std::pair<std::pair<ParticleID, Voxel>, bool>
SpatiocyteWorld::new_voxel_structure(const Voxel& v)
{
const bool is_succeeded((*space_).update_voxel_private(ParticleID(), v));
const coordinate_type coord(private2coord(v.coordinate()));
return std::make_pair(std::make_pair(ParticleID(),
Voxel(v.species(), coord, v.radius(), v.D(), v.loc())),
is_succeeded);
}
virtual void add_voxel_without_checking(const particle_info& info)
{
if (info.second != ParticleID())
{
throw NotSupported("No ParticleID is allowed.");
}
; // do nothing
}
void load_particle_space(const H5::Group& root, Tspace_* space)
{
typedef ParticleSpaceHDF5Traits traits_type;
typedef typename traits_type::h5_species_struct h5_species_struct;
typedef typename traits_type::h5_particle_struct h5_particle_struct;
Real3 edge_lengths;
const hsize_t dims[] = {3};
const H5::ArrayType lengths_type(H5::PredType::NATIVE_DOUBLE, 1, dims);
root.openAttribute("edge_lengths").read(lengths_type, &edge_lengths);
space->reset(edge_lengths);
double t;
root.openAttribute("t").read(H5::PredType::IEEE_F64LE, &t);
space->set_t(t);
{
H5::DataSet species_dset(root.openDataSet("species"));
const unsigned int num_species(
species_dset.getSpace().getSimpleExtentNpoints());
boost::scoped_array<h5_species_struct> h5_species_table(
new h5_species_struct[num_species]);
species_dset.read(
h5_species_table.get(), traits_type::get_species_comp_type());
species_dset.close();
H5::DataSet particle_dset(root.openDataSet("particles"));
const unsigned int num_particles(
particle_dset.getSpace().getSimpleExtentNpoints());
boost::scoped_array<h5_particle_struct> h5_particle_table(
new h5_particle_struct[num_particles]);
particle_dset.read(
h5_particle_table.get(), traits_type::get_particle_comp_type());
particle_dset.close();
typedef utils::get_mapper_mf<unsigned int, Species::serial_type>::type
species_id_map_type;
species_id_map_type species_id_map;
for (unsigned int i(0); i < num_species; ++i)
{
species_id_map[h5_species_table[i].id] = h5_species_table[i].serial;
}
for (unsigned int i(0); i < num_particles; ++i)
{
space->update_particle(ParticleID(std::make_pair(h5_particle_table[i].lot, h5_particle_table[i].serial)), Particle(Species(species_id_map[h5_particle_table[i].sid]), Real3(h5_particle_table[i].posx, h5_particle_table[i].posy, h5_particle_table[i].posz), h5_particle_table[i].radius, h5_particle_table[i].D));
}
// boost::scoped_array<h5_particle_struct>
// h5_particle_table(new h5_particle_struct[num_particles]);
// for (unsigned int i(0); i < num_particles; ++i)
// {
// species_id_map_type::const_iterator
// it(species_id_map.find(particles[i].second.species_serial()));
// if (it == species_id_map.end())
// {
// species.push_back(particles[i].second.species());
// it = species_id_map.insert(
// std::make_pair(particles[i].second.species_serial(),
// species.size())).first;
// }
// h5_particle_table[i].lot = particles[i].first.lot();
// h5_particle_table[i].serial = particles[i].first.serial();
// h5_particle_table[i].sid = (*it).second;
// h5_particle_table[i].posx = particles[i].second.position()[0];
// h5_particle_table[i].posy = particles[i].second.position()[1];
// h5_particle_table[i].posz = particles[i].second.position()[2];
// h5_particle_table[i].radius = particles[i].second.radius();
// h5_particle_table[i].D = particles[i].second.D();
// }
// boost::scoped_array<h5_species_struct>
// h5_species_table(new h5_species_struct[species.size()]);
// for (unsigned int i(0); i < species.size(); ++i)
// {
// h5_species_table[i].id = i + 1;
// std::strcpy(h5_species_table[i].serial,
// species[i].serial().c_str());
// }
}
}
void load_lattice_space(const H5::Group& root, Tspace_* space)
{
typedef LatticeSpaceHDF5Traits traits_type;
uint32_t space_type; // not use
double t;
double voxel_radius;
Real3 edge_lengths;
const hsize_t dims[] = {3};
uint32_t is_periodic;
#define OPEN_ATTRIBUTE(attribute, type) \
root.openAttribute(#attribute).read(type, &attribute)
OPEN_ATTRIBUTE(space_type, H5::PredType::STD_I32LE);
OPEN_ATTRIBUTE(t, H5::PredType::IEEE_F64LE);
OPEN_ATTRIBUTE(voxel_radius, H5::PredType::IEEE_F64LE);
OPEN_ATTRIBUTE(edge_lengths, H5::ArrayType(H5::PredType::NATIVE_DOUBLE, 1, dims));
OPEN_ATTRIBUTE(is_periodic, H5::PredType::STD_I32LE);
#undef OPEN_ATTRIBUTE
space->set_t(t);
space->reset(edge_lengths, voxel_radius, (is_periodic != 0));
std::map<Species, traits_type::h5_species_struct> struct_map;
std::map<Species, std::vector<std::pair<ParticleID, Integer> > > voxels_map;
std::multimap<std::string, Species> location_map;
std::map<Species, std::pair<traits_type::h5_species_struct,
std::vector<std::pair<ParticleID, Integer> > > > tmp_map;
H5::Group spgroup(root.openGroup("species"));
char name_C[32 + 1];
for (hsize_t idx(0); idx < spgroup.getNumObjs(); ++idx)
{
memset(name_C, 0, 32 + 1); // clear buffer
const ssize_t name_len = H5Lget_name_by_idx(spgroup.getLocId(), ".", H5_INDEX_NAME, H5_ITER_INC, idx, name_C, 32, H5P_DEFAULT);
H5::Group group(spgroup.openGroup(name_C));
const std::string name_S(name_C);
Species species(name_S);
// const H5std_string serial = spgroup.getObjnameByIdx(idx);
// H5::Group group(spgroup.openGroup(serial.c_str()));
// Species species(std::string(serial.c_str()));
traits_type::h5_species_struct property;
group.openAttribute("property").read(
traits_type::get_property_comp(), &property);
struct_map.insert(std::make_pair(species, property));
location_map.insert(std::make_pair(property.location, species));
H5::DataSet voxel_dset(group.openDataSet("voxels"));
const unsigned int num_voxels(
voxel_dset.getSpace().getSimpleExtentNpoints());
boost::scoped_array<traits_type::h5_voxel_struct> h5_voxel_array(
new traits_type::h5_voxel_struct[num_voxels]);
voxel_dset.read(
h5_voxel_array.get(), traits_type::get_voxel_comp());
voxel_dset.close();
group.close();
std::vector<std::pair<ParticleID, Integer> > voxels;
for (unsigned int idx(0); idx < num_voxels; ++idx)
{
voxels.push_back(std::make_pair(
ParticleID(std::make_pair(h5_voxel_array[idx].lot, h5_voxel_array[idx].serial)),
h5_voxel_array[idx].coordinate));
}
voxels_map.insert(std::make_pair(species, voxels));
}
spgroup.close();
std::vector<Species> sp_list;
traits_type::sort_by_location(location_map, sp_list);
for (std::vector<Species>::iterator itr(sp_list.begin());
itr != sp_list.end(); ++itr)
{
Species species(*itr);
traits_type::h5_species_struct property((*struct_map.find(species)).second);
std::vector<std::pair<ParticleID, Integer> > voxels((*voxels_map.find(species)).second);
if (property.is_structure == 0)
space->make_molecular_type(species, property.radius, property.D, property.location);
else
space->make_structure_type(species, static_cast<Shape::dimension_kind>(property.dimension), property.location);
space->add_voxels(species, voxels);
}
}
virtual particle_info pop(const private_coordinate_type& coord)
{
return particle_info(coord, ParticleID());
}