def get_energies(rootdir, reanalyze, verbose, detailed, sort): """ Doc string. """ if verbose: FORMAT = "%(relativeCreated)d msecs : %(message)s" logging.basicConfig(level=logging.INFO, format=FORMAT) if not detailed: drone = SimpleVaspToComputedEntryDrone(inc_structure=True) else: drone = VaspToComputedEntryDrone(inc_structure=True, data=["filename", "initial_structure"]) ncpus = multiprocessing.cpu_count() logging.info("Detected {} cpus".format(ncpus)) queen = BorgQueen(drone, number_of_drones=ncpus) if os.path.exists(SAVE_FILE) and not reanalyze: msg = "Using previously assimilated data from {}.".format(SAVE_FILE) \ + " Use -f to force re-analysis." queen.load_data(SAVE_FILE) else: if ncpus > 1: queen.parallel_assimilate(rootdir) else: queen.serial_assimilate(rootdir) msg = "Analysis results saved to {} for faster ".format(SAVE_FILE) + \ "subsequent loading." queen.save_data(SAVE_FILE) entries = queen.get_data() if sort == "energy_per_atom": entries = sorted(entries, key=lambda x: x.energy_per_atom) elif sort == "filename": entries = sorted(entries, key=lambda x: x.data["filename"]) all_data = [] for e in entries: if not detailed: delta_vol = "{:.2f}".format(e.data["delta_volume"] * 100) else: delta_vol = e.structure.volume / \ e.data["initial_structure"].volume - 1 delta_vol = "{:.2f}".format(delta_vol * 100) all_data.append((e.data["filename"].replace("./", ""), re.sub("\s+", "", e.composition.formula), "{:.5f}".format(e.energy), "{:.5f}".format(e.energy_per_atom), delta_vol)) if len(all_data) > 0: headers = ("Directory", "Formula", "Energy", "E/Atom", "% vol chg") t = PrettyTable(headers) t.align["Directory"] = "l" for d in all_data: t.add_row(d) print(t) print(msg) else: print("No valid vasp run found.")
def get_energies(rootdir, reanalyze, verbose, pretty): if verbose: FORMAT = "%(relativeCreated)d msecs : %(message)s" logging.basicConfig(level=logging.INFO, format=FORMAT) drone = GaussianToComputedEntryDrone(inc_structure=True, parameters=['filename']) ncpus = multiprocessing.cpu_count() logging.info('Detected {} cpus'.format(ncpus)) queen = BorgQueen(drone, number_of_drones=ncpus) if os.path.exists(save_file) and not reanalyze: msg = 'Using previously assimilated data from {}. ' + \ 'Use -f to force re-analysis'.format(save_file) queen.load_data(save_file) else: queen.parallel_assimilate(rootdir) msg = 'Results saved to {} for faster reloading.'.format(save_file) queen.save_data(save_file) entries = queen.get_data() entries = sorted(entries, key=lambda x: x.parameters['filename']) all_data = [(e.parameters['filename'].replace("./", ""), re.sub("\s+", "", e.composition.formula), "{}".format(e.parameters['charge']), "{}".format(e.parameters['spin_mult']), "{:.5f}".format(e.energy), "{:.5f}".format(e.energy_per_atom), ) for e in entries] headers = ("Directory", "Formula", "Charge", "Spin Mult.", "Energy", "E/Atom") print(tabulate(all_data, headers=headers)) print("") print(msg)
def get_energies(rootdir, reanalyze, verbose, pretty, detailed, sort): if verbose: FORMAT = "%(relativeCreated)d msecs : %(message)s" logging.basicConfig(level=logging.INFO, format=FORMAT) if not detailed: drone = SimpleVaspToComputedEntryDrone(inc_structure=True) else: drone = VaspToComputedEntryDrone( inc_structure=True, data=["filename", "initial_structure"]) ncpus = multiprocessing.cpu_count() logging.info("Detected {} cpus".format(ncpus)) queen = BorgQueen(drone, number_of_drones=ncpus) if os.path.exists(save_file) and not reanalyze: msg = "Using previously assimilated data from {}.".format(save_file) \ + " Use -f to force re-analysis." queen.load_data(save_file) else: if ncpus > 1: queen.parallel_assimilate(rootdir) else: queen.serial_assimilate(rootdir) msg = "Analysis results saved to {} for faster ".format(save_file) + \ "subsequent loading." queen.save_data(save_file) entries = queen.get_data() if sort == "energy_per_atom": entries = sorted(entries, key=lambda x: x.energy_per_atom) elif sort == "filename": entries = sorted(entries, key=lambda x: x.data["filename"]) all_data = [] for e in entries: if not detailed: delta_vol = "{:.2f}".format(e.data["delta_volume"] * 100) else: delta_vol = e.structure.volume / \ e.data["initial_structure"].volume - 1 delta_vol = "{:.2f}".format(delta_vol * 100) all_data.append( (e.data["filename"].replace("./", ""), re.sub("\s+", "", e.composition.formula), "{:.5f}".format(e.energy), "{:.5f}".format(e.energy_per_atom), delta_vol)) if len(all_data) > 0: headers = ("Directory", "Formula", "Energy", "E/Atom", "% vol chg") if pretty: from prettytable import PrettyTable t = PrettyTable(headers) t.set_field_align("Directory", "l") map(t.add_row, all_data) print t else: print str_aligned(all_data, headers) print msg else: print "No valid vasp run found."
def get_energies(rootdir, reanalyze, verbose, detailed, sort, fmt): """ Doc string. """ if verbose: logformat = "%(relativeCreated)d msecs : %(message)s" logging.basicConfig(level=logging.INFO, format=logformat) if not detailed: drone = SimpleVaspToComputedEntryDrone(inc_structure=True) else: drone = VaspToComputedEntryDrone( inc_structure=True, data=["filename", "initial_structure"]) ncpus = multiprocessing.cpu_count() logging.info("Detected {} cpus".format(ncpus)) queen = BorgQueen(drone, number_of_drones=ncpus) if os.path.exists(SAVE_FILE) and not reanalyze: msg = "Using previously assimilated data from {}.".format(SAVE_FILE) \ + " Use -r to force re-analysis." queen.load_data(SAVE_FILE) else: if ncpus > 1: queen.parallel_assimilate(rootdir) else: queen.serial_assimilate(rootdir) msg = "Analysis results saved to {} for faster ".format(SAVE_FILE) + \ "subsequent loading." queen.save_data(SAVE_FILE) entries = queen.get_data() if sort == "energy_per_atom": entries = sorted(entries, key=lambda x: x.energy_per_atom) elif sort == "filename": entries = sorted(entries, key=lambda x: x.data["filename"]) all_data = [] for e in entries: if not detailed: delta_vol = "{:.2f}".format(e.data["delta_volume"] * 100) else: delta_vol = e.structure.volume / \ e.data["initial_structure"].volume - 1 delta_vol = "{:.2f}".format(delta_vol * 100) all_data.append( (e.data["filename"].replace("./", ""), re.sub(r"\s+", "", e.composition.formula), "{:.5f}".format(e.energy), "{:.5f}".format(e.energy_per_atom), delta_vol)) if len(all_data) > 0: headers = ("Directory", "Formula", "Energy", "E/Atom", "% vol chg") print(tabulate(all_data, headers=headers, tablefmt=fmt)) print("") print(msg) else: print("No valid vasp run found.") os.unlink(SAVE_FILE)
def submit_vasp_directory(self, rootdir, authors, projects=None, references='', remarks=None, master_data=None, master_history=None, created_at=None, ncpus=None): """ Assimilates all vasp run directories beneath a particular directory using BorgQueen to obtain structures, and then submits thhem to the Materials Project as SNL files. VASP related meta data like initial structure and final energies are automatically incorporated. .. note:: As of now, this MP REST feature is open only to a select group of users. Opening up submissions to all users is being planned for the future. Args: rootdir (str): Rootdir to start assimilating VASP runs from. authors: *List* of {"name":'', "email":''} dicts, *list* of Strings as 'John Doe <*****@*****.**>', or a single String with commas separating authors. The same list of authors should apply to all runs. projects ([str]): List of Strings ['Project A', 'Project B']. This applies to all structures. references (str): A String in BibTeX format. Again, this applies to all structures. remarks ([str]): List of Strings ['Remark A', 'Remark B'] master_data (dict): A free form dict. Namespaced at the root level with an underscore, e.g. {"_materialsproject":<custom data>}. This data is added to all structures detected in the directory, in addition to other vasp data on a per structure basis. master_history: A master history to be added to all entries. created_at (datetime): A datetime object ncpus (int): Number of cpus to use in using BorgQueen to assimilate. Defaults to None, which means serial. """ from pymatgen.apps.borg.hive import VaspToComputedEntryDrone from pymatgen.apps.borg.queen import BorgQueen drone = VaspToComputedEntryDrone( inc_structure=True, data=["filename", "initial_structure"]) queen = BorgQueen(drone, number_of_drones=ncpus) queen.parallel_assimilate(rootdir) structures = [] metadata = [] histories = [] for e in queen.get_data(): structures.append(e.structure) m = { "_vasp": { "parameters": e.parameters, "final_energy": e.energy, "final_energy_per_atom": e.energy_per_atom, "initial_structure": e.data["initial_structure"].as_dict() } } if "history" in e.parameters: histories.append(e.parameters["history"]) if master_data is not None: m.update(master_data) metadata.append(m) if master_history is not None: histories = master_history * len(structures) return self.submit_structures(structures, authors, projects=projects, references=references, remarks=remarks, data=metadata, histories=histories, created_at=created_at)
# coding: utf-8 # Copyright (c) Henniggroup. # Distributed under the terms of the MIT License. from __future__ import division, print_function, unicode_literals, \ absolute_import from pymatgen.apps.borg.queen import BorgQueen from mpinterfaces.database import MPINTVaspToDbTaskDrone # import multiprocessing additional_fields = {"author": "kiran"} # "doi":"10.1063/1.4865107" drone = MPINTVaspToDbTaskDrone(host="127.0.0.1", port=27017, database="vasp", collection="collection_name", user="******", password="******", additional_fields=additional_fields) ncpus = 4 # multiprocessing.cpu_count() queen = BorgQueen(drone, number_of_drones=ncpus) queen.parallel_assimilate('path_to_vasp_calculation_folders')
def submit_vasp_directory(self, rootdir, authors, projects=None, references='', remarks=None, master_data=None, master_history=None, created_at=None, ncpus=None): """ Assimilates all vasp run directories beneath a particular directory using BorgQueen to obtain structures, and then submits thhem to the Materials Project as SNL files. VASP related meta data like initial structure and final energies are automatically incorporated. .. note:: As of now, this MP REST feature is open only to a select group of users. Opening up submissions to all users is being planned for the future. Args: rootdir: Rootdir to start assimilating VASP runs from. authors: *List* of {"name":'', "email":''} dicts, *list* of Strings as 'John Doe <*****@*****.**>', or a single String with commas separating authors. The same list of authors should apply to all runs. projects: List of Strings ['Project A', 'Project B']. This applies to all structures. references: A String in BibTeX format. Again, this applies to all structures. remarks: List of Strings ['Remark A', 'Remark B'] masterdata: A free form dict. Namespaced at the root level with an underscore, e.g. {"_materialsproject":<custom data>}. This data is added to all structures detected in the directory, in addition to other vasp data on a per structure basis. created_at: A datetime object ncpus: Number of cpus to use in using BorgQueen to assimilate """ drone = VaspToComputedEntryDrone(inc_structure=True, data=["filename", "initial_structure"]) queen = BorgQueen(drone, number_of_drones=ncpus) queen.parallel_assimilate(rootdir) structures = [] metadata = [] # TODO: Get histories from the data. for e in queen.get_data(): structures.append(e.structure) m = { "_vasp": { "parameters": e.parameters, "final_energy": e.energy, "final_energy_per_atom": e.energy_per_atom, "initial_structure": e.data["initial_structure"].to_dict } } if master_data is not None: m.update(master_data) metadata.append(m) histories = None if master_history is not None: histories = master_history * len(structures) return self.submit_structures( structures, authors, projects=projects, references=references, remarks=remarks, data=metadata, histories=histories, created_at=created_at)
def get_energies(rootdir, reanalyze, verbose, quick, sort, fmt): """ Get energies of all vaspruns in directory (nested). Args: rootdir (str): Root directory. reanalyze (bool): Whether to ignore saved results and reanalyze verbose (bool): Verbose mode or not. quick (bool): Whether to perform a quick analysis (using OSZICAR instead of vasprun.xml sort (bool): Whether to sort the results in ascending order. fmt (str): tablefmt passed to tabulate. """ if verbose: logformat = "%(relativeCreated)d msecs : %(message)s" logging.basicConfig(level=logging.INFO, format=logformat) if quick: drone = SimpleVaspToComputedEntryDrone(inc_structure=True) else: drone = VaspToComputedEntryDrone( inc_structure=True, data=["filename", "initial_structure"]) ncpus = multiprocessing.cpu_count() logging.info("Detected {} cpus".format(ncpus)) queen = BorgQueen(drone, number_of_drones=ncpus) if os.path.exists(SAVE_FILE) and not reanalyze: msg = ("Using previously assimilated data from {}.".format(SAVE_FILE) + " Use -r to force re-analysis.") queen.load_data(SAVE_FILE) else: if ncpus > 1: queen.parallel_assimilate(rootdir) else: queen.serial_assimilate(rootdir) msg = ("Analysis results saved to {} for faster ".format(SAVE_FILE) + "subsequent loading.") queen.save_data(SAVE_FILE) entries = queen.get_data() if sort == "energy_per_atom": entries = sorted(entries, key=lambda x: x.energy_per_atom) elif sort == "filename": entries = sorted(entries, key=lambda x: x.data["filename"]) all_data = [] for e in entries: if quick: delta_vol = "NA" else: delta_vol = e.structure.volume / e.data[ "initial_structure"].volume - 1 delta_vol = "{:.2f}".format(delta_vol * 100) all_data.append(( e.data["filename"].replace("./", ""), re.sub(r"\s+", "", e.composition.formula), "{:.5f}".format(e.energy), "{:.5f}".format(e.energy_per_atom), delta_vol, )) if len(all_data) > 0: headers = ("Directory", "Formula", "Energy", "E/Atom", "% vol chg") print(tabulate(all_data, headers=headers, tablefmt=fmt)) print("") print(msg) else: print("No valid vasp run found.") os.unlink(SAVE_FILE) return 0
from __future__ import division, unicode_literals, print_function from mpinterfaces.database import MPINTVaspToDbTaskDrone from pymatgen.apps.borg.queen import BorgQueen #import multiprocessing additional_fields = {"author":"kiran"} #"doi":"10.1063/1.4865107" drone = MPINTVaspToDbTaskDrone(host="127.0.0.1", port=27017, database="vasp", collection="collection_name", user="******", password="******", additional_fields=additional_fields) ncpus = 4 #multiprocessing.cpu_count() queen = BorgQueen(drone, number_of_drones=ncpus) queen.parallel_assimilate('path_to_vasp_calculation_folders')
def get_energies(rootdir, reanalyze, verbose, detailed, sort, formulaunit, debug, hull, threshold, args, templatestructure): ion_list = 'Novalue' ave_key_list = 'Novalue' threscount = 0 """ Doc string. """ if (verbose and not debug): FORMAT = "%(relativeCreated)d msecs : %(message)s" logging.basicConfig(level=logging.INFO, format=FORMAT) elif debug: logging.basicConfig(level=logging.DEBUG) if not detailed: drone = SimpleVaspToComputedEntryDrone(inc_structure=True) else: drone = VaspToComputedEntryDrone(inc_structure=True, data=["filename", "initial_structure"]) ncpus = multiprocessing.cpu_count() logging.info("Detected {} cpus".format(ncpus)) queen = BorgQueen(drone, number_of_drones=ncpus) if os.path.exists(SAVE_FILE) and not reanalyze: msg = "Using previously assimilated data from {}.".format(SAVE_FILE) \ + " Use -f to force re-analysis." queen.load_data(SAVE_FILE) else: if ncpus > 1: queen.parallel_assimilate(rootdir) else: queen.serial_assimilate(rootdir) msg = "Analysis results saved to {} for faster ".format(SAVE_FILE) + \ "subsequent loading." queen.save_data(SAVE_FILE) entries = queen.get_data() if sort == "energy_per_atom": entries = sorted(entries, key=lambda x: x.energy_per_atom) elif sort == "filename": entries = sorted(entries, key=lambda x: x.data["filename"]) # logging.debug('First Energy entry is {}'.format(entries[0])) base_energy = entries[0].energy logging.debug('Type of entries is: {}'.format(type(entries))) logging.debug('First Element of Entries is:{}'.format(entries[0])) # logging.debug('First Energy entry structure is {}'.format(entries[0].structure)) xy_direction = int(args.XYdirection) tolerance = float(args.tolerance) if args.template: logging.debug('Temp Structure site info is: {}'.format(Na12(['Co','Mn'],['Na'],templatestructure,templatestructure,XY_Direction=xy_direction,tol=tolerance))) template_site_info = Na12(['Co','Mn'],['Na'],templatestructure,templatestructure,XY_Direction=xy_direction,tol=tolerance) all_data = [] energy_diff = [] threshold=float(threshold) Structure_info_dict = {} check_ion_seq = [args.dupion] for e in entries: if not detailed: delta_vol = "{:.2f}".format(e.data["delta_volume"] * 100) else: delta_vol = e.structure.volume / \ e.data["initial_structure"].volume - 1 delta_vol = "{:.2f}".format(delta_vol * 100) entry_path = e.data['filename'].rsplit('/',1)[0] entry_site_info = Na12(['Co','Mn'],['Na'],e.structure,e.structure,XY_Direction=xy_direction,tol=tolerance) logging.debug('Total Na site: {}'.format(entry_site_info['Total_Na_Site'])) #Coordination extraction part # na_layer_site_fcoords = [site._fcoords for site in s if site.specie.symbol == "Na"] # if 'Cif_Structure' in e.data.keys(): # na_sites_fcoords = [site._fcoords for site in e.data['Cif_Structure'] if site.specie.symbol == 'Na'] # na_sites_fcoords_list_tuple = [tuple(coord) for coord in na_sites_fcoords] na_sites_fcoords = [site._fcoords for site in e.data['CONTCAR_Structure'] if site.specie.symbol == 'Na'] na_sites_fcoords_list_tuple = [tuple(coord) for coord in na_sites_fcoords] if args.nupdown: entry_data= [rootdir,e.data["filename"].replace("./", ""), re.sub("\s+", "", e.composition.formula), "{:.5f}".format(e.energy), "{:.5f}".format(1000*(e.energy-base_energy)/int(formulaunit)), "{:.5f}".format(e.energy_per_atom), delta_vol,e.parameters['run_type'], e.data['NUPDOWN'],e.data['ISMEAR'],na_sites_fcoords_list_tuple] else: entry_data= [rootdir,e.data["filename"].replace("./", ""), re.sub("\s+", "", e.composition.formula), "{:.5f}".format(e.energy), "{:.5f}".format(1000*(e.energy-base_energy)/int(formulaunit)), "{:.5f}".format(e.energy_per_atom), delta_vol,e.parameters['run_type'],na_sites_fcoords_list_tuple] if args.structure: entry_data.extend([entry_site_info['Total_Na_Site'],entry_site_info['Na2_Site'],entry_site_info['Na1_Mn_Site'], entry_site_info['Na1_Co_Site'],entry_site_info['Na1_Mn_Co_Site']]) if args.template: entry_data.extend([template_site_info['Total_Na_Site'],template_site_info['Na2_Site'],template_site_info['Na1_Mn_Site'], template_site_info['Na1_Co_Site'],template_site_info['Na1_Mn_Co_Site']]) # sitelist = ['Existed','Duplicate_Entry'] logging.debug(e.data) if args.duplicate: # filename.rsplit('/',2)[-2] Duplicate, Duplicat_Entry, Structure_info_dict = check_ex(check_ion_seq,Structure_info_dict, e,args.tolerance) entry_data.extend([Duplicate,Duplicat_Entry]) if args.ion_list: if args.ion_list[0] == "All": ion_list = None else: (start, end) = [int(i) for i in re.split("-", args.ion_list[0])] ion_list = list(range(start, end + 1)) for d in entry_path: magdata = get_magnetization(d, ion_list) entry_data.extend(magdata) if args.ion_avg_list: ave_mag_data, ave_key_list = get_ave_magnetization(entry_path,args.ion_avg_list) entry_data.extend(ave_mag_data) if threshold != 0: all_data.append(entry_data) if float(entry_data[4])<threshold: threscount +=1 elif threshold == 0: all_data.append(entry_data) energy_diff.append("{:.5f}".format(1000*(e.energy-base_energy)/int(formulaunit))) # if len(all_data) > 0: # headers = ("Directory", "Formula", "Energy", "Energy Diff (meV)/F.U.","E/Atom", "% vol chg") # t = PrettyTable(headers) # t.align["Directory"] = "l" # for d in all_data: # logging.debug('data row in all data is: \n {}'.format(d)) # t.add_row(d) # print(t) # print(msg) # else: # print("No valid vasp run found.") if hull: print 'Analyzing group: {}\n'.format(rootdir) print 'Energy above hull is: \n' print map(lambda x: x.encode('ascii'), energy_diff) logging.info('In group: {}, number of entries fall in threshold is {}'.format(rootdir,threscount)) all_data.append([]) return all_data