Merge pull request #90 from dlparkhurst/mix_error

Mix error

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.
 

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).

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*).

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

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.
 

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.
 

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.
 

examples/Makefile.am

@@ -8,6 +8,8 @@ examplesdir = $(docdir)/examples
 dist_examples_DATA = $(EXAMPLES)
 
 EXAMPLES= \
+	co2.dat \
+	co2_VP.dat \
 	co2.tsv \
 	ex1 \
 	ex2 \

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

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

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

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

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

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

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

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

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

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

examples/ex20b

@@ -96,6 +96,7 @@ USER_PUNCH
 END
 PRINT
 	-selected_output false
+	-warnings        0
 END
 INCLUDE$ ex20_open
 END

examples/ex21

@@ -357,5 +357,6 @@ USER_PUNCH
 END
 PRINT
  -selected_out false
+ -status       false
 INCLUDE$ radial
 END

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

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

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(); */

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++)