mirror of
https://git.gfz-potsdam.de/naaice/poet.git
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BREAKING CHANGE: use dump mechanism of PhreeqcRM-GFZ to get and set
internal variables feat: enables exchange data: added exchange only benchmark data: applied required changes to benchmarks
This commit is contained in:
Max Luebke
parent
315ac84423
commit
3fdf586e0d
@ -21,7 +21,6 @@
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#include "poet/ChemistryModule.hpp"
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#include <RInside.h>
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#include <Rcpp.h>
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#include <Rcpp/internal/wrap.h>
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#include <cstdint>
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#include <cstdlib>
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#include <poet/DiffusionModule.hpp>
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@ -100,7 +99,8 @@ inline double RunMasterLoop(SimParams ¶ms, RInside &R, Grid &grid,
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ChemistryParams &chem_params,
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const GridParams &g_params, uint32_t nxyz_master) {
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DiffusionModule diffusion(poet::DiffusionParams(R), grid);
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DiffusionParams d_params{R};
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DiffusionModule diffusion(d_params, grid);
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/* Iteration Count is dynamic, retrieving value from R (is only needed by
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* master for the following loop) */
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uint32_t maxiter = R.parseEval("mysetup$iterations");
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@ -112,7 +112,8 @@ inline double RunMasterLoop(SimParams ¶ms, RInside &R, Grid &grid,
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set_chem_parameters(chem, nxyz_master, chem_params.database_path);
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chem.RunInitFile(chem_params.input_script);
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chem.InitializeField(grid.GetTotalCellCount(), DFToHashMap(g_params.init_df));
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poet::ChemistryModule::SingleCMap init_df = DFToHashMap(d_params.initial_t);
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chem.mergeFieldWithModule(init_df, grid.GetTotalCellCount());
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if (params.getNumParams().dht_enabled) {
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chem.SetDHTEnabled(true, params.getNumParams().dht_size_per_process);
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@ -21,7 +21,6 @@
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#include "poet/ChemistryModule.hpp"
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#include <RInside.h>
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#include <Rcpp.h>
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#include <Rcpp/internal/wrap.h>
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#include <cstdint>
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#include <cstdlib>
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#include <poet/DiffusionModule.hpp>
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@ -99,7 +98,6 @@ inline double RunMasterLoop(SimParams ¶ms, RInside &R, Grid &grid,
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set_chem_parameters(chem, nxyz_master, chem_params.database_path);
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chem.RunInitFile(chem_params.input_script);
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chem.SetSelectedOutputOn(true);
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chem.SetTimeStep(0);
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chem.RunCells();
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@ -1,4 +1,4 @@
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## Time-stamp: "Last modified 2023-04-13 17:10:30 mluebke"
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## Time-stamp: "Last modified 2023-04-14 11:02:31 mluebke"
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database <- normalizePath("../share/poet/bench/barite/db_barite.dat")
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input_script <- normalizePath("../share/poet/bench/barite/barite.pqi")
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@ -29,7 +29,7 @@ grid <- list(
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n_cells = c(n, m),
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s_cells = c(1, 1),
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type = types[1],
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init_cell = as.data.frame(init_cell),
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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@ -43,13 +43,13 @@ grid <- list(
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## initial conditions
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init_diffu <- c(
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init_diffu <- list(
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"H" = 110.0124,
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"O" = 55.5087,
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"Charge" = -1.217E-09,
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"Ba" = 1.E-10,
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"Cl" = 1.E-10,
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"S" = 6.205E-4,
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"S(6)" = 6.205E-4,
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"Sr" = 6.205E-4
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)
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@ -60,7 +60,7 @@ injection_diff <- list(
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"Charge" = -3.337E-08,
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"Ba" = 0.1,
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"Cl" = 0.2,
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"S" = 0,
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"S(6)" = 0,
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"Sr" = 0)
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)
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@ -71,7 +71,7 @@ alpha_diffu <- c(
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"Charge" = 1E-06,
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"Ba" = 1E-06,
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"Cl" = 1E-06,
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"S" = 1E-06,
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"S(6)" = 1E-06,
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"Sr" = 1E-06
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)
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@ -91,9 +91,12 @@ boundary <- list(
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diffu_list <- names(alpha_diffu)
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vecinj <- do.call(rbind.data.frame, injection_diff)
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names(vecinj) <- names(init_diffu)
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diffusion <- list(
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init = init_diffu,
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vecinj = do.call(rbind.data.frame, injection_diff),
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init = as.data.frame(init_diffu, check.names = FALSE),
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vecinj = vecinj,
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# vecinj_inner = vecinj_inner,
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vecinj_index = boundary,
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alpha = alpha_diffu
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@ -1,4 +1,4 @@
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## Time-stamp: "Last modified 2023-01-10 13:51:40 delucia"
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## Time-stamp: "Last modified 2023-04-17 12:25:25 mluebke"
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database <- normalizePath("../share/poet/examples/phreeqc_kin.dat")
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input_script <- normalizePath("../share/poet/bench/dolo_inner.pqi")
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@ -17,7 +17,7 @@ init_cell <- list(
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"H" = 110.683,
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"O" = 55.3413,
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"Charge" = -5.0822e-19,
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"C" = 1.2279E-4,
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"C(4)" = 1.2279E-4,
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"Ca" = 1.2279E-4,
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"Cl" = 0,
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"Mg" = 0,
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@ -30,7 +30,7 @@ grid <- list(
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n_cells = c(n, m),
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s_cells = c(1, 1),
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type = types[1],
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init_cell = as.data.frame(init_cell),
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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@ -43,11 +43,11 @@ grid <- list(
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##################################################################
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## initial conditions
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init_diffu <- c(
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init_diffu <- list(
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"H" = 110.683,
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"O" = 55.3413,
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"Charge" = -5.0822e-19,
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"C" = 1.2279E-4,
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"C(4)" = 1.2279E-4,
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"Ca" = 1.2279E-4,
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"Cl" = 0,
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"Mg" = 0
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@ -58,7 +58,7 @@ alpha_diffu <- c(
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"H" = 1E-6,
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"O" = 1E-6,
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"Charge" = 1E-6,
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"C" = 1E-6,
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"C(4)" = 1E-6,
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"Ca" = 1E-6,
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"Cl" = 1E-6,
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"Mg" = 1E-6
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@ -70,7 +70,7 @@ vecinj_diffu <- list(
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"H" = 110.683,
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"O" = 55.3413,
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"Charge" = 1.90431e-16,
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"C" = 0,
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"C(4)" = 0,
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"Ca" = 0,
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"Cl" = 0.002,
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"Mg" = 0.001
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@ -79,7 +79,7 @@ vecinj_diffu <- list(
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"H" = 110.683,
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"O" = 55.3413,
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"Charge" = 1.90431e-16,
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"C" = 0,
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"C(4)" = 0,
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"Ca" = 0.0,
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"Cl" = 0.004,
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"Mg" = 0.002
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@ -102,9 +102,12 @@ boundary <- list(
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diffu_list <- names(alpha_diffu)
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vecinj <- do.call(rbind.data.frame, vecinj_diffu)
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names(vecinj) <- names(init_diffu)
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diffusion <- list(
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init = init_diffu,
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vecinj = do.call(rbind.data.frame, vecinj_diffu),
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init = as.data.frame(init_diffu, check.names = FALSE),
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vecinj = vecinj,
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vecinj_inner = vecinj_inner,
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vecinj_index = boundary,
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alpha = alpha_diffu
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@ -1,4 +1,4 @@
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## Time-stamp: "Last modified 2023-01-10 13:51:40 delucia"
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## Time-stamp: "Last modified 2023-04-17 12:27:27 mluebke"
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database <- normalizePath("../share/poet/examples/phreeqc_kin.dat")
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input_script <- normalizePath("../share/poet/bench/dolo_inner.pqi")
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@ -30,7 +30,7 @@ grid <- list(
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n_cells = c(n, m),
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s_cells = c(2, 1),
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type = types[1],
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init_cell = as.data.frame(init_cell),
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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@ -43,7 +43,7 @@ grid <- list(
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##################################################################
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## initial conditions
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init_diffu <- c(
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init_diffu <- list(
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"H" = 110.683,
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"O" = 55.3413,
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"Charge" = -5.0822e-19,
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@ -102,9 +102,12 @@ boundary <- list(
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diffu_list <- names(alpha_diffu)
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vecinj <- do.call(rbind.data.frame, vecinj_diffu)
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names(vecinj) <- names(init_diffu)
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diffusion <- list(
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init = init_diffu,
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vecinj = do.call(rbind.data.frame, vecinj_diffu),
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init = as.data.frame(init_diffu, check.names = FALSE),
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vecinj = vecinj,
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vecinj_inner = vecinj_inner,
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vecinj_index = boundary,
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alpha = alpha_diffu
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@ -1,6 +1,8 @@
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install(FILES
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surfex.R
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SurfExBase.pqi
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ExBase.pqi
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ex.R
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#surfex.R
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#SurfExBase.pqi
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SMILE_2021_11_01_TH.dat
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DESTINATION
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share/poet/bench/surfex
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39
bench/surfex/ExBase.pqi
Normal file
39
bench/surfex/ExBase.pqi
Normal file
@ -0,0 +1,39 @@
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## Time-stamp: "Last modified 2023-03-21 11:49:43 mluebke"
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KNOBS
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-logfile false
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-iterations 10000
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-convergence_tolerance 1E-12
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-step_size 2
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-pe_step_size 2
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SELECTED_OUTPUT
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-reset false
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-high_precision true
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-solution true
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-state true
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-step true
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-pH true
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-pe true
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-ionic_strength true
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-water true
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SOLUTION 1
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temp 13
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units mol/kgw
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pH 7.06355
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pe -2.626517
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C(4) 0.001990694
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Ca 0.02172649
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Cl 0.3227673 charge
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Fe 0.0001434717
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K 0.001902357
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Mg 0.01739704
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Na 0.2762882
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S(6) 0.01652701
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Sr 0.0004520361
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U(4) 8.147792e-12
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U(6) 2.237946e-09
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-water 0.00133
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EXCHANGE 1
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-equil 1
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Z 0.0012585
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Y 0.0009418
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END
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144
bench/surfex/ex.R
Normal file
144
bench/surfex/ex.R
Normal file
@ -0,0 +1,144 @@
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## Time-stamp: "Last modified 2023-04-17 12:29:27 mluebke"
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database <- normalizePath("./SMILE_2021_11_01_TH.dat")
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input_script <- normalizePath("./ExBase.pqi")
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cat(paste(":: R This is a test 1\n"))
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#################################################################
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## Section 1 ##
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## Grid initialization ##
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#################################################################
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n <- 100
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m <- 100
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types <- c("scratch", "phreeqc", "rds")
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init_cell <- list(H = 1.476571028625e-01,
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O = 7.392297218936e-02,
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Charge = -1.765225732724e-18,
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`C(-4)` = 2.477908970828e-21,
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`C(4)` = 2.647623016916e-06,
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Ca = 2.889623169138e-05,
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Cl = 4.292806181039e-04,
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`Fe(2)` =1.908142472666e-07,
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`Fe(3)` =3.173306589931e-12,
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`H(0)` =2.675642675119e-15,
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K = 2.530134809667e-06,
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Mg =2.313806319294e-05,
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Na =3.674633059628e-04,
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`S(-2)` = 8.589766637180e-15,
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`S(2)` = 1.205284362720e-19,
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`S(4)` = 9.108958772790e-18,
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`S(6)` = 2.198092329098e-05,
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Sr = 6.012080128154e-07,
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`U(4)` = 1.039668623852e-14,
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`U(5)` = 1.208394829796e-15,
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`U(6)` = 2.976409147150e-12)
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(1, 1),
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type = "scratch",
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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)
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##################################################################
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## Section 2 ##
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## Diffusion parameters and boundary conditions ##
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##################################################################
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vecinj_diffu <- list(
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list(H = 0.147659686316291,
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O = 0.0739242798146046,
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Charge = 7.46361643222701e-20,
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`C(-4)` = 2.92438561098248e-21,
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`C(4)` = 2.65160558871092e-06,
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Ca = 2.89001071336443e-05,
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Cl = 0.000429291158114428,
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`Fe(2)` = 1.90823391198114e-07,
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`Fe(3)` = 3.10832423034763e-12,
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`H(0)` = 2.7888235127385e-15,
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K = 2.5301787e-06,
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Mg = 2.31391999937907e-05,
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Na = 0.00036746969,
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`S(-2)` = 1.01376078438546e-14,
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`S(2)` = 1.42247026981542e-19,
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`S(4)` = 9.49422092568557e-18,
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`S(6)` = 2.19812504654191e-05,
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Sr = 6.01218519999999e-07,
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`U(4)` = 4.82255946569383e-12,
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`U(5)` = 5.49050615347901e-13,
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`U(6)` = 1.32462838991902e-09)
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)
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vecinj <- do.call(rbind.data.frame, vecinj_diffu)
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names(vecinj) <- grid$props
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## diffusion coefficients
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alpha_diffu <- c(H = 1E-6, O = 1E-6, Charge = 1E-6, `C(-4)` = 1E-6,
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`C(4)` = 1E-6, Ca = 1E-6, Cl = 1E-6, `Fe(2)` = 1E-6,
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`Fe(3)` = 1E-6, `H(0)` = 1E-6, K = 1E-6, Mg = 1E-6,
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Na = 1E-6, `S(-2)` = 1E-6, `S(2)` = 1E-6,
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`S(4)` = 1E-6, `S(6)` = 1E-6, Sr = 1E-6,
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`U(4)` = 1E-6, `U(5)` = 1E-6, `U(6)` = 1E-6)
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## list of boundary conditions/inner nodes
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## vecinj_inner <- list(
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## list(1,1,1)
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## )
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boundary <- list(
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"N" = rep(1, n),
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"E" = rep(0, n),
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"S" = rep(0, n),
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"W" = rep(0, n)
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)
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diffu_list <- names(alpha_diffu)
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vecinj <- do.call(rbind.data.frame, vecinj_diffu)
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names(vecinj) <- names(init_cell)
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diffusion <- list(
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init = as.data.frame(init_cell, check.names = FALSE),
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vecinj = vecinj,
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# vecinj_inner = vecinj_inner,
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vecinj_index = boundary,
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alpha = alpha_diffu
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)
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#################################################################
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## Section 3 ##
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## Chemistry module (Phreeqc) ##
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#################################################################
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chemistry <- list(
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database = database,
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input_script = input_script
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)
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#################################################################
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## Section 4 ##
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## Putting all those things together ##
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#################################################################
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iterations <- 10
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dt <- 200
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setup <- list(
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grid = grid,
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diffusion = diffusion,
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chemistry = chemistry,
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iterations = iterations,
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timesteps = rep(dt, iterations),
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store_result = TRUE
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)
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@ -1 +1 @@
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Subproject commit f862889b693507458d450c6319abe5e1dce030f7
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Subproject commit ade4f56605b8d0e81b7ccad510f2db21f46b5ff9
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@ -5,8 +5,10 @@
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#include "PhreeqcRM.h"
|
||||
#include "poet/DHT_Wrapper.hpp"
|
||||
|
||||
#include <array>
|
||||
#include <cstddef>
|
||||
#include <cstdint>
|
||||
#include <map>
|
||||
#include <mpi.h>
|
||||
#include <string>
|
||||
#include <unordered_map>
|
||||
@ -127,35 +129,14 @@ public:
|
||||
};
|
||||
|
||||
/**
|
||||
* Initializes field with a "DataFrame" containing a single value for each
|
||||
* species.
|
||||
* Merge initial values from existing module with the chemistry module and set
|
||||
* according internal variables.
|
||||
*
|
||||
* Each species must have been previously found by
|
||||
* ChemistryModule::RunInitFile.
|
||||
*
|
||||
* \exception std::domain_error Species name of map is not defined.
|
||||
*
|
||||
* \param n_cells Count of cells for each species.
|
||||
* \param mapped_values Unordered map containing one double value for each
|
||||
* specified species.
|
||||
* \param input_map Map with name and initial values of another module like
|
||||
* Diffusion.
|
||||
* \param n_cells number of cells used to initialize the field with.
|
||||
*/
|
||||
void InitializeField(uint32_t n_cells, const SingleCMap &mapped_values);
|
||||
|
||||
/**
|
||||
* Initializes field with a "DataFrame" containing a vector of values for each
|
||||
* species.
|
||||
*
|
||||
* Each species must have been previously found by
|
||||
* ChemistryModule::RunInitFile.
|
||||
*
|
||||
* There is no check if vector length matches count of grid cells defined.
|
||||
*
|
||||
* \exception std::domain_error Species name of map is not defined.
|
||||
*
|
||||
* \param mapped_values Unordered map containing a vector of multiple values.
|
||||
* Size of the vectors shall be the count of grid cells defined previously.
|
||||
*/
|
||||
void InitializeField(const VectorCMap &mapped_values);
|
||||
void mergeFieldWithModule(const SingleCMap &input_map, std::uint32_t n_cells);
|
||||
|
||||
/**
|
||||
* **Only called by workers!** Start the worker listening loop.
|
||||
@ -298,6 +279,7 @@ protected:
|
||||
enum {
|
||||
CHEM_INIT,
|
||||
CHEM_WP_SIZE,
|
||||
CHEM_INIT_SPECIES,
|
||||
CHEM_DHT_ENABLE,
|
||||
CHEM_DHT_SIGNIF_VEC,
|
||||
CHEM_DHT_PROP_TYPE_VEC,
|
||||
@ -365,9 +347,6 @@ protected:
|
||||
std::vector<int32_t> &vecMapping,
|
||||
double dSimTime, double dTimestep);
|
||||
|
||||
void GetWPFromInternals(std::vector<double> &vecWP, uint32_t wp_size);
|
||||
void SetInternalsFromWP(const std::vector<double> &vecWP, uint32_t wp_size);
|
||||
|
||||
std::vector<uint32_t> CalculateWPSizesVector(uint32_t n_cells,
|
||||
uint32_t wp_size) const;
|
||||
|
||||
@ -397,6 +376,7 @@ protected:
|
||||
double idle_t = 0.;
|
||||
double seq_t = 0.;
|
||||
double send_recv_t = 0.;
|
||||
|
||||
#endif
|
||||
|
||||
double chem_t = 0.;
|
||||
@ -405,8 +385,9 @@ protected:
|
||||
uint32_t prop_count = 0;
|
||||
std::vector<std::string> prop_names;
|
||||
std::vector<double> field;
|
||||
std::vector<uint32_t> speciesPerModule;
|
||||
static constexpr uint32_t MODULE_COUNT = 5;
|
||||
static constexpr uint32_t MODULE_COUNT = 4;
|
||||
|
||||
std::array<std::uint32_t, 4> speciesPerModule{};
|
||||
};
|
||||
} // namespace poet
|
||||
|
||||
|
||||
@ -21,7 +21,6 @@
|
||||
#ifndef PARSER_H
|
||||
#define PARSER_H
|
||||
|
||||
#include <bits/stdint-uintn.h>
|
||||
#include <string>
|
||||
#include <string_view>
|
||||
#include <vector>
|
||||
@ -85,7 +84,7 @@ using GridParams = struct s_GridParams {
|
||||
};
|
||||
|
||||
using DiffusionParams = struct s_DiffusionParams {
|
||||
std::vector<std::string> prop_names;
|
||||
Rcpp::DataFrame initial_t;
|
||||
|
||||
Rcpp::NumericVector alpha;
|
||||
Rcpp::List vecinj_inner;
|
||||
|
||||
@ -2,11 +2,15 @@
|
||||
#include "PhreeqcRM.h"
|
||||
#include "poet/DHT_Wrapper.hpp"
|
||||
|
||||
#include <algorithm>
|
||||
#include <bits/stdint-uintn.h>
|
||||
#include <cassert>
|
||||
#include <cstdint>
|
||||
#include <map>
|
||||
#include <mpi.h>
|
||||
#include <stdexcept>
|
||||
#include <string>
|
||||
#include <utility>
|
||||
#include <vector>
|
||||
|
||||
#ifndef POET_USE_PRM
|
||||
@ -58,44 +62,12 @@ void poet::ChemistryModule::RunInitFile(const std::string &input_script_path) {
|
||||
|
||||
this->FindComponents();
|
||||
|
||||
std::vector<std::string> props;
|
||||
this->speciesPerModule.reserve(this->MODULE_COUNT);
|
||||
PhreeqcRM::initializePOET(this->speciesPerModule, this->prop_names);
|
||||
this->prop_count = prop_names.size();
|
||||
|
||||
std::vector<std::string> curr_prop_names = this->GetComponents();
|
||||
props.insert(props.end(), curr_prop_names.begin(), curr_prop_names.end());
|
||||
this->speciesPerModule.push_back(curr_prop_names.size());
|
||||
|
||||
curr_prop_names = this->GetEquilibriumPhases();
|
||||
props.insert(props.end(), curr_prop_names.begin(), curr_prop_names.end());
|
||||
char equilibrium = (curr_prop_names.empty() ? -1 : 1);
|
||||
this->speciesPerModule.push_back(curr_prop_names.size());
|
||||
|
||||
curr_prop_names = this->GetExchangeNames();
|
||||
props.insert(props.end(), curr_prop_names.begin(), curr_prop_names.end());
|
||||
char exchange = (curr_prop_names.empty() ? -1 : 1);
|
||||
this->speciesPerModule.push_back(curr_prop_names.size());
|
||||
|
||||
curr_prop_names = this->GetSurfaceNames();
|
||||
props.insert(props.end(), curr_prop_names.begin(), curr_prop_names.end());
|
||||
char surface = (curr_prop_names.empty() ? -1 : 1);
|
||||
this->speciesPerModule.push_back(curr_prop_names.size());
|
||||
|
||||
// curr_prop_names = this->GetGasComponents();
|
||||
// props.insert(props.end(), curr_prop_names.begin(), curr_prop_names.end());
|
||||
// char gas = (curr_prop_names.empty() ? -1 : 1);
|
||||
// this->speciesPerModule.push_back(curr_prop_names.size());
|
||||
|
||||
// curr_prop_names = this->GetSolidSolutionNames();
|
||||
// props.insert(props.end(), curr_prop_names.begin(), curr_prop_names.end());
|
||||
// char ssolutions = (curr_prop_names.empty() ? -1 : 1);
|
||||
// this->speciesPerModule.push_back(curr_prop_names.size());
|
||||
|
||||
curr_prop_names = this->GetKineticReactions();
|
||||
props.insert(props.end(), curr_prop_names.begin(), curr_prop_names.end());
|
||||
char kinetics = (curr_prop_names.empty() ? -1 : 1);
|
||||
this->speciesPerModule.push_back(curr_prop_names.size());
|
||||
|
||||
this->prop_count = props.size();
|
||||
char exchange = (speciesPerModule[1] == 0 ? -1 : 1);
|
||||
char kinetics = (speciesPerModule[2] == 0 ? -1 : 1);
|
||||
char equilibrium = (speciesPerModule[3] == 0 ? -1 : 1);
|
||||
|
||||
#ifdef POET_USE_PRM
|
||||
std::vector<int> ic1;
|
||||
@ -105,7 +77,7 @@ void poet::ChemistryModule::RunInitFile(const std::string &input_script_path) {
|
||||
ic1[i] = 1; // Solution 1
|
||||
ic1[nxyz + i] = equilibrium; // Equilibrium 1
|
||||
ic1[2 * nxyz + i] = exchange; // Exchange none
|
||||
ic1[3 * nxyz + i] = surface; // Surface none
|
||||
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] = kinetics; // Kinetics 1
|
||||
@ -113,61 +85,105 @@ void poet::ChemistryModule::RunInitFile(const std::string &input_script_path) {
|
||||
|
||||
this->InitialPhreeqc2Module(ic1);
|
||||
#else
|
||||
if (!this->is_master || this->is_sequential) {
|
||||
std::vector<int> ic1;
|
||||
ic1.resize(this->nxyz * 7, -1);
|
||||
// TODO: hardcoded reaction modules
|
||||
for (int i = 0; i < nxyz; i++) {
|
||||
ic1[i] = 1; // Solution 1
|
||||
ic1[nxyz + i] = equilibrium; // Equilibrium 1
|
||||
ic1[2 * nxyz + i] = exchange; // Exchange none
|
||||
ic1[3 * nxyz + i] = surface; // Surface none
|
||||
ic1[4 * nxyz + i] = -1; // Gas phase none
|
||||
ic1[5 * nxyz + i] = -1; // Solid solutions none
|
||||
ic1[6 * nxyz + i] = kinetics; // Kinetics 1
|
||||
}
|
||||
|
||||
this->InitialPhreeqc2Module(ic1);
|
||||
std::vector<int> ic1;
|
||||
ic1.resize(this->nxyz * 7, -1);
|
||||
// TODO: hardcoded reaction modules
|
||||
for (int i = 0; i < nxyz; i++) {
|
||||
ic1[i] = 1; // Solution 1
|
||||
ic1[nxyz + i] = equilibrium; // Equilibrium 1
|
||||
ic1[2 * nxyz + i] = exchange; // Exchange none
|
||||
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] = kinetics; // Kinetics 1
|
||||
}
|
||||
|
||||
this->InitialPhreeqc2Module(ic1);
|
||||
#endif
|
||||
this->prop_names = props;
|
||||
}
|
||||
|
||||
#ifndef POET_USE_PRM
|
||||
void poet::ChemistryModule::InitializeField(
|
||||
uint32_t n_cells, const poet::ChemistryModule::SingleCMap &mapped_values) {
|
||||
if (this->is_master) {
|
||||
this->field.reserve(this->prop_count * n_cells);
|
||||
for (const std::string &prop_name : this->prop_names) {
|
||||
const auto m_it = mapped_values.find(prop_name);
|
||||
if (m_it == mapped_values.end()) {
|
||||
throw std::domain_error(
|
||||
"Prop names vector does not match any key in given map.");
|
||||
}
|
||||
void poet::ChemistryModule::mergeFieldWithModule(const SingleCMap &input_map,
|
||||
std::uint32_t n_cells) {
|
||||
|
||||
const std::vector<double> field_row(n_cells, m_it->second);
|
||||
const auto chem_field_end = this->field.end();
|
||||
this->field.insert(chem_field_end, field_row.begin(), field_row.end());
|
||||
}
|
||||
this->n_cells = n_cells;
|
||||
if (is_master) {
|
||||
int f_type = CHEM_INIT_SPECIES;
|
||||
PropagateFunctionType(f_type);
|
||||
}
|
||||
}
|
||||
|
||||
void poet::ChemistryModule::InitializeField(
|
||||
const poet::ChemistryModule::VectorCMap &mapped_values) {
|
||||
if (this->is_master) {
|
||||
for (const std::string &prop_name : this->prop_names) {
|
||||
const auto m_it = mapped_values.find(prop_name);
|
||||
if (m_it == mapped_values.end()) {
|
||||
throw std::domain_error(
|
||||
"Prop names vector does not match any key in given map.");
|
||||
std::vector<std::string> essentials_backup{
|
||||
prop_names.begin() + speciesPerModule[0], prop_names.end()};
|
||||
|
||||
std::vector<std::string> new_solution_names{
|
||||
this->prop_names.begin(), this->prop_names.begin() + speciesPerModule[0]};
|
||||
|
||||
if (is_master) {
|
||||
for (const auto &init_val : input_map) {
|
||||
std::string name = init_val.first;
|
||||
if (std::find(new_solution_names.begin(), new_solution_names.end(),
|
||||
name) == new_solution_names.end()) {
|
||||
int size = name.size();
|
||||
ChemBCast(&size, 1, MPI_INT);
|
||||
ChemBCast(name.data(), name.size(), MPI_CHAR);
|
||||
new_solution_names.push_back(name);
|
||||
}
|
||||
|
||||
const auto field_row = m_it->second;
|
||||
const auto chem_field_end = this->field.end();
|
||||
this->field.insert(chem_field_end, field_row.begin(), field_row.end());
|
||||
}
|
||||
this->n_cells = mapped_values.begin()->second.size();
|
||||
int end = 0;
|
||||
ChemBCast(&end, 1, MPI_INT);
|
||||
} else {
|
||||
constexpr int MAXSIZE = 128;
|
||||
MPI_Status status;
|
||||
int recv_size;
|
||||
char recv_buffer[MAXSIZE];
|
||||
while (1) {
|
||||
ChemBCast(&recv_size, 1, MPI_INT);
|
||||
if (recv_size == 0) {
|
||||
break;
|
||||
}
|
||||
ChemBCast(recv_buffer, recv_size, MPI_CHAR);
|
||||
recv_buffer[recv_size] = '\0';
|
||||
new_solution_names.push_back(std::string(recv_buffer));
|
||||
}
|
||||
}
|
||||
|
||||
// now sort the new values
|
||||
std::sort(new_solution_names.begin() + 3, new_solution_names.end());
|
||||
|
||||
// and append other processes than solutions
|
||||
std::vector<std::string> new_prop_names = new_solution_names;
|
||||
new_prop_names.insert(new_prop_names.end(), essentials_backup.begin(),
|
||||
essentials_backup.end());
|
||||
|
||||
std::vector<std::string> old_prop_names{this->prop_names};
|
||||
this->prop_names = std::move(new_prop_names);
|
||||
this->prop_count = prop_names.size();
|
||||
|
||||
this->SetPOETSolutionNames(new_solution_names);
|
||||
|
||||
if (is_master) {
|
||||
this->n_cells = n_cells;
|
||||
|
||||
this->field.clear();
|
||||
this->field.reserve(this->prop_count * n_cells);
|
||||
|
||||
std::vector<double> init_values;
|
||||
this->getDumpedField(init_values);
|
||||
|
||||
const std::vector<std::string> ess_names = old_prop_names;
|
||||
|
||||
for (const auto &name : this->prop_names) {
|
||||
auto it_find = std::find(ess_names.begin(), ess_names.end(), name);
|
||||
double value;
|
||||
if (it_find != ess_names.end()) {
|
||||
int index = it_find - ess_names.begin();
|
||||
value = init_values[index];
|
||||
} else {
|
||||
auto map_it = input_map.find(name);
|
||||
value = map_it->second;
|
||||
}
|
||||
std::vector<double> curr_vec(n_cells, value);
|
||||
this->field.insert(field.end(), curr_vec.begin(), curr_vec.end());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -274,89 +290,26 @@ void poet::ChemistryModule::ReadDHTFile(const std::string &input_file) {
|
||||
}
|
||||
}
|
||||
|
||||
void poet::ChemistryModule::GetWPFromInternals(std::vector<double> &vecWP,
|
||||
uint32_t wp_size) {
|
||||
std::vector<double> vecCurrOutput;
|
||||
|
||||
vecWP.clear();
|
||||
vecWP.reserve(this->prop_count * wp_size);
|
||||
|
||||
this->GetConcentrations(vecCurrOutput);
|
||||
vecWP.insert(vecWP.end(), vecCurrOutput.begin(), vecCurrOutput.end());
|
||||
|
||||
if (this->speciesPerModule[1] != 0) {
|
||||
this->GetPPhaseMoles(vecCurrOutput);
|
||||
vecWP.insert(vecWP.end(), vecCurrOutput.begin(), vecCurrOutput.end());
|
||||
}
|
||||
|
||||
// NOTE: Block for 'Surface' and 'Exchange' is missing because of missing
|
||||
// Getters @ PhreeqcRM
|
||||
// ...
|
||||
// BLOCK_END
|
||||
|
||||
if (this->speciesPerModule[4] != 0) {
|
||||
this->GetKineticsMoles(vecCurrOutput);
|
||||
vecWP.insert(vecWP.end(), vecCurrOutput.begin(), vecCurrOutput.end());
|
||||
}
|
||||
}
|
||||
void poet::ChemistryModule::SetInternalsFromWP(const std::vector<double> &vecWP,
|
||||
uint32_t wp_size) {
|
||||
uint32_t iCurrElements;
|
||||
|
||||
auto itStart = vecWP.begin();
|
||||
auto itEnd = itStart;
|
||||
|
||||
// this->SetMappingForWP(iCurrWPSize);
|
||||
|
||||
int nchem = this->GetChemistryCellCount();
|
||||
|
||||
iCurrElements = this->speciesPerModule[0];
|
||||
|
||||
itEnd += iCurrElements * wp_size;
|
||||
this->SetConcentrations(std::vector<double>(itStart, itEnd));
|
||||
itStart = itEnd;
|
||||
|
||||
// Equlibirum Phases
|
||||
if ((iCurrElements = this->speciesPerModule[1]) != 0) {
|
||||
itEnd += iCurrElements * wp_size;
|
||||
this->SetPPhaseMoles(std::vector<double>(itStart, itEnd));
|
||||
itStart = itEnd;
|
||||
}
|
||||
|
||||
// // NOTE: Block for 'Surface' and 'Exchange' is missing because of missing
|
||||
// // setters @ PhreeqcRM
|
||||
// // ...
|
||||
// // BLOCK_END
|
||||
|
||||
if ((iCurrElements = this->speciesPerModule[4]) != 0) {
|
||||
itEnd += iCurrElements * wp_size;
|
||||
this->SetKineticsMoles(std::vector<double>(itStart, itEnd));
|
||||
itStart = itEnd;
|
||||
}
|
||||
}
|
||||
|
||||
#else //POET_USE_PRM
|
||||
#else // POET_USE_PRM
|
||||
|
||||
inline void poet::ChemistryModule::PrmToPoetField(std::vector<double> &field) {
|
||||
GetConcentrations(field);
|
||||
int col = GetSelectedOutputColumnCount();
|
||||
int rows = GetSelectedOutputRowCount();
|
||||
|
||||
field.reserve(field.size() + 3 * rows);
|
||||
|
||||
std::vector<double> so;
|
||||
GetSelectedOutput(so);
|
||||
|
||||
for (int j = 0; j < col; j += 2) {
|
||||
const auto start = so.begin() + (j * rows);
|
||||
const auto end = start + rows;
|
||||
field.insert(field.end(), start, end);
|
||||
}
|
||||
this->getDumpedField(field);
|
||||
}
|
||||
|
||||
void poet::ChemistryModule::RunCells() {
|
||||
PhreeqcRM::RunCells();
|
||||
PrmToPoetField(this->field);
|
||||
|
||||
std::vector<double> tmp_field;
|
||||
|
||||
PrmToPoetField(tmp_field);
|
||||
this->field = tmp_field;
|
||||
|
||||
for (uint32_t i = 0; i < field.size(); i++) {
|
||||
uint32_t back_i = static_cast<uint32_t>(i / this->nxyz);
|
||||
uint32_t mod_i = i % this->nxyz;
|
||||
|
||||
field[i] = tmp_field[back_i + (mod_i * this->prop_count)];
|
||||
}
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
@ -233,9 +233,12 @@ void poet::ChemistryModule::RunCells() {
|
||||
}
|
||||
|
||||
void poet::ChemistryModule::MasterRunSequential() {
|
||||
SetInternalsFromWP(this->field, this->nxyz);
|
||||
std::vector<double> shuffled_field =
|
||||
shuffleField(field, n_cells, prop_count, 1);
|
||||
this->setDumpedField(shuffled_field);
|
||||
PhreeqcRM::RunCells();
|
||||
GetWPFromInternals(this->field, this->nxyz);
|
||||
this->getDumpedField(shuffled_field);
|
||||
unshuffleField(shuffled_field, n_cells, prop_count, 1, this->field);
|
||||
}
|
||||
|
||||
void poet::ChemistryModule::MasterRunParallel() {
|
||||
|
||||
@ -5,6 +5,7 @@
|
||||
#include <cstdint>
|
||||
#include <iomanip>
|
||||
#include <iostream>
|
||||
#include <map>
|
||||
#include <mpi.h>
|
||||
#include <stdexcept>
|
||||
#include <string>
|
||||
@ -42,6 +43,12 @@ void poet::ChemistryModule::WorkerLoop() {
|
||||
RunInitFile(get_string(0, this->group_comm));
|
||||
break;
|
||||
}
|
||||
case CHEM_INIT_SPECIES: {
|
||||
SingleCMap dummy_map;
|
||||
std::uint32_t n_cells_dummy;
|
||||
mergeFieldWithModule(dummy_map, n_cells_dummy);
|
||||
break;
|
||||
}
|
||||
case CHEM_DHT_ENABLE: {
|
||||
bool enable;
|
||||
ChemBCast(&enable, 1, MPI_CXX_BOOL);
|
||||
@ -339,32 +346,16 @@ poet::ChemistryModule::WorkerRunWorkPackage(std::vector<double> &vecWP,
|
||||
return IRM_OK;
|
||||
}
|
||||
|
||||
std::vector<double> vecCopy;
|
||||
|
||||
vecCopy = vecWP;
|
||||
for (uint32_t i = 0; i < this->prop_count; i++) {
|
||||
for (uint32_t j = 0; j < this->wp_size; j++) {
|
||||
vecWP[(i * this->wp_size) + j] = vecCopy[(j * this->prop_count) + i];
|
||||
}
|
||||
}
|
||||
|
||||
IRM_RESULT result;
|
||||
this->PhreeqcRM::CreateMapping(vecMapping);
|
||||
this->SetInternalsFromWP(vecWP, this->wp_size);
|
||||
this->setDumpedField(vecWP);
|
||||
|
||||
this->PhreeqcRM::SetTime(dSimTime);
|
||||
this->PhreeqcRM::SetTimeStep(dTimestep);
|
||||
|
||||
result = this->PhreeqcRM::RunCells();
|
||||
|
||||
this->GetWPFromInternals(vecWP, this->wp_size);
|
||||
|
||||
vecCopy = vecWP;
|
||||
for (uint32_t i = 0; i < this->prop_count; i++) {
|
||||
for (uint32_t j = 0; j < this->wp_size; j++) {
|
||||
vecWP[(j * this->prop_count) + i] = vecCopy[(i * this->wp_size) + j];
|
||||
}
|
||||
}
|
||||
this->getDumpedField(vecWP);
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
@ -74,7 +74,8 @@ void DiffusionModule::initialize(poet::DiffusionParams args) {
|
||||
// const poet::DiffusionParams args(this->R);
|
||||
|
||||
// name of props
|
||||
this->prop_names = args.prop_names;
|
||||
//
|
||||
this->prop_names = Rcpp::as<std::vector<std::string>>(args.initial_t.names());
|
||||
this->prop_count = this->prop_names.size();
|
||||
|
||||
this->state =
|
||||
@ -91,7 +92,9 @@ void DiffusionModule::initialize(poet::DiffusionParams args) {
|
||||
// initial input
|
||||
this->alpha.push_back(args.alpha[this->prop_names[i]]);
|
||||
|
||||
std::vector<double> prop_vec = grid.GetSpeciesByName(this->prop_names[i]);
|
||||
double val = args.initial_t[prop_names[i]];
|
||||
|
||||
std::vector<double> prop_vec(n_cells_per_prop, val);
|
||||
std::copy(prop_vec.begin(), prop_vec.end(),
|
||||
field.begin() + (i * this->n_cells_per_prop));
|
||||
if (this->dim == this->DIM_2D) {
|
||||
|
||||
@ -21,7 +21,6 @@
|
||||
#include "poet/SimParams.hpp"
|
||||
#include <RInside.h>
|
||||
#include <Rcpp.h>
|
||||
#include <Rcpp/internal/wrap.h>
|
||||
#include <algorithm>
|
||||
#include <cassert>
|
||||
#include <cstdint>
|
||||
|
||||
@ -19,7 +19,6 @@
|
||||
*/
|
||||
|
||||
#include "poet/DHT_Types.hpp"
|
||||
#include <bits/stdint-uintn.h>
|
||||
#include <poet/SimParams.hpp>
|
||||
|
||||
#include <RInside.h>
|
||||
@ -51,8 +50,8 @@ poet::GridParams::s_GridParams(RInside &R) {
|
||||
}
|
||||
|
||||
poet::DiffusionParams::s_DiffusionParams(RInside &R) {
|
||||
this->prop_names = Rcpp::as<std::vector<std::string>>(
|
||||
R.parseEval("names(mysetup$diffusion$init)"));
|
||||
this->initial_t =
|
||||
Rcpp::as<Rcpp::DataFrame>(R.parseEval("mysetup$diffusion$init"));
|
||||
this->alpha =
|
||||
Rcpp::as<Rcpp::NumericVector>(R.parseEval("mysetup$diffusion$alpha"));
|
||||
if (Rcpp::as<bool>(
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user