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Update scripts to aiida 2.6.2 #45

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Update scripts to aiida 2.6.2 #45

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2 changes: 1 addition & 1 deletion 0-preliminary-do-not-run/oxides/1-create-aiida-archive-from-cifs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
STRUCTURES_FULL_GROUP_LABEL = f'acwf-verification/{SET_NAME}/structures'

Structure = DataFactory('structure')
group, _ = orm.Group.objects.get_or_create(label=STRUCTURES_FULL_GROUP_LABEL)
group, _ = orm.Group.collection.get_or_create(label=STRUCTURES_FULL_GROUP_LABEL)

query = orm.QueryBuilder()
query.append(Structure, tag='structure', project=['extras', 'id'])
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2 changes: 1 addition & 1 deletion 0-preliminary-do-not-run/oxides/upload-test-structure.py
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Expand Up @@ -22,7 +22,7 @@
STRUCTURES_FULL_GROUP_LABEL = f'acwf-verification/{set_name}/structures/{code_name}'

Structure = DataFactory('structure')
group, created = orm.Group.objects.get_or_create(label=STRUCTURES_FULL_GROUP_LABEL)
group, created = orm.Group.collection.get_or_create(label=STRUCTURES_FULL_GROUP_LABEL)

if not created and len(group.nodes) > 0:
print(f"Stopping, non-empty group '{STRUCTURES_FULL_GROUP_LABEL}' already exists")
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2 changes: 1 addition & 1 deletion 0-preliminary-do-not-run/unaries/1-create_unaries_structures_group.py
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Expand Up @@ -118,7 +118,7 @@ def get_aiida_structures(alats):
print(f"# {len(existing)} structures already in the group")
print(f"# {len(missing)} structures that I will add to the group")

group, _ = Group.objects.get_or_create(label=AIIDA_GROUP_LABEL)
group, _ = Group.collection.get_or_create(label=AIIDA_GROUP_LABEL)
structures_to_add = [all_structures[extras] for extras in missing]
# I need to store all these structures first
for structure in structures_to_add:
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2 changes: 1 addition & 1 deletion 0-preliminary-do-not-run/unaries/old-sets/1-create_unaries_structures_group-set1.py
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Expand Up @@ -112,7 +112,7 @@ def get_aiida_structures(alats):
print(f"# {len(existing)} structures already in the group")
print(f"# {len(missing)} structures that I will add to the group")

group, _ = Group.objects.get_or_create(label=AIIDA_GROUP_LABEL)
group, _ = Group.collection.get_or_create(label=AIIDA_GROUP_LABEL)
structures_to_add = [all_structures[extras] for extras in missing]
# I need to store all these structures first
for structure in structures_to_add:
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4 changes: 2 additions & 2 deletions 1-preliminary/create_starting_subgroup.py
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Expand Up @@ -39,8 +39,8 @@ def get_plugin_name():
STRUCTURES_FULL_GROUP_LABEL = f'acwf-verification/{SET_NAME}/structures'
STRUCTURES_GROUP_LABEL = f'acwf-verification/{SET_NAME}/structures/{PLUGIN_NAME}'

group = orm.Group.objects.get(label=STRUCTURES_FULL_GROUP_LABEL)
subgroup, _ = orm.Group.objects.get_or_create(label=STRUCTURES_GROUP_LABEL)
group = orm.Group.collection.get(label=STRUCTURES_FULL_GROUP_LABEL)
subgroup, _ = orm.Group.collection.get_or_create(label=STRUCTURES_GROUP_LABEL)

#####################################################################################
## PLUGIN-SPECIFIC PART: ADD THE ELIF FOR YOUR CODE
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2 changes: 1 addition & 1 deletion 2-submit/launch_calculations_qe.py
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Expand Up @@ -74,7 +74,7 @@ def get_inputs_and_processclass_from_extras(self, extras_values):
'sub_process' : { # optional code-dependent overrides
'base': {
'pw': {
'settings' : orm.Dict(dict= {
'settings' : orm.Dict({
'cmdline': ['-nk', '32'],
})
}
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28 changes: 19 additions & 9 deletions 3-analyze/get_results.py
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Expand Up @@ -32,7 +32,7 @@ def extract_from_failed(node):
streses=[]
num_atoms = None
num_attempt_vols = 0
for i in node.get_outgoing(link_type=LinkType.CALL_WORK).all():
for i in node.base.links.get_outgoing(link_type=LinkType.CALL_WORK).all():
num_attempt_vols = num_attempt_vols + 1
if i.node.is_finished_ok:
if num_atoms is None:
Expand Down Expand Up @@ -109,8 +109,8 @@ def get_plugin_name():
progress_bar = tqdm.tqdm(wf_nodes)
for node in progress_bar:
structure = node.inputs.structure
element = structure.extras['element']
configuration = structure.extras['configuration']
element = structure.base.extras.all['element']
configuration = structure.base.extras.all['configuration']

uuid_mapping[f'{element}-{configuration}'] = {
'structure': structure.uuid,
Expand Down Expand Up @@ -141,7 +141,7 @@ def get_plugin_name():
# For successfully finished workflows, collect the data from outputs
if node.process_state.value == 'finished' and node.exit_status == 0:
# Extract volumes and energies for this system
outputs = node.get_outgoing(link_type=LinkType.RETURN).nested()
outputs = node.base.links.get_outgoing(link_type=LinkType.RETURN).nested()
for index, sub_structure in sorted(outputs['structures'].items()):
if num_atoms is None:
num_atoms = len(sub_structure.sites)
Expand All @@ -152,7 +152,7 @@ def get_plugin_name():
volumes.append(sub_structure.get_cell_volume())
energy_node = outputs['total_energies'][index]
energies.append(energy_node.value)
parent_workflows_links = energy_node.get_incoming(link_type=LinkType.RETURN).all()
parent_workflows_links = energy_node.base.links.get_incoming(link_type=LinkType.RETURN).all()
parent_workflows = [
triple.node for triple in parent_workflows_links
if issubclass(triple.node.process_class, CommonRelaxWorkChain)]
Expand Down Expand Up @@ -214,8 +214,13 @@ def get_plugin_name():
bulk_modulus_GPa = bulk_modulus_internal * echarge * 1.0e21
#1 eV/Angstrom3 = 160.21766208 GPa
bulk_modulus_ev_ang3 = bulk_modulus_GPa / 160.21766208
data_to_print[(structure.extras['element'], structure.extras['configuration'])] = (
min_volume, E0, bulk_modulus_GPa, bulk_deriv)
data_to_print[
(
structure.base.extras.all['element'], structure.base.extras.all['configuration']
)
] = (
min_volume, E0, bulk_modulus_GPa, bulk_deriv
)
BM_fit_data = {
'min_volume': min_volume,
'E0': E0,
Expand All @@ -224,11 +229,16 @@ def get_plugin_name():
'residuals': residuals[0]
}
if residuals[0] > 1.e-3:
warning_lines.append(f"WARNING! High fit residuals: {residuals[0]} for {structure.extras['element']} {structure.extras['configuration']}")
warning_lines.append(
f"WARNING! High fit residuals: {residuals[0]} for {structure.base.extras.all['element']} "
f"{structure.base.extras.all['configuration']}"
)
except ValueError:
# If we cannot find a minimum
# Note that BM_fit_data was already set to None at the top
warning_lines.append(f"WARNING! Unable to fit for {structure.extras['element']} {structure.extras['configuration']}")
warning_lines.append(
f"WARNING! Unable to fit for {structure.base.extras.all['element']} {structure.base.extras.all['configuration']}"
)

all_eos_data[f'{element}-{configuration}'] = eos_data
num_atoms_in_sim_cell[f'{element}-{configuration}'] = num_atoms
Expand Down