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https://git.gfz-potsdam.de/naaice/poet.git
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refactor: make Grid class a bit more generic
This commit is contained in:
Max Luebke
parent
fc20d7a7f0
commit
689c55bf32
@ -179,11 +179,11 @@ int main(int argc, char *argv[]) {
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// TODO: Grid anpassen
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GridParams grid_params = GridParams(R);
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Grid grid(grid_params);
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// grid.init_from_R();
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Grid grid;
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params.initVectorParams(R, grid.getSpeciesCount());
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grid.InitModuleFromParams(GridParams(R));
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params.initVectorParams(R, grid.GetSpeciesCount());
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// MDL: store all parameters
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if (world_rank == 0) {
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@ -1 +1 @@
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Subproject commit a9e3d9fa355160ef7efdb5e421076e72c0e58893
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Subproject commit e7769e1a718c9993c1500c5df13dc64b39362b9a
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2
ext/tug
2
ext/tug
@ -1 +1 @@
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Subproject commit 0abd4e04ae40724f9ddb62da9f7c6ebd234330bb
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Subproject commit d4e3ab8544628c72921bf60d4462d6d131b0ffb5
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@ -2,7 +2,7 @@
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** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
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** Potsdam)
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**
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** Copyright (C) 2018-2022 Marco De Lucia, Max Luebke (GFZ Potsdam)
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** Copyright (C) 2018-2023 Marco De Lucia, Max Luebke (GFZ Potsdam)
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**
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** POET is free software; you can redistribute it and/or modify it under the
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** terms of the GNU General Public License as published by the Free Software
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@ -21,10 +21,10 @@
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#ifndef GRID_H
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#define GRID_H
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#include "PhreeqcRM.h"
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#include "poet/SimParams.hpp"
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#include <Rcpp.h>
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#include <array>
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#include <cstddef>
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#include <cstdint>
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#include <map>
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#include <string>
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@ -53,65 +53,54 @@ constexpr const char *GRID_MODULE_NAME = "grid_init";
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*
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*/
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class Grid {
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private:
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using prop_vec = std::vector<std::string>;
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public:
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/**
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* @brief Construct a new Grid object
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*
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* This will call the default constructor and initializes private RRuntime
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* with given R runtime.
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*
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* @param R
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*/
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Grid(poet::GridParams grid_args);
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Grid();
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~Grid();
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/**
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* @brief Init the grid
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*
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* At this moment init will only declare and define a variable inside the R
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* runtime called grid_tmp since the whole Grid initialization and management
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* is done by the R runtime. This may change in the future.
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*
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*/
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void init_from_R();
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auto getGridDimension() -> uint8_t;
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auto getTotalCellCount() -> uint32_t;
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auto getGridCellsCount(uint8_t direction) -> uint32_t;
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auto getDomainSize(uint8_t dircetion) -> uint32_t;
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void InitModuleFromParams(const poet::GridParams &grid_args);
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StateMemory *registerState(std::string module_name,
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std::vector<std::string> props);
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StateMemory *getStatePointer(std::string module_name);
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void deregisterState(std::string module_name);
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void SetGridDimension(uint8_t dim);
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void SetGridCellCount(uint32_t n_x, uint32_t n_y = 0, uint32_t n_z = 0);
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void SetGridSize(double s_x, double s_y = 0., double s_z = 0.);
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void SetPropNames(const std::vector<std::string> &prop_names);
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auto getSpeciesCount() -> uint32_t;
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auto getPropNames() -> prop_vec;
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void InitGridFromScratch(const Rcpp::DataFrame &init_cell);
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void InitGridFromRDS();
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void InitGridFromPhreeqc();
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auto getSpeciesByName(std::string name,
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std::string module_name = poet::GRID_MODULE_NAME)
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auto GetGridDimension() const -> uint8_t;
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auto GetTotalCellCount() const -> uint32_t;
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auto GetGridCellsCount(uint8_t direction) const -> uint32_t;
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auto GetGridSize(uint8_t direction) const -> uint32_t;
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auto RegisterState(std::string module_name, std::vector<std::string> props)
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-> StateMemory *;
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auto GetStatePointer(std::string module_name) -> StateMemory *;
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auto GetInitialGrid() const -> StateMemory *;
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auto GetSpeciesCount() const -> uint32_t;
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auto GetPropNames() const -> std::vector<std::string>;
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auto GetSpeciesByName(std::string name,
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std::string module_name = poet::GRID_MODULE_NAME) const
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-> std::vector<double>;
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private:
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PhreeqcRM *initPhreeqc(const poet::GridParams ¶ms);
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// auto InitPhreeqc(const poet::GridParams ¶ms) -> PhreeqcRM *;
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std::uint8_t dim;
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std::array<std::uint32_t, MAX_DIM> d_spatial;
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std::uint8_t dim = 0;
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std::array<double, MAX_DIM> grid_size;
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std::array<std::uint32_t, MAX_DIM> n_cells;
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std::map<std::string, StateMemory *> state_register;
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std::map<std::string, std::vector<double>> grid_init;
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StateMemory *grid_init = std::nullptr_t();
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prop_vec prop_names;
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std::vector<std::string> prop_names;
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PhreeqcRM *phreeqc_rm = std::nullptr_t();
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void initFromPhreeqc(const poet::GridParams &grid_args);
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void initFromRDS(const poet::GridParams &grid_args);
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void initFromScratch(const poet::GridParams &grid_args);
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// PhreeqcRM *phreeqc_rm = std::nullptr_t();
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};
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} // namespace poet
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#endif // GRID_H
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@ -6,7 +6,7 @@ poet::BaseChemModule::BaseChemModule(SimParams ¶ms, RInside &R_,
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t_simparams tmp = params.getNumParams();
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this->world_rank = tmp.world_rank;
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this->world_size = tmp.world_size;
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this->prop_names = this->grid.getPropNames();
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this->prop_names = this->grid.GetPropNames();
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this->n_cells_per_prop = this->grid.getTotalCellCount();
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this->n_cells_per_prop = this->grid.GetTotalCellCount();
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}
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@ -42,7 +42,7 @@ ChemMaster::ChemMaster(SimParams ¶ms, RInside &R_, Grid &grid_)
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this->wp_size = tmp.wp_size;
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this->dht_enabled = tmp.dht_enabled;
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uint32_t grid_size = grid.getTotalCellCount() * this->prop_names.size();
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uint32_t grid_size = grid.GetTotalCellCount() * this->prop_names.size();
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/* allocate memory */
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this->workerlist = new worker_struct[this->world_size - 1];
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@ -52,8 +52,8 @@ ChemMaster::ChemMaster(SimParams ¶ms, RInside &R_, Grid &grid_)
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this->mpi_buffer = new double[grid_size];
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/* calculate distribution of work packages */
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uint32_t mod_pkgs = grid.getTotalCellCount() % this->wp_size;
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uint32_t n_packages = (uint32_t)(grid.getTotalCellCount() / this->wp_size) +
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uint32_t mod_pkgs = grid.GetTotalCellCount() % this->wp_size;
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uint32_t n_packages = (uint32_t)(grid.GetTotalCellCount() / this->wp_size) +
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(mod_pkgs != 0 ? 1 : 0);
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this->wp_sizes_vector = std::vector<uint32_t>(n_packages, this->wp_size);
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@ -64,14 +64,14 @@ ChemMaster::ChemMaster(SimParams ¶ms, RInside &R_, Grid &grid_)
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}
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}
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this->state = this->grid.registerState(
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this->state = this->grid.RegisterState(
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poet::BaseChemModule::CHEMISTRY_MODULE_NAME, this->prop_names);
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std::vector<double> &field = this->state->mem;
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field.resize(this->n_cells_per_prop * this->prop_names.size());
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for (uint32_t i = 0; i < this->prop_names.size(); i++) {
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std::vector<double> prop_vec =
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this->grid.getSpeciesByName(this->prop_names[i]);
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this->grid.GetSpeciesByName(this->prop_names[i]);
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std::copy(prop_vec.begin(), prop_vec.end(),
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field.begin() + (i * this->n_cells_per_prop));
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@ -105,7 +105,7 @@ void ChemMaster::Simulate(double dt) {
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for (uint32_t i = 0; i < this->prop_names.size(); i++) {
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try {
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std::vector<double> t_prop_vec = this->grid.getSpeciesByName(
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std::vector<double> t_prop_vec = this->grid.GetSpeciesByName(
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this->prop_names[i], poet::DIFFUSION_MODULE_NAME);
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std::copy(t_prop_vec.begin(), t_prop_vec.end(),
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@ -233,7 +233,7 @@ inline void ChemMaster::sendPkgs(int &pkg_to_send, int &count_pkgs,
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workerlist[p].send_addr = work_pointer;
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/* push work pointer to next work package */
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end_of_wp = local_work_package_size * grid.getSpeciesCount();
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end_of_wp = local_work_package_size * grid.GetSpeciesCount();
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work_pointer = &(work_pointer[end_of_wp]);
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// fill send buffer starting with work_package ...
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@ -37,14 +37,14 @@ using namespace poet;
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ChemSeq::ChemSeq(SimParams ¶ms, RInside &R_, Grid &grid_)
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: BaseChemModule(params, R_, grid_) {
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this->state = this->grid.registerState(
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this->state = this->grid.RegisterState(
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poet::BaseChemModule::CHEMISTRY_MODULE_NAME, this->prop_names);
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std::vector<double> &field = this->state->mem;
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field.resize(this->n_cells_per_prop * this->prop_names.size());
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for (uint32_t i = 0; i < this->prop_names.size(); i++) {
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std::vector<double> prop_vec =
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this->grid.getSpeciesByName(this->prop_names[i]);
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this->grid.GetSpeciesByName(this->prop_names[i]);
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std::copy(prop_vec.begin(), prop_vec.end(),
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field.begin() + (i * this->n_cells_per_prop));
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@ -52,7 +52,6 @@ ChemSeq::ChemSeq(SimParams ¶ms, RInside &R_, Grid &grid_)
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}
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poet::ChemSeq::~ChemSeq() {
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this->grid.deregisterState(poet::BaseChemModule::CHEMISTRY_MODULE_NAME);
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if (this->phreeqc_rm) {
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delete this->phreeqc_rm;
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}
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@ -75,7 +74,7 @@ void ChemSeq::Simulate(double dt) {
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for (uint32_t i = 0; i < this->prop_names.size(); i++) {
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try {
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std::vector<double> t_prop_vec = this->grid.getSpeciesByName(
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std::vector<double> t_prop_vec = this->grid.GetSpeciesByName(
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this->prop_names[i], poet::DIFFUSION_MODULE_NAME);
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std::copy(t_prop_vec.begin(), t_prop_vec.end(),
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@ -24,13 +24,11 @@
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#include <Rcpp.h>
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#include <algorithm>
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#include <cstdint>
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#include <ostream>
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#include <poet/ChemSimSeq.hpp>
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#include <poet/DiffusionModule.hpp>
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#include <poet/Grid.hpp>
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#include <array>
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#include <bits/stdint-uintn.h>
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#include <cassert>
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#include <mpi.h>
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#include <string>
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@ -58,14 +56,14 @@ inline const char *convert_bc_to_config_file(uint8_t in) {
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DiffusionModule::DiffusionModule(poet::DiffusionParams diffu_args, Grid &grid_)
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: grid(grid_) {
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this->diff_input.setGridCellN(grid_.getGridCellsCount(GRID_X_DIR),
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grid_.getGridCellsCount(GRID_Y_DIR));
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this->diff_input.setDomainSize(grid_.getDomainSize(GRID_X_DIR),
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grid_.getDomainSize(GRID_Y_DIR));
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this->diff_input.setGridCellN(grid_.GetGridCellsCount(GRID_X_DIR),
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grid_.GetGridCellsCount(GRID_Y_DIR));
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this->diff_input.setDomainSize(grid_.GetGridSize(GRID_X_DIR),
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grid_.GetGridSize(GRID_Y_DIR));
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this->dim = grid_.getGridDimension();
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this->dim = grid_.GetGridDimension();
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this->n_cells_per_prop = grid_.getTotalCellCount();
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this->n_cells_per_prop = grid_.GetTotalCellCount();
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this->initialize(diffu_args);
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}
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@ -78,7 +76,7 @@ void DiffusionModule::initialize(poet::DiffusionParams args) {
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this->prop_count = this->prop_names.size();
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this->state =
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this->grid.registerState(DIFFUSION_MODULE_NAME, this->prop_names);
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this->grid.RegisterState(DIFFUSION_MODULE_NAME, this->prop_names);
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std::vector<double> &field = this->state->mem;
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@ -91,15 +89,15 @@ void DiffusionModule::initialize(poet::DiffusionParams args) {
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// initial input
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this->alpha.push_back(args.alpha[this->prop_names[i]]);
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std::vector<double> prop_vec = grid.getSpeciesByName(this->prop_names[i]);
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std::vector<double> prop_vec = grid.GetSpeciesByName(this->prop_names[i]);
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std::copy(prop_vec.begin(), prop_vec.end(),
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field.begin() + (i * this->n_cells_per_prop));
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if (this->dim == this->DIM_2D) {
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tug::bc::BoundaryCondition bc(this->grid.getGridCellsCount(GRID_X_DIR),
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this->grid.getGridCellsCount(GRID_Y_DIR));
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tug::bc::BoundaryCondition bc(this->grid.GetGridCellsCount(GRID_X_DIR),
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this->grid.GetGridCellsCount(GRID_Y_DIR));
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this->bc_vec.push_back(bc);
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} else {
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tug::bc::BoundaryCondition bc(this->grid.getGridCellsCount(GRID_X_DIR));
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tug::bc::BoundaryCondition bc(this->grid.GetGridCellsCount(GRID_X_DIR));
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this->bc_vec.push_back(bc);
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}
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}
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@ -173,7 +171,7 @@ void DiffusionModule::simulate(double dt) {
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// module) as input for diffusion
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for (uint32_t i = 0; i < this->prop_names.size(); i++) {
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try {
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std::vector<double> t_prop_vec = this->grid.getSpeciesByName(
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std::vector<double> t_prop_vec = this->grid.GetSpeciesByName(
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this->prop_names[i], poet::BaseChemModule::CHEMISTRY_MODULE_NAME);
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std::copy(t_prop_vec.begin(), t_prop_vec.end(),
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267
src/Grid.cpp
267
src/Grid.cpp
@ -2,7 +2,7 @@
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** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
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** Potsdam)
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**
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** Copyright (C) 2018-2022 Marco De Lucia, Max Luebke (GFZ Potsdam)
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** Copyright (C) 2018-2023 Marco De Lucia, Max Luebke (GFZ Potsdam)
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**
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** POET is free software; you can redistribute it and/or modify it under the
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** terms of the GNU General Public License as published by the Free Software
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@ -18,7 +18,6 @@
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** Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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*/
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#include "PhreeqcRM.h"
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#include "poet/SimParams.hpp"
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#include <Rcpp.h>
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#include <algorithm>
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@ -49,62 +48,100 @@ static inline int8_t get_type_id(std::string type) {
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return -1;
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}
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Grid::Grid(poet::GridParams grid_args) {
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// get dimension of grid
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this->dim = grid_args.n_cells.size();
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void poet::Grid::InitModuleFromParams(const poet::GridParams &grid_args) {
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assert(grid_args.n_cells.size() == grid_args.s_cells.size());
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// assert that dim is 1 or 2
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assert(this->dim <= MAX_DIM && this->dim > 0);
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// also assert that vetor spatial discretization is equal in size of
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// dimensions
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assert(this->dim == grid_args.s_cells.size());
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this->SetGridDimension(grid_args.n_cells.size());
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this->n_cells.fill(0);
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this->d_spatial.fill(0);
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// store grid dimensions
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std::copy(grid_args.n_cells.begin(), grid_args.n_cells.end(),
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this->n_cells.begin());
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std::copy(grid_args.s_cells.begin(), grid_args.s_cells.end(),
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this->d_spatial.begin());
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this->grid_size.begin());
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auto init_type = get_type_id(grid_args.type);
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assert(init_type >= 0);
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uint32_t vec_size = this->getTotalCellCount();
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if (init_type != INIT_PHREEQC) {
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this->prop_names = grid_args.props;
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switch (init_type) {
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case INIT_SCRATCH:
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this->SetPropNames(grid_args.props);
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this->InitGridFromScratch(grid_args.init_df);
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break;
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case INIT_RDS:
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this->SetPropNames(grid_args.props);
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this->InitGridFromRDS();
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break;
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case INIT_PHREEQC:
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this->InitGridFromPhreeqc();
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}
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}
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for (auto const &prop : this->prop_names) {
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std::vector<double> prop_vec(vec_size);
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// size of the vector shall be 1
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if (init_type == INIT_SCRATCH) {
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double prop_val =
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((Rcpp::NumericVector)grid_args.init_df[prop.c_str()])[0];
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std::fill(prop_vec.begin(), prop_vec.end(), prop_val);
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} else if (init_type == INIT_RDS) {
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prop_vec = Rcpp::as<std::vector<double>>(grid_args.init_df[prop.c_str()]);
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}
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// TODO: define behaviour for phreeqc script input
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void poet::Grid::SetGridDimension(uint8_t dim) {
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assert(dim < MAX_DIM + 1);
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// NOTE: if there are props defined more than once the first written value
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// will be used
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this->grid_init.insert(std::pair(prop, prop_vec));
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}
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this->dim = dim;
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}
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|
||||
void poet::Grid::SetGridCellCount(uint32_t n_x, uint32_t n_y, uint32_t n_z) {
|
||||
assert(this->dim < MAX_DIM + 1);
|
||||
|
||||
this->n_cells[0] = n_x;
|
||||
this->n_cells[1] = n_y;
|
||||
// this->n_cells[2] = n_z;
|
||||
}
|
||||
|
||||
void poet::Grid::SetGridSize(double s_x, double s_y, double s_z) {
|
||||
assert(this->dim < MAX_DIM + 1);
|
||||
|
||||
this->grid_size[0] = s_x;
|
||||
this->grid_size[1] = s_y;
|
||||
// this->grid_size[2] = s_z;
|
||||
}
|
||||
|
||||
void poet::Grid::SetPropNames(const std::vector<std::string> &prop_names) {
|
||||
this->prop_names = prop_names;
|
||||
}
|
||||
|
||||
Grid::Grid() {
|
||||
this->n_cells.fill(0);
|
||||
this->grid_size.fill(0);
|
||||
};
|
||||
|
||||
Grid::~Grid() {
|
||||
for (auto &[key, val] : this->state_register) {
|
||||
delete val;
|
||||
}
|
||||
if (this->phreeqc_rm != nullptr) {
|
||||
delete this->phreeqc_rm;
|
||||
}
|
||||
// if (this->phreeqc_rm != nullptr) {
|
||||
// delete this->phreeqc_rm;
|
||||
// }
|
||||
}
|
||||
|
||||
poet::StateMemory *Grid::registerState(std::string module_name,
|
||||
void poet::Grid::InitGridFromScratch(const Rcpp::DataFrame &init_cell) {
|
||||
const uint32_t vec_size = this->GetTotalCellCount();
|
||||
|
||||
StateMemory *curr_state =
|
||||
this->RegisterState(poet::GRID_MODULE_NAME, this->prop_names);
|
||||
curr_state->props = this->prop_names;
|
||||
|
||||
std::vector<double> &curr_field = curr_state->mem;
|
||||
|
||||
for (auto const &prop : this->prop_names) {
|
||||
// size of the vector shall be 1
|
||||
double prop_val = ((Rcpp::NumericVector)init_cell[prop.c_str()])[0];
|
||||
std::vector<double> prop_vec(vec_size, prop_val);
|
||||
|
||||
curr_field.insert(curr_field.end(), prop_vec.begin(), prop_vec.end());
|
||||
}
|
||||
|
||||
this->grid_init = curr_state;
|
||||
}
|
||||
void poet::Grid::InitGridFromRDS() {
|
||||
// TODO
|
||||
}
|
||||
void poet::Grid::InitGridFromPhreeqc() {
|
||||
// TODO
|
||||
}
|
||||
|
||||
poet::StateMemory *Grid::RegisterState(std::string module_name,
|
||||
std::vector<std::string> props) {
|
||||
poet::StateMemory *mem = new poet::StateMemory;
|
||||
|
||||
@ -120,7 +157,7 @@ poet::StateMemory *Grid::registerState(std::string module_name,
|
||||
return mem;
|
||||
}
|
||||
|
||||
poet::StateMemory *Grid::getStatePointer(std::string module_name) {
|
||||
poet::StateMemory *Grid::GetStatePointer(std::string module_name) {
|
||||
const auto it = this->state_register.find(module_name);
|
||||
|
||||
if (it == this->state_register.end()) {
|
||||
@ -131,27 +168,27 @@ poet::StateMemory *Grid::getStatePointer(std::string module_name) {
|
||||
return it->second;
|
||||
}
|
||||
|
||||
void Grid::deregisterState(std::string module_name) {
|
||||
const auto it = this->state_register.find(module_name);
|
||||
// void Grid::DeregisterState(std::string module_name) {
|
||||
// const auto it = this->state_register.find(module_name);
|
||||
|
||||
if (it == this->state_register.end()) {
|
||||
throw std::range_error(
|
||||
std::string("Requested module " + module_name + " was not found"));
|
||||
}
|
||||
// if (it == this->state_register.end()) {
|
||||
// throw std::range_error(
|
||||
// std::string("Requested module " + module_name + " was not found"));
|
||||
// }
|
||||
|
||||
auto *p = it->second;
|
||||
delete p;
|
||||
// auto *p = it->second;
|
||||
// delete p;
|
||||
|
||||
this->state_register.erase(it);
|
||||
// this->state_register.erase(it);
|
||||
// }
|
||||
|
||||
auto Grid::GetGridSize(uint8_t direction) const -> uint32_t {
|
||||
return this->grid_size.at(direction);
|
||||
}
|
||||
|
||||
auto Grid::getDomainSize(uint8_t dircetion) -> uint32_t {
|
||||
return this->d_spatial.at(dircetion);
|
||||
}
|
||||
auto Grid::GetGridDimension() const -> uint8_t { return this->dim; }
|
||||
|
||||
auto Grid::getGridDimension() -> uint8_t { return this->dim; }
|
||||
|
||||
auto Grid::getTotalCellCount() -> uint32_t {
|
||||
auto Grid::GetTotalCellCount() const -> uint32_t {
|
||||
uint32_t sum = 1;
|
||||
for (auto const &dim : this->n_cells) {
|
||||
sum *= (dim != 0 ? dim : 1);
|
||||
@ -160,28 +197,38 @@ auto Grid::getTotalCellCount() -> uint32_t {
|
||||
return sum;
|
||||
}
|
||||
|
||||
auto Grid::getGridCellsCount(uint8_t direction) -> uint32_t {
|
||||
auto Grid::GetGridCellsCount(uint8_t direction) const -> uint32_t {
|
||||
return this->n_cells.at(direction);
|
||||
}
|
||||
|
||||
auto Grid::getSpeciesCount() -> uint32_t { return this->prop_names.size(); }
|
||||
auto poet::Grid::GetInitialGrid() const -> StateMemory * {
|
||||
return this->grid_init;
|
||||
}
|
||||
|
||||
auto Grid::getPropNames() -> prop_vec { return this->prop_names; }
|
||||
auto Grid::GetSpeciesCount() const -> uint32_t {
|
||||
return this->prop_names.size();
|
||||
}
|
||||
|
||||
auto poet::Grid::getSpeciesByName(std::string name, std::string module_name)
|
||||
auto Grid::GetPropNames() const -> std::vector<std::string> {
|
||||
return this->prop_names;
|
||||
}
|
||||
|
||||
auto poet::Grid::GetSpeciesByName(std::string name,
|
||||
std::string module_name) const
|
||||
-> std::vector<double> {
|
||||
|
||||
// if module name references to initial grid
|
||||
if (module_name == poet::GRID_MODULE_NAME) {
|
||||
auto const it = this->grid_init.find(name);
|
||||
// if (module_name == poet::GRID_MODULE_NAME) {
|
||||
// auto const it = this->grid_init.find(name);
|
||||
|
||||
if (it == this->grid_init.end()) {
|
||||
throw std::range_error(
|
||||
std::string("Species " + name + " was not found for initial grid"));
|
||||
}
|
||||
// if (it == this->grid_init.end()) {
|
||||
// throw std::range_error(
|
||||
// std::string("Species " + name + " was not found for initial
|
||||
// grid"));
|
||||
// }
|
||||
|
||||
return it->second;
|
||||
}
|
||||
// return it->second;
|
||||
// }
|
||||
|
||||
// else find module with name
|
||||
auto const it = this->state_register.find(module_name);
|
||||
@ -201,59 +248,59 @@ auto poet::Grid::getSpeciesByName(std::string name, std::string module_name)
|
||||
}
|
||||
uint32_t prop_index = find_res - prop_vector.begin();
|
||||
|
||||
uint32_t begin_vec = prop_index * this->getTotalCellCount(),
|
||||
end_vec = ((prop_index + 1) * this->getTotalCellCount());
|
||||
uint32_t begin_vec = prop_index * this->GetTotalCellCount(),
|
||||
end_vec = ((prop_index + 1) * this->GetTotalCellCount());
|
||||
|
||||
return std::vector<double>(module_memory->mem.begin() + begin_vec,
|
||||
module_memory->mem.begin() + end_vec);
|
||||
}
|
||||
|
||||
PhreeqcRM *poet::Grid::initPhreeqc(const poet::GridParams ¶ms) {
|
||||
PhreeqcRM *chem_model = new PhreeqcRM(this->getTotalCellCount(), 1);
|
||||
// PhreeqcRM *poet::Grid::InitPhreeqc(const poet::GridParams ¶ms) {
|
||||
// PhreeqcRM *chem_model = new PhreeqcRM(this->GetTotalCellCount(), 1);
|
||||
|
||||
// FIXME: hardcoded options ...
|
||||
chem_model->SetErrorHandlerMode(1);
|
||||
chem_model->SetComponentH2O(false);
|
||||
chem_model->SetRebalanceFraction(0.5);
|
||||
chem_model->SetRebalanceByCell(true);
|
||||
chem_model->UseSolutionDensityVolume(false);
|
||||
chem_model->SetPartitionUZSolids(false);
|
||||
// // FIXME: hardcoded options ...
|
||||
// chem_model->SetErrorHandlerMode(1);
|
||||
// chem_model->SetComponentH2O(false);
|
||||
// chem_model->SetRebalanceFraction(0.5);
|
||||
// chem_model->SetRebalanceByCell(true);
|
||||
// chem_model->UseSolutionDensityVolume(false);
|
||||
// chem_model->SetPartitionUZSolids(false);
|
||||
|
||||
// Set concentration units
|
||||
// 1, mg/L; 2, mol/L; 3, kg/kgs
|
||||
chem_model->SetUnitsSolution(2);
|
||||
// 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
chem_model->SetUnitsPPassemblage(1);
|
||||
// 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
chem_model->SetUnitsExchange(1);
|
||||
// 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
chem_model->SetUnitsSurface(1);
|
||||
// 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
chem_model->SetUnitsGasPhase(1);
|
||||
// 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
chem_model->SetUnitsSSassemblage(1);
|
||||
// 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
chem_model->SetUnitsKinetics(1);
|
||||
// // Set concentration units
|
||||
// // 1, mg/L; 2, mol/L; 3, kg/kgs
|
||||
// chem_model->SetUnitsSolution(2);
|
||||
// // 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
// chem_model->SetUnitsPPassemblage(1);
|
||||
// // 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
// chem_model->SetUnitsExchange(1);
|
||||
// // 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
// chem_model->SetUnitsSurface(1);
|
||||
// // 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
// chem_model->SetUnitsGasPhase(1);
|
||||
// // 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
// chem_model->SetUnitsSSassemblage(1);
|
||||
// // 0, mol/L cell; 1, mol/L water; 2 mol/L rock
|
||||
// chem_model->SetUnitsKinetics(1);
|
||||
|
||||
// Set representative volume
|
||||
std::vector<double> rv;
|
||||
rv.resize(this->getTotalCellCount(), 1.0);
|
||||
chem_model->SetRepresentativeVolume(rv);
|
||||
// // Set representative volume
|
||||
// std::vector<double> rv;
|
||||
// rv.resize(this->GetTotalCellCount(), 1.0);
|
||||
// chem_model->SetRepresentativeVolume(rv);
|
||||
|
||||
// Set initial porosity
|
||||
std::vector<double> por;
|
||||
por.resize(this->getTotalCellCount(), 0.05);
|
||||
chem_model->SetPorosity(por);
|
||||
// // Set initial porosity
|
||||
// std::vector<double> por;
|
||||
// por.resize(this->GetTotalCellCount(), 0.05);
|
||||
// chem_model->SetPorosity(por);
|
||||
|
||||
// Set initial saturation
|
||||
std::vector<double> sat;
|
||||
sat.resize(this->getTotalCellCount(), 1.0);
|
||||
chem_model->SetSaturation(sat);
|
||||
// // Set initial saturation
|
||||
// std::vector<double> sat;
|
||||
// sat.resize(this->GetTotalCellCount(), 1.0);
|
||||
// chem_model->SetSaturation(sat);
|
||||
|
||||
// Load database
|
||||
chem_model->LoadDatabase(params.database_path);
|
||||
chem_model->RunFile(true, true, true, params.input_script);
|
||||
chem_model->RunString(true, false, true, "DELETE; -all");
|
||||
// // Load database
|
||||
// chem_model->LoadDatabase(params.database_path);
|
||||
// chem_model->RunFile(true, true, true, params.input_script);
|
||||
// chem_model->RunString(true, false, true, "DELETE; -all");
|
||||
|
||||
return chem_model;
|
||||
}
|
||||
// return chem_model;
|
||||
// }
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user