def move_random(self, entry_id, factor=0.2, in_place=False, kind='move'):
entry = self.get_entry(entry_id)
pos = np.array(entry['structure']['positions']).reshape((-1, 3))
# Unit Vectors
uv = unit_vectors(2 * np.random.rand(*pos.shape) - 1)
new_pos = generic_serializer(pos + factor * uv)
structure = Structure(positions=new_pos, symbols=entry['structure']['symbols'], periodicity=False)
if in_place:
self.update_properties(entry_id=entry_id, new_properties={})
return self.set_structure(entry_id, structure)
else:
structure = Structure(positions=new_pos, symbols=entry['structure']['symbols'], periodicity=False)
return self.new_entry(structure, active=False)
def move_random(self, entry_id, factor=0.2, in_place=False, kind='move'):
entry = self.get_entry(entry_id)
pos = np.array(entry['structure']['positions']).reshape((-1, 3))
# Unit Vectors
uv = unit_vectors(2 * np.random.rand(*pos.shape) - 1)
new_pos = generic_serializer(pos + factor * uv)
structure = Structure(positions=new_pos,
symbols=entry['structure']['symbols'],
periodicity=False)
if in_place:
self.update_properties(entry_id=entry_id, new_properties={})
return self.set_structure(entry_id, structure)
else:
structure = Structure(positions=new_pos,
symbols=entry['structure']['symbols'],
periodicity=False)
return self.new_entry(structure, active=False)
def from_structure(self, structure):
"""
Set input variables for a given structure
:param structure: (pychemia.Structure) Structure to set ABINIT input variables
:return:
"""
natom = structure.natom
ntypat = len(structure.species)
znucl = atomic_number(structure.species)
typat_dict = {}
index = 1
for ispec in structure.species:
typat_dict[ispec] = index
index += 1
typat = [typat_dict[i] for i in structure.symbols]
xcart = angstrom_bohr * structure.positions.flatten()
acell = angstrom_bohr * np.array(structure.lattice.lengths)
rprim = unit_vectors(structure.cell).T.flatten()
for i in ['natom', 'ntypat', 'znucl', 'typat', 'xcart', 'acell', 'rprim']:
self.set_value(i, eval(i))
def from_structure(self, structure):
"""
Set input variables for a given structure
:param structure: (pychemia.Structure) Structure to set ABINIT input variables
:return:
"""
natom = structure.natom
ntypat = len(structure.species)
znucl = atomic_number(structure.species)
typat_dict = {}
index = 1
for ispec in structure.species:
typat_dict[ispec] = index
index += 1
typat = [typat_dict[i] for i in structure.symbols]
xcart = angstrom_bohr * structure.positions.flatten()
acell = angstrom_bohr * np.array(structure.lattice.lengths)
rprim = unit_vectors(structure.cell).T.flatten()
for i in ['natom', 'ntypat', 'znucl', 'typat', 'xcart', 'acell', 'rprim']:
self.set_value(i, eval(i))