3 8.747e-05 1.022e-04 -4.058 -3.991 0.067 -17.09
MgOH+ 1.151e-05 8.107e-06 -4.939 -5.091 -0.152 (0)
Mn(2) 3.773e-09
Mn+2 2.097e-09 4.806e-10 -8.678 -9.318 -0.640 -16.36
MnCl+ 1.053e-09 6.985e-10 -8.977 -9.156 -0.178 -2.79
MnCO3 2.550e-10 2.979e-10 -9.593 -9.526 0.067 (0)
MnSO4 1.905e-10 2.225e-10 -9.720 -9.653 0.067 22.54
MnCl2 9.314e-11 1.088e-10 -10.031 -9.963 0.067 85.89
MnHCO3+ 6.475e-11 4.294e-11 -10.189 -10.367 -0.178 (0)
MnCl3- 1.612e-11 1.069e-11 -10.793 -10.971 -0.178 45.79
MnOH+ 3.031e-12 2.010e-12 -11.518 -11.697 -0.178 (0)
Mn(OH)3- 4.949e-20 3.282e-20 -19.305 -19.484 -0.178 (0)
Mn(NO3)2 1.325e-20 1.548e-20 -19.878 -19.810 0.067 41.04
Mn(3) 5.279e-26
Mn+3 5.279e-26 4.195e-27 -25.277 -26.377 -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- 4.064e-08 3.035e-08 -7.391 -7.518 -0.127 39.98
N(5) 4.847e-06
NO3- 4.847e-06 2.844e-06 -5.314 -5.546 -0.232 30.29
Mn(NO3)2 1.325e-20 1.548e-20 -19.878 -19.810 0.067 41.04
Na 4.854e-01
Na+ 4.785e-01 3.434e-01 -0.320 -0.464 -0.144 -0.50
NaSO4- 6.637e-03 4.482e-03 -2.178 -2.349 -0.171 21.21
NaHCO3 1.658e-04 1.936e-04 -3.781 -3.713 0.067 1.80
NaCO3- 6.682e-05 4.990e-05 -4.175 -4.302 -0.127 2.88
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
S(6) 2.926e-02
SO4-2 1.432e-02 2.604e-03 -1.844 -2.584 -0.740 17.49
MgSO4 7.170e-03 8.375e-03 -2.144 -2.077 0.067 5.84
NaSO4- 6.637e-03 4.482e-03 -2.178 -2.349 -0.171 21.21
CaSO4 9.548e-04 1.115e-03 -3.020 -2.953 0.067 7.50
KSO4- 1.756e-04 1.186e-04 -3.755 -3.926 -0.171 34.85
NH4SO4- 4.064e-08 3.035e-08 -7.391 -7.518 -0.127 39.98
HSO4- 2.042e-09 1.525e-09 -8.690 -8.817 -0.127 40.96
MnSO4 1.905e-10 2.225e-10 -9.720 -9.653 0.067 22.54
CaHSO4+ 5.915e-11 4.418e-11 -10.228 -10.355 -0.127 (0)
FeSO4+ 1.174e-18 7.786e-19 -17.930 -18.109 -0.178 (0)
Fe(SO4)2- 5.939e-20 4.436e-20 -19.226 -19.353 -0.127 (0)
FeSO4 4.443e-20 5.190e-20 -19.352 -19.285 0.067 18.97
FeHSO4+2 4.038e-26 1.256e-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)
U(4) 1.088e-21
U(OH)5- 1.088e-21 8.128e-22 -20.963 -21.090 -0.127 (0)
U(OH)4 1.738e-25 2.030e-25 -24.760 -24.692 0.067 (0)
U+4 0.000e+00 0.000e+00 -46.972 -49.000 -2.028 (0)
U(5) 1.707e-18
UO2+ 1.707e-18 1.275e-18 -17.768 -17.894 -0.127 (0)
U(6) 1.437e-08
UO2(CO3)3-4 1.252e-08 1.173e-10 -7.902 -9.931 -2.028 (0)
UO2(CO3)2-2 1.837e-09 5.716e-10 -8.736 -9.243 -0.507 (0)
UO2CO3 7.662e-12 8.950e-12 -11.116 -11.048 0.067 (0)
UO2OH+ 3.563e-14 2.661e-14 -13.448 -13.575 -0.127 (0)
UO2+2 3.182e-16 9.898e-17 -15.497 -16.004 -0.507 (0)
(UO2)2(OH)2+2 1.973e-21 6.139e-22 -20.705 -21.212 -0.507 (0)
(UO2)3(OH)5+ 3.387e-23 2.530e-23 -22.470 -22.597 -0.127 (0)
------------------------------Saturation indices-------------------------------
Phase SI** log IAP log K(298 K, 1 atm)
Anhydrite -0.93 -5.20 -4.28 CaSO4
Aragonite 0.61 -7.73 -8.34 CaCO3
Calcite 0.75 -7.73 -8.48 CaCO3
Chalcedony -0.52 -4.07 -3.55 SiO2
Chrysotile 3.36 35.56 32.20 Mg3Si2O5(OH)4
CO2(g) -3.39 -4.86 -1.47 CO2
Dolomite 2.39 -14.70 -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 1.55 62.58 61.03 Mn3O4
Hematite 14.17 10.17 -4.01 Fe2O3
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 -8.10 7.10 15.20 Mn(OH)2
Pyrolusite 6.97 48.35 41.38 MnO2:H2O
Quartz -0.09 -4.07 -3.98 SiO2
Rhodochrosite -3.30 -14.43 -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 -13.17 -24.06 -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
Uraninite -12.65 -16.14 -3.49 UO2
**For a gas, SI = log10(fugacity). Fugacity = pressure * phi / 1 atm.
For ideal gases, phi = 1.
------------------
End of simulation.
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Reading input data for simulation 2.
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End of Run after 0.013884 Seconds.
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