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feat: add surface module

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This commit is contained in:
Max Luebke 2023-04-17 15:51:51 +02:00
parent 4c430ff819
commit 5492560f6c
5 changed files with 16 additions and 20 deletions
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4
bench/surfex/CMakeLists.txt
View File

@ -1,8 +1,8 @@
install(FILES
ExBase.pqi
ex.R
#surfex.R
#SurfExBase.pqi
surfex.R
SurfExBase.pqi
SMILE_2021_11_01_TH.dat
DESTINATION
share/poet/bench/surfex

7
bench/surfex/surfex.R
View File

@ -1,4 +1,4 @@
## Time-stamp: "Last modified 2023-04-13 17:11:52 mluebke"
## Time-stamp: "Last modified 2023-04-17 15:48:21 mluebke"
database <- normalizePath("../share/poet/bench/surfex/SMILE_2021_11_01_TH.dat")
input_script <- normalizePath("../share/poet/bench/surfex/SurfExBase.pqi")
@ -103,8 +103,11 @@ boundary <- list(
diffu_list <- names(alpha_diffu)
vecinj <- do.call(rbind.data.frame, vecinj_diffu)
names(vecinj) <- names(init_cell)
diffusion <- list(
init = init_cell,
init = as.data.frame(init_cell, check.names = FALSE),
vecinj = vecinj,
# vecinj_inner = vecinj_inner,
vecinj_index = boundary,

2
ext/phreeqcrm

@ -1 +1 @@
Subproject commit ade4f56605b8d0e81b7ccad510f2db21f46b5ff9
Subproject commit 6a4c14c2857f0ad3558af3f1e1aa7555a805e8e2

4
include/poet/ChemistryModule.hpp
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@ -385,9 +385,9 @@ protected:
uint32_t prop_count = 0;
std::vector<std::string> prop_names;
std::vector<double> field;
static constexpr uint32_t MODULE_COUNT = 4;
static constexpr int MODULE_COUNT = 5;
std::array<std::uint32_t, 4> speciesPerModule{};
std::array<std::uint32_t, MODULE_COUNT> speciesPerModule{};
};
} // namespace poet

19
src/ChemistryModule/ChemistryModule.cpp
View File

@ -68,6 +68,7 @@ void poet::ChemistryModule::RunInitFile(const std::string &input_script_path) {
char exchange = (speciesPerModule[1] == 0 ? -1 : 1);
char kinetics = (speciesPerModule[2] == 0 ? -1 : 1);
char equilibrium = (speciesPerModule[3] == 0 ? -1 : 1);
char surface = (speciesPerModule[4] == 0 ? -1 : 1);
#ifdef POET_USE_PRM
std::vector<int> ic1;
@ -77,7 +78,7 @@ 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] = -1; // Surface 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
@ -92,7 +93,7 @@ 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] = -1; // Surface 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
@ -104,7 +105,7 @@ void poet::ChemistryModule::RunInitFile(const std::string &input_script_path) {
#ifndef POET_USE_PRM
void poet::ChemistryModule::mergeFieldWithModule(const SingleCMap &input_map,
std::uint32_t n_cells) {
std::uint32_t n_cells) {
if (is_master) {
int f_type = CHEM_INIT_SPECIES;
@ -171,16 +172,8 @@ void poet::ChemistryModule::mergeFieldWithModule(const SingleCMap &input_map,
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;
}
for (int i = 0; i < prop_names.size(); i++) {
double value = init_values[i];
std::vector<double> curr_vec(n_cells, value);
this->field.insert(field.end(), curr_vec.begin(), curr_vec.end());
}