mirror of
https://git.gfz-potsdam.de/naaice/iphreeqc.git
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Merge commit 'e9737db628620156e968e184e2a42a7bdffc408f'
This commit is contained in:
Darth Vader
commit
7e117b6c66
@ -41,12 +41,16 @@ trigger-downstream:
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script:
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- echo triggering iphreeqc
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- curl -X POST -F token=${IPHREEQC_TRIGGER} -F ref=master https://code.chs.usgs.gov/api/v4/projects/${IPHREEQC_ID}/trigger/pipeline
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- sleep 180
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- echo triggering iphreeqccom
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- curl -X POST -F token=${IPHREEQCCOM_TRIGGER} -F ref=master https://code.chs.usgs.gov/api/v4/projects/${IPHREEQCCOM_ID}/trigger/pipeline
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- sleep 120
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- echo triggering phast3-doc PHAST3_DOC_TRIGGER PHAST3_DOC_ID
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- curl -X POST -F token=${PHAST3_DOC_TRIGGER} -F ref=master https://code.chs.usgs.gov/api/v4/projects/${PHAST3_DOC_ID}/trigger/pipeline
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- sleep 180
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- echo triggering phreeqc3 PHREEQC3_TRIGGER PHREEQC3_ID
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- curl -X POST -F token=${PHREEQC3_TRIGGER} -F ref=master https://code.chs.usgs.gov/api/v4/projects/${PHREEQC3_ID}/trigger/pipeline
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- sleep 360
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## Upstream Projects
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## none
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@ -1,4 +1,211 @@
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Version @PHREEQC_VER@: @PHREEQC_DATE@
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-----------------
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May 22, 2023
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-----------------
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PHREEQC: (See https://hydrochemistry.eu/ph3/release.html for html version of changes.)
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Added Basic function f_visc("H+") that returns the fractional contribution of a species to
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viscosity of the solution when parameters are defined for the species with -viscosity.
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Actually, it gives the contribution of the species to the B and D terms in the Jones-Dole
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eqution, assuming that the A term is small. The fractional contribution can be negative, for
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example f_visc("K+") is usually smaller than zero.
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Bug-fix: When -Vm parameters of SOLUTION_SPECIES were read after -viscosity parameters, the
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first viscosity parameter was set to 0.
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Defined -analytical_expression and -gamma for Na2SO4, K2SO4 and MgSO4 and Mg(SO4)22- species in
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PHREEQC.dat, fitting the activities from pitzer.dat from 0 - 200 °C, and the solubilities of
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mirabilite/thenardite (Na2SO4), arcanite (K2SO4), and epsomite, hexahydrite, kieserite (MgSO4
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and new species Mg(SO4)22-). The parameters for calculating the apparent volume (-Vm) and the
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diffusion coefficients (-Dw) of the species were adapted using measured data of density and
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conductance (SC).
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Removed the NaCO3- species in PHREEQC.dat since they are not necessary for the calculation of
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the specific conductance (SC) and their origin is unknown. Defined parameters in the
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-analytical_expression, -gamma, -dw, -Vm and -viscosity for the NaHCO3 species in PHREEQC.dat,
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using the data in Appelo, 2015, Appl. Geochem. 55, 62-71. (These data were used for defining
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interaction parameters in pitzer.dat.) The parameters for the apparent volume (-Vm), the
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diffusion coefficient (-Dw) and the viscosity of CO32- and HCO3- were adapted using measured
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data of density, conductance and viscosity of binary solutions.
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The viscosity of the solution at P, T is now calculated and printed in the output file, and can
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be retrieved in Basic programs with the function viscos (in previous versions, viscos returned
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the viscosity of pure water at P, T).
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The calculation uses a modified Jones-Dole equation which sums the contributions of individual
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solutes:
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eta / eta0 = 1 + A sqrt(0.5 sum(zi*mi)) + sum fan (Bi*mi + Di*mi*ni),
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where eta is the viscosity of the solution (mPa s), eta0 is viscosity of pure water at the
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temperature and pressure of the solution, mi is the molality of species i, made dimensionless
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by dividing by 1 molal, and zi is the absolute charge number. A is derived from Debye-Hückel
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theory, and fan, B, D and n are coefficients that incorporate volume, ionic strength and
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temperature effects. The coefficients are:
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B = b0 + b1 exp(-b2 tC)
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where b0, b1, and b2 are coefficients, and tC is the temperature in ºC. The temperature is
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limited to 200°C.
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fan = (2 - tan * Van / VCl-)
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for anions, with tan a coefficient and Van the P, T and I dependent, apparent volume of the
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anion relative to the one of Cl-, which is used as reference species. For cations, fan = 1
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and tan need not be defined.
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D = d1 exp(-d2 tC)
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where d1 and d2 are coefficients.
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n = ((1 + fI)^d3 + ((zi^2 + zi) / 2 * mi)^d3 / (2 + fI)
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where fI averages ionic strength effects and d3 is a parameter.
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The coefficients are fitted on measured viscosities of binary solutions and entered
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with item -viscosity under keyword SOLUTION_SPECIES, for example for H+:
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SOLUTION_SPECIES
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H+ = H+
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-viscosity 9.35e-2 -8.31e-2 2.487e-2 4.49e-4 2.01e-2 1.570 0
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# b0 b1 b2 d1 d2 d3 tan
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When the solute concentrations are seawater-like or higher, the viscosity is different
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from pure water (see figure at). To obtain a valid model for natural waters with phreeqc.dat,
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the complexes of SO42- with the major cations were redefined, as noted above.
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The A parameter in the Jones-Dole equation needs temperature dependent diffusion coefficients of the species, and therefore the parameters for calculating the I and T dependency of the diffusion coefficients (-dw parameters of SOLUTION_SPECIES) were refitted for SO42- and CO32- species.
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Example files are in c:\phreeqc\viscosity.
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Implicit calculations with option -fix_current will now account for changing concentrations in
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the boundary solutions of the column.
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Activated the print of statements defined in USER_PRINT when the initial EXCHANGE, SURFACE and
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GAS_PHASE are calculated.
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Changed the dw_t parameter for CO3-2 to 30 (was 0) and for HCO3- to -150 (was 0) to better fit
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McCleskey's data
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Bug fix: removed the factor (TK / 298.15) from the calculation of the temperature dependence of
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the diffusion coefficient. For an example, see the calculation of Dw(TK) of H+ in the next
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paragraph.
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Bug fixes in printing/punching of diffusion coefficients with diff_c and setdiff_c: the numbers
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are now corrected for I and T effects when the appropriate factors are defined in keyword
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SOLUTION_SPECIES, item -dw. For example:
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H+ = H+
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-gamma 9.0 0
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-dw 9.31e-9 1000 0.46 1e-10 # The dw parameters are defined in Appelo, 2017, CCR 101, 102-113.
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It will set Dw(TK) = 9.31e-9 * exp(1000 / TK - 1000 / 298.15) * viscos_0_25 / viscos_0_tc
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and Dw(I) = Dw(TK) * exp(-0.46 * DH_A * |zi| * I 0.5 / (1 + DH_B * I 0.5 * 1e-10 / (1 + I 0.75))),
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where viscos_0_25 is the viscosity of pure water at 25 °C, viscos_0_tc is the viscosity of pure
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water at the temperature of the solution. DH_A and DH_B are Debye-Hückel parameters,
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retrievable with PHREEQC Basic.
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The temperature correction is always applied in multicomponent, diffusive transport and for
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calculating the viscosity.
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The ionic strength correction is for electromigration calculations (Appelo, 2017, CCR 101, 102). The correction is applied when the option is set true in TRANSPORT, item -multi_D:
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-multi_d true 1e-9 0.3 0.05 1.0 true # multicomponent diffusion
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# true/false, default tracer diffusion coefficient (Dw = 1e-9 m2/s) in water at 25 °C (used in
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case -dw is not defined for a species), porosity (por = 0.3), limiting porosity (0.05) below
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which diffusion stops, exponent n (1.0) used in calculating the porewater diffusion coefficient
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Dp = Dw * por^n, true/false: correct Dw for ionic strength (false by default).
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-----------------
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May 19, 2023
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-----------------
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PhreeqcRM:
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Renamed GetDensity and related functions to GetDensityCalculated.
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Renamed SetDensity and related functions to SetDensityUser.
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Density is used to convert user-model concentrations to module solution definitions only if the
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units of the user-model concentrations are specified to be parts per million. The density specified by
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SetDensityUser is used by SetConcentrations to convert from per kg of solution to
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per L of solution. For GetConcentrations, two options are available to convert from module solutions
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to user-model concentrations, depending on the value used for the method SetUseSolutionDensityVolume:
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(1) the module-calculated density is used to convert from the calculated volume of solution
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to the mass (kg) of solution, or (2) the user-specified value of density is used to make the conversion.
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Again, density is only used if the user-model concentration units are ppm.
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The change in method names is intended to emphasize the difference between the user-specified densities
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and the module-calculated densities.
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Renamed GetSaturation and related functions to GetSaturationCalculated.
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Renamed SetSaturation and related functions to SetSaturationUser.
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The values specified by SetSaturation are used to convert user-model concentrations to module solution definitions.
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For SetConcentrations, the volume of solution is calculated to be the user-specified saturation * porosity *
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representative volume. For GetConcentrations, two options are available to determine the solution volume, depending
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on the value specified for SetUseSolutionDensityVolume: (1) the solution volume is calculated by the reaction module
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and used to convert to user-model concentrations, or (2) the solution volume is again calculated by
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user-specified saturation * porosity * representative volume, and those values are used to convert to user-model
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concentrations. In either case, the values returned by GetSaturationCalculated are the calculated solution volume divided
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by (porosity * representative volume).
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The change in method names is intended to emphasize the difference between the user-specified saturations and
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and the module-calculated saturations.
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-----------------
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April 16, 2023
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-----------------
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PhreeqcRM: Added new methods to simplify getting and setting component and
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aqueous species concentrations.
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New methods:
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GetIthConcentration(int i, std::vector<double>& c)--Gets the ith component concentration as
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of the last RunCells calculation. Total number of components is retrieved with GetComponentCount.
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GetIthSpeciesConcentration(int i, std::vector<double>& c)--Gets the ith aqueous species concentration as
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of the last RunCells calculation. Total number of aqueous species is retrieved with GetSpeciesCount.
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This method is for use with multicomponent diffusion, and SetSpeciesSaveOn must be set to true.
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SetIthConcentration(int i, std::vector<double>& c)--Sets the ith component concentration; done after
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transport calculations and before RunCells calculation. Total number of components is retrieved
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with GetComponentCount. SetIthConcentration must be run for every component before RunCells is called.
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SetIthConcentration(int i, std::vector<double>& c)--Sets the ith aqueous species concentration; done after
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transport calculations and before RunCells calculation. Total number of aqueous species is
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retrieved with GetSpeciesCount. This method is for use with multicomponent diffusion,
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and SetSpeciesSaveOn must be set to true. SetIthSpeciesConcentration must be run for every aqueous
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species before RunCells is called.
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Fortran versions are
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RM_GetIthConcentration(id, i, c)
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RM_GetIthSpeciesConcentration(id, i, c)
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RM_SetIthConcentration(id, i, c)
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RM_SetIthSpeciesConcentration(id, i, c)
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-----------------
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April 14, 2023
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-----------------
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PhreeqcRM: Added new methods to simplify setting initial conditions.
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New initial conditions methods:
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InitialEquilibriumPhases2Module(equilibrium_phases);
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InitialExchanges2Module(exchanges);
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InitialGasPhases2Module(gas_phases);
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InitialKinetics2Module(kinetics);
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InitialSolutions2Module(solutions);
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InitialSolidSolutions2Module(solid_solutions);
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InitialSurfaces2Module(surfaces);
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These methods are an alternative to InitialPhreeqc2Module, which used a 7 x nxyz array to
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set all initial conditions in one method call. The new methods set only one reactant at a
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time, and all methods use a single array of index numbers (referring to definitions in
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the InitialPhreeqc instance) of length nxyz (the number of user grid cells). The methods
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copy definitions from the InitialPhreeqc instance to define initial conditions in the
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model cells.
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Fortran implementation is as follows:
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RM_InitialEquilibriumPhases2Module(id, equilibrium_phases);
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RM_InitialExchanges2Module(id, exchanges);
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RM_InitialGasPhases2Module(id, gas_phases);
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RM_InitialKinetics2Module(id, kinetics);
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RM_InitialSolutions2Module(id, solutions);
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RM_InitialSolidSolutions2Module(id, solid_solutions);
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RM_InitialSurfaces2Module(id, surfaces);
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-----------------
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April 3, 2023
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-----------------
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@ -59,9 +266,9 @@ Version @PHREEQC_VER@: @PHREEQC_DATE@
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-----------------
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February 26, 2023
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-----------------
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PhreeqcRM: Added a BMI (Basic Model Interface) for C++.
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PhreeqcRM: Added a BMI (Basic Model Interface) for C++ and Fortran.
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The interface is a repackaging of the available methods of
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PhreeqcRM. All PhreeqcRM methods are available, in addition
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PhreeqcRM. All PhreeqcRM methods are available in addition
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to the BMI methods.
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New capabilities include (1) the capability to
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@ -82,95 +289,99 @@ Version @PHREEQC_VER@: @PHREEQC_DATE@
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the YAML file with BMI_Initialize to execute the specified PhreeqcRM methods
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to apply the data specified in the YAML file.
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The following is represents the way BMI methods would be used to implement
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The following represents the way BMI methods would be used to implement
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a sequential, noniterative transport calculation:
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PhreeqcRM phreeqc_rm(nxyz, nthreads);
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phreeqc_rm.BMI_Initialize("myfile.yaml");
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phreeqc_rm.Initialize("myfile.yaml");
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int ncomps;
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phreeqc_rm.BMI_GetValue("ComponentCount", &ncomps);
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phreeqc_rm.GetValue("ComponentCount", &ncomps);
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int ngrid;
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phreeqc_rm.BMI_GetValue("GridCellCount", ngrid);
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phreeqc_rm.GetValue("GridCellCount", ngrid);
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std::vector c(ngrid*ncomps, 0.0);
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phreeqc_rm.BMI_GetValue("Concentrations", c.data());
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phreeqc_rm.BMI_SetValue("TimeStep", 86400);
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phreeqc_rm.GetValue("Concentrations", c.data());
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phreeqc_rm.SetValue("TimeStep", 86400);
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for(double time = 0; time < 864000; time+=86400)
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{
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// Take a transport time step here and update the vector c.
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your_transport(c);
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phreeqc_rm.BMI_SetValue("Time", time);
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phreeqc_rm.BMI_SetValue("Concentrations", c.data());
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phreeqc_rm.BMI_Update();
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phreeqc_rm.BMI_GetValue("Concentrations", c.data());
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phreeqc_rm.SetValue("Time", time);
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phreeqc_rm.SetValue("Concentrations", c.data());
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phreeqc_rm.Update();
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phreeqc_rm.GetValue("Concentrations", c.data());
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}
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The set of BMI methods is as follows:
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std::string BMI_GetComponentName()
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std::string GetComponentName()
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Returns "PhreeqcRM".
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double BMI_GetCurrentTime()
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double GetCurrentTime()
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Returns current time that has been set by the user.
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double BMI_GetEndTime()
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double GetEndTime()
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Returns current time plus the time step.
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int BMI_GetInputItemCount()
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int GetInputItemCount()
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Returns the number of variables that it is possible to set
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with BMI_SetValue.
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with SetValue.
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std::vector<std::string> BMI_GetInputVarNames()
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std::vector<std::string> GetInputVarNames()
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Returns a list of the names of variables that can be set
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with BMI_SetValue.
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with SetValue.
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int BMI_GetOutputItemCount()
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int GetOutputItemCount()
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Returns the number of variables that it is possible to retrieve
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with BMI_GetValue.
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with GetValue.
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std::vector<std::string> BMI_GetOutputVarNames()
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std::vector<std::string> GetOutputVarNames()
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Returns a list of the names of variables that can be retrieved
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with BMI_GetValue.
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with GetValue.
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double BMI_GetTimeStep()
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double GetTimeStep()
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Returns the current time step that has been set by the user.
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std::string BMI_GetTimeUnits()
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std::string GetTimeUnits()
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Returns "seconds".
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void BMI_GetValue(std::string name, void* dest)
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void GetValue(std::string name, void* dest)
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Returns a value or vector of values for the variable identified by name
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void BMI_GetValuePtr(std::string name, void* dest)
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void GetValuePtr(std::string name, void* dest)
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Returns a pointer to current values of a variable. This method
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is available for selected variables.
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int BMI_GetVarItemsize(std::string name)
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int GetVarItemsize(std::string name)
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Returns the number of bytes needed for one element of the variable
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identified by name.
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int BMI_GetVarNbytes(std::string name)
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int GetVarNbytes(std::string name)
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Returns the total number of bytes neded to store the value or vector
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of values identified by name.
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std::string BMI_GetVarType(std::string name)
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std::string GetVarType(std::string name)
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Returns the type of the variable identified by name: "int", "double", or
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"string".
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std::string BMI_GetVarUnits(std::string name)
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std::string GetVarUnits(std::string name)
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Returns the units associated with the variable identified by name.
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void BMI_Initialize(std::string config_file)
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void Initialize(std::string config_file)
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Same as InitializeYAML discussed above.
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void BMI_SetValue(std::string name, void* src)
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void SetValue(std::string name, void* src)
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Sets the value or vector of values for the variable identified by name.
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void BMI_Update(void)
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void Update(void)
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Calculates chemical reactions for a time step. It is equivalent to
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the method RunCells. Equilibrium will be calculated between the solution
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and all equilibrium reactants (EQUILIBRIUM_PHASES, EXCHANGE, etc), and
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KINETICS will be integrated for the time step.
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BMI is implemented in Fortran with USE BMIPhreeqcRM. Methods are nemed with a
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prefix "bmif" and have an additional initial argument to identify the instance of
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BMIPhreeqcRM that is being used.
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||||
-----------------
|
||||
February 26, 2023
|
||||
-----------------
|
||||
|
||||
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