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perf: use compact array format for TRISO particle HDF5 I/O
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cn-skywalker
parent
a657bcb6c2
commit
2b371c606c
2 changed files with 186 additions and 4 deletions
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@ -112,6 +112,10 @@ class Summary:
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if "dagmc" not in self._f['geometry'].attrs.keys():
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self._read_surfaces()
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cell_fills = self._read_cells()
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# Read compact TRISO particle data if present
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if 'geometry/triso_particles' in self._f:
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triso_fills = self._read_triso_particles()
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cell_fills.update(triso_fills)
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self._read_universes()
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self._read_lattices()
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self._finalize_geometry(cell_fills)
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@ -194,6 +198,69 @@ class Summary:
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return cell_fills
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def _read_triso_particles(self):
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"""Read compact TRISO particle data from HDF5 and reconstruct objects.
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Returns
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-------
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dict
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Cell fill information for all TRISO and background cells
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"""
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triso_grp = self._f['geometry/triso_particles']
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n_triso = int(triso_grp.attrs['n_triso'])
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if n_triso == 0:
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return {}
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# Batch-read all arrays
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positions = triso_grp['positions'][()] # (N, 4) array
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surface_ids = triso_grp['surface_ids'][()] # (N,) array
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cell_ids = triso_grp['cell_ids'][()] # (N,) array
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fill_universes = triso_grp['fill_universes'][()] # (N,) array
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group_offsets = triso_grp['group_offsets'][()] # (n_groups+1,) array
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cell_fills = {}
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# Create all TRISO Sphere surfaces in batch
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for i in range(n_triso):
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x0, y0, z0, r = positions[i]
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sid = int(surface_ids[i])
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surf = openmc.Sphere(x0=float(x0), y0=float(y0),
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z0=float(z0), r=float(r),
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surface_id=sid)
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self._fast_surfaces[sid] = surf
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# Create all TRISO Cell objects in batch
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for i in range(n_triso):
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cid = int(cell_ids[i])
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sid = int(surface_ids[i])
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fill_univ_id = int(fill_universes[i])
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x0, y0, z0, _ = positions[i]
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cell = openmc.Cell(cell_id=cid)
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cell.region = -self._fast_surfaces[sid]
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cell.translation = np.array([x0, y0, z0], dtype=np.float64)
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cell_fills[cid] = ('universe', fill_univ_id)
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self._fast_cells[cid] = cell
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# Create background cells for each group
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n_groups = len(group_offsets) - 1
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groups_grp = triso_grp['groups']
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for g in range(n_groups):
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grp = groups_grp[str(g)]
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bg_cell_id = int(grp['background_cell_id'][()])
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bg_material_id = int(grp['background_material_id'][()])
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bg_universe_id = int(grp['background_universe_id'][()])
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bg_cell = openmc.Cell(cell_id=bg_cell_id)
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bg_cell.virtual_lattice = True
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bg_cell.lower_left = list(grp['vl_lower_left'][()])
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bg_cell.pitch = list(grp['vl_pitch'][()])
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bg_cell.shape = list(grp['vl_shape'][()])
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cell_fills[bg_cell_id] = ('material', bg_material_id)
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self._fast_cells[bg_cell_id] = bg_cell
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return cell_fills
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def _read_universes(self):
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for group in self._f['geometry/universes'].values():
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geom_type = group.get('geom_type')
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123
src/summary.cpp
123
src/summary.cpp
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@ -1,6 +1,7 @@
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#include "openmc/summary.h"
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#include <fmt/core.h>
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#include <map>
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#include "openmc/capi.h"
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#include "openmc/cell.h"
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@ -93,25 +94,139 @@ void write_nuclides(hid_t file)
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close_group(macro_group);
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}
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void write_triso_particles(hid_t geom_group)
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{
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// Collect all TRISO surfaces and group by background cell ID
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std::map<int32_t, vector<int32_t>> bg_to_surfs;
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for (int i = 0; i < model::surfaces.size(); ++i) {
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const auto& surf = model::surfaces[i];
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if (surf->is_triso_surface_) {
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bg_to_surfs[surf->triso_base_index_].push_back(i);
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}
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}
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int n_groups = bg_to_surfs.size();
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if (n_groups == 0)
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return;
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// Count total TRISO particles
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int n_triso = 0;
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for (const auto& [bg_id, surfs] : bg_to_surfs) {
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n_triso += surfs.size();
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}
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// Build flat arrays
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vector<double> positions(n_triso * 4);
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vector<int32_t> surface_ids(n_triso);
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vector<int32_t> cell_ids(n_triso);
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vector<int32_t> fill_universes(n_triso);
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vector<int32_t> group_offsets(n_groups + 1);
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int idx = 0;
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int g = 0;
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group_offsets[0] = 0;
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for (const auto& [bg_cell_id, surfs] : bg_to_surfs) {
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for (const auto& i_surf : surfs) {
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const auto& surf = model::surfaces[i_surf];
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vector<double> center = surf->get_center();
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double radius = surf->get_radius();
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positions[idx * 4 + 0] = center[0];
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positions[idx * 4 + 1] = center[1];
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positions[idx * 4 + 2] = center[2];
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positions[idx * 4 + 3] = radius;
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surface_ids[idx] = surf->id_;
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// Get TRISO particle cell via triso_particle_index_
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int32_t i_cell = model::cell_map.at(surf->triso_particle_index_);
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const auto& cell = model::cells[i_cell];
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cell_ids[idx] = cell->id_;
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fill_universes[idx] = model::universes[cell->fill_]->id_;
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++idx;
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}
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group_offsets[g + 1] = idx;
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++g;
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}
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// Write compact TRISO data to HDF5
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hid_t triso_group = create_group(geom_group, "triso_particles");
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write_attribute(triso_group, "n_groups", n_groups);
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write_attribute(triso_group, "n_triso", n_triso);
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// Write positions as 2D dataset [n_triso, 4]
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hsize_t pos_dims[] = {static_cast<hsize_t>(n_triso), 4};
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write_dataset_lowlevel(triso_group, 2, pos_dims, "positions",
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H5TypeMap<double>::type_id, H5S_ALL, false, positions.data());
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write_dataset(triso_group, "surface_ids", surface_ids);
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write_dataset(triso_group, "cell_ids", cell_ids);
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write_dataset(triso_group, "fill_universes", fill_universes);
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write_dataset(triso_group, "group_offsets", group_offsets);
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// Write per-group metadata (background cell info)
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hid_t groups_group = create_group(triso_group, "groups");
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g = 0;
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for (const auto& [bg_cell_id, surfs] : bg_to_surfs) {
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auto grp = create_group(groups_group, std::to_string(g));
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int32_t i_bg_cell = model::cell_map.at(bg_cell_id);
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const auto& bg_cell = model::cells[i_bg_cell];
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write_dataset(grp, "background_cell_id", bg_cell->id_);
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write_dataset(grp, "background_material_id",
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model::materials[bg_cell->material_[0]]->id_);
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write_dataset(
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grp, "background_universe_id", model::universes[bg_cell->universe_]->id_);
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write_dataset(grp, "vl_lower_left", bg_cell->vl_lower_left_);
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write_dataset(grp, "vl_pitch", bg_cell->vl_pitch_);
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write_dataset(grp, "vl_shape", bg_cell->vl_shape_);
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close_group(grp);
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++g;
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}
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close_group(groups_group);
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close_group(triso_group);
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}
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void write_geometry(hid_t file)
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{
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auto geom_group = create_group(file, "geometry");
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write_attribute(geom_group, "n_cells", model::cells.size());
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write_attribute(geom_group, "n_surfaces", model::surfaces.size());
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// Count non-TRISO cells and surfaces for accurate counts
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int n_cells = 0;
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int n_surfaces = 0;
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for (const auto& c : model::cells) {
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if (!c->triso_particle_ && !c->virtual_lattice_)
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++n_cells;
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}
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for (const auto& surf : model::surfaces) {
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if (!surf->is_triso_surface_)
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++n_surfaces;
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}
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write_attribute(geom_group, "n_cells", n_cells);
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write_attribute(geom_group, "n_surfaces", n_surfaces);
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write_attribute(geom_group, "n_universes", model::universes.size());
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write_attribute(geom_group, "n_lattices", model::lattices.size());
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auto cells_group = create_group(geom_group, "cells");
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for (const auto& c : model::cells)
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for (const auto& c : model::cells) {
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if (c->triso_particle_ || c->virtual_lattice_)
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continue;
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c->to_hdf5(cells_group);
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}
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close_group(cells_group);
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auto surfaces_group = create_group(geom_group, "surfaces");
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for (const auto& surf : model::surfaces)
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for (const auto& surf : model::surfaces) {
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if (surf->is_triso_surface_)
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continue;
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surf->to_hdf5(surfaces_group);
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}
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close_group(surfaces_group);
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// Write compact TRISO particle data
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write_triso_particles(geom_group);
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auto universes_group = create_group(geom_group, "universes");
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for (const auto& u : model::universes)
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u->to_hdf5(universes_group);
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