def start(self):
"""
Retrieve and initialize paramters of the WorkChain, validate inputs
"""
self.report(
'INFO: Started structure relaxation workflow version {}\n'.format(
self._workflowversion))
self.ctx.info = [] # Collects Hints
self.ctx.warnings = [] # Collects Warnings
self.ctx.errors = [] # Collects Errors
# Pre-initialization of some variables
self.ctx.loop_count = 0 # Counts relax restarts
self.ctx.forces = [] # Collects forces
self.ctx.final_cell = None # The relaxed Bravais matrix
self.ctx.final_atom_positions = None # Relaxed atom positions
self.ctx.pbc = None # Boundary conditions
self.ctx.reached_relax = False # Bool if is relaxed
self.ctx.switch_bfgs = False # Bool if BFGS should be switched on
self.ctx.scf_res = None # Last scf results
self.ctx.final_structure = None # The optimized structure
self.ctx.total_magnetic_moment = None
# initialize the dictionary using defaults if no wf paramters are given
wf_default = copy.deepcopy(self._default_wf_para)
if 'wf_parameters' in self.inputs:
wf_dict = self.inputs.wf_parameters.get_dict()
else:
wf_dict = wf_default
extra_keys = []
for key in wf_dict.keys():
if key not in wf_default.keys():
extra_keys.append(key)
if extra_keys:
error = 'ERROR: input wf_parameters for Relax contains extra keys: {}'.format(
extra_keys)
self.report(error)
return self.exit_codes.ERROR_INVALID_INPUT_PARAM
# extend wf parameters given by user using defaults
for key, val in six.iteritems(wf_default):
wf_dict[key] = wf_dict.get(key, val)
self.ctx.wf_dict = wf_dict
if '49' in wf_dict['atoms_off']:
error = '"49" label for atoms_off is reserved for internal use'
self.report(error)
return self.exit_codes.ERROR_INVALID_INPUT_PARAM
# Check if final scf can be run
run_final = wf_dict.get('run_final_scf', False)
if run_final:
# We need inpgen to be there
input_scf = AttributeDict(
self.exposed_inputs(FleurScfWorkChain, namespace='scf'))
# policy, reuse as much as possible from scf namespace
input_final_scf = input_scf
if 'remote_data' in input_final_scf:
del input_final_scf.remote_data
if 'structure' in input_final_scf:
del input_final_scf.structure
if 'fleurinp' in input_final_scf:
del input_final_scf.fleurinp
if 'wf_parameters' in input_final_scf:
del input_final_scf.wf_parameters
if 'final_scf' in self.inputs:
# Will defaults of namespace override other given options?
input_final_scf_given = AttributeDict(
self.exposed_inputs(FleurScfWorkChain,
namespace='final_scf'))
for key, val in input_final_scf_given.items():
input_final_scf[key] = val
self.ctx.input_final_scf = input_final_scf
if 'inpgen' not in input_scf and 'inpgen' not in input_final_scf:
self.report(
'Error: Wrong input: inpgen missing for final scf.')
return self.exit_codes.ERROR_INPGEN_MISSING
def _generate_calc_job_node(
entry_point_name,
results_folder,
inputs=None,
computer=None,
outputs=None,
outfile_override=None,
):
"""
Generate a CalcJob node with fake retrieved node in the
tests/data
"""
calc_class = CalculationFactory(entry_point_name)
entry_point = format_entry_point_string('aiida.calculations',
entry_point_name)
builder = calc_class.get_builder()
if not computer:
computer = db_test_app.localhost
node = CalcJobNode(computer=computer, process_type=entry_point)
# Monkypatch the inputs
if inputs is not None:
inputs = AttributeDict(inputs)
node.__dict__['inputs'] = inputs
# Add direct inputs, pseudos are omitted
for k, v in inputs.items():
if isinstance(v, Node):
if not v.is_stored:
v.store()
node.add_incoming(v,
link_type=LinkType.INPUT_CALC,
link_label=k)
options = builder.metadata.options
options.update(inputs.metadata.options)
node.set_attribute('input_filename', options.input_filename)
node.set_attribute('seedname', options.seedname)
node.set_attribute('output_filename', options.output_filename)
node.set_attribute('error_filename', 'aiida.err')
node.set_option('resources', {
'num_machines': 1,
'num_mpiprocs_per_machine': 1
})
node.set_option('max_wallclock_seconds', 1800)
node.store()
filepath = this_folder.parent / 'data' / results_folder
retrieved = FolderData()
retrieved.put_object_from_tree(str(filepath.resolve()))
# Apply overriding output files
if outfile_override is not None:
for key, content in outfile_override.items():
if content is None:
retrieved.delete_object(key)
continue
buf = BytesIO(content.encode())
retrieved.put_object_from_filelike(buf, key)
retrieved.add_incoming(node,
link_type=LinkType.CREATE,
link_label='retrieved')
retrieved.store()
if outputs is not None:
for label, out_node in outputs.items():
out_node.add_incoming(node,
link_type=LinkType.CREATE,
link_label=label)
if not out_node.is_stored:
out_node.store()
return node
