def is_valid(self, indices, tag):
"""Checks that the given atom specifiers are correctly given. Does not
yet check that they exist or don't overlap with other subssystems.
"""
# Determine how the atoms are specified: indices, tag or special set
if isinstance(indices, str):
if indices != "remaining":
error("Use \"remaining\" if you want to assign the yet unassigned atoms to a subsystem")
elif (indices is None) and (tag is None):
error("Provide system as indices or tag",)
def is_valid(self, indices, tag):
"""Checks that the given atom specifiers are correctly given. Does not
yet check that they exist or don't overlap with other subssystems.
"""
# Determine how the atoms are specified: indices, tag or special set
if isinstance(indices, str):
if indices != "remaining":
error(
"Use \"remaining\" if you want to assign the yet unassigned atoms to a subsystem"
)
elif (indices is None) and (tag is None):
error("Provide system as indices or tag", )
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 get_bader_charges(atoms, calc, charge_source="all-electron", gridrefinement=4):
"""This function uses an external Bader charge calculator from
http://theory.cm.utexas.edu/henkelman/code/bader/. This tool is
provided also in pysic/tools. Before using this function the bader
executable directory has to be added to PATH.
Parameters:
atoms: ASE Atoms
The structure from which we want to calculate the charges from.
calc: ASE calculator
charge_source: string
Indicates the electron density that is used in charge calculation.
Can be "pseudo" or "all-electron".
gridrefinement: int
The factor by which the calculation grid is densified in charge
calculation.
Returns: numpy array of the atomic charges
"""
# First check that the bader executable is in PATH
if spawn.find_executable("bader") is None:
error((
"Cannot find the \"bader\" executable in PATH. The bader "
"executable is provided in the pysic/tools folder, or it can be "
"downloaded from http://theory.cm.utexas.edu/henkelman/code/bader/. "
"Ensure that the executable is named \"bader\", place it in any "
"directory you want and then add that directory to your system"
"PATH."))
atoms_copy = atoms.copy()
calc.set_atoms(atoms_copy)
if charge_source == "pseudo":
try:
density = np.array(calc.get_pseudo_density())
except AttributeError:
error("The calculator doesn't provide pseudo density.")
if charge_source == "all-electron":
try:
density = np.array(calc.get_all_electron_density(gridrefinement=gridrefinement))
except AttributeError:
error("The calculator doesn't provide all electron density.")
wrk_dir = os.getcwd()+"/.BADERTEMP"
dir_created = False
# Write the density in bader supported units and format
if rank == 0:
# Create temporary folder for calculations
if not os.path.exists(wrk_dir):
os.makedirs(wrk_dir)
dir_created = True
else:
error("Tried to create a temporary folder in " + wrk_dir + ", but the folder already existed. Please remove it manually first.")
rho = density * Bohr**3
write(wrk_dir + '/electron_density.cube', atoms, data=rho)
# Run the bader executable in terminal. The bader executable included
# int pysic/tools has to be in the PATH/PYTHONPATH
command = "cd " + wrk_dir + "; bader electron_density.cube"
subprocess.check_output(command, shell=True)
#os.system("gnome-terminal --disable-factory -e '"+command+"'")
# Wait for the main process to write the file
barrier()
# ASE provides an existing function for attaching the charges to the
# atoms (safe because using a copy). Although we don't want to actually
# attach the charges to anything, we use this function and extract the
# charges later.
bader.attach_charges(atoms_copy, wrk_dir + "/ACF.dat")
# The call for charges was changed between
# ASE 3.6 and 3.7
try:
bader_charges = np.array(atoms_copy.get_initial_charges())
except:
bader_charges = np.array(atoms_copy.get_charges())
# Remove the temporary files
if rank == 0:
if dir_created:
shutil.rmtree(wrk_dir)
return bader_charges
def get_bader_charges(atoms,
calc,
charge_source="all-electron",
gridrefinement=4):
"""This function uses an external Bader charge calculator from
http://theory.cm.utexas.edu/henkelman/code/bader/. This tool is
provided also in pysic/tools. Before using this function the bader
executable directory has to be added to PATH.
Parameters:
atoms: ASE Atoms
The structure from which we want to calculate the charges from.
calc: ASE calculator
charge_source: string
Indicates the electron density that is used in charge calculation.
Can be "pseudo" or "all-electron".
gridrefinement: int
The factor by which the calculation grid is densified in charge
calculation.
Returns: numpy array of the atomic charges
"""
# First check that the bader executable is in PATH
if spawn.find_executable("bader") is None:
error((
"Cannot find the \"bader\" executable in PATH. The bader "
"executable is provided in the pysic/tools folder, or it can be "
"downloaded from http://theory.cm.utexas.edu/henkelman/code/bader/. "
"Ensure that the executable is named \"bader\", place it in any "
"directory you want and then add that directory to your system"
"PATH."))
atoms_copy = atoms.copy()
calc.set_atoms(atoms_copy)
if charge_source == "pseudo":
try:
density = np.array(calc.get_pseudo_density())
except AttributeError:
error("The calculator doesn't provide pseudo density.")
if charge_source == "all-electron":
try:
density = np.array(
calc.get_all_electron_density(gridrefinement=gridrefinement))
except AttributeError:
error("The calculator doesn't provide all electron density.")
wrk_dir = os.getcwd() + "/.BADERTEMP"
dir_created = False
# Write the density in bader supported units and format
if rank == 0:
# Create temporary folder for calculations
if not os.path.exists(wrk_dir):
os.makedirs(wrk_dir)
dir_created = True
else:
error(
"Tried to create a temporary folder in " + wrk_dir +
", but the folder already existed. Please remove it manually first."
)
rho = density * Bohr**3
write(wrk_dir + '/electron_density.cube', atoms, data=rho)
# Run the bader executable in terminal. The bader executable included
# int pysic/tools has to be in the PATH/PYTHONPATH
command = "cd " + wrk_dir + "; bader electron_density.cube"
subprocess.check_output(command, shell=True)
#os.system("gnome-terminal --disable-factory -e '"+command+"'")
# Wait for the main process to write the file
barrier()
# ASE provides an existing function for attaching the charges to the
# atoms (safe because using a copy). Although we don't want to actually
# attach the charges to anything, we use this function and extract the
# charges later.
bader.attach_charges(atoms_copy, wrk_dir + "/ACF.dat")
# The call for charges was changed between
# ASE 3.6 and 3.7
try:
bader_charges = np.array(atoms_copy.get_initial_charges())
except:
bader_charges = np.array(atoms_copy.get_charges())
# Remove the temporary files
if rank == 0:
if dir_created:
shutil.rmtree(wrk_dir)
return bader_charges
def update_charges_van_der_waals(self):
"""Updates the atomic charges by using the electron density within a
sphere of van Der Waals radius.
The charge for each atom in the system is integrated from the electron
density inside the van Der Waals radius of the atom in hand. The link
atoms will affect the distribution of the electron density.
"""
self.timer.start("van Der Waals charge calculation")
# Turn debugging on or off here
debugging = False
atoms_with_links = self.atoms_for_subsystem
calc = self.calculator
# The electron density is calculated from the system with link atoms.
# This way the link atoms can modify the charge distribution
calc.set_atoms(atoms_with_links)
if self.charge_source == "pseudo":
try:
density = np.array(calc.get_pseudo_density())
except AttributeError:
error("The DFT calculator on subsystem \"" + self.name +
"\" doesn't provide pseudo density.")
if self.charge_source == "all-electron":
try:
density = np.array(
calc.get_all_electron_density(gridrefinement=1))
except AttributeError:
error("The DFT calculator on subsystem \"" + self.name +
"\" doesn't provide all electron density.")
# Write the charge density as .cube file for VMD
if debugging:
write('nacl.cube', atoms_with_links, data=density)
grid = self.density_grid
if debugging:
debug_list = []
# The link atoms are at the end of the list
n_atoms = len(atoms_with_links)
projected_charges = np.zeros((1, n_atoms))
for i_atom, atom in enumerate(atoms_with_links):
r_atom = atom.position
z = atom.number
# Get the van Der Waals radius
R = ase.data.vdw.vdw_radii[z]
# Create a 3 x 3 x 3 x 3 array that can be used for vectorized
# operations with the density grid
r_atom_array = np.tile(
r_atom, (grid.shape[0], grid.shape[1], grid.shape[2], 1))
diff = grid - r_atom_array
# Numpy < 1.8 doesn't recoxnize axis argument on norm. This is a
# workaround for diff = np.linalg.norm(diff, axis=3)
diff = np.apply_along_axis(np.linalg.norm, 3, diff)
indices = np.where(diff <= R)
densities = density[indices]
atom_charge = np.sum(densities)
projected_charges[0, i_atom] = atom_charge
if debugging:
debug_list.append((atom, indices, densities))
#DEBUG: Visualize the grid and contributing grid points as atoms
if debugging:
d = Atoms()
d.set_cell(atoms_with_links.get_cell())
# Visualize the integration spheres with atoms
for point in debug_list:
atom = point[0]
indices = point[1]
densities = point[2]
d.append(atom)
print "Atom: " + str(atom.symbol) + ", Density sum: " + str(
np.sum(densities))
print "Density points included: " + str(len(densities))
for i in range(len(indices[0])):
x = indices[0][i]
y = indices[1][i]
z = indices[2][i]
a = Atom('H')
a.position = grid[x, y, z, :]
d.append(a)
view(d)
# Normalize the projected charges according to the electronic charge in
# the whole system excluding the link atom to preserve charge neutrality
atomic_numbers = np.array(atoms_with_links.get_atomic_numbers())
total_electron_charge = -np.sum(atomic_numbers)
total_charge = np.sum(np.array(projected_charges))
projected_charges *= total_electron_charge / total_charge
# Add the nuclear charges and initial charges
projected_charges += atomic_numbers
# Set the calculated charges to the atoms. The call for charges was
# changed between ASE 3.6 and 3.7
try:
self.atoms_for_interaction.set_initial_charges(
projected_charges[0, :].tolist())
except:
self.atoms_for_interaction.set_charges(
projected_charges[0, :].tolist())
self.pseudo_density = density
self.timer.stop()
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 update_charges_van_der_waals(self):
"""Updates the atomic charges by using the electron density within a
sphere of van Der Waals radius.
The charge for each atom in the system is integrated from the electron
density inside the van Der Waals radius of the atom in hand. The link
atoms will affect the distribution of the electron density.
"""
self.timer.start("van Der Waals charge calculation")
# Turn debugging on or off here
debugging = False
atoms_with_links = self.atoms_for_subsystem
calc = self.calculator
# The electron density is calculated from the system with link atoms.
# This way the link atoms can modify the charge distribution
calc.set_atoms(atoms_with_links)
if self.charge_source == "pseudo":
try:
density = np.array(calc.get_pseudo_density())
except AttributeError:
error("The DFT calculator on subsystem \"" + self.name + "\" doesn't provide pseudo density.")
if self.charge_source == "all-electron":
try:
density = np.array(calc.get_all_electron_density(gridrefinement=1))
except AttributeError:
error("The DFT calculator on subsystem \"" + self.name + "\" doesn't provide all electron density.")
# Write the charge density as .cube file for VMD
if debugging:
write('nacl.cube', atoms_with_links, data=density)
grid = self.density_grid
if debugging:
debug_list = []
# The link atoms are at the end of the list
n_atoms = len(atoms_with_links)
projected_charges = np.zeros((1, n_atoms))
for i_atom, atom in enumerate(atoms_with_links):
r_atom = atom.position
z = atom.number
# Get the van Der Waals radius
R = ase.data.vdw.vdw_radii[z]
# Create a 3 x 3 x 3 x 3 array that can be used for vectorized
# operations with the density grid
r_atom_array = np.tile(r_atom, (grid.shape[0], grid.shape[1], grid.shape[2], 1))
diff = grid - r_atom_array
# Numpy < 1.8 doesn't recoxnize axis argument on norm. This is a
# workaround for diff = np.linalg.norm(diff, axis=3)
diff = np.apply_along_axis(np.linalg.norm, 3, diff)
indices = np.where(diff <= R)
densities = density[indices]
atom_charge = np.sum(densities)
projected_charges[0, i_atom] = atom_charge
if debugging:
debug_list.append((atom, indices, densities))
#DEBUG: Visualize the grid and contributing grid points as atoms
if debugging:
d = Atoms()
d.set_cell(atoms_with_links.get_cell())
# Visualize the integration spheres with atoms
for point in debug_list:
atom = point[0]
indices = point[1]
densities = point[2]
d.append(atom)
print "Atom: " + str(atom.symbol) + ", Density sum: " + str(np.sum(densities))
print "Density points included: " + str(len(densities))
for i in range(len(indices[0])):
x = indices[0][i]
y = indices[1][i]
z = indices[2][i]
a = Atom('H')
a.position = grid[x, y, z, :]
d.append(a)
view(d)
# Normalize the projected charges according to the electronic charge in
# the whole system excluding the link atom to preserve charge neutrality
atomic_numbers = np.array(atoms_with_links.get_atomic_numbers())
total_electron_charge = -np.sum(atomic_numbers)
total_charge = np.sum(np.array(projected_charges))
projected_charges *= total_electron_charge/total_charge
# Add the nuclear charges and initial charges
projected_charges += atomic_numbers
# Set the calculated charges to the atoms. The call for charges was
# changed between ASE 3.6 and 3.7
try:
self.atoms_for_interaction.set_initial_charges(projected_charges[0, :].tolist())
except:
self.atoms_for_interaction.set_charges(projected_charges[0, :].tolist())
self.pseudo_density = density
self.timer.stop()
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()