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add MultiSystem for ASE traj(or any other format can be read by ASE) #190

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Merged
amcadmus merged 2 commits into from
Aug 31, 2021
Merged

add MultiSystem for ASE traj(or any other format can be read by ASE) #190

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cb67000
add MultiSystem for ASE traj(or any other format can be read by ASE)
bigd4 Aug 27, 2021
de57e31
add unittest
bigd4 Aug 30, 2021
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47 changes: 45 additions & 2 deletions dpdata/plugins/ase.py
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from dpdata.format import Format
import numpy as np
try:
import ase.io
from ase.calculators.calculator import PropertyNotImplementedError
except ImportError:
pass


@Format.register("ase/structure")
class ASEStructureFormat(Format):
def from_labeled_system(self, data, **kwargs):
return data

def from_multi_systems(self, file_name, begin=None, end=None, step=None, fmt='traj', **kwargs):
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frames = ase.io.read(file_name, format=fmt, index=slice(begin, end, step))
for atoms in frames:
symbols = atoms.get_chemical_symbols()
atom_names = list(set(symbols))
atom_numbs = [symbols.count(symbol) for symbol in atom_names]
atom_types = np.array([atom_names.index(symbol) for symbol in symbols]).astype(int)

cells = atoms.cell[:]
coords = atoms.get_positions()
try:
energies = atoms.get_potential_energy(force_consistent=True)
except PropertyNotImplementedError:
energies = atoms.get_potential_energy()
forces = atoms.get_forces()
info_dict = {
'atom_names': atom_names,
'atom_numbs': atom_numbs,
'atom_types': atom_types,
'cells': np.array([cells]).astype('float32'),
'coords': np.array([coords]).astype('float32'),
'energies': np.array([energies]).astype('float32'),
'forces': np.array([forces]).astype('float32'),
'orig': [0,0,0],
}
try:
stress = atoms.get_stress(False)
virials = np.array([-atoms.get_volume() * stress]).astype('float32')
info_dict['virials'] = virials
except PropertyNotImplementedError:
pass
yield info_dict

def to_system(self, data, **kwargs):
'''
convert System to ASE Atom obj
Expand Down Expand Up @@ -42,9 +84,10 @@ def to_labeled_system(self, data, *args, **kwargs):
}
if "virials" in data:
# convert to GPa as this is ase convention
v_pref = 1 * 1e4 / 1.602176621e6
# v_pref = 1 * 1e4 / 1.602176621e6
vol = structure.get_volume()
results['stress'] = data["virials"][ii] / (v_pref * vol)
# results['stress'] = data["virials"][ii] / (v_pref * vol)
results['stress'] = -data["virials"][ii] / vol

structure.calc = SinglePointCalculator(structure, **results)
structures.append(structure)
Expand Down
2 changes: 1 addition & 1 deletion dpdata/plugins/rdkit.py
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from dpdata.format import Format
try:
import rdkit.Chem
import dpdata.rdkit.utils
except ModuleNotFoundError:
pass
import dpdata.rdkit.utils


@Format.register("mol")
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