def initialize_phreeqcrm_yaml(yamlfile, nxyz): #initialize phreeqc from yaml file phreeqc_rm = phreeqcrm.PhreeqcRM(nxyz, 1) status = phreeqc_rm.InitializeYAML(yamlfile) status = phreeqc_rm.SetScreenOn(True) sout_columns = phreeqc_rm.GetSelectedOutputHeadings() soutdf = pd.DataFrame(columns = sout_columns) return phreeqc_rm, soutdf, sout_columns
- key: SetComponentH2O tf: false- key: UseSolutionDensityVolume tf: false- key: SetFilePrefix prefix: test01\_phreeqc- key: OpenFiles- key: SetUnitsSolution option: 2- key: SetPorosity por: !!python/object/apply:numpy.core.multiarray._reconstruct args: - &id001 !!python/name:numpy.ndarray '' - !!python/tuple - 0 - !!binary | Yg== state: !!python/tuple - 1 - !!python/tuple - 50 - !!python/object/apply:numpy.dtype args: - f8 - false - true state: !!python/tuple - 3 - < - null - null - null - -1 - -1 - 0 - false - !!binary | AAAAAAAA8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA8D8A AAAAAADwPwAAAAAAAPA/AAAAAAAA8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA8D8AAAAAAADwPwAA AAAAAPA/AAAAAAAA8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA8D8AAAAAAADwPwAAAAAAAPA/AAAA AAAA8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA8D8AAAAA AADwPwAAAAAAAPA/AAAAAAAA8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA8D8AAAAAAADwPwAAAAAA APA/AAAAAAAA8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA 8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA8D8AAAAAAADwPwAAAAAAAPA/AAAAAAAA8D8AAAAAAADw Pw==- key: SetPrintChemistryMask cell_mask: !!python/object/apply:numpy.core.multiarray._reconstruct args: - *id001 - !!python/tuple - 0 - !!binary | Yg== state: !!python/tuple - 1 - !!python/tuple - 50 - &id002 !!python/object/apply:numpy.dtype args: - i4 - false - true state: !!python/tuple - 3 - < - null - null - null - -1 - -1 - 0 - false - !!binary | AQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAAB AAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEA AAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAA AAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAA=- key: SetPrintChemistryOn workers: false initial_phreeqc: true utility: false- key: LoadDatabase database: database\pht3d_datab.dat- key: RunFile workers: true initial_phreeqc: true utility: true chemistry_name: test01\phinp.dat- key: RunString workers: true initial_phreeqc: false utility: true input_string: DELETE; -all- key: SetTime time: 0.0- key: SetTimeStep time_step: 0.0- key: SetGridCellCount count: 50- key: InitialPhreeqc2Module ic: !!python/object/apply:numpy.core.multiarray._reconstruct args: - *id001 - !!python/tuple - 0 - !!binary | Yg== state: !!python/tuple - 1 - !!python/tuple - 350 - *id002 - false - !!binary | AQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAAB AAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEA AAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAA AAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAA AQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAAB AAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEA AAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAA AP////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////8=- key: RunCells
import numpy as npimport yamlphreeqcrmfrom constants import FilePathsdef WriteYAMLFile_py(): # Create YAMLPhreeqcRM document yrm = yamlphreeqcrm.YAMLPhreeqcRM() # Number of cells nxyz = 40; # Set GridCellCount yrm.YAMLSetGridCellCount(nxyz) # Set ThreadCount yrm.YAMLThreadCount(3) # Set some properties yrm.YAMLSetErrorHandlerMode(1) yrm.YAMLSetComponentH2O(False) yrm.YAMLSetRebalanceFraction(0.5) yrm.YAMLSetRebalanceByCell(True) yrm.YAMLUseSolutionDensityVolume(False) yrm.YAMLSetPartitionUZSolids(False) # Open files yrm.YAMLSetFilePrefix("AdvectBMI_py"); yrm.YAMLOpenFiles(); # Set concentration units yrm.YAMLSetUnitsSolution(2) # 1, mg/L; 2, mol/L; 3, kg/kgs yrm.YAMLSetUnitsPPassemblage(1) # 0, mol/L cell; 1, mol/L water; 2 mol/L rock yrm.YAMLSetUnitsExchange(1) # 0, mol/L cell; 1, mol/L water; 2 mol/L rock yrm.YAMLSetUnitsSurface(1) # 0, mol/L cell; 1, mol/L water; 2 mol/L rock yrm.YAMLSetUnitsGasPhase(1) # 0, mol/L cell; 1, mol/L water; 2 mol/L rock yrm.YAMLSetUnitsSSassemblage(1) # 0, mol/L cell; 1, mol/L water; 2 mol/L rock yrm.YAMLSetUnitsKinetics(1) # 0, mol/L cell; 1, mol/L water; 2 mol/L rock # Set conversion from seconds to user units (days) Only affects one print statement time_conversion = 1.0 / 86400.0 yrm.YAMLSetTimeConversion(time_conversion) # Set representative volume rv = [1] * nxyz yrm.YAMLSetRepresentativeVolume(rv) # Set initial density density = [1.0] * nxyz yrm.YAMLSetDensityUser(density) # Set initial porosity por = [0.2] * nxyz yrm.YAMLSetPorosity(por) # Set initial saturation sat = [1] * nxyz yrm.YAMLSetSaturationUser(sat) # Set cells to print chemistry when print chemistry is turned on print_chemistry_mask = [0] * nxyz for i in range(nxyz // 2): print_chemistry_mask[i] = 1 yrm.YAMLSetPrintChemistryMask(print_chemistry_mask) # Demonstation of mapping, two equivalent rows by symmetry # zero-based indexing grid2chem = [-1] * nxyz for i in range(nxyz // 2): grid2chem[i] = i grid2chem[i + nxyz // 2] = i yrm.YAMLCreateMapping(grid2chem) # Set printing of chemistry file yrm.YAMLSetPrintChemistryOn(False, True, False) # workers, initial_phreeqc, utility # Load database yrm.YAMLLoadDatabase("phreeqc.dat") # Run file to define solutions and reactants for initial conditions, selected output workers = True # Worker instances do the reaction calculations for transport initial_phreeqc = True # InitialPhreeqc instance accumulates initial and boundary conditions utility = True # Utility instance is available for processing yrm.YAMLRunFile(workers, initial_phreeqc, utility, "advect.pqi") # Clear contents of workers and utility initial_phreeqc = False input = "DELETE; -all" yrm.YAMLRunString(workers, initial_phreeqc, utility, input) yrm.YAMLAddOutputVars("AddOutputVars", "true") # Determine number of components to transport yrm.YAMLFindComponents() # set array of initial conditions ic1 = [-1]*(nxyz*7) ic2 = [-1]*(nxyz*7) f1 = [1]*(nxyz*7) for i in range(nxyz): ic1[i] = 1; # Solution 1 ic1[nxyz + i] = -1; # Equilibrium phases none ic1[2 * nxyz + i] = 1; # Exchange 1 ic1[3 * nxyz + i] = -1; # Surface none ic1[4 * nxyz + i] = -1; # Gas phase none ic1[5 * nxyz + i] = -1; # Solid solutions none ic1[6 * nxyz + i] = -1; # Kinetics none yrm.YAMLInitialPhreeqc2Module_mix(ic1, ic2, f1) # No mixing is defined, so the following is equivalent #yrm.YAMLInitialPhreeqc2Module(ic1) # alternative for setting initial conditions # cell number in first argument (-1 indicates last solution, 40 in this case) # in advect.pqi and any reactants with the same number-- # Equilibrium phases, exchange, surface, gas phase, solid solution, and (or) kinetics-- # will be written to cells 18 and 19 (0 based) module_cells = [18, 19] yrm.YAMLInitialPhreeqcCell2Module(-1, module_cells) # Initial equilibration of cells time_step = 0.0 # no kinetics yrm.YAMLSetTimeStep(time_step) time = 0.0 yrm.YAMLSetTime(time) yrm.YAMLRunCells() time_step = 86400.0 yrm.YAMLSetTimeStep(time_step) # Write YAML file yrm.WriteYAMLDoc(FilePaths.YAML) print("Done.")if __name__ == '__main__': WriteYAMLFile_py()
phreeqcrm_yaml.YAMLInitialPhreeqc2Module(self.ic1_flatten)
phreeqcrm_yaml.YAMLInitialPhreeqc2Module([1] * (7*nxyz))
def ndarray_representer(dumper: yaml.Dumper, array: np.ndarray) -> yaml.Node: return dumper.represent_list(array.tolist())yaml.add_representer(np.ndarray, ndarray_representer)
