def gen_input():
os.mkdir(workflow_path)
structure = get_structure_from_pass_path(start_path)
write_workflow_convergence_file(workflow_path, False)
scaled_structure = structure_scaler([
structure
]) # resizes structure to compare with o-vacancy calculations
structure_list, compound_path = get_structures_with_element_removed(
workflow_path, 'O', scaled_structure)
batch_write_input(structure_list,
vasp_input_set=MPRelaxSet,
output_dir=compound_path,
make_dir_if_not_present=True)
for root, dirs, files in os.walk(workflow_path):
for file in files:
if file == 'POTCAR':
kpoints1 = get_kpoints(os.path.join(root, 'POSCAR'), 300)
kpoints2 = get_kpoints(os.path.join(root, 'POSCAR'), 1000)
natoms = len(
Poscar.from_file(os.path.join(root, 'POSCAR')).structure)
convergence_writelines = bulk_convergence(
kpoints1, kpoints2, natoms)
write_vasp_convergence_file(root, convergence_writelines)
def read_input_files(filename, to_scale=True):
if os.path.isdir(workflow_path) == False:
os.mkdir(workflow_path)
paths_list = get_paths_from_file(os.path.join(pwd, filename))
structures = get_structures_from_paths(paths_list)
if to_scale == True:
scaled_structures = structure_scaler(
structures
) # resizes structure to compare with o-vacancy calculations
else:
scaled_structures = structures # for just regular bulk relaxations of Materials Project structures
batch_write_input(scaled_structures,
vasp_input_set=MPRelaxSet,
output_dir=workflow_path,
make_dir_if_not_present=True)
append_to_incars(pwd, tags_to_add)
for root, dirs, files in os.walk(workflow_path):
for file in files:
if file == 'POTCAR':
kpoints1 = get_kpoints(os.path.join(root, 'POSCAR'), 300)
kpoints2 = get_kpoints(os.path.join(root, 'POSCAR'), 1000)
natoms = len(
Poscar.from_file(os.path.join(root, 'POSCAR')).structure)
convergence_writelines = bulk_convergence(
kpoints1, kpoints2, natoms)
write_vasp_convergence_file(root, convergence_writelines)
write_workflow_convergence_file(workflow_path, False)
return
def read_input_files(filename, scale_factors):
if os.path.isdir(workflow_path) == False:
os.mkdir(workflow_path)
paths_list = get_paths_from_file(os.path.join(pwd, filename))
base_structures = []
sub_structures = []
for path in paths_list:
base = Poscar.from_file(path).structure
structures = get_Structures(path, elements_to_ignore)
if structures != None:
sub_structures.append(structures)
base_structures.append(base)
else:
print('No structures to append')
continue
for base_ind in range(len(base_structures)):
compound_parent_directory = str(
base_structures[base_ind].formula).replace(' ', '')
compound_path = os.path.join(workflow_path, compound_parent_directory)
os.mkdir(compound_path)
for structure in sub_structures[base_ind]:
structure_directory = str(structure.formula).replace(' ', '')
structure_path = os.path.join(compound_path, structure_directory)
scaled_structures = []
for sf in scale_factors:
copy = structure.copy()
init_volume = copy.volume
copy.scale_lattice(sf * init_volume)
scaled_structures.append(copy)
batch_write_input(scaled_structures,
vasp_input_set=MPRelaxSet,
output_dir=structure_path,
make_dir_if_not_present=True)
append_to_incars(pwd, tags_to_add)
for root, dirs, files in os.walk(workflow_path):
for file in files:
if file == 'POTCAR':
kpoints1 = get_kpoints(os.path.join(root, 'POSCAR'), 300)
kpoints2 = get_kpoints(os.path.join(root, 'POSCAR'), 1000)
natoms = len(
Poscar.from_file(os.path.join(root, 'POSCAR')).structure)
convergence_writelines = volume_bulk_convergence(
kpoints1, kpoints2)
write_vasp_convergence_file(root, convergence_writelines)
write_workflow_convergence_file(workflow_path, False)
return
def gen_input(scale_factors):
os.mkdir(workflow_path)
start_path = get_previous_pass_path(pwd, workflow_name)
structure = get_structure_from_pass_path(start_path)
write_workflow_convergence_file(workflow_path, False)
init_volume = structure.volume
scaled_structures = []
for sf in scale_factors:
structure.scale_lattice(sf * init_volume)
scaled_structures.append(structure)
batch_write_input(scaled_structures,
vasp_input_set=MPRelaxSet,
output_dir=workflow_path)
for root, dirs, files in os.walk(workflow_path):
for file in files:
if file == 'POTCAR':
kpoints1 = get_kpoints(os.path.join(root, 'POSCAR'), 300)
kpoints2 = get_kpoints(os.path.join(root, 'POSCAR'), 1000)
convergence_writelines = volume_bulk_convergence(
kpoints1, kpoints2)
write_vasp_convergence_file(root, convergence_writelines)
return
def gen_input():
structure = get_structure_from_pass_path(start_path)
if check_magnetism(pwd, structure):
os.mkdir(workflow_path)
write_workflow_convergence_file(workflow_path, False)
mag_structures = MagneticStructureEnumerator(structure)
ordered_structures = mag_structures.ordered_structures[:
max_num_mag_structs]
batch_write_input(ordered_structures,
vasp_input_set=MPRelaxSet,
output_dir=workflow_path)
for root, dirs, files in os.walk(workflow_path):
for file in files:
if file == 'POTCAR':
kpoints1 = get_kpoints(os.path.join(root, 'POSCAR'), 300)
kpoints2 = get_kpoints(os.path.join(root, 'POSCAR'), 1000)
natoms = len(
Poscar.from_file(os.path.join(root,
'POSCAR')).structure)
convergence_writelines = bulk_convergence(
kpoints1, kpoints2, natoms)
write_vasp_convergence_file(root, convergence_writelines)
def generate_input_files(filename, mp_key):
if os.path.isdir(workflow_path) == False:
os.mkdir(workflow_path)
id_list = get_mpids_from_file(os.path.join(pwd, filename))
structures = get_structures_from_materials_project(id_list, mp_key)
for structure in structures:
try:
mag_structures_obj = MagneticStructureEnumerator(structure)
ordered_structures = mag_structures_obj.ordered_structures[:
max_num_mag_structs]
compound_parent_directory = str(structure.formula).replace(' ', '')
compound_path = os.path.join(workflow_path,
compound_parent_directory)
if os.path.isdir(compound_path) == False:
os.mkdir(compound_path)
batch_write_input(ordered_structures,
vasp_input_set=MPRelaxSet,
output_dir=compound_path,
make_dir_if_not_present=True)
except:
print('%s is not magnetic!' %
str(structure.formula).replace(' ', ''))
continue
append_to_incars(pwd, tags_to_add)
for root, dirs, files in os.walk(workflow_path):
for file in files:
if file == 'POTCAR':
kpoints1 = get_kpoints(os.path.join(root, 'POSCAR'), 300)
kpoints2 = get_kpoints(os.path.join(root, 'POSCAR'), 1000)
natoms = len(
Poscar.from_file(os.path.join(root, 'POSCAR')).structure)
convergence_writelines = bulk_convergence(
kpoints1, kpoints2, natoms)
write_vasp_convergence_file(root, convergence_writelines)
write_workflow_convergence_file(workflow_path, False)
return
def gen_input():
os.mkdir(workflow_path)
structure = get_structure_from_pass_path(start_path)
write_workflow_convergence_file(workflow_path, False)
batch_write_input([structure],
vasp_input_set=MPRelaxSet,
output_dir=workflow_path)
for root, dirs, files in os.walk(workflow_path):
for file in files:
if file == 'POTCAR':
kpoints1 = get_kpoints(os.path.join(root, 'POSCAR'), 300)
kpoints2 = get_kpoints(os.path.join(root, 'POSCAR'), 1000)
natoms = len(
Poscar.from_file(os.path.join(root, 'POSCAR')).structure)
convergence_writelines = bulk_convergence(
kpoints1, kpoints2, natoms)
write_vasp_convergence_file(root, convergence_writelines)