mirror of
https://git.gfz-potsdam.de/naaice/poet.git
synced 2025-12-16 12:54:50 +01:00
Update getModuleSizes function to use new API
This commit is contained in:
Max Lübke
parent
c9cf6c92e7
commit
8d6aafbec4
@ -1 +1 @@
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Subproject commit d92ab31765d3850beb0b9e980b7b82696e56e4fc
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Subproject commit b34c327377e2e06fb1d79b546996b9b401e850bc
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@ -1,6 +1,7 @@
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#include "InitialList.hpp"
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#include "InitialList.hpp"
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#include <IPhreeqcPOET.hpp>
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#include <IPhreeqcPOET.hpp>
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#include <RInside.h>
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#include <Rcpp/Function.h>
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#include <Rcpp/Function.h>
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#include <Rcpp/vector/instantiation.h>
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#include <Rcpp/vector/instantiation.h>
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#include <algorithm>
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#include <algorithm>
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@ -12,28 +13,25 @@
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namespace poet {
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namespace poet {
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static Rcpp::NumericMatrix pqcScriptToGrid(IPhreeqcPOET &phreeqc, RInside &R) {
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static Rcpp::NumericMatrix pqcScriptToGrid(IPhreeqcPOET &phreeqc, RInside &R) {
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IPhreeqcPOET::PhreeqcMat phreeqc_mat = phreeqc.getPhreeqcMat();
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const auto solution_ids = phreeqc.getSolutionIds();
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auto col_names = phreeqc.getInitNames();
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const auto concentrations = phreeqc.getInitValues();
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// add "id" to the front of the column names
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// add "id" to the front of the column names
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const std::size_t ncols = col_names.size();
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const std::size_t ncols = phreeqc_mat.names.size();
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const std::size_t nrows = solution_ids.size();
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const std::size_t nrows = phreeqc_mat.values.size();
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col_names.insert(col_names.begin(), "id");
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phreeqc_mat.names.insert(phreeqc_mat.names.begin(), "ID");
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Rcpp::NumericMatrix mat(nrows, ncols + 1);
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Rcpp::NumericMatrix mat(nrows, ncols + 1);
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for (std::size_t i = 0; i < nrows; i++) {
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for (std::size_t i = 0; i < nrows; i++) {
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mat(i, 0) = solution_ids[i];
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mat(i, 0) = phreeqc_mat.ids[i];
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for (std::size_t j = 0; j < ncols; ++j) {
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for (std::size_t j = 0; j < ncols; ++j) {
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mat(i, j + 1) = concentrations[i][j];
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mat(i, j + 1) = phreeqc_mat.values[i][j];
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}
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}
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}
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}
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Rcpp::colnames(mat) = Rcpp::wrap(col_names);
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Rcpp::colnames(mat) = Rcpp::wrap(phreeqc_mat.names);
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return mat;
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return mat;
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}
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}
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@ -59,18 +57,22 @@ replaceRawKeywordIDs(std::map<int, std::string> raws) {
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}
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}
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static inline IPhreeqcPOET::ModulesArray
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static inline IPhreeqcPOET::ModulesArray
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modifyModuleSizes(IPhreeqcPOET::ModulesArray sizes,
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getModuleSizes(IPhreeqcPOET &phreeqc, const Rcpp::List &initial_grid) {
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const Rcpp::NumericMatrix &phreeqc_mat,
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IPhreeqcPOET::ModulesArray mod_array;
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const Rcpp::List &initial_grid) {
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Rcpp::Function unique("unique");
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std::vector<std::uint32_t> sizes_vec(sizes.begin(), sizes.end());
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Rcpp::Function modify_sizes("modify_module_sizes");
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std::vector<int> row_ids =
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sizes_vec = Rcpp::as<std::vector<std::uint32_t>>(
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Rcpp::as<std::vector<int>>(unique(initial_grid["ID"]));
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modify_sizes(sizes_vec, phreeqc_mat, initial_grid));
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std::copy(sizes_vec.begin(), sizes_vec.end(), sizes.begin());
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// std::vector<std::uint32_t> sizes_vec(sizes.begin(), sizes.end());
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return sizes;
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// Rcpp::Function modify_sizes("modify_module_sizes");
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// sizes_vec = Rcpp::as<std::vector<std::uint32_t>>(
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// modify_sizes(sizes_vec, phreeqc_mat, initial_grid));
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// std::copy(sizes_vec.begin(), sizes_vec.end(), sizes.begin());
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return phreeqc.getModuleSizes(row_ids);
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}
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}
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void InitialList::initGrid(const Rcpp::List &grid_input) {
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void InitialList::initGrid(const Rcpp::List &grid_input) {
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@ -123,8 +125,7 @@ void InitialList::initGrid(const Rcpp::List &grid_input) {
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this->phreeqc_mat = pqcScriptToGrid(phreeqc, R);
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this->phreeqc_mat = pqcScriptToGrid(phreeqc, R);
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this->initial_grid = matToGrid(R, this->phreeqc_mat, grid_def);
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this->initial_grid = matToGrid(R, this->phreeqc_mat, grid_def);
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this->module_sizes = modifyModuleSizes(phreeqc.getModuleSizes(),
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this->module_sizes = getModuleSizes(phreeqc, this->initial_grid);
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this->phreeqc_mat, this->initial_grid);
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// print module sizes
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// print module sizes
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for (std::size_t i = 0; i < this->module_sizes.size(); i++) {
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for (std::size_t i = 0; i < this->module_sizes.size(); i++) {
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396
src/poet.hpp
396
src/poet.hpp
@ -1,396 +0,0 @@
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#ifndef POET_H
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#define POET_H
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#include <string>
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static const char *poet_version = "tmp/ml/v0.2-107-g9990c12";
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// using the Raw string literal to avoid escaping the quotes
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static inline std::string kin_r_library = R"(## Time-stamp: "Last modified 2023-08-15 11:58:23 delucia"
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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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### Foundation; either version 2 of the License, or (at your option) any later
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### version.
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###
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### POET is distributed in the hope that it will be useful, but WITHOUT ANY
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### WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
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### A PARTICULAR PURPOSE. See the GNU General Public License for more details.
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###
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### You should have received a copy of the GNU General Public License along with
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### this program; if not, write to the Free Software Foundation, Inc., 51
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### Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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## Simple function to check file extension. It is needed to check if
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## the GridFile is SUM (MUFITS format) or rds/RData
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FileExt <- function(x) {
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pos <- regexpr("\\.([[:alnum:]]+)$", x)
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ifelse(pos > -1L, substring(x, pos + 1L), "")
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}
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master_init <- function(setup) {
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msgm("Process with rank 0 reading GRID properties")
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## Setup the directory where we will store the results
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verb <- FALSE
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if (local_rank == 0) {
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verb <- TRUE ## verbosity loading MUFITS results
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if (!dir.exists(fileout)) {
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dir.create(fileout)
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msgm("created directory ", fileout)
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} else {
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msgm("dir ", fileout, " already exists, I will overwrite!")
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}
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if (!exists("store_result")) {
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msgm("store_result doesn't exist!")
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} else {
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msgm("store_result is ", store_result)
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}
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} else {
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}
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setup$iter <- 1
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setup$maxiter <- setup$iterations
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setup$timesteps <- setup$timesteps
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setup$simulation_time <- 0
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if (is.null(setup[["store_result"]])) {
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setup$store_result <- TRUE
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}
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if (setup$store_result) {
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if (is.null(setup[["out_save"]])) {
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setup$out_save <- seq(1, setup$iterations)
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}
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}
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return(setup)
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}
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## This function, called only by master, stores on disk the last
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## calculated time step if store_result is TRUE and increments the
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## iteration counter
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master_iteration_end <- function(setup) {
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iter <- setup$iter
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## max digits for iterations
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dgts <- as.integer(ceiling(log10(setup$iterations + 1)))
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## string format to use in sprintf
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fmt <- paste0("%0", dgts, "d")
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## Write on disk state_T and state_C after every iteration
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## comprised in setup$out_save
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if (setup$store_result) {
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if (iter %in% setup$out_save) {
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nameout <- paste0(fileout, "/iter_", sprintf(fmt=fmt, iter), ".rds")
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info <- list(
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tr_req_dt = as.integer(setup$req_dt)
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## tr_allow_dt = setup$allowed_dt,
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## tr_inniter = as.integer(setup$inniter)
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)
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saveRDS(list(
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T = setup$state_T, C = setup$state_C,
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simtime = as.integer(setup$simtime),
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tr_info = info
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), file = nameout)
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msgm("results stored in <", nameout, ">")
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}
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}
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msgm("done iteration", iter, "/", setup$maxiter)
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setup$iter <- setup$iter + 1
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return(setup)
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}
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## function for the workers to compute chemistry through PHREEQC
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slave_chemistry <- function(setup, data) {
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base <- setup$base
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first <- setup$first
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prop <- setup$prop
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immobile <- setup$immobile
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kin <- setup$kin
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ann <- setup$ann
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iter <- setup$iter
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timesteps <- setup$timesteps
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dt <- timesteps[iter]
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state_T <- data ## not the global field, but the work-package
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## treat special H+/pH, e-/pe cases
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state_T <- RedModRphree::Act2pH(state_T)
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## reduction of the problem
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if (setup$reduce) {
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reduced <- ReduceStateOmit(state_T, omit = setup$ann)
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} else {
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reduced <- state_T
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}
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## form the PHREEQC input script for the current work package
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inplist <- SplitMultiKin(
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data = reduced, procs = 1, base = base, first = first,
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ann = ann, prop = prop, minerals = immobile, kin = kin, dt = dt
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)
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## if (local_rank==1 & iter==1)
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## RPhreeWriteInp("FirstInp", inplist)
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tmpC <- RunPQC(inplist, procs = 1, second = TRUE)
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## recompose after the reduction
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if (setup$reduce) {
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state_C <- RecomposeState(tmpC, reduced)
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} else {
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state_C <- tmpC
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}
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## the next line is needed since we don't need all columns of
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## PHREEQC output
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return(state_C[, prop])
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}
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## This function, called by master
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master_chemistry <- function(setup, data) {
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state_T <- setup$state_T
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msgm(" chemistry iteration", setup$iter)
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## treat special H+/pH, e-/pe cases
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state_T <- RedModRphree::Act2pH(state_T)
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## reduction of the problem
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if (setup$reduce) {
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reduced <- ReduceStateOmit(state_T, omit = setup$ann)
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} else {
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reduced <- state_T
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}
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## inject data from workers
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res_C <- data
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rownames(res_C) <- NULL
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## print(res_C)
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if (nrow(res_C) > nrow(reduced)) {
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res_C <- res_C[seq(2, nrow(res_C), by = 2), ]
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}
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## recompose after the reduction
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if (setup$reduce) {
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state_C <- RecomposeState(res_C, reduced)
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} else {
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state_C <- res_C
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}
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setup$state_C <- state_C
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setup$reduced <- reduced
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return(setup)
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}
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## Adapted version for "reduction"
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ReduceStateOmit <- function(data, omit = NULL, sign = 6) {
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require(mgcv)
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rem <- colnames(data)
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if (is.list(omit)) {
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indomi <- match(names(omit), colnames(data))
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datao <- data[, -indomi]
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} else {
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datao <- data
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}
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datao <- signif(datao, sign)
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red <- mgcv::uniquecombs(datao)
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inds <- attr(red, "index")
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now <- ncol(red)
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## reattach the omitted column(s)
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## FIXME: control if more than one ann is present
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if (is.list(omit)) {
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red <- cbind(red, rep(data[1, indomi], nrow(red)))
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colnames(red)[now + 1] <- names(omit)
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ret <- red[, colnames(data)]
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} else {
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ret <- red
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}
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rownames(ret) <- NULL
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attr(ret, "index") <- inds
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return(ret)
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}
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## Attach the name of the calling function to the message displayed on
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## R's stdout
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msgm <- function(...) {
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if (local_rank == 0) {
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fname <- as.list(sys.call(-1))[[1]]
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prefix <- paste0("R: ", fname, " ::")
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cat(paste(prefix, ..., "\n"))
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}
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invisible()
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}
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## Function called by master R process to store on disk all relevant
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## parameters for the simulation
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StoreSetup <- function(setup) {
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to_store <- vector(mode = "list", length = 4)
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## names(to_store) <- c("Sim", "Flow", "Transport", "Chemistry", "DHT")
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names(to_store) <- c("Sim", "Transport", "DHT", "Cmdline")
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## read the setup R file, which is sourced in kin.cpp
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tmpbuff <- file(filesim, "r")
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setupfile <- readLines(tmpbuff)
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close.connection(tmpbuff)
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to_store$Sim <- setupfile
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## to_store$Flow <- list(
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## snapshots = setup$snapshots,
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## gridfile = setup$gridfile,
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## phase = setup$phase,
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## density = setup$density,
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## dt_differ = setup$dt_differ,
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## prolong = setup$prolong,
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## maxiter = setup$maxiter,
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## saved_iter = setup$iter_output,
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## out_save = setup$out_save )
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to_store$Transport <- setup$diffusion
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## to_store$Chemistry <- list(
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## nprocs = n_procs,
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## wp_size = work_package_size,
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## base = setup$base,
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## first = setup$first,
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## init = setup$initsim,
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## db = db,
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## kin = setup$kin,
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## ann = setup$ann)
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if (dht_enabled) {
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to_store$DHT <- list(
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enabled = dht_enabled,
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log = dht_log
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## signif = dht_final_signif,
|
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||||||
## proptype = dht_final_proptype
|
|
||||||
)
|
|
||||||
} else {
|
|
||||||
to_store$DHT <- FALSE
|
|
||||||
}
|
|
||||||
|
|
||||||
if (dht_enabled) {
|
|
||||||
to_store$DHT <- list(
|
|
||||||
enabled = dht_enabled,
|
|
||||||
log = dht_log
|
|
||||||
#signif = dht_final_signif,
|
|
||||||
#proptype = dht_final_proptype
|
|
||||||
)
|
|
||||||
} else {
|
|
||||||
to_store$DHT <- FALSE
|
|
||||||
}
|
|
||||||
|
|
||||||
saveRDS(to_store, file = paste0(fileout, "/setup.rds"))
|
|
||||||
msgm("initialization stored in ", paste0(fileout, "/setup.rds"))
|
|
||||||
}
|
|
||||||
|
|
||||||
GetWorkPackageSizesVector <- function(n_packages, package_size, len) {
|
|
||||||
ids <- rep(1:n_packages, times=package_size, each = 1)[1:len]
|
|
||||||
return(as.integer(table(ids)))
|
|
||||||
}
|
|
||||||
)";
|
|
||||||
|
|
||||||
static inline std::string init_r_library = R"(input <- readRDS("/home/max/Storage/poet/build/apps/out.rds")
|
|
||||||
|
|
||||||
grid_def <- matrix(c(2, 3), nrow = 2, ncol = 5)
|
|
||||||
|
|
||||||
library(data.table)
|
|
||||||
|
|
||||||
pqc_to_grid <- function(pqc_in, grid) {
|
|
||||||
# Convert the input DataFrame to a data.table
|
|
||||||
dt <- data.table(pqc_in)
|
|
||||||
|
|
||||||
# Flatten the matrix into a vector
|
|
||||||
id_vector <- as.vector(t(grid))
|
|
||||||
|
|
||||||
# Initialize an empty data.table to store the results
|
|
||||||
result_dt <- data.table()
|
|
||||||
|
|
||||||
# Iterate over each ID in the vector
|
|
||||||
for (id_mat in id_vector) {
|
|
||||||
# Find the matching row in the data.table
|
|
||||||
matching_dt <- dt[id == id_mat]
|
|
||||||
|
|
||||||
# Append the matching data.table row to the result data.table
|
|
||||||
result_dt <- rbind(result_dt, matching_dt)
|
|
||||||
}
|
|
||||||
|
|
||||||
# Remove all columns which only contain NaN
|
|
||||||
# result_dt <- result_dt[, colSums(is.na(result_dt)) != nrow(result_dt)]
|
|
||||||
|
|
||||||
res_df <- as.data.frame(result_dt)
|
|
||||||
|
|
||||||
return(res_df[, colSums(is.na(res_df)) != nrow(res_df)])
|
|
||||||
}
|
|
||||||
|
|
||||||
pqc_init <- pqc_to_grid(input, grid_def)
|
|
||||||
test <- pqc_init
|
|
||||||
|
|
||||||
modify_module_sizes <- function(mod_sizes, pqc_mat, init_grid) {
|
|
||||||
# Find all unique IDs in init_grid
|
|
||||||
unique_ids <- unique(as.vector(init_grid$id))
|
|
||||||
|
|
||||||
# remove rows from pqc_mat that are not in init_grid
|
|
||||||
pqc_mat <- as.data.frame(pqc_mat)
|
|
||||||
pqc_mat <- pqc_mat[pqc_mat$id %in% unique_ids, ]
|
|
||||||
|
|
||||||
# Find the column indices where all rows are NA
|
|
||||||
na_cols <- which(colSums(is.na(pqc_mat)) == nrow(pqc_mat))
|
|
||||||
|
|
||||||
# Build cumsum over mod_sizes
|
|
||||||
cum_mod_sizes <- cumsum(mod_sizes)
|
|
||||||
|
|
||||||
# Find the indices where the value of na_cols is equal to the value of cum_mod_sizes
|
|
||||||
idx <- which(cum_mod_sizes %in% na_cols)
|
|
||||||
|
|
||||||
# Set the value of mod_sizes to 0 at the indices found in the previous step
|
|
||||||
mod_sizes[idx] <- 0
|
|
||||||
|
|
||||||
return(mod_sizes)
|
|
||||||
}
|
|
||||||
|
|
||||||
# mod_sizes <- c(7, 0, 4, 2, 0)
|
|
||||||
|
|
||||||
# unique_ids <- unique(as.vector(pqc_init$id))
|
|
||||||
|
|
||||||
# tmp <- as.data.frame(input)
|
|
||||||
# pqc_test <- tmp[tmp$id %in% unique_ids, ]
|
|
||||||
# na_cols <- which(colSums(is.na(pqc_test)) == nrow(pqc_test))
|
|
||||||
# cum_mod_sizes <- cumsum(mod_sizes)
|
|
||||||
|
|
||||||
# # Get the indices of the columns of cum_mod_sizes where the value of the column is equal to the value of na_cols
|
|
||||||
# idx <- which(cum_mod_sizes %in% na_cols)
|
|
||||||
# mod_sizes[idx] <- 0
|
|
||||||
|
|
||||||
# idx <- which(na_cols == cum_mod_sizes)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
# idx <- which(na_cols[1] >= cum_mod_sizes)
|
|
||||||
|
|
||||||
# mod_sizes <- modify_module_sizes(mod_sizes, pqc_init, pqc_init)
|
|
||||||
|
|
||||||
# remove column with all NA
|
|
||||||
)";
|
|
||||||
|
|
||||||
#endif // POET_H
|
|
||||||
Loading…
x
Reference in New Issue
Block a user