Author Topic: Question about PhreeqcRM Python examples (AdvectBMI_py.py / SimpleAdvect.py) (Read 631 times)

ZYWTDaEO6 · « **on:** 19/04/25 19:20 »

Dear Parkhurst,

I am currently learning to use PhreeqcRM through the Python examples provided in the swig/python directory.

Specifically, I have run both AdvectBMI_py.py (using the BMI interface) and SimpleAdvect.py (using the native PhreeqcRM interface). In both cases, when I examine the output concentrations, I observe that the values for all chemical species appear to remain constant throughout the entire simulation time. The concentrations in the cells seem identical at t=0 and all subsequent time steps reported.

My expectation was that, particularly in an advection example, I would see changes in concentrations within the cells over time as the initial or boundary solution propagates through the domain.

Thank you very much for your time and expertise.

Code: [Select]

```
Number of threads:                                3
20
Number of components for transport:               8
         H  1.008
         O  16.0
    Charge  1.0
        Ca  40.08
        Cl  35.453
         K  39.102
         N  14.0067
        Na  22.9898

Beginning transport calculation [0.] days
          Time step             [1.] days
Beginning reaction calculation  [1.] days
Beginning transport calculation [1.] days
          Time step             [1.] days
Beginning reaction calculation  [2.] days
Selected output sequence number: 0
Selected output user number:     333
Cell number  0
     Density:    0.9970430229481125
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  1
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  2
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  3
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  4
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  5
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  6
     Density:    0.9970430229481125
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  7
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  8
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  9
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  10
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  11
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  12
     Density:    0.9970430229481125
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  13
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  14
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  15
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  16
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  17
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  18
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  19
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Beginning transport calculation [2.] days
          Time step             [1.] days
Beginning reaction calculation  [3.] days
Selected output sequence number: 0
Selected output user number:     333
Cell number  0
     Density:    0.9970430229481125
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  1
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  2
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  3
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  4
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  5
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  6
     Density:    0.9970430229481125
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  7
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  8
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  9
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  10
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  11
     Density:    0.9983196873286277
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11
7, solution_specific_conductance, 131.01871540268837
8, solution_total_molality_Ca, 0.0
9, solution_total_molality_Cl, 0.0
10, solution_total_molality_H, 111.0124335644499
11, solution_total_molality_H(0), 0.0
12, solution_total_molality_H(1), 0.0
13, solution_total_molality_K, 0.00019689283893444917
14, solution_total_molality_N, 0.0011999999996000533
15, solution_total_molality_N(-3), 0.0
16, solution_total_molality_N(0), 5.774276373580111e-20
17, solution_total_molality_N(3), 1.258138975296026e-16
18, solution_total_molality_N(5), 0.0011999999995999276
19, solution_total_molality_Na, 0.0010031071606652637
20, solution_total_molality_O, 55.51035192033384
21, solution_total_molality_O(-2), 0.0
22, solution_total_molality_O(0), 0.0005351381100779916
23, exchange_total_molality_X, 0.001103310572667991
24, exchange_X_species_log_molality_CaX2, -99.99
25, exchange_X_species_log_molality_KX, -3.9556562321114286
26, exchange_X_species_log_molality_NaX, -3.9615785875174336
27, exchange_X_species_log_molality_X-, 2.694683055658531
Cell number  12
     Density:    0.9970430229481125
     Volume:     0.19975821827868964
     Components: 
0, H: 110.81329495518257
1, O: 55.41077519792159
2, Charge: -3.3889300648929136e-16
3, Ca: 0.0
4, Cl: 0.0
5, K: 0.00019653964456818623
6, N: 0.0011978473908933682
7, Na: 0.0010013077463248419
     Selected output: 
0, solution_ph, 7.081624630524877
1, solution_pe, 13.966528092709469
2, solution_alkalinity, -9.89431379916503e-19
3, solution_ionic_strength, 0.0012000859545712812
4, solution_water_mass, 0.19939988387865468
5, solution_charge_balance, -3.395020189911757e-16
6, solution_percent_error, -1.4144904275313323e-11

dlparkhurst · « **Reply #1 on:** 19/04/25 20:06 »

If you run SimpleAdvect_py.py, a file named SimpleAdvect_py.chem.txt should be generated. The file presents the compositions of cell 0-19 after 10 advection steps. Whereas initially all cells were Na-dominated, you should find a transition from a Ca-dominated solution in cell 0

Code: [Select]

Time:                   10
Chemistry cell:         0
Grid cell(s) (0-based): 0 
------------------------------------
Reading input data for simulation 1.
------------------------------------

	RUN_CELLS
	  -start_time 777600
	  -time_step  86400
	  -cells      0
	END
--------------------------
Beginning of run as cells.
--------------------------

-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------

Reaction step 1.

Using solution 0.	Solution after simulation 1.
Using exchange 0.	Exchange assemblage after simulation 1.

-----------------------------Exchange composition------------------------------

X                2.200e-04 mol

	                               Equiv-    Equivalent      Log 
	Species             Moles      alents      Fraction     Gamma

	CaX2              1.100e-04   2.200e-04   1.000e+00    -0.080
	KX                5.579e-15   5.579e-15   2.536e-11    -0.020
	NaX               9.246e-22   9.246e-22   4.203e-18    -0.020

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

	Elements           Molality       Moles

	Ca                6.000e-04   1.196e-04
	Cl                1.200e-03   2.393e-04
	K                 2.946e-13   5.875e-14
	Na                2.522e-19   5.029e-20

to a Na-dominated solution in cell 19

Code: [Select]

Time:                   10
Chemistry cell:         19
Grid cell(s) (0-based): 19 
------------------------------------
Reading input data for simulation 1.
------------------------------------

	RUN_CELLS
	  -start_time 777600
	  -time_step  86400
	  -cells      19
	END
--------------------------
Beginning of run as cells.
--------------------------

-----------------------------------------
Beginning of batch-reaction calculations.
-----------------------------------------

Reaction step 1.

Using solution 19.	Solution after simulation 1.
Using exchange 19.	Exchange assemblage after simulation 1.

-----------------------------Exchange composition------------------------------

X                2.200e-04 mol

	                               Equiv-    Equivalent      Log 
	Species             Moles      alents      Fraction     Gamma

	KX                1.108e-04   1.108e-04   5.034e-01    -0.017
	NaX               1.092e-04   1.092e-04   4.966e-01    -0.017
	NH4X              3.892e-65   3.892e-65   1.769e-61    -0.017

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

	Elements           Molality       Moles

	K                 1.969e-04   3.926e-05
	N                 1.200e-03   2.393e-04
	Na                1.003e-03   2.000e-04

ZYWTDaEO6 · « **Reply #2 on:** 20/04/25 06:50 »

Hi Parkhurst,

Thank you for your response. After reviewing the SimpleAdvect_py.chem.txt, I can clearly see the transition from the solution in cell 0 to cell 19 after 10 advection steps.

However, When I examine AdvectBMI_py.chem.txt, I still observe that the concentrations seem identical across different cells at the same time step. For example, at Time = 9, the solution compositions reported for Chemistry cells 0, 8, and 19 appear to be exactly the same:

Time: 9
Chemistry cell: 0
Grid cell(s) (0-based): 0 20

Elements Molality Moles

K 1.969e-04 3.926e-05
N 1.200e-03 2.393e-04
Na 1.003e-03 2.000e-04

-------------------------------------------------

Time: 9
Chemistry cell: 8
Grid cell(s) (0-based): 8 28

Elements Molality Moles

K 1.969e-04 3.926e-05
N 1.200e-03 2.393e-04
Na 1.003e-03 2.000e-04

-------------------------------------------------

Time: 9
Chemistry cell: 19
Grid cell(s) (0-based): 19 39

Elements Molality Moles

K 1.969e-04 3.926e-05
N 1.200e-03 2.393e-04
Na 1.003e-03 2.000e-04

This lack of change in the BMI example output is confusing, as I expected to see the same output as SimpleAdvect_py.chem.txt.

My reason for focusing on the BMI interface is that I need to extract detailed output, specifically mineral phase information, at each output time step. I recall reading in other forum posts that the BMI interface might be necessary and more suitable for this task.

My questions: Why the AdvectBMI_py.py example might not be showing the expected concentration changes in its .chem.txt output?

Thanks again for your help and expertise.

dlparkhurst · « **Reply #3 on:** 21/04/25 00:01 »

The file AdvectBMI_py.py was contributed by a user, and I apparently did not check it carefully enough (plus my Python abilities are limited). They used a pointer for concentrations, which works in one direction, in that the values of c (concentration) in Python are always equal to the concentrations in PhreeqcRM. However, setting values of c in Python through the pointer does not set values of concentrations in PhreeqcRM; a call to set_value("Concentrations") is required.

The following should cause Ca to be transported through the column. The differences (I think 4 lines of code) are all related to the variable c in three places. I have used c as an array rather than a pointer, except in the output section.

Code: [Select]

def AdvectBMI_py():

	# Based on PHREEQC Example 11

	# --------------------------------------------------------------------------
	# Create PhreeqcRM
	# --------------------------------------------------------------------------
	yaml_file = FilePaths.YAML
	
	# phreeqc_rm.GetGridCellCountYAML must be called BEFORE
	# the PhreeqcRM instance is created. The
	# return value can be used to create the
	# PhreeqcRM instance.
	#
	# If the YAML file does not contain
	# a node "SetGridCellCount:" (usually written
	# using the YAMLPhreeqcRM class and the method
	# YAMLSetGridCellCount), the return
	# value is zero.
	###nxyz = GetGridCellCountYAML(yaml_file)
	#nxyz = 40
	# Bogus conductivity field for Basic callback demonstration
	#hydraulic_K = [i*2.0 for i in range(nxyz)] 
	#nthreads = 3
	
	##bmi = phreeqcrm.BMIPhreeqcRM()
	bmi = AdvectBMI(yaml_file)

	# Initialize with YAML file
	##status = bmi.initialize(yaml_file)

    # Demonstrate add to Basic: Set a function for Basic CALLBACK after LoadDatabase
    #TODO CALL register_basic_callback_fortran()
#ifdef USE_MPI
    # Optional callback for MPI
    #TODO status = do_something()   # only root is calling do_something here
#endif

	# print(bmi.get_pointable_var_names())

	components = bmi.get_value_ptr("Components")
	ncomps = bmi.get_value_ptr("ComponentCount")[0]
	nxyz = bmi.get_value_ptr("GridCellCount")[0]

	# print(components)
	# print(ncomps)
	# print(nxyz)

	time = bmi.get_value_ptr("Time")
	time_step = bmi.get_value_ptr("TimeStep")


	hydraulic_K = [0.0] * nxyz
	for i in range(nxyz):
		hydraulic_K[i] = i*2.0

	nthreads = bmi.GetThreadCount()

	print(f"Number of threads:                                {nthreads}")

	nbytes = bmi.get_var_nbytes("FilePrefix")
	dest = np.full(1, " " * nbytes)
	prefix = bmi.get_value('FilePrefix', dest)[0]

	nchem = bmi.GetChemistryCellCount()
	print(nchem)

	print(f"Number of components for transport:               {ncomps}")

	# Get component information)
	gfw = bmi.get_value_ptr("Gfw")
	for i in range(ncomps):
		print(f"{components[i].rjust(10,' ')}  {gfw[i]}")
	print()

	# Get initial temperatures
	temperature = bmi.get_value_ptr("Temperature")
	# Get initial saturation
	sat = bmi.get_value_ptr("SaturationCalculated")
	# Get initial porosity
	por = bmi.get_value_ptr("Porosity")

	# print(temperature)
	# print(sat)
	# print(por)

	# Get initial volume
	volume = bmi.get_value_ptr("SolutionVolume")
	# Get initial concentrations
	#c = bmi.get_value_ptr("Concentrations")
	dest = np.empty(nxyz*ncomps, dtype=float)
	c = bmi.get_value("Concentrations", dest)

	# print("volume")
	# print(volume)
	# print("c")
	# print(c)

	# Set density, pressure, and temperature
	density = [1.0] * nxyz
	bmi.set_value("DensityUser", density)
	pressure = [2.0] * nxyz
	bmi.set_value("Pressure", pressure)
	temperature = [20.0] * nxyz
	bmi.set_value("Temperature", temperature)

    # --------------------------------------------------------------------------
    # Set boundary condition
    # --------------------------------------------------------------------------
	nbound = 1
	bc1 = [0]           # solution 0 from Initial IPhreeqc instance
	bc2 = [-1]          # no bc2 solution for mixing
	bc_f1 = [1.0]       # mixing fraction for bc1

	bc_conc = bmi.InitialPhreeqc2Concentrations(bc1)

	bmi.SetScreenOn(True)
	time[0] = 0.0
	time_step[0] = 86400.0

	# --------------------------------------------------------------------------
	# Transient loop
	# --------------------------------------------------------------------------
	dummy_int_scalar = np.empty((1,), dtype=int)
	selected_output = bmi.get_value_ptr("SelectedOutputOn")
	nsteps = 10
	for step in range(nsteps):
		print(f"Beginning transport calculation {time*bmi.GetTimeConversion()} days")
		print(f"          Time step             {time_step*bmi.GetTimeConversion()} days")

		advectionbmi_py(c, bc_conc, ncomps, nxyz, nbound)

		if (step == (nsteps - 1)):
			print_chemistry_on = 1
		else:
			print_chemistry_on = 0
		selected_output[0] = print_chemistry_on

		bmi.SetPrintChemistryOn(print_chemistry_on==1, False, False)  # workers, initial_phreeqc, utility
		time[0] += time_step
		# bmi.set_value("Time", time)

		# Optionally, if values changed during transport
		##bmi.set_value("Porosity", por)
		bmi.set_value("SaturationUser", sat)
		##bmi.set_value("Temperature", temperature)
		##bmi.set_value("Pressure", pressure)
		##bmi.set_value("TimeStep", time_step)
		
		# Run cells with transported conditions
		print(f"Beginning reaction calculation  {time*bmi.GetTimeConversion()} days")
		bmi.set_value("Concentrations", c)
		bmi.update()
		bmi.get_value("Concentrations", c)

		# Print results at last time step
		if (step == (nsteps - 1)):
			bmi.display_results()

	# Clean up
	bmi.finalize()
	print("Done.")

As an aside, I think BMI has some shortcomings. They seem to think that data is laid out in nice contiguous blocks that can be pointed to, whereas a parallel program may have data that needs to be assembled from multiple storage areas or even different processors. In addition, the use of void pointers to pass data of different types can be error prone and possibly nonstandard.

ZYWTDaEO6 · « **Reply #4 on:** 21/04/25 05:49 »

Hi Parkhurst,

Thanks a lot for pointing out the need to call `set_value("Concentrations", c)` in the BMI example, after making that change I do see concentration changes over time.

I actually prefer the native PhreeqcRM interface because it's more straightforward to me. However, my main goal is to extract the remaining mineral amounts after each reaction step.

From previous forum discussions I got the impression that only the BMI interface lets me pull out per-time‑step mineral data. Is that still the case?

Thanks again for all your help!

dlparkhurst · « **Reply #5 on:** 21/04/25 06:19 »

If you instantiate a BMIPhreeqcRM instance, you can still use all the native PhreeqcRM methods for doing the simulations. BMI simply adds methods, including being able to use get_value for mineral amounts and other data.

If the values that you want are not available with get_value (see add_output_vars), then you can always use SELECTED_OUTPUT and USER_PUNCH to obtain almost any result and customized results (units conversion ,for example) with the PhreeqcRM method GetSelectedOutput and related methods.

ZYWTDaEO6 · « **Reply #6 on:** 21/04/25 17:19 »

Hi Parkhurst,

Thank you so much for all your detailed explanations and suggestions. After our discussion I switched to PhreeqcRM?s native interface and have now successfully coupled it with MODFLOW ? the transport and reaction steps run as expected and I?m able to extract the mineral amounts after each step.

I really appreciate your time and expertise in helping me get this working.

Author Topic: Question about PhreeqcRM Python examples (AdvectBMI_py.py / SimpleAdvect.py) (Read 631 times)

ZYWTDaEO6

Question about PhreeqcRM Python examples (AdvectBMI_py.py / SimpleAdvect.py)

dlparkhurst

Re: Question about PhreeqcRM Python examples (AdvectBMI_py.py / SimpleAdvect.py)

ZYWTDaEO6

Re: Question about PhreeqcRM Python examples (AdvectBMI_py.py / SimpleAdvect.py)

dlparkhurst

Re: Question about PhreeqcRM Python examples (AdvectBMI_py.py / SimpleAdvect.py)

ZYWTDaEO6

Re: Question about PhreeqcRM Python examples (AdvectBMI_py.py / SimpleAdvect.py)

dlparkhurst

Re: Question about PhreeqcRM Python examples (AdvectBMI_py.py / SimpleAdvect.py)

ZYWTDaEO6

Re: Question about PhreeqcRM Python examples (AdvectBMI_py.py / SimpleAdvect.py)