def snl_to_wf_phonon(snl, parameters): # parameters["user_vasp_settings"] specifies user defined incar/kpoints parameters fws = [] connections = defaultdict(list) parameters = parameters if parameters else {} snl_priority = parameters.get('priority', 1) priority = snl_priority * 2 # once we start a job, keep going! f = Composition(snl.structure.composition.reduced_formula).alphabetical_formula # add the SNL to the SNL DB and figure out duplicate group tasks = [AddSNLTask()] spec = {'task_type': 'Add to SNL database', 'snl': snl.as_dict(), '_queueadapter': QA_DB, '_priority': snl_priority} if 'snlgroup_id' in parameters and isinstance(snl, MPStructureNL): spec['force_mpsnl'] = snl.as_dict() spec['force_snlgroup_id'] = parameters['snlgroup_id'] del spec['snl'] fws.append(Firework(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=0)) connections[0] = [1] parameters["exact_structure"] = True # run GGA structure optimization for force convergence spec = snl_to_wf._snl_to_spec(snl, parameters=parameters) user_vasp_settings = parameters.get("user_vasp_settings") spec = update_spec_force_convergence(spec, user_vasp_settings) spec['run_tags'].append("origin") spec['_priority'] = priority spec['_queueadapter'] = QA_VASP del spec['_dupefinder'] spec['task_type'] = "Vasp force convergence optimize structure (2x)" tasks = [VaspWriterTask(), get_custodian_task(spec)] fws.append(Firework(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=1)) # insert into DB - GGA structure optimization spec = {'task_type': 'VASP db insertion', '_priority': priority, '_allow_fizzled_parents': True, '_queueadapter': QA_DB, 'clean_task_doc':True, 'elastic_constant':"force_convergence"} fws.append(Firework([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=2)) connections[1] = [2] spec = {'task_type': 'Setup Deformed Struct Task', '_priority': priority, '_queueadapter': QA_CONTROL} fws.append(Firework([SetupDeformedStructTask()], spec, name=get_slug(f + '--' + spec['task_type']),fw_id=3)) connections[2] = [3] wf_meta = get_meta_from_structure(snl.structure) wf_meta['run_version'] = 'May 2013 (1)' if '_materialsproject' in snl.data and 'submission_id' in snl.data['_materialsproject']: wf_meta['submission_id'] = snl.data['_materialsproject']['submission_id'] return Workflow(fws, connections, name=Composition( snl.structure.composition.reduced_formula).alphabetical_formula, metadata=wf_meta)
def snl_to_wf_elastic(snl, parameters): # parameters["user_vasp_settings"] specifies user defined incar/kpoints parameters fws = [] connections = defaultdict(list) parameters = parameters if parameters else {} snl_priority = parameters.get('priority', 1) priority = snl_priority * 2 # once we start a job, keep going! f = Composition(snl.structure.composition.reduced_formula).alphabetical_formula # add the SNL to the SNL DB and figure out duplicate group tasks = [AddSNLTask()] spec = {'task_type': 'Add to SNL database', 'snl': snl.as_dict(), '_queueadapter': QA_DB, '_priority': snl_priority} if 'snlgroup_id' in parameters and isinstance(snl, MPStructureNL): spec['force_mpsnl'] = snl.as_dict() spec['force_snlgroup_id'] = parameters['snlgroup_id'] del spec['snl'] fws.append(Firework(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=0)) connections[0] = [1] parameters["exact_structure"] = True # run GGA structure optimization for force convergence spec = snl_to_wf._snl_to_spec(snl, parameters=parameters) user_vasp_settings = parameters.get("user_vasp_settings") spec = update_spec_force_convergence(spec, user_vasp_settings) spec['run_tags'].append("origin") spec['_priority'] = priority spec['_queueadapter'] = QA_VASP del spec['_dupefinder'] spec['task_type'] = "Vasp force convergence optimize structure (2x)" tasks = [VaspWriterTask(), get_custodian_task(spec)] fws.append(Firework(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=1)) # insert into DB - GGA structure optimization spec = {'task_type': 'VASP db insertion', '_priority': priority, '_allow_fizzled_parents': True, '_queueadapter': QA_DB, 'clean_task_doc':True, 'elastic_constant':"force_convergence"} fws.append(Firework([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=2)) connections[1] = [2] spec = {'task_type': 'Setup Deformed Struct Task', '_priority': priority, '_queueadapter': QA_CONTROL} fws.append(Firework([SetupDeformedStructTask()], spec, name=get_slug(f + '--' + spec['task_type']),fw_id=3)) connections[2] = [3] wf_meta = get_meta_from_structure(snl.structure) wf_meta['run_version'] = 'May 2013 (1)' if '_materialsproject' in snl.data and 'submission_id' in snl.data['_materialsproject']: wf_meta['submission_id'] = snl.data['_materialsproject']['submission_id'] return Workflow(fws, connections, name=Composition( snl.structure.composition.reduced_formula).alphabetical_formula, metadata=wf_meta)
def run_task(self, fw_spec): # Read structure from previous relaxation relaxed_struct = fw_spec['output']['crystal'] # Generate deformed structures d_struct_set = DeformedStructureSet(relaxed_struct, ns=0.06) wf=[] for i, d_struct in enumerate(d_struct_set.def_structs): fws=[] connections={} f = Composition(d_struct.formula).alphabetical_formula snl = StructureNL(d_struct, 'Joseph Montoya <*****@*****.**>', projects=["Elasticity"]) tasks = [AddSNLTask()] snl_priority = fw_spec.get('priority', 1) spec = {'task_type': 'Add Deformed Struct to SNL database', 'snl': snl.as_dict(), '_queueadapter': QA_DB, '_priority': snl_priority} if 'snlgroup_id' in fw_spec and isinstance(snl, MPStructureNL): spec['force_mpsnl'] = snl.as_dict() spec['force_snlgroup_id'] = fw_spec['snlgroup_id'] del spec['snl'] fws.append(Firework(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-1000+i*10)) connections[-1000+i*10] = [-999+i*10] spec = snl_to_wf._snl_to_spec(snl, parameters={'exact_structure':True}) spec = update_spec_force_convergence(spec) spec['deformation_matrix'] = d_struct_set.deformations[i].tolist() spec['original_task_id'] = fw_spec["task_id"] spec['_priority'] = fw_spec['_priority']*2 #Turn off dupefinder for deformed structure del spec['_dupefinder'] spec['task_type'] = "Optimize deformed structure" fws.append(Firework([VaspWriterTask(), SetupElastConstTask(), get_custodian_task(spec)], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-999+i*10)) priority = fw_spec['_priority']*3 spec = {'task_type': 'VASP db insertion', '_priority': priority, '_allow_fizzled_parents': True, '_queueadapter': QA_DB, 'elastic_constant':"deformed_structure", 'clean_task_doc':True, 'deformation_matrix':d_struct_set.deformations[i].tolist(), 'original_task_id':fw_spec["task_id"]} fws.append(Firework([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-998+i*10)) connections[-999+i*10] = [-998+i*10] wf.append(Workflow(fws, connections)) return FWAction(additions=wf)
def run_task(self, fw_spec): # Read structure from previous relaxation relaxed_struct = fw_spec['output']['crystal'] # Generate deformed structures d_struct_set = DeformedStructureSet(relaxed_struct, ns=0.06) wf=[] for i, d_struct in enumerate(d_struct_set.def_structs): fws=[] connections={} f = Composition(d_struct.formula).alphabetical_formula snl = StructureNL(d_struct, 'Joseph Montoya <*****@*****.**>', projects=["Elasticity"]) tasks = [AddSNLTask()] snl_priority = fw_spec.get('priority', 1) spec = {'task_type': 'Add Deformed Struct to SNL database', 'snl': snl.as_dict(), '_queueadapter': QA_DB, '_priority': snl_priority} if 'snlgroup_id' in fw_spec and isinstance(snl, MPStructureNL): spec['force_mpsnl'] = snl.as_dict() spec['force_snlgroup_id'] = fw_spec['snlgroup_id'] del spec['snl'] fws.append(Firework(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-1000+i*10)) connections[-1000+i*10] = [-999+i*10] spec = snl_to_wf._snl_to_spec(snl, parameters={'exact_structure':True}) spec = update_spec_force_convergence(spec) spec['deformation_matrix'] = d_struct_set.deformations[i].tolist() spec['original_task_id'] = fw_spec["task_id"] spec['_priority'] = fw_spec['_priority']*2 #Turn off dupefinder for deformed structure del spec['_dupefinder'] spec['task_type'] = "Optimize deformed structure" fws.append(Firework([VaspWriterTask(), SetupElastConstTask(), get_custodian_task(spec)], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-999+i*10)) priority = fw_spec['_priority']*3 spec = {'task_type': 'VASP db insertion', '_priority': priority, '_allow_fizzled_parents': True, '_queueadapter': QA_DB, 'elastic_constant':"deformed_structure", 'clean_task_doc':True, 'deformation_matrix':d_struct_set.deformations[i].tolist(), 'original_task_id':fw_spec["task_id"]} fws.append(Firework([VaspToDBTask(), AddElasticDataToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=-998+i*10)) connections[-999+i*10] = [-998+i*10] wf.append(Workflow(fws, connections)) 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: 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 snl_to_wf(snl, parameters=None): fws = [] connections = defaultdict(list) parameters = parameters if parameters else {} snl_priority = parameters.get('priority', 1) priority = snl_priority * 2 # once we start a job, keep going! f = Composition(snl.structure.composition.reduced_formula).alphabetical_formula snl_spec = {} if 'snlgroup_id' in parameters: if 'mpsnl' in parameters: snl_spec['mpsnl'] = parameters['mpsnl'] elif isinstance(snl, MPStructureNL): snl_spec['mpsnl'] = snl.as_dict() else: raise ValueError("improper use of force SNL") snl_spec['snlgroup_id'] = parameters['snlgroup_id'] else: # add the SNL to the SNL DB and figure out duplicate group tasks = [AddSNLTask()] spec = {'task_type': 'Add to SNL database', 'snl': snl.as_dict(), '_queueadapter': QA_DB, '_priority': snl_priority} fws.append(Firework(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=0)) connections[0] = [1] trackers = [Tracker('FW_job.out'), Tracker('FW_job.error'), Tracker('vasp.out'), Tracker('OUTCAR'), Tracker('OSZICAR'), Tracker('OUTCAR.relax1'), Tracker('OUTCAR.relax2')] trackers_db = [Tracker('FW_job.out'), Tracker('FW_job.error')] # run GGA structure optimization spec = _snl_to_spec(snl, enforce_gga=True, parameters=parameters) spec.update(snl_spec) spec['_priority'] = priority spec['_queueadapter'] = QA_VASP spec['_trackers'] = trackers tasks = [VaspWriterTask(), get_custodian_task(spec)] fws.append(Firework(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=1)) # insert into DB - GGA structure optimization spec = {'task_type': 'VASP db insertion', '_priority': priority*2, '_allow_fizzled_parents': True, '_queueadapter': QA_DB, "_dupefinder": DupeFinderDB().to_dict(), '_trackers': trackers_db} fws.append( Firework([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=2)) connections[1] = [2] # determine if GGA+U FW is needed incar = MPVaspInputSet().get_incar(snl.structure).as_dict() ggau_compound = ('LDAU' in incar and incar['LDAU']) if not parameters.get('skip_bandstructure', False) and (not ggau_compound or parameters.get('force_gga_bandstructure', False)): spec = {'task_type': 'Controller: add Electronic Structure v2', '_priority': priority, '_queueadapter': QA_CONTROL} fws.append( Firework([AddEStructureTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=3)) connections[2] = [3] if ggau_compound: spec = _snl_to_spec(snl, enforce_gga=False, parameters=parameters) del spec['vasp'] # we are stealing all VASP params and such from previous run spec['_priority'] = priority spec['_queueadapter'] = QA_VASP spec['_trackers'] = trackers fws.append(Firework( [VaspCopyTask(), SetupGGAUTask(), get_custodian_task(spec)], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=10)) connections[2].append(10) spec = {'task_type': 'VASP db insertion', '_queueadapter': QA_DB, '_allow_fizzled_parents': True, '_priority': priority, "_dupefinder": DupeFinderDB().to_dict(), '_trackers': trackers_db} fws.append( Firework([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=11)) connections[10] = [11] if not parameters.get('skip_bandstructure', False): spec = {'task_type': 'Controller: add Electronic Structure v2', '_priority': priority, '_queueadapter': QA_CONTROL} fws.append( Firework([AddEStructureTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=12)) connections[11] = [12] wf_meta = get_meta_from_structure(snl.structure) wf_meta['run_version'] = 'May 2013 (1)' # not maintained if '_materialsproject' in snl.data and 'submission_id' in snl.data['_materialsproject']: wf_meta['submission_id'] = snl.data['_materialsproject']['submission_id'] return Workflow(fws, connections, name=Composition( snl.structure.composition.reduced_formula).alphabetical_formula, metadata=wf_meta)
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...")
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'] 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) 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']} snl = StructureNL.from_dict(spec['mpsnl']) spec['run_tags'].append(unconverged_tag) spec['_queueadapter'] = QA_VASP fws = [] connections = {} f = Composition.from_formula( 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'])} 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...")
def snl_to_wf(snl, parameters=None): fws = [] connections = defaultdict(list) parameters = parameters if parameters else {} snl_priority = parameters.get('priority', 1) priority = snl_priority * 2 # once we start a job, keep going! f = Composition( snl.structure.composition.reduced_formula).alphabetical_formula snl_spec = {} if 'snlgroup_id' in parameters: if 'mpsnl' in parameters: snl_spec['mpsnl'] = parameters['mpsnl'] elif isinstance(snl, MPStructureNL): snl_spec['mpsnl'] = snl.as_dict() else: raise ValueError("improper use of force SNL") snl_spec['snlgroup_id'] = parameters['snlgroup_id'] else: # add the SNL to the SNL DB and figure out duplicate group tasks = [AddSNLTask()] spec = { 'task_type': 'Add to SNL database', 'snl': snl.as_dict(), '_queueadapter': QA_DB, '_priority': snl_priority } fws.append( Firework(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=0)) connections[0] = [1] trackers = [ Tracker('FW_job.out'), Tracker('FW_job.error'), Tracker('vasp.out'), Tracker('OUTCAR'), Tracker('OSZICAR'), Tracker('OUTCAR.relax1'), Tracker('OUTCAR.relax2') ] trackers_db = [Tracker('FW_job.out'), Tracker('FW_job.error')] # run GGA structure optimization spec = _snl_to_spec(snl, enforce_gga=True, parameters=parameters) spec.update(snl_spec) spec['_priority'] = priority spec['_queueadapter'] = QA_VASP spec['_trackers'] = trackers tasks = [VaspWriterTask(), get_custodian_task(spec)] fws.append( Firework(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=1)) # insert into DB - GGA structure optimization spec = { 'task_type': 'VASP db insertion', '_priority': priority * 2, '_allow_fizzled_parents': True, '_queueadapter': QA_DB, "_dupefinder": DupeFinderDB().to_dict(), '_trackers': trackers_db } fws.append( Firework([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=2)) connections[1] = [2] # determine if GGA+U FW is needed incar = MPVaspInputSet().get_incar(snl.structure).as_dict() ggau_compound = ('LDAU' in incar and incar['LDAU']) if not parameters.get('skip_bandstructure', False) and ( not ggau_compound or parameters.get('force_gga_bandstructure', False)): spec = { 'task_type': 'Controller: add Electronic Structure v2', '_priority': priority, '_queueadapter': QA_CONTROL } fws.append( Firework([AddEStructureTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=3)) connections[2] = [3] if ggau_compound: spec = _snl_to_spec(snl, enforce_gga=False, parameters=parameters) del spec[ 'vasp'] # we are stealing all VASP params and such from previous run spec['_priority'] = priority spec['_queueadapter'] = QA_VASP spec['_trackers'] = trackers fws.append( Firework( [VaspCopyTask(), SetupGGAUTask(), get_custodian_task(spec)], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=10)) connections[2].append(10) spec = { 'task_type': 'VASP db insertion', '_queueadapter': QA_DB, '_allow_fizzled_parents': True, '_priority': priority, "_dupefinder": DupeFinderDB().to_dict(), '_trackers': trackers_db } fws.append( Firework([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=11)) connections[10] = [11] if not parameters.get('skip_bandstructure', False): spec = { 'task_type': 'Controller: add Electronic Structure v2', '_priority': priority, '_queueadapter': QA_CONTROL } fws.append( Firework([AddEStructureTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=12)) connections[11] = [12] wf_meta = get_meta_from_structure(snl.structure) wf_meta['run_version'] = 'May 2013 (1)' if '_materialsproject' in snl.data and 'submission_id' in snl.data[ '_materialsproject']: wf_meta['submission_id'] = snl.data['_materialsproject'][ 'submission_id'] return Workflow( fws, connections, name=Composition( snl.structure.composition.reduced_formula).alphabetical_formula, metadata=wf_meta)
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.from_formula(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} 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} 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} 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 snl_to_wf(snl, parameters=None): fws = [] connections = {} parameters = parameters if parameters else {} snl_priority = parameters.get('priority', 1) priority = snl_priority * 2 # once we start a job, keep going! f = Composition.from_formula(snl.structure.composition.reduced_formula).alphabetical_formula # add the SNL to the SNL DB and figure out duplicate group tasks = [AddSNLTask()] spec = {'task_type': 'Add to SNL database', 'snl': snl.to_dict, '_queueadapter': QA_DB, '_priority': snl_priority} if 'snlgroup_id' in parameters and isinstance(snl, MPStructureNL): spec['force_mpsnl'] = snl.to_dict spec['force_snlgroup_id'] = parameters['snlgroup_id'] del spec['snl'] fws.append(FireWork(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=0)) connections[0] = [1] # run GGA structure optimization spec = _snl_to_spec(snl, enforce_gga=True) spec['_priority'] = priority spec['_queueadapter'] = QA_VASP tasks = [VaspWriterTask(), get_custodian_task(spec)] fws.append(FireWork(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=1)) # insert into DB - GGA structure optimization spec = {'task_type': 'VASP db insertion', '_priority': priority, '_allow_fizzled_parents': True, '_queueadapter': QA_DB} fws.append( FireWork([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=2)) connections[1] = [2] if not parameters.get('skip_bandstructure', False): spec = {'task_type': 'Controller: add Electronic Structure v2', '_priority': priority, '_queueadapter': QA_CONTROL} fws.append( FireWork([AddEStructureTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=3)) connections[2] = [3] # determine if GGA+U FW is needed incar = MPVaspInputSet().get_incar(snl.structure).to_dict if 'LDAU' in incar and incar['LDAU']: spec = _snl_to_spec(snl, enforce_gga=False) del spec['vasp'] # we are stealing all VASP params and such from previous run spec['_priority'] = priority spec['_queueadapter'] = QA_VASP fws.append(FireWork( [VaspCopyTask(), SetupGGAUTask(), get_custodian_task(spec)], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=10)) connections[2].append(10) spec = {'task_type': 'VASP db insertion', '_queueadapter': QA_DB, '_allow_fizzled_parents': True, '_priority': priority} fws.append( FireWork([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=11)) connections[10] = [11] if not parameters.get('skip_bandstructure', False): spec = {'task_type': 'Controller: add Electronic Structure v2', '_priority': priority, '_queueadapter': QA_CONTROL} fws.append( FireWork([AddEStructureTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=12)) connections[11] = [12] wf_meta = get_meta_from_structure(snl.structure) wf_meta['run_version'] = 'May 2013 (1)' if '_materialsproject' in snl.data and 'submission_id' in snl.data['_materialsproject']: wf_meta['submission_id'] = snl.data['_materialsproject']['submission_id'] return Workflow(fws, connections, name=Composition.from_formula( snl.structure.composition.reduced_formula).alphabetical_formula, metadata=wf_meta)
def snl_to_wf(snl, parameters=None): fws = [] connections = {} parameters = parameters if parameters else {} snl_priority = parameters.get('priority', 1) priority = snl_priority * 2 # once we start a job, keep going! f = Composition.from_formula( snl.structure.composition.reduced_formula).alphabetical_formula # add the SNL to the SNL DB and figure out duplicate group tasks = [AddSNLTask()] spec = { 'task_type': 'Add to SNL database', 'snl': snl.to_dict, '_queueadapter': QA_DB, '_priority': snl_priority } if 'snlgroup_id' in parameters and isinstance(snl, MPStructureNL): spec['force_mpsnl'] = snl.to_dict spec['force_snlgroup_id'] = parameters['snlgroup_id'] del spec['snl'] fws.append( FireWork(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=0)) connections[0] = [1] # run GGA structure optimization spec = _snl_to_spec(snl, enforce_gga=True) spec['_priority'] = priority spec['_queueadapter'] = QA_VASP tasks = [VaspWriterTask(), get_custodian_task(spec)] fws.append( FireWork(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=1)) # insert into DB - GGA structure optimization spec = { 'task_type': 'VASP db insertion', '_priority': priority, '_allow_fizzled_parents': True, '_queueadapter': QA_DB } fws.append( FireWork([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=2)) connections[1] = [2] if not parameters.get('skip_bandstructure', False): spec = { 'task_type': 'Controller: add Electronic Structure v2', '_priority': priority, '_queueadapter': QA_CONTROL } fws.append( FireWork([AddEStructureTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=3)) connections[2] = [3] # determine if GGA+U FW is needed incar = MPVaspInputSet().get_incar(snl.structure).to_dict if 'LDAU' in incar and incar['LDAU']: spec = _snl_to_spec(snl, enforce_gga=False) del spec[ 'vasp'] # we are stealing all VASP params and such from previous run spec['_priority'] = priority spec['_queueadapter'] = QA_VASP fws.append( FireWork( [VaspCopyTask(), SetupGGAUTask(), get_custodian_task(spec)], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=10)) connections[2].append(10) spec = { 'task_type': 'VASP db insertion', '_queueadapter': QA_DB, '_allow_fizzled_parents': True, '_priority': priority } fws.append( FireWork([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=11)) connections[10] = [11] if not parameters.get('skip_bandstructure', False): spec = { 'task_type': 'Controller: add Electronic Structure v2', '_priority': priority, '_queueadapter': QA_CONTROL } fws.append( FireWork([AddEStructureTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=12)) connections[11] = [12] wf_meta = get_meta_from_structure(snl.structure) wf_meta['run_version'] = 'May 2013 (1)' if '_materialsproject' in snl.data and 'submission_id' in snl.data[ '_materialsproject']: wf_meta['submission_id'] = snl.data['_materialsproject'][ 'submission_id'] return Workflow( fws, connections, name=Composition.from_formula( snl.structure.composition.reduced_formula).alphabetical_formula, metadata=wf_meta)
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 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)