def set(self, **kwargs):
"""Set parameters like set(key1=value1, key2=value2, ...).
A dictionary containing the parameters that have been changed
is returned.
The special keyword 'parameters' can be used to read
parameters from a file."""
if 'parameters' in kwargs:
filename = kwargs.pop('parameters')
parameters = Parameters.read(filename)
parameters.update(kwargs)
kwargs = parameters
changed_parameters = {}
for key, value in kwargs.items():
oldvalue = self.parameters.get(key)
if key not in self.parameters or not (value == oldvalue):
if isinstance(oldvalue, dict):
# Special treatment for dictionary parameters:
for name in value:
if name not in oldvalue:
raise KeyError('Unknown subparameter "{}" in '
'dictionary parameter "{}"'.format(
name, key))
oldvalue.update(value)
value = oldvalue
changed_parameters[key] = value
self.parameters[key] = value
return changed_parameters
def read(self, label):
'Read atoms, parameters and calculated results from restart files.'
self.atoms = ase.io.read(label + '_restart.traj')
self.parameters = Parameters.read(label + '_params.ase')
from ase.io.jsonio import read_json
with open(label + '_results.json') as fd:
self.results = read_json(fd)
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(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):
"""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_input(self, label):
""" Read MyMD input and restart file
Initializes self.frames with frame from restart file
and self.parameters with data form input file.
WARNING: This function is not yet properly implemented
"""
# TODO: make it take an arbitrary input filename
self.label = label
# If the input was generated by ASE, it is simple
if False and os.path.isfile(self.label + '.ase'):
self.parameters = Parameters.read(self.label + '.ase')
else:
if not os.path.isfile(self.label + '.inp'):
raise ReadError
f = open(self.label + '.inp')
s = f.readlines()
parse = self.parse_line
p = self.parameters
natoms = int(parse(s[0]))
# mass = float( parse(s[1]) ) #not needed, default in
# read_restart
epsilon = float(parse(s[2]))
sigma = float(parse(s[3]))
rcut = float(parse(s[4]))
box = parse(s[5])
restfile = parse(s[6])
trajfile = parse(s[7])
enerfile = parse(s[8])
nsteps = int(parse(s[9]))
dt = float(parse(s[10]))
nprint = int(parse(s[11]))
# TODO: start parsing the format...
atoms = io.read_restart(label + '.rest')
atoms.set_cell([box, box, box])
if len(atoms) != natoms:
s = "natoms = {} from {} does not match with\n".\
format(natoms, self.label + '.inp')
s = "natoms = {} from restart file {}".\
format(len(atoms), self.label + '.rest')
raise RuntimeError(s)
self.potentials = potentials.LJPotential(
epsilon=epsilon,
sigma=sigma,
rcut=rcut)
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):
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):
"""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)
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):
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)
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
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):
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 set(self, **kwargs):
"""Set all parameters.
Parameters:
kwargs : Dictionary containing the keywords for deMon
"""
# Put in the default arguments.
kwargs = self.default_parameters.__class__(**kwargs)
if 'parameters' in kwargs:
filename = kwargs.pop('parameters')
parameters = Parameters.read(filename)
parameters.update(kwargs)
kwargs = parameters
changed_parameters = {}
for key, value in kwargs.items():
oldvalue = self.parameters.get(key)
if key not in self.parameters or not equal(value, oldvalue):
changed_parameters[key] = value
self.parameters[key] = value
return changed_parameters
def set(self, **kwargs):
"""Set all parameters.
Parameters:
kwargs : Dictionary containing the keywords for deMon
"""
# Put in the default arguments.
kwargs = self.default_parameters.__class__(**kwargs)
if 'parameters' in kwargs:
filename = kwargs.pop('parameters')
parameters = Parameters.read(filename)
parameters.update(kwargs)
kwargs = parameters
changed_parameters = {}
for key, value in kwargs.items():
oldvalue = self.parameters.get(key)
if key not in self.parameters or not equal(value, oldvalue):
changed_parameters[key] = value
self.parameters[key] = value
return changed_parameters
def read(self, label):
'Read atoms, parameters and calculated results from restart files.'
from numpy import array # needed by eval(<label_results.ase>)
self.atoms = ase.io.read(label + '_restart.traj')
self.parameters = Parameters.read(label + '_params.ase')
self.results = eval(open(label + '_results.ase').read())
def read(self, label):
'Read atoms, parameters and calculated results from restart files.'
self.atoms = ase.io.read(label + '_restart.traj')
self.parameters = Parameters.read(label + '_params.ase')
results_txt = open(label + '_results.ase').read()
self.results = eval(results_txt, {'array': np.array})
def read_ase_and_abinit_inputs(label):
with open(label + '.in') as fd:
atoms = read_abinit_in(fd)
parameters = Parameters.read(label + '.ase')
return atoms, parameters
def read(self, label):
'Read atoms, parameters and calculated results from restart files.'
self.atoms = ase.io.read(label + '_restart.traj')
self.parameters = Parameters.read(label + '_params.ase')
results_txt = open(label + '_results.ase').read()
self.results = eval(results_txt, {'array': np.array})
