def run_stage(self):
"""Check for restart, prepare input, submit and direct output to context."""
# Update structure
self.ctx.base_inp['cp2k']['structure'] = self.ctx.structure
# Check if it is needed to restart the calculation and provide the parent folder and new structure
if self.ctx.parent_calc_folder:
self.ctx.base_inp['cp2k']['parent_calc_folder'] = self.ctx.parent_calc_folder
self.ctx.cp2k_param['FORCE_EVAL']['DFT']['SCF']['SCF_GUESS'] = 'RESTART'
self.ctx.cp2k_param['FORCE_EVAL']['DFT']['WFN_RESTART_FILE_NAME'] = './parent_calc/aiida-RESTART.wfn'
else:
self.ctx.cp2k_param['FORCE_EVAL']['DFT']['SCF']['SCF_GUESS'] = 'ATOMIC'
# Overwrite the generated input with the custom cp2k/parameters
if 'parameters' in self.exposed_inputs(Cp2kBaseWorkChain, 'cp2k_base')['cp2k']:
merge_dict(
self.ctx.cp2k_param,
AttributeDict(self.exposed_inputs(Cp2kBaseWorkChain, 'cp2k_base')['cp2k']['parameters'].get_dict()))
self.ctx.base_inp['cp2k']['parameters'] = Dict(dict=self.ctx.cp2k_param).store()
# Update labels
self.ctx.base_inp['metadata'].update({
'label': '{}_{}'.format(self.ctx.stage_tag, self.ctx.settings_tag),
'call_link_label': 'run_{}_{}'.format(self.ctx.stage_tag, self.ctx.settings_tag),
})
self.ctx.base_inp['cp2k']['metadata'].update(
{'label': self.ctx.base_inp['cp2k']['parameters'].get_dict()['GLOBAL']['RUN_TYPE']})
running_base = self.submit(Cp2kBaseWorkChain, **self.ctx.base_inp)
self.report("submitted Cp2kBaseWorkChain for {}/{}".format(self.ctx.stage_tag, self.ctx.settings_tag))
return ToContext(stages=append_(running_base))
def inspect_and_update_stage(self):
"""Update geometry, parent folder and the new &MOTION settings."""
last_stage = self.ctx.stages[-1]
if 'output_structure' in last_stage.outputs:
self.ctx.structure = last_stage.outputs.output_structure
self.report('Structure updated for next stage')
else:
self.report(
'New structure NOT found and NOT updated for next stage')
self.ctx.parent_calc_folder = last_stage.outputs.remote_folder
last_stage.outputs.output_parameters.label = '{}_{}_valid'.format(
self.ctx.stage_tag, self.ctx.settings_tag)
self.ctx.stage_idx += 1
next_stage_tag = 'stage_{}'.format(self.ctx.stage_idx)
if next_stage_tag in self.ctx.protocol:
self.ctx.stage_tag = next_stage_tag
self.ctx.next_stage_exists = True
merge_dict(self.ctx.cp2k_param,
self.ctx.protocol[self.ctx.stage_tag])
else:
self.ctx.next_stage_exists = False
self.report("All stages computed, finishing...")
def setup_multistage(self):
"""Setup initial parameters."""
# Store the workchain inputs in context (to be modified later)
self.ctx.base_inp = AttributeDict(self.exposed_inputs(Cp2kBaseWorkChain, 'cp2k_base'))
# Check if an input parent_calc_folder is provided
if 'parent_calc_folder' in self.inputs:
self.ctx.parent_calc_folder = self.inputs.parent_calc_folder
else:
self.ctx.parent_calc_folder = None
# Read yaml file selected as SinglefileData or chosen with the tag, and overwrite with custom modifications
if 'protocol_yaml' in self.inputs:
self.ctx.protocol = yaml.safe_load(self.inputs.protocol_yaml.open())
else:
thisdir = os.path.dirname(os.path.abspath(__file__))
yamlfullpath = os.path.join(thisdir, 'multistage_protocols', self.inputs.protocol_tag.value + '.yaml')
with open(yamlfullpath, 'r') as stream:
self.ctx.protocol = yaml.safe_load(stream)
merge_dict(self.ctx.protocol, self.inputs.protocol_modify.get_dict())
# Initialize
self.ctx.settings_ok = False
self.ctx.stage_idx = 0
self.ctx.stage_tag = 'stage_{}'.format(self.ctx.stage_idx)
self.ctx.settings_idx = 0
self.ctx.settings_tag = 'settings_{}'.format(self.ctx.settings_idx)
self.ctx.structure = self.inputs.structure
# Resize the unit cell if min(perp_with) < inputs.min_cell_size
self.ctx.resize = check_resize_unit_cell(self.ctx.structure, self.inputs.min_cell_size) # Dict
if self.ctx.resize['nx'] > 1 or self.ctx.resize['ny'] > 1 or self.ctx.resize['nz'] > 1:
resized_struct = resize_unit_cell(self.ctx.structure, self.ctx.resize)
self.ctx.structure = resized_struct
self.report("Unit cell resized by {}x{}x{} (StructureData<{}>)".format(self.ctx.resize['nx'],
self.ctx.resize['ny'],
self.ctx.resize['nz'],
resized_struct.pk))
else:
self.report("Unit cell was NOT resized")
# Generate input parameters and store them
self.ctx.cp2k_param = deepcopy(self.ctx.protocol['settings_0'])
while self.inputs.starting_settings_idx < self.ctx.settings_idx:
# overwrite untill the desired starting setting are obtained
self.ctx.settings_idx += 1
self.ctx.settings_tag = 'settings_{}'.format(self.ctx.settings_idx)
if self.ctx.settings_tag in self.ctx.protocol:
merge_dict(self.ctx.cp2k_param, self.ctx.protocol[self.ctx.settings_tag])
else:
return self.exit_codes.ERROR_MISSING_INITIAL_SETTINGS # pylint: disable=no-member
kinds = get_kinds_section(self.ctx.structure, self.ctx.protocol)
merge_dict(self.ctx.cp2k_param, kinds)
multiplicity = get_input_multiplicity(self.ctx.structure, self.ctx.protocol)
merge_dict(self.ctx.cp2k_param, multiplicity)
merge_dict(self.ctx.cp2k_param, self.ctx.protocol['stage_0'])
def inspect_and_update_settings_stage0(self): # pylint: disable=inconsistent-return-statements
"""Inspect the stage0/settings_{idx} calculation and check if it is
needed to update the settings and resubmint the calculation."""
self.ctx.settings_ok = True
# Settings/structure are bad: there are problems in parsing the output file
# and, most probably, the calculation didn't even start the scf cycles
if 'output_parameters' in self.ctx.stages[-1].outputs:
cp2k_out = self.ctx.stages[-1].outputs.output_parameters
else:
self.report('ERROR_PARSING_OUTPUT')
return self.exit_codes.ERROR_PARSING_OUTPUT # pylint: disable=no-member
# Settings are bad: the SCF did not converge in the final step
if not cp2k_out["motion_step_info"]["scf_converged"][-1]:
self.report("BAD SETTINGS: the SCF did not converge")
self.ctx.settings_ok = False
self.ctx.settings_idx += 1
else:
# SCF converged, but the computed bandgap needs to be checked
self.report("Bandgaps spin1/spin2: {:.3f} and {:.3f} ev".format(
cp2k_out["bandgap_spin1_au"] * HARTREE2EV,
cp2k_out["bandgap_spin2_au"] * HARTREE2EV))
bandgap_thr_ev = self.ctx.protocol['bandgap_thr_ev']
if ot_has_small_bandgap(self.ctx.cp2k_param, cp2k_out,
bandgap_thr_ev):
self.report("BAD SETTINGS: band gap is < {:.3f} eV".format(
bandgap_thr_ev))
self.ctx.settings_ok = False
self.ctx.settings_idx += 1
# Update the settings tag, check if it is available and overwrite
if not self.ctx.settings_ok:
cp2k_out.label = '{}_{}_discard'.format(self.ctx.stage_tag,
self.ctx.settings_tag)
next_settings_tag = 'settings_{}'.format(self.ctx.settings_idx)
if next_settings_tag in self.ctx.protocol:
self.ctx.settings_tag = next_settings_tag
merge_dict(self.ctx.cp2k_param,
self.ctx.protocol[self.ctx.settings_tag])
else:
return self.exit_codes.ERROR_NO_MORE_SETTINGS # pylint: disable=no-member