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BREAKING CHANGE: use Field data structure instead of plain 1D vector to

Browse Source 
store concentrations
This commit is contained in:
Max Luebke 2023-04-24 14:20:31 +02:00
parent 2e7af244e2
commit 89fc291e79
11 changed files with 199 additions and 150 deletions
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43
app/poet.cpp
View File

@ -51,6 +51,22 @@ poet::ChemistryModule::SingleCMap DFToHashMap(const Rcpp::DataFrame &df) {
return out_map;
}
// HACK: this is a step back as the order and also the count of fields is
// predefined, but it will change in the future
void writeFieldsToR(RInside &R, const Field &trans, const Field &chem) {
R["TMP"] = Rcpp::wrap(trans.AsVector());
R["TMP_PROPS"] = Rcpp::wrap(trans.GetProps());
R.parseEval(std::string(
"mysetup$state_T <- setNames(data.frame(matrix(TMP, nrow=" +
std::to_string(trans.GetRequestedVecSize()) + ")), TMP_PROPS)"));
R["TMP"] = Rcpp::wrap(chem.AsVector());
R["TMP_PROPS"] = Rcpp::wrap(chem.GetProps());
R.parseEval(std::string(
"mysetup$state_C <- setNames(data.frame(matrix(TMP, nrow=" +
std::to_string(chem.GetRequestedVecSize()) + ")), TMP_PROPS)"));
}
void set_chem_parameters(poet::ChemistryModule &chem, uint32_t wp_size,
const std::string &database_path) {
chem.SetErrorHandlerMode(1);
@ -95,12 +111,12 @@ void set_chem_parameters(poet::ChemistryModule &chem, uint32_t wp_size,
chem.LoadDatabase(database_path);
}
inline double RunMasterLoop(SimParams &params, RInside &R, Grid &grid,
inline double RunMasterLoop(SimParams &params, RInside &R,
ChemistryParams &chem_params,
const GridParams &g_params, uint32_t nxyz_master) {
DiffusionParams d_params{R};
DiffusionModule diffusion(d_params, grid);
DiffusionModule diffusion(d_params, g_params);
/* Iteration Count is dynamic, retrieving value from R (is only needed by
* master for the following loop) */
uint32_t maxiter = R.parseEval("mysetup$iterations");
@ -113,7 +129,7 @@ inline double RunMasterLoop(SimParams &params, RInside &R, Grid &grid,
chem.RunInitFile(chem_params.input_script);
poet::ChemistryModule::SingleCMap init_df = DFToHashMap(d_params.initial_t);
chem.mergeFieldWithModule(init_df, grid.GetTotalCellCount());
chem.initializeField(diffusion.getField());
if (params.getNumParams().dht_enabled) {
chem.SetDHTEnabled(true, params.getNumParams().dht_size_per_process);
@ -131,8 +147,6 @@ inline double RunMasterLoop(SimParams &params, RInside &R, Grid &grid,
}
}
StateMemory *chem_state = grid.RegisterState("state_C", chem.GetPropNames());
chem_state->mem = chem.GetField();
/* SIMULATION LOOP */
double dStartTime = MPI_Wtime();
@ -154,19 +168,17 @@ inline double RunMasterLoop(SimParams &params, RInside &R, Grid &grid,
// TODO: transport to diffusion
diffusion.simulate(dt);
grid.PreModuleFieldCopy(tick++);
chem.getField().UpdateFromField(diffusion.getField());
cout << "CPP: Chemistry" << endl;
chem.SetTimeStep(dt);
chem.SetField(chem_state->mem);
chem.SetTimeStep(dt);
chem.RunCells();
chem_state->mem = chem.GetField();
grid.WriteFieldsToR(R);
grid.PreModuleFieldCopy(tick++);
writeFieldsToR(R, diffusion.getField(), chem.GetField());
diffusion.getField().UpdateFromField(chem.GetField());
R["req_dt"] = dt;
R["simtime"] = (sim_time += dt);
@ -302,14 +314,9 @@ int main(int argc, char *argv[]) {
std::string master_init_code = "mysetup <- master_init(setup=setup)";
R.parseEval(master_init_code);
Grid grid;
GridParams g_params(R);
grid.InitModuleFromParams(g_params);
grid.PushbackModuleFlow(poet::DIFFUSION_MODULE_NAME, CHEMISTRY_MODULE_NAME);
grid.PushbackModuleFlow(CHEMISTRY_MODULE_NAME, poet::DIFFUSION_MODULE_NAME);
params.initVectorParams(R, grid.GetSpeciesCount());
params.initVectorParams(R);
// MDL: store all parameters
if (world_rank == 0) {
@ -331,9 +338,9 @@ int main(int argc, char *argv[]) {
MPI_Bcast(&c_size, 1, MPI_UINT32_T, 0, MPI_COMM_WORLD);
MPI_Bcast(db_path.data(), c_size, MPI_CHAR, 0, MPI_COMM_WORLD);
uint32_t nxyz_master = (world_size == 1 ? grid.GetTotalCellCount() : 1);
uint32_t nxyz_master = (world_size == 1 ? g_params.total_n : 1);
dSimTime = RunMasterLoop(params, R, grid, chem_params, g_params, nxyz_master);
dSimTime = RunMasterLoop(params, R, chem_params, g_params, nxyz_master);
cout << "CPP: finished simulation loop" << endl;

4
bench/dolo_diffu_inner/dolo_diffu_inner.R
View File

@ -1,7 +1,7 @@
## Time-stamp: "Last modified 2023-04-17 12:25:25 mluebke"
## Time-stamp: "Last modified 2023-04-24 14:11:01 mluebke"
database <- normalizePath("../share/poet/examples/phreeqc_kin.dat")
input_script <- normalizePath("../share/poet/bench/dolo_inner.pqi")
input_script <- normalizePath("../share/poet/bench/dolo/dolo_inner.pqi")
#################################################################
## Section 1 ##

40
include/poet/ChemistryModule.hpp
View File

@ -1,6 +1,7 @@
#ifndef CHEMISTRYMODULE_H_
#define CHEMISTRYMODULE_H_
#include "Field.hpp"
#include "IrmResult.h"
#include "PhreeqcRM.h"
#include "poet/DHT_Wrapper.hpp"
@ -77,7 +78,7 @@ public:
/**
* Returns the chemical field.
*/
auto GetField() const { return this->field; }
auto GetField() const { return this->chem_field; }
/**
* Returns all known species names, including not only aqueous species, but
* also equilibrium, exchange, surface and kinetic reactants.
@ -129,14 +130,15 @@ public:
};
/**
* **This function has to be run!**
*
* Merge initial values from existing module with the chemistry module and set
* according internal variables.
*
* \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.
* \param other Field to merge chemistry with. Most likely it is something
* like the diffusion field.
*/
void mergeFieldWithModule(const SingleCMap &input_map, std::uint32_t n_cells);
void initializeField(const Field &other);
/**
* **Only called by workers!** Start the worker listening loop.
@ -187,16 +189,6 @@ public:
*/
void ReadDHTFile(const std::string &input_file);
/**
* Overwrite the current field state by another field.
*
* There are no checks if new vector dimensions matches expected sizes etc.
*
* \param field New input field. Current field state of the instance will be
* overwritten.
*/
void SetField(const std::vector<double> &field) { this->field = field; }
/**
* **Master only** Return count of grid cells.
*/
@ -271,6 +263,13 @@ public:
* \return Vector of all count of DHT evictions.
*/
std::vector<uint32_t> GetWorkerDHTEvictions() const;
/**
* **Master only** Returns the current state of the chemical field.
*
* \return Reference to the chemical field.
*/
Field &getField() { return this->chem_field; }
#endif
protected:
#ifdef POET_USE_PRM
@ -350,6 +349,13 @@ protected:
std::vector<uint32_t> CalculateWPSizesVector(uint32_t n_cells,
uint32_t wp_size) const;
std::vector<double> shuffleField(const std::vector<double> &in_field,
uint32_t size_per_prop, uint32_t prop_count,
uint32_t wp_count);
void unshuffleField(const std::vector<double> &in_buffer,
uint32_t size_per_prop, uint32_t prop_count,
uint32_t wp_count, std::vector<double> &out_field);
int comm_size, comm_rank;
MPI_Comm group_comm;
@ -384,7 +390,9 @@ protected:
uint32_t n_cells = 0;
uint32_t prop_count = 0;
std::vector<std::string> prop_names;
std::vector<double> field;
Field chem_field{0};
static constexpr int MODULE_COUNT = 5;
std::array<std::uint32_t, MODULE_COUNT> speciesPerModule{};

18
include/poet/DiffusionModule.hpp
View File

@ -21,9 +21,12 @@
#ifndef DIFFUSION_MODULE_H
#define DIFFUSION_MODULE_H
#include "Field.hpp"
#include "SimParams.hpp"
#include "poet/SimParams.hpp"
#include <array>
#include <cmath>
#include <cstdint>
#include <poet/Grid.hpp>
#include <string>
#include <tug/BoundaryCondition.hpp>
@ -49,7 +52,8 @@ public:
*
* @param R RRuntime object
*/
DiffusionModule(poet::DiffusionParams diffu_args, Grid &grid_);
DiffusionModule(const poet::DiffusionParams &diffu_args,
const poet::GridParams &grid_params);
/**
* @brief Run simulation for one iteration
@ -74,6 +78,13 @@ public:
*/
double getTransportTime();
/**
* \brief Returns the current diffusion field.
*
* \return Reference to the diffusion field.
*/
Field &getField() { return this->t_field; }
private:
/**
* @brief Instance of RRuntime
@ -83,9 +94,8 @@ private:
enum { DIM_1D = 1, DIM_2D };
void initialize(poet::DiffusionParams args);
void initialize(const poet::DiffusionParams &args);
Grid &grid;
uint8_t dim;
uint32_t prop_count;
@ -96,7 +106,7 @@ private:
std::vector<std::string> prop_names;
std::vector<tug::bc::BoundaryCondition> bc_vec;
poet::StateMemory *state;
Field t_field;
uint32_t n_cells_per_prop;

14
include/poet/Field.hpp
View File

@ -63,6 +63,12 @@ public:
void InitFromVec(const std::vector<double> &input,
const std::vector<std::string> &prop_vec);
Field &operator=(const Field &rhs) {
this->req_vec_size = rhs.req_vec_size;
this->props = rhs.props;
return *this;
}
/**
* Returns a reference to the column vector with given name. Creates a new
* vector if prop was not found. The prop name will be added to the end of the
@ -79,14 +85,16 @@ public:
*
* \return Vector containing all species names in output order.
*/
auto GetProps() const { return this->props; };
auto GetProps() const -> std::vector<std::string> { return this->props; }
/**
* Return the requested vector size.
*
* \return Requested vector size set in the instanciation of the object.
*/
auto GetRequestedVecSize() const { return this->req_vec_size; };
auto GetRequestedVecSize() const -> std::uint32_t {
return this->req_vec_size;
};
/**
* Updates all species with values from another field. If one element of the
@ -142,7 +150,7 @@ public:
void SetFromVector(const std::vector<FieldColumn> &cont_field);
private:
const uint32_t req_vec_size;
std::uint32_t req_vec_size;
std::vector<std::string> props;
};

11
include/poet/SimParams.hpp
View File

@ -21,6 +21,7 @@
#ifndef PARSER_H
#define PARSER_H
#include <cstdint>
#include <string>
#include <string_view>
#include <vector>
@ -69,8 +70,10 @@ typedef struct {
} t_simparams;
using GridParams = struct s_GridParams {
std::vector<uint32_t> n_cells;
std::vector<double> s_cells;
std::array<uint32_t, 2> n_cells;
std::array<double, 2> s_cells;
std::uint8_t dim;
std::uint32_t total_n;
std::string type;
@ -161,10 +164,8 @@ public:
* 'init_chemistry' must be run beforehand.
*
* @param R R runtime
* @param col_count Count of variables per grid cell (typically the count of
* columns of each grid cell)
*/
void initVectorParams(RInside &R, int col_count);
void initVectorParams(RInside &R);
/**
* @brief Get the numerical params struct

80
src/ChemistryModule/ChemistryModule.cpp
View File

@ -104,8 +104,7 @@ 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) {
void poet::ChemistryModule::initializeField(const Field &trans_field) {
if (is_master) {
int f_type = CHEM_INIT_SPECIES;
@ -119,14 +118,13 @@ void poet::ChemistryModule::mergeFieldWithModule(const SingleCMap &input_map,
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;
for (auto &prop : trans_field.GetProps()) {
if (std::find(new_solution_names.begin(), new_solution_names.end(),
name) == new_solution_names.end()) {
int size = name.size();
prop) == new_solution_names.end()) {
int size = prop.size();
ChemBCast(&size, 1, MPI_INT);
ChemBCast(name.data(), name.size(), MPI_CHAR);
new_solution_names.push_back(name);
ChemBCast(prop.data(), prop.size(), MPI_CHAR);
new_solution_names.push_back(prop);
}
}
int end = 0;
@ -162,21 +160,27 @@ void poet::ChemistryModule::mergeFieldWithModule(const SingleCMap &input_map,
this->SetPOETSolutionNames(new_solution_names);
if (is_master) {
this->n_cells = n_cells;
this->n_cells = trans_field.GetRequestedVecSize();
chem_field = Field(n_cells);
this->field.clear();
this->field.reserve(this->prop_count * n_cells);
std::vector<double> phreeqc_init;
this->getDumpedField(phreeqc_init);
std::vector<double> init_values;
this->getDumpedField(init_values);
const std::vector<std::string> ess_names = old_prop_names;
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());
if (is_sequential) {
std::vector<double> init_vec{phreeqc_init};
this->unshuffleField(phreeqc_init, n_cells, prop_count, 1, init_vec);
chem_field.InitFromVec(init_vec, prop_names);
return;
}
std::vector<std::vector<double>> initial_values;
for (int i = 0; i < phreeqc_init.size(); i++) {
std::vector<double> init(n_cells, phreeqc_init[i]);
initial_values.push_back(std::move(init));
}
chem_field.InitFromVec(initial_values, prop_names);
}
}
@ -283,6 +287,42 @@ void poet::ChemistryModule::ReadDHTFile(const std::string &input_file) {
}
}
std::vector<double>
poet::ChemistryModule::shuffleField(const std::vector<double> &in_field,
uint32_t size_per_prop, uint32_t prop_count,
uint32_t wp_count) {
std::vector<double> out_buffer(in_field.size());
uint32_t write_i = 0;
for (uint32_t i = 0; i < wp_count; i++) {
for (uint32_t j = i; j < size_per_prop; j += wp_count) {
for (uint32_t k = 0; k < prop_count; k++) {
out_buffer[(write_i * prop_count) + k] =
in_field[(k * size_per_prop) + j];
}
write_i++;
}
}
return out_buffer;
}
void poet::ChemistryModule::unshuffleField(const std::vector<double> &in_buffer,
uint32_t size_per_prop,
uint32_t prop_count,
uint32_t wp_count,
std::vector<double> &out_field) {
uint32_t read_i = 0;
for (uint32_t i = 0; i < wp_count; i++) {
for (uint32_t j = i; j < size_per_prop; j += wp_count) {
for (uint32_t k = 0; k < prop_count; k++) {
out_field[(k * size_per_prop) + j] =
in_buffer[(read_i * prop_count) + k];
}
read_i++;
}
}
}
#else // POET_USE_PRM
inline void poet::ChemistryModule::PrmToPoetField(std::vector<double> &field) {

49
src/ChemistryModule/MasterFunctions.cpp
View File

@ -77,40 +77,6 @@ std::vector<uint32_t> poet::ChemistryModule::GetWorkerDHTEvictions() const {
return MasterGatherWorkerMetrics(WORKER_DHT_EVICTIONS);
}
inline std::vector<double> shuffleField(const std::vector<double> &in_field,
uint32_t size_per_prop,
uint32_t prop_count,
uint32_t wp_count) {
std::vector<double> out_buffer(in_field.size());
uint32_t write_i = 0;
for (uint32_t i = 0; i < wp_count; i++) {
for (uint32_t j = i; j < size_per_prop; j += wp_count) {
for (uint32_t k = 0; k < prop_count; k++) {
out_buffer[(write_i * prop_count) + k] =
in_field[(k * size_per_prop) + j];
}
write_i++;
}
}
return out_buffer;
}
inline void unshuffleField(const std::vector<double> &in_buffer,
uint32_t size_per_prop, uint32_t prop_count,
uint32_t wp_count, std::vector<double> &out_field) {
uint32_t read_i = 0;
for (uint32_t i = 0; i < wp_count; i++) {
for (uint32_t j = i; j < size_per_prop; j += wp_count) {
for (uint32_t k = 0; k < prop_count; k++) {
out_field[(k * size_per_prop) + j] =
in_buffer[(read_i * prop_count) + k];
}
read_i++;
}
}
}
inline void printProgressbar(int count_pkgs, int n_wp, int barWidth = 70) {
/* visual progress */
double progress = (float)(count_pkgs + 1) / n_wp;
@ -234,11 +200,13 @@ void poet::ChemistryModule::RunCells() {
void poet::ChemistryModule::MasterRunSequential() {
std::vector<double> shuffled_field =
shuffleField(field, n_cells, prop_count, 1);
shuffleField(chem_field.AsVector(), n_cells, prop_count, 1);
this->setDumpedField(shuffled_field);
PhreeqcRM::RunCells();
this->getDumpedField(shuffled_field);
unshuffleField(shuffled_field, n_cells, prop_count, 1, this->field);
std::vector<double> out_vec{shuffled_field};
unshuffleField(shuffled_field, n_cells, prop_count, 1, out_vec);
chem_field.SetFromVector(out_vec);
}
void poet::ChemistryModule::MasterRunParallel() {
@ -270,8 +238,9 @@ void poet::ChemistryModule::MasterRunParallel() {
/* shuffle grid */
// grid.shuffleAndExport(mpi_buffer);
std::vector<double> mpi_buffer = shuffleField(
this->field, this->n_cells, this->prop_count, wp_sizes_vector.size());
std::vector<double> mpi_buffer =
shuffleField(chem_field.AsVector(), this->n_cells, this->prop_count,
wp_sizes_vector.size());
/* setup local variables */
pkg_to_send = wp_sizes_vector.size();
@ -317,8 +286,10 @@ void poet::ChemistryModule::MasterRunParallel() {
/* unshuffle grid */
// grid.importAndUnshuffle(mpi_buffer);
std::vector<double> out_vec{mpi_buffer};
unshuffleField(mpi_buffer, this->n_cells, this->prop_count,
wp_sizes_vector.size(), this->field);
wp_sizes_vector.size(), out_vec);
chem_field.SetFromVector(out_vec);
/* do master stuff */

5
src/ChemistryModule/WorkerFunctions.cpp
View File

@ -44,9 +44,8 @@ void poet::ChemistryModule::WorkerLoop() {
break;
}
case CHEM_INIT_SPECIES: {
SingleCMap dummy_map;
std::uint32_t n_cells_dummy;
mergeFieldWithModule(dummy_map, n_cells_dummy);
Field dummy{0};
initializeField(dummy);
break;
}
case CHEM_DHT_ENABLE: {

63
src/DiffusionModule.cpp
View File

@ -55,21 +55,19 @@ inline const char *convert_bc_to_config_file(uint8_t in) {
return "";
}
DiffusionModule::DiffusionModule(poet::DiffusionParams diffu_args, Grid &grid_)
: grid(grid_) {
this->diff_input.setGridCellN(grid_.GetGridCellsCount(GRID_X_DIR),
grid_.GetGridCellsCount(GRID_Y_DIR));
this->diff_input.setDomainSize(grid_.GetGridSize(GRID_X_DIR),
grid_.GetGridSize(GRID_Y_DIR));
DiffusionModule::DiffusionModule(const poet::DiffusionParams &diffu_args,
const poet::GridParams &grid_params)
: t_field{grid_params.total_n}, n_cells_per_prop(grid_params.total_n) {
this->diff_input.setGridCellN(grid_params.n_cells[0], grid_params.n_cells[1]);
this->diff_input.setDomainSize(grid_params.s_cells[0],
grid_params.s_cells[1]);
this->dim = grid_.GetGridDimension();
this->n_cells_per_prop = grid_.GetTotalCellCount();
this->dim = grid_params.dim;
this->initialize(diffu_args);
}
void DiffusionModule::initialize(poet::DiffusionParams args) {
void DiffusionModule::initialize(const poet::DiffusionParams &args) {
// const poet::DiffusionParams args(this->R);
// name of props
@ -77,35 +75,32 @@ void DiffusionModule::initialize(poet::DiffusionParams args) {
this->prop_names = Rcpp::as<std::vector<std::string>>(args.initial_t.names());
this->prop_count = this->prop_names.size();
this->state =
this->grid.RegisterState(DIFFUSION_MODULE_NAME, this->prop_names);
std::vector<double> &field = this->state->mem;
// initialize field and alphas
field.resize(this->n_cells_per_prop * this->prop_count);
this->alpha.reserve(this->prop_count);
std::vector<std::vector<double>> initial_values;
for (uint32_t i = 0; i < this->prop_count; i++) {
// get alphas - we cannot assume alphas are provided in same order as
// initial input
this->alpha.push_back(args.alpha[this->prop_names[i]]);
double val = args.initial_t[prop_names[i]];
const double val = args.initial_t[prop_names[i]];
std::vector<double> init_val(t_field.GetRequestedVecSize(), val);
initial_values.push_back(std::move(init_val));
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) {
tug::bc::BoundaryCondition bc(this->grid.GetGridCellsCount(GRID_X_DIR),
this->grid.GetGridCellsCount(GRID_Y_DIR));
tug::bc::BoundaryCondition bc(diff_input.grid.grid_cells[0],
diff_input.grid.grid_cells[1]);
this->bc_vec.push_back(bc);
} else {
tug::bc::BoundaryCondition bc(this->grid.GetGridCellsCount(GRID_X_DIR));
tug::bc::BoundaryCondition bc(diff_input.grid.grid_cells[0]);
this->bc_vec.push_back(bc);
}
}
t_field.InitFromVec(initial_values, prop_names);
// apply boundary conditions to each ghost node
uint8_t bc_size = (this->dim == this->DIM_1D ? 2 : 4);
for (uint8_t i = 0; i < bc_size; i++) {
@ -133,14 +128,6 @@ void DiffusionModule::initialize(poet::DiffusionParams args) {
// apply inner grid constant cells
// NOTE: opening a scope here for distinguish variable names
if (args.vecinj_inner.size() != 0) {
// get indices of constant grid cells
// Rcpp::NumericVector indices_const_cells = args.vecinj_inner(Rcpp::_, 0);
// this->index_constant_cells =
// Rcpp::as<std::vector<uint32_t>>(indices_const_cells);
// // get indices to vecinj for constant cells
// Rcpp::NumericVector vecinj_indices = args.vecinj_inner(Rcpp::_, 1);
// apply inner constant cells for every concentration
for (int i = 0; i < this->prop_count; i++) {
std::vector<double> bc_vec = args.vecinj[this->prop_names[i]];
@ -169,23 +156,25 @@ void DiffusionModule::simulate(double dt) {
std::cout << "DiffusionModule::simulate(): Starting diffusion ..."
<< std::flush;
std::vector<double> &curr_field = this->state->mem;
std::vector<std::vector<double>> field_2d = t_field.As2DVector();
this->diff_input.setTimestep(dt);
double *field = curr_field.data();
for (int i = 0; i < this->prop_count; i++) {
double *in_field = &field[i * this->n_cells_per_prop];
for (int i = 0; i < field_2d.size(); i++) {
std::vector<double> in_alpha(this->n_cells_per_prop, this->alpha[i]);
this->diff_input.setBoundaryCondition(this->bc_vec[i]);
if (this->dim == this->DIM_1D) {
tug::diffusion::BTCS_1D(this->diff_input, in_field, in_alpha.data());
tug::diffusion::BTCS_1D(this->diff_input, field_2d[i].data(),
in_alpha.data());
} else {
tug::diffusion::ADI_2D(this->diff_input, in_field, in_alpha.data());
tug::diffusion::ADI_2D(this->diff_input, field_2d[i].data(),
in_alpha.data());
}
}
t_field.SetFromVector(field_2d);
std::cout << " done!\n";
sim_a_transport = MPI_Wtime();

22
src/SimParams.cpp
View File

@ -19,6 +19,8 @@
*/
#include "poet/DHT_Types.hpp"
#include <algorithm>
#include <cassert>
#include <poet/SimParams.hpp>
#include <RInside.h>
@ -34,10 +36,24 @@ using namespace std;
using namespace Rcpp;
poet::GridParams::s_GridParams(RInside &R) {
this->n_cells =
auto tmp_n_cells =
Rcpp::as<std::vector<uint32_t>>(R.parseEval("mysetup$grid$n_cells"));
this->s_cells =
assert(tmp_n_cells.size() < 3);
this->dim = tmp_n_cells.size();
std::copy(tmp_n_cells.begin(), tmp_n_cells.end(), this->n_cells.begin());
auto tmp_s_cells =
Rcpp::as<std::vector<double>>(R.parseEval("mysetup$grid$s_cells"));
assert(tmp_s_cells.size() == this->dim);
std::copy(tmp_s_cells.begin(), tmp_s_cells.end(), this->s_cells.begin());
this->total_n =
(dim == 1 ? this->n_cells[0] : this->n_cells[0] * this->n_cells[1]);
this->type = Rcpp::as<std::string>(R.parseEval("mysetup$grid$type"));
this->init_df =
Rcpp::as<Rcpp::DataFrame>(R.parseEval("mysetup$grid$init_cell"));
@ -191,7 +207,7 @@ int SimParams::parseFromCmdl(char *argv[], RInside &R) {
return poet::PARSER_OK;
}
void SimParams::initVectorParams(RInside &R, int col_count) {
void SimParams::initVectorParams(RInside &R) {
if (simparams.dht_enabled) {
/*Load significance vector from R setup file (or set default)*/
bool signif_vector_exists = R.parseEval("exists('signif_vector')");