def _write_fdf_arguments(self, f):
"""Write directly given fdf-arguments.
"""
fdf_arguments = self.parameters['fdf_arguments']
fdf_arguments["XC.functional"], \
fdf_arguments["XC.authors"] = self.parameters['xc']
energy_shift = self['energy_shift']
fdf_arguments["PAO.EnergyShift"] = energy_shift
mesh_cutoff = '%.4f eV' % self['mesh_cutoff']
fdf_arguments["MeshCutoff"] = mesh_cutoff
if self['spin'] == 'UNPOLARIZED':
fdf_arguments["SpinPolarized"] = False
elif self['spin'] == 'COLLINEAR':
fdf_arguments["SpinPolarized"] = True
elif self['spin'] == 'FULL':
fdf_arguments["SpinPolarized"] = True
fdf_arguments["NonCollinearSpin"] = True
for key, value in self.allowed_fdf_keywords.items():
if key in fdf_arguments.keys():
if key in self.unit_fdf_keywords:
val = '%.8f %s' % (fdf_arguments[key],
self.unit_fdf_keywords[key])
f.write(format_fdf(key, val))
elif fdf_arguments[key] != value:
f.write(format_fdf(key, fdf_arguments[key]))
def write_input(self, atoms, properties=None, system_changes=None):
"""Write input (fdf)-file.
See calculator.py for further details.
Parameters:
- atoms : The Atoms object to write.
- properties : The properties which should be calculated.
- system_changes : List of properties changed since last run.
"""
# Call base calculator.
FileIOCalculator.write_input(self,
atoms=atoms,
properties=properties,
system_changes=system_changes)
if system_changes is None and properties is None:
return
filename = self.label + '.fdf'
# On any changes, remove all analysis files.
if system_changes is not None:
self.remove_analysis()
# Start writing the file.
with open(filename, 'w') as f:
# Write system name and label.
f.write(format_fdf('SystemName', self.label))
f.write(format_fdf('SystemLabel', self.label))
f.write("\n")
# Write the minimal arg
self._write_species(f, atoms)
self._write_structure(f, atoms)
# First write explicitly given options to
# allow the user to overwrite anything.
self._write_fdf_arguments(f)
# Use the saved density matrix if only 'cell' and 'positions'
# haved changes.
if (system_changes is None
or ('numbers' not in system_changes
and 'initial_magmoms' not in system_changes
and 'initial_charges' not in system_changes)):
f.write(format_fdf('DM.UseSaveDM', True))
# Save density.
if 'density' in properties:
f.write(format_fdf('SaveRho', True))
# Force siesta to return error on no convergence.
# Why?? maybe we don't want to force convergency??
# f.write(format_fdf('SCFMustConverge', True))
self._write_kpts(f)
def write_input(self, atoms, properties=None, system_changes=None):
"""Write input (fdf)-file.
See calculator.py for further details.
Parameters:
- atoms : The Atoms object to write.
- properties : The properties which should be calculated.
- system_changes : List of properties changed since last run.
"""
# Call base calculator.
FileIOCalculator.write_input(
self,
atoms=atoms,
properties=properties,
system_changes=system_changes)
if system_changes is None and properties is None:
return
filename = self.label + '.fdf'
# On any changes, remove all analysis files.
if system_changes is not None:
self.remove_analysis()
# Start writing the file.
with open(filename, 'w') as f:
# First write explicitly given options to
# allow the user to overwrite anything.
self._write_fdf_arguments(f)
# Use the saved density matrix if only 'cell' and 'positions'
# haved changes.
if (system_changes is None or
('numbers' not in system_changes and
'initial_magmoms' not in system_changes and
'initial_charges' not in system_changes)):
f.write(format_fdf('DM.UseSaveDM', True))
# Save density.
if 'density' in properties:
f.write(format_fdf('SaveRho', True))
# Write system name and label.
f.write(format_fdf('SystemName', self.label))
f.write(format_fdf('SystemLabel', self.label))
# Force siesta to return error on no convergence.
f.write(format_fdf('SCFMustConverge', True))
# Write the rest.
self._write_species(f, atoms)
self._write_kpts(f)
self._write_structure(f, atoms)
def _write_fdf_arguments(self, f):
"""Write directly given fdf-arguments.
"""
fdf_arguments = self.parameters['fdf_arguments']
# Early return
if fdf_arguments is None:
return
for key, value in fdf_arguments.iteritems():
if key in self.unit_fdf_keywords.keys():
value = ('%.8f ' % value, self.unit_fdf_keywords[key])
f.write(format_fdf(key, value))
elif key in self.allowed_fdf_keywords:
f.write(format_fdf(key, value))
else:
raise ValueError("%s not in allowed keywords." % key)
def _write_fdf_arguments(self, f):
"""Write directly given fdf-arguments.
"""
fdf_arguments = self.parameters['fdf_arguments']
# Early return
if fdf_arguments is None:
return
for key, value in fdf_arguments.iteritems():
if key in self.unit_fdf_keywords.keys():
value = '%.8f %s' % (value, self.unit_fdf_keywords[key])
f.write(format_fdf(key, value))
elif key in self.allowed_fdf_keywords:
f.write(format_fdf(key, value))
else:
raise ValueError("%s not in allowed keywords." % key)
def _write_structure(self, f, atoms):
"""Translate the Atoms object to fdf-format.
Parameters:
- f: An open file object.
- atoms: An atoms object.
"""
unit_cell = atoms.get_cell()
xyz = atoms.get_positions()
f.write('\n')
f.write(format_fdf('NumberOfAtoms', len(xyz)))
# Write lattice vectors
default_unit_cell = np.eye(3, dtype=float)
if np.any(unit_cell != default_unit_cell):
f.write(format_fdf('LatticeConstant', '1.0 Ang'))
f.write('%block LatticeVectors\n')
for i in range(3):
for j in range(3):
s = string.rjust(' %.15f' % unit_cell[i, j], 16) + ' '
f.write(s)
f.write('\n')
f.write('%endblock LatticeVectors\n')
f.write('\n')
self._write_atomic_coordinates(f, atoms)
# Write magnetic moments.
magmoms = atoms.get_initial_magnetic_moments()
# The DM.InitSpin block must be written to initialize to
# no spin. SIESTA default is FM initialization, if the
# block is not written, but we must conform to the
# atoms object.
if self['spin'] != 'UNPOLARIZED':
f.write('%block DM.InitSpin\n')
for n, M in enumerate(magmoms):
if M != 0:
f.write(' %d %.14f\n' % (n + 1, M))
f.write('%endblock DM.InitSpin\n')
f.write('\n')
def _write_structure(self, f, atoms):
"""Translate the Atoms object to fdf-format.
Parameters:
- f: An open file object.
- atoms: An atoms object.
"""
unit_cell = atoms.get_cell()
xyz = atoms.get_positions()
f.write('\n')
f.write(format_fdf('NumberOfAtoms', len(xyz)))
# Write lattice vectors
default_unit_cell = np.eye(3, dtype=float)
if np.any(unit_cell != default_unit_cell):
f.write(format_fdf('LatticeConstant', '1.0 Ang'))
f.write('%block LatticeVectors\n')
for i in range(3):
for j in range(3):
s = string.rjust(' %.15f' % unit_cell[i, j], 16) + ' '
f.write(s)
f.write('\n')
f.write('%endblock LatticeVectors\n')
f.write('\n')
self._write_atomic_coordinates(f, atoms)
# Write magnetic moments.
magmoms = atoms.get_initial_magnetic_moments()
# The DM.InitSpin block must be written to initialize to
# no spin. SIESTA default is FM initialization, if the
# block is not written, but we must conform to the
# atoms object.
if self['spin'] != 'UNPOLARIZED':
f.write('%block DM.InitSpin\n')
for n, M in enumerate(magmoms):
if M != 0:
f.write(' %d %.14f\n' % (n + 1, M))
f.write('%endblock DM.InitSpin\n')
f.write('\n')
def _write_structure(self, f, atoms):
"""Translate the Atoms object to fdf-format.
Parameters:
- f: An open file object.
- atoms: An atoms object.
"""
cell = atoms.cell
f.write('\n')
if cell.rank in [1, 2]:
raise ValueError('Expected 3D unit cell or no unit cell. You may '
'wish to add vacuum along some directions.')
# Write lattice vectors
if np.any(cell):
f.write(format_fdf('LatticeConstant', '1.0 Ang'))
f.write('%block LatticeVectors\n')
for i in range(3):
for j in range(3):
s = (' %.15f' % cell[i, j]).rjust(16) + ' '
f.write(s)
f.write('\n')
f.write('%endblock LatticeVectors\n')
f.write('\n')
self._write_atomic_coordinates(f, atoms)
# Write magnetic moments.
magmoms = atoms.get_initial_magnetic_moments()
# The DM.InitSpin block must be written to initialize to
# no spin. SIESTA default is FM initialization, if the
# block is not written, but we must conform to the
# atoms object.
if magmoms is not None:
if len(magmoms) == 0:
f.write('#Empty block forces ASE initialization.\n')
f.write('%block DM.InitSpin\n')
if len(magmoms) != 0 and isinstance(magmoms[0], np.ndarray):
for n, Mcart in enumerate(magmoms):
M = cart2sph(Mcart)
if M[0] != 0:
f.write(' %d %.14f %.14f %.14f \n' %
(n + 1, M[0], M[1], M[2]))
elif len(magmoms) != 0 and isinstance(magmoms[0], float):
for n, M in enumerate(magmoms):
if M != 0:
f.write(' %d %.14f \n' % (n + 1, M))
f.write('%endblock DM.InitSpin\n')
f.write('\n')
def _write_species(self, f, atoms):
"""Write input related the different species.
Parameters:
- f: An open file object.
- atoms: An atoms object.
"""
species, species_numbers = self.species(atoms)
if self['pseudo_path'] is not None:
pseudo_path = self['pseudo_path']
elif 'SIESTA_PP_PATH' in os.environ:
pseudo_path = os.environ['SIESTA_PP_PATH']
else:
mess = "Please set the environment variable 'SIESTA_PP_PATH'"
raise Exception(mess)
f.write(format_fdf('NumberOfSpecies', len(species)))
f.write(format_fdf('NumberOfAtoms', len(atoms)))
pao_basis = []
chemical_labels = []
basis_sizes = []
synth_blocks = []
for species_number, spec in enumerate(species):
species_number += 1
symbol = spec['symbol']
atomic_number = atomic_numbers[symbol]
if spec['pseudopotential'] is None:
if self.pseudo_qualifier() == '':
label = symbol
pseudopotential = label + '.psf'
else:
label = '.'.join([symbol, self.pseudo_qualifier()])
pseudopotential = label + '.psf'
else:
pseudopotential = spec['pseudopotential']
label = os.path.basename(pseudopotential)
label = '.'.join(label.split('.')[:-1])
if not os.path.isabs(pseudopotential):
pseudopotential = join(pseudo_path, pseudopotential)
if not os.path.exists(pseudopotential):
mess = "Pseudopotential '%s' not found" % pseudopotential
raise RuntimeError(mess)
name = os.path.basename(pseudopotential)
name = name.split('.')
name.insert(-1, str(species_number))
if spec['ghost']:
name.insert(-1, 'ghost')
atomic_number = -atomic_number
name = '.'.join(name)
pseudo_targetpath = self.getpath(name)
if join(os.getcwd(), name) != pseudopotential:
if islink(pseudo_targetpath) or isfile(pseudo_targetpath):
os.remove(pseudo_targetpath)
symlink_pseudos = self['symlink_pseudos']
if symlink_pseudos is None:
symlink_pseudos = not os.name == 'nt'
if symlink_pseudos:
os.symlink(pseudopotential, pseudo_targetpath)
else:
shutil.copy(pseudopotential, pseudo_targetpath)
if not spec['excess_charge'] is None:
atomic_number += 200
n_atoms = sum(np.array(species_numbers) == species_number)
paec = float(spec['excess_charge']) / n_atoms
vc = get_valence_charge(pseudopotential)
fraction = float(vc + paec) / vc
pseudo_head = name[:-4]
fractional_command = os.environ['SIESTA_UTIL_FRACTIONAL']
cmd = '%s %s %.7f' % (fractional_command,
pseudo_head,
fraction)
os.system(cmd)
pseudo_head += '-Fraction-%.5f' % fraction
synth_pseudo = pseudo_head + '.psf'
synth_block_filename = pseudo_head + '.synth'
os.remove(name)
shutil.copyfile(synth_pseudo, name)
synth_block = read_vca_synth_block(
synth_block_filename,
species_number=species_number)
synth_blocks.append(synth_block)
if len(synth_blocks) > 0:
f.write(format_fdf('SyntheticAtoms', list(synth_blocks)))
label = '.'.join(np.array(name.split('.'))[:-1])
string = ' %d %d %s' % (species_number, atomic_number, label)
chemical_labels.append(string)
if isinstance(spec['basis_set'], PAOBasisBlock):
pao_basis.append(spec['basis_set'].script(label))
else:
basis_sizes.append((" " + label, spec['basis_set']))
f.write((format_fdf('ChemicalSpecieslabel', chemical_labels)))
f.write('\n')
f.write((format_fdf('PAO.Basis', pao_basis)))
f.write((format_fdf('PAO.BasisSizes', basis_sizes)))
f.write('\n')
def write_input(self, atoms, properties=None, system_changes=None):
"""Write input (fdf)-file.
See calculator.py for further details.
Parameters:
- atoms : The Atoms object to write.
- properties : The properties which should be calculated.
- system_changes : List of properties changed since last run.
"""
# Call base calculator.
FileIOCalculator.write_input(
self,
atoms=atoms,
properties=properties,
system_changes=system_changes)
if system_changes is None and properties is None:
return
filename = self.getpath(ext='fdf')
# On any changes, remove all analysis files.
if system_changes is not None:
self.remove_analysis()
# Start writing the file.
with open(filename, 'w') as f:
# Write system name and label.
f.write(format_fdf('SystemName', self.prefix))
f.write(format_fdf('SystemLabel', self.prefix))
f.write("\n")
# Write explicitly given options first to
# allow the user to override anything.
fdf_arguments = self['fdf_arguments']
keys = sorted(fdf_arguments.keys())
for key in keys:
f.write(format_fdf(key, fdf_arguments[key]))
# Force siesta to return error on no convergence.
# as default consistent with ASE expectations.
if 'SCFMustConverge' not in fdf_arguments.keys():
f.write(format_fdf('SCFMustConverge', True))
f.write("\n")
# Write spin level.
f.write(format_fdf('Spin ', self['spin']))
# Spin backwards compatibility.
if self['spin'] == 'collinear':
f.write(format_fdf('SpinPolarized', (True, "# Backwards compatibility.")))
elif self['spin'] == 'non-collinear':
f.write(format_fdf('NonCollinear', (True, "# Backwards compatibility.")))
# Write functional.
functional, authors = self['xc']
f.write(format_fdf('XC.functional', functional))
f.write(format_fdf('XC.authors', authors))
f.write("\n")
# Write mesh cutoff and energy shift.
f.write(format_fdf('MeshCutoff',
(self['mesh_cutoff'], 'eV')))
f.write(format_fdf('PAO.EnergyShift',
(self['energy_shift'], 'eV')))
f.write("\n")
# Write the minimal arg
self._write_species(f, atoms)
self._write_structure(f, atoms)
# Use the saved density matrix if only 'cell' and 'positions'
# have changed.
if (system_changes is None or
('numbers' not in system_changes and
'initial_magmoms' not in system_changes and
'initial_charges' not in system_changes)):
f.write(format_fdf('DM.UseSaveDM', True))
# Save density.
if 'density' in properties:
f.write(format_fdf('SaveRho', True))
self._write_kpts(f)
if self['bandpath'] is not None:
lines = bandpath2bandpoints(self['bandpath'])
f.write(lines)
f.write('\n')
def _write_species(self, f, atoms):
"""Write input related the different species.
Parameters:
- f: An open file object.
- atoms: An atoms object.
"""
energy_shift = '%.4f eV' % self['energy_shift']
f.write('\n')
f.write(format_fdf('PAO_EnergyShift', energy_shift))
mesh_cutoff = '%.4f eV' % self['mesh_cutoff']
f.write(format_fdf('MeshCutoff', mesh_cutoff))
species, species_numbers = self.species(atoms)
if self['spin'] == 'UNPOLARIZED':
f.write(format_fdf('SpinPolarized', False))
elif self['spin'] == 'COLLINEAR':
f.write(format_fdf('SpinPolarized', True))
elif self['spin'] == 'FULL':
f.write(format_fdf('SpinPolarized', True))
f.write(format_fdf('NonCollinearSpin', True))
functional, authors = self.parameters['xc']
f.write('\n')
f.write(format_fdf('XC_functional', functional))
if authors is not None:
f.write(format_fdf('XC_authors', authors))
f.write('\n')
if not self['pseudo_path'] is None:
pseudo_path = self['pseudo_path']
elif 'SIESTA_PP_PATH' in os.environ:
pseudo_path = os.environ['SIESTA_PP_PATH']
else:
mess = "Please set the environment variable 'SIESTA_PP_PATH'"
raise Exception(mess)
f.write(format_fdf('NumberOfSpecies', len(species)))
pao_basis = []
chemical_labels = []
basis_sizes = []
for species_number, specie in enumerate(species):
species_number += 1
symbol = specie['symbol']
atomic_number = atomic_numbers[symbol]
if specie['pseudopotential'] is None:
if self.pseudo_qualifier() == '':
label = symbol
pseudopotential = label + '.psf'
else:
label = '.'.join([symbol, self.pseudo_qualifier()])
pseudopotential = label + '.psf'
else:
pseudopotential = specie['pseudopotential']
label = os.path.basename(pseudopotential)
label = '.'.join(label.split('.')[:-1])
if not os.path.isabs(pseudopotential):
pseudopotential = join(pseudo_path, pseudopotential)
if not os.path.exists(pseudopotential):
mess = "Pseudopotential '%s' not found" % pseudopotential
raise RuntimeError(mess)
name = os.path.basename(pseudopotential)
name = name.split('.')
name.insert(-1, str(species_number))
if specie['ghost']:
name.insert(-1, 'ghost')
atomic_number = -atomic_number
name = '.'.join(name)
if join(os.getcwd(), name) != pseudopotential:
if islink(name) or isfile(name):
os.remove(name)
os.symlink(pseudopotential, name)
label = '.'.join(np.array(name.split('.'))[:-1])
string = ' %d %d %s' % (species_number, atomic_number, label)
chemical_labels.append(string)
if isinstance(specie['basis_set'], PAOBasisBlock):
pao_basis.append(specie['basis_set'].script(label))
else:
basis_sizes.append((label, specie['basis_set']))
f.write((format_fdf('ChemicalSpecieslabel', chemical_labels)))
f.write('\n')
f.write((format_fdf('PAO.Basis', pao_basis)))
f.write((format_fdf('PAO.BasisSizes', basis_sizes)))
f.write('\n')
def _write_species(self, f, atoms):
"""Write input related the different species.
Parameters:
- f: An open file object.
- atoms: An atoms object.
"""
energy_shift = '%.4f eV' % self['energy_shift']
f.write('\n')
f.write(format_fdf('PAO_EnergyShift', energy_shift))
mesh_cutoff = '%.4f eV' % self['mesh_cutoff']
f.write(format_fdf('MeshCutoff', mesh_cutoff))
species, species_numbers = self.species(atoms)
if self['spin'] == 'UNPOLARIZED':
f.write(format_fdf('SpinPolarized', False))
elif self['spin'] == 'COLLINEAR':
f.write(format_fdf('SpinPolarized', True))
elif self['spin'] == 'FULL':
f.write(format_fdf('SpinPolarized', True))
f.write(format_fdf('NonCollinearSpin', True))
functional, authors = self.parameters['xc']
f.write('\n')
f.write(format_fdf('XC_functional', functional))
if authors is not None:
f.write(format_fdf('XC_authors', authors))
f.write('\n')
if not self['pseudo_path'] is None:
pseudo_path = self['pseudo_path']
elif 'SIESTA_PP_PATH' in os.environ:
pseudo_path = os.environ['SIESTA_PP_PATH']
else:
mess = "Please set the environment variable 'SIESTA_PP_PATH'"
raise Exception(mess)
f.write(format_fdf('NumberOfSpecies', len(species)))
pao_basis = []
chemical_labels = []
basis_sizes = []
synth_blocks = []
for species_number, specie in enumerate(species):
species_number += 1
symbol = specie['symbol']
atomic_number = atomic_numbers[symbol]
if specie['pseudopotential'] is None:
if self.pseudo_qualifier() == '':
label = symbol
pseudopotential = label + '.psf'
else:
label = '.'.join([symbol, self.pseudo_qualifier()])
pseudopotential = label + '.psf'
else:
pseudopotential = specie['pseudopotential']
label = os.path.basename(pseudopotential)
label = '.'.join(label.split('.')[:-1])
if not os.path.isabs(pseudopotential):
pseudopotential = join(pseudo_path, pseudopotential)
if not os.path.exists(pseudopotential):
mess = "Pseudopotential '%s' not found" % pseudopotential
raise RuntimeError(mess)
name = os.path.basename(pseudopotential)
name = name.split('.')
name.insert(-1, str(species_number))
if specie['ghost']:
name.insert(-1, 'ghost')
atomic_number = -atomic_number
name = '.'.join(name)
if join(os.getcwd(), name) != pseudopotential:
if islink(name) or isfile(name):
os.remove(name)
os.symlink(pseudopotential, name)
if not specie['excess_charge'] is None:
atomic_number += 200
n_atoms = sum(np.array(species_numbers) == species_number)
paec = float(specie['excess_charge']) / n_atoms
vc = get_valence_charge(pseudopotential)
fraction = float(vc + paec) / vc
pseudo_head = name[:-4]
fractional_command = os.environ['SIESTA_UTIL_FRACTIONAL']
cmd = '%s %s %.7f' % (fractional_command,
pseudo_head,
fraction)
os.system(cmd)
pseudo_head += '-Fraction-%.5f' % fraction
synth_pseudo = pseudo_head + '.psf'
synth_block_filename = pseudo_head + '.synth'
os.remove(name)
shutil.copyfile(synth_pseudo, name)
synth_block = read_vca_synth_block(
synth_block_filename,
species_number=species_number)
synth_blocks.append(synth_block)
if len(synth_blocks) > 0:
f.write(format_fdf('SyntheticAtoms', list(synth_blocks)))
label = '.'.join(np.array(name.split('.'))[:-1])
string = ' %d %d %s' % (species_number, atomic_number, label)
chemical_labels.append(string)
if isinstance(specie['basis_set'], PAOBasisBlock):
pao_basis.append(specie['basis_set'].script(label))
else:
basis_sizes.append((label, specie['basis_set']))
f.write((format_fdf('ChemicalSpecieslabel', chemical_labels)))
f.write('\n')
f.write((format_fdf('PAO.Basis', pao_basis)))
f.write((format_fdf('PAO.BasisSizes', basis_sizes)))
f.write('\n')
