Skip to content

Add pqi_pqo_files to tests #289

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
rkingsbury merged 3 commits into from
Nov 6, 2025
Merged

Add pqi_pqo_files to tests #289

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
c619d47
Add pqi_pqo_files to tests
Nov 6, 2025
89b792b
Add sophisticated pqi pqo files
Nov 6, 2025
c46f935
Change directory name to files_phreeqc
Nov 6, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 14 additions & 0 deletions tests/files_phreeqc/sophisticated_test_case.pqi
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
DATABASE C:\Program Files (x86)\USGS\Phreeqc Interactive 3.7.3-15968\database\phreeqc.dat
Copy link
Member

@rkingsbury rkingsbury Nov 6, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Is this line necessary? Since it points to a local directory (C:\...) it's not going to be useful (or readable) by our wrapper). Same goes for the other input files. If omitted, does PHREEQC just use its default database?

Copy link
Collaborator Author

@SuixiongTay SuixiongTay Nov 6, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Let's cross validate the current DATABASE directory structure with Vineet's IPHREEQC schema to check. Tagging @vineetbansal

We could also specify the parser to skip entries containing the keyword DATABASE. Ideally, the test will check the following lines in the pqo output to validate the initial solution block:

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

------------------------------------
Reading input data for simulation 1.
------------------------------------

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

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

And we can remove the below:

   Input file: C:\Users\...
  Output file: C:\Users\...
Database file: C:\Program Files (x86)\USGS\Phreeqc Interactive 3.7.3-15968\database\phreeqc.dat
------------------------------------
Reading input data for simulation 2.
------------------------------------

-------------------------------
End of Run after 0.084 Seconds.
-------------------------------

What do you think? @rkingsbury

Copy link
Member

@rkingsbury rkingsbury Nov 6, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Agreed; that sounds like a good approach.

SOLUTION 0
temp 25.00
pH 7.00
pe 4.0
Ca 3.0 # total dissolved Ca
Na 1.0
Alkalinity 3.8 # mmol charge / kgw
S 1.0 # total sulfur, mainly sulfate, S(6), at pe = 4
N(5) 0.2 # nitrogen in the form of nitrate, N(5)
Cl 1.0
water 1 # kg water, default = 1 kg
density 1
END
151 changes: 151 additions & 0 deletions tests/files_phreeqc/sophisticated_test_case.pqo
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,151 @@
Input file: C:\Users\st2591\Downloads\test.pqi
Output file: C:\Users\st2591\Downloads\test.pqo
Database file: C:\Program Files (x86)\USGS\Phreeqc Interactive 3.7.3-15968\database\phreeqc.dat

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

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

DATABASE C:\Program Files (x86)\USGS\Phreeqc Interactive 3.7.3-15968\database\phreeqc.dat
SOLUTION 0
temp 25.00
pH 7.00
pe 4.0
Ca 3.0 # total dissolved Ca
Na 1.0
Alkalinity 3.8 # mmol charge / kgw
S 1.0 # total sulfur, mainly sulfate, S(6), at pe = 4
N(5) 0.2 # nitrogen in the form of nitrate, N(5)
Cl 1.0
water 1 # kg water, default = 1 kg
density 1
END
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------

Initial solution 0.

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

Elements Molality Moles

Alkalinity 3.800e-03 3.800e-03
Ca 3.000e-03 3.000e-03
Cl 1.000e-03 1.000e-03
N(5) 2.000e-04 2.000e-04
Na 1.000e-03 1.000e-03
S 1.000e-03 1.000e-03

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

pH = 7.000
pe = 4.000
Specific Conductance (µS/cm, 25°C) = 666
Density (g/cm³) = 0.99749
Volume (L) = 1.00307
Activity of water = 1.000
Ionic strength (mol/kgw) = 1.010e-02
Mass of water (kg) = 1.000e+00
Total carbon (mol/kg) = 4.543e-03
Total CO2 (mol/kg) = 4.543e-03
Temperature (°C) = 25.00
Electrical balance (eq) = 4.207e-17
Percent error, 100*(Cat-|An|)/(Cat+|An|) = 0.00
Iterations = 8
Total H = 1.110162e+02
Total O = 5.552370e+01

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

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

OH- 1.125e-07 1.012e-07 -6.949 -6.995 -0.046 -4.03
H+ 1.095e-07 1.000e-07 -6.960 -7.000 -0.040 0.00
H2O 5.551e+01 9.998e-01 1.744 -0.000 0.000 18.07
C(4) 4.543e-03
HCO3- 3.698e-03 3.345e-03 -2.432 -2.476 -0.044 24.77
CO2 7.505e-04 7.523e-04 -3.125 -3.124 0.001 34.43
CaHCO3+ 8.613e-05 7.805e-05 -4.065 -4.108 -0.043 9.72
CaCO3 4.808e-06 4.820e-06 -5.318 -5.317 0.001 -14.60
CO3-2 2.342e-06 1.569e-06 -5.630 -5.804 -0.174 -5.01
NaHCO3 1.687e-06 1.691e-06 -5.773 -5.772 0.001 1.80
NaCO3- 2.913e-08 2.626e-08 -7.536 -7.581 -0.045 -0.92
(CO2)2 1.036e-08 1.039e-08 -7.984 -7.983 0.001 68.87
Ca 3.000e-03
Ca+2 2.732e-03 1.829e-03 -2.564 -2.738 -0.174 -17.93
CaSO4 1.772e-04 1.777e-04 -3.751 -3.750 0.001 7.50
CaHCO3+ 8.613e-05 7.805e-05 -4.065 -4.108 -0.043 9.72
CaCO3 4.808e-06 4.820e-06 -5.318 -5.317 0.001 -14.60
CaOH+ 3.366e-09 3.034e-09 -8.473 -8.518 -0.045 (0)
CaHSO4+ 1.295e-10 1.168e-10 -9.888 -9.933 -0.045 (0)
Cl 1.000e-03
Cl- 1.000e-03 9.003e-04 -3.000 -3.046 -0.046 18.14
H(0) 1.413e-25
H2 7.063e-26 7.079e-26 -25.151 -25.150 0.001 28.61
N(5) 2.000e-04
NO3- 2.000e-04 1.796e-04 -3.699 -3.746 -0.047 29.55
Na 1.000e-03
Na+ 9.956e-04 8.989e-04 -3.002 -3.046 -0.044 -1.38
NaSO4- 2.721e-06 2.461e-06 -5.565 -5.609 -0.044 14.33
NaHCO3 1.687e-06 1.691e-06 -5.773 -5.772 0.001 1.80
NaCO3- 2.913e-08 2.626e-08 -7.536 -7.581 -0.045 -0.92
NaOH 9.076e-21 9.097e-21 -20.042 -20.041 0.001 (0)
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -42.081 -42.080 0.001 30.40
S(-2) 0.000e+00
HS- 0.000e+00 0.000e+00 -64.566 -64.612 -0.046 20.67
H2S 0.000e+00 0.000e+00 -64.672 -64.671 0.001 36.27
S-2 0.000e+00 0.000e+00 -70.354 -70.530 -0.176 (0)
(H2S)2 0.000e+00 0.000e+00 -130.620 -130.619 0.001 30.09
S(6) 1.000e-03
SO4-2 8.200e-04 5.463e-04 -3.086 -3.263 -0.176 14.77
CaSO4 1.772e-04 1.777e-04 -3.751 -3.750 0.001 7.50
NaSO4- 2.721e-06 2.461e-06 -5.565 -5.609 -0.044 14.33
HSO4- 5.892e-09 5.312e-09 -8.230 -8.275 -0.045 40.34
CaHSO4+ 1.295e-10 1.168e-10 -9.888 -9.933 -0.045 (0)

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

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

Anhydrite -1.72 -6.00 -4.28 CaSO4
Aragonite -0.21 -8.54 -8.34 CaCO3
Calcite -0.06 -8.54 -8.48 CaCO3
CO2(g) -1.66 -3.12 -1.47 CO2
Gypsum -1.42 -6.00 -4.58 CaSO4:2H2O
H2(g) -22.05 -25.15 -3.10 H2
H2O(g) -1.50 -0.00 1.50 H2O
H2S(g) -63.68 -71.61 -7.94 H2S
Halite -7.66 -6.09 1.57 NaCl
O2(g) -39.19 -42.08 -2.89 O2
Sulfur -47.55 -42.67 4.88 S

**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 0.05 Seconds.
------------------------------
5 changes: 5 additions & 0 deletions tests/files_phreeqc/water_pH7_temp25.pqi
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
DATABASE C:\Program Files (x86)\USGS\Phreeqc Interactive 3.7.3-15968\database\phreeqc.dat
SOLUTION 0
temp 25.00
pH 7.00
END
91 changes: 91 additions & 0 deletions tests/files_phreeqc/water_pH7_temp25.pqo
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,91 @@
Input file: C:\Users\st2591\Downloads\Phrqc1.pqi
Output file: C:\Users\st2591\Downloads\Phrqc1.pqo
Database file: C:\Program Files (x86)\USGS\Phreeqc Interactive 3.7.3-15968\database\phreeqc.dat

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

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

DATABASE C:\Program Files (x86)\USGS\Phreeqc Interactive 3.7.3-15968\database\phreeqc.dat
SOLUTION 0
temp 25.00
pH 7.00
END
-------------------------------------------
Beginning of initial solution calculations.
-------------------------------------------

Initial solution 0.

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

Elements Molality Moles

Pure water

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

pH = 7.000
pe = 4.000
Specific Conductance (µS/cm, 25°C) = 0
Density (g/cm³) = 0.99704
Volume (L) = 1.00297
Activity of water = 1.000
Ionic strength (mol/kgw) = 1.007e-07
Mass of water (kg) = 1.000e+00
Total alkalinity (eq/kg) = 1.217e-09
Temperature (°C) = 25.00
Electrical balance (eq) = -1.217e-09
Percent error, 100*(Cat-|An|)/(Cat+|An|) = -0.60
Iterations = 0
Total H = 1.110124e+02
Total O = 5.550622e+01

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

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

OH- 1.013e-07 1.012e-07 -6.995 -6.995 -0.000 -4.14
H+ 1.001e-07 1.000e-07 -7.000 -7.000 -0.000 0.00
H2O 5.551e+01 1.000e+00 1.744 0.000 0.000 18.07
H(0) 1.416e-25
H2 7.079e-26 7.079e-26 -25.150 -25.150 0.000 28.61
O(0) 0.000e+00
O2 0.000e+00 0.000e+00 -42.080 -42.080 0.000 30.40

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

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

H2(g) -22.05 -25.15 -3.10 H2
H2O(g) -1.50 0.00 1.50 H2O
O2(g) -39.19 -42.08 -2.89 O2

**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 0.084 Seconds.
-------------------------------
Loading