def test_array_equal(a, b, rtol, atol):
assert a is not b
assert equal(a, b, rtol=rtol, atol=atol)
assert equal({'size': a, 'gamma': True},
{'size': b, 'gamma': True}, rtol=rtol, atol=atol)
assert not equal({'size': a, 'gamma': True},
{'size': b, 'gamma': False}, rtol=rtol, atol=atol)
assert not equal({'size': a}, b, rtol=rtol, atol=atol)
assert not equal(a, {'size': b}, rtol=rtol, atol=atol)
def check_state(self, atoms, tol=1e-15):
"""Check for system changes since last calculation."""
from ase.calculators.calculator import all_changes, equal
if self.atoms is None:
system_changes = all_changes[:]
else:
system_changes = []
if not equal(self.atoms.positions, atoms.positions, atol=tol):
system_changes.append('positions')
if not equal(self.atoms.numbers, atoms.numbers):
system_changes.append('numbers')
if not equal(self.atoms.cell, atoms.cell, atol=tol):
system_changes.append('cell')
if not equal(self.atoms.pbc, atoms.pbc):
system_changes.append('pbc')
if not equal(self.atoms.get_initial_magnetic_moments(),
atoms.get_initial_magnetic_moments(),
atol=tol):
system_changes.append('initial_magmoms')
if not equal(self.atoms.get_initial_charges(),
atoms.get_initial_charges(),
atol=tol):
system_changes.append('initial_charges')
return system_changes
def set(self, **kwargs):
"""Set all parameters.
Parameters:
-kwargs : Dictionary containing the keywords defined in
OpenMXParameters.
"""
for key, value in kwargs.items():
if key not in self.default_parameters.keys():
raise KeyError('Unkown keyword "%s" and value "%s".' %
(key, value))
if key == 'xc' and value not in self.default_parameters.allowed_xc:
raise KeyError('Given xc "%s" is not allowed' % value)
if key in ['dat_arguments'] and isinstance(value, dict):
# For values that are dictionaries, verify subkeys, too.
default_dict = self.default_parameters[key]
for subkey in kwargs[key]:
if subkey not in default_dict:
allowed = ', '.join(list(default_dict.keys()))
raise TypeError('Unknown subkeyword "{0}" of keyword '
'"{1}". Must be one of: {2}'.format(
subkey, key, allowed))
# Find out what parameter has been changed
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
# Set the parameters
for key, value in kwargs.items():
# print(' Setting the %s as %s'%(key, value))
self.parameters[key] = value
# If Changed Parameter is Critical, we have to reset the results
for key, value in changed_parameters.items():
if key in ['xc', 'kpts', 'energy_cutoff']:
self.results = {}
value = kwargs.get('energy_cutoff')
if value is not None and not (isinstance(value,
(float, int)) and value > 0):
mess = "'%s' must be a positive number(in eV), \
got '%s'" % ('energy_cutoff', value)
raise ValueError(mess)
atoms = kwargs.get('atoms')
if atoms is not None and self.atoms is None:
self.atoms = atoms.copy()
def my_set(self, **kwargs):
"""Set parameters like set(key1=value1, key2=value2, ...).
A dictionary containing the parameters that have been changed
is returned.
Subclasses must implement a set() method that will look at the
chaneged parameters and decide if a call to reset() is needed.
If the changed parameters are harmless, like a change in
verbosity, then there is no need to call reset().
The special keyword 'parameters' can be used to read
parameters from a file."""
from ase.calculators.calculator import equal
with open('ts_data_EPB.txt', 'a') as tempText:
tempText.write('\n Entering my Vasp.set() method. - EPB')
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)
with open('ts_data_EPB.txt', 'a') as tempText:
tempText.write(
f" self.parameters['{key}'] = {oldvalue}; new value = {value}\n"
)
if key not in self.parameters or not equal(value, oldvalue):
changed_parameters[key] = value
self.parameters[key] = value
if self.discard_results_on_any_change and changed_parameters:
self.reset()
with open('ts_data_EPB.txt', 'a') as tempText:
tempText.write('\n Exiting my Vasp.set() method. - EPB')
return changed_parameters
def get_terminations(self, slab, layers):
'''
determine how many terminations for a surface index
for a slab with SrO, TiO2, SrO, TiO2 ... ordering, there will be two terminations
'SrO' and 'TiO2'
Search from the top to the bottom
'''
from ase.build import minimize_rotation_and_translation
from ase.calculators.calculator import compare_atoms, equal
import pprint
nlayer = max(layers) + 1
terminations = {}
natoms = len(slab)
for i in range(nlayer - 2, 0, -1):
atoms = slab[layers == i]
formula = atoms.get_chemical_formula(mode='hill')
print(formula)
inds = [
j for j in range(natoms)
if layers[j] in range(i, i - self.nlayer, -1)
]
atoms = slab[inds]
atoms.wrap()
if not terminations:
terminations['%s-%s' % (formula, i)] = atoms.copy()
else:
flag = True
atoms1 = atoms.copy()
for ter, atoms2 in terminations.items():
if len(atoms1) != len(atoms2):
flag = False
else:
minimize_rotation_and_translation(atoms2, atoms1)
if equal(atoms1.arrays, atoms2.arrays, tol=0.1):
flag = False
if flag:
terminations['%s-%s' % (formula, i)] = atoms.copy()
print(formula, ter)
# view([atoms1, atoms2])
pprint.pprint(terminations)
# view(terminations.values())
return terminations
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 set(self, **kwargs):
"""Sets parameters list and determines if calculation needs to be reset
*for now it is reset if any parameters change*
"""
# Read parameters from 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 equal(value, oldvalue):
changed_parameters[key] = value
self.parameters[key] = value
if changed_parameters:
self.reset()
return changed_parameters
def check_state(self, atoms, tol=1e-15):
"""Check for system changes since last calculation."""
from ase.calculators.calculator import all_changes, equal
if self.atoms is None:
system_changes = all_changes[:]
else:
system_changes = []
if not equal(self.atoms.positions, atoms.positions, tol):
system_changes.append('positions')
if not equal(self.atoms.numbers, atoms.numbers):
system_changes.append('numbers')
if not equal(self.atoms.cell, atoms.cell, tol):
system_changes.append('cell')
if not equal(self.atoms.pbc, atoms.pbc):
system_changes.append('pbc')
if not equal(self.atoms.get_initial_magnetic_moments(),
atoms.get_initial_magnetic_moments(), tol):
system_changes.append('initial_magmoms')
if not equal(self.atoms.get_initial_charges(),
atoms.get_initial_charges(), tol):
system_changes.append('initial_charges')
return system_changes
def test_array_almost_equal(a, b, rtol, atol):
assert a is not b
assert equal(a, b, rtol=rtol, atol=atol)
assert equal({'size': a, 'gamma': True},
{'size': b, 'gamma': True}, rtol=rtol, atol=atol)
def test_single_value(a, b, rtol, atol):
assert equal(a, b, rtol=rtol, atol=atol)
