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grid.cc
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#include "grid.h"
#include <algorithm>
#include <array>
#include <cctype>
#include <cmath>
#include <cstddef>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <ctime>
#include <filesystem>
#include <fstream>
#include <iostream>
#include <limits>
#ifdef MPI_ON
#include <mpi.h>
#endif
#include <span>
#include <sstream>
#include <string>
#include <tuple>
#include <utility>
#include <vector>
#include "artisoptions.h"
#include "atomic.h"
#include "constants.h"
#include "decay.h"
#include "globals.h"
#include "input.h"
#include "nltepop.h"
#include "nonthermal.h"
#include "packet.h"
#include "radfield.h"
#include "rpkt.h"
#include "sn3d.h"
#include "vectors.h"
namespace grid {
namespace {
std::array<char, 3> coordlabel{'?', '?', '?'};
std::array<int, 3> ncoordgrid{0}; // propagation grid dimensions
auto model_type = GridType::SPHERICAL1D;
ptrdiff_t npts_model = 0; // number of model grid cells
ptrdiff_t nonempty_npts_model = 0; // number of allocated non-empty model grid cells
double t_model = -1.; // time at which densities in input model are correct.
std::vector<double> vout_model{};
std::array<int, 3> ncoord_model{0}; // the model.txt input grid dimensions
double min_den; // minimum model density
double mfegroup = 0.; // Total mass of Fe group elements in ejecta
int first_cellindex = -1; // auto-determine first cell index in model.txt (usually 1 or 0)
struct PropGridCell {
std::array<double, 3> pos_min{}; // Initial co-ordinates of inner most corner of cell.
int modelgridindex{-1};
};
std::vector<PropGridCell> cell{};
std::vector<int> mg_associated_cells;
std::vector<int> nonemptymgi_of_mgi;
std::vector<int> mgi_of_nonemptymgi;
std::span<double> totmassradionuclide{}; // total mass of each radionuclide in the ejecta
double *nltepops_allcells{};
#ifdef MPI_ON
MPI_Win win_nltepops_allcells = MPI_WIN_NULL;
MPI_Win win_initnucmassfrac_allcells = MPI_WIN_NULL;
#endif
float *initnucmassfrac_allcells{};
float *initmassfracuntrackedstable_allcells{};
float *elem_meanweight_allcells{};
std::vector<int> ranks_nstart;
std::vector<int> ranks_ndo;
std::vector<int> ranks_ndo_nonempty;
int maxndo = -1;
void set_rho_tmin(const int modelgridindex, const float x) { modelgrid[modelgridindex].rhoinit = x; }
void set_initelectronfrac(const int modelgridindex, const double electronfrac) {
modelgrid[modelgridindex].initelectronfrac = electronfrac;
}
void read_possible_yefile() {
if (!std::filesystem::exists("Ye.txt")) {
printout("Ye.txt not found\n");
return;
}
FILE *filein = fopen_required("Ye.txt", "r");
int nlines_in = 0;
assert_always(fscanf(filein, "%d", &nlines_in) == 1);
for (int n = 0; n < nlines_in; n++) {
int mgiplusone = -1;
double initelecfrac = 0.;
assert_always(fscanf(filein, "%d %lg", &mgiplusone, &initelecfrac) == 2);
const int mgi = mgiplusone - 1;
if (mgi >= 0 && mgi < get_npts_model()) {
set_initelectronfrac(mgi, initelecfrac);
// printout("Ye.txt: setting mgi %d init_ye %g\n", mgi, initelecfrac);
} else {
// printout("Ye.txt: ignoring mgi %d init_ye %g\n", mgi, initelecfrac);
}
}
fclose(filein);
}
void set_npts_model(const int new_npts_model) {
npts_model = new_npts_model;
assert_always(modelgrid.data() == nullptr);
modelgrid = std::span(static_cast<ModelGridCell *>(calloc(npts_model + 1, sizeof(ModelGridCell))), npts_model + 1);
assert_always(modelgrid.data() != nullptr);
mg_associated_cells.resize(npts_model + 1, 0);
nonemptymgi_of_mgi.resize(npts_model + 1, -1);
}
void allocate_initradiobund() {
assert_always(npts_model > 0);
const ptrdiff_t num_nuclides = decay::get_num_nuclides();
const size_t totalradioabundsize = (npts_model + 1) * num_nuclides * sizeof(float);
#ifdef MPI_ON
const auto [_, noderank_cells] = get_range_chunk(npts_model + 1, globals::node_nprocs, globals::rank_in_node);
auto size = static_cast<MPI_Aint>(noderank_cells * num_nuclides * sizeof(float));
int disp_unit = sizeof(float);
assert_always(MPI_Win_allocate_shared(size, disp_unit, MPI_INFO_NULL, globals::mpi_comm_node,
&initnucmassfrac_allcells, &win_initnucmassfrac_allcells) == MPI_SUCCESS);
assert_always(MPI_Win_shared_query(win_initnucmassfrac_allcells, 0, &size, &disp_unit, &initnucmassfrac_allcells) ==
MPI_SUCCESS);
#else
initnucmassfrac_allcells = static_cast<float *>(malloc(totalradioabundsize));
#endif
printout(
"[info] mem_usage: radioabundance data for %td nuclides for %td cells occupies %.3f MB (node shared memory)\n",
num_nuclides, npts_model, static_cast<double>(totalradioabundsize) / 1024. / 1024.);
#ifdef MPI_ON
MPI_Barrier(globals::mpi_comm_node);
#endif
assert_always(initnucmassfrac_allcells != nullptr);
for (ptrdiff_t mgi = 0; mgi < (npts_model + 1); mgi++) {
modelgrid[mgi].initnucmassfrac = &initnucmassfrac_allcells[mgi * num_nuclides];
if (mgi % static_cast<ptrdiff_t>(globals::node_nprocs) == globals::rank_in_node) {
for (int i = 0; i < decay::get_num_nuclides(); i++) {
modelgrid[mgi].initnucmassfrac[i] = 0.;
}
}
}
#ifdef MPI_ON
MPI_Barrier(globals::mpi_comm_node);
#endif
}
auto get_cell_r_inner(const int cellindex) -> double {
if constexpr (GRID_TYPE == GridType::SPHERICAL1D) {
return get_cellcoordmin(cellindex, 0);
}
if constexpr (GRID_TYPE == GridType::CYLINDRICAL2D) {
const auto rcyl_inner = get_cellcoordmin(cellindex, 0);
const auto z_inner = std::min(std::abs(get_cellcoordmin(cellindex, 1)), std::abs(get_cellcoordmax(cellindex, 1)));
return std::sqrt(std::pow(rcyl_inner, 2) + std::pow(z_inner, 2));
}
if constexpr (GRID_TYPE == GridType::CARTESIAN3D) {
const auto x_inner = std::min(std::abs(get_cellcoordmin(cellindex, 0)), std::abs(get_cellcoordmax(cellindex, 0)));
const auto y_inner = std::min(std::abs(get_cellcoordmin(cellindex, 1)), std::abs(get_cellcoordmax(cellindex, 1)));
const auto z_inner = std::min(std::abs(get_cellcoordmin(cellindex, 2)), std::abs(get_cellcoordmax(cellindex, 2)));
return std::sqrt(std::pow(x_inner, 2) + std::pow(y_inner, 2) + std::pow(z_inner, 2));
}
assert_always(false);
return NAN;
}
void set_ffegrp(const int modelgridindex, float x) {
if (!(x >= 0.)) {
printout("WARNING: Fe-group mass fraction %g is negative in cell %d\n", x, modelgridindex);
assert_always(x > -1e-6);
x = 0.;
}
assert_always(x >= 0);
assert_always(x <= 1.001);
modelgrid[modelgridindex].ffegrp = x;
}
void set_cell_modelgridindex(const int cellindex, const int new_modelgridindex) {
assert_testmodeonly(cellindex < ngrid);
assert_testmodeonly(new_modelgridindex <= get_npts_model());
cell[cellindex].modelgridindex = new_modelgridindex;
}
void set_modelinitnucmassfrac(const int modelgridindex, const int nucindex, float abund) {
// set the mass fraction of a nuclide in a model grid cell at t=t_model by nuclide index
// initnucmassfrac array is in node shared memory
assert_always(nucindex >= 0);
if (!(abund >= 0.)) {
printout("WARNING: nuclear mass fraction for nucindex %d = %g is negative in cell %d\n", nucindex, abund,
modelgridindex);
assert_always(abund > -1e-6);
abund = 0.;
}
assert_always(abund >= 0.);
assert_always(abund <= 1.);
assert_always(modelgrid[modelgridindex].initnucmassfrac != nullptr);
modelgrid[modelgridindex].initnucmassfrac[nucindex] = abund;
}
void set_initenergyq(const int modelgridindex, const double initenergyq) {
modelgrid[modelgridindex].initenergyq = initenergyq;
}
void set_elem_untrackedstable_abund_from_total(const int mgi, const int element, const float elemabundance) {
// set the stable mass fraction of an element from the total element mass fraction
// by subtracting the abundances of radioactive isotopes.
// if the element Z=anumber has no specific stable abundance variable then the function does nothing
const int atomic_number = get_atomicnumber(element);
double isofracsum = 0.; // mass fraction sum of radioactive isotopes
for (int nucindex = 0; nucindex < decay::get_num_nuclides(); nucindex++) {
if (decay::get_nuc_z(nucindex) == atomic_number) {
// radioactive isotope of this element
isofracsum += get_modelinitnucmassfrac(mgi, nucindex);
}
}
double massfrac_untrackedstable = elemabundance - isofracsum;
if (massfrac_untrackedstable < 0.) {
// allow some roundoff error before we complain
if ((isofracsum - elemabundance - 1.) > 1e-4 && std::abs(isofracsum - elemabundance) > 1e-6) {
printout("WARNING: cell %d Z=%d element abundance is less than the sum of its radioisotope abundances\n", mgi,
atomic_number);
printout(" massfrac(Z) %g massfrac_radioisotopes(Z) %g\n", elemabundance, isofracsum);
printout(" increasing elemental abundance to %g and setting stable isotopic abundance to zero\n", isofracsum);
}
assert_always(massfrac_untrackedstable >=
-1e-2); // result is allowed to be slightly negative due to roundoff error
massfrac_untrackedstable = 0.; // bring up to zero if negative
}
// if (globals::rank_in_node == 0)
{
modelgrid[mgi].initmassfracuntrackedstable[element] = massfrac_untrackedstable;
}
// (isofracsum + massfracstable) might not exactly match elemabundance if we had to boost it to reach isofracsum
set_elem_abundance(mgi, element, isofracsum + massfrac_untrackedstable);
}
void allocate_nonemptycells_composition_cooling()
// Initialise composition dependent cell data for the given cell
{
const ptrdiff_t npts_nonempty = get_nonempty_npts_model();
#ifdef MPI_ON
const auto [_, noderank_nonemptycellcount] =
get_range_chunk(nonempty_npts_model, globals::node_nprocs, globals::rank_in_node);
{
auto size = static_cast<MPI_Aint>(noderank_nonemptycellcount * get_nelements() * sizeof(float));
int disp_unit = sizeof(float);
MPI_Win mpiwin = MPI_WIN_NULL;
assert_always(MPI_Win_allocate_shared(size, disp_unit, MPI_INFO_NULL, globals::mpi_comm_node,
&initmassfracuntrackedstable_allcells, &mpiwin) == MPI_SUCCESS);
assert_always(MPI_Win_shared_query(mpiwin, 0, &size, &disp_unit, &initmassfracuntrackedstable_allcells) ==
MPI_SUCCESS);
}
{
auto size = static_cast<MPI_Aint>(noderank_nonemptycellcount * get_nelements() * sizeof(float));
int disp_unit = sizeof(float);
MPI_Win mpiwin = MPI_WIN_NULL;
assert_always(MPI_Win_allocate_shared(size, disp_unit, MPI_INFO_NULL, globals::mpi_comm_node,
&elem_meanweight_allcells, &mpiwin) == MPI_SUCCESS);
assert_always(MPI_Win_shared_query(mpiwin, 0, &size, &disp_unit, &elem_meanweight_allcells) == MPI_SUCCESS);
MPI_Barrier(globals::mpi_comm_node);
}
#else
initmassfracuntrackedstable_allcells = static_cast<float *>(malloc(npts_nonempty * get_nelements() * sizeof(float)));
elem_meanweight_allcells = static_cast<float *>(malloc(npts_nonempty * get_nelements() * sizeof(float)));
#endif
if (globals::total_nlte_levels > 0) {
#ifdef MPI_ON
auto size = static_cast<MPI_Aint>(noderank_nonemptycellcount * globals::total_nlte_levels * sizeof(double));
int disp_unit = sizeof(double);
assert_always(MPI_Win_allocate_shared(size, disp_unit, MPI_INFO_NULL, globals::mpi_comm_node, &nltepops_allcells,
&win_nltepops_allcells) == MPI_SUCCESS);
assert_always(MPI_Win_shared_query(win_nltepops_allcells, 0, &size, &disp_unit, &nltepops_allcells) == MPI_SUCCESS);
MPI_Barrier(globals::mpi_comm_node);
#else
nltepops_allcells = static_cast<double *>(malloc(npts_nonempty * globals::total_nlte_levels * sizeof(double)));
#endif
assert_always(nltepops_allcells != nullptr);
}
for (ptrdiff_t nonemptymgi = 0; nonemptymgi < npts_nonempty; nonemptymgi++) {
const int modelgridindex = grid::get_mgi_of_nonemptymgi(nonemptymgi);
modelgrid[modelgridindex].elements_uppermost_ion = static_cast<int *>(malloc(get_nelements() * sizeof(int)));
assert_always(modelgrid[modelgridindex].elements_uppermost_ion != nullptr);
modelgrid[modelgridindex].elem_massfracs = static_cast<float *>(malloc(get_nelements() * sizeof(float)));
if (modelgrid[modelgridindex].elem_massfracs == nullptr) {
printout("[fatal] input: not enough memory to initialize compositionlist for cell %d... abort\n", modelgridindex);
std::abort();
}
modelgrid[modelgridindex].initmassfracuntrackedstable =
&initmassfracuntrackedstable_allcells[nonemptymgi * get_nelements()];
assert_always(modelgrid[modelgridindex].initmassfracuntrackedstable != nullptr);
modelgrid[modelgridindex].elem_meanweight = &elem_meanweight_allcells[nonemptymgi * get_nelements()];
assert_always(modelgrid[modelgridindex].elem_meanweight != nullptr);
if (globals::total_nlte_levels > 0) {
modelgrid[modelgridindex].nlte_pops =
std::span(&nltepops_allcells[nonemptymgi * globals::total_nlte_levels], globals::total_nlte_levels);
assert_always(modelgrid[modelgridindex].nlte_pops.data() != nullptr);
// -1 indicates that there is currently no information on the nlte populations
std::ranges::fill(modelgrid[modelgridindex].nlte_pops, -1.);
}
std::fill_n(modelgrid[modelgridindex].elem_massfracs, get_nelements(), -1.);
modelgrid[modelgridindex].ion_groundlevelpops = static_cast<float *>(calloc(get_includedions(), sizeof(float)));
if (modelgrid[modelgridindex].ion_groundlevelpops == nullptr) {
printout("[fatal] input: not enough memory to initialize ion_groundlevelpops in cell %d... abort\n",
modelgridindex);
std::abort();
}
modelgrid[modelgridindex].ion_partfuncts = static_cast<float *>(calloc(get_includedions(), sizeof(float)));
if (modelgrid[modelgridindex].ion_partfuncts == nullptr) {
printout("[fatal] input: not enough memory to initialize partfunctlist in cell %d... abort\n", modelgridindex);
std::abort();
}
modelgrid[modelgridindex].ion_cooling_contribs = static_cast<double *>(malloc(get_includedions() * sizeof(double)));
if (modelgrid[modelgridindex].ion_cooling_contribs == nullptr) {
printout("[fatal] input: not enough memory to initialize ion_cooling_contribs for cell %d... abort\n",
modelgridindex);
std::abort();
}
}
}
void allocate_nonemptymodelcells() {
// Determine the number of simulation cells associated with the model cells
for (int mgi = 0; mgi < (get_npts_model() + 1); mgi++) {
mg_associated_cells[mgi] = 0;
modelgrid[mgi].initial_radial_pos_sum = 0.;
}
for (int cellindex = 0; cellindex < ngrid; cellindex++) {
const auto radial_pos_mid = get_cellradialposmid(cellindex);
if (FORCE_SPHERICAL_ESCAPE_SURFACE && radial_pos_mid > globals::vmax * globals::tmin) {
// for 1D models, the final shell outer v should already be at vmax
assert_always(model_type != GridType::SPHERICAL1D || cell[cellindex].modelgridindex == get_npts_model());
cell[cellindex].modelgridindex = get_npts_model();
}
const int mgi = get_cell_modelgridindex(cellindex);
assert_always(!(get_model_type() == GridType::CARTESIAN3D) || (get_rho_tmin(mgi) > 0) || (mgi == get_npts_model()));
mg_associated_cells[mgi] += 1;
modelgrid[mgi].initial_radial_pos_sum += radial_pos_mid;
assert_always(!(get_model_type() == GridType::CARTESIAN3D) || (mg_associated_cells[mgi] == 1) ||
(mgi == get_npts_model()));
}
// find number of non-empty cells and allocate nonempty list
nonempty_npts_model = 0;
for (int mgi = 0; mgi < get_npts_model(); mgi++) {
if (get_numassociatedcells(mgi) > 0) {
nonempty_npts_model++;
}
}
assert_always(nonempty_npts_model > 0);
mgi_of_nonemptymgi.resize(nonempty_npts_model, -2);
int nonemptymgi = 0; // index within list of non-empty modelgrid cells
for (int mgi = 0; mgi < get_npts_model(); mgi++) {
if (get_numassociatedcells(mgi) > 0) {
if (get_rho_tmin(mgi) <= 0) {
printout("Error: negative or zero density. Abort.\n");
std::abort();
}
nonemptymgi_of_mgi[mgi] = nonemptymgi;
mgi_of_nonemptymgi[nonemptymgi] = mgi;
nonemptymgi++;
} else {
nonemptymgi_of_mgi[mgi] = -1;
set_rho_tmin(mgi, 0.);
set_rho(mgi, 0.);
if (modelgrid[mgi].initnucmassfrac != nullptr) {
for (int nucindex = 0; nucindex < decay::get_num_nuclides(); nucindex++) {
set_modelinitnucmassfrac(mgi, nucindex, 0.);
}
}
}
}
allocate_nonemptycells_composition_cooling();
if constexpr (EXPANSIONOPACITIES_ON || RPKT_BOUNDBOUND_THERMALISATION_PROBABILITY > 0.) {
allocate_expansionopacities();
}
globals::dep_estimator_gamma.resize(nonempty_npts_model, 0.);
globals::dep_estimator_positron.resize(nonempty_npts_model, 0.);
globals::dep_estimator_electron.resize(nonempty_npts_model, 0.);
globals::dep_estimator_alpha.resize(nonempty_npts_model, 0.);
const auto ionestimcount = nonempty_npts_model * globals::nbfcontinua_ground;
const auto ionestimsize = ionestimcount * sizeof(double);
if (USE_LUT_PHOTOION && ionestimsize > 0) {
#ifdef MPI_ON
const auto [_, noderank_nonemptycellcount] =
get_range_chunk(nonempty_npts_model, globals::node_nprocs, globals::rank_in_node);
auto size = static_cast<MPI_Aint>(noderank_nonemptycellcount * globals::nbfcontinua_ground * sizeof(double));
int disp_unit = sizeof(double);
assert_always(MPI_Win_allocate_shared(size, disp_unit, MPI_INFO_NULL, globals::mpi_comm_node,
&globals::corrphotoionrenorm,
&globals::win_corrphotoionrenorm) == MPI_SUCCESS);
assert_always(MPI_Win_shared_query(globals::win_corrphotoionrenorm, 0, &size, &disp_unit,
&globals::corrphotoionrenorm) == MPI_SUCCESS);
#else
globals::corrphotoionrenorm = static_cast<double *>(malloc(ionestimsize));
#endif
globals::gammaestimator.resize(ionestimcount, 0.);
#ifdef DO_TITER
globals::gammaestimator_save.resize(nonempty_npts_model, 0.);
#endif
} else {
globals::corrphotoionrenorm = nullptr;
globals::gammaestimator.clear();
#ifdef DO_TITER
globals::gammaestimator_save.clear();
#endif
}
if (USE_LUT_BFHEATING && ionestimsize > 0) {
globals::bfheatingestimator.resize(ionestimcount, 0.);
#ifdef DO_TITER
globals::bfheatingestimator_save.resize(nonempty_npts_model, 0.);
#endif
} else {
globals::bfheatingestimator.clear();
#ifdef DO_TITER
globals::bfheatingestimator_save.clear();
#endif
}
globals::ffheatingestimator.resize(nonempty_npts_model, 0.);
globals::colheatingestimator.resize(nonempty_npts_model, 0.);
#ifdef DO_TITER
globals::ffheatingestimator_save.resize(nonempty_npts_model, 0.);
globals::colheatingestimator_save.resize(nonempty_npts_model, 0.);
#endif
#ifdef MPI_ON
// barrier to make sure node master has set abundance values to node shared memory
MPI_Barrier(MPI_COMM_WORLD);
#endif
printout("[info] mem_usage: the modelgrid array occupies %.3f MB\n",
(get_npts_model() + 1) * sizeof(modelgrid[0]) / 1024. / 1024.);
printout("There are %td modelgrid cells with associated propagation cells (nonempty_npts_model)\n",
nonempty_npts_model);
printout(
"[info] mem_usage: NLTE populations for all allocated cells occupy a total of %.3f MB (node shared memory)\n",
get_nonempty_npts_model() * globals::total_nlte_levels * sizeof(double) / 1024. / 1024.);
}
void map_1dmodelto3dgrid()
// Map 1D spherical model grid onto propagation grid
{
for (int cellindex = 0; cellindex < ngrid; cellindex++) {
const double cellvmid = get_cellradialposmid(cellindex) / globals::tmin;
const int mgi = static_cast<int>(std::ranges::lower_bound(vout_model, cellvmid) - vout_model.begin());
if (mgi < get_npts_model() && modelgrid[mgi].rhoinit > 0) {
set_cell_modelgridindex(cellindex, mgi);
assert_always(vout_model[mgi] >= cellvmid);
assert_always((mgi > 0 ? vout_model[mgi - 1] : 0.0) <= cellvmid);
} else {
// corner cells outside of the outermost model shell are empty
// and so are any shells with zero density
set_cell_modelgridindex(cellindex, get_npts_model());
}
}
}
void map_2dmodelto3dgrid()
// Map 2D cylindrical model onto propagation grid
{
for (int cellindex = 0; cellindex < ngrid; cellindex++) {
// map to 3D Cartesian grid
const auto pos_mid = std::array<double, 3>{get_cellcoordmin(cellindex, 0) + (0.5 * wid_init(cellindex, 0)),
get_cellcoordmin(cellindex, 1) + (0.5 * wid_init(cellindex, 1)),
get_cellcoordmin(cellindex, 2) + (0.5 * wid_init(cellindex, 2))};
const double rcylindrical = std::sqrt(std::pow(pos_mid[0], 2) + std::pow(pos_mid[1], 2));
// 2D grid is uniform so rcyl and z indicies can be calculated with no lookup
const int n_rcyl = static_cast<int>(rcylindrical / globals::tmin / globals::vmax * ncoord_model[0]);
const int n_z =
static_cast<int>((pos_mid[2] / globals::tmin + globals::vmax) / (2 * globals::vmax) * ncoord_model[1]);
if (n_rcyl >= 0 && n_rcyl < ncoord_model[0] && n_z >= 0 && n_z < ncoord_model[1]) {
const int mgi = (n_z * ncoord_model[0]) + n_rcyl;
if (modelgrid[mgi].rhoinit > 0) {
set_cell_modelgridindex(cellindex, mgi);
} else {
set_cell_modelgridindex(cellindex, get_npts_model());
}
} else {
set_cell_modelgridindex(cellindex, get_npts_model());
}
}
}
// mgi and cellindex are interchangeable in this mode (except for empty cells that associated with mgi ==
// get_npts_model())
void map_modeltogrid_direct() {
for (int cellindex = 0; cellindex < ngrid; cellindex++) {
const int mgi = (modelgrid[cellindex].rhoinit > 0) ? cellindex : get_npts_model();
set_cell_modelgridindex(cellindex, mgi);
}
}
void abundances_read() {
#ifdef MPI_ON
// barrier to make sure node master has set values in node shared memory
MPI_Barrier(MPI_COMM_WORLD);
#endif
printout("reading abundances.txt...");
const bool threedimensional = (get_model_type() == GridType::CARTESIAN3D);
// Open the abundances file
auto abundance_file = fstream_required("abundances.txt", std::ios::in);
// and process through the grid to read in the abundances per cell
// The abundance file should only contain information for non-empty
// cells. Its format must be cellnumber (integer), abundance for
// element Z=1 (float) up to abundance for element Z=30 (float)
// i.e. in total one integer and 30 floats.
// loop over propagation cells for 3D models, or modelgrid cells
for (int mgi = 0; mgi < get_npts_model(); mgi++) {
std::string line;
assert_always(get_noncommentline(abundance_file, line));
std::istringstream ssline(line);
int cellnumberinput = -1;
assert_always(ssline >> cellnumberinput);
assert_always(cellnumberinput == mgi + first_cellindex);
// the abundances.txt file specifies the elemental mass fractions for each model cell
// (or proportial to mass frac, e.g. element densities because they will be normalised anyway)
// The abundances begin with hydrogen, helium, etc, going as far up the atomic numbers as required
double normfactor = 0.;
float abundances_in[150] = {0.};
double abund_in = 0.;
for (int anumber = 1; anumber <= 150; anumber++) {
abundances_in[anumber - 1] = 0.;
if (!(ssline >> abund_in)) {
// at least one element (hydrogen) should have been specified for nonempty cells
assert_always(anumber > 1 || get_numassociatedcells(mgi) == 0);
break;
}
if (abund_in < 0. || abund_in < std::numeric_limits<float>::min()) {
assert_always(abund_in > -1e-6);
abund_in = 0.;
}
abundances_in[anumber - 1] = static_cast<float>(abund_in);
normfactor += abundances_in[anumber - 1];
}
if (get_numassociatedcells(mgi) > 0) {
if (threedimensional || normfactor <= 0.) {
normfactor = 1.;
}
for (int element = 0; element < get_nelements(); element++) {
// now set the abundances (by mass) of included elements, i.e.
// read out the abundances specified in the atomic data file
const int anumber = get_atomicnumber(element);
const float elemabundance = abundances_in[anumber - 1] / normfactor;
assert_always(elemabundance >= 0.);
// radioactive nuclide abundances should have already been set by read_??_model
set_elem_untrackedstable_abund_from_total(mgi, element, elemabundance);
}
}
}
#ifdef MPI_ON
// barrier to make sure node master has set values in node shared memory
MPI_Barrier(MPI_COMM_WORLD);
#endif
printout("done.\n");
}
void parse_model_headerline(const std::string &line, std::vector<int> &zlist, std::vector<int> &alist,
std::vector<std::string> &colnames) {
// custom header line
std::istringstream iss(line);
std::string token;
int columnindex = -1;
while (std::getline(iss, token, ' ')) {
if (std::ranges::all_of(token, isspace)) { // skip whitespace tokens
continue;
}
columnindex++;
if (token == "#inputcellid") {
assert_always(columnindex == 0);
} else if (token == "velocity_outer") {
assert_always(columnindex == 1);
} else if (token == "vel_r_max_kmps") {
assert_always(columnindex == 1);
} else if (token.starts_with("pos_")) {
continue;
} else if (token == "logrho") {
// 1D models have log10(rho [g/cm3])
assert_always(columnindex == 2);
assert_always(get_model_type() == GridType::SPHERICAL1D);
} else if (token == "rho") {
// 2D and 3D models have rho [g/cm3]
assert_always(get_model_type() != GridType::SPHERICAL1D);
assert_always((columnindex == 4 && get_model_type() == GridType::CARTESIAN3D) ||
(columnindex == 3 && get_model_type() == GridType::CYLINDRICAL2D));
continue;
} else if (token.starts_with("X_") && token != "X_Fegroup") {
colnames.push_back(token);
const int z = decay::get_nucstring_z(token.substr(2)); // + 2 skips the 'X_'
const int a = decay::get_nucstring_a(token.substr(2));
assert_always(z >= 0);
assert_always(a >= 0);
// printout("Custom column: '%s' Z %d A %d\n", token.c_str(), z, a);
zlist.push_back(z);
alist.push_back(a);
} else {
// printout("Custom column: '%s' Z %d A %d\n", token.c_str(), -1, -1);
colnames.push_back(token);
zlist.push_back(-1);
alist.push_back(-1);
}
}
}
auto get_token_count(std::string &line) -> int {
std::string token;
int abundcolcount = 0;
auto ssline = std::istringstream(line);
while (std::getline(ssline, token, ' ')) {
if (!std::ranges::all_of(token, isspace)) { // skip whitespace tokens
abundcolcount++;
}
}
return abundcolcount;
}
void read_model_radioabundances(std::fstream &fmodel, std::istringstream &ssline_in, const int mgi, const bool keepcell,
const std::vector<std::string> &colnames, const std::vector<int> &nucindexlist,
const bool one_line_per_cell) {
std::string line;
if (!one_line_per_cell) {
assert_always(std::getline(fmodel, line));
}
auto ssline = one_line_per_cell ? std::move(ssline_in) : std::istringstream(line);
if (!keepcell) {
return;
}
for (ptrdiff_t i = 0; i < std::ssize(colnames); i++) {
double valuein = 0.;
assert_always(ssline >> valuein); // usually a mass fraction, but now can be anything
if (nucindexlist[i] >= 0) {
assert_testmodeonly(valuein <= 1.);
set_modelinitnucmassfrac(mgi, nucindexlist[i], valuein);
} else if (colnames[i] == "X_Fegroup") {
set_ffegrp(mgi, valuein);
} else if (colnames[i] == "cellYe") {
set_initelectronfrac(mgi, valuein);
} else if (colnames[i] == "q") {
// use value for t_model and adjust to tmin with expansion factor
set_initenergyq(mgi, valuein * t_model / globals::tmin);
} else if (colnames[i] == "tracercount") {
;
} else {
if (mgi == 0) {
printout("WARNING: ignoring column '%s' nucindex %d valuein[mgi=0] %lg\n", colnames[i].c_str(), nucindexlist[i],
valuein);
}
}
}
double valuein = 0.;
assert_always(!(ssline >> valuein)); // should be no tokens left!
}
auto read_model_columns(std::fstream &fmodel) -> std::tuple<std::vector<std::string>, std::vector<int>, bool> {
auto pos_data_start = fmodel.tellg(); // get position in case we need to undo getline
std::vector<int> zlist;
std::vector<int> alist;
std::vector<std::string> colnames;
std::string line;
std::getline(fmodel, line);
std::string headerline;
const bool header_specified = lineiscommentonly(line);
if (header_specified) {
// line is the header
headerline = line;
pos_data_start = fmodel.tellg();
std::getline(fmodel, line);
} else {
// line is not a comment, so it must be the first line of data
// add a default header for unlabelled columns
switch (model_type) {
case GridType::SPHERICAL1D:
headerline = std::string("#inputcellid vel_r_max_kmps logrho");
break;
case GridType::CYLINDRICAL2D:
headerline = std::string("#inputcellid pos_rcyl_mid pos_z_mid rho");
break;
case GridType::CARTESIAN3D:
headerline = std::string("#inputcellid pos_x_min pos_y_min pos_z_min rho");
break;
}
headerline += std::string(" X_Fegroup X_Ni56 X_Co56 X_Fe52 X_Cr48");
}
int colcount = get_token_count(line);
const bool one_line_per_cell = (colcount >= get_token_count(headerline));
printout("model.txt has %s line per cell format\n", one_line_per_cell ? "one" : "two");
if (!one_line_per_cell) { // add columns from the second line
std::getline(fmodel, line);
colcount += get_token_count(line);
}
if (!header_specified && colcount > get_token_count(headerline)) {
headerline += " X_Ni57 X_Co57";
}
assert_always(colcount == get_token_count(headerline));
fmodel.seekg(pos_data_start); // get back to start of data
if (header_specified) {
printout("model.txt has header line: %s\n", headerline.c_str());
} else {
printout("model.txt has no header line. Using default: %s\n", headerline.c_str());
}
parse_model_headerline(headerline, zlist, alist, colnames);
decay::init_nuclides(zlist, alist);
std::vector<int> nucindexlist(zlist.size());
for (ptrdiff_t i = 0; i < std::ssize(zlist); i++) {
nucindexlist[i] = (zlist[i] > 0) ? decay::get_nucindex(zlist[i], alist[i]) : -1;
}
allocate_initradiobund();
return {colnames, nucindexlist, one_line_per_cell};
}
// Read in a 1D spherical model
void read_1d_model() {
auto fmodel = fstream_required("model.txt", std::ios::in);
std::string line;
// 1st read the number of data points in the table of input model.
int npts_model_in = 0;
assert_always(get_noncommentline(fmodel, line));
std::istringstream(line) >> npts_model_in;
set_npts_model(npts_model_in);
ncoord_model[0] = npts_model_in;
vout_model.resize(get_npts_model(), NAN);
// Now read the time (in days) at which the model is specified.
double t_model_days{NAN};
assert_always(get_noncommentline(fmodel, line));
std::istringstream(line) >> t_model_days;
t_model = t_model_days * DAY;
// Now read in the lines of the model. Each line has 5 entries: the
// cell number (integer) the velocity at outer boundary of cell (float),
// the mass density in the cell (float), the abundance of Ni56 by mass
// in the cell (float) and the total abundance of all Fe-grp elements
// in the cell (float). For now, the last number is recorded but never
// used.
const auto [colnames, nucindexlist, one_line_per_cell] = read_model_columns(fmodel);
int mgi = 0;
while (std::getline(fmodel, line)) {
double vout_kmps{NAN};
double log_rho{NAN};
int cellnumberin = 0;
std::istringstream ssline(line);
if (ssline >> cellnumberin >> vout_kmps >> log_rho) {
if (mgi == 0) {
first_cellindex = cellnumberin;
printout("first_cellindex %d\n", first_cellindex);
}
assert_always(cellnumberin == mgi + first_cellindex);
vout_model[mgi] = vout_kmps * 1.e5;
const double rho_tmin = pow(10., log_rho) * pow(t_model / globals::tmin, 3);
set_rho_tmin(mgi, rho_tmin);
set_rho(mgi, rho_tmin);
} else {
printout("Unexpected number of values in model.txt\n");
printout("line: %s\n", line.c_str());
assert_always(false);
}
read_model_radioabundances(fmodel, ssline, mgi, true, colnames, nucindexlist, one_line_per_cell);
mgi += 1;
if (mgi == get_npts_model()) {
break;
}
}
if (mgi != get_npts_model()) {
printout("ERROR in model.txt. Found only %d cells instead of %d expected.\n", mgi - 1, get_npts_model());
std::abort();
}
globals::vmax = vout_model[get_npts_model() - 1];
}
// Read in a 2D axisymmetric cylindrical model
void read_2d_model() {
auto fmodel = fstream_required("model.txt", std::ios::in);
std::string line;
// 1st read the number of data points in the table of input model.
assert_always(get_noncommentline(fmodel, line));
std::istringstream(line) >> ncoord_model[0] >> ncoord_model[1]; // r and z (cylindrical polar)
ncoord_model[2] = 0.;
set_npts_model(ncoord_model[0] * ncoord_model[1]);
// Now read the time (in days) at which the model is specified.
double t_model_days{NAN};
assert_always(get_noncommentline(fmodel, line));
std::istringstream(line) >> t_model_days;
t_model = t_model_days * DAY;
// Now read in vmax for the model (in cm s^-1).
assert_always(get_noncommentline(fmodel, line));
std::istringstream(line) >> globals::vmax;
const auto [colnames, nucindexlist, one_line_per_cell] = read_model_columns(fmodel);
// Now read in the model. Each point in the model has two lines of input.
// First is an index for the cell then its r-mid point then its z-mid point
// then its total mass density.
// Second is the total FeG mass, initial 56Ni mass, initial 56Co mass
int mgi = 0;
while (std::getline(fmodel, line)) {
int cellnumberin = 0;
float cell_r_in{NAN};
float cell_z_in{NAN};
double rho_tmodel{NAN};
std::istringstream ssline(line);
assert_always(ssline >> cellnumberin >> cell_r_in >> cell_z_in >> rho_tmodel);
if (mgi == 0) {
first_cellindex = cellnumberin;
}
assert_always(cellnumberin == mgi + first_cellindex);
const int n_rcyl = (mgi % ncoord_model[0]);
const double pos_r_cyl_mid = (n_rcyl + 0.5) * globals::vmax * t_model / ncoord_model[0];
assert_always(fabs((cell_r_in / pos_r_cyl_mid) - 1) < 1e-3);
const int n_z = (mgi / ncoord_model[0]);
const double pos_z_mid = globals::vmax * t_model * (-1 + 2 * (n_z + 0.5) / ncoord_model[1]);
assert_always(fabs((cell_z_in / pos_z_mid) - 1) < 1e-3);
if (rho_tmodel < 0) {
printout("negative input density %g %d\n", rho_tmodel, mgi);
std::abort();
}
const bool keepcell = (rho_tmodel > 0);
const double rho_tmin = rho_tmodel * pow(t_model / globals::tmin, 3);
set_rho_tmin(mgi, rho_tmin);
set_rho(mgi, rho_tmin);
read_model_radioabundances(fmodel, ssline, mgi, keepcell, colnames, nucindexlist, one_line_per_cell);
mgi++;
}
if (mgi != get_npts_model()) {
printout("ERROR in model.txt. Found %d only cells instead of %d expected.\n", mgi - 1, get_npts_model());
std::abort();
}
}
// read a 3D Cartesian model
void read_3d_model() {
auto fmodel = fstream_required("model.txt", std::ios::in);
std::string line;
// 1st read the number of data points in the table of input model.
// This MUST be the same number as the maximum number of points used in the grid - if not, abort.
int npts_model_in = 0;
assert_always(get_noncommentline(fmodel, line));
std::istringstream(line) >> npts_model_in;
set_npts_model(npts_model_in);
ncoord_model[0] = ncoord_model[1] = ncoord_model[2] = static_cast<int>(round(pow(npts_model_in, 1 / 3.)));
assert_always(ncoord_model[0] * ncoord_model[1] * ncoord_model[2] == npts_model_in);
// for a 3D input model, the propagation cells will match the input cells exactly
ncoordgrid = ncoord_model;
ngrid = npts_model_in;
double t_model_days{NAN};
assert_always(get_noncommentline(fmodel, line));
std::istringstream(line) >> t_model_days;
t_model = t_model_days * DAY;
// Now read in vmax for the model (in cm s^-1).
assert_always(get_noncommentline(fmodel, line));
std::istringstream(line) >> globals::vmax;