def __init__(self, structure):
"""
Creates a new StructureSymmetry object for a given structure
This class allows interaction with spglib for several operations related
to symmetry
:param structure:
Example:
>>> import pychemia
>>> a = 4.05
>>> b = a/2
>>> fcc = pychemia.Structure(symbols=['Au'], cell=[[0, b, b], [b, 0, b], [b, b, 0]], periodicity=True)
>>> symm = pychemia.crystal.CrystalSymmetry(fcc)
>>> symm.number()
225
>>> symm.symbol() == u'Fm-3m'
True
"""
assert structure.is_crystal
assert structure.is_perfect
self.structure = structure
# Spglib"s convention for the lattice definition is the transpose of cell
# self._transposed_cell = structure.cell.transpose().copy()
self.spglib_lattice = generic_serializer(structure.cell.copy())
# Spglib requires numpy floats.
# self._transposed_cell = np.array(self._transposed_cell, dtype='double', order='C')
# self._reduced = np.array(structure.reduced, dtype='double', order='C')
self.spglib_positions = generic_serializer(structure.reduced)
# Get a list of indices for each atom in structure
# Indices starting in 1
# self._numbers = np.array([structure.species.index(x) + 1 for x in structure.symbols], dtype='intc')
self.spglib_numbers = [structure.species.index(x) + 1 for x in structure.symbols]
def __init__(self, structure):
"""
Creates a new StructureSymmetry object for a given structure
This class allows interaction with spglib for several operations related
to symmetry
:param structure:
Example:
>>> import pychemia
>>> a = 4.05
>>> b = a/2
>>> fcc = pychemia.Structure(symbols=['Au'], cell=[[0, b, b], [b, 0, b], [b, b, 0]], periodicity=True)
>>> symm = pychemia.crystal.CrystalSymmetry(fcc)
>>> symm.number()
225
>>> symm.symbol() == u'Fm-3m'
True
"""
assert structure.is_crystal
assert structure.is_perfect
self.structure = structure
# Spglib"s convention for the lattice definition is the transpose of cell
# self._transposed_cell = structure.cell.transpose().copy()
self.spglib_lattice = generic_serializer(structure.cell.copy())
# Spglib requires numpy floats.
# self._transposed_cell = np.array(self._transposed_cell, dtype='double', order='C')
# self._reduced = np.array(structure.reduced, dtype='double', order='C')
self.spglib_positions = generic_serializer(structure.reduced)
# Get a list of indices for each atom in structure
# Indices starting in 1
# self._numbers = np.array([structure.species.index(x) + 1 for x in structure.symbols], dtype='intc')
self.spglib_numbers = [structure.species.index(x) + 1 for x in structure.symbols]
def evaluate(self, imember):
entry = self.population.get_entry(imember)
pcm_structure = pychemia.Structure.from_dict(entry['structure'])
ase_structure = pychemia.external.ase.pychemia2ase(pcm_structure)
ase_structure.set_calculator(LennardJones())
dyn = QuasiNewton(ase_structure)
dyn.run()
ase_structure.set_constraint(
FixAtoms(mask=[True for atom in ase_structure]))
ucf = UnitCellFilter(ase_structure)
qn = QuasiNewton(ucf)
qn.run()
new_structure = pychemia.external.ase.ase2pychemia(ase_structure)
energy = ase_structure.get_potential_energy()
forces = ase_structure.get_forces()
stress = ase_structure.get_stress()
new_properties = {
'energy': float(energy),
'forces': generic_serializer(forces),
'stress': generic_serializer(stress)
}
self.population.db.update(imember,
structure=new_structure,
properties=new_properties)
def run(self, nparal=4):
vj = VaspJob()
vj.initialize(self.structure, self.workdir, self.kpoints, binary=self.binary)
vj.clean()
vj.job_static()
vj.input_variables.set_density_for_restart()
vj.input_variables.set_encut(ENCUT=self.encut, POTCAR=self.workdir + os.sep + 'POTCAR')
vj.input_variables.variables['NBANDS'] = nparal * ((int(self.structure.valence_electrons()) +
self.structure.natom) / nparal + 1)
vj.input_variables.set_ismear(self.kpoints)
vj.input_variables.variables['SIGMA'] = 0.2
vj.input_variables.variables['ISPIN'] = 2
if self.task_params['extra_incar'] is not None:
for i in self.task_params['extra_incar']:
vj.input_variables.variables[i] = self.task_params['extra_incar'][i]
vj.set_inputs()
self.encut = vj.input_variables.variables['ENCUT']
vj.run(use_mpi=True, mpi_num_procs=nparal)
pcm_log.debug('Starting VASP')
while True:
energy_str = ''
filename = self.workdir + os.sep + 'vasp_stdout.log'
if os.path.exists(filename):
vasp_stdout = read_vasp_stdout(filename=filename)
if len(vasp_stdout['data']) > 2:
scf_energies = [i[2] for i in vasp_stdout['data']]
energy_str = ' %7.3f' % scf_energies[1]
for i in range(1, len(scf_energies)):
if scf_energies[i] < scf_energies[i - 1]:
energy_str += ' >'
else:
energy_str += ' <'
pcm_log.debug(energy_str)
if vj.runner is not None and vj.runner.poll() is not None:
filename = self.workdir + os.sep + 'vasp_stdout.log'
if os.path.exists(filename):
vasp_stdout = read_vasp_stdout(filename=filename)
if len(vasp_stdout['data']) > 2:
scf_energies = [i[2] for i in vasp_stdout['data']]
energy_str += ' %7.3f' % scf_energies[-1]
pcm_log.debug(energy_str)
pcm_log.debug('Execution complete')
break
time.sleep(5)
vj.get_outputs()
self.output = {'forces': generic_serializer(vj.outcar.forces), 'stress': generic_serializer(vj.outcar.stress),
'energy': vj.outcar.energy, 'energies': generic_serializer(vj.outcar.energies),
'INCAR': vj.input_variables.variables}
if vj.outcar.is_finished:
self.finished = True
def test_serializer(self):
"""
Test (pychemia.utils.serializer) :
"""
a = np.array([1, 2, 3])
assert generic_serializer(a) == [1, 2, 3]
b = np.array([[1, 2, 3], [4, 5, 6]])
assert generic_serializer(b) == [[1, 2, 3], [4, 5, 6]]
c = np.array([[[1, 2, 3], [4, 5, 6]], [[7, 8, 9], [0, 1, 2]]])
assert generic_serializer(c) == [[[1, 2, 3], [4, 5, 6]], [[7, 8, 9], [0, 1, 2]]]
mydict = {'a': a, 'b': b, 'c': c}
assert generic_serializer(mydict) == {u'a': [1, 2, 3],
u'b': [[1, 2, 3], [4, 5, 6]],
u'c': [[[1, 2, 3], [4, 5, 6]], [[7, 8, 9], [0, 1, 2]]]}
def test_serializer(self):
"""
Tests (pychemia.utils.serializer) :
"""
a = np.array([1, 2, 3])
assert generic_serializer(a) == [1, 2, 3]
b = np.array([[1, 2, 3], [4, 5, 6]])
assert generic_serializer(b) == [[1, 2, 3], [4, 5, 6]]
c = np.array([[[1, 2, 3], [4, 5, 6]], [[7, 8, 9], [0, 1, 2]]])
assert generic_serializer(c) == [[[1, 2, 3], [4, 5, 6]], [[7, 8, 9], [0, 1, 2]]]
mydict = {'a': a, 'b': b, 'c': c}
generic_serializer(mydict) == {u'a': [1, 2, 3],
u'b': [[1, 2, 3], [4, 5, 6]],
u'c': [[[1, 2, 3], [4, 5, 6]], [[7, 8, 9], [0, 1, 2]]]}
def set_kpoints_list(self, kpoints_list, weights=None):
"""
Set an explicit list of kpoints with a proper check of correct arguments
:param kpoints_list: Explicit list of k-points (Only for 'cartesian' and 'reduced')
:param weights: List of weights associated to each k-point (Only for 'cartesian' and 'reduced')
"""
assert (self.kmode in ['cartesian', 'reduced'])
if kpoints_list is None:
self.kpoints_list = [[0, 0, 0]]
else:
if np.array(kpoints_list).shape == (3, ):
self.kpoints_list = np.array(kpoints_list).reshape((-1, 3))
elif np.array(kpoints_list).shape[1] == 3:
self.kpoints_list = np.array(kpoints_list)
else:
raise ValueError(
"Wrong value for kpoints_list, should be an array with shape (nkpt,3)"
)
self.kpoints_list = generic_serializer(self.kpoints_list)
nkpt = len(self.kpoints_list)
if weights is None:
self.weights = np.ones(nkpt)
elif len(np.array(weights)) == nkpt:
self.weights = np.array(weights)
else:
raise ValueError(
"Wrong value for weights, should be an array with shape (nkpt,)"
)
self.weights = list(self.weights)
def cluster_fb_worker(db_settings):
while True:
pcdb = pychemia.db.get_database(db_settings)
population = pychemia.population.LJCluster(pcdb)
entry = population.pcdb.db.pychemia_entries.find_one({'status.' + population.tag: True,
'status.lock': {'$exists': False},
'properties': {}}, {'_id': 1})
if entry is not None:
population.pcdb.lock(entry['_id'])
structure = population.pcdb.get_structure(entry['_id'])
fb = pychemia.code.fireball.FireBall(fdata_path='../Fdata')
fb.initialize(structure, workdir=str(entry['_id']))
fb.cluster_relaxation()
fb.set_inputs()
sp = fb.run()
sp.wait()
so = pychemia.code.fireball.read_fireball_stdout(fb.workdir + os.sep + 'fireball.log')
forces = generic_serializer(so['forces'][-1])
energy = so['energy'][-1]['ETOT']
properties = {'forces': forces, 'energy': energy}
structure = pychemia.code.fireball.read_geometry_bas(fb.workdir + os.sep + 'answer.bas')
population.pcdb.update(entry['_id'], structure=structure, properties=properties)
population.pcdb.unlock(entry['_id'])
else:
break
def move_random(self, entry_id, factor=0.2, in_place=False, kind='move'):
entry = self.get_entry(entry_id)
pos = np.array(entry['structure']['positions']).reshape((-1, 3))
# Unit Vectors
uv = pychemia.utils.mathematics.unit_vectors(
2 * np.random.rand(*pos.shape) - 1)
new_pos = generic_serializer(pos + factor * uv)
structure = pychemia.Structure(positions=new_pos,
symbols=entry['structure']['symbols'],
periodicity=False)
if in_place:
return self.pcdb.db.pychemia_entries.update_one(
{'_id': entry_id},
{'$set': {
'structure': structure.to_dict,
'properties': {}
}})
else:
structure = pychemia.Structure(
positions=new_pos,
symbols=entry['structure']['symbols'],
periodicity=False)
return self.new_entry(structure, active=False)
def set_kpoints_list(self, kpoints_list, weights=None):
"""
Set an explicit list of kpoints with a proper check of correct arguments
:param kpoints_list: Explicit list of k-points (Only for 'cartesian' and 'reduced')
:param weights: List of weights associated to each k-point (Only for 'cartesian' and 'reduced')
"""
assert (self.kmode in ['cartesian', 'reduced'])
if kpoints_list is None:
self.kpoints_list = [[0, 0, 0]]
else:
if np.array(kpoints_list).shape == (3,):
self.kpoints_list = np.array(kpoints_list).reshape((-1, 3))
elif np.array(kpoints_list).shape[1] == 3:
self.kpoints_list = np.array(kpoints_list)
else:
raise ValueError("Wrong value for kpoints_list, should be an array with shape (nkpt,3)")
self.kpoints_list = generic_serializer(self.kpoints_list)
nkpt = len(self.kpoints_list)
if weights is None:
self.weights = np.ones(nkpt)
elif len(np.array(weights)) == nkpt:
self.weights = np.array(weights)
else:
raise ValueError("Wrong value for weights, should be an array with shape (nkpt,)")
self.weights = list(self.weights)
def read_fireball_stdout(filename):
rf = open(filename, 'r')
data = rf.read()
atom_data = re.findall(r'Atom Coordinates from Basis File:([\d\w\s=\-\.#]+)===\n', data)[0]
symbols = []
positions = []
for iline in atom_data.split('\n'):
# print iline
tmp = iline.split()
if len(tmp) == 6 and tmp[0].isdigit():
symbols.append(tmp[1])
positions.append([float(x) for x in tmp[2:5]])
natom = len(symbols)
initial_positions = np.array(positions)
# print symbols
# print initial_positions
forces_data = re.findall(r'The grand total force \(eV/A\):([\w\d\s\.\-=\+]*)Cartesian', data)
# print len(forces_data)
forces = np.zeros((len(forces_data), natom, 3))
# print forces.shape
iteration = 0
for idata in forces_data:
for iline in idata.split('\n'):
if 'iatom' in iline:
fields = iline.split()
forces[iteration, int(fields[2]) - 1] = np.array(fields[-3:], dtype=float)
iteration += 1
ret = re.findall('Cartesian Forces:\s*Max = ([=\w\s\d.]*)RMS = ([\s\d.]*)\n', data)
ret = [[float(x) for x in y] for y in ret]
max_force = [x[0] for x in ret]
rms = [x[1] for x in ret]
energy_data = re.findall(r'---------- T H E T O T A L E N E R G Y -----------([\s\w\d\.\-=/]+)--- \n', data)
energy = []
for idata in energy_data:
for iline in idata.split('\n'):
if 'Time step' in iline:
tmp = iline.split()
ienergy = {'Time_step': int(tmp[3]), 'SCF_step': int(tmp[7]), 'etot/atom': float(tmp[10])}
elif len(iline.split('=')) == 2:
tmp = iline.split('=')
ienergy[tmp[0].strip()] = float(tmp[1])
energy.append(ienergy)
ret = {'symbols': symbols,
'initial_positions': initial_positions,
'forces': generic_serializer(forces),
'energetics': energy,
'max_force': max_force,
'rms_force': rms}
return ret
def read_fireball_stdout(filename):
rf = open(filename, 'r')
data = rf.read()
atom_data = re.findall(r'Atom Coordinates from Basis File:([\d\w\s=\-\.#]+)===\n', data)[0]
symbols = []
positions = []
for iline in atom_data.split('\n'):
# print iline
tmp = iline.split()
if len(tmp) == 6 and tmp[0].isdigit():
symbols.append(tmp[1])
positions.append([float(x) for x in tmp[2:5]])
natom = len(symbols)
initial_positions = np.array(positions)
# print symbols
# print initial_positions
forces_data = re.findall(r'The grand total force \(eV/A\):([\w\d\s\.\-=\+]*)Cartesian', data)
# print len(forces_data)
forces = np.zeros((len(forces_data), natom, 3))
# print forces.shape
iteration = 0
for idata in forces_data:
for iline in idata.split('\n'):
if 'iatom' in iline:
fields = iline.split()
forces[iteration, int(fields[2]) - 1] = np.array(fields[-3:], dtype=float)
iteration += 1
ret = re.findall('Cartesian Forces:\s*Max = ([=\w\s\d.]*)RMS = ([\s\d.]*)\n', data)
ret = [[float(x) for x in y] for y in ret]
max_force = [x[0] for x in ret]
rms = [x[1] for x in ret]
energy_data = re.findall(r'---------- T H E T O T A L E N E R G Y -----------([\s\w\d\.\-=/]+)--- \n', data)
energy = []
for idata in energy_data:
for iline in idata.split('\n'):
if 'Time step' in iline:
tmp = iline.split()
ienergy = {'Time_step': int(tmp[3]), 'SCF_step': int(tmp[7]), 'etot/atom': float(tmp[10])}
elif len(iline.split('=')) == 2:
tmp = iline.split('=')
ienergy[tmp[0].strip()] = float(tmp[1])
energy.append(ienergy)
ret = {'symbols': symbols,
'initial_positions': initial_positions,
'forces': generic_serializer(forces),
'energetics': energy,
'max_force': max_force,
'rms_force': rms}
return ret
def to_dict(self):
ret = {}
for i in ['charge', 'energy', 'forces', 'stress']:
ret[i] = eval('self.' + i)
for i in ret:
if isinstance(ret[i], np.ndarray):
ret[i] = generic_serializer(ret[i])
return ret
def to_dict(self):
ret = {}
for i in ['charge', 'energy', 'forces', 'stress']:
ret[i] = eval('self.' + i)
for i in ret:
if isinstance(ret[i], np.ndarray):
ret[i] = generic_serializer(ret[i])
return ret
def elastic_moduli(filename='OUTCAR'):
ret = {}
rf = open(filename)
data = rf.read()
subblock = re.findall('ELASTIC MODULI CONTR FROM IONIC RELAXATION \(kBar\)[\s\d\w]*-*([\s\d\w.-]*)\n\n\n',
data)
ret['elastic_moduli_contr'] = np.array(np.array(subblock[0].split()[:42]).reshape(6, -1)[:, 1:], dtype=float)
subblock = re.findall('TOTAL ELASTIC MODULI \(kBar\)[\s\d\w]*-*([\s\d\w.-]*)\n\n\n', data)
ret['total_elastic_moduli'] = np.array(np.array(subblock[0].split()[:42]).reshape(6, -1)[:, 1:], dtype=float)
return generic_serializer(ret)
def evaluate(self, imember):
entry = self.population.get_entry(imember)
pcm_structure = pychemia.Structure.from_dict(entry['structure'])
ase_structure = pychemia.external.ase.pychemia2ase(pcm_structure)
ase_structure.set_calculator(LennardJones())
dyn = QuasiNewton(ase_structure)
dyn.run()
ase_structure.set_constraint(FixAtoms(mask=[True for atom in ase_structure]))
ucf = UnitCellFilter(ase_structure)
qn = QuasiNewton(ucf)
qn.run()
new_structure = pychemia.external.ase.ase2pychemia(ase_structure)
energy = ase_structure.get_potential_energy()
forces = ase_structure.get_forces()
stress = ase_structure.get_stress()
new_properties = {'energy': float(energy), 'forces': generic_serializer(forces),
'stress': generic_serializer(stress)}
self.population.db.update(imember, structure=new_structure, properties=new_properties)
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 evaluate(self, structure, gtol=None):
if gtol is None:
gtol = self.target_forces
positions, forces, energy = lj_compact_evaluate(structure, gtol, self.minimal_density)
structure.set_positions(positions)
structure.relocate_to_cm()
if structure.natom > 2:
structure.align_inertia_momenta()
sorted_indices = structure.sort_sites()
forces = forces[sorted_indices]
pg = get_point_group(structure, executable='symmol')
properties = {'forces': generic_serializer(forces), 'energy': energy, 'point_group': pg}
return structure, properties
def evaluate(self, entry_id, gtol=None):
if gtol is None:
gtol = self.target_forces
print('Evaluating %s target density= %7.3F' % (entry_id, self.minimal_density))
structure = self.get_structure(entry_id)
positions, forces, energy = lj_compact_evaluate(structure, gtol, self.minimal_density)
structure.set_positions(positions)
structure.relocate_to_cm()
if structure.natom > 2:
structure.align_inertia_momenta()
sorted_indices = structure.sort_sites()
forces = forces[sorted_indices]
properties = {'forces': generic_serializer(forces), 'energy': energy}
return structure, properties, energy
def set_grid(self, grid, shifts=None):
"""
Set a grid of kpoints with a proper check of correct arguments
:param grid: Number of kpoints on each direction (Only for 'gamma' and 'monkhorst-pack')
:param shifts: Shift applied to the grid (Only for 'gamma' and 'monkhorst-pack')
"""
assert (self.kmode in ['gamma', 'monkhorst-pack'])
if grid is None:
self.grid = [1, 1, 1]
elif len(grid) == 3:
self.grid = [int(x) for x in grid]
else:
raise ValueError("Wrong value for grid, should be an array with shape (-1,3)")
if shifts is None:
self.shifts = [0, 0, 0]
else:
self.shifts = generic_serializer(np.array(shifts).reshape(3))
def set_grid(self, grid, shifts=None):
"""
Set a grid of kpoints with a proper check of correct arguments
:param grid: Number of kpoints on each direction (Only for 'gamma' and 'monkhorst-pack')
:param shifts: Shift applied to the grid (Only for 'gamma' and 'monkhorst-pack')
"""
assert (self.kmode in ['gamma', 'monkhorst-pack'])
if grid is None:
self.grid = [1, 1, 1]
elif len(grid) == 3:
self.grid = [int(x) for x in grid]
else:
raise ValueError(
"Wrong value for grid, should be an array with shape (-1,3)")
if shifts is None:
self.shifts = [0, 0, 0]
else:
self.shifts = generic_serializer(np.array(shifts).reshape((-1, 3)))
def evaluate(self, entry_id, gtol=None):
if gtol is None:
gtol = self.target_forces
print('Evaluating %s target density= %7.3F' %
(entry_id, self.minimal_density))
structure = self.get_structure(entry_id)
positions, forces, energy = lj_compact_evaluate(
structure, gtol, self.minimal_density)
structure.set_positions(positions)
structure.relocate_to_cm()
if structure.natom > 2:
structure.align_inertia_momenta()
sorted_indices = structure.sort_sites()
forces = forces[sorted_indices]
properties = {'forces': generic_serializer(forces), 'energy': energy}
return structure, properties, energy
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 = pychemia.utils.mathematics.unit_vectors(2 * np.random.rand(*pos.shape) - 1)
new_pos = generic_serializer(pos + factor * uv)
structure = pychemia.Structure(positions=new_pos,
symbols=entry['structure']['symbols'],
periodicity=False)
if in_place:
return self.pcdb.db.pychemia_entries.update_one({'_id': entry_id},
{'$set': {'structure': structure.to_dict,
'properties': {}}})
else:
structure = pychemia.Structure(positions=new_pos,
symbols=entry['structure']['symbols'],
periodicity=False)
return self.new_entry(structure, active=False)
def evaluate(self, structure, gtol=None):
if gtol is None:
gtol = self.target_forces
positions, forces, energy = lj_compact_evaluate(
structure, gtol, self.minimal_density)
structure.set_positions(positions)
structure.relocate_to_cm()
if structure.natom > 2:
structure.align_inertia_momenta()
sorted_indices = structure.sort_sites()
forces = forces[sorted_indices]
pg = get_point_group(structure, executable='symmol')
properties = {
'forces': generic_serializer(forces),
'energy': energy,
'point_group': pg
}
return structure, properties
def cluster_fb_worker(db_settings):
while True:
pcdb = pychemia.db.get_database(db_settings)
population = pychemia.population.LJCluster(pcdb)
entry = population.pcdb.db.pychemia_entries.find_one(
{
'status.' + population.tag: True,
'status.lock': {
'$exists': False
},
'properties': {}
}, {'_id': 1})
if entry is not None:
population.pcdb.lock(entry['_id'])
structure = population.pcdb.get_structure(entry['_id'])
fb = pychemia.code.fireball.FireBall(fdata_path='../Fdata')
fb.initialize(structure, workdir=str(entry['_id']))
fb.cluster_relaxation()
fb.set_inputs()
sp = fb.run()
sp.wait()
so = pychemia.code.fireball.read_fireball_stdout(fb.workdir +
os.sep +
'fireball.log')
forces = generic_serializer(so['forces'][-1])
energy = so['energy'][-1]['ETOT']
properties = {'forces': forces, 'energy': energy}
structure = pychemia.code.fireball.read_geometry_bas(fb.workdir +
os.sep +
'answer.bas')
population.pcdb.update(entry['_id'],
structure=structure,
properties=properties)
population.pcdb.unlock(entry['_id'])
else:
break
def test_orbital(self):
"""
Test (pychemia.population.OrbitalDFTU) :
"""
if not pychemia.db.has_connection():
return
pychemia_path = pychemia.__path__[0]
abiinput = pychemia.code.abinit.AbinitInput('tests/data/abinit_dmatpawu/abinit.in')
dmatpawu = np.array(abiinput['dmatpawu']).reshape(-1, 5, 5)
params = pychemia.population.orbitaldftu.dmatpawu2params(dmatpawu, 5)
dmatpawu_new = pychemia.population.orbitaldftu.params2dmatpawu(params)
self.assertLess(np.min(dmatpawu-dmatpawu_new), 0.01)
with self.assertRaises(ValueError) as context:
pychemia.population.orbitaldftu.OrbitalDFTU('test', '/tmp/no_abinit.in')
with self.assertRaises(ValueError) as context:
pychemia.population.orbitaldftu.OrbitalDFTU('test', input_path='tests/data/abinit_01/abinit.in')
popu = pychemia.population.orbitaldftu.OrbitalDFTU('test', input_path='tests/data/abinit_dmatpawu/abinit.in')
popu.pcdb.clean()
ea = [[-0.1, -0.2, -0.3, -0.4, -0.5, -0.6, -0.7, -0.8, -0.9, -1.0],
[0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
params['euler_angles'] = ea
params = generic_serializer(params)
entry_id = popu.new_entry(params)
ea = [[0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0],
[-0.1, -0.2, -0.3, -0.4, -0.5, -0.6, -0.7, -0.8, -0.9, -1.0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
params['euler_angles'] = ea
params = generic_serializer(params)
entry_jd = popu.new_entry(params)
popu.add_random()
popu.random_population(16)
print(popu)
self.assertFalse(popu.is_evaluated(entry_id))
for entry_id in popu.members:
params = popu.get_correlation_params(entry_id, final=False)
popu.set_final_results(entry_id, params, 0.0, 1E-13)
self.assertTrue(popu.is_evaluated(entry_id))
popu.get_duplicates(popu.members, tolerance=0.1)
popu.cross([entry_id, entry_jd])
entry_idm = popu.move_random(entry_id)
popu.get_entry(entry_idm, {'properties': 1})
entry_imj = popu.move(entry_id, entry_jd)
popu.get_entry(entry_imj, {'properties': 1})
# pd = popu.to_dict
# popu.from_dict(pd)
tmpdir = tempfile.mkdtemp()
for i in popu.members:
popu.prepare_folder(i, workdir=tmpdir, source_dir=pychemia_path + 'tests/data/abinit_dmatpawu')
popu.pcdb.clean()
shutil.rmtree(tmpdir)
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 run(self, nparal=1):
self.started = True
self.cleaner()
vj = self.vaspjob
ncalls = 1
self.first_run(nparal)
while True:
if vj.runner is not None and vj.runner.poll() is not None:
pcm_log.info('Execution completed. Return code %d' % vj.runner.returncode)
filename = self.workdir + os.sep + 'vasp_stdout.log'
if os.path.exists(filename):
read_vasp_stdout(filename=filename)
ncalls += 1
va = VaspAnalyser(self.workdir)
va.run()
max_force, max_stress = self.get_max_force_stress()
print('Max Force: %9.3E Stress: %9.3E (target forces= %E)' %
(max_force, max_stress, self.target_forces))
if max_force is not None and max_force < self.target_forces:
# Conditions to finish the run
if max_stress < self.target_forces:
self.success = True
break
elif not self.relax_cell:
self.success = True
break
elif ncalls >= self.max_calls:
self.success = False
break
self.update()
vj.run(use_mpi=True, mpi_num_procs=nparal)
if self.waiting:
vj.runner.wait()
else:
filename = self.workdir + os.sep + 'vasp_stdout.log'
if os.path.exists(filename):
vasp_stdout = read_vasp_stdout(filename=filename)
if len(vasp_stdout['iterations']) > 0:
pcm_log.debug('[%s] SCF: %s' % (os.path.basename(self.workdir), str(vasp_stdout['iterations'])))
# if len(vasp_stdout['energies']) > 2:
# energy_str = ' %9.3E' % vasp_stdout['energies'][0]
# for i in range(1, len(vasp_stdout['energies'])):
# if vasp_stdout['energies'][i] < vasp_stdout['energies'][i-1]:
# energy_str += ' >'
# else:
# energy_str += ' <'
# pcm_log.debug(energy_str)
time.sleep(30)
outcars = sorted([x for x in os.listdir(self.workdir) if x.startswith('OUTCAR')])[::-1]
vo = VaspOutput(self.workdir + os.sep + outcars[0])
forces = vo.forces
stress = vo.stress
if len(outcars) > 1:
for i in outcars[1:]:
vo = VaspOutput(self.workdir + os.sep + i)
forces = np.concatenate((forces, vo.forces))
stress = np.concatenate((stress, vo.stress))
vj.get_outputs()
self.output = {'forces': generic_serializer(forces), 'stress': generic_serializer(stress),
'energy': vj.outcar.energy, 'energies': generic_serializer(vj.outcar.energies)}
if vj.outcar.is_finished:
self.finished = True
def worker(db_settings, entry_id, workdir, target_forces, relaxator_params):
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)
structure = structure.scale()
print('relaxator_params', relaxator_params)
relaxer = IonRelaxation2(structure, workdir=workdir, target_forces=target_forces, waiting=False,
binary=relaxator_params['binary'], encut=1.3, kp_grid=None, kp_density=1E4,
relax_cell=True)
print('relaxing on:', relaxer.workdir)
relaxer.run(relaxator_params['nmpiparal'])
pcm_log.info('[%s]: Finished relaxation. Target forces: %7.3e' % (str(entry_id), target_forces))
filename = workdir + os.sep + 'OUTCAR'
if os.path.isfile(filename):
forces, stress, total_energy = relaxer.get_forces_stress_energy()
if forces is not None:
magnitude_forces = np.apply_along_axis(np.linalg.norm, 1, forces)
print('Forces: Max: %9.3e Avg: %9.3e' % (np.max(magnitude_forces), np.average(magnitude_forces)))
print('Stress: ', np.max(np.abs(stress.flatten())))
if forces is None:
pcm_log.error('No forces found on %s' % filename)
if stress is None:
pcm_log.error('No stress found on %s' % filename)
if total_energy is None:
pcm_log.error('No total_energy found on %s' % filename)
new_structure = relaxer.get_final_geometry()
if forces is not None and stress is not None and total_energy is not None and new_structure is not None:
pcm_log.info('[%s]: Updating properties' % str(entry_id))
pcdb.update(entry_id, structure=new_structure)
te = total_energy
pcdb.entries.update({'_id': entry_id},
{'$set': {'status.relaxation': 'succeed',
'status.target_forces': target_forces,
'properties.forces': generic_serializer(forces),
'properties.stress': generic_serializer(stress),
'properties.energy': te,
'properties.energy_pa': te / new_structure.natom,
'properties.energy_pf': te / new_structure.get_composition().gcd}})
# Fingerprint
# Update the fingerprints only if the two structures are really different
diffnatom = structure.natom != new_structure.natom
diffcell = np.max(np.abs((structure.cell - new_structure.cell).flatten()))
diffreduced = np.max(np.abs((structure.reduced - new_structure.reduced).flatten()))
if diffnatom != 0 or diffcell > 1E-7 or diffreduced > 1E-7:
analysis = StructureAnalysis(new_structure, radius=50)
x, ys = analysis.fp_oganov(delta=0.01, sigma=0.01)
fingerprint = {'_id': entry_id}
for k in ys:
atomic_number1 = atomic_number(new_structure.species[k[0]])
atomic_number2 = atomic_number(new_structure.species[k[1]])
pair = '%06d' % min(atomic_number1 * 1000 + atomic_number2,
atomic_number2 * 1000 + atomic_number1)
fingerprint[pair] = list(ys[k])
if pcdb.db.fingerprints.find_one({'_id': entry_id}) is None:
pcdb.db.fingerprints.insert(fingerprint)
else:
pcdb.db.fingerprints.update({'_id': entry_id}, fingerprint)
else:
pcm_log.debug('Original and new structures are very similar.')
pcm_log.debug('Max diff cell: %10.3e' % np.max(np.absolute((structure.cell -
new_structure.cell).flatten())))
if structure.natom == new_structure.natom:
pcm_log.debug('Max diff reduced coordinates: %10.3e' %
np.max(np.absolute((structure.reduced - new_structure.reduced).flatten())))
else:
pcdb.entries.update({'_id': entry_id}, {'$set': {'status.relaxation': 'failed'}})
pcm_log.error('Bad data after relaxation. Tagging relaxation as failed')
else:
pcm_log.error('ERROR: File not found %s' % filename)
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)
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(db_settings, entry_id, workdir, target_forces, relaxator_params):
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)
structure = structure.scale()
print('relaxator_params', relaxator_params)
relaxer = IonRelaxation(structure,
workdir=workdir,
target_forces=target_forces,
waiting=False,
binary=relaxator_params['binary'],
encut=1.3,
kp_grid=None,
kp_density=1E4,
relax_cell=True,
max_calls=10)
print('relaxing on:', relaxer.workdir)
relaxer.run(relaxator_params['nmpiparal'])
pcm_log.info('[%s]: Finished relaxation. Target forces: %7.3e' %
(str(entry_id), target_forces))
filename = workdir + os.sep + 'OUTCAR'
if os.path.isfile(filename):
forces, stress, total_energy = relaxer.get_forces_stress_energy()
if forces is not None:
magnitude_forces = np.apply_along_axis(np.linalg.norm, 1, forces)
print('Forces: Max: %9.3e Avg: %9.3e' %
(np.max(magnitude_forces), np.average(magnitude_forces)))
print('Stress: ', np.max(np.abs(stress.flatten())))
if forces is None:
pcm_log.error('No forces found on %s' % filename)
if stress is None:
pcm_log.error('No stress found on %s' % filename)
if total_energy is None:
pcm_log.error('No total_energy found on %s' % filename)
new_structure = relaxer.get_final_geometry()
if forces is not None and stress is not None and total_energy is not None and new_structure is not None:
pcm_log.info('[%s]: Updating properties' % str(entry_id))
pcdb.update(entry_id, structure=new_structure)
te = total_energy
pcdb.entries.update({'_id': entry_id}, {
'$set': {
'status.relaxation':
'succeed',
'status.target_forces':
target_forces,
'properties.forces':
generic_serializer(forces),
'properties.stress':
generic_serializer(stress),
'properties.energy':
te,
'properties.energy_pa':
te / new_structure.natom,
'properties.energy_pf':
te / new_structure.get_composition().gcd
}
})
# Fingerprint
# Update the fingerprints only if the two structures are really different
diffnatom = structure.natom != new_structure.natom
diffcell = np.max(
np.abs((structure.cell - new_structure.cell).flatten()))
diffreduced = np.max(
np.abs((structure.reduced - new_structure.reduced).flatten()))
if diffnatom != 0 or diffcell > 1E-7 or diffreduced > 1E-7:
analysis = StructureAnalysis(new_structure, radius=50)
x, ys = analysis.fp_oganov(delta=0.01, sigma=0.01)
fingerprint = {'_id': entry_id}
for k in ys:
atomic_number1 = atomic_number(new_structure.species[k[0]])
atomic_number2 = atomic_number(new_structure.species[k[1]])
pair = '%06d' % min(atomic_number1 * 1000 + atomic_number2,
atomic_number2 * 1000 + atomic_number1)
fingerprint[pair] = list(ys[k])
if pcdb.db.fingerprints.find_one({'_id': entry_id}) is None:
pcdb.db.fingerprints.insert(fingerprint)
else:
pcdb.db.fingerprints.update({'_id': entry_id}, fingerprint)
else:
pcm_log.debug('Original and new structures are very similar.')
pcm_log.debug('Max diff cell: %10.3e' % np.max(
np.absolute(
(structure.cell - new_structure.cell).flatten())))
if structure.natom == new_structure.natom:
pcm_log.debug(
'Max diff reduced coordinates: %10.3e' % np.max(
np.absolute((structure.reduced -
new_structure.reduced).flatten())))
else:
pcdb.entries.update({'_id': entry_id},
{'$set': {
'status.relaxation': 'failed'
}})
pcm_log.error(
'Bad data after relaxation. Tagging relaxation as failed')
else:
pcm_log.error('ERROR: File not found %s' % filename)
pcm_log.info('[%s]: Unlocking the entry' % str(entry_id))
pcdb.unlock(entry_id)
def read_dftb_stdout(filename='dftb_stdout.log'):
"""
Read the standard output stored in a file
(by default 'dftb_stdout.log') and extract
relevant information useful for a relaxation
procedure
:param filename: The standard output stored in a file
:return:
"""
rf = open(filename, 'r')
data = rf.read()
ret = {}
start_ini = re.findall(r'Starting initialization...[\s-]+([.\s\d\w\-:\(\),+]+)---', data)
if len(start_ini) == 1:
start_ini = start_ini[0].replace('\n ', ' ').split('\n')
ret['Starting_Initialization'] = {}
for line in start_ini:
if len(line.split(':')) == 2:
left, right = line.split(':')
elif line[:3] != '---':
left = line[:29].replace(':', '')
right = line[29:]
ret['Starting_Initialization'][left.strip()] = parse_value(right.strip())
if left.strip() == 'K-points and weights':
right = right.replace(':', '')
right = np.array(right.split(), dtype=float).reshape((-1, 5))
ret['Starting_Initialization'][left.strip()] = {'kpoints': generic_serializer(right[:, 1:-1]),
'weights': generic_serializer(right[:, -1])}
geom_blocks = re.findall(r'Geometry step:([\^*.\s\d\w\-:\(\),+]+)Pa', data)
ret['Geometry_Steps'] = []
for iblock in geom_blocks:
ib = iblock.split('\n')
if 'Lattice' in ib[0]:
tmp = {'iter': int(ib[0].split(',')[0]), 'scc': {}}
else:
tmp = {'iter': int(ib[0]), 'scc': {}}
tmp['scc']['tot_electronic'] = []
tmp['scc']['diff_electronic'] = []
tmp['scc']['scc_error'] = []
for iline in ib[4:]:
fields = iline.split()
if len(fields) > 0 and fields[0].strip().isdigit():
tmp['scc']['tot_electronic'].append(float(fields[1]))
tmp['scc']['diff_electronic'].append(float(fields[2]))
tmp['scc']['scc_error'].append(float(fields[3]))
elif len(iline.split(':')) == 2:
left, right = iline.split(':')
tmp[left.strip()] = {'value': float(right.split()[0]), 'units': right.split()[1]}
ret['Geometry_Steps'].append(tmp)
max_force = re.findall(r'Maximal force component:\s*([\s\dE+-.]+)\s*\n', data)
if len(max_force) > 0:
ret['max_force'] = float(max_force[-1])
if re.findall('Geometry did NOT converge', data):
pcm_log.debug('Convergence not achieved!')
ret['ion_convergence'] = False
else:
ret['ion_convergence'] = True
if re.findall('Geometry converged', data):
pcm_log.debug('Convergence achieved!')
ret['ion_convergence'] = True
else:
ret['ion_convergence'] = False
return ret
def run(self, nparal=1):
self.started = True
self.cleaner()
vj = self.vaspjob
ncalls = 1
self.first_run(nparal)
while True:
if vj.runner is not None and vj.runner.poll() is not None:
pcm_log.info('Execution completed. Return code %d' %
vj.runner.returncode)
filename = self.workdir + os.sep + 'vasp_stdout.log'
if os.path.exists(filename):
read_vasp_stdout(filename=filename)
ncalls += 1
va = VaspAnalyser(self.workdir)
va.run()
max_force, max_stress = self.get_max_force_stress()
print('Max Force: %9.3E Stress: %9.3E (target forces= %E)' %
(max_force, max_stress, self.target_forces))
if max_force is not None and max_force < self.target_forces:
# Conditions to finish the run
if max_stress < self.target_forces:
self.success = True
break
elif not self.relax_cell:
self.success = True
break
elif ncalls >= self.max_calls:
self.success = False
break
self.update()
vj.run(use_mpi=True, mpi_num_procs=nparal)
if self.waiting:
vj.runner.wait()
else:
filename = self.workdir + os.sep + 'vasp_stdout.log'
if os.path.exists(filename):
vasp_stdout = read_vasp_stdout(filename=filename)
if len(vasp_stdout['iterations']) > 0:
pcm_log.debug('[%s] SCF: %s' % (os.path.basename(
self.workdir), str(vasp_stdout['iterations'])))
# if len(vasp_stdout['energies']) > 2:
# energy_str = ' %9.3E' % vasp_stdout['energies'][0]
# for i in range(1, len(vasp_stdout['energies'])):
# if vasp_stdout['energies'][i] < vasp_stdout['energies'][i-1]:
# energy_str += ' >'
# else:
# energy_str += ' <'
# pcm_log.debug(energy_str)
time.sleep(30)
outcars = sorted([
x for x in os.listdir(self.workdir) if x.startswith('OUTCAR')
])[::-1]
vo = VaspOutput(self.workdir + os.sep + outcars[0])
forces = vo.forces
stress = vo.stress
if len(outcars) > 1:
for i in outcars[1:]:
vo = VaspOutput(self.workdir + os.sep + i)
forces = np.concatenate((forces, vo.forces))
stress = np.concatenate((stress, vo.stress))
vj.get_outputs()
self.output = {
'forces': generic_serializer(forces),
'stress': generic_serializer(stress),
'energy': vj.outcar.energy,
'energies': generic_serializer(vj.outcar.energies)
}
if vj.outcar.is_finished:
self.finished = True
def test_orbital(self):
"""
Tests (pychemia.population.OrbitalDFTU) :
"""
if not pychemia.db.has_connection():
return
pychemia_path = pychemia.__path__[0]
abiinput = pychemia.code.abinit.AbinitInput('tests/data/abinit_dmatpawu/abinit.in')
dmatpawu = np.array(abiinput['dmatpawu']).reshape(-1, 5, 5)
params = pychemia.population.orbitaldftu.dmatpawu2params(dmatpawu, 5)
dmatpawu_new = pychemia.population.orbitaldftu.params2dmatpawu(params)
self.assertLess(np.min(dmatpawu-dmatpawu_new), 0.01)
with self.assertRaises(ValueError) as context:
pychemia.population.orbitaldftu.OrbitalDFTU('test', '/tmp/no_abinit.in')
with self.assertRaises(ValueError) as context:
pychemia.population.orbitaldftu.OrbitalDFTU('test', input_path='tests/data/abinit_01/abinit.in')
popu = pychemia.population.orbitaldftu.OrbitalDFTU('test', input_path='tests/data/abinit_dmatpawu/abinit.in')
popu.pcdb.clean()
ea = [[-0.1, -0.2, -0.3, -0.4, -0.5, -0.6, -0.7, -0.8, -0.9, -1.0],
[0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
params['euler_angles'] = ea
params = generic_serializer(params)
entry_id = popu.new_entry(params)
ea = [[0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0],
[-0.1, -0.2, -0.3, -0.4, -0.5, -0.6, -0.7, -0.8, -0.9, -1.0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
params['euler_angles'] = ea
params = generic_serializer(params)
entry_jd = popu.new_entry(params)
popu.add_random()
popu.random_population(16)
print(popu)
self.assertFalse(popu.is_evaluated(entry_id))
for entry_id in popu.members:
params = popu.get_correlation_params(entry_id, final=False)
popu.set_final_results(entry_id, params, 0.0, 1E-13)
self.assertTrue(popu.is_evaluated(entry_id))
popu.get_duplicates(popu.members, tolerance=0.1)
popu.cross([entry_id, entry_jd])
entry_idm = popu.move_random(entry_id)
popu.get_entry(entry_idm, {'properties': 1})
entry_imj = popu.move(entry_id, entry_jd)
popu.get_entry(entry_imj, {'properties': 1})
# pd = popu.to_dict
# popu.from_dict(pd)
tmpdir = tempfile.mkdtemp()
for i in popu.members:
popu.prepare_folder(i, workdir=tmpdir, source_dir=pychemia_path + 'tests/data/abinit_dmatpawu')
popu.pcdb.clean()
shutil.rmtree(tmpdir)