def read_results(self):
FileIOCalculator.read(self, self.label)
if not os.path.isfile(self.label + '.got'):
raise ReadError
with open(self.label + '.got') as f:
lines = f.readlines()
cycles = -1
self.optimized = None
for i, line in enumerate(lines):
m = re.match(r'\s*Total lattice energy\s*=\s*(\S+)\s*eV', line)
if m:
energy = float(m.group(1))
self.results['energy'] = energy
self.results['free_energy'] = energy
elif line.find('Optimisation achieved') != -1:
self.optimized = True
elif line.find('Final Gnorm') != -1:
self.Gnorm = float(line.split()[-1])
elif line.find('Cycle:') != -1:
cycles += 1
elif line.find('Final Cartesian derivatives') != -1:
s = i + 5
forces = []
while(True):
s = s + 1
if lines[s].find("------------") != -1:
break
if lines[s].find(" s ") != -1:
continue
g = lines[s].split()[3:6]
G = [-float(x) * eV / Ang for x in g]
forces.append(G)
forces = np.array(forces)
self.results['forces'] = forces
elif line.find('Final cartesian coordinates of atoms') != -1:
s = i + 5
positions = []
while True:
s = s + 1
if lines[s].find("------------") != -1:
break
if lines[s].find(" s ") != -1:
continue
xyz = lines[s].split()[3:6]
XYZ = [float(x) * Ang for x in xyz]
positions.append(XYZ)
positions = np.array(positions)
self.atoms.set_positions(positions)
self.steps = cycles
def read(self, label):
FileIOCalculator.read(self, label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
self.parameters = Parameters.read(self.label + '.ase')
self.atoms = read_gamess_us_input(self.label + '.inp')
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
self.parameters = Parameters.read(self.label + '.ase')
self.atoms = read_orca_input(self.label + '.inp')
self.read_results()
def read_results(self):
"""Read the results, such as energy, forces, eigenvalues, etc.
"""
FileIOCalculator.read(self, self.label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
with open(self.label + '.out') as f:
lines = f.readlines()
for i, line in enumerate(lines):
if line.find('TOTAL ENERGY') != -1:
self.results['energy'] = float(line.split()[3])
elif line.find('FINAL HEAT OF FORMATION') != -1:
self.final_hof = float(line.split()[5]) * kcal / mol
elif line.find('NO. OF FILLED LEVELS') != -1:
self.nspins = 1
self.no_occ_levels = int(line.split()[-1])
elif line.find('NO. OF ALPHA ELECTRON') != -1:
self.nspins = 2
self.no_alpha_electrons = int(line.split()[-1])
self.no_beta_electrons = int(lines[i + 1].split()[-1])
self.results['magmom'] = abs(self.no_alpha_electrons -
self.no_beta_electrons)
elif line.find('FINAL POINT AND DERIVATIVES') != -1:
forces = [
-float(line.split()[6])
for line in lines[i + 3:i + 3 + 3 * len(self.atoms)]
]
self.results['forces'] = np.array(forces).reshape(
(-1, 3)) * kcal / mol
elif line.find('EIGENVALUES') != -1:
if line.find('ALPHA') != -1:
j = i + 1
eigs_alpha = []
while not lines[j].isspace():
eigs_alpha += [float(eps) for eps in lines[j].split()]
j += 1
elif line.find('BETA') != -1:
j = i + 1
eigs_beta = []
while not lines[j].isspace():
eigs_beta += [float(eps) for eps in lines[j].split()]
j += 1
eigs = np.array([eigs_alpha, eigs_beta]).reshape(2, 1, -1)
self.eigenvalues = eigs
else:
eigs = []
j = i + 1
while not lines[j].isspace():
eigs += [float(e) for e in lines[j].split()]
j += 1
self.eigenvalues = np.array(eigs).reshape(1, 1, -1)
elif line.find('DIPOLE ') != -1:
self.results['dipole'] = np.array(
lines[i + 3].split()[1:1 + 3], float) * Debye
def read_results(self):
FileIOCalculator.read(self, self.label)
if not os.path.isfile(self.label + '.got'):
raise ReadError
with open(self.label + '.got') as f:
lines = f.readlines()
cycles = -1
self.optimized = None
for i, line in enumerate(lines):
if line.startswith(" Final energy") and 'eV' in line:
energy = float(line.split()[-2])
self.results['energy'] = energy
self.results['free_energy'] = energy
elif line.find('Optimisation achieved') != -1:
self.optimized = True
elif line.find('Final Gnorm') != -1:
self.Gnorm = float(line.split()[-1])
elif line.find('Cycle:') != -1:
cycles += 1
elif line.find('Final Cartesian derivatives') != -1:
s = i + 5
forces = []
while (True):
s = s + 1
if lines[s].find("------------") != -1:
break
if lines[s].find(" s ") != -1:
continue
g = lines[s].split()[3:6]
G = [-float(x) * eV / Ang for x in g]
forces.append(G)
forces = np.array(forces)
self.results['forces'] = forces
elif line.find('Final cartesian coordinates of atoms') != -1:
s = i + 5
positions = []
while True:
s = s + 1
if lines[s].find("------------") != -1:
break
if lines[s].find(" s ") != -1:
continue
xyz = lines[s].split()[3:6]
XYZ = [float(x) * Ang for x in xyz]
positions.append(XYZ)
positions = np.array(positions)
self.atoms.set_positions(positions)
self.steps = cycles
def read_results(self):
"""Read the results, such as energy, forces, eigenvalues, etc.
"""
FileIOCalculator.read(self, self.label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
parser = MopacParser(self.label)
self.parser = parser
self.atoms = parser.atoms
self.results = parser.get_properties()
def read(self, label):
"""Read a onetep .out file into the current instance."""
FileIOCalculator.read(self, label)
onetep_file = self.label + '.out'
warnings = []
try:
out = paropen(onetep_file, 'r')
except IOError:
raise ReadError('Could not open output file "%s"' % onetep_file)
# keep track of what we've read in
read_lattice = False
read_species = False
read_positions = False
line = out.readline()
if self.atoms is None:
self.atoms = Atoms()
self.atoms.calc = self
while line:
clean_line = line.strip().lower()
if '%block lattice_cart' in clean_line:
self._read_lattice(out)
read_lattice = True
elif '%block species_pot' in clean_line:
self._read_species_pot(out)
elif '%block species' in clean_line:
self._read_species(out)
read_species = True
elif '%block positions_abs' in clean_line:
self._read_positions(out)
read_positions = True
elif '%block species_cond' in clean_line:
self._read_species_cond(out)
elif 'warn' in line.lower():
warnings.append(line)
line = out.readline()
out.close()
if warnings:
warn('WARNING: %s contains warnings' % onetep_file)
for warning in warnings:
warn(warning)
if not (read_lattice and read_species and read_positions):
raise ReadError('Failed to read in essential calculation'
' data from output file "%s"' % onetep_file)
self.read_results(label)
def read(self, label):
"""Read a onetep .out file into the current instance."""
FileIOCalculator.read(self, label)
onetep_file = self.label + '.out'
warnings = []
try:
out = paropen(onetep_file, 'r')
except IOError:
raise ReadError('Could not open output file "%s"' % onetep_file)
# keep track of what we've read in
read_lattice = False
read_species = False
read_positions = False
line = out.readline()
if self.atoms is None:
self.atoms = Atoms()
self.atoms.calc = self
while line:
clean_line = line.strip().lower()
if '%block lattice_cart' in clean_line:
self._read_lattice(out)
read_lattice = True
elif '%block species_pot' in clean_line:
self._read_species_pot(out)
elif '%block species' in clean_line:
self._read_species(out)
read_species = True
elif '%block positions_abs' in clean_line:
self._read_positions(out)
read_positions = True
elif '%block species_cond' in clean_line:
self._read_species_cond(out)
elif 'warn' in line.lower():
warnings.append(line)
line = out.readline()
out.close()
if warnings:
warn('WARNING: %s contains warnings' % onetep_file)
for warning in warnings:
warn(warning)
if not (read_lattice and read_species and read_positions):
raise ReadError('Failed to read in essential calculation'
' data from output file "%s"' % onetep_file)
self.read_results(label)
def read_results(self):
"""Read the results, such as energy, forces, eigenvalues, etc.
"""
FileIOCalculator.read(self, self.label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
with open(self.label + '.out') as f:
lines = f.readlines()
for i, line in enumerate(lines):
if line.find('TOTAL ENERGY') != -1:
self.results['energy'] = float(line.split()[3])
elif line.find('FINAL HEAT OF FORMATION') != -1:
self.final_hof = float(line.split()[5]) * kcal / mol
elif line.find('NO. OF FILLED LEVELS') != -1:
self.nspins = 1
self.no_occ_levels = int(line.split()[-1])
elif line.find('NO. OF ALPHA ELECTRON') != -1:
self.nspins = 2
self.no_alpha_electrons = int(line.split()[-1])
self.no_beta_electrons = int(lines[i+1].split()[-1])
self.results['magmom'] = abs(self.no_alpha_electrons -
self.no_beta_electrons)
elif line.find('FINAL POINT AND DERIVATIVES') != -1:
forces = [-float(line.split()[6])
for line in lines[i + 3:i + 3 + 3 * len(self.atoms)]]
self.results['forces'] = np.array(
forces).reshape((-1, 3)) * kcal / mol
elif line.find('EIGENVALUES') != -1:
if line.find('ALPHA') != -1:
j = i + 1
eigs_alpha = []
while not lines[j].isspace():
eigs_alpha += [float(eps) for eps in lines[j].split()]
j += 1
elif line.find('BETA') != -1:
j = i + 1
eigs_beta = []
while not lines[j].isspace():
eigs_beta += [float(eps) for eps in lines[j].split()]
j += 1
eigs = np.array([eigs_alpha, eigs_beta]).reshape(2, 1, -1)
self.eigenvalues = eigs
else:
eigs = []
j = i + 1
while not lines[j].isspace():
eigs += [float(e) for e in lines[j].split()]
j += 1
self.eigenvalues = np.array(eigs).reshape(1, 1, -1)
elif line.find('DIPOLE ') != -1:
self.results['dipole'] = np.array(
lines[i + 3].split()[1:1 + 3], float) * Debye
def read(self, label):
# Set the label
FileIOCalculator.read(self, label)
# We can read the output file from cp2k
outfile = open("%s.out" % label, "r")
outlines = [line.strip() for line in outfile.readlines() ]
outfile.close()
unit_cell = np.zeros((3,3), dtype = np.float64)
reading_atoms = False
nat = 0
atm_coords = []
atm_type = []
__start__ = 0
for i, line in enumerate(outlines):
data_line = line.strip()
if len(data_line) == 0:
continue
if data_line[0] == "CELL|" and data_line[1] == "Vector" :
index = {"a" : 0, "b" : 1, "c" : 2}
v_i = index[data_line[2]]
unit_cell[v_i, 0] = float( data_line[4])
unit_cell[v_i, 1] = float( data_line[5])
unit_cell[v_i, 2] = float( data_line[6])
if "ATOMIC COORDINATES" in line:
reading_atoms = True
if reading_atoms:
if len(data_line) != 8:
reading_atoms = False
continue
if data_line[0] == "Atom":
continue
atm_type_conv = {"H": "H", "D": "H", "O":"O"} # Avoid deuterium
nat += 1
atm_coords.append( [float(data_line[3]), float(data_line[4]), float(data_line[5])])
atm_type.append( atm_type_conv[data_line[2]])
# Generate the ASE ATOM structure
self.atoms = Atoms(atm_type, atm_coords, cell=unit_cell)
self.read_results()
print ("Test results:")
print ("energy:", self.results["energy"])
print ("forces:", self.results["forces"])
print ("stress:", self.results["stress"])
def read(self, label):
"""Read results from ABINIT's text-output file."""
FileIOCalculator.read(self, label)
filename = self.label + '.txt'
if not os.path.isfile(filename):
raise ReadError
self.atoms = read_abinit(self.label + '.in')
self.parameters = Parameters.read(self.label + '.ase')
self.initialize(self.atoms)
self.read_results()
def read(self, label):
"""Read results from ABINIT's text-output file."""
FileIOCalculator.read(self, label)
filename = self.label + '.txt'
if not os.path.isfile(filename):
raise ReadError('ABINIT output file ' + filename + ' is missing.')
self.atoms = read_abinit(self.label + '.in')
self.parameters = Parameters.read(self.label + '.ase')
self.initialize(self.atoms)
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
geometry = os.path.join(self.directory, 'geometry.in')
control = os.path.join(self.directory, 'control.in')
for filename in [geometry, control, self.out]:
if not os.path.isfile(filename):
raise ReadError
self.atoms = read_aims(geometry)
self.parameters = Parameters.read(os.path.join(self.directory,
'parameters.ase'))
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
geometry = self.label + '.car'
output = self.label + '.outmol'
force = self.label + '.grad'
for filename in [force, output, geometry]:
if not os.path.isfile(filename):
raise ReadError
self.atoms = read(geometry)
self.parameters = Parameters.read(self.label + 'parameters.ase')
self.read_results()
def read(self, label):
"""Used to read the results of a previous calculation if restarting"""
FileIOCalculator.read(self, label)
from ase.io.orca import read_orca_out
filename = self.label
if not os.path.isfile(filename + ".log"):
raise ReadError
self.atoms = read_orca_out(filename, quantity='atoms')
self.parameters = Parameters.read(self.label + '.ase')
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
geometry = self.label + '.car'
output = self.label + '.outmol'
force = self.label + '.grad'
for filename in [force, output, geometry]:
if not os.path.isfile(filename):
raise ReadError
self.atoms = read(geometry)
self.parameters = Parameters.read(self.label + 'parameters.ase')
self.read_results()
def read(self, label):
""" Read results and input from a MyMD calculation.
The FileIOCalculator API of ASE prescribes this method and states
that it should read both input and output.
"""
FileIOCalculator.read(self, label)
self.read_input(label)
# Here start reading the trajectories etc.
self.state = Atoms(symbols, positions,
magmoms=self.parameters.pop('magmoms'))
self.read_results()
def read(self, label):
"""Used to read the results of a previous calculation if restarting"""
FileIOCalculator.read(self, label)
from ase.io.gaussian import read_gaussian_out
filename = self.label + '.log'
if not os.path.isfile(filename):
raise ReadError
self.atoms = read_gaussian_out(filename, quantity='atoms')
self.parameters = Parameters.read(self.label + '.ase')
initial_magmoms = self.parameters.pop('initial_magmoms')
self.atoms.set_initial_magnetic_moments(initial_magmoms)
self.read_results()
def read(self, label):
"""Used to read the results of a previous calculation if restarting"""
FileIOCalculator.read(self, label)
from ase.io.gaussian import read_gaussian_out
filename = self.label + '.log'
if not os.path.isfile(filename):
raise ReadError
self.atoms = read_gaussian_out(filename, quantity='atoms')
self.parameters = Parameters.read(self.label + '.ase')
initial_magmoms = self.parameters.pop('initial_magmoms')
self.atoms.set_initial_magnetic_moments(initial_magmoms)
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
filename = self.label + ".log"
with open(filename, 'r') as f:
lines = f.readlines()
if 'WARNING' in lines:
raise ReadError("Not convergy energy in log file {}.".format(filename))
if not '! total energy' in lines:
raise ReadError("Wrong ACE-Molecule log file {}.".format(filename))
if not os.path.isfile(filename):
raise ReadError("Wrong ACE-Molecule input file {}.".format(filename))
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
totenergy = os.path.join(self.directory, 'TOTENERGY.OUT')
eigval = os.path.join(self.directory, 'EIGVAL.OUT')
kpoints = os.path.join(self.directory, 'KPOINTS.OUT')
for filename in [totenergy, eigval, kpoints, self.out]:
if not os.path.isfile(filename):
raise ReadError('ELK output file ' + filename + ' is missing.')
# read state from elk.in because *.OUT do not provide enough digits!
self.atoms = read_elk(os.path.join(self.directory, 'elk.in'))
self.parameters = Parameters.read(
os.path.join(self.directory, 'parameters.ase'))
self.initialize(self.atoms)
self.read_results()
def read(self, label=None):
if label is None: label = self.label
FileIOCalculator.read(self, label)
geometry = os.path.join(self.directory, 'geometry.in')
control = os.path.join(self.directory, 'control.in')
for filename in [geometry, control, self.out]:
if not os.path.isfile(filename):
raise ReadError
self.atoms, symmetry_block = read_aims(geometry, True)
self.parameters = Parameters.read(
os.path.join(self.directory, 'parameters.ase'))
if symmetry_block:
self.parameters["symmetry_block"] = symmetry_block
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
totenergy = os.path.join(self.directory, 'TOTENERGY.OUT')
eigval = os.path.join(self.directory, 'EIGVAL.OUT')
kpoints = os.path.join(self.directory, 'KPOINTS.OUT')
for filename in [totenergy, eigval, kpoints, self.out]:
if not os.path.isfile(filename):
raise ReadError
# read state from elk.in because *.OUT do not provide enough digits!
self.atoms = read_elk(os.path.join(self.directory, 'elk.in'))
self.parameters = Parameters.read(os.path.join(self.directory,
'parameters.ase'))
self.initialize(self.atoms)
self.read_results()
def read(self, label):
# XXX label of restart file may not be the same as actual label!
# This makes things rather tricky. We first set the label to
# that of the restart file and arbitrarily expect the remaining code
# to rectify any consequent inconsistencies.
self.set_label(label)
FileIOCalculator.read(self, label)
inp_path = self._getpath('inp')
fd = open(inp_path)
names, values = parse_input_file(fd)
kwargs = purify(dict(zip(names, values)))
self.atoms, kwargs = kwargs2atoms(kwargs)
self.kwargs.update(kwargs)
fd.close()
self.read_results()
def read_results(self):
FileIOCalculator.read(self, self.label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
with open(self.label + '.out') as f:
lines = f.readlines()
for i, line in enumerate(lines):
if line.find('TOTAL ENERGY') != -1:
self.results['energy'] = float(line.split()[3])
elif line.find('FINAL POINT AND DERIVATIVES') != -1:
forces = [
-float(line.split()[6])
for line in lines[i + 3:i + 3 + 3 * len(self.atoms)]
]
forces = np.array(forces).reshape((-1, 3)) * kcal / mol
self.results['forces'] = forces
break
def read(self, label):
# XXX label of restart file may not be the same as actual label!
# This makes things rather tricky. We first set the label to
# that of the restart file and arbitrarily expect the remaining code
# to rectify any consequent inconsistencies.
self.set_label(label)
FileIOCalculator.read(self, label)
inp_path = self._getpath('inp')
fd = open(inp_path)
kwargs = parse_input_file(fd)
if self.octopus_keywords is not None:
self.check_keywords_exist(kwargs)
self.atoms, kwargs = kwargs2atoms(kwargs)
self.kwargs.update(kwargs)
fd.close()
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
with open(self.label + '.inp') as fd:
for line in fd:
if line.startswith('geometry'):
break
symbols = []
positions = []
for line in fd:
if line.startswith('end'):
break
words = line.split()
symbols.append(words[0])
positions.append([float(word) for word in words[1:]])
self.parameters = Parameters.read(self.label + '.ase')
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
if not os.path.isfile(self.label + ".out"):
raise ReadError
f = open(self.label + ".nw")
for line in f:
if line.startswith("geometry"):
break
symbols = []
positions = []
for line in f:
if line.startswith("end"):
break
words = line.split()
symbols.append(words[0])
positions.append([float(word) for word in words[1:]])
self.parameters = Parameters.read(self.label + ".ase")
self.state = Atoms(symbols, positions, magmoms=self.parameters.pop("magmoms"))
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
with open(self.label + '.out') as f:
lines = f.readlines()
self.parameters = Parameters(task='', method='')
p = self.parameters
parm_line = self.read_parameters_from_file(lines)
for keyword in parm_line.split():
if 'RELSCF' in keyword:
p.relscf = float(keyword.split('=')[-1])
elif keyword in self.methods:
p.method = keyword
else:
p.task += keyword + ' '
p.task.rstrip()
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
f = open(self.label + '.nw')
for line in f:
if line.startswith('geometry'):
break
symbols = []
positions = []
for line in f:
if line.startswith('end'):
break
words = line.split()
symbols.append(words[0])
positions.append([float(word) for word in words[1:]])
self.parameters = Parameters.read(self.label + '.ase')
self.atoms = Atoms(symbols, positions,
magmoms=self.parameters.pop('initial_magmoms'))
self.read_results()
def read(self, label):
"""Read results from ABINIT's text-output file."""
# XXX I think we should redo the concept of 'restarting'.
# It makes sense to load a previous calculation as
#
# * static, calculator-independent results
# * an actual calculator capable of calculating
#
# Either of which is simpler than our current mechanism which
# implies both at the same time. Moreover, we don't need
# something like calc.read(label).
#
# What we need for these two purposes is
#
# * calc = MyCalculator.read(basefile)
# (or maybe it should return Atoms with calc attached)
# * results = read_results(basefile, format='abinit')
#
# where basefile determines the file tree.
FileIOCalculator.read(self, label)
self.atoms, self.parameters = io.read_ase_and_abinit_inputs(self.label)
self.results = io.read_results(self.label, self._output_filename())
def read(self, label):
FileIOCalculator.read(self, label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
with open(self.label + '.out') as f:
lines = f.readlines()
self.parameters = Parameters(task='', method='')
p = self.parameters
parm_line = self.read_parameters_from_file(lines)
for keyword in parm_line.split():
if 'RELSCF' in keyword:
p.relscf = float(keyword.split('=')[-1])
elif keyword in self.methods:
p.method = keyword
else:
p.task += keyword + ' '
p.task.rstrip()
self.atoms = self.read_atoms_from_file(lines)
self.read_results()
def read(self, label):
FileIOCalculator.read(self, label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
f = open(self.label + '.nw')
for line in f:
if line.startswith('geometry'):
break
symbols = []
positions = []
for line in f:
if line.startswith('end'):
break
words = line.split()
symbols.append(words[0])
positions.append([float(word) for word in words[1:]])
self.parameters = Parameters.read(self.label + '.ase')
self.atoms = Atoms(symbols, positions,
magmoms=self.parameters.pop('initial_magmoms'))
self.read_results()
def read(self, label=None):
"""Read results from VASP output files.
Files which are read: OUTCAR, CONTCAR and vasprun.xml
Raises ReadError if they are not found"""
if label is None:
label = self.label
FileIOCalculator.read(self, label)
# If we restart, self.parameters isn't initialized
if self.parameters is None:
self.parameters = self.get_default_parameters()
# Check for existence of the necessary output files
for file in ['OUTCAR', 'CONTCAR', 'vasprun.xml']:
filename = os.path.join(self.directory, file)
if not os.path.isfile(filename):
raise ReadError(
'VASP outputfile {} was not found'.format(filename))
# Read atoms
self.atoms = self.read_atoms()
# Build sorting and resorting lists
self.read_sort()
# Read parameters
olddir = os.getcwd()
try:
os.chdir(self.directory)
self.read_incar()
self.read_kpoints()
self.read_potcar()
finally:
os.chdir(olddir)
# Read the results from the calculation
self.read_results()
def read_results(self):
"""Read the results, such as energy, forces, eigenvalues, etc.
"""
FileIOCalculator.read(self, self.label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
with open(self.label + '.out') as f:
lines = f.readlines()
for i, line in enumerate(lines):
if line.find('TOTAL ENERGY') != -1:
self.results['energy'] = float(line.split()[3])
elif line.find('FINAL HEAT OF FORMATION') != -1:
self.final_hof = float(line.split()[5]) * kcal / mol
elif line.find('BOND ORDERS AND VALENCIES') != -1:
bo = []
for k in range(math.ceil(len(self.atoms) / 6)):
if k == 0: kf = 0
else: kf = ((len(self.atoms) + 1) * k - 3 * k * k)
for j in range(min(6, len(self.atoms) - 6 * k - 1)):
bo.append([
line.split()[2 + j]
for line in lines[i + j + 6 + kf + 6 * k:i + 5 +
len(self.atoms) + kf]
])
self.bond_order = [item for sublist in bo for item in sublist]
elif line.find('NO. OF FILLED LEVELS') != -1:
self.nspins = 1
self.no_occ_levels = int(line.split()[-1])
elif line.find('NO. OF ALPHA ELECTRON') != -1:
self.nspins = 2
self.no_alpha_electrons = int(line.split()[-1])
self.no_beta_electrons = int(lines[i + 1].split()[-1])
self.results['magmom'] = abs(self.no_alpha_electrons -
self.no_beta_electrons)
elif line.find('FINAL POINT AND DERIVATIVES') != -1:
nf = [
len(line.split()) == 8
for line in lines[i + 3:i + 3 + 3 * len(self.atoms)]
]
if not False in nf:
self.forces_permission = True
forces = [
-float(line.split()[6])
for line in lines[i + 3:i + 3 + 3 * len(self.atoms)]
]
self.results['forces'] = np.array(forces).reshape(
(-1, 3)) * kcal / mol
else:
self.forces_permission = False
self.results['forces'] = np.array(
np.zeros(3 * len(self.atoms))).reshape((-1, 3))
elif line.find('EIGENVALUES') != -1:
if line.find('ALPHA') != -1:
j = i + 1
eigs_alpha = []
while not lines[j].isspace():
eigs_alpha += [float(eps) for eps in lines[j].split()]
j += 1
elif line.find('BETA') != -1:
j = i + 1
eigs_beta = []
while not lines[j].isspace():
eigs_beta += [float(eps) for eps in lines[j].split()]
j += 1
eigs = np.array([eigs_alpha, eigs_beta]).reshape(2, 1, -1)
self.eigenvalues = eigs
else:
eigs = []
j = i + 1
while not lines[j].isspace():
eigs += [float(e) for e in lines[j].split()]
j += 1
self.eigenvalues = np.array(eigs).reshape(1, 1, -1)
elif line.find('DIPOLE ') != -1:
self.results['dipole'] = np.array(
lines[i + 3].split()[1:1 + 3], float) * Debye
def read(self, label):
"""Used to read the results of a previous calculation if restarting"""
FileIOCalculator.read(self, label)
def read_results(self):
FileIOCalculator.read(self, self.label)
if not os.path.isfile(self.label + '.got'):
raise ReadError
with open(self.label + '.got') as f:
lines = f.readlines()
cycles = -1
self.optimized = None
for i, line in enumerate(lines):
m = re.match(r'\s*Total lattice energy\s*=\s*(\S+)\s*eV', line)
if m:
energy = float(m.group(1))
self.results['energy'] = energy
self.results['free_energy'] = energy
elif line.find('Optimisation achieved') != -1:
self.optimized = True
elif line.find('Final Gnorm') != -1:
self.Gnorm = float(line.split()[-1])
elif line.find('Cycle:') != -1:
cycles += 1
elif line.find('Final Cartesian derivatives') != -1:
s = i + 5
forces = []
while (True):
s = s + 1
if lines[s].find("------------") != -1:
break
if lines[s].find(" s ") != -1:
continue
g = lines[s].split()[3:6]
G = [-float(x) * eV / Ang for x in g]
forces.append(G)
forces = np.array(forces)
self.results['forces'] = forces
elif line.find('Final internal derivatives') != -1:
s = i + 5
forces = []
while (True):
s = s + 1
if lines[s].find("------------") != -1:
break
g = lines[s].split()[3:6]
# Uncomment the section below to separate the numbers when there is no space between them, in the case of long numbers. This prevents the code to break if numbers are too big.
'''for t in range(3-len(g)):
g.append(' ')
for j in range(2):
min_index=[i+1 for i,e in enumerate(g[j][1:]) if e == '-']
if j==0 and len(min_index) != 0:
if len(min_index)==1:
g[2]=g[1]
g[1]=g[0][min_index[0]:]
g[0]=g[0][:min_index[0]]
else:
g[2]=g[0][min_index[1]:]
g[1]=g[0][min_index[0]:min_index[1]]
g[0]=g[0][:min_index[0]]
break
if j==1 and len(min_index) != 0:
g[2]=g[1][min_index[0]:]
g[1]=g[1][:min_index[0]]'''
G = [-float(x) * eV / Ang for x in g]
forces.append(G)
forces = np.array(forces)
self.results['forces'] = forces
elif line.find('Final cartesian coordinates of atoms') != -1:
s = i + 5
positions = []
while True:
s = s + 1
if lines[s].find("------------") != -1:
break
if lines[s].find(" s ") != -1:
continue
xyz = lines[s].split()[3:6]
XYZ = [float(x) * Ang for x in xyz]
positions.append(XYZ)
positions = np.array(positions)
self.atoms.set_positions(positions)
elif line.find('Final stress tensor components') != -1:
res = [0., 0., 0., 0., 0., 0.]
for j in range(3):
var = lines[i + j + 3].split()[1]
res[j] = float(var)
var = lines[i + j + 3].split()[3]
res[j + 3] = float(var)
stress = np.array(res)
self.results['stress'] = stress
elif line.find('Final Cartesian lattice vectors') != -1:
lattice_vectors = np.zeros((3, 3))
s = i + 2
for j in range(s, s + 3):
temp = lines[j].split()
for k in range(3):
lattice_vectors[j - s][k] = float(temp[k])
self.atoms.set_cell(lattice_vectors)
if self.fractional_coordinates is not None:
self.fractional_coordinates = np.array(
self.fractional_coordinates)
self.atoms.set_scaled_positions(
self.fractional_coordinates)
elif line.find('Final fractional coordinates of atoms') != -1:
s = i + 5
scaled_positions = []
while True:
s = s + 1
if lines[s].find("------------") != -1:
break
if lines[s].find(" s ") != -1:
continue
xyz = lines[s].split()[3:6]
XYZ = [float(x) for x in xyz]
scaled_positions.append(XYZ)
self.fractional_coordinates = scaled_positions
self.steps = cycles
def read(self, label):
"""Used to read the results of a previous calculation if restarting"""
FileIOCalculator.read(self, label)
def read(self, label):
FileIOCalculator.read(self, label)
self.read_results()
