def add_random(self, random_probability=0.3):
"""
Add one random structure to the population
"""
structure = Structure()
if self.composition is None:
raise ValueError('No composition associated to this population')
comp = self.composition.composition.copy()
rnd = random.random()
natom_limit = self.max_comp_mult * self.composition.natom / self.composition.gcd
condition = {
'structure.nspecies': self.composition.nspecies,
'structure.natom': {
'$lte': natom_limit
}
}
if self.pcdb_source is None or self.pcdb_source.entries.find(
condition).count() <= len(self.source_blacklist):
rnd = 0
origin = None
if self.pcdb_source is None or rnd < random_probability or self.composition.nspecies > 1:
pcm_log.debug('Random Structure')
factor = np.random.randint(self.min_comp_mult,
self.max_comp_mult + 1)
for i in comp:
comp[i] *= factor
structure = Structure.random_cell(comp,
method='stretching',
stabilization_number=5,
nparal=5,
periodic=True)
else:
pcm_log.debug('From source')
while True:
entry = None
condition['properties.spacegroup'] = random.randint(1, 230)
print('Trying', condition['properties.spacegroup'])
for ientry in self.pcdb_source.entries.find(condition):
if ientry['_id'] not in self.source_blacklist:
entry = ientry
break
if entry is not None:
origin = entry['_id']
structure = self.pcdb_source.get_structure(entry['_id'])
factor = covalent_radius(
self.composition.species[0]) / covalent_radius(
structure.species[0])
print('From source: %s Spacegroup: %d Scaling: %7.3f' %
(structure.formula,
entry['properties']['spacegroup'], factor))
structure.set_cell(
np.dot(factor * np.eye(3), structure.cell))
structure.symbols = structure.natom * self.composition.species
self.source_blacklist.append(entry['_id'])
break
return self.new_entry(structure), origin
def add_random(self, random_probability=0.3):
"""
Add one random structure to the population
"""
entry_id = None
structure = Structure()
if self.composition is None:
raise ValueError('No composition associated to this population')
factor = np.random.randint(self.min_comp_mult, self.max_comp_mult + 1)
comp = self.composition.composition.copy()
#print("Initial composition: %s" % comp)
#print(Composition(comp))
#print(Composition(comp).symbols)
for i in comp:
comp[i] *= factor
new_comp = Composition(comp)
while True:
rnd = random.random()
condition = {
'structure.nspecies': new_comp.nspecies,
'structure.natom': new_comp.natom
}
if self.pcdb_source is None:
rnd = 0
elif len(self.sources[factor]) == 0:
rnd = 0
if self.pcdb_source is None or rnd < random_probability:
pcm_log.debug('Random Structure')
structure = Structure.random_cell(new_comp,
method='stretching',
stabilization_number=5,
nparal=5,
periodic=True)
break
else:
pcm_log.debug('From source')
entry_id = self.sources[factor][np.random.randint(
0, len(self.sources[factor]))]
structure = self.pcdb_source.get_structure(entry_id)
print("chosen structure from database =", structure)
sym = CrystalSymmetry(structure)
scale_factor = float(
np.max(covalent_radius(new_comp.species)) /
np.max(covalent_radius(structure.species)))
reduce_scale = scale_factor**(1. / 3) # WIH
msg = 'Mult: %d natom: %d From source: %s Spacegroup: %d Scaling: %7.3f'
print(msg % (factor, structure.natom, structure.formula,
sym.number(), scale_factor))
# structure.set_cell(np.dot(scale_factor * np.eye(3), structure.cell)) # WIH
structure.set_cell(
np.dot(reduce_scale * np.eye(3), structure.cell)) # WIH
print("symbols before change = ", structure.symbols)
structure.symbols = new_comp.symbols
print("symbols after change = ", structure.symbols)
self.sources[factor].remove(entry_id)
break
return self.new_entry(structure), entry_id
def replace_failed(self):
for entry in self.entries.find({'status.relaxation': 'failed'}):
st = self.get_structure(entry['_id'])
comp = st.composition
new_structure = Structure.random_cell(comp)
self.entries.update({'_id': entry['_id']}, {'$unset': {'status.relaxation': 1,
'status.target_forces': 1,
'properties.energy': 1,
'properties.forces': 1,
'properties.stress': 1}})
self.update(entry['_id'], structure=new_structure)
def replace_failed(self):
for entry in self.entries.find({'status.relaxation': 'failed'}):
st = self.get_structure(entry['_id'])
comp = st.composition
new_structure = Structure.random_cell(comp)
self.entries.update({'_id': entry['_id']}, {'$unset': {'status.relaxation': 1,
'status.target_forces': 1,
'properties.energy': 1,
'properties.forces': 1,
'properties.stress': 1}})
self.update(entry['_id'], structure=new_structure)
def add_random(self, random_probability=0.3):
"""
Add one random structure to the population
"""
entry_id = None
structure = Structure()
if self.composition is None:
raise ValueError('No composition associated to this population')
factor = np.random.randint(self.min_comp_mult, self.max_comp_mult + 1)
comp = self.composition.composition.copy()
# print("Initial composition: %s" % comp)
# print(Composition(comp))
# print(Composition(comp).symbols)
for i in comp:
comp[i] *= factor
new_comp = Composition(comp)
while True:
rnd = random.random()
condition = {'structure.nspecies': new_comp.nspecies,
'structure.natom': new_comp.natom}
if self.pcdb_source is None:
rnd = 0
elif len(self.sources[factor]) == 0:
rnd = 0
if self.pcdb_source is None or rnd < random_probability:
pcm_log.debug('Random Structure')
structure = Structure.random_cell(new_comp, method='stretching', stabilization_number=5, nparal=5,
periodic=True)
break
else:
pcm_log.debug('From source')
entry_id = self.sources[factor][np.random.randint(0, len(self.sources[factor]))]
structure = self.pcdb_source.get_structure(entry_id)
print("chosen structure from database =", structure)
sym = CrystalSymmetry(structure)
scale_factor = float(np.max(covalent_radius(new_comp.species)) /
np.max(covalent_radius(structure.species)))
reduce_scale = scale_factor ** (1. / 3) # WIH
msg = 'Mult: %d natom: %d From source: %s Spacegroup: %d Scaling: %7.3f'
print(msg % (factor, structure.natom, structure.formula, sym.number(), scale_factor))
# structure.set_cell(np.dot(scale_factor * np.eye(3), structure.cell)) # WIH
structure.set_cell(np.dot(reduce_scale * np.eye(3), structure.cell)) # WIH
print("symbols before change = ", structure.symbols)
structure.symbols = new_comp.symbols
print("symbols after change = ", structure.symbols)
self.sources[factor].remove(entry_id)
break
return self.new_entry(structure), entry_id
def add_random(self, random_probability=0.3):
"""
Add one random structure to the population
"""
structure = Structure()
if self.composition is None:
raise ValueError('No composition associated to this population')
comp = self.composition.composition.copy()
rnd = random.random()
natom_limit = self.max_comp_mult * self.composition.natom / self.composition.gcd
condition = {'structure.nspecies': self.composition.nspecies,
'structure.natom': {'$lte': natom_limit}}
if self.pcdb_source is None or self.pcdb_source.entries.find(condition).count() <= len(self.source_blacklist):
rnd = 0
origin = None
if self.pcdb_source is None or rnd < random_probability or self.composition.nspecies > 1:
pcm_log.debug('Random Structure')
factor = np.random.randint(self.min_comp_mult, self.max_comp_mult + 1)
for i in comp:
comp[i] *= factor
structure = Structure.random_cell(comp, method='stretching', stabilization_number=5, nparal=5,
periodic=True)
else:
pcm_log.debug('From source')
while True:
entry = None
condition['properties.spacegroup'] = random.randint(1, 230)
print('Trying', condition['properties.spacegroup'])
for ientry in self.pcdb_source.entries.find(condition):
if ientry['_id'] not in self.source_blacklist:
entry = ientry
break
if entry is not None:
origin = entry['_id']
structure = self.pcdb_source.get_structure(entry['_id'])
factor = covalent_radius(self.composition.species[0]) / covalent_radius(structure.species[0])
print('From source: %s Spacegroup: %d Scaling: %7.3f' % (structure.formula,
entry['properties']['spacegroup'],
factor))
structure.set_cell(np.dot(factor * np.eye(3), structure.cell))
structure.symbols = structure.natom * self.composition.species
self.source_blacklist.append(entry['_id'])
break
return self.new_entry(structure), origin
def worker_maise(db_settings, entry_id, workdir, relaxator_params):
"""
Relax and return evaluate the energy of the structure stored with identifier 'entry_id'
using the MAISE code
:param db_settings: (dict) Dictionary of DB parameters needed to create a PyChemiaDB object
:param entry_id: MongoDB identifier of one entry of the database created from db_settings
:param workdir: (str) Working directory where input and output from MAISE is written
:param relaxator_params: (dict) Arguments needed to control the relaxation using MAISE
Arguments are store as keys and they include:
'target_forces' : Used to defined the tolerance to consider one candidate as relaxed.
'source_dir': Directory with executable maise and directory INI
:return:
"""
max_ncalls = 6
pcdb = get_database(db_settings)
target_forces = relaxator_params['target_forces']
source_dir = relaxator_params['source_dir']
pcm_log.info('[%s]: Starting relaxation. Target forces: %7.3e' % (str(entry_id), target_forces))
if pcdb.is_locked(entry_id):
return
else:
pcdb.lock(entry_id)
structure = pcdb.get_structure(entry_id)
status = pcdb.get_dicts(entry_id)[2]
if 'ncalls' in status and status['ncalls'] > 0:
ncalls = status['ncalls'] + 1
print('ncalls = ', status['ncalls'])
else:
ncalls = 1
print('Verifing initial structure...')
while np.min(structure.distance_matrix()+(np.eye(structure.natom)*5)) < 1.9:
print('ERROR: Bad initial guess, two atoms are to close. Creating new random structure for id: %s' %
str(entry_id))
write_poscar(structure, workdir + os.sep + 'Fail_initial_POSCAR') # WIH
structure = Structure.random_cell(structure.composition)
write_poscar(structure, workdir + os.sep + 'POSCAR')
if not os.path.exists(workdir + os.sep + 'setup') and ncalls == 1: # WIH
print('First run.') # WIH
# print('Verifying that everything runs smoothly') # WIH
print(workdir + os.sep + 'setup')
shutil.copy2(source_dir + os.sep + 'setup_1', workdir + os.sep + 'setup') # WIH
elif ncalls > 1: # WIH
shutil.copy2(source_dir + os.sep + 'setup_2', workdir + os.sep + 'setup') # WIH
if not os.path.exists(workdir + os.sep + 'INI'):
os.symlink(source_dir + os.sep + 'INI', workdir + os.sep + 'INI')
if not os.path.exists(workdir + os.sep + 'maise'):
os.symlink(source_dir + os.sep + 'maise', workdir + os.sep + 'maise')
# Get the Current Working Directory
# cwd = os.getcwd()
# Move to the actual directory where maise will run
os.chdir(workdir)
wf = open('maise.stdout', 'w')
subprocess.call(['./maise'], stdout=wf)
wf.close()
if os.path.isfile('OSZICAR'):
energies = np.loadtxt('OSZICAR')
else:
energies = None
forces = None
stress = None
stress_kb = None
if os.path.isfile('OUTCAR'):
rf = open('OUTCAR', 'r')
data = rf.read()
pos_forces = re.findall(r'TOTAL-FORCE \(eV/Angst\)\s*-*\s*([-.\d\s]+)\s+-{2}', data)
pos_forces = np.array([x.split() for x in pos_forces], dtype=float)
if len(pos_forces) > 0 and len(pos_forces[-1]) % 7 == 0:
pos_forces.shape = (len(pos_forces), -1, 7)
forces = pos_forces[:, :, 3:6]
# positions = pos_forces[:, :, :3]
else:
print('Forces and Positions could not be parsed : ', pos_forces.shape)
print('pos_forces =\n%s ' % pos_forces)
str_stress = re.findall('Total([.\d\s-]*)in', data)
if len(str_stress) == 2:
stress = np.array([[float(y) for y in x.split()] for x in str_stress])
str_stress = re.findall('in kB([.\d\s-]*)energy', data)
if len(str_stress) == 2:
stress_kb = np.array([[float(y) for y in x.split()] for x in str_stress])
create_new = False
if not os.path.isfile('CONTCAR') or os.path.getsize("CONTCAR") == 0:
create_new = True
print('CONTCAR not found in entry: %s' % str(entry_id))
i = 1
while True:
if not os.path.isfile('POSCAR-failed-%03s' % str(i)):
os.rename('POSCAR', 'POSCAR-failed-%03s' % str(i))
break
else:
i += 1
else:
new_structure = read_poscar('CONTCAR')
# min_dist = np.min(new_structure.distance_matrix+np.ones((new_structure.natom,new_structure.natom)))
min_dist = np.min(new_structure.distance_matrix()+(np.eye(new_structure.natom)*5)) # WIH
print('Minimal distance= %8.7f' % min_dist) # WIH
if min_dist < 2.0:
print('ERROR: MAISE finished with and structure with distances too close:', entry_id) # WIH
write_poscar(new_structure, workdir + os.sep + 'Collapsed_CONTCAR') # WIH
create_new = True # WIH
if create_new:
new_structure = Structure.random_cell(structure.composition)
ncalls = 0 # WIH
if ncalls > max_ncalls:
print('WARNING: Too many calls to MAISE and no relaxation succeeded, replacing structure: ', entry_id) # WIH
new_structure = Structure.random_cell(structure.composition)
pcdb.entries.update({'_id': entry_id}, {'$set': {'status.ncalls': 0}})
create_new = True
else:
pcdb.entries.update({'_id': entry_id}, {'$set': {'status.ncalls': ncalls}})
pcdb.update(entry_id, structure=new_structure, properties={})
# if not create_new and energies is not None and forces is not None and stress is not None:
if energies is not None and forces is not None and stress is not None:
te = energies[1]
pcdb.entries.update({'_id': entry_id},
{'$set': {'status.relaxation': 'succeed',
'status.target_forces': target_forces,
'properties.initial_forces': generic_serializer(forces[0]),
'properties.initial_stress': generic_serializer(stress[0]),
'properties.initial_stress_kB': generic_serializer(stress_kb[0]),
'properties.forces': generic_serializer(forces[1]),
'properties.stress': generic_serializer(stress[1]),
'properties.stress_kB': generic_serializer(stress_kb[1]),
'properties.energy': te,
'properties.energy_pa': te / new_structure.natom,
'properties.energy_pf': te / new_structure.get_composition().gcd}})
for ifile in ['POSCAR', 'CONTCAR', 'setup', 'OUTCAR', 'maise.stdout', 'list.dat']:
if not os.path.exists(ifile):
wf = open(ifile, 'w')
wf.write('')
wf.close()
n = 1
while True:
if os.path.exists(ifile + ('_%03d' % n)):
n += 1
else:
break
os.rename(ifile, ifile+('_%03d' % n))
pcm_log.info('[%s]: Unlocking the entry' % str(entry_id))
pcdb.unlock(entry_id)
def worker_maise(db_settings, entry_id, workdir, target_forces, relaxator_params):
max_ncalls = 6
pcdb = get_database(db_settings)
pcm_log.info('[%s]: Starting relaxation. Target forces: %7.3e' % (str(entry_id), target_forces))
if pcdb.is_locked(entry_id):
return
else:
pcdb.lock(entry_id)
structure = pcdb.get_structure(entry_id)
status = pcdb.get_dicts(entry_id)[2]
if 'ncalls' in status:
ncalls = status['ncalls'] + 1
else:
ncalls = 1
#print('Current directory: '+os.getcwd() )
#print('Working directory: '+workdir)
write_poscar(structure,workdir+os.sep+'POSCAR')
if not os.path.exists(workdir+os.sep+'setup'):
shutil.copy2('setup', workdir)
if not os.path.exists(workdir+os.sep+'INI'):
os.symlink(os.getcwd()+os.sep+'INI', workdir+os.sep+'INI')
if not os.path.exists(workdir+os.sep+'maise'):
os.symlink(os.getcwd()+os.sep+'maise', workdir+os.sep+'maise')
cwd=os.getcwd()
os.chdir(workdir)
wf=open('maise.stdout','w')
subprocess.call(['./maise'], stdout=wf)
wf.close()
if os.path.isfile('OSZICAR'):
energies=np.loadtxt('OSZICAR')
else:
energies=None
if os.path.isfile('OUTCAR'):
rf = open('OUTCAR', 'r')
data = rf.read()
pos_forces = re.findall(r'TOTAL-FORCE \(eV/Angst\)\s*-*\s*([-.\d\s]+)\s+-{2}', data)
pos_forces = np.array([x.split() for x in pos_forces], dtype=float)
if len(pos_forces) > 0 and len(pos_forces[-1]) % 7 == 0:
pos_forces.shape = (len(pos_forces), -1, 7)
forces = pos_forces[:, :, 3:6]
positions = pos_forces[:, :, :3]
else:
print('Forces and Positions could not be parsed : ', pos_forces.shape)
print('pos_forces =\n%s ' % pos_forces)
str_stress=re.findall('Total([\.\d\s-]*)in',data)
if len(str_stress)==2:
stress = np.array([[float(y) for y in x.split()] for x in str_stress])
str_stress=re.findall('in kB([\.\d\s-]*)energy',data)
if len(str_stress)==2:
stress_kB = np.array([[float(y) for y in x.split()] for x in str_stress])
else:
forces=None
stress=None
stress_kB=None
new_structure=read_poscar('CONTCAR')
if np.min(new_structure.distance_matrix()+np.eye(new_structure.natom))<0.23:
print('WARNING: Structure collapse 2 atoms, creating a new random structure')
new_structure=Structure.random_cell(new_structure.composition)
if ncalls > max_ncalls:
print('WARNING: Too many calls to MAISE and no relaxation succeeded, replacing structure')
new_structure=Structure.random_cell(new_structure.composition)
pcdb.entries.update({'_id': entry_id}, {'$set': {'status.ncalls': 0}})
else:
pcdb.entries.update({'_id': entry_id}, {'$set': {'status.ncalls': ncalls}})
pcdb.update(entry_id, structure=new_structure)
if energies is not None and forces is not None and stress is not None:
te = energies[1]
pcdb.entries.update({'_id': entry_id},
{'$set': {'status.relaxation': 'succeed',
'status.target_forces': target_forces,
'properties.initial_forces': generic_serializer(forces[0]),
'properties.initial_stress': generic_serializer(stress[0]),
'properties.initial_stress_kB': generic_serializer(stress_kB[0]),
'properties.forces': generic_serializer(forces[1]),
'properties.stress': generic_serializer(stress[1]),
'properties.stress_kB': generic_serializer(stress_kB[1]),
'properties.energy': te,
'properties.energy_pa': te / new_structure.natom,
'properties.energy_pf': te / new_structure.get_composition().gcd}})
for ifile in ['POSCAR', 'CONTCAR', 'setup', 'OUTCAR', 'maise.stdout', 'list.dat']:
if not os.path.exists(ifile):
wf = open(ifile, 'w')
wf.write('')
wf.close()
n=1
while True:
if os.path.exists(ifile+ ('_%03d' % n)):
n+=1
else:
break
os.rename(ifile,ifile+('_%03d' % n))
pcm_log.info('[%s]: Unlocking the entry' % str(entry_id))
pcdb.unlock(entry_id)
def worker_maise(db_settings, entry_id, workdir, relaxator_params):
"""
Relax and return evaluate the energy of the structure stored with identifier 'entry_id'
using the MAISE code
:param db_settings: (dict) Dictionary of DB parameters needed to create a PyChemiaDB object
:param entry_id: MongoDB identifier of one entry of the database created from db_settings
:param workdir: (str) Working directory where input and output from MAISE is written
:param relaxator_params: (dict) Arguments needed to control the relaxation using MAISE
Arguments are store as keys and they include:
'target_forces' : Used to defined the tolerance to consider one candidate as relaxed.
'source_dir': Directory with executable maise and directory INI
:return:
"""
max_ncalls = 6
pcdb = get_database(db_settings)
target_forces = relaxator_params['target_forces']
source_dir = relaxator_params['source_dir']
pcm_log.info('[%s]: Starting relaxation. Target forces: %7.3e' %
(str(entry_id), target_forces))
if pcdb.is_locked(entry_id):
return
else:
pcdb.lock(entry_id)
structure = pcdb.get_structure(entry_id)
status = pcdb.get_dicts(entry_id)[2]
if 'ncalls' in status and status['ncalls'] > 0:
ncalls = status['ncalls'] + 1
print('ncalls = ', status['ncalls'])
else:
ncalls = 1
print('Verifing initial structure...')
while np.min(structure.distance_matrix() +
(np.eye(structure.natom) * 5)) < 1.9:
print(
'ERROR: Bad initial guess, two atoms are to close. Creating new random structure for id: %s'
% str(entry_id))
write_poscar(structure,
workdir + os.sep + 'Fail_initial_POSCAR') # WIH
structure = Structure.random_cell(structure.composition)
write_poscar(structure, workdir + os.sep + 'POSCAR')
if not os.path.exists(workdir + os.sep + 'setup') and ncalls == 1: # WIH
print('First run.') # WIH
# print('Verifying that everything runs smoothly') # WIH
print(workdir + os.sep + 'setup')
shutil.copy2(source_dir + os.sep + 'setup_1',
workdir + os.sep + 'setup') # WIH
elif ncalls > 1: # WIH
shutil.copy2(source_dir + os.sep + 'setup_2',
workdir + os.sep + 'setup') # WIH
if not os.path.exists(workdir + os.sep + 'INI'):
os.symlink(source_dir + os.sep + 'INI', workdir + os.sep + 'INI')
if not os.path.exists(workdir + os.sep + 'maise'):
os.symlink(source_dir + os.sep + 'maise', workdir + os.sep + 'maise')
# Get the Current Working Directory
# cwd = os.getcwd()
# Move to the actual directory where maise will run
os.chdir(workdir)
wf = open('maise.stdout', 'w')
subprocess.call(['./maise'], stdout=wf)
wf.close()
if os.path.isfile('OSZICAR'):
energies = np.loadtxt('OSZICAR')
else:
energies = None
forces = None
stress = None
stress_kb = None
if os.path.isfile('OUTCAR'):
rf = open('OUTCAR', 'r')
data = rf.read()
pos_forces = re.findall(
r'TOTAL-FORCE \(eV/Angst\)\s*-*\s*([-.\d\s]+)\s+-{2}', data)
pos_forces = np.array([x.split() for x in pos_forces], dtype=float)
if len(pos_forces) > 0 and len(pos_forces[-1]) % 7 == 0:
pos_forces.shape = (len(pos_forces), -1, 7)
forces = pos_forces[:, :, 3:6]
# positions = pos_forces[:, :, :3]
else:
print('Forces and Positions could not be parsed : ',
pos_forces.shape)
print('pos_forces =\n%s ' % pos_forces)
str_stress = re.findall('Total([.\d\s-]*)in', data)
if len(str_stress) == 2:
stress = np.array([[float(y) for y in x.split()]
for x in str_stress])
str_stress = re.findall('in kB([.\d\s-]*)energy', data)
if len(str_stress) == 2:
stress_kb = np.array([[float(y) for y in x.split()]
for x in str_stress])
create_new = False
if not os.path.isfile('CONTCAR') or os.path.getsize("CONTCAR") == 0:
create_new = True
print('CONTCAR not found in entry: %s' % str(entry_id))
i = 1
while True:
if not os.path.isfile('POSCAR-failed-%03s' % str(i)):
os.rename('POSCAR', 'POSCAR-failed-%03s' % str(i))
break
else:
i += 1
else:
new_structure = read_poscar('CONTCAR')
# min_dist = np.min(new_structure.distance_matrix+np.ones((new_structure.natom,new_structure.natom)))
min_dist = np.min(new_structure.distance_matrix() +
(np.eye(new_structure.natom) * 5)) # WIH
print('Minimal distance= %8.7f' % min_dist) # WIH
if min_dist < 2.0:
print(
'ERROR: MAISE finished with and structure with distances too close:',
entry_id) # WIH
write_poscar(new_structure,
workdir + os.sep + 'Collapsed_CONTCAR') # WIH
create_new = True # WIH
if create_new:
new_structure = Structure.random_cell(structure.composition)
ncalls = 0 # WIH
if ncalls > max_ncalls:
print(
'WARNING: Too many calls to MAISE and no relaxation succeeded, replacing structure: ',
entry_id) # WIH
new_structure = Structure.random_cell(structure.composition)
pcdb.entries.update({'_id': entry_id}, {'$set': {'status.ncalls': 0}})
create_new = True
else:
pcdb.entries.update({'_id': entry_id},
{'$set': {
'status.ncalls': ncalls
}})
pcdb.update(entry_id, structure=new_structure, properties={})
# if not create_new and energies is not None and forces is not None and stress is not None:
if energies is not None and forces is not None and stress is not None:
te = energies[1]
pcdb.entries.update({'_id': entry_id}, {
'$set': {
'status.relaxation': 'succeed',
'status.target_forces': target_forces,
'properties.initial_forces': generic_serializer(forces[0]),
'properties.initial_stress': generic_serializer(stress[0]),
'properties.initial_stress_kB': generic_serializer(
stress_kb[0]),
'properties.forces': generic_serializer(forces[1]),
'properties.stress': generic_serializer(stress[1]),
'properties.stress_kB': generic_serializer(stress_kb[1]),
'properties.energy': te,
'properties.energy_pa': te / new_structure.natom,
'properties.energy_pf':
te / new_structure.get_composition().gcd
}
})
for ifile in [
'POSCAR', 'CONTCAR', 'setup', 'OUTCAR', 'maise.stdout', 'list.dat'
]:
if not os.path.exists(ifile):
wf = open(ifile, 'w')
wf.write('')
wf.close()
n = 1
while True:
if os.path.exists(ifile + ('_%03d' % n)):
n += 1
else:
break
os.rename(ifile, ifile + ('_%03d' % n))
pcm_log.info('[%s]: Unlocking the entry' % str(entry_id))
pcdb.unlock(entry_id)