pyne::Material::Material(pyne::comp_map cm, double m, std::string s, double apm)
{
// Initializes the mass stream based on an isotopic component dictionary.
comp = cm;
mass = m;
name = s;
atoms_per_mol = apm;
norm_comp();
};
void pyne::Material::from_atom_frac(std::map<int, double> atom_fracs)
{
// atom frac must be of the form {nuc: af}, eg, water
// 80160: 1.0
// 10010: 2.0
// clear existing components
comp.clear();
atoms_per_mol = 0.0;
for (std::map<int, double>::iterator afi = atom_fracs.begin(); afi != atom_fracs.end(); afi++)
{
comp[afi->first] = (afi->second) * pyne::atomic_mass(afi->first);
atoms_per_mol += (afi->second);
};
norm_comp();
};
void pyne::Material::from_hdf5(std::string filename, std::string datapath, int row, int protocol) {
// Turn off annoying HDF5 errors
herr_t status;
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
// Check that the file is there
if (!pyne::file_exists(filename))
throw pyne::FileNotFound(filename);
// Check to see if the file is in HDF5 format.
bool ish5 = H5Fis_hdf5(filename.c_str());
if (!ish5)
throw h5wrap::FileNotHDF5(filename);
//Set file access properties so it closes cleanly
hid_t fapl;
fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fclose_degree(fapl,H5F_CLOSE_STRONG);
// Open the database
hid_t db = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, fapl);
bool datapath_exists = h5wrap::path_exists(db, datapath);
if (!datapath_exists)
throw h5wrap::PathNotFound(filename, datapath);
// Clear current content
comp.clear();
// Load via various protocols
if (protocol == 0)
_load_comp_protocol0(db, datapath, row);
else if (protocol == 1)
_load_comp_protocol1(db, datapath, row);
else
throw pyne::MaterialProtocolError();
// Close the database
status = H5Fclose(db);
// Renomalize the composition, just to be safe.
norm_comp();
};
void pyne::Material::from_hdf5(std::string filename, std::string datapath, int row, int protocol)
{
// Turn off annoying HDF5 errors
H5::Exception::dontPrint();
// Check that the file is there
if (!pyne::file_exists(filename))
throw pyne::FileNotFound(filename);
// Check to see if the file is in HDF5 format.
bool isH5 = H5::H5File::isHdf5(filename);
if (!isH5)
throw h5wrap::FileNotHDF5(filename);
// Open the database
H5::H5File db (filename, H5F_ACC_RDONLY);
bool datapath_exists = h5wrap::path_exists(&db, datapath);
if (!datapath_exists)
throw h5wrap::PathNotFound(filename, datapath);
// Clear current content
comp.clear();
// Load via various protocols
if (protocol == 0)
_load_comp_protocol0(&db, datapath, row);
else if (protocol == 1)
_load_comp_protocol1(&db, datapath, row);
else
throw pyne::MaterialProtocolError();
// Close the database
db.close();
// Renomalize the composition, just to be safe.
norm_comp();
};
void pyne::Material::from_text(std::string filename)
{
// Check that the file is there
if (!pyne::file_exists(filename))
throw pyne::FileNotFound(filename);
// New filestream
std::ifstream f;
f.open(filename.c_str());
// Read in
comp.clear();
std::string keystr, valstr;
while ( !f.eof() )
{
f >> keystr;
if (0 == keystr.length())
continue;
else
f >> valstr;
if (keystr == "Name")
name = valstr;
else if (keystr == "Mass")
mass = pyne::to_dbl(valstr);
else if (keystr == "APerM")
atoms_per_mol = pyne::to_dbl(valstr);
else
comp[pyne::nucname::zzaaam(keystr)] = pyne::to_dbl(valstr);
};
f.close();
norm_comp();
};
