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fix: setting of inner constant cells

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Max Luebke 2022-12-15 15:56:52 +01:00 committed by Max Lübke
parent ded8fbd0ae
commit 2e675d8139
4 changed files with 33 additions and 29 deletions
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14
data/SimDol2D_diffu.R
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@ -95,13 +95,17 @@ vecinj_diffu <- list(
) )
) )
inner_index <- c(5, 15, 25) #inner_index <- c(5, 15, 25)
inner_vecinj_index <- rep(1, 3) #inner_vecinj_index <- rep(1, 3)
#
#vecinj_inner <- cbind(inner_index, inner_vecinj_index)
vecinj_inner <- list(
l1 = c(1,2,2)
)
vecinj_inner <- cbind(inner_index, inner_vecinj_index)
boundary <- list( boundary <- list(
"N" = rep(1, n), "N" = rep(0, n),
"E" = rep(0, n), "E" = rep(0, n),
"S" = rep(0, n), "S" = rep(0, n),
"W" = rep(0, n) "W" = rep(0, n)
@ -112,7 +116,7 @@ diffu_list <- names(alpha_diffu)
diffusion <- list( diffusion <- list(
init = init_diffu, init = init_diffu,
vecinj = do.call(rbind.data.frame, vecinj_diffu), vecinj = do.call(rbind.data.frame, vecinj_diffu),
# vecinj_inner = vecinj_inner, vecinj_inner = vecinj_inner,
vecinj_index = boundary, vecinj_index = boundary,
alpha = alpha_diffu alpha = alpha_diffu
) )

2
include/poet/SimParams.hpp
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@ -87,7 +87,7 @@ using DiffusionParams = struct s_DiffusionParams {
std::vector<std::string> prop_names; std::vector<std::string> prop_names;
Rcpp::NumericVector alpha; Rcpp::NumericVector alpha;
Rcpp::NumericMatrix vecinj_inner; Rcpp::List vecinj_inner;
Rcpp::DataFrame vecinj; Rcpp::DataFrame vecinj;
Rcpp::DataFrame vecinj_index; Rcpp::DataFrame vecinj_index;

27
src/DiffusionModule.cpp
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@ -130,29 +130,28 @@ void DiffusionModule::initialize(poet::DiffusionParams args) {
// apply inner grid constant cells // apply inner grid constant cells
// NOTE: opening a scope here for distinguish variable names // NOTE: opening a scope here for distinguish variable names
if (args.vecinj_inner.rows() != 0) { if (args.vecinj_inner.size() != 0) {
// get indices of constant grid cells // get indices of constant grid cells
Rcpp::NumericVector indices_const_cells = args.vecinj_inner(Rcpp::_, 0); // Rcpp::NumericVector indices_const_cells = args.vecinj_inner(Rcpp::_, 0);
this->index_constant_cells = // this->index_constant_cells =
Rcpp::as<std::vector<uint32_t>>(indices_const_cells); // Rcpp::as<std::vector<uint32_t>>(indices_const_cells);
// get indices to vecinj for constant cells // // get indices to vecinj for constant cells
Rcpp::NumericVector vecinj_indices = args.vecinj_inner(Rcpp::_, 1); // Rcpp::NumericVector vecinj_indices = args.vecinj_inner(Rcpp::_, 1);
// apply inner constant cells for every concentration // apply inner constant cells for every concentration
for (int i = 0; i < this->prop_count; i++) { for (int i = 0; i < this->prop_count; i++) {
std::vector<double> bc_vec = args.vecinj[this->prop_names[i]]; std::vector<double> bc_vec = args.vecinj[this->prop_names[i]];
tug::bc::BoundaryCondition &curr_bc = *(this->bc_vec.begin() + i); tug::bc::BoundaryCondition &curr_bc = *(this->bc_vec.begin() + i);
for (int j = 0; j < indices_const_cells.size(); j++) { for (int j = 0; j < args.vecinj_inner.size(); j++) {
std::vector<double> inner_tuple =
Rcpp::as<std::vector<double>>(args.vecinj_inner[j]);
tug::bc::boundary_condition bc = {tug::bc::BC_TYPE_CONSTANT, tug::bc::boundary_condition bc = {tug::bc::BC_TYPE_CONSTANT,
bc_vec[vecinj_indices[j] - 1]}; bc_vec[inner_tuple[0] - 1]};
uint32_t x = this->index_constant_cells[j] % this->index_constant_cells.push_back(inner_tuple[1]);
this->grid.getGridCellsCount(GRID_X_DIR); uint32_t x = inner_tuple[1];
uint32_t y = (this->dim == this->DIM_1D uint32_t y = (this->dim == this->DIM_1D ? 0 : inner_tuple[2]);
? 0
: this->index_constant_cells[j] /
this->grid.getGridCellsCount(GRID_Y_DIR));
curr_bc.setInnerBC(bc, x, y); curr_bc.setInnerBC(bc, x, y);
} }

15
src/SimParams.cpp
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@ -53,9 +53,10 @@ poet::DiffusionParams::s_DiffusionParams(RInside &R) {
R.parseEval("names(mysetup$diffusion$init)")); R.parseEval("names(mysetup$diffusion$init)"));
this->alpha = this->alpha =
Rcpp::as<Rcpp::NumericVector>(R.parseEval("mysetup$diffusion$alpha")); Rcpp::as<Rcpp::NumericVector>(R.parseEval("mysetup$diffusion$alpha"));
if (Rcpp::as<bool>(R.parseEval("exists('mysetup$diffusion$vecinj_inner')"))) { if (Rcpp::as<bool>(
this->vecinj_inner = Rcpp::as<Rcpp::NumericMatrix>( R.parseEval("'vecinj_inner' %in% names(mysetup$diffusion)"))) {
R.parseEval("mysetup$diffusion$vecinj_inner")); this->vecinj_inner =
Rcpp::as<Rcpp::List>(R.parseEval("mysetup$diffusion$vecinj_inner"));
} }
this->vecinj = this->vecinj =
Rcpp::as<Rcpp::DataFrame>(R.parseEval("mysetup$diffusion$vecinj")); Rcpp::as<Rcpp::DataFrame>(R.parseEval("mysetup$diffusion$vecinj"));
@ -64,10 +65,10 @@ poet::DiffusionParams::s_DiffusionParams(RInside &R) {
} }
poet::ChemistryParams::s_ChemistryParams(RInside &R) { poet::ChemistryParams::s_ChemistryParams(RInside &R) {
this->database_path = Rcpp::as<std::string>( this->database_path =
R.parseEval("mysetup$chemistry$database")); Rcpp::as<std::string>(R.parseEval("mysetup$chemistry$database"));
this->input_script = Rcpp::as<std::string>( this->input_script =
R.parseEval("mysetup$chemistry$input_script")); Rcpp::as<std::string>(R.parseEval("mysetup$chemistry$input_script"));
} }
SimParams::SimParams(int world_rank_, int world_size_) { SimParams::SimParams(int world_rank_, int world_size_) {