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updated RELEASE.TXT, revised PR_P and PR_PHI functions and the test case PR_error_incremental
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David Parkhurst
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166
RELEASE.TXT
166
RELEASE.TXT
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Version @PHREEQC_VER@: @PHREEQC_DATE@
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-----------------
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February 28, 2023
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-----------------
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PhreeqcRM: Revised names for PhreeqcRM test case source and output
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files (Tests subdirectory of distribution). Added tests SimpleAdvect_cpp
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and SimpleAdvect_f90, which produce the same results as Advect_cpp
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and Advect_f90, but with a minimal set of PhreeqcRM method calls.
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-----------------
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February 26, 2023
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-----------------
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PhreeqcRM: Added method InitializeYAML to initialize a PhreeqcRM
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instance.
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It is possible to use a YAML file to initialize the PhreeqcRM instance.
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If a GUI is used to define model input, a YAML file could be used to
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transfer the data from the GUI to a PhreeqcRM instance. The YAML file
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contains names of PhreeqcRM methods and associated data, for example:
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RunFile:
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workers: true
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initial_phreeqc: true
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utility: true
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chemistry_name: advect.pqi
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InitializeYAML can be used to process the directives defined in
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the YAML file. The method InitializeYAML is equivalent to BMI_Initialize.
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A C++ class named YAMLPhreeqcRM is included in the Tests subdirectory
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of the PhreeqcRM distribution, which provides the capability to generate
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a PhreeqcRM YAML file. The file WriteYAMLFile.cpp generates a YAML file
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and advection_bmi_cpp.cpp reads and processes the file to initialize
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a PhreeqcRM instance.
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-----------------
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February 26, 2023
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-----------------
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PhreeqcRM: Added a rudimentary BMI (Basic Model Interface) for C++.
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The interface adds minimal capabilities to the other methods of
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PhreeqcRM. The only new capabilities are (1) the capability to
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retrieve units for the variables for BMI_GetValues and BMI_SetValues,
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and (2) the capability to use YAML (YAML ain't Markup Language)
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to initialize a PhreeqcRM instance with the method BMI_Initialize
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(which is equivalent to the method InitializeYAML). The YAML
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capability would be especially useful if a GUI (Graphical User Interface)
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is used to set up model initial conditions. The GUI could write a YAML file
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that contains directives for PhreeqcRM methods that need to be run and
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the corresonding data needed to initialize a PhreeqcRM instance--for example,
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setting units; running a PHREEQC input file to define initial and
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boundary conditions; distribution of initial conditions to the model cells;
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setting initial porosity, saturation, temperature, and pressure.
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When a PhreeqcRM instance is created by the simulator, it can process
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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 complete 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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int ncomps;
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phreeqc_rm.BMI_GetValue("ComponentCount", &ncomps);
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int ngrid;
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phreeqc_rm.BMI_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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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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}
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The complete set of BMI methods is as follows:
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std::string BMI_GetComponentName()
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Returns "PhreeqcRM".
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double BMI_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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Returns current time plus the time step.
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int BMI_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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std::vector<std::string> BMI_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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int BMI_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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std::vector<std::string> BMI_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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double BMI_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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Returns "seconds".
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void BMI_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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int BMI_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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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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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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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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Same as InitializeYAML discussed above.
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void BMI_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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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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-----------------
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February 26, 2023
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-----------------
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PHREEQC: Fixed bug with Basic functions PR_P and PR_PHI. Values
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were incorrect after the first step when INCREMENTAL_REACTIONS
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was set to true.
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-----------------
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February 25, 2023
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-----------------
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ALL PROGRAMS: Added the latest version of the database Thermoddem to
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the distributions of PHREEQC programs. The database was downloaded
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from https://thermoddem.brgm.fr/.
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-----------------
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March 23, 2022
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-----------------
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PHREEQC: "MacInnes" was misspelled in one of the warning messages.
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-----------------
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December 18, 2021
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-----------------
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PHREEQC: Fixed transport bug where the end cell should not have
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been processed in part of the calculation.
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Version 3.7.3: December 2, 2021
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-----------------
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November 27, 2021
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-----------------
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