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Merge commit 'dd597b1187b6cbfbb271fa39575dea62c2f7247e'
This commit is contained in:
Scott R Charlton
commit
e3da23912a
@ -1,62 +1,292 @@
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Version @PHREEQC_VER@: @PHREEQC_DATE@
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-----------------
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July 17, 2018
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-----------------
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PHREEQC: Fixed bug where an element name like "1W" in SOLUTION or SOLUTION_SPREAD
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was interpreted as an isotope, but caused a NULL pointer if the ISOTOPE definitions
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did not exist.
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-----------------
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July 8, 2018
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-----------------
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PHREEQC: Added option -ddl to SURFACE. Sets surface type to
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diffuse double layer, which is the default if -no_edl and -cd_music
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are not defined.
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-----------------
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June 27, 2018
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-----------------
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PhreeqcRM: Added methods to provide lists of exchange species, surface species,
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reactants, and relevant minerals and gases defined in the reaction module. The lists
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are derived from the SOLUTION, EXCHANGE, SURFACE, EQUILIBRIUM_PHASES, GAS_PHASES,
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and KINETICS definitions in the "initial phreeqc" IPhreeqc object.
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See documentation of PhreeqcRM in download distributions.
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-----------
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C++ methods
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-----------
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EXCHANGE
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--------
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Number of exchange species
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int GetExchangeSpeciesCount(void)
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Names of all exchange species (for example, NaX)
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const std::vector<std::string> & GetExchangeSpeciesNames(void)
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Name of exchanger in exchange species (for example, X)
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const std::vector<std::string> & GetExchangeNames(void)
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Surface
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-------
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Number of surface species
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int GetSurfaceSpeciesCount(void)
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Names of all surface species (for example Hfo_wOH)
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const std::vector<std::string> & GetSurfaceSpeciesNames(void)
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Surface type for surface species (for example Hfo_w)
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const std::vector<std::string> & GetSurfaceTypes(void)
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Surface name for surface species (for example Hfo)
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const std::vector<std::string> & GetSurfaceNames(void)
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Equilibrium phases
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------------------
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Number of equilibrium phases
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int GetEquilibriumPhasesCount(void)
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Names of equilibrium phases; suitable for definitions of -equilibrium_phases
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in SELECTED_OUTPUT
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const std::vector<std::string> & GetEquilibriumPhases(void)
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Gas phase components
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--------------------
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Number of gas phase components
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int GetGasComponentsCount(void)
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Names of gas phase components; suitable for definitions of -gas
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in SELECTED_OUTPUT
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const std::vector<std::string> & GetGasComponents(void)
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Kinetics
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--------
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Number of kinetic reactions
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int GetKineticReactionsCount(void)
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Names of kinetic reactions; suitable for definitions of -kinetics
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in SELECTED_OUTPUT
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const std::vector<std::string> & GetKineticReactions(void)
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Solid solutions
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---------------
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Number of solid solution components
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int GetSolidSolutionComponentsCount(void)
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Names of solid solution components; suitable for definitions of
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-solid_solution in SELECTED_OUTPUT
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const std::vector<std::string> & GetSolidSolutionComponents(void)
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Solid solution name containing the solid solution component
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const std::vector<std::string> & GetSolidSolutionNames(void)
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Saturation index phases
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-----------------------
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Number of phases appropriate for the elements defined in the reaction module
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int GetSICount(void)
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Names of phases in the reaction module; suitable for definitions of
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-si in SELECTED_OUTPUT
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const std::vector<std::string> & GetSINames(void)
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---------------
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Fortran methods
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---------------
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Exchange
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--------
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Number of exchange species
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integer function RM_GetExchangeSpeciesCount(id)
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Name of exchange species (for example, NaX)
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integer function RM_GetExchangeSpeciesName(id, i, line)
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Name of exchanger in exchange species (for example, X)
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integer function RM_GetExchangeName(id, i, line1)
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Surface
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-------
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Number of surface species
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integer function RM_GetSurfaceSpeciesCount(id)
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Name of all surface species (for example Hfo_wOH)
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integer function RM_GetSurfaceSpeciesName(id, i, line)
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Surface type for surface species (for example Hfo_w)
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integer function RM_GetSurfaceType(id, i, line1)
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Surface name for surface species (for example Hfo)
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integer function RM_GetSurfaceName(id, i, line2)
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Equilibrium phases
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------------------
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Number of equilibrium phases
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integer function RM_GetEquilibriumPhasesCount(id)
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Name of equilibrium phase; suitable for definitions of -equilibrium_phases
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in SELECTED_OUTPUT
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integer function RM_GetEquilibriumPhasesName(id, i, line)
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Gas phase components
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--------------------
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Number of gas phase components
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integer function RM_GetGasComponentsCount(id)
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Name of gas phase component; suitable for definitions of -gas
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in SELECTED_OUTPUT
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integer function RM_GetGasComponentsName(id, i, line)
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Kinetics
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--------
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Number of kinetic reactions
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integer function RM_GetKineticReactionsCount(id)
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Name of kinetic reaction; suitable for definitions of -kinetics
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in SELECTED_OUTPUT
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integer function RM_GetKineticReactionsName(id, i, line)
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Solid solutions
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---------------
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Number of solid solution components
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integer function RM_GetSolidSolutionComponentsCount(id)
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Name of solid solution component; suitable for definitions of
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-solid_solution in SELECTED_OUTPUT
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integer function RM_GetSolidSolutionComponentsName(id, i, line)
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Solid solution name containing the solid solution component
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integer function RM_GetSolidSolutionName(id, i, line1)
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Saturation index phases
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-----------------------
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Number of phases appropriate for the elements defined in the reaction module
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integer function RM_GetSICount(id)
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Name of phase in the reaction module; suitable for definitions of
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-si in SELECTED_OUTPUT
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integer function RM_GetSIName(id, i, line)
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---------------
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C methods
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---------------
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Exchange
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--------
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Number of exchange species
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int RM_GetExchangeSpeciesCount(id)
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Name of exchange species (for example, NaX)
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IRM_RESULT RM_GetExchangeSpeciesName(id, i, line1, length)
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Name of exchanger in exchange species (for example, X)
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IRM_RESULT RM_GetExchangeName(id, i, line1, length)
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Surface
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-------
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Number of surface species
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int RM_GetSurfaceSpeciesCount(id)
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Name of all surface species (for example Hfo_wOH)
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IRM_RESULT RM_GetSurfaceSpeciesName(id, i, line, length)
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Surface type for surface species (for example Hfo_w)
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IRM_RESULT RM_GetSurfaceType(id, i, line1, length)
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Surface name for surface species (for example Hfo)
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IRM_RESULT RM_GetSurfaceName(id, i, line2, length)
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Equilibrium phases
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------------------
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Number of equilibrium phases
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int RM_GetEquilibriumPhasesCount(id)
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Name of equilibrium phase; suitable for definitions of -equilibrium_phases
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in SELECTED_OUTPUT
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IRM_RESULT RM_GetEquilibriumPhasesName(id, i, line, length)
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Gas phase components
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--------------------
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Number of gas phase components
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int RM_GetGasComponentsCount(id)
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Name of gas phase component; suitable for definitions of -gas
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in SELECTED_OUTPUT
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IRM_RESULT RM_GetGasComponentsName(id, i, line, length)
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Kinetics
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--------
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Number of kinetic reactions
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int RM_GetKineticReactionsCount(id)
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Name of kinetic reaction; suitable for definitions of -kinetics
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in SELECTED_OUTPUT
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IRM_RESULT RM_GetKineticReactionsName(id, i, line, length)
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Solid solutions
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---------------
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Number of solid solution components
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int RM_GetSolidSolutionComponentsCount(id)
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Name of solid solution component; suitable for definitions of
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-solid_solution in SELECTED_OUTPUT
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IRM_RESULT RM_GetSolidSolutionComponentsName(id, i, line, length)
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Solid solution name containing the solid solution component
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IRM_RESULT RM_GetSolidSolutionName(id, i, line1, length)
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Saturation index phases
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-----------------------
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Number of phases appropriate for the elements defined in the reaction module
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int RM_GetSICount(id)
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Name of phase in the reaction module; suitable for definitions of
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-si in SELECTED_OUTPUT
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IRM_RESULT RM_GetSIName(id, i, line, length)
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-----------------
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June 24, 2018
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-----------------
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PHREEQC:
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Made the solid solution calculation with the Pitzer-model similar to the numerical
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derivatives used in ion-association calculations.
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PHREEQC:
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Made the solid solution calculation with the Pitzer-model similar to the numerical
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derivatives used in ion-association calculations.
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Bug-fix for porosities, which could be set incorrectly when porosities were not
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defined in TRANSPORT simulations with more cells than before.
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Bug-fix for porosities, which could be set incorrectly when porosities were not
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defined in TRANSPORT simulations with more cells than before.
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Modified the diffusion properties for (possible) boundary cells in stagnant
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calculations with enhanced transport through a Donnan layer. In version 3.4.2,
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the harmonic mean of all the diffusional properties was introduced for all the
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stagnant cells. However, many models use cell 3 and cell [2 + stagnant cells]
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as outer, well-mixed reservoir solutions, and diffusion is then determined by
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the properties of the boundary cells in the column (similar to the regular column,
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where cells 0 and [cells + 1] are well-mixed). If cells 3 and [2 + stagnant cells]
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are without a surface with a Donnan layer, they are taken as well-mixed now.
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Modified the diffusion properties for (possible) boundary cells in stagnant
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calculations with enhanced transport through a Donnan layer. In version 3.4.2,
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the harmonic mean of all the diffusional properties was introduced for all the
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stagnant cells. However, many models use cell 3 and cell [2 + stagnant cells]
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as outer, well-mixed reservoir solutions, and diffusion is then determined by
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the properties of the boundary cells in the column (similar to the regular column,
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where cells 0 and [cells + 1] are well-mixed). If cells 3 and [2 + stagnant cells]
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are without a surface with a Donnan layer, they are taken as well-mixed now.
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Thus:
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--cell 3 without donnan layer, cell 4 with a donnan layer: diffusion is determined
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by the properties of cell 4.
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Thus:
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--cell 3 without donnan layer, cell 4 with a donnan layer: diffusion is determined
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by the properties of cell 4.
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--cell 3 without donnan layer, cell 4 without a donnan layer: diffusion is determined
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by the harmonic mean of the properties of cells 3 & 4.
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--cell 3 without donnan layer, cell 4 without a donnan layer: diffusion is determined
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by the harmonic mean of the properties of cells 3 & 4.
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PHREEQC's choice can be manipulated, adding a surface with a very small number of sites
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and a tiny Donnan layer in cell 3 and/or the cells it diffuses into, and similar
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for cell [2 + stagnant cells]. See example opa_col3.phr (http://www.hydrohemistry.eu).
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PHREEQC's choice can be manipulated, adding a surface with a very small number of sites
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and a tiny Donnan layer in cell 3 and/or the cells it diffuses into, and similar
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for cell [2 + stagnant cells]. See example opa_col3.phr (http://www.hydrohemistry.eu).
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A Donnan layer on SURFACEs can now be calculated with the Pitzer database.
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A Donnan layer on SURFACEs can now be calculated with the Pitzer database.
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Bug-fixes for option -numerical_derivatives in KNOBS, setting it true may
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improve convergence of donnan layer calculations
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(for example, try it in http://www.hydrochemistry.eu/exmpls/membrane.phr).
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Overall iterations (this is, all the calls to CLI in a reaction step) are
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printed in the output file if different from the iterations in the final set.
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It can be USER_PRINTED/PUNCHED with the variable 'iterations'.
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Streamlined the output of -debug_prep in KNOBS. Added options
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-debug_mass_balance (total moles of elements), and -debug_mass_action
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(species data: log_k, dz, reaction stoichiometry).
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The numbers in the matrix for CLI can be inspected in
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my_array[row * (count_unknowns + 1) + col].
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Bug-fixes for option -numerical_derivatives in KNOBS, setting it true may
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improve convergence of donnan layer calculations
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(for example, try it in http://www.hydrochemistry.eu/exmpls/membrane.phr).
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Overall iterations (this is, all the calls to CLI in a reaction step) are
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printed in the output file if different from the iterations in the final set.
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It can be USER_PRINTED/PUNCHED with the variable 'iterations'.
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Streamlined the output of -debug_prep in KNOBS. Added options
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-debug_mass_balance (total moles of elements), and -debug_mass_action
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(species data: log_k, dz, reaction stoichiometry).
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The numbers in the matrix for CLI can be inspected in
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my_array[row * (count_unknowns + 1) + col].
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-----------------
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May 1, 2018
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-----------------
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PhreeqcRM: Added new methods to retrieve log10 activity coefficients
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of aqueous species: GetSpeciesLog10Gammas(lg) (C++) and
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RM_GetSpeciesLog10Gammas(lg) (C++ and Fortran).
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See documentation of PhreeqcRM in download distributions
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of aqueous species.
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C++ method:
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IRM_RESULT GetSpeciesLog10Gammas (std::vector< double > &species_log10gammas)
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Fortran method:
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integer function RM_GetSpeciesLog10Gammas(integer, intent(in) id,
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double precision, dimension(:,:), intent(out) species_log10gammas)
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C method:
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IRM_RESULT RM_GetSpeciesLog10Gammas(int id, double * species_log10gammas)
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See documentation of PhreeqcRM in download distributions.
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-----------------
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April 28, 2018
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