def run_misfit_strain(path, misfit_strain, input_dictionary,
initial_relaxation_input_dictionary, dfpt_incar_settings,
derivative_evaluation_vasp_run_inputs_dictionary,
minima_relaxation_input_dictionary,
epitaxial_relaxation_input_dictionary):
Path.make(path)
species_list = input_dictionary['species_list']
reference_lattice_constant = input_dictionary['reference_lattice_constant']
Nx = input_dictionary['supercell_dimensions_list'][0]
Ny = input_dictionary['supercell_dimensions_list'][1]
Nz = input_dictionary['supercell_dimensions_list'][2]
displacement_finite_differrences_step_size = input_dictionary[
'displacement_finite_differrences_step_size']
perturbation_magnitudes_dictionary = input_dictionary[
'perturbation_magnitudes_dictionary']
a = reference_lattice_constant * (1.0 + misfit_strain)
initial_structure = Perovskite(
supercell_dimensions=[Nx, Ny, Nz],
lattice=[[a * Nx, 0.0, 0.0], [0.0, a * Ny, 0.0],
[
0.0, 0.0, reference_lattice_constant * Nz *
(1.0 + 0.3 * (1.0 - (a / reference_lattice_constant)))
]],
species_list=species_list)
relaxation = VaspRelaxation(
path=Path.join(path, 'relaxation'),
initial_structure=initial_structure,
input_dictionary=initial_relaxation_input_dictionary)
if not relaxation.complete:
relaxation.update()
return False
relaxed_structure = relaxation.final_structure
relaxed_structure_path = Path.join(path, 'output_relaxed_structure')
relaxed_structure.to_poscar_file_path(relaxed_structure_path)
force_calculation_path = Path.join(path, 'dfpt_force_calculation')
kpoints = Kpoints(scheme_string=kpoint_scheme,
subdivisions_list=kpoint_subdivisions_list)
incar = IncarMaker.get_dfpt_hessian_incar(dfpt_incar_settings)
input_set = VaspInputSet(relaxed_structure,
kpoints,
incar,
auto_change_lreal=False,
auto_change_npar=False)
dfpt_force_run = VaspRun(path=force_calculation_path, input_set=input_set)
if not dfpt_force_run.complete:
dfpt_force_run.update()
return False
hessian = Hessian(dfpt_force_run.outcar)
hessian.print_eigenvalues_to_file(Path.join(path, 'output_eigen_values'))
hessian.print_eigen_components_to_file(
Path.join(path, 'output_eigen_components'))
variable_specialty_points_dictionary = input_dictionary[
'variable_specialty_points_dictionary_set'][
misfit_strain] if input_dictionary.has_key(misfit_strain) else {}
derivative_evaluation_path = Path.join(
path, 'expansion_coefficient_calculations')
derivative_evaluator = DerivativeEvaluator(
path=derivative_evaluation_path,
reference_structure=relaxed_structure,
hessian=hessian,
reference_completed_vasp_relaxation_run=relaxation,
vasp_run_inputs_dictionary=
derivative_evaluation_vasp_run_inputs_dictionary,
perturbation_magnitudes_dictionary=perturbation_magnitudes_dictionary,
displacement_finite_differrences_step_size=
displacement_finite_differrences_step_size,
status_file_path=Path.join(path, 'output_derivative_plot_data'),
variable_specialty_points_dictionary=
variable_specialty_points_dictionary)
derivative_evaluator.update()
guessed_minima_data_path = Path.join(path, 'guessed_chromosomes')
minima_path = Path.join(path, 'minima_relaxations')
if Path.exists(guessed_minima_data_path):
minima_relaxer = MinimaRelaxer(
path=minima_path,
reference_structure=relaxed_structure,
reference_completed_vasp_relaxation_run=relaxation,
hessian=hessian,
vasp_relaxation_inputs_dictionary=
minima_relaxation_input_dictionary,
eigen_chromosome_energy_pairs_file_path=guessed_minima_data_path)
minima_relaxer.update()
minima_relaxer.print_status_to_file(
Path.join(path, 'output_minima_relaxations_status'))
if minima_relaxer.complete:
minima_relaxer.print_selected_uniques_to_file(file_path=Path.join(
path, 'output_selected_unique_minima_relaxations'))
sorted_uniques = minima_relaxer.get_sorted_unique_relaxation_data_list(
)
return sorted_uniques
def run_misfit_strain(path, misfit_strain, input_dictionary,
initial_relaxation_input_dictionary, dfpt_incar_settings,
derivative_evaluation_vasp_run_inputs_dictionary,
minima_relaxation_input_dictionary,
epitaxial_relaxation_input_dictionary):
Path.make(path)
guessed_minima_data_path = Path.join(path, 'guessed_chromosomes')
species_list = input_dictionary['species_list']
reference_lattice_constant = input_dictionary['reference_lattice_constant']
Nx = input_dictionary['supercell_dimensions_list'][0]
Ny = input_dictionary['supercell_dimensions_list'][1]
Nz = input_dictionary['supercell_dimensions_list'][2]
displacement_finite_differences_step_size = input_dictionary[
'displacement_finite_differences_step_size']
perturbation_magnitudes_dictionary = input_dictionary[
'perturbation_magnitudes_dictionary']
a = reference_lattice_constant * (1.0 + misfit_strain)
initial_structure = Perovskite(
supercell_dimensions=[Nx, Ny, Nz],
lattice=[[a * Nx, 0.0, 0.0], [0.0, a * Ny, 0.0],
[
0.0, 0.0, reference_lattice_constant * Nz *
(1.0 + 0.3 * (1.0 - (a / reference_lattice_constant)))
]],
species_list=species_list)
relaxation = VaspRelaxation(
path=Path.join(path, 'relaxation'),
initial_structure=initial_structure,
input_dictionary=initial_relaxation_input_dictionary)
if not relaxation.complete:
relaxation.update()
return False
relaxed_structure = relaxation.final_structure
relaxed_structure_path = Path.join(path, 'output_relaxed_structure')
relaxed_structure.to_poscar_file_path(relaxed_structure_path)
force_calculation_path = Path.join(path, 'dfpt_force_calculation')
kpoints = Kpoints(scheme_string=kpoint_scheme,
subdivisions_list=kpoint_subdivisions_list)
incar = IncarMaker.get_dfpt_hessian_incar(dfpt_incar_settings)
input_set = VaspInputSet(relaxed_structure,
kpoints,
incar,
auto_change_lreal=False,
auto_change_npar=False)
input_set.incar['lepsilon'] = True
dfpt_force_run = VaspRun(path=force_calculation_path, input_set=input_set)
if not dfpt_force_run.complete:
dfpt_force_run.update()
return False
hessian = Hessian(dfpt_force_run.outcar)
if input_dictionary['write_hessian_data']:
hessian.print_eigenvalues_to_file(
Path.join(path, 'output_eigen_values'))
hessian.print_eigen_components_to_file(
Path.join(path, 'output_eigen_components'))
hessian.print_mode_effective_charge_vectors_to_file(
Path.join(path, 'output_mode_effective_charge_vectors'),
relaxed_structure)
eigen_structure = EigenStructure(reference_structure=relaxed_structure,
hessian=hessian)
mode_structures_path = Path.join(path, 'mode_rendered_structures')
Path.make(mode_structures_path)
mode_charge_file = File(
Path.join(path, 'output_mode_effective_charge_vectors'))
sorted_eigen_pairs = hessian.get_sorted_hessian_eigen_pairs_list()
for i, structure in enumerate(
eigen_structure.get_mode_distorted_structures_list(
amplitude=0.6)):
if i > 30:
break
structure.to_poscar_file_path(
Path.join(
mode_structures_path, 'u' + str(i + 1) + '_' +
str(round(sorted_eigen_pairs[i].eigenvalue, 2)) + '.vasp'))
structure.lattice = Lattice([[8.0, 0.0, 0.0], [0.0, 8.0, 0.0],
[0.0, 0.0, 8.0]])
mode_charge_file[i] += ' ' + structure.get_spacegroup_string(
symprec=0.2) + ' ' + structure.get_spacegroup_string(
symprec=0.1) + ' ' + structure.get_spacegroup_string(
symprec=0.001)
mode_charge_file.write_to_path()
#sys.exit()
################################################### random structure searcher
if True:
rand_path = Path.join(path, 'random_trials')
Path.make(rand_path)
num_guesses = 1
num_modes = 12
max_amplitude = 0.6
if misfit_strain == 0.02:
eigen_structure = EigenStructure(
reference_structure=relaxed_structure, hessian=hessian)
for i in range(num_guesses):
trial_path = Path.join(rand_path, str(i))
if not Path.exists(trial_path):
initial_structure_trial = eigen_structure.get_random_structure(
mode_count_cutoff=num_modes,
max_amplitude=max_amplitude)
trial_relaxation = VaspRelaxation(
path=trial_path,
initial_structure=initial_structure_trial,
input_dictionary=minima_relaxation_input_dictionary)
else:
trial_relaxation = VaspRelaxation(path=trial_path)
print "Updating random trial relaxation at " + trial_relaxation.path + " Status is " + trial_relaxation.get_status_string(
)
trial_relaxation.update()
if trial_relaxation.complete:
print "Trial " + str(i)
print trial_relaxation.get_data_dictionary()
return None
###################################################
if not Path.exists(guessed_minima_data_path):
variable_specialty_points_dictionary = input_dictionary[
'variable_specialty_points_dictionary_set'][
misfit_strain] if input_dictionary.has_key(
misfit_strain) else {}
derivative_evaluation_path = Path.join(
path, 'expansion_coefficient_calculations')
derivative_evaluator = DerivativeEvaluator(
path=derivative_evaluation_path,
reference_structure=relaxed_structure,
hessian=hessian,
reference_completed_vasp_relaxation_run=relaxation,
vasp_run_inputs_dictionary=
derivative_evaluation_vasp_run_inputs_dictionary,
perturbation_magnitudes_dictionary=
perturbation_magnitudes_dictionary,
displacement_finite_differences_step_size=
displacement_finite_differences_step_size,
status_file_path=Path.join(path, 'output_derivative_plot_data'),
variable_specialty_points_dictionary=
variable_specialty_points_dictionary,
max_displacement_variables=input_dictionary[
'max_displacement_variables'])
derivative_evaluator.update()
else:
minima_path = Path.join(path, 'minima_relaxations')
minima_relaxer = MinimaRelaxer(
path=minima_path,
reference_structure=relaxed_structure,
reference_completed_vasp_relaxation_run=relaxation,
hessian=hessian,
vasp_relaxation_inputs_dictionary=
minima_relaxation_input_dictionary,
eigen_chromosome_energy_pairs_file_path=guessed_minima_data_path,
log_base_path=path,
max_minima=input_dictionary['max_minima'])
minima_relaxer.update()
minima_relaxer.print_status_to_file(
Path.join(path, 'output_minima_relaxations_status'))
if minima_relaxer.complete:
print "Minima relaxer complete: sorting the relaxations to find the lowest energy structure."
#minima_relaxer.print_selected_uniques_to_file(file_path=Path.join(path, 'output_selected_unique_minima_relaxations'))
sorted_uniques = minima_relaxer.get_sorted_unique_relaxation_data_list(
)
return sorted_uniques
'nsw': 1,
'npar': 'Remove',
}
dfpt_force_run = VaspCalculationGenerator(vasp_calculation_input_dictionary)
dfpt_force_run.update()
if not dfpt_force_run.complete:
sys.exit()
hessian = Hessian(dfpt_force_run.outcar)
if input_dictionary['write_hessian_data']:
hessian.print_eigenvalues_to_file(Path.join(path, 'output_eigen_values'))
hessian.print_eigen_components_to_file(
Path.join(path, 'output_eigen_components'))
hessian.print_mode_effective_charge_vectors_to_file(
Path.join(path, 'output_mode_effective_charge_vectors'),
relaxed_structure)
eigen_structure = EigenStructure(reference_structure=relaxed_structure,
hessian=hessian)
mode_structures_path = Path.join(path, 'mode_rendered_structures')
Path.make(mode_structures_path)
mode_charge_file = File(
Path.join(path, 'output_mode_effective_charge_vectors'))
sorted_eigen_pairs = hessian.get_sorted_hessian_eigen_pairs_list()
for i, structure in enumerate(