def _snl_to_spec(snl, enforce_gga=False, parameters=None): parameters = parameters if parameters else {} parameters.setdefault('boltztrap', True) # by default run boltztrap parameters.setdefault('force_gamma', False) # by default not force gamma parameters.setdefault('exact_structure', True) spec = {'parameters': parameters} incar_enforce = {'NCORE': 8} if parameters['exact_structure']: structure = snl.structure else: structure = snl.structure.get_primitive_structure() if enforce_gga: incar_enforce.update({"LDAU": False}) mpvis = MPRelaxSet(structure, user_incar_settings=incar_enforce, force_gamma=parameters['force_gamma']) incar = mpvis.incar poscar = mpvis.poscar kpoints = mpvis.kpoints potcar = mpvis.potcar spec['vasp'] = {} spec['vasp']['incar'] = incar.as_dict() spec['vasp']['poscar'] = poscar.as_dict() spec['vasp']['kpoints'] = kpoints.as_dict() spec['vasp']['potcar'] = potcar.as_dict() # Add run tags of pseudopotential spec['run_tags'] = spec.get('run_tags', [potcar.functional]) spec['run_tags'].extend(potcar.symbols) # Add run tags of +U u_tags = [ '%s=%s' % t for t in zip(poscar.site_symbols, incar.get('LDAUU', [0] * len(poscar.site_symbols))) ] spec['run_tags'].extend(u_tags) # add user run tags if 'run_tags' in parameters: spec['run_tags'].extend(parameters['run_tags']) del spec['parameters']['run_tags'] # add exact structure run tag automatically if we have a unique situation if 'exact_structure' in parameters and parameters['exact_structure'] and \ structure != snl.structure.get_primitive_structure(): spec['run_tags'].extend('exact_structure') spec['_dupefinder'] = DupeFinderVasp().to_dict() spec['vaspinputset_name'] = mpvis.__class__.__name__ spec['task_type'] = 'GGA+U optimize structure (2x)' if spec['vasp'][ 'incar'].get('LDAU', False) else 'GGA optimize structure (2x)' return spec
def _snl_to_spec(snl, enforce_gga=False, parameters=None): parameters = parameters if parameters else {} spec = {'parameters': parameters} incar_enforce = {'NPAR': 2} if 'exact_structure' in parameters and parameters['exact_structure']: structure = snl.structure else: structure = snl.structure.get_primitive_structure() mpvis = MPGGAVaspInputSet( user_incar_settings=incar_enforce) if enforce_gga else MPVaspInputSet( user_incar_settings=incar_enforce) incar = mpvis.get_incar(structure) poscar = mpvis.get_poscar(structure) kpoints = mpvis.get_kpoints(structure) potcar = mpvis.get_potcar(structure) spec['vasp'] = {} spec['vasp']['incar'] = incar.to_dict spec['vasp']['poscar'] = poscar.to_dict spec['vasp']['kpoints'] = kpoints.to_dict spec['vasp']['potcar'] = potcar.to_dict # Add run tags of pseudopotential spec['run_tags'] = spec.get('run_tags', [potcar.functional]) spec['run_tags'].extend(potcar.symbols) # Add run tags of +U u_tags = [ '%s=%s' % t for t in zip(poscar.site_symbols, incar.get('LDAUU', [0] * len(poscar.site_symbols))) ] spec['run_tags'].extend(u_tags) # add user run tags if 'run_tags' in parameters: spec['run_tags'].extend(parameters['run_tags']) del spec['parameters']['run_tags'] # add exact structure run tag automatically if we have a unique situation if 'exact_structure' in parameters and parameters[ 'exact_structure'] and snl.structure != snl.structure.get_primitive_structure( ): spec['run_tags'].extend('exact_structure') spec['_dupefinder'] = DupeFinderVasp().to_dict() spec['vaspinputset_name'] = mpvis.__class__.__name__ spec['task_type'] = 'GGA+U optimize structure (2x)' if spec['vasp'][ 'incar'].get('LDAU', False) else 'GGA optimize structure (2x)' return spec
def _snl_to_spec(snl, enforce_gga=False): spec = {} incar_enforce = {'NPAR': 2} structure = snl.structure mpvis = MPGGAVaspInputSet( user_incar_settings=incar_enforce) if enforce_gga else MPVaspInputSet( user_incar_settings=incar_enforce) incar = mpvis.get_incar(structure) poscar = mpvis.get_poscar(structure) kpoints = mpvis.get_kpoints(structure) potcar = mpvis.get_potcar(structure) spec['vasp'] = {} spec['vasp']['incar'] = incar.to_dict spec['vasp']['poscar'] = poscar.to_dict spec['vasp']['kpoints'] = kpoints.to_dict spec['vasp']['potcar'] = potcar.to_dict # Add run tags of pseudopotential spec['run_tags'] = spec.get('run_tags', [potcar.functional]) spec['run_tags'].extend(potcar.symbols) # Add run tags of +U u_tags = [ '%s=%s' % t for t in zip(poscar.site_symbols, incar.get('LDAUU', [0] * len(poscar.site_symbols))) ] spec['run_tags'].extend(u_tags) spec['_dupefinder'] = DupeFinderVasp().to_dict() spec['vaspinputset_name'] = mpvis.__class__.__name__ spec['task_type'] = 'GGA+U optimize structure (2x)' if spec['vasp'][ 'incar'].get('LDAU', False) else 'GGA optimize structure (2x)' return spec
def run_task(self, fw_spec): print 'sleeping 10s for Mongo' time.sleep(10) print 'done sleeping' print 'the gap is {}, the cutoff is {}'.format( fw_spec['analysis']['bandgap'], self.gap_cutoff) if fw_spec['analysis']['bandgap'] >= self.gap_cutoff: static_dens = 90 uniform_dens = 1000 line_dens = 20 else: static_dens = 450 uniform_dens = 1500 line_dens = 30 if fw_spec['analysis']['bandgap'] <= self.metal_cutoff: user_incar_settings = {"ISMEAR": 1, "SIGMA": 0.2} else: user_incar_settings = {} print 'Adding more runs...' type_name = 'GGA+U' if 'GGA+U' in fw_spec['prev_task_type'] else 'GGA' snl = StructureNL.from_dict(fw_spec['mpsnl']) f = Composition( snl.structure.composition.reduced_formula).alphabetical_formula fws = [] connections = {} priority = fw_spec['_priority'] trackers = [ Tracker('FW_job.out'), Tracker('FW_job.error'), Tracker('vasp.out'), Tracker('OUTCAR'), Tracker('OSZICAR') ] trackers_db = [Tracker('FW_job.out'), Tracker('FW_job.error')] # run GGA static spec = fw_spec # pass all the items from the current spec to the new spec.update({ 'task_type': '{} static v2'.format(type_name), '_queueadapter': QA_VASP_SMALL, '_dupefinder': DupeFinderVasp().to_dict(), '_priority': priority, '_trackers': trackers }) fws.append( Firework([ VaspCopyTask({ 'use_CONTCAR': True, 'skip_CHGCAR': True }), SetupStaticRunTask({ "kpoints_density": static_dens, 'user_incar_settings': user_incar_settings }), get_custodian_task(spec) ], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-10)) # insert into DB - GGA static spec = { 'task_type': 'VASP db insertion', '_queueadapter': QA_DB, '_allow_fizzled_parents': True, '_priority': priority * 2, "_dupefinder": DupeFinderDB().to_dict(), '_trackers': trackers_db } fws.append( Firework([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-9)) connections[-10] = -9 # run GGA Uniform spec = { 'task_type': '{} Uniform v2'.format(type_name), '_queueadapter': QA_VASP, '_dupefinder': DupeFinderVasp().to_dict(), '_priority': priority, '_trackers': trackers } fws.append( Firework([ VaspCopyTask({'use_CONTCAR': False}), SetupNonSCFTask({ 'mode': 'uniform', "kpoints_density": uniform_dens }), get_custodian_task(spec) ], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-8)) connections[-9] = -8 # insert into DB - GGA Uniform spec = { 'task_type': 'VASP db insertion', '_queueadapter': QA_DB, '_allow_fizzled_parents': True, '_priority': priority * 2, "_dupefinder": DupeFinderDB().to_dict(), '_trackers': trackers_db } fws.append( Firework([VaspToDBTask({'parse_uniform': True})], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-7)) connections[-8] = -7 # run GGA Band structure spec = { 'task_type': '{} band structure v2'.format(type_name), '_queueadapter': QA_VASP, '_dupefinder': DupeFinderVasp().to_dict(), '_priority': priority, '_trackers': trackers } fws.append( Firework([ VaspCopyTask({'use_CONTCAR': False}), SetupNonSCFTask({ 'mode': 'line', "kpoints_line_density": line_dens }), get_custodian_task(spec) ], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-6)) connections[-7] = [-6] # insert into DB - GGA Band structure spec = { 'task_type': 'VASP db insertion', '_queueadapter': QA_DB, '_allow_fizzled_parents': True, '_priority': priority * 2, "_dupefinder": DupeFinderDB().to_dict(), '_trackers': trackers_db } fws.append( Firework([VaspToDBTask({})], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-5)) connections[-6] = -5 if fw_spec.get('parameters') and fw_spec['parameters'].get( 'boltztrap'): # run Boltztrap from mpworks.firetasks.boltztrap_tasks import BoltztrapRunTask spec = { 'task_type': '{} Boltztrap'.format(type_name), '_queueadapter': QA_DB, '_dupefinder': DupeFinderDB().to_dict(), '_priority': priority } fws.append( Firework([BoltztrapRunTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-4)) connections[-7].append(-4) wf = Workflow(fws, connections) print 'Done adding more runs...' return FWAction(additions=wf)
def run_task(self, fw_spec): print 'sleeping 10s for Mongo' time.sleep(10) print 'done sleeping' print 'the gap is {}, the cutoff is {}'.format( fw_spec['analysis']['bandgap'], self.gap_cutoff) if fw_spec['analysis']['bandgap'] >= self.gap_cutoff: print 'Adding more runs...' type_name = 'GGA+U' if 'GGA+U' in fw_spec[ 'prev_task_type'] else 'GGA' snl = StructureNL.from_dict(fw_spec['mpsnl']) f = Composition( snl.structure.composition.reduced_formula).alphabetical_formula fws = [] connections = {} priority = fw_spec['_priority'] # run GGA static spec = fw_spec # pass all the items from the current spec to the new # one spec.update({ 'task_type': '{} static'.format(type_name), '_queueadapter': QA_VASP, '_dupefinder': DupeFinderVasp().to_dict(), '_priority': priority }) fws.append( Firework([ VaspCopyTask({'use_CONTCAR': True}), SetupStaticRunTask(), get_custodian_task(spec) ], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-10)) # insert into DB - GGA static spec = { 'task_type': 'VASP db insertion', '_queueadapter': QA_DB, '_allow_fizzled_parents': True, '_priority': priority, "_dupefinder": DupeFinderDB().to_dict() } fws.append( Firework([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-9)) connections[-10] = -9 # run GGA Uniform spec = { 'task_type': '{} Uniform'.format(type_name), '_queueadapter': QA_VASP, '_dupefinder': DupeFinderVasp().to_dict(), '_priority': priority } fws.append( Firework([ VaspCopyTask({'use_CONTCAR': False}), SetupNonSCFTask({'mode': 'uniform'}), get_custodian_task(spec) ], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-8)) connections[-9] = -8 # insert into DB - GGA Uniform spec = { 'task_type': 'VASP db insertion', '_queueadapter': QA_DB, '_allow_fizzled_parents': True, '_priority': priority, "_dupefinder": DupeFinderDB().to_dict() } fws.append( Firework([VaspToDBTask({'parse_uniform': True})], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-7)) connections[-8] = -7 # run GGA Band structure spec = { 'task_type': '{} band structure'.format(type_name), '_queueadapter': QA_VASP, '_dupefinder': DupeFinderVasp().to_dict(), '_priority': priority } fws.append( Firework([ VaspCopyTask({'use_CONTCAR': False}), SetupNonSCFTask({'mode': 'line'}), get_custodian_task(spec) ], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-6)) connections[-7] = -6 # insert into DB - GGA Band structure spec = { 'task_type': 'VASP db insertion', '_queueadapter': QA_DB, '_allow_fizzled_parents': True, '_priority': priority, "_dupefinder": DupeFinderDB().to_dict() } fws.append( Firework([VaspToDBTask({})], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-5)) connections[-6] = -5 wf = Workflow(fws, connections) print 'Done adding more runs...' return FWAction(additions=wf) return FWAction()
def run_task(self, fw_spec): if '_fizzled_parents' in fw_spec and not 'prev_vasp_dir' in fw_spec: prev_dir = get_loc( fw_spec['_fizzled_parents'][0]['launches'][0]['launch_dir']) update_spec = {} # add this later when creating new FW fizzled_parent = True parse_dos = False else: prev_dir = get_loc(fw_spec['prev_vasp_dir']) update_spec = { 'prev_vasp_dir': prev_dir, 'prev_task_type': fw_spec['prev_task_type'], 'run_tags': fw_spec['run_tags'], 'parameters': fw_spec.get('parameters') } fizzled_parent = False parse_dos = 'Uniform' in fw_spec['prev_task_type'] if 'run_tags' in fw_spec: self.additional_fields['run_tags'] = fw_spec['run_tags'] else: self.additional_fields['run_tags'] = fw_spec['_fizzled_parents'][ 0]['spec']['run_tags'] if MOVE_TO_GARDEN_DEV: prev_dir = move_to_garden(prev_dir, prod=False) elif MOVE_TO_GARDEN_PROD: prev_dir = move_to_garden(prev_dir, prod=True) # get the directory containing the db file db_dir = os.environ['DB_LOC'] db_path = os.path.join(db_dir, 'tasks_db.json') logging.basicConfig(level=logging.INFO) logger = logging.getLogger('MPVaspDrone') logger.setLevel(logging.INFO) sh = logging.StreamHandler(stream=sys.stdout) sh.setLevel(getattr(logging, 'INFO')) logger.addHandler(sh) with open(db_path) as f: db_creds = json.load(f) drone = MPVaspDrone(host=db_creds['host'], port=db_creds['port'], database=db_creds['database'], user=db_creds['admin_user'], password=db_creds['admin_password'], collection=db_creds['collection'], parse_dos=parse_dos, additional_fields=self.additional_fields, update_duplicates=self.update_duplicates) t_id, d = drone.assimilate( prev_dir, launches_coll=LaunchPad.auto_load().launches) mpsnl = d['snl_final'] if 'snl_final' in d else d['snl'] snlgroup_id = d['snlgroup_id_final'] if 'snlgroup_id_final' in d else d[ 'snlgroup_id'] update_spec.update({'mpsnl': mpsnl, 'snlgroup_id': snlgroup_id}) print 'ENTERED task id:', t_id stored_data = {'task_id': t_id} if d['state'] == 'successful': update_spec['analysis'] = d['analysis'] update_spec['output'] = d['output'] update_spec['vasp'] = { 'incar': d['calculations'][-1]['input']['incar'], 'kpoints': d['calculations'][-1]['input']['kpoints'] } update_spec["task_id"] = t_id return FWAction(stored_data=stored_data, update_spec=update_spec) # not successful - first test to see if UnconvergedHandler is needed if not fizzled_parent: unconverged_tag = 'unconverged_handler--{}'.format( fw_spec['prev_task_type']) output_dir = last_relax(os.path.join(prev_dir, 'vasprun.xml')) ueh = UnconvergedErrorHandler(output_filename=output_dir) # TODO: make this a little more flexible if ueh.check() and unconverged_tag not in fw_spec['run_tags']: print 'Unconverged run! Creating dynamic FW...' spec = { 'prev_vasp_dir': prev_dir, 'prev_task_type': fw_spec['task_type'], 'mpsnl': mpsnl, 'snlgroup_id': snlgroup_id, 'task_type': fw_spec['prev_task_type'], 'run_tags': list(fw_spec['run_tags']), 'parameters': fw_spec.get('parameters'), '_dupefinder': DupeFinderVasp().to_dict(), '_priority': fw_spec['_priority'] } # Pass elastic tensor spec if 'deformation_matrix' in fw_spec.keys(): spec['deformation_matrix'] = fw_spec['deformation_matrix'] spec['original_task_id'] = fw_spec['original_task_id'] snl = StructureNL.from_dict(spec['mpsnl']) spec['run_tags'].append(unconverged_tag) spec['_queueadapter'] = QA_VASP fws = [] connections = {} f = Composition(snl.structure.composition.reduced_formula ).alphabetical_formula fws.append( Firework([ VaspCopyTask({ 'files': [ 'INCAR', 'KPOINTS', 'POSCAR', 'POTCAR', 'CONTCAR' ], 'use_CONTCAR': False }), SetupUnconvergedHandlerTask(), get_custodian_task(spec) ], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-2)) spec = { 'task_type': 'VASP db insertion', '_allow_fizzled_parents': True, '_priority': fw_spec['_priority'], '_queueadapter': QA_DB, 'run_tags': list(fw_spec['run_tags']) } if 'deformation_matrix' in fw_spec.keys(): spec['deformation_matrix'] = fw_spec['deformation_matrix'] spec['original_task_id'] = fw_spec['original_task_id'] spec['run_tags'].append(unconverged_tag) fws.append( Firework([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-1)) connections[-2] = -1 wf = Workflow(fws, connections) return FWAction(detours=wf) # not successful and not due to convergence problem - FIZZLE raise ValueError("DB insertion successful, but don't know how to \ fix this Firework! Can't continue with workflow...")