def get_orig_EV(self, db_file, tag):
vasp_db = VaspCalcDb.from_db_file(db_file=db_file, admin=True)
volumes, energies, dos_objs, _ \
= get_static_calculations(vasp_db, tag)
print('%s Volumes = %s' % (len(volumes), volumes))
print('%s Energies = %s' % (len(energies), energies))
return (list(volumes), list(energies), dos_objs)
def get_vol_ene(self):
tag = self["tag"]
admin = self.get('admin', False)
_db_file = self.get('db_file', db_file)
vasp_db = VaspCalcDb.from_db_file(db_file=_db_file, admin=admin)
volumes, energies, _, _ = get_static_calculations(vasp_db, tag)
return volumes, energies
def test_get_static_calculations():
tag = '8e7b216d-c6b6-4da4-905e-e7afd44195aa'
vasp_db = VaspCalcDb.from_db_file(db_file=db_file, admin=True)
volumes, energies, dos_objs, _ = get_static_calculations(vasp_db, tag)
#print(volumes, energies)
assert False
def test_get_static_calculations():
tag = '0267947f-b5a0-4993-8b5e-58f9dfb4e362'
vasp_db = VaspCalcDb.from_db_file(db_file=db_file, admin=True)
volumes, energies, dos_objs, _ = get_static_calculations(vasp_db, tag)
#print(volumes, energies)
assert False
def run_task(self):
tag = self["tag"]
admin = self.get('admin', False)
_db_file = self.get('db_file', db_file)
vasp_db = VaspCalcDb.from_db_file(db_file=_db_file, admin=admin)
volumes, energies, dos_objs, _calc = get_static_calculations(
vasp_db, tag)
structure = Structure.from_dict(_calc['output']['structure'])
qha_result = {}
qha_result['structure'] = structure.as_dict()
qha_result['formula_pretty'] = structure.composition.reduced_formula
qha_result['elements'] = sorted(
[el.name for el in structure.composition.elements])
qha_result['metadata'] = self.get('metadata', {'tag': tag})
#qha_result['has_phonon'] = self['phonon']
poisson = self.get('poisson')
val, idx = min((val, idx) for (idx, val) in enumerate(energies))
poisson_Cij = get_Poisson_Ratio(vasp_db, tag, volumes[idx])
if poisson is None:
poisson = poisson_Cij or 0.363615
print("Used Poisson ratio:", poisson)
bp2gru = self.get('bp2gru', 2. / 3.)
# phonon properties
# check if phonon calculations existed
#always perform phonon calculations when when enough phonon calculations found
num_phonons = len(
list(vasp_db.db['phonon'].find(
{'$and': [{
'metadata': {
'tag': tag
}
}, {
'adopted': True
}]})))
#num_phonons = len(list(vasp_db.db['phonon'].find({'$and':[ {'metadata.tag': tag}, {'adopted': True} ]})))
qha_result['has_phonon'] = num_phonons >= 5
#if self['phonon']:
if qha_result['has_phonon']:
# get the vibrational properties from the FW spec
phonon_calculations = list(vasp_db.db['phonon'].find(
{'$and': [{
'metadata.tag': tag
}, {
'adopted': True
}]}))
#phonon_calculations = list(vasp_db.db['phonon'].find({'$and':[ {'metadata': {'tag':tag}}, {'adopted': True} ]}))
vol_vol = []
vol_f_vib = []
vol_s_vib = []
vol_c_vib = []
for calc in phonon_calculations:
if calc['volume'] in vol_vol: continue
if calc['volume'] not in volumes: continue
vol_vol.append(calc['volume'])
vol_f_vib.append(calc['F_vib'])
vol_s_vib.append(calc['S_vib'])
vol_c_vib.append(calc['CV_vib'])
# sort them order of the unit cell volumes
vol_f_vib = sort_x_by_y(vol_f_vib, vol_vol)
vol_s_vib = sort_x_by_y(vol_s_vib, vol_vol)
vol_c_vib = sort_x_by_y(vol_c_vib, vol_vol)
f_vib = np.vstack(vol_f_vib)
# by Yi Wang, after a long day debug, finally I fixex the bug below
# i.e, sometimes, the number of phonon volumes is less than that of static!
_volumes = []
_energies = []
_dos_objs = []
for iv, vol in enumerate(volumes):
if vol not in vol_vol: continue
_volumes.append(vol)
_energies.append(energies[iv])
_dos_objs.append(dos_objs[iv])
volumes = _volumes
energies = _energies
dos_objs = _dos_objs
self.volumes = volumes
self.energies = energies
qha = Quasiharmonic(energies,
volumes,
structure,
dos_objects=dos_objs,
F_vib=f_vib,
t_min=self['t_min'],
t_max=self['t_max'],
t_step=self['t_step'],
poisson=poisson,
bp2gru=bp2gru)
qha_result['phonon'] = qha.get_summary_dict()
qha_result['phonon']['entropies'] = vol_s_vib
qha_result['phonon']['heat_capacities'] = vol_c_vib
qha_result['phonon']['temperatures'] = qha_result['phonon'][
'temperatures'].tolist()
# calculate the Debye model results no matter what
qha_debye = Quasiharmonic(energies,
volumes,
structure,
dos_objects=dos_objs,
F_vib=None,
t_min=self['t_min'],
t_max=self['t_max'],
t_step=self['t_step'],
poisson=poisson,
bp2gru=bp2gru)
# fit 0 K EOS for good measure
eos = Vinet(volumes, energies)
eos.fit()
errors = eos.func(volumes) - energies
sum_square_error = float(np.sum(np.square(errors)))
eos_res = {}
eos_res['b0_GPa'] = float(eos.b0_GPa)
eos_res['b0'] = float(eos.b0)
eos_res['b1'] = float(eos.b1)
eos_res['eq_volume'] = float(eos.v0)
eos_res['eq_energy'] = float(eos.e0)
eos_res['energies'] = list(energies)
eos_res['volumes'] = list(volumes)
eos_res['name'] = 'Vinet'
eos_res['error'] = {}
eos_res['error']['difference'] = errors.tolist(
) # volume by volume differences
eos_res['error']['sum_square_error'] = sum_square_error
qha_result['eos'] = eos_res
qha_result['debye'] = qha_debye.get_summary_dict()
qha_result['debye']['poisson'] = poisson
qha_result['debye']['bp2gru'] = bp2gru
qha_result['debye']['temperatures'] = qha_result['debye'][
'temperatures'].tolist()
qha_result['version_atomate'] = atomate_ver
qha_result['version_dfttk'] = dfttk_ver
volumes_false = []
energies_false = []
static_falses = vasp_db.collection.find(
{'$and': [{
'metadata.tag': tag
}, {
'adopted': False
}]})
for static_false in static_falses:
volumes_false.append(
static_false['output']['structure']['lattice']['volume'])
energies_false.append(static_false['output']['energy'])
qha_result['Volumes_fitting_false'] = volumes_false
qha_result['Energies_fitting_false'] = energies_false
print('Volumes_fitting_false : %s' % volumes_false)
print('Energies_fitting_false: %s' % energies_false)
print('number of phonon calculations found : %s' % num_phonons)
"""
# write to JSON for debugging purposes
import json
with open('qha_summary.json', 'w') as fp:
json.dump(qha_result, fp, indent=4)
"""
if self.get("test_failure", False): return
#if self['phonon']:
if qha_result['has_phonon']:
vasp_db.db['qha_phonon'].insert_one(qha_result)
qha_result.pop('phonon')
vasp_db.db['qha'].insert_one(qha_result)
else:
vasp_db.db['qha'].insert_one(qha_result)