Skip to content

Commit

Permalink
Replace PhotoionTarget *phixstargets with int phixstargetstart
Browse files Browse the repository at this point in the history
  • Loading branch information
@lukeshingles
lukeshingles committed Sep 9, 2024
1 parent d008552 commit 197fd1e
Show file tree
Hide file tree
Showing 3 changed files with 52 additions and 40 deletions.
8 changes: 6 additions & 2 deletions atomic.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,9 @@ inline auto get_nphixstargets(const int element, const int ion, const int level)
assert_testmodeonly(phixstargetindex >= 0);
assert_testmodeonly(phixstargetindex < get_nphixstargets(element, ion, level));

return globals::elements[element].ions[ion].levels[level].phixstargets[phixstargetindex].levelindex;
return globals::allphixstargets[globals::elements[element].ions[ion].levels[level].phixstargetstart +
phixstargetindex]
.levelindex;
}

// Return the probability of a target state for photoionization of (element,ion,level).
Expand All @@ -106,7 +108,9 @@ inline auto get_nphixstargets(const int element, const int ion, const int level)
assert_testmodeonly(phixstargetindex >= 0);
assert_testmodeonly(phixstargetindex < get_nphixstargets(element, ion, level));

return globals::elements[element].ions[ion].levels[level].phixstargets[phixstargetindex].probability;
return globals::allphixstargets[globals::elements[element].ions[ion].levels[level].phixstargetstart +
phixstargetindex]
.probability;
}

// Return the statistical weight of (element,ion,level).
Expand Down
19 changes: 11 additions & 8 deletions globals.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -82,14 +82,16 @@ struct PhotoionTarget {

struct EnergyLevel {
double epsilon{-1}; // Excitation energy of this level relative to the neutral ground level.
int alltrans_startdown{}; // Allowed downward transitions from this level
int ndowntrans{0};
int nuptrans{0};
int phixsstart{-1}; // index to start of photoionisation cross-sections table in global::allphixs
int nphixstargets{0}; // length of phixstargets array:
float stat_weight{0.}; // Statistical weight of this level.
PhotoionTarget *phixstargets{}; // pointer to table of target states and probabilities
int cont_index{-1}; // Index of the continuum associated to this level. Negative number.
int alltrans_startdown{}; // index into globals::alltrans for first down transition from this level
int ndowntrans{0}; // Number of down transitions from this level
int nuptrans{0}; // Number of up transitions to this level
int phixsstart{-1}; // index to start of photoionisation cross-sections table in global::allphixs
int nphixstargets{0}; // number of target levels for photoionisation
float stat_weight{0.}; // statistical weight of this level
int phixstargetstart{}; // index into globals::allphixstargets
int cont_index{-1}; // index of the bound-free continuum (for first target) sorted by
// element/ion/level/phixstargetindex
// (not an index into the nu_edge-sorted allcont list!)
int closestgroundlevelcont{-1};
};

Expand Down Expand Up @@ -256,6 +258,7 @@ inline std::vector<float> ion_alpha_sp; // alpha_sp for each ion and temperatur

inline float *allphixs{};
inline LevelTransition *alltrans;
inline std::vector<PhotoionTarget> allphixstargets;

inline std::vector<Element> elements;

Expand Down
65 changes: 35 additions & 30 deletions input.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@
#include <functional>
#include <ios>
#include <iterator>
#include <limits>
#ifndef GPU_ON
#include <random>
#endif
Expand Down Expand Up @@ -87,29 +86,34 @@ constexpr std::array<std::string_view, 24> inputlinecomments = {

CellCachePhixsTargets *chphixstargetsblock{};

// use the temporary list, before it has been copied to node-shared memory
auto get_phixsupperlevel_tmp(const std::vector<PhotoionTarget> &temp_allphixstargets, const int element, const int ion,
const int level, const int phixstargetindex) {
return temp_allphixstargets[globals::elements[element].ions[ion].levels[level].phixstargetstart + phixstargetindex]
.levelindex;
}

void read_phixs_data_table(std::fstream &phixsfile, const int nphixspoints_inputtable, const int element,
const int lowerion, const int lowerlevel, const int upperion, int upperlevel_in,
std::vector<float> &tmpallphixs, size_t *mem_usage_phixs, const int phixs_file_version) {
std::vector<float> &tmpallphixs, std::vector<PhotoionTarget> &temp_allphixstargets,
size_t *mem_usage_phixs, const int phixs_file_version) {
std::string phixsline;
assert_always(globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargetstart == -1);
globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargetstart =
static_cast<int>(std::ssize(temp_allphixstargets));
if (upperlevel_in >= 0) { // file gives photoionisation to a single target state only
int upperlevel = upperlevel_in - groundstate_index_in;
assert_always(upperlevel >= 0);
assert_always(globals::elements[element].ions[lowerion].levels[lowerlevel].nphixstargets == 0);
globals::elements[element].ions[lowerion].levels[lowerlevel].nphixstargets = 1;
*mem_usage_phixs += sizeof(PhotoionTarget);

assert_always(globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets == nullptr);
globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets =
static_cast<PhotoionTarget *>(malloc(sizeof(PhotoionTarget)));
assert_always(globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets != nullptr);

if (single_level_top_ion && (upperion == get_nions(element) - 1)) {
// top ion has only one level, so send it to that level
upperlevel = 0;
}

globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets[0].levelindex = upperlevel;
globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets[0].probability = 1.;
temp_allphixstargets.push_back({.probability = 1., .levelindex = upperlevel});
} else { // upperlevel < 0, indicating that a table of upper levels and their probabilities will follow
int in_nphixstargets = 0;
assert_always(get_noncommentline(phixsfile, phixsline));
Expand All @@ -121,10 +125,6 @@ void read_phixs_data_table(std::fstream &phixsfile, const int nphixspoints_input
globals::elements[element].ions[lowerion].levels[lowerlevel].nphixstargets = in_nphixstargets;
*mem_usage_phixs += in_nphixstargets * sizeof(PhotoionTarget);

globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets =
static_cast<PhotoionTarget *>(malloc(in_nphixstargets * sizeof(PhotoionTarget)));
assert_always(globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets != nullptr);

double probability_sum = 0.;
for (int i = 0; i < in_nphixstargets; i++) {
double phixstargetprobability{NAN};
Expand All @@ -133,9 +133,8 @@ void read_phixs_data_table(std::fstream &phixsfile, const int nphixspoints_input
const int upperlevel = upperlevel_in - groundstate_index_in;
assert_always(upperlevel >= 0);
assert_always(phixstargetprobability > 0);
globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets[i].levelindex = upperlevel;
globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets[i].probability =
phixstargetprobability;
temp_allphixstargets.push_back({.probability = phixstargetprobability, .levelindex = upperlevel});

probability_sum += phixstargetprobability;
}
if (fabs(probability_sum - 1.0) > 0.01) {
Expand All @@ -145,17 +144,13 @@ void read_phixs_data_table(std::fstream &phixsfile, const int nphixspoints_input
} else { // file has table of target states and probabilities but our top ion is limited to one level
globals::elements[element].ions[lowerion].levels[lowerlevel].nphixstargets = 1;
*mem_usage_phixs += sizeof(PhotoionTarget);
globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets =
static_cast<PhotoionTarget *>(malloc(sizeof(PhotoionTarget)));
assert_always(globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets != nullptr);

for (int i = 0; i < in_nphixstargets; i++) {
assert_always(get_noncommentline(phixsfile, phixsline));
}

// send it to the ground state of the top ion
globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets[0].levelindex = 0;
globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargets[0].probability = 1.;
temp_allphixstargets.push_back({.probability = 1., .levelindex = 0});
}
}

Expand All @@ -167,7 +162,10 @@ void read_phixs_data_table(std::fstream &phixsfile, const int nphixspoints_input
if (lowerion < get_nions(element) - 1) {
for (int phixstargetindex = 0; phixstargetindex < get_nphixstargets(element, lowerion, lowerlevel);
phixstargetindex++) {
const int upperlevel = get_phixsupperlevel(element, lowerion, lowerlevel, phixstargetindex);
const int upperlevel =
temp_allphixstargets[globals::elements[element].ions[lowerion].levels[lowerlevel].phixstargetstart +
phixstargetindex]
.levelindex;
if (upperlevel > get_maxrecombininglevel(element, lowerion + 1)) {
globals::elements[element].ions[lowerion + 1].maxrecombininglevel = upperlevel;
}
Expand All @@ -183,7 +181,7 @@ void read_phixs_data_table(std::fstream &phixsfile, const int nphixspoints_input
auto *levelphixstable = &tmpallphixs[tmpphixsstart];
if (phixs_file_version == 1) {
assert_always(get_nphixstargets(element, lowerion, lowerlevel) == 1);
assert_always(get_phixsupperlevel(element, lowerion, lowerlevel, 0) == 0);
assert_always(get_phixsupperlevel_tmp(temp_allphixstargets, element, lowerion, lowerlevel, 0) == 0);

const double nu_edge = (epsilon(element, upperion, 0) - epsilon(element, lowerion, lowerlevel)) / H;

Expand Down Expand Up @@ -241,7 +239,8 @@ void read_phixs_data_table(std::fstream &phixsfile, const int nphixspoints_input
}
}

void read_phixs_file(const int phixs_file_version, std::vector<float> &tmpallphixs) {
void read_phixs_file(const int phixs_file_version, std::vector<float> &tmpallphixs,
std::vector<PhotoionTarget> &temp_allphixstargets) {
size_t mem_usage_phixs = 0;

printout("readin phixs data from %s\n", phixsdata_filenames[phixs_file_version]);
Expand Down Expand Up @@ -309,7 +308,7 @@ void read_phixs_file(const int phixs_file_version, std::vector<float> &tmpallphi
// store only photoionization crosssections for ions that are part of the current model atom
if (lowerion >= 0 && upperion < get_nions(element) && lowerlevel < get_ionisinglevels(element, lowerion)) {
read_phixs_data_table(phixsfile, nphixspoints_inputtable, element, lowerion, lowerlevel, upperion,
upperlevel_in, tmpallphixs, &mem_usage_phixs, phixs_file_version);
upperlevel_in, tmpallphixs, temp_allphixstargets, &mem_usage_phixs, phixs_file_version);

skip_this_phixs_table = false;
}
Expand Down Expand Up @@ -364,7 +363,7 @@ void read_ion_levels(std::fstream &adata, const int element, const int ion, cons
const double currentlevelenergy = (energyoffset + levelenergy) * EV;
globals::elements[element].ions[ion].levels[level].nphixstargets = 0;
globals::elements[element].ions[ion].levels[level].phixsstart = -1;
globals::elements[element].ions[ion].levels[level].phixstargets = nullptr;
globals::elements[element].ions[ion].levels[level].phixstargetstart = -1;
globals::elements[element].ions[ion].levels[level].epsilon = currentlevelenergy;
globals::elements[element].ions[ion].levels[level].stat_weight = statweight;
assert_always(statweight > 0.);
Expand Down Expand Up @@ -843,6 +842,7 @@ void read_phixs_data() {
globals::nbfcontinua_ground = 0;
globals::nbfcontinua = 0;
std::vector<float> tmpallphixs;
std::vector<PhotoionTarget> temp_allphixstargets;

// read in photoionisation cross sections
phixs_file_version_exists[0] = false;
Expand All @@ -860,10 +860,10 @@ void read_phixs_data() {
"from phixsdata_v2.txt to interpolate the phixsdata.txt data\n");
}
if (phixs_file_version_exists[2]) {
read_phixs_file(2, tmpallphixs);
read_phixs_file(2, tmpallphixs, temp_allphixstargets);
}
if (phixs_file_version_exists[1]) {
read_phixs_file(1, tmpallphixs);
read_phixs_file(1, tmpallphixs, temp_allphixstargets);
}

int cont_index = 0;
Expand All @@ -887,8 +887,9 @@ void read_phixs_data() {
// all levels in the ground term should be photoionisation targets from the lower ground state
if (ion > 0 && ion < get_nions(element) - 1) {
const int nphixstargets = get_nphixstargets(element, ion - 1, 0);
if (nphixstargets > 0 && get_phixsupperlevel(element, ion - 1, 0, 0) == 0) {
const int phixstargetlevels = get_phixsupperlevel(element, ion - 1, 0, nphixstargets - 1) + 1;
if (nphixstargets > 0 && get_phixsupperlevel_tmp(temp_allphixstargets, element, ion - 1, 0, 0) == 0) {
const int phixstargetlevels =
get_phixsupperlevel_tmp(temp_allphixstargets, element, ion - 1, 0, nphixstargets - 1) + 1;

if (nlevels_groundterm != phixstargetlevels) {
printout("WARNING: Z=%d ionstage %d nlevels_groundterm %d phixstargetlevels(ion-1) %d.\n",
Expand Down Expand Up @@ -936,6 +937,10 @@ void read_phixs_data() {
#endif
}

temp_allphixstargets.shrink_to_fit();
globals::allphixstargets = temp_allphixstargets;
// TODO: copy to node-shared memory

setup_phixs_list();
}

Expand Down

0 comments on commit 197fd1e

Please sign in to comment.