def set_parameters(self, params):
"""Sets the numeric values of all parameters.
Equivalent to :meth:`~pysic.interactions.bondorder.BondOrderParameters.set_parameter_values`.
Parameters:
params: list of doubles
list of values to be assigned to parameters
"""
if self.accepts_parameters(params):
self.parameters = params
else:
new_params = [[], []]
if len(params) == self.n_params[0] + self.n_params[1]:
new_params[0] = params[0:self.n_params[0]]
new_params[1] = params[self.n_params[0]:self.n_params[1]]
if self.accepts_parameters(new_params):
warn("Using parameters \n"+str(new_params)+\
"\ninstead of \n"+str(params),3)
self.parameters = new_params
else:
raise InvalidParametersError(
'The bond order factor "{bof}" requires {num} parameters.'.
format(bof=self.bond_order_type, num=str(self.n_params)))
def set_parameters(self, params):
"""Sets the numeric values of all parameters.
Equivalent to :meth:`~pysic.interactions.bondorder.BondOrderParameters.set_parameter_values`.
Parameters:
params: list of doubles
list of values to be assigned to parameters
"""
if self.accepts_parameters(params):
self.parameters = params
else:
new_params = [[], []]
if len(params) == self.n_params[0] + self.n_params[1]:
new_params[0] = params[0 : self.n_params[0]]
new_params[1] = params[self.n_params[0] : self.n_params[1]]
if self.accepts_parameters(new_params):
warn("Using parameters \n" + str(new_params) + "\ninstead of \n" + str(params), 3)
self.parameters = new_params
else:
raise InvalidParametersError(
'The bond order factor "{bof}" requires {num} parameters.'.format(
bof=self.bond_order_type, num=str(self.n_params)
)
)
def get_pseudo_density(self):
"""Returns the electron pseudo density if available.
"""
if self.pseudo_density is not None:
return copy.copy(self.pseudo_density)
else:
if hasattr(self.calculator, "get_pseudo_density"):
return copy.copy(self.calculator.get_pseudo_density(self.atoms_for_subsystem))
else:
warn("The pseudo density for subsystem \"" + self.name + "\" is not available.", 2)
def get_pseudo_density(self):
"""Returns the electron pseudo density if available.
"""
if self.pseudo_density is not None:
return copy.copy(self.pseudo_density)
else:
if hasattr(self.calculator, "get_pseudo_density"):
return copy.copy(
self.calculator.get_pseudo_density(
self.atoms_for_subsystem))
else:
warn(
"The pseudo density for subsystem \"" + self.name +
"\" is not available.", 2)
def enable_charge_calculation(self,
division="Bader",
source="all-electron",
gridrefinement=4):
"""Enable the dynamic calculation of atom-centered charges with the
specified algorithm and from the specified electron density. These
charges are only used for the interaction between other subsystems.
Parameters:
division: string
Indicates the division algorithm that is used. Available options are:
- "Bader": Bader algorithm
- "van Der Waals": Spheres with van Der Waals radius
source: string
Indicates what type of electron density is used. Available
options are:
- "pseudo": Use the pseudo electron density provided by all ASE DFT calculators
- "all-electron": Use the all-electron density provided by at least GPAW
gridrefinement: int
Indicates the subdivision that is used for the all-electron
density. Can be other than unity only for Bader algorithm with
all-electron density.
"""
divisions = ["Bader", "van Der Waals"]
charge_sources = ["pseudo", "all-electron"]
if division not in divisions:
error("Invalid division algorithm: " + division)
if source not in charge_sources:
error("Invalid source for electron density: " + source)
if gridrefinement != 1:
if (division != "Bader") or (division == "Bader"
and source != "all-electron"):
warn(
"The gridrefinement is available only for the Bader algorithm with all-electron density, it is ignored.",
3)
self.charge_calculation_enabled = True
self.division = division
self.charge_source = source
self.gridrefinement = gridrefinement
def enable_charge_calculation(self, division="Bader", source="all-electron", gridrefinement=4):
"""Enable the dynamic calculation of atom-centered charges with the
specified algorithm and from the specified electron density. These
charges are only used for the interaction between other subsystems.
Parameters:
division: string
Indicates the division algorithm that is used. Available options are:
- "Bader": Bader algorithm
- "van Der Waals": Spheres with van Der Waals radius
source: string
Indicates what type of electron density is used. Available
options are:
- "pseudo": Use the pseudo electron density provided by all ASE DFT calculators
- "all-electron": Use the all-electron density provided by at least GPAW
gridrefinement: int
Indicates the subdivision that is used for the all-electron
density. Can be other than unity only for Bader algorithm with
all-electron density.
"""
divisions = ["Bader", "van Der Waals"]
charge_sources = ["pseudo", "all-electron"]
if division not in divisions:
error("Invalid division algorithm: " + division)
if source not in charge_sources:
error("Invalid source for electron density: " + source)
if gridrefinement != 1:
if (division != "Bader") or (division == "Bader" and source != "all-electron"):
warn("The gridrefinement is available only for the Bader algorithm with all-electron density, it is ignored.", 3)
self.charge_calculation_enabled = True
self.division = division
self.charge_source = source
self.gridrefinement = gridrefinement
def __init__(self, atoms, info, index_map, reverse_index_map, n_atoms):
"""
Parameters:
atoms: ASE Atoms
The subsystem atoms.
info: SubSystem object
Contains all the information about the subsystem
index_map: dictionary of int to int
The keys are the atom indices in the full system, values are
indices in the subssystem.
reverse_index_map: dicitonary of int to int
The keys are the atom indices in the subsystem, values are the
keys in the full system.
n_atoms: int
Number of atoms in the full system.
"""
# Extract data from info
self.name = info.name
self.calculator = copy.copy(info.calculator)
self.cell_size_optimization_enabled = info.cell_size_optimization_enabled
self.cell_padding = info.cell_padding
self.charge_calculation_enabled = info.charge_calculation_enabled
self.charge_source = info.charge_source
self.division = info.division
self.gridrefinement = info.gridrefinement
self.n_atoms = n_atoms
self.atoms_for_interaction = atoms.copy()
self.atoms_for_subsystem = atoms.copy()
self.index_map = index_map
self.reverse_index_map = reverse_index_map
self.potential_energy = None
self.forces = None
self.density_grid = None
self.pseudo_density = None
self.link_atom_indices = []
self.timer = Timer([
"Bader charge calculation", "van Der Waals charge calculation",
"Energy", "Forces", "Density grid update", "Cell minimization"
])
# The older ASE versions do not support get_initial_charges()
try:
charges = np.array(atoms.get_initial_charges())
except:
charges = np.array(atoms.get_charges())
self.initial_charges = charges
## Can't enable charge calculation on non-DFT calculator
self.dft_system = hasattr(self.calculator, "get_pseudo_density")
if self.charge_calculation_enabled is True and not self.dft_system:
error("Can't enable charge calculation on non-DFT calculator!")
# If the cell size minimization flag has been enabled, then try to reduce the
# cell size
if self.cell_size_optimization_enabled:
pbc = atoms.get_pbc()
if pbc[0] or pbc[1] or pbc[2]:
warn(("Cannot optimize cell size when periodic boundary"
"condition have been enabled, disabling optimization."),
2)
self.cell_size_optimization_enabled = False
else:
self.optimize_cell()
def __init__(self, atoms, info, index_map, reverse_index_map, n_atoms):
"""
Parameters:
atoms: ASE Atoms
The subsystem atoms.
info: SubSystem object
Contains all the information about the subsystem
index_map: dictionary of int to int
The keys are the atom indices in the full system, values are
indices in the subssystem.
reverse_index_map: dicitonary of int to int
The keys are the atom indices in the subsystem, values are the
keys in the full system.
n_atoms: int
Number of atoms in the full system.
"""
# Extract data from info
self.name = info.name
self.calculator = copy.copy(info.calculator)
self.cell_size_optimization_enabled = info.cell_size_optimization_enabled
self.cell_padding = info.cell_padding
self.charge_calculation_enabled = info.charge_calculation_enabled
self.charge_source = info.charge_source
self.division = info.division
self.gridrefinement = info.gridrefinement
self.n_atoms = n_atoms
self.atoms_for_interaction = atoms.copy()
self.atoms_for_subsystem = atoms.copy()
self.index_map = index_map
self.reverse_index_map = reverse_index_map
self.potential_energy = None
self.forces = None
self.density_grid = None
self.pseudo_density = None
self.link_atom_indices = []
self.timer = Timer([
"Bader charge calculation",
"van Der Waals charge calculation",
"Energy",
"Forces",
"Density grid update",
"Cell minimization"])
# The older ASE versions do not support get_initial_charges()
try:
charges = np.array(atoms.get_initial_charges())
except:
charges = np.array(atoms.get_charges())
self.initial_charges = charges
## Can't enable charge calculation on non-DFT calculator
self.dft_system = hasattr(self.calculator, "get_pseudo_density")
if self.charge_calculation_enabled is True and not self.dft_system:
error("Can't enable charge calculation on non-DFT calculator!")
# If the cell size minimization flag has been enabled, then try to reduce the
# cell size
if self.cell_size_optimization_enabled:
pbc = atoms.get_pbc()
if pbc[0] or pbc[1] or pbc[2]:
warn(("Cannot optimize cell size when periodic boundary"
"condition have been enabled, disabling optimization."), 2)
self.cell_size_optimization_enabled = False
else:
self.optimize_cell()