def launch(dataset_path, group_name, group_description, parse_comments_path,
parse_comments_structure):
print("loading dataset: {} to group: {}".format(dataset_path, group_name))
# Setup/Retrieve the Group
g = Group.objects.get_or_create(name=group_name,
description=group_description)[0]
# Loop over structures in the dataset_path, storing the nodes then adding them to the group
i = 0
while True:
try:
ase_structure = ase.io.read(dataset_path, index=i, format="runner")
except StopIteration:
break
# setup and store the ase structure as an aiida StructureData node
aiida_structure = StructureData()
aiida_structure.set_ase(ase_structure)
aiida_structure_stored = aiida_structure.store()
# add in the dataset_path line if possible
if parse_comments_path:
try:
structure_path = ase_structure.comment.strip().split()[-1][3:]
aiida_structure_stored.set_extra("structure_path",
structure_path)
except AttributeError:
print(
"could not set structure_path on {}".format(ase_structure))
pass
# Add in details of parent structure uuid
if parse_comments_structure:
try:
parent_uuid = ase_structure.comment.strip().split()[-1]
aiida_structure_stored.set_extra("parent_uuid", parent_uuid)
add_parentstructure_extras(aiida_structure_stored, parent_uuid)
except AttributeError:
print("could not set parent_uuid on {}".format(ase_structure))
pass
# add in the chemical formula and number of atoms if possible
try:
aiida_structure_stored.set_extra("num_atoms", len(ase_structure))
aiida_structure_stored.set_extra(
"chem_formula", ase_structure.get_chemical_formula())
except AttributeError:
print("could not set either num_atoms or chemical_formula " \
" on {}".format(ase_structure))
pass
# add the structure to the group
g.add_nodes(aiida_structure_stored)
g.store()
i += 1
def store_asestructure(ase_structure, extras, structure_group, dryrun):
ase_structure = sort(ase_structure)
ase_structure.set_tags(
[0] *
len(ase_structure)) #force AiiDA to use the same kind for each element
# convert any instances of vacancy internal symbol use back to user symbol use
for key in extras:
if extras[key] == VACANCY_INTERNAL_SYMBOL:
extras[key] = VACANCY_USER_SYMBOL
if key == 'matrix_elements':
extras[key] = [
(lambda x: x
if x != VACANCY_INTERNAL_SYMBOL else VACANCY_USER_SYMBOL)(x)
for x in extras[key]
]
# delete all the vacancy sites prior to storage
del ase_structure[[
x.index for x in ase_structure if x.symbol == VACANCY_INTERNAL_SYMBOL
or x.symbol == VACANCY_USER_SYMBOL
]]
alreadyin_group = checkif_structure_alreadyin_group(
ase_structure, structure_group)
if alreadyin_group:
print(("skiping structure, already stored in group: {}".format(
ase_structure)))
return
if dryrun:
print(("structure: {}".format(ase_structure)))
print(("extras: {}".format(extras)))
else:
print(("storing structure: {}".format(ase_structure)))
aiida_structure = StructureData()
aiida_structure.set_ase(ase_structure)
aiida_structure_stored = aiida_structure.store()
for key in extras:
aiida_structure_stored.set_extra(key, extras[key])
aiida_structure_stored.set_extra("num_atoms", len(ase_structure))
aiida_structure_stored.set_extra("chem_formula",
ase_structure.get_chemical_formula())
structure_group.add_nodes(aiida_structure_stored)
print(("{} stored".format(aiida_structure_stored)))
return
def cli(dataset_path, group_name, group_description, parse_comments_path,
parse_comments_structure, dryrun):
print("loading dataset: {} to group: {}".format(dataset_path, group_name))
# Setup/Retrieve the Group
structure_group = Group.objects.get_or_create(
name=group_name, description=group_description)[0]
# Loop over structures in the dataset_path, storing the nodes then adding them to the group
i = 0
while True:
try:
ase_structure = ase.io.read(dataset_path, index=i, format="runner")
except StopIteration:
break
# setup and store the ase structure as an aiida StructureData node
aiida_structure = StructureData()
aiida_structure.set_ase(ase_structure)
extras = {}
# add in the dataset_path line if possible
if parse_comments_path:
try:
structure_path = ase_structure.comment.strip().split()[-1][3:]
extras['structure_path'] = str(structure_path)
except AttributeError:
print(
"could not set structure_path on {}".format(ase_structure))
print(
"Can your version of ase parse comments for runner data?")
pass
# Add in details of parent structure uuid
if parse_comments_structure:
try:
parent_uuid = ase_structure.comment.strip().split()[-1]
aiida_structure.set_extra("parent_uuid", parent_uuid)
add_parentstructure_extras(aiida_structure, parent_uuid)
except AttributeError:
print("could not set parent_uuid on {}".format(ase_structure))
pass
# add the structure to the group
store_asestructure(ase_structure, extras, structure_group, dryrun)
i += 1
