from molsysmt._private.digestion import digest
from molsysmt import pyunitwizard as puw
import numpy as np
[docs]
@digest(form='molsysmt.Structures')
def to_file_h5msm(item, atom_indices='all', structure_indices='all', output_filename=None,
compression='gzip', compression_opts=4, int_precision='single', float_precision='single',
skip_digestion=False):
from molsysmt.native import H5MSMFileHandler
handler = H5MSMFileHandler(output_filename, io_mode='w', compression=compression,
compression_opts=compression_opts, int_precision=int_precision,
float_precision=float_precision, closed=False)
dump_structures_to_h5msm(item, handler, atom_indices=atom_indices,
structure_indices=structure_indices)
handler.close()
return output_filename
[docs]
def dump_structures_to_h5msm(item, file, atom_indices='all', structure_indices='all'):
from h5py._hl.files import File as h5py_File
from molsysmt.native import H5MSMFileHandler
file_is_h5msm = False
needs_to_be_closed = False
if isinstance(file, h5py_File):
if 'type' in file.attrs:
file_is_h5msm = (file.attrs['type']=='h5msm')
elif isinstance(file, H5MSMFileHandler):
file = file.file
file_is_h5msm = True
else:
from molsysmt.form.file_h5msm.is_form import is_form as is_file_h5msm_form
file_is_h5msm = is_file_h5msm_form(file)
if file_is_h5msm:
file = h5py.File(file, "w")
needs_to_be_closed = True
if not file_is_h5msm:
raise ValueError
int_precision = file.attrs['int_precision']
float_precision = file.attrs['float_precision']
if int_precision=='single':
int_type=np.int32
elif int_precision=='double':
int_type=np.int64
if float_precision=='single':
float_type=np.float32
elif float_precision=='double':
float_type=np.float64
structures_ds = file['structures']
n_atoms = item.n_atoms
n_structures = item.n_structures
length_unit = puw.get_standard_units(dimensionality={'[L]':1})
time_unit = puw.get_standard_units(dimensionality={'[T]':1})
energy_unit = puw.get_standard_units(dimensionality={'[L]':2, '[M]':1, '[T]':-2,
'[mol]': -1})
temperature_unit = puw.get_standard_units(dimensionality={'[K]':1})
structures_ds.attrs['length_unit']=str(length_unit)
structures_ds.attrs['time_unit']=str(time_unit)
structures_ds.attrs['energy_unit']=str(energy_unit)
if item.coordinates is not None:
structures_ds['coordinates'].resize((n_structures,n_atoms,3))
if puw.check(item.coordinates, unit=length_unit):
aux = puw.get_value(item.coordinates).astype(float_precision)
else:
aux = puw.get_value(item.coordinates, to_unit=length_unit).astype(float_precision)
structures_ds['coordinates'][:,:,:] = aux
if item.velocities is not None:
structures_ds['velocities'].resize((n_structures,n_atoms,3))
if puw.check(item.velocities, unit=length_unit/length_time):
aux = puw.get_value(item.velocities).astype(float_precision)
else:
aux = puw.get_value(item.velocities, to_unit=length_unit/length_time).astype(float_precision)
structures_ds['velocities'][:,:,:] = aux
if item.box is not None:
structures_ds['box'].resize((n_structures,3,3))
if puw.check(item.box, unit=length_unit):
aux = puw.get_value(item.box).astype(float_precision)
else:
aux = puw.get_value(item.box, to_unit=length_unit).astype(float_precision)
structures_ds['box'][:,:,:] = aux
if item.kinetic_energy is not None:
structures_ds['kinetic_energy'].resize((n_structures))
if puw.check(item.kinetic_energy, unit=energy_unit):
aux = puw.get_value(item.kinetic_energy).astype(float_precision)
else:
aux = puw.get_value(item.kinetic_energy, to_unit=length_unit).astype(float_precision)
structures_ds['kinetic_energy'][:] = aux
if item.potential_energy is not None:
structures_ds['potential_energy'].resize((n_structures))
if puw.check(item.potential_energy, unit=energy_unit):
aux = puw.get_value(item.potential_energy).astype(float_precision)
else:
aux = puw.get_value(item.potential_energy, to_unit=length_unit).astype(float_precision)
structures_ds['potential_energy'][:] = aux
if item.temperature is not None:
structures_ds['temperature'].resize((n_structures))
if puw.check(item.temperature, unit=temperature_unit):
aux = puw.get_value(item.temperature).astype(float_precision)
else:
aux = puw.get_value(item.temperature, to_unit=length_unit).astype(float_precision)
structures_ds['temperature'][:] = aux
structures_ds.attrs['n_atoms'] = n_atoms
structures_ds.attrs['n_structures'] = n_structures
structures_ds.attrs['n_structures_written'] = n_structures
if needs_to_be_closed:
file.close()
pass
