diff --git a/database/Amm.dat b/database/Amm.dat index d38840e9..c095a395 100644 --- a/database/Amm.dat +++ b/database/Amm.dat @@ -1,4 +1,4 @@ -# PHREEQC.DAT for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Based on: +# Amm.dat for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Based on: # diffusion coefficients and molal volumina of aqueous species, solubility and volume of minerals, and critical temperatures and pressures of gases in Peng-Robinson's EOS. # Details are given at the end of this file. diff --git a/database/Kinec.v2.dat b/database/Kinec.v2.dat index e4c1339b..e3cb6865 100644 --- a/database/Kinec.v2.dat +++ b/database/Kinec.v2.dat @@ -1,4 +1,4 @@ -# KINEC.v2.dat - last edited April 18, 2024 by MA and EHO. +# Kinec.v2.dat - last edited April 18, 2024 by MA and EHO. # # This database contains the parameters for calculating mineral dissolution rates for primary and secondary silicate minerals using the equations and parameters reported by Hermanska et al. (2022, 2023), # and dissolution rates for other non)-silicate mineral systems using the equations and parameters reported by Oelkers and Addassi (2024, in preparation). diff --git a/database/Kinec_v3.dat b/database/Kinec_v3.dat index fd613fd7..8a753756 100644 --- a/database/Kinec_v3.dat +++ b/database/Kinec_v3.dat @@ -1,4 +1,4 @@ -# KINEC_v3.dat - last edited July 23, 2024 by MA and EHO. +# Kinec_v3.dat - last edited July 23, 2024 by MA and EHO. # # This database contains the parameters for calculating mineral dissolution rates for primary and secondary silicate minerals using the equations and parameters reported by Hermanska et al. (2022, 2023), # and dissolution rates for other mineral systems using the equations and parameters reported by Oelkers and addassi (2024*). diff --git a/database/Tipping_Hurley.dat b/database/Tipping_Hurley.dat index 471fe128..ea61af2b 100644 --- a/database/Tipping_Hurley.dat +++ b/database/Tipping_Hurley.dat @@ -2,7 +2,6 @@ # Created 17 May 2024 14:30:44 # c:\3rdParty\lsp\lsp.exe -f2 -k="asis" -ts "Tipping_Hurley.dat" -# $Id: wateq4f.dat 6895 2012-08-21 18:10:05Z dlpark $ # Revised arsenic data from Archer and Nordstrom (2002) SOLUTION_MASTER_SPECIES diff --git a/database/phreeqc.dat b/database/phreeqc.dat index 01cdbe3c..d89cef0d 100644 --- a/database/phreeqc.dat +++ b/database/phreeqc.dat @@ -1,8 +1,8 @@ -# File 1 = C:\GitPrograms\phreeqc3-1\database\Amm.dat, 22/05/2024 19:38, 1948 lines, 55817 bytes, md5=78b3659799b73ddca128328b6ee7533b +# File 1 = C:\GitPrograms\phreeqc3-1\database\phreeqc.dat, 22/05/2024 19:38, 1948 lines, 55817 bytes, md5=78b3659799b73ddca128328b6ee7533b # Created 22 May 2024 19:55:37 -# C:\3rdParty\lsp\lsp.exe -f2 -k=asis -ts Amm.dat +# C:\3rdParty\lsp\lsp.exe -f2 -k=asis -ts phreeqc.dat -# PHREEQC.DAT for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Based on: +# phreeqc.dat for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Based on: # diffusion coefficients and molal volumina of aqueous species, solubility and volume of minerals, and critical temperatures and pressures of gases in Peng-Robinson's EOS. # Details are given at the end of this file. diff --git a/database/phreeqc_rates.dat b/database/phreeqc_rates.dat index 2c777a45..2721908d 100644 --- a/database/phreeqc_rates.dat +++ b/database/phreeqc_rates.dat @@ -1,4 +1,4 @@ -# PHREEQC.DAT for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Augmented with kinetic rates for minerals from compilations. Based on: +# phreeqc_rates.dat for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Augmented with kinetic rates for minerals from compilations. Based on: # diffusion coefficients and molal volumina of aqueous species, solubility and volume of minerals, and critical temperatures and pressures of gases in Peng-Robinson's EOS. # Details are given at the end of this file. diff --git a/database/pitzer.dat b/database/pitzer.dat index eb1c87f2..d18b8023 100644 --- a/database/pitzer.dat +++ b/database/pitzer.dat @@ -1,4 +1,4 @@ -# Pitzer.DAT for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution, using +# pitzer.dat for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution, using # diffusion coefficients of species, molal volumina of aqueous species and minerals, and critical temperatures and pressures of gases used in Peng-Robinson's EOS. # Details are given at the end of this file. diff --git a/examples/Makefile.am b/examples/Makefile.am index 2987311e..39faa04d 100644 --- a/examples/Makefile.am +++ b/examples/Makefile.am @@ -8,6 +8,8 @@ examplesdir = $(docdir)/examples dist_examples_DATA = $(EXAMPLES) EXAMPLES= \ + co2.dat \ + co2_VP.dat \ co2.tsv \ ex1 \ ex2 \ diff --git a/examples/ex11 b/examples/ex11 index 963492ce..4e79007a 100644 --- a/examples/ex11 +++ b/examples/ex11 @@ -58,13 +58,13 @@ USER_GRAPH 1 END TRANSPORT -cells 40 - -lengths 0.002 + -lengths 40*0.002 -shifts 100 -time_step 720.0 -flow_direction forward -boundary_conditions flux flux -diffusion_coefficient 0.0e-9 - -dispersivities 0.002 + -dispersivities 40*0.002 -correct_disp true -punch_cells 40 -punch_frequency 1 diff --git a/examples/ex12 b/examples/ex12 index ec562301..512e4b75 100644 --- a/examples/ex12 +++ b/examples/ex12 @@ -47,8 +47,8 @@ TRANSPORT # Make column temperature 0C, displace Cl -shifts 60 -flow_direction forward -boundary_conditions flux flux - -lengths 0.333333 - -dispersivities 0.0 # No dispersion + -lengths 60*0.333333 + -dispersivities 60*0.0 # No dispersion -diffusion_coefficient 0.0 # No diffusion -thermal_diffusion 1.0 # No retardation for heat END diff --git a/examples/ex12a b/examples/ex12a index cfbe4262..d0209b7c 100644 --- a/examples/ex12a +++ b/examples/ex12a @@ -56,9 +56,9 @@ TRANSPORT # Diffuse 24C, NaCl solution from column ends -shifts 1 -flow_direction diffusion -boundary_conditions constant closed - -lengths 1.0 + -lengths 20*1.0 -thermal_diffusion 3.0 # Heat is retarded equal to Na - -dispersivities 0.0 # No dispersion + -dispersivities 20*0.0 # No dispersion -diffusion_coefficient 0.3e-9 # m^2/s -time_step 1.0e+10 # 317 years, 19 substeps will be used SELECTED_OUTPUT @@ -121,7 +121,8 @@ END # TRANSPORT # no need to redefine parameters that don't change from 20 cell model -cells 60 - -lengths 0.33333333333333333 + -lengths 60*0.33333333333333333 + -disp 60*0.0 -punch_cells 1-60 SELECTED_OUTPUT -active true # See also PRINT; selected_output false diff --git a/examples/ex13a b/examples/ex13a index 129b568c..97d393df 100644 --- a/examples/ex13a +++ b/examples/ex13a @@ -34,8 +34,8 @@ TRANSPORT -time_step 3600 -boundary_conditions flux flux -diffusion_coefficient 0.0 - -lengths 0.1 - -dispersivities 0.015 + -lengths 20*0.1 + -dispersivities 20*0.015 -stagnant 1 6.8e-6 0.3 0.1 # 1 stagnant layer^, ^alpha, ^epsil(m), ^epsil(im) END diff --git a/examples/ex13ac b/examples/ex13ac index eeb735ac..2f5b8d8f 100644 --- a/examples/ex13ac +++ b/examples/ex13ac @@ -34,8 +34,8 @@ TRANSPORT -time_step 3600 -boundary_conditions flux flux -diffusion_coefficient 0.0 - -lengths 0.1 - -dispersivities 0.015 + -lengths 20*0.1 + -dispersivities 20*0.015 -stagnant 1 6.8e-6 0.3 0.1 # 1 stagnant layer^, ^alpha, ^epsil(m), ^epsil(im) END @@ -228,8 +228,8 @@ TRANSPORT -time_step 3600 -boundary_conditions flux flux -diffusion_coefficient 0.0 - -lengths 0.1 - -dispersivities 0.015 + -lengths 20*0.1 + -dispersivities 20*0.015 -stagnant 5 END SOLUTION 0 # Original solution reenters diff --git a/examples/ex13b b/examples/ex13b index 259d0236..500f8a3d 100644 --- a/examples/ex13b +++ b/examples/ex13b @@ -55,8 +55,8 @@ TRANSPORT -time_step 3600 -boundary_conditions flux flux -diffusion_coefficient 0.0 - -lengths 0.1 - -dispersivities 0.015 + -lengths 20*0.1 + -dispersivities 20*0.015 -stagnant 1 END SOLUTION 0 # Original solution reenters diff --git a/examples/ex13c b/examples/ex13c index f5abdca9..49cf2903 100644 --- a/examples/ex13c +++ b/examples/ex13c @@ -155,8 +155,8 @@ TRANSPORT -time_step 3600 -boundary_conditions flux flux -diffusion_coefficient 0.0 - -lengths 0.1 - -dispersivities 0.015 + -lengths 20*0.1 + -dispersivities 20*0.015 -stagnant 5 END SOLUTION 0 # Original solution reenters diff --git a/examples/ex15 b/examples/ex15 index c6b73165..61a92d25 100644 --- a/examples/ex15 +++ b/examples/ex15 @@ -135,12 +135,12 @@ USER_GRAPH 2 Example 15 -end -end TRANSPORT First 20 hours have NTA and cobalt in infilling solution -cells 10 - -lengths 1 + -lengths 10*1 -shifts 20 -time_step 3600 -flow_direction forward -boundary_conditions flux flux - -dispersivities .05 + -dispersivities 10*.05 -correct_disp true -diffusion_coefficient 0.0 -punch_cells 10 @@ -183,13 +183,13 @@ USER_GRAPH 2 -end TRANSPORT First 20 hours have NTA and cobalt in infilling solution -cells 20 - -lengths 0.5 + -lengths 20*0.5 -shifts 40 -initial_time 0 -time_step 1800 -flow_direction forward -boundary_conditions flux flux - -dispersivities .05 + -dispersivities 20*.05 -correct_disp true -diffusion_coefficient 0.0 -punch_cells 20 diff --git a/examples/ex15a b/examples/ex15a index aa49f946..05baccd3 100644 --- a/examples/ex15a +++ b/examples/ex15a @@ -118,12 +118,12 @@ USER_GRAPH Example 15A -end TRANSPORT First 20 hours have NTA and cobalt in infilling solution -cells 10 - -lengths 1 + -lengths 10*1 -shifts 20 -time_step 3600 -flow_direction forward -boundary_conditions flux flux - -dispersivities .05 + -dispersivities 10*.05 -correct_disp true -diffusion_coefficient 0.0 -punch_cells 10 @@ -156,13 +156,13 @@ USER_GRAPH -end TRANSPORT First 20 hours have NTA and cobalt in infilling solution -cells 20 - -lengths 0.5 + -lengths 20*0.5 -shifts 40 -initial_time 0 -time_step 1800 -flow_direction forward -boundary_conditions flux flux - -dispersivities .05 + -dispersivities 20*.05 -correct_disp true -diffusion_coefficient 0.0 -punch_cells 20 diff --git a/examples/ex15b b/examples/ex15b index 219074e7..e836b898 100644 --- a/examples/ex15b +++ b/examples/ex15b @@ -103,12 +103,12 @@ USER_PUNCH -end TRANSPORT First 20 hours have NTA and cobalt in infilling solution -cells 10 - -lengths 1 + -lengths 10*1 -shifts 20 -time_step 3600 -flow_direction forward -boundary_conditions flux flux - -dispersivities .05 + -dispersivities 10*.05 -correct_disp true -diffusion_coefficient 0.0 -punch_cells 10 @@ -147,13 +147,13 @@ USER_PUNCH -end TRANSPORT First 20 hours have NTA and cobalt in infilling solution -cells 20 - -lengths 0.5 + -lengths 20*0.5 -shifts 40 -initial_time 0 -time_step 1800 -flow_direction forward -boundary_conditions flux flux - -dispersivities .05 + -dispersivities 20*.05 -correct_disp true -diffusion_coefficient 0.0 -punch_cells 20 diff --git a/examples/ex20b b/examples/ex20b index 9fc9687c..52fbd08b 100644 --- a/examples/ex20b +++ b/examples/ex20b @@ -96,6 +96,7 @@ USER_PUNCH END PRINT -selected_output false + -warnings 0 END INCLUDE$ ex20_open END diff --git a/examples/ex21 b/examples/ex21 index e255d814..6ba0a3c8 100644 --- a/examples/ex21 +++ b/examples/ex21 @@ -357,5 +357,6 @@ USER_PUNCH END PRINT -selected_out false + -status false INCLUDE$ radial END diff --git a/examples/ex22 b/examples/ex22 index 7309ad8e..5dc3a51e 100644 --- a/examples/ex22 +++ b/examples/ex22 @@ -1,6 +1,8 @@ TITLE Example 22.--Compare experimental CO2 solubilities at high CO2 pressure with Peng-Robinson calc`ns with fixed-volume gas_phase, 25, 50, 75, 100, 150 oC. #PRINT; -reset false +PRINT +-warnings 0 SOLUTION 1 GAS_PHASE 1 -fixed_volume diff --git a/examples/ex9 b/examples/ex9 index 48855840..cd34f3fe 100644 --- a/examples/ex9 +++ b/examples/ex9 @@ -96,6 +96,8 @@ Goethite Fe_triOOH + 3 H+ = Fe_tri+3 + 2 H2O log_k -1.0 END +PRINT +-warnings 0 SOLUTION 1 pH 7.0 pe 10.0 O2(g) -0.67 diff --git a/src/mainsubs.cpp b/src/mainsubs.cpp index ba317af0..11ee782d 100644 --- a/src/mainsubs.cpp +++ b/src/mainsubs.cpp @@ -681,9 +681,15 @@ initial_gas_phases(int print) if (pr.user_print) print_user_print(); if (PR /*&& use.Get_gas_phase_ptr()->total_p > 1.0*/) - warning_msg("While initializing gas phase composition by equilibrating:\n" - " Found definitions of gas` critical temperature and pressure.\n" - " Going to use Peng-Robinson in subsequent calculations.\n"); + { + std::ostringstream msg; + msg << "\nWhile initializing gas phase composition by equilibrating:\n"; + msg << " Found definitions of gas critical temperature and pressure.\n"; + msg << " Going to use Peng-Robinson in subsequent calculations.\n"; + screen_msg(msg.str().c_str()); + output_msg(msg.str().c_str()); + log_msg(msg.str().c_str()); + } xgas_save(n_user); punch_all(); /* free_model_allocs(); */ diff --git a/src/transport.cpp b/src/transport.cpp index 7bde99d4..f7ee9b4e 100644 --- a/src/transport.cpp +++ b/src/transport.cpp @@ -508,13 +508,17 @@ transport(void) /* * Now transport */ - if (implicit) - snprintf(token, sizeof(token), "\nCalculating implicit transport: %d (mobile) cells, %d shifts, %d mixruns, max. mixf = %g.\n\n", - count_cells, count_shifts - transport_start + 1, nmix, max_mixf); - else - snprintf(token, sizeof(token), "\nCalculating transport: %d (mobile) cells, %d shifts, %d mixruns...\n\n", - count_cells, count_shifts - transport_start + 1, nmix); - warning_msg(token); + { + if (implicit) + snprintf(token, sizeof(token), "\nCalculating implicit transport: %d (mobile) cells, %d shifts, %d mixruns, max. mixf = %g.\n\n", + count_cells, count_shifts - transport_start + 1, nmix, max_mixf); + else + snprintf(token, sizeof(token), "\nCalculating transport: %d (mobile) cells, %d shifts, %d mixruns...\n\n", + count_cells, count_shifts - transport_start + 1, nmix); + screen_msg(token); + output_msg(token); + log_msg(token); + } max_iter = 0; for (transport_step = transport_start; transport_step <= count_shifts; transport_step++)