def collect_data(self, entry_id, workdir):
if os.path.isfile(workdir + '/OUTCAR'):
vo = VaspOutput(workdir + '/OUTCAR')
if 'energy' in vo.final_data:
if 'free_energy' in vo.final_data['energy']:
energy = vo.final_data['energy']['free_energy']
print('Uploading energy data for %s' % entry_id)
self.set_in_properties(entry_id, 'energy', energy)
return True
else:
return False
else:
return False
else:
return False
def update(self, workdir):
"""
This routine determines how to proceed with the relaxation
for one specific work directory
:param workdir: (str) String representation of the id in the mongodb
:return:
"""
# workdir = self.basedir + os.sep + entry_id
entry_id = os.path.basename(workdir)
vj = self.vasp_jobs[entry_id]
runj = self.runs[entry_id]
if os.path.isfile(workdir + os.sep + 'OUTCAR'):
vj.get_outputs()
self.update_history(entry_id)
if os.path.isfile(workdir + os.sep + 'RELAXED'):
self.add_status(entry_id, 'RELAXED')
elif not os.path.isfile(workdir + os.sep + 'PROCAR'):
self.add_status(entry_id, 'NOPROCAR')
else:
self.del_status(entry_id, 'NOPROCAR')
if not os.path.isfile(workdir + os.sep + 'OUTCAR'):
self.add_status(entry_id, 'NOOUTCAR')
else:
self.del_status(entry_id, 'NOOUTCAR')
print('-')
vo = VaspOutput(workdir + os.sep + 'OUTCAR')
relaxation_info = vo.relaxation_info()
if len(relaxation_info) != 3:
print('[' + str(entry_id) + ']' +
' Missing some data in OUTCAR (forces or stress)')
self.add_status(entry_id, 'NOOUTCAR')
print('[' + str(entry_id) + ']' + 'Results:')
for i in relaxation_info:
print('[' + str(entry_id) + '] %20s %12.5e' %
(i, relaxation_info[i]))
# Conditions to consider the structure relaxed
if relaxation_info['avg_force'] < self.target_force:
if relaxation_info['avg_stress_diag'] < self.target_stress:
if relaxation_info[
'avg_stress_non_diag'] < self.target_stress:
wf = open(workdir + os.sep + 'RELAXED', 'w')
for i in relaxation_info:
wf.write("%15s %12.3f" %
(i, relaxation_info[i]))
wf.close()
wf = open(workdir + os.sep + 'COMPLETE', 'w')
for i in relaxation_info:
wf.write("%15s %12.3f" %
(i, relaxation_info[i]))
wf.close()
self.add_status(entry_id, 'RELAXED')
if self.modify_input(entry_id):
# How to change ISIF
if relaxation_info['avg_force'] < 0.1:
if relaxation_info['avg_stress_diag'] < 0.1:
if relaxation_info['avg_stress_non_diag'] < 0.1:
vj.input_variables.variables['ISIF'] = 3
else:
vj.input_variables.variables['ISIF'] = 3
else:
vj.input_variables.variables['ISIF'] = 3
else:
vj.input_variables.variables['ISIF'] = 2
# How to change IBRION
# if info['avg_force'] < 0.1 and info['avg_stress_diag'] < 0.1 and info['avg_stress_non_diag'] < 0.1:
# vj.input_variables.variables['IBRION'] = 1
# elif info['avg_force'] < 1 and info['avg_stress_diag'] < 1 and info['avg_stress_non_diag'] < 1:
# vj.input_variables.variables['IBRION'] = 2
# else:
# vj.input_variables.variables['IBRION'] = 3
# How to change EDIFF
if vj.input_variables.variables['EDIFF'] > 2 * 1E-4:
vj.input_variables.variables['EDIFF'] = round_small(
vj.input_variables.variables['EDIFF'] / 2)
else:
vj.input_variables.variables['EDIFF'] = 1E-4
# How to change EDIFFG
if vj.input_variables.variables['EDIFFG'] < -2 * self.target_force:
vj.input_variables.variables['EDIFFG'] = round_small(
vj.input_variables.variables['EDIFFG'] / 2)
else:
vj.input_variables.variables['EDIFFG'] = -self.target_force
# Print new values
print('[' + str(entry_id) + ']' + 'New Values:')
for i in ['ISIF', 'IBRION', 'EDIFF', 'EDIFFG']:
print('[' + str(entry_id) + ']' + i + ' : ',
vj.input_variables.variables[i])
print('-')
for i in ['OUTCAR']:
if not os.path.exists(workdir + os.sep + i):
wf = open(workdir + os.sep + i, 'w')
wf.write('')
wf.close()
log = logging.handlers.RotatingFileHandler(workdir + os.sep +
i,
maxBytes=1,
backupCount=1000)
log.doRollover()
try:
vj.structure = read_poscar(workdir + os.sep + 'CONTCAR')
except ValueError:
print('Error reading CONTCAR')
vj.set_inputs()
properties = vj.outcar
status = self.status[entry_id]
newentry = self.population.db.update(entry_id,
structure=vj.structure,
properties=properties,
status=status)
vj.save_json(workdir + os.sep + 'vaspjob.json')
wf = open(workdir + os.sep + 'entry.json', 'w')
json.dump(newentry,
wf,
sort_keys=True,
indent=4,
separators=(',', ': '))
wf.close()
return True
else:
vj.set_inputs()
status = self.status[entry_id]
newentry = self.population.db.update(entry_id,
structure=vj.structure,
status=status)
vj.save_json(workdir + os.sep + 'vaspjob.json')
wf = open(workdir + os.sep + 'entry.json', 'w')
json.dump(newentry,
wf,
sort_keys=True,
indent=4,
separators=(',', ': '))
wf.close()
return True
def update(self, workdir):
"""
This routine determines how to proceed with the relaxation
for one specific work directory
:param workdir: (str) String representation of the id in the mongodb
:return:
"""
# workdir = self.basedir + os.sep + entry_id
entry_id = os.path.basename(workdir)
vj = self.vasp_jobs[entry_id]
runj = self.runs[entry_id]
if os.path.isfile(workdir + os.sep + 'OUTCAR'):
vj.get_outputs()
self.update_history(entry_id)
if os.path.isfile(workdir + os.sep + 'RELAXED'):
self.add_status(entry_id, 'RELAXED')
elif not os.path.isfile(workdir + os.sep + 'PROCAR'):
self.add_status(entry_id, 'NOPROCAR')
else:
self.del_status(entry_id, 'NOPROCAR')
if not os.path.isfile(workdir + os.sep + 'OUTCAR'):
self.add_status(entry_id, 'NOOUTCAR')
else:
self.del_status(entry_id, 'NOOUTCAR')
print('-')
vo = VaspOutput(workdir + os.sep + 'OUTCAR')
relaxation_info = vo.relaxation_info()
if len(relaxation_info) != 3:
print('[' + str(entry_id) + ']' + ' Missing some data in OUTCAR (forces or stress)')
self.add_status(entry_id, 'NOOUTCAR')
print('[' + str(entry_id) + ']' + 'Results:')
for i in relaxation_info:
print('[' + str(entry_id) + '] %20s %12.5e' % (i, relaxation_info[i]))
# Conditions to consider the structure relaxed
if relaxation_info['avg_force'] < self.target_force:
if relaxation_info['avg_stress_diag'] < self.target_stress:
if relaxation_info['avg_stress_non_diag'] < self.target_stress:
wf = open(workdir + os.sep + 'RELAXED', 'w')
for i in relaxation_info:
wf.write("%15s %12.3f" % (i, relaxation_info[i]))
wf.close()
wf = open(workdir + os.sep + 'COMPLETE', 'w')
for i in relaxation_info:
wf.write("%15s %12.3f" % (i, relaxation_info[i]))
wf.close()
self.add_status(entry_id, 'RELAXED')
if self.modify_input(entry_id):
# How to change ISIF
if relaxation_info['avg_force'] < 0.1:
if relaxation_info['avg_stress_diag'] < 0.1:
if relaxation_info['avg_stress_non_diag'] < 0.1:
vj.input_variables.variables['ISIF'] = 3
else:
vj.input_variables.variables['ISIF'] = 3
else:
vj.input_variables.variables['ISIF'] = 3
else:
vj.input_variables.variables['ISIF'] = 2
# How to change IBRION
# if info['avg_force'] < 0.1 and info['avg_stress_diag'] < 0.1 and info['avg_stress_non_diag'] < 0.1:
# vj.input_variables.variables['IBRION'] = 1
# elif info['avg_force'] < 1 and info['avg_stress_diag'] < 1 and info['avg_stress_non_diag'] < 1:
# vj.input_variables.variables['IBRION'] = 2
# else:
# vj.input_variables.variables['IBRION'] = 3
# How to change EDIFF
if vj.input_variables.variables['EDIFF'] > 2 * 1E-4:
vj.input_variables.variables['EDIFF'] = round_small(vj.input_variables.variables['EDIFF'] / 2)
else:
vj.input_variables.variables['EDIFF'] = 1E-4
# How to change EDIFFG
if vj.input_variables.variables['EDIFFG'] < - 2 * self.target_force:
vj.input_variables.variables['EDIFFG'] = round_small(vj.input_variables.variables['EDIFFG'] / 2)
else:
vj.input_variables.variables['EDIFFG'] = - self.target_force
# Print new values
print('[' + str(entry_id) + ']' + 'New Values:')
for i in ['ISIF', 'IBRION', 'EDIFF', 'EDIFFG']:
print('[' + str(entry_id) + ']' + i + ' : ', vj.input_variables.variables[i])
print('-')
for i in ['OUTCAR']:
if not os.path.exists(workdir + os.sep + i):
wf = open(workdir + os.sep + i, 'w')
wf.write('')
wf.close()
log = logging.handlers.RotatingFileHandler(workdir + os.sep + i, maxBytes=1, backupCount=1000)
log.doRollover()
try:
vj.structure = read_poscar(workdir + os.sep + 'CONTCAR')
except ValueError:
print('Error reading CONTCAR')
vj.set_inputs()
properties = vj.outcar
status = self.status[entry_id]
newentry = self.population.db.update(entry_id, structure=vj.structure, properties=properties, status=status)
vj.save_json(workdir + os.sep + 'vaspjob.json')
wf = open(workdir + os.sep + 'entry.json', 'w')
json.dump(newentry, wf, sort_keys=True, indent=4, separators=(',', ': '))
wf.close()
return True
else:
vj.set_inputs()
status = self.status[entry_id]
newentry = self.population.db.update(entry_id, structure=vj.structure, status=status)
vj.save_json(workdir + os.sep + 'vaspjob.json')
wf = open(workdir + os.sep + 'entry.json', 'w')
json.dump(newentry, wf, sort_keys=True, indent=4, separators=(',', ': '))
wf.close()
return True