def get_nebs_analysis(cls, wf):
assert wf.metadata['workflow_class'] == cls.workflow_class
assert wf.metadata['workflow_module'] == cls.workflow_module
terminal_start_step_index = -1
terminal_start_final_fw_id = None
terminal_end_step_index = -1
terminal_end_final_fw_id = None
neb_tasks_step_index = {}
neb_tasks_step_final_fw_id = {}
neb_setup_tasks_step_index = {}
neb_setup_tasks_step_final_fw_id = {}
for fw_id, fw in wf.id_fw.items():
if 'SRC_task_index' in fw.spec:
src_type = fw.tasks[-1].src_type
if src_type in ['run', 'setup']:
task_index = fw.spec['SRC_task_index']
match = re.match("neb\d+$", task_index.task_type)
if match and match.string == task_index.task_type:
if src_type == 'run':
if task_index.task_type not in neb_tasks_step_index:
neb_tasks_step_index[task_index.task_type] = task_index.index
neb_tasks_step_final_fw_id[task_index.task_type] = fw_id
else:
if task_index.index > neb_tasks_step_index[task_index.task_type]:
neb_tasks_step_index[task_index.task_type] = task_index.index
neb_tasks_step_final_fw_id[task_index.task_type] = fw_id
elif src_type == 'setup':
if task_index.task_type not in neb_setup_tasks_step_index:
neb_setup_tasks_step_index[task_index.task_type] = task_index.index
neb_setup_tasks_step_final_fw_id[task_index.task_type] = fw_id
else:
if task_index.index > neb_setup_tasks_step_index[task_index.task_type]:
neb_setup_tasks_step_index[task_index.task_type] = task_index.index
neb_setup_tasks_step_final_fw_id[task_index.task_type] = fw_id
elif task_index.task_type == 'MPRelaxVasp-start':
if src_type == 'run':
if task_index.index > terminal_start_step_index:
terminal_start_step_index = task_index.index
terminal_start_final_fw_id = fw_id
elif task_index.task_type == 'MPRelaxVasp-end':
if src_type == 'run':
if task_index.index > terminal_end_step_index:
terminal_end_step_index = task_index.index
terminal_end_final_fw_id = fw_id
if terminal_start_final_fw_id is None:
raise RuntimeError('No terminal-start relaxation found ...')
if terminal_end_final_fw_id is None:
raise RuntimeError('No terminal-end relaxation found ...')
if len(neb_tasks_step_index) == 0:
raise RuntimeError('No NEB analysis found ...')
# Terminal start dir
terminal_start_fw = wf.id_fw[terminal_start_final_fw_id]
terminal_start_last_launch = (terminal_start_fw.archived_launches + terminal_start_fw.launches)[-1]
terminal_start_run_dir = terminal_start_last_launch.launch_dir
# Terminal end dir
terminal_end_fw = wf.id_fw[terminal_end_final_fw_id]
terminal_end_last_launch = (terminal_end_fw.archived_launches + terminal_end_fw.launches)[-1]
terminal_end_run_dir = terminal_end_last_launch.launch_dir
nebs_analysis = []
nebs_calculations_parameters = []
helper = MPNEBTaskHelper()
for ineb in range(1, len(neb_tasks_step_index)+1):
neb_task_type = 'neb{:d}'.format(ineb)
nebfw = wf.id_fw[neb_tasks_step_final_fw_id[neb_task_type]]
last_launch = (nebfw.archived_launches + nebfw.launches)[-1]
neb_analysis = NEBAnalysis.from_dir(last_launch.launch_dir,
relaxation_dirs=(terminal_start_run_dir, terminal_end_run_dir))
nebs_analysis.append(neb_analysis)
nebsetupfw = wf.id_fw[neb_setup_tasks_step_final_fw_id[neb_task_type]]
nebsetuptask = nebsetupfw.tasks[-1]
neb_vasp_input_set = nebsetuptask.vasp_input_set
kpoints_generation_description = get_kpoints_generation_description(neb_vasp_input_set)
neb_task = nebfw.tasks[-1]
last_launch = (nebfw.archived_launches + nebfw.launches)[-1]
helper.set_task(neb_task)
helper.task.setup_rundir(last_launch.launch_dir)
vasprun = helper.get_vasprun()
if vasprun == 'vasprun.xml malformed':
incar = helper.get_incar()
calculation_parameters = {'origin': 'incar',
'INCAR': incar,
'INCAR_ALL': 'unknown',
'potcar_symbols': 'unknown',
'ENCUT': incar.get('ENCUT', 'DEFAULT'),
'EDIFFG': incar.get('EDIFFG', 'DEFAULT'),
'ISMEAR': incar.get('ISMEAR', 'DEFAULT'),
'SIGMA': incar.get('SIGMA', 'DEFAULT'),
'kpoints_generation_description': kpoints_generation_description}
else:
calculation_parameters = {'origin': 'vasprun.xml',
'INCAR': vasprun.incar,
'INCAR_ALL': vasprun.parameters,
'potcar_symbols': vasprun.potcar_symbols,
'ENCUT': vasprun.incar['ENCUT'] or vasprun.parameters['ENCUT'],
'EDIFFG': vasprun.incar.get('EDIFFG') or vasprun.parameters.get('EDIFFG'),
'ISMEAR': vasprun.incar.get('ISMEAR') or vasprun.parameters.get('ISMEAR'),
'SIGMA': vasprun.incar.get('SIGMA') or vasprun.parameters.get('SIGMA'),
'kpoints_generation_description': kpoints_generation_description}
nebs_calculations_parameters.append(calculation_parameters)
return {'nebs_analysis': [neb_analysis.as_dict() for neb_analysis in nebs_analysis],
'nebs_calculations_parameters': nebs_calculations_parameters}
def get_terminal_computed_entries(cls, wf):
assert wf.metadata['workflow_class'] == cls.workflow_class
assert wf.metadata['workflow_module'] == cls.workflow_module
terminal_start_step_index = -1
terminal_start_final_fw_id = None
terminal_start_setup_step_index = -1
terminal_start_setup_fw_id = None
terminal_end_step_index = -1
terminal_end_final_fw_id = None
terminal_end_setup_step_index = -1
terminal_end_setup_fw_id = None
for fw_id, fw in wf.id_fw.items():
if 'SRC_task_index' in fw.spec:
src_type = fw.tasks[-1].src_type
if src_type in ['run', 'setup']:
task_index = fw.spec['SRC_task_index']
if task_index.task_type == 'MPRelaxVasp-start':
if src_type == 'run':
if task_index.index > terminal_start_step_index:
terminal_start_step_index = task_index.index
terminal_start_final_fw_id = fw_id
elif src_type == 'setup':
if task_index.index > terminal_start_setup_step_index:
terminal_start_setup_step_index = task_index.index
terminal_start_setup_fw_id = fw_id
elif task_index.task_type == 'MPRelaxVasp-end':
if src_type == 'run':
if task_index.index > terminal_end_step_index:
terminal_end_step_index = task_index.index
terminal_end_final_fw_id = fw_id
elif src_type == 'setup':
if task_index.index > terminal_end_setup_step_index:
terminal_end_setup_step_index = task_index.index
terminal_end_setup_fw_id = fw_id
if terminal_start_final_fw_id is None:
raise RuntimeError('No terminal-start relaxation found ...')
if terminal_end_final_fw_id is None:
raise RuntimeError('No terminal-end relaxation found ...')
# Terminal start dir
terminal_start_fw = wf.id_fw[terminal_start_final_fw_id]
terminal_start_last_launch = (terminal_start_fw.archived_launches + terminal_start_fw.launches)[-1]
terminal_start_run_dir = terminal_start_last_launch.launch_dir
# Terminal end dir
terminal_end_fw = wf.id_fw[terminal_end_final_fw_id]
terminal_end_last_launch = (terminal_end_fw.archived_launches + terminal_end_fw.launches)[-1]
terminal_end_run_dir = terminal_end_last_launch.launch_dir
helper = MPRelaxTaskHelper()
# Get the information for the terminal start
terminal_start_task = terminal_start_fw.tasks[-1]
helper.set_task(terminal_start_task)
helper.task.setup_rundir(terminal_start_run_dir)
terminal_start_all_info = helper.get_all_info(raise_error=True)
terminal_start_setup_fw = wf.id_fw[terminal_start_setup_fw_id]
terminal_start_setup_task = terminal_start_setup_fw.tasks[-1]
terminal_start_vasp_input_set = terminal_start_setup_task.vasp_input_set
terminal_start_kpts_generation_description = get_kpoints_generation_description(terminal_start_vasp_input_set)
terminal_start_computed_entry = terminal_start_all_info['computed_entry']
terminal_start_vasprun = terminal_start_all_info['vasprun']
terminal_start_calculation_parameters = {'INCAR': terminal_start_vasprun.incar,
'INCAR_ALL': terminal_start_vasprun.parameters,
'potcar_symbols': terminal_start_vasprun.potcar_symbols,
'ENCUT': terminal_start_vasprun.incar['ENCUT'] or terminal_start_vasprun.parameters['ENCUT'],
'EDIFFG': terminal_start_vasprun.incar.get('EDIFFG') or terminal_start_vasprun.parameters.get('EDIFFG'),
'ISMEAR': terminal_start_vasprun.incar.get('ISMEAR') or terminal_start_vasprun.parameters.get('ISMEAR'),
'SIGMA': terminal_start_vasprun.incar.get('SIGMA') or terminal_start_vasprun.parameters.get('SIGMA'),
'kpoints_generation_description': terminal_start_kpts_generation_description}
if terminal_start_computed_entry.data is None:
terminal_start_computed_entry.data = {}
terminal_start_computed_entry.data['calculation_parameters'] = terminal_start_calculation_parameters
# Get the information for the terminal end
terminal_end_task = terminal_end_fw.tasks[-1]
helper.set_task(terminal_end_task)
helper.task.setup_rundir(terminal_end_run_dir)
terminal_end_all_info = helper.get_all_info(raise_error=True)
terminal_end_setup_fw = wf.id_fw[terminal_end_setup_fw_id]
terminal_end_setup_task = terminal_end_setup_fw.tasks[-1]
terminal_end_vasp_input_set = terminal_end_setup_task.vasp_input_set
terminal_end_kpts_generation_description = get_kpoints_generation_description(
terminal_end_vasp_input_set)
terminal_end_computed_entry = terminal_end_all_info['computed_entry']
terminal_end_vasprun = terminal_end_all_info['vasprun']
terminal_end_calculation_parameters = {'INCAR': terminal_end_vasprun.incar,
'INCAR_ALL': terminal_end_vasprun.parameters,
'potcar_symbols': terminal_end_vasprun.potcar_symbols,
'ENCUT': terminal_end_vasprun.incar['ENCUT'] or
terminal_end_vasprun.parameters['ENCUT'],
'EDIFFG': terminal_end_vasprun.incar.get(
'EDIFFG') or terminal_end_vasprun.parameters.get('EDIFFG'),
'ISMEAR': terminal_end_vasprun.incar.get(
'ISMEAR') or terminal_end_vasprun.parameters.get('ISMEAR'),
'SIGMA': terminal_end_vasprun.incar.get(
'SIGMA') or terminal_end_vasprun.parameters.get('SIGMA'),
'kpoints_generation_description': terminal_end_kpts_generation_description}
if terminal_end_computed_entry.data is None:
terminal_end_computed_entry.data = {}
terminal_end_computed_entry.data['calculation_parameters'] = terminal_end_calculation_parameters
return {'computed_entry_terminal_start': terminal_start_computed_entry.as_dict(),
'computed_entry_terminal_end': terminal_end_computed_entry.as_dict()}
def get_final_results(cls, wf):
assert wf.metadata['workflow_class'] == cls.workflow_class
assert wf.metadata['workflow_module'] == cls.workflow_module
step_index = -1
final_fw_id = None
nrelaxations = 1
fw_ids = {}
final_setup_fw_id = None
final_setup_step_index = -1
final_setup_nrelaxations = 1
for fw_id, fw in wf.id_fw.items():
if 'SRC_task_index' in fw.spec:
src_type = fw.tasks[-1].src_type
if src_type in ['run', 'setup']:
task_index = fw.spec['SRC_task_index']
if 'MPRelaxVasp' in task_index.task_type:
if task_index.task_type == 'MPRelaxVasp':
if src_type == 'run':
fw_ids[(1, task_index.index)] = fw_id
if task_index.index > step_index:
step_index = task_index.index
final_fw_id = fw_id
elif src_type == 'setup':
if task_index.index > final_setup_step_index:
final_setup_step_index = task_index.index
final_setup_fw_id = fw_id
else:
match = re.match("MPRelaxVasp-\d+", task_index.task_type)
if match and match.string == task_index.task_type:
nn = int(task_index.task_type[12:])
if src_type == 'run':
fw_ids[(nn, task_index.index)] = fw_id
if nn == nrelaxations:
if task_index.index > step_index:
step_index = task_index.index
final_fw_id = fw_id
elif nn > nrelaxations:
step_index = task_index.index
final_fw_id = fw_id
nrelaxations = nn
elif src_type == 'setup':
if nn == final_setup_nrelaxations:
if task_index.index > final_setup_step_index:
final_setup_step_index = task_index.index
final_setup_fw_id = fw_id
elif nn > final_setup_nrelaxations:
final_setup_step_index = task_index.index
final_setup_fw_id = fw_id
final_setup_nrelaxations = nn
if final_fw_id is None:
raise RuntimeError('Final structure not found ...')
rlx_and_task_indices = sorted(fw_ids.keys())
ionic_steps = []
helper = MPRelaxTaskHelper()
for rlx_and_task_index in rlx_and_task_indices:
fw_id = fw_ids[rlx_and_task_index]
myfw = wf.id_fw[fw_id]
mytask = myfw.tasks[-1]
last_launch = (myfw.archived_launches + myfw.launches)[-1]
helper.set_task(mytask)
helper.task.setup_rundir(last_launch.launch_dir)
all_info = helper.get_all_info(raise_error=False)
if all_info:
task_ionic_steps = all_info['ionic_steps']
for ionstep in task_ionic_steps:
ionstep.pop('structure')
ionic_steps.append(task_ionic_steps)
final_setup_fw = wf.id_fw[final_setup_fw_id]
final_setup_task = final_setup_fw.tasks[-1]
final_vasp_input_set = final_setup_task.vasp_input_set
kpoints_generation_description = get_kpoints_generation_description(final_vasp_input_set)
all_info_final = helper.get_all_info(raise_error=True)
computed_entry = all_info_final['computed_entry']
vasprun = all_info_final['vasprun']
calculation_parameters = {'INCAR': vasprun.incar,
'INCAR_ALL': vasprun.parameters,
'potcar_symbols': vasprun.potcar_symbols,
'ENCUT': vasprun.incar['ENCUT'] or vasprun.parameters['ENCUT'],
'EDIFFG': vasprun.incar.get('EDIFFG') or vasprun.parameters.get('EDIFFG'),
'ISMEAR': vasprun.incar.get('ISMEAR') or vasprun.parameters.get('ISMEAR'),
'SIGMA': vasprun.incar.get('SIGMA') or vasprun.parameters.get('SIGMA'),
'kpoints_generation_description': kpoints_generation_description}
if computed_entry.data is None:
computed_entry.data = {}
computed_entry.data['calculation_parameters'] = calculation_parameters
return {'computed_entry': computed_entry.as_dict(),
'final_structure': all_info_final['final_structure'].as_dict(),
'ionic_steps': ionic_steps}
