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Merged
avdudchenko merged 2 commits into from
May 24, 2026
Merged

Dropped second action #4

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021c6c4
cleaned up egg-info
TimBartholomew May 20, 2026
21915d0
dropped the second action, simplified osmotic pressure calc
TimBartholomew May 20, 2026
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4 changes: 3 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@

*.egg-info/
*.egg-info
*.dat
*.pyc
*.inp
.vscode/
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59 changes: 6 additions & 53 deletions src/phreeqcinwt/core/solution_state_utils.py
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Expand Up @@ -6,41 +6,15 @@


class solution_utils:
def _process_activities(self, result):

@avdudchenko avdudchenko May 24, 2026 •
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So we are completely dropping reporting activity coefficients for phases/species?
Osmotic pressure use this - hence the dependence (we get activities for all specie/h2o) and then use h2o to get osmotic pressure.

I think it is fine to drop all of this as I do not seem many/any use cases (I only added as I tried to see if useing raw activites would make better surrogates -it did not...)

# print(result)
activities = {}
for element, name in self.return_dict.items():
idx = np.where("la_" + element == np.array(result[0]))[0]
if len(idx) > 0:
activities[element] = {
"value": 10 ** result[1][idx[0]],
"units": "dimensionless",
}
activities["log10_{}".format(element)] = {
"value": result[1][idx[0]],
"units": "dimensionless",
}
else:
activities[element] = {"value": None, "units": "dimensionless"}
activities["log10_{}".format(element)] = {
"value": None,
"units": "dimensionless",
}
idx = np.where("la_H2O" == np.array(result[0]))[0]
# print(idx)
activities["H2O"] = {"value": 10 ** result[1][idx[0]], "units": "dimensionless"}
activities["log10_{}".format("H2O")] = {
"value": result[1][idx[0]],
"units": "dimensionless",
}
# print(activities)
return activities

def _get_osmotic_pressure(self, result, solution_state, activities):
def _get_osmotic_pressure(self, result, solution_state):
idx = np.where("h2o_vm" == np.array(result[0]))[0]
activity_idx = np.where("la_H2O" == np.array(result[0]))[0]

if len(idx) == 0 or len(activity_idx) == 0:
return {"units": "Pa", "value": None}

vm = result[1][idx[0]] # cm3/mol
activity = activities["H2O"]["value"]
activity = 10 ** result[1][activity_idx[0]]
R = 8.31446261815324 # m3⋅Pa⋅K−1⋅mol−1
T = solution_state["Temperature"]["value"] + 273.15
if vm == 0:
Expand Down Expand Up @@ -103,27 +77,6 @@ def _get_solution_comp(
}
return aque_species_comp

def _get_diffusion_transfer_number(
self,
result,
):
transport_data = {"diffusion": {}, "transfer_number": {}}
for i in range(len(result[1])):
if isinstance(result[1][i], str) and "diffusion" in result[1][i]:
species = result[1][i].split(" ")[1]
transport_data["diffusion"][species] = {
"value": result[1][i + 1],
"units": "m2/s",
}
for i in range(len(result[1])):
if isinstance(result[1][i], str) and "transfer_number" in result[1][i]:
species = result[1][i].split(" ")[1]
transport_data["transfer_number"][species] = {
"value": result[1][i + 1],
"units": "unitless",
}
return transport_data

def _get_scaling_tendencies(self, result, report=False):
result_dict = {}
for i in range(len(result[1])):
Expand Down
61 changes: 1 addition & 60 deletions src/phreeqcinwt/phreeqc_wt_api.py
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Expand Up @@ -460,6 +460,7 @@ def get_solution_state(
command += " -charge_balance true\n"
command += " -water true\n"
command += " -percent_error true\n"
command += " -activities H2O\n"
command += " -user_punch true\n"

command += "\n"
Expand All @@ -477,47 +478,13 @@ def get_solution_state(
solution_composition["composition"] = self._get_solution_comp(
result,
)

command = "USE SOLUTION {}\n".format(str(solution_number))

command += "EQUILIBRIUM_PHASES\n"
command += "USER_PUNCH\n"
command += "-start\n"
cur_count = 10
for element in solution_composition["composition"]["species"].keys():
command += '{} PUNCH "diffusion\t{element}" DIFF_C("{element}")\n'.format(
cur_count, element=element
)
cur_count += 10
for element in solution_composition["composition"]["species"].keys():
command += (
'{} PUNCH "transfer_number\t{element}" T_SC("{element}")\n'.format(
cur_count, element=element
)
)
cur_count += 10
command += "-end\n"
command += "SELECTED_OUTPUT\n"
command += " -user_punch true\n"
command += " -activities "
for element in solution_composition["composition"]["species"].keys():
command += " {} ".format(element)
command += " H2O\n"
command += "\n"
command += "END\n"
self.run_string(command)

result2 = self.phreeqc.get_selected_output_array()
solution_composition["activities"] = self._process_activities(result2)
solution_composition["transport"] = self._get_diffusion_transfer_number(result2)
solution_composition["solution_state"].update(
self.get_total_concetration(solution_composition)
)
solution_composition["solution_state"]["Osmotic pressure"] = (
self._get_osmotic_pressure(
result,
solution_composition["solution_state"],
solution_composition["activities"],
)
)
self.current_state = solution_composition
Expand Down Expand Up @@ -554,32 +521,6 @@ def get_solution_state(
mass["mw (g/mol)"],
"g/mol",
)

print("activities------------------")
for scalant, SI in solution_composition["activities"].items():
print(
"\t",
scalant,
SI,
)

# print("diffusion------------------")
# for scalant, SI in solution_composition["transport"]["diffusion"].items():
# print(
# "\t",
# scalant,
# SI,
# )

# print("transfer number------------------")
# for scalant, SI in solution_composition["transport"][
# "transfer_number"
# ].items():
# print(
# "\t",
# scalant,
# SI,
# )
print("scaling tendendencies------------------")
for scalant, SI in solution_composition["scaling_tendencies"].items():
if scalant == "max":
Expand Down
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