Merge pull request #102 from dlparkhurst/mix_error

Mix error

Author: scharlton2

.github/workflows/cmake.yml

@@ -231,7 +231,7 @@ jobs:
     - name: CTest
       shell: bash
       run: |
-        if [ "${{ inputs.Regression }}" = "true" ]; then
+        if [ "${{ github.event_name }}" = "pull_request" ] || [ "${{ inputs.Regression }}" = "true" ]; then
           echo "Running regression tests..."
           ctest -S ctest.regression.cmake -DCTEST_TEST_TIMEOUT=1200
         else
@@ -240,9 +240,9 @@ jobs:
         fi
 
     - name: Run Optional CMemCheck (Linux)
-      if: runner.os == 'Linux' && (github.event_name == 'schedule' || inputs.CMemCheck == true)
+      if: runner.os == 'Linux' && (github.event_name == 'schedule' || github.event_name == 'pull_request' || inputs.CMemCheck == true)
       run: |
-        if [ "${{ inputs.Regression }}" = "true" ]; then
+        if [ "${{ github.event_name }}" = "pull_request" ] || [ "${{ inputs.Regression }}" = "true" ]; then
           echo "Running CMemCheck Regression tests..."
           ctest -S cmemcheck.regression.cmake -DCTEST_TEST_TIMEOUT=2400
         else

database/Amm.dat

@@ -1,4 +1,4 @@
-# Amm.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.
 
@@ -165,9 +165,9 @@ PO4-3 = PO4-3
 	-dw 0.612e-9
 F- = F-
 	-gamma 3.5 0
-	-Vm 0.928 1.36 6.27 -2.84 1.84 0 0 -0.318 0 1
-	-viscosity 0 2.85e-2 1.35e-2 6.11e-2 4.38e-3 1.384 0.586
-	-dw 1.46e-9 -36 4.352
+	-Vm 2.235 -3.39 7.6 -2.5 1.71 15 -1 -39.3 5.68e-2 0.913 # Majer et al., 1997, JSC 26, 847, with NaF and KF.
+	-viscosity 0 -0.448 4.67e-2 0.46 4.03e-2 -0.057 -2
+	-dw 1.46e-9 -62 5 0.854 1.66
 Br- = Br-
 	-gamma 3 0.045
 	-Vm 6.72 2.85 4.21 -3.14 1.38 0 -9.56e-2 7.08 -1.56e-3 1
@@ -475,8 +475,18 @@ Na+ + HPO4-2 = NaHPO4-
 	-gamma 5.4 0
 	-Vm 5.2 8.1 13 -3 0.9 0 0 1.62e-2 1
 Na+ + F- = NaF
-	-log_k -0.24
-	-Vm 2.7483 -1.0708 6.1709 -2.7347 -.03 # supcrt
+	-gamma 0 0.2
+	-log_k -2.38; -delta_h 24.5
+	-analytic -5 1.159e-2 -250
+	-Vm -0.6 2.14 20 -2.40 -9.6e-2
+	-dw 8e-10
+K+ + F- = KF
+	-gamma 0 -6.3e-3
+	-log_k -0.82; -delta_h 14.5
+	-analytic -1.568 5.87e-3 -234.6
+	-Vm 1.94 -9.2 20 -2.4 2.6e-2
+	-viscosity 0.9 -0.769 -1e-3 2 6.76e-2 -0.889 -2
+	-dw 8e-10
 K+ + HCO3- = KHCO3
 	-log_k -0.35; -delta_h 12 kJ
 	-gamma 0 0.1
@@ -1057,9 +1067,8 @@ Hydroxyapatite
 	-Vm 128.9
 Fluorite
 	CaF2 = Ca+2 + 2 F-
-	-log_k -10.6
-	-delta_h 4.69 kcal
-	-analytic 66.348 0 -4298.2 -25.271
+	-log_k -10.61; -delta_h 10.6
+	-analytic 57.313 0 -3495 -22.714 # Str�bel, 1965, NJbM,M 83-95; Henry, 2018, PhD, Colorado School of Mines.
 	-Vm 15.7
 SiO2(a)
 	SiO2 + 2 H2O = H4SiO4
@@ -1363,9 +1372,9 @@ EXCHANGE_SPECIES
 	-delta_h 1.4 # Merriam & Thomas, 1956
 
 # !!!!!
-#	  H+ + X- = HX # better: active fraction model, see https://hydrochemistry.eu/exmpls/a_f.html
-#	  -log_k  1.0
-#	  -gamma  9.0	0
+#	H+ + X- = HX # better use: active fraction model, see https://hydrochemistry.eu/exmpls/a_f.html 
+#	-log_k  1.0
+#	-gamma  9.0	0
 
 	AmmH+ + X- = AmmHX
 #	NH4+ + X- = NH4X
@@ -1954,10 +1963,11 @@ END
 # For details, consult ref. 1 and subroutine calc_vm(tc, pa) in prep.cpp.
 # =============================================================================================
 # The viscosity is calculated with a (modified) Jones-Dole equation:
-#    viscos / viscos_0 = 1 + A * Sum(0.5 z_i m_i) + fan * Sum(B_i m_i + D_i m_i n_i)
+#    viscos / viscos_0 = 1 + A * Sum(0.5 z_i m_i)^0.5 + fan * Sum(B_i m_i + D_i m_i n_i)
 # Parameters are for calculating the B and D terms:
 #    -viscosity 9.35e-2 -8.31e-2 2.487e-2 4.49e-4 2.01e-2 1.570 0
 #    #	        b0      b1	    b2	   d1	  d2	d3  tan
+#    A = calculated according to Falkenhagen
 #    z_i is absolute charge number, m_i is molality of i
 #    B_i = b0 + b1 exp(-b2 * tc)
 #    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions and neutral species

database/phreeqc.dat

@@ -159,9 +159,9 @@ PO4-3 = PO4-3
 	-dw 0.612e-9
 F- = F-
 	-gamma 3.5 0
-	-Vm 0.928 1.36 6.27 -2.84 1.84 0 0 -0.318 0 1
-	-viscosity 0 2.85e-2 1.35e-2 6.11e-2 4.38e-3 1.384 0.586
-	-dw 1.46e-9 -36 4.352
+	-Vm 2.235 -3.39 7.6 -2.5 1.71 15 -1 -39.3 5.68e-2 0.913 # Majer et al., 1997, JSC 26, 847, with NaF and KF.
+	-viscosity 0 -0.448 4.67e-2 0.46 4.03e-2 -0.057 -2
+	-dw 1.46e-9 -62 5 0.854 1.66
 Br- = Br-
 	-gamma 3 0.045
 	-Vm 6.72 2.85 4.21 -3.14 1.38 0 -9.56e-2 7.08 -1.56e-3 1
@@ -467,8 +467,18 @@ Na+ + HPO4-2 = NaHPO4-
 	-gamma 5.4 0
 	-Vm 5.2 8.1 13 -3 0.9 0 0 1.62e-2 1
 Na+ + F- = NaF
-	-log_k -0.24
-	-Vm 2.7483 -1.0708 6.1709 -2.7347 -.03 # supcrt
+	-gamma 0 0.2
+	-log_k -2.38; -delta_h 24.5
+	-analytic -5 1.159e-2 -250
+	-Vm -0.6 2.14 20 -2.40 -9.6e-2
+	-dw 8e-10
+K+ + F- = KF
+	-gamma 0 -6.3e-3
+	-log_k -0.82; -delta_h 14.5
+	-analytic -1.568 5.87e-3 -234.6
+	-Vm 1.94 -9.2 20 -2.4 2.6e-2
+	-viscosity 0.9 -0.769 -1e-3 2 6.76e-2 -0.889 -2
+	-dw 8e-10
 K+ + HCO3- = KHCO3
 	-log_k -0.35; -delta_h 12 kJ
 	-gamma 0 0.1
@@ -1049,9 +1059,8 @@ Hydroxyapatite
 	-Vm 128.9
 Fluorite
 	CaF2 = Ca+2 + 2 F-
-	-log_k -10.6
-	-delta_h 4.69 kcal
-	-analytic 66.348 0 -4298.2 -25.271
+	-log_k -10.61; -delta_h 10.6
+	-analytic 57.313 0 -3495 -22.714 # Str�bel, 1965, NJbM,M 83-95; Henry, 2018, PhD, Colorado School of Mines.
 	-Vm 15.7
 SiO2(a)
 	SiO2 + 2 H2O = H4SiO4
@@ -1943,10 +1952,11 @@ END
 # For details, consult ref. 1 and subroutine calc_vm(tc, pa) in prep.cpp.
 # =============================================================================================
 # The viscosity is calculated with a (modified) Jones-Dole equation:
-#    viscos / viscos_0 = 1 + A * Sum(0.5 z_i m_i) + fan * Sum(B_i m_i + D_i m_i n_i)
+#    viscos / viscos_0 = 1 + A * Sum(0.5 z_i m_i)^0.5 + fan * Sum(B_i m_i + D_i m_i n_i)
 # Parameters are for calculating the B and D terms:
 #    -viscosity 9.35e-2 -8.31e-2 2.487e-2 4.49e-4 2.01e-2 1.570 0
 #    #	        b0      b1	    b2	   d1	  d2	d3  tan
+#    A = calculated according to Falkenhagen
 #    z_i is absolute charge number, m_i is molality of i
 #    B_i = b0 + b1 exp(-b2 * tc)
 #    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions and neutral species

database/phreeqc_rates.dat

@@ -1,6 +1,20 @@
-# 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.
+# PHREEQC_RATES.DAT for calculating kinetic rates for minerals from compilations by:
+
+# Hermansk�, M., Voigt, M.J., Marieni, C., Declercq, J. and Oelkers, E.H., 2022. A comprehensive and internally consistent mineral dissolution rate database: Part I: Primary silicate minerals and glasses. Chem. Geol., 597, p.120807
+# Hermansk�, M., Voigt, M.J., Marieni, C., Declercq, J. and Oelkers, E.H., 2023. A comprehensive and consistent mineral dissolution rate database: Part II: Secondary silicate minerals. Chem. Geol., p.121632.
+# Palandri, J.L. and Kharaka, J.K., 2004. A compilation of rate parameters of water-mineral interaction kinetics for application to geochemical modeling. USGS Open-File Report 2004-1068, 71 p.
+# Sverdrup, H., Oelkers, E., Erlandsson Lampa, M., Belyazid, S., Kurz, D. and Akselsson, C., 2019. Reviews and syntheses: Weathering of silicate minerals in soils and watersheds: Parameterization of the weathering kinetics module in the PROFILE and ForSAFE models. Biogeosciences Discuss. 1-58.
+
+# For explanation and examples see https://hydrochemistry.eu/exmpls/kin_silicates.html
+
+# Rate parameter blocks were added to PHREEQC.DAT:
+# RATE_PARAMETERS_PK
+# RATE_PARAMETERS_SVD
+# RATE_PARAMETERS_HERMANSKA
+
+# Missing PHASES were copied from ThermoddemV1.10_15Dec2020.dat
+
+# at the end: Example input files with RATES for KINETICS calculations
 
 SOLUTION_MASTER_SPECIES
 #
@@ -159,9 +173,9 @@ PO4-3 = PO4-3
 	-dw 0.612e-9
 F- = F-
 	-gamma 3.5 0
-	-Vm 0.928 1.36 6.27 -2.84 1.84 0 0 -0.318 0 1
-	-viscosity 0 2.85e-2 1.35e-2 6.11e-2 4.38e-3 1.384 0.586
-	-dw 1.46e-9 -36 4.352
+	-Vm 2.235 -3.39 7.6 -2.5 1.71 15 -1 -39.3 5.68e-2 0.913 # Majer et al., 1997, JSC 26, 847, with NaF and KF.
+	-viscosity 0 -0.448 4.67e-2 0.46 4.03e-2 -0.057 -2
+	-dw 1.46e-9 -62 5 0.854 1.66
 Br- = Br-
 	-gamma 3 0.045
 	-Vm 6.72 2.85 4.21 -3.14 1.38 0 -9.56e-2 7.08 -1.56e-3 1
@@ -467,8 +481,18 @@ Na+ + HPO4-2 = NaHPO4-
 	-gamma 5.4 0
 	-Vm 5.2 8.1 13 -3 0.9 0 0 1.62e-2 1
 Na+ + F- = NaF
-	-log_k -0.24
-	-Vm 2.7483 -1.0708 6.1709 -2.7347 -.03 # supcrt
+	-gamma 0 0.2
+	-log_k -2.38; -delta_h 24.5
+	-analytic -5 1.159e-2 -250
+	-Vm -0.6 2.14 20 -2.40 -9.6e-2
+	-dw 8e-10
+K+ + F- = KF
+	-gamma 0 -6.3e-3
+	-log_k -0.82; -delta_h 14.5
+	-analytic -1.568 5.87e-3 -234.6
+	-Vm 1.94 -9.2 20 -2.4 2.6e-2
+	-viscosity 0.9 -0.769 -1e-3 2 6.76e-2 -0.889 -2
+	-dw 8e-10
 K+ + HCO3- = KHCO3
 	-log_k -0.35; -delta_h 12 kJ
 	-gamma 0 0.1
@@ -1049,9 +1073,8 @@ Hydroxyapatite
 	-Vm 128.9
 Fluorite
 	CaF2 = Ca+2 + 2 F-
-	-log_k -10.6
-	-delta_h 4.69 kcal
-	-analytic 66.348 0 -4298.2 -25.271
+	-log_k -10.61; -delta_h 10.6
+	-analytic 57.313 0 -3495 -22.714 # Str�bel, 1965, NJbM,M 83-95; Henry, 2018, PhD, Colorado School of Mines.
 	-Vm 15.7
 SiO2(a)
 	SiO2 + 2 H2O = H4SiO4
@@ -3134,10 +3157,11 @@ Wollastonite    -6.97   700             56      0.4     0       0
 # For details, consult ref. 1 and subroutine calc_vm(tc, pa) in prep.cpp.
 # =============================================================================================
 # The viscosity is calculated with a (modified) Jones-Dole equation:
-#    viscos / viscos_0 = 1 + A * Sum(0.5 z_i m_i) + fan * Sum(B_i m_i + D_i m_i n_i)
+#    viscos / viscos_0 = 1 + A * Sum(0.5 z_i m_i)^0.5 + fan * Sum(B_i m_i + D_i m_i n_i)
 # Parameters are for calculating the B and D terms:
 #    -viscosity 9.35e-2 -8.31e-2 2.487e-2 4.49e-4 2.01e-2 1.570 0
 #    #	        b0      b1	    b2	   d1	  d2	d3  tan
+#    A = calculated according to Falkenhagen
 #    z_i is absolute charge number, m_i is molality of i
 #    B_i = b0 + b1 exp(-b2 * tc)
 #    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions and neutral species

database/pitzer.dat

@@ -1,4 +1,5 @@
-# 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.
 
@@ -92,18 +93,18 @@ Cl- = Cl-
 	-dw 2.033e-9 216 3.16 0.2071 0.7432
 CO3-2 = CO3-2
 	-Vm 6.706 -9.119 -9 -1.888 3.461 2.221 3.977 11.4 -1.519e-2 0.666
-	-viscosity -6.6E-4 0.275 3.26E-2 7E-5 -1E-3 2.24 -1.81
-	-dw 0.955e-9 -81.4 1.975 0.158 0.438
+	-viscosity -3.5e-3 0.272 3.16e-2 2.9e-5 -1e-3 2.5 -1.887
+	-dw 0.955e-9 -83 1.99 0.15 0.4205
 SO4-2 = SO4-2
 	-Vm -7.77 43.17 176 -51.45 3.794 0 4.97 20.5 -5.77e-2 0.45
-	-viscosity -4.1e-2 0.1735 1.308e-2 2.16e-4 2.83e-2 3.375 0.21
-	-dw 1.07e-9 -63 0.397 0.982 1.01
+	-viscosity -0.119 0.297 1.16e-2 5.58e-4 -1e-3 2.497 0.239
+	-dw 1.07e-9 9 0.3554 1.219 1.273
 B(OH)3 = B(OH)3
 	-Vm 7.0643 8.8547 3.5844 -3.1451 -.2 # supcrt
 	-dw 1.1e-9
 Br- = Br-
 	-Vm 6.72 2.85 4.21 -3.14 1.38 0 -9.56e-2 7.08 -1.56e-3 1
-	-viscosity -6.98e-2 -0.141 1.78e-2 0.159 7.76e-3 6.25e-2 0.859
+	-viscosity 0.254 -0.684 2.26e-3 0.399 3.54e-3 9.52e-3 0.753
 	-dw 2.09e-9 208 3.5 0 0.5737
 H4SiO4 = H4SiO4
 	-Vm 10.5 1.7 20 -2.7 0.1291 # supcrt  2*H2O in a1
@@ -128,14 +129,14 @@ H2Sg = H2Sg # H2S
 H2O = OH- + H+
 	-analytic 293.29227 0.1360833 -10576.913 -123.73158 0 -6.996455e-5
 	-Vm -9.66 28.5 80 -22.9 1.89 0 1.09 0 0 1
-	-viscosity -2.26e-2 0.106 2.184e-2  -3.2e-3 0 0.4082 -1.634 # < 5 M Li,Na,KOH
+	-viscosity -2.26e-2 0.106 2.184e-2 -3.2e-3 0 0.4082 -1.634 # < 5 M Li,Na,KOH
  	-dw 5.27e-9 491 1.851 0 0.3256
 CO3-2 + H+ = HCO3-
 	log_k 10.329;  delta_h -3.561 kcal
 	-analytic 107.8975 0.03252849 -5151.79 -38.92561 563713.9
 	-Vm 9.962 -4.891 -19.198 1.101 1.356 0 5 100 -2.608e-2 0.118
-	-viscosity -1.5 1.42 -7E-4 0.259 2.09E-2 0.412 -2.58E-2
-	-dw 1.18e-9 -214 2.164 0 0.173
+	-viscosity -1.5 1.454 -5.45e-4 0.405 2.931e-2 0.4058 -9.24e-3
+	-dw 1.18e-9 -215 2.15 1e-9 0.2866
 CO3-2 + 2 H+ = CO2 + H2O
 	log_k 16.6767
 	delta_h -5.738 kcal
@@ -283,7 +284,7 @@ Chrysotile
 	-log_k 32.2
 	-delta_h -46.8 kcal
 	-analytic 13.248 0 10217.1 -6.1894
-	-Vm 110
+	-Vm 106.6
 Diopside
 	CaMgSi2O6 + 4 H+ = Ca+2 + Mg+2 - 2 H2O + 2 H4SiO4 # llnl.dat
 	log_k 20.96

doc/RELEASE.TXT

@@ -2,23 +2,55 @@ Version @PHREEQC_VER@: @PHREEQC_DATE@
 	-----------------
 	October 13, 2025
 	-----------------
-	PHREEQC:  Updated phreeqc.dat, Amm.dat, and phreeqc_rates.dat.
-	--Additional updates to viscosity and specific conductance.
+	PHREEQC:  
+	Updated PHREEQC.DAT: SOLUTION_SPECIES: F-, NaF, KF, using high P, T using data 
+	from Majer et al., 1997, JSC 26, 847. PHASES: Fluorite, solubility data from 
+	Strübel, 1965, NJbM,M 83-95; Henry, 2018, PhD, Colorado School of Mines.
+
+	Updated PITZER.DAT: SOLUTION_SPECIES: SO4-2
+
+	Updated PHREEQC.DAT: SOLUTION_SPECIES: SO4-2, NaSO4-, Na2SO4, KSO4-, MgSO4, 
+	Mg(SO4)2-2, AmmHSO4-
+
+	Modified viscosity parameters for Br-, using high temperature data from 
+	Abdulagatov and Azizov, 2006, J.S.C. 35, 705 (NaBr), and 2008, J.S.C 37, 3 
+	(KBr). 
 
 	-----------------
 	October 28, 2025
 	-----------------
+	PHREEQC: 
+	Corrected -Vm of K-mica in PHREEQC.DAT.
+
+	Added -Vm and modified -viscosity of SOLUTION_SPECIES HCl in PHREEQC.DAT. 
+
 	PHREEQC: A new option was added to the keyword data block LLNL_AQUEOUS_MODEL_PARAMETERS.
 
 		-use_phreeqc_dha_dhb [True or False]
 
-	True uses alternate pressure- and temperature-dependent formulations for Debye-Hückel A and B 
-	and the density of pure water, which are the same formulations used in phreeqc.dat and pitzer.dat. 
-	In addition, pressure dependence of log Ks through the molar volume parameters (-Vm) of 
-	SOLUTION_SPECIES and PHASES is allowed. False uses the definitions in the LLNL_AQUEOUS_MODEL_PARAMETERS
-	options -dh_a and -dh_b for Debye-Hückel A and B, and -Vm values are not used. If the option is 
-	absent False is assumed, which is consistent with all previous uses of the llnl.dat database. 
-	If the option is defined without True or False, True is assumed.
+-use_phreeqc_dha_dhb True
+
+	--Debye-Hückel A and B values and the density of pure water are calculated 
+		pressure- and temperature-dependent as done with phreeqc.dat and pitzer.dat
+	--the value of bdot can be defined for individual SOLUTE_SPECIES as in 
+		phreeqc.dat with -gamma adot bdot
+	--the density of the solution is calculated using the molar volume 
+		parameters (-Vm) in SOLUTION_SPECIES
+	--the pressure dependence of log K's is calculated from the molar volume 
+		parameters in SOLUTION_SPECIES and PHASES
+
+-use_phreeqc_dha_dhb False
+	--Gives results as previously with a llnl-type database
+	 
+	--Debye-Hückel A and B are calculated temperature-dependent by 
+		interpolating the numbers in -dh_a and -dh_b in the 
+		LLNL_AQUEOUS_MODEL_PARAMETERS.
+
+	--The value of bdot is the same for all aqueous species, from 
+		interpolating the numbers in -bdot in the LLNL_AQUEOUS_MODEL_PARAMETERS.
+		
+	--Vm values are not used for calculating the pressure dependence of 
+		reactions and, if present, solution densities are not correct 
 
 	-----------------
 	October 13, 2025