def main(api="", queryid=""): """Get VASP inputs for Materials Project structure Args: api <str>: Materials Project API key queryid <str>: Materials Project ID of the structure Returns: creates a folder named with that mpid, and including some VASP input files. """ if api == "": print "Must have an API key from materialsproject.org" return None if queryid == "": print "No MP structure ID given. Exiting." return None rest_adapter = MPRester(api) entries=list() proplist=list() proplist.append('pretty_formula') proplist.append('structure') proplist.append('potcar') proplist.append('material_id') myentry = rest_adapter.mpquery(criteria={'material_id':queryid}, properties=proplist) if len(myentry) == 0: print "Could not find entry for %s as material_id. Trying entry_id." % queryid myentry = rest_adapter.mpquery(criteria={'entry_id':queryid}, properties=proplist) if len(myentry) == 0: print "Could not find entry for %s" % queryid return None entries.extend(myentry) workdir = os.getcwd() from pymatgen.io.vaspio_set import MITVaspInputSet, MPVaspInputSet for entry in entries: mpvis = MPVaspInputSet() myname = str(entry['pretty_formula']) #print entry['structure'].composition #print entry['structure'].formula #myname = entry['pretty_formula'] myname = myname.replace("(","_").replace(")","_") myname = myname + "_" + entry['material_id'] os.mkdir(myname) os.chdir(myname) mystructure = entry['structure'] if mystructure.num_sites <= 10: mystructure.make_supercell([2,2,2]) #mystructure.perturb(0.01) incar = mpvis.get_incar(mystructure) incar.write_file("INCAR") potcar = mpvis.get_potcar(mystructure) potcar.write_file("POTCAR") #potcar_symbols = mpvis.get_potcar_symbols(mystructure) myposcar=Poscar(mystructure) mykpoints=mpvis.get_kpoints(mystructure) mykpoints.write_file("KPOINTS") myposcar.write_file("POSCAR") os.chdir(workdir)
class MPResterTest(unittest.TestCase): def setUp(self): self.rester = MPRester() def test_get_data(self): props = ["energy", "energy_per_atom", "formation_energy_per_atom", "nsites", "unit_cell_formula", "pretty_formula", "is_hubbard", "elements", "nelements", "e_above_hull", "hubbards", "is_compatible", "task_ids", "density", "icsd_id", "total_magnetization"] expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749, 28, {u'P': 4, u'Fe': 4, u'O': 16, u'Li': 4}, "LiFePO4", True, [u'Li', u'O', u'P', u'Fe'], 4, 0.0, {u'Fe': 5.3, u'Li': 0.0, u'O': 0.0, u'P': 0.0}, True, ['mp-540081', 'mp-601412', 'mp-19017'], 3.4662026991351147, [159107, 154117, 160776, 99860, 181272, 166815, 260571, 92198, 165000, 155580, 38209, 161479, 153699, 260569, 260570, 200155, 260572, 181341, 181342, 72545, 56291, 97764, 162282, 155635], 16.0002716] for (i, prop) in enumerate(props): if prop not in ['hubbards', 'unit_cell_formula', 'elements', 'icsd_id']: val = self.rester.get_data("mp-19017", prop=prop)[0][prop] self.assertAlmostEqual(expected_vals[i], val) elif prop in ["elements", "icsd_id"]: self.assertEqual(set(expected_vals[i]), set(self.rester.get_data("mp-19017", prop=prop)[0][prop])) else: self.assertEqual(expected_vals[i], self.rester.get_data("mp-19017", prop=prop)[0][prop]) props = ['structure', 'initial_structure', 'final_structure', 'entry'] for prop in props: obj = self.rester.get_data("mp-19017", prop=prop)[0][prop] if prop.endswith("structure"): self.assertIsInstance(obj, Structure) elif prop == "entry": obj = self.rester.get_data("mp-19017", prop=prop)[0][prop] self.assertIsInstance(obj, ComputedEntry) #Test chemsys search data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula') self.assertTrue(len(data) > 1) elements = {Element("Li"), Element("Fe"), Element("O")} for d in data: self.assertTrue( set(Composition(d['unit_cell_formula']).elements).issubset( elements)) self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3", "badmethod") def test_get_materials_id_from_task_id(self): self.assertEqual(self.rester.get_materials_id_from_task_id( "mp-540081"), "mp-19017") def test_get_entries_in_chemsys(self): syms = ["Li", "Fe", "O"] all_entries = self.rester.get_entries_in_chemsys(syms, False) entries = self.rester.get_entries_in_chemsys(syms) self.assertTrue(len(entries) <= len(all_entries)) elements = set([Element(sym) for sym in syms]) for e in entries: self.assertIsInstance(e, ComputedEntry) self.assertTrue(set(e.composition.elements).issubset(elements)) def test_get_structure_by_material_id(self): s1 = self.rester.get_structure_by_material_id("mp-1") self.assertEqual(s1.formula, "Cs1") def test_get_entry_by_material_id(self): e = self.rester.get_entry_by_material_id("mp-19017") self.assertIsInstance(e, ComputedEntry) self.assertTrue(e.composition.reduced_formula, "LiFePO4") def test_mpquery(self): criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}} props = ['formula', 'energy'] data = self.rester.mpquery(criteria=criteria, properties=props) self.assertTrue(len(data) > 6) def test_get_exp_thermo_data(self): data = self.rester.get_exp_thermo_data("Fe2O3") self.assertTrue(len(data) > 0) for d in data: self.assertEqual(d.formula, "Fe2O3") def test_get_dos_by_id(self): dos = self.rester.get_dos_by_material_id("mp-2254") self.assertIsInstance(dos, CompleteDos) def test_get_bandstructure_by_material_id(self): bs = self.rester.get_bandstructure_by_material_id("mp-2254") self.assertIsInstance(bs, BandStructureSymmLine) def test_get_structures(self): structs = self.rester.get_structures("Mn3O4") self.assertTrue(len(structs) > 0) for s in structs: self.assertEqual(s.composition.reduced_formula, "Mn3O4") def test_get_entries(self): entries = self.rester.get_entries("TiO2") self.assertTrue(len(entries) > 1) for e in entries: self.assertEqual(e.composition.reduced_formula, "TiO2") entries = self.rester.get_entries("TiO2", inc_structure="final") self.assertTrue(len(entries) > 1) for e in entries: self.assertEqual(e.structure.composition.reduced_formula, "TiO2") def test_get_exp_entry(self): entry = self.rester.get_exp_entry("Fe2O3") self.assertEqual(entry.energy, -825.5) def test_submit_query_delete_snl(self): s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]]) # d = self.rester.submit_snl( # [s, s], remarks=["unittest"], # authors="Test User <*****@*****.**>") # self.assertEqual(len(d), 2) # data = self.rester.query_snl({"about.remarks": "unittest"}) # self.assertEqual(len(data), 2) # snlids = [d["_id"] for d in data] # self.rester.delete_snl(snlids) # data = self.rester.query_snl({"about.remarks": "unittest"}) # self.assertEqual(len(data), 0) def test_get_stability(self): entries = self.rester.get_entries("Fe-O") modified_entries = [] for entry in entries: # Create modified entries with energies that are 0.01eV higher # than the corresponding entries. if entry.composition.reduced_formula == "Fe2O3": modified_entries.append( ComputedEntry(entry.composition, entry.uncorrected_energy + 0.01, parameters=entry.parameters, entry_id="mod_{}".format(entry.entry_id))) rest_ehulls = self.rester.get_stability(modified_entries) all_entries = entries + modified_entries compat = MaterialsProjectCompatibility() all_entries = compat.process_entries(all_entries) pd = PhaseDiagram(all_entries) a = PDAnalyzer(pd) for e in all_entries: if str(e.entry_id).startswith("mod"): for d in rest_ehulls: if d["entry_id"] == e.entry_id: data = d break self.assertAlmostEqual(a.get_e_above_hull(e), data["e_above_hull"])
class MPResterTest(unittest.TestCase): def setUp(self): self.rester = MPRester() def test_get_data(self): props = ["energy", "energy_per_atom", "formation_energy_per_atom", "nsites", "unit_cell_formula", "pretty_formula", "is_hubbard", "elements", "nelements", "e_above_hull", "hubbards", "is_compatible", "task_ids", "density", "icsd_id", "total_magnetization"] expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749, 28, {u'P': 4, u'Fe': 4, u'O': 16, u'Li': 4}, "LiFePO4", True, [u'Li', u'O', u'P', u'Fe'], 4, 0.0, {u'Fe': 5.3, u'Li': 0.0, u'O': 0.0, u'P': 0.0}, True, ['mp-540081', 'mp-601412', 'mp-19017'], 3.4662026991351147, [159107, 154117, 160776, 99860, 181272, 166815, 260571, 92198, 165000, 155580, 38209, 161479, 153699, 260569, 260570, 200155, 260572, 181341, 181342, 72545, 56291, 97764, 162282, 155635], 16.0002716] for (i, prop) in enumerate(props): if prop not in ['hubbards', 'unit_cell_formula', 'elements', 'icsd_id']: val = self.rester.get_data("mp-540081", prop=prop)[0][prop] self.assertAlmostEqual(expected_vals[i], val) elif prop in ["elements", "icsd_id"]: self.assertEqual(set(expected_vals[i]), set(self.rester.get_data("mp-540081", prop=prop)[0][prop])) else: self.assertEqual(expected_vals[i], self.rester.get_data("mp-540081", prop=prop)[0][prop]) props = ['structure', 'initial_structure', 'final_structure', 'entry'] for prop in props: obj = self.rester.get_data("mp-540081", prop=prop)[0][prop] if prop.endswith("structure"): self.assertIsInstance(obj, Structure) elif prop == "entry": obj = self.rester.get_data("mp-540081", prop=prop)[0][prop] self.assertIsInstance(obj, ComputedEntry) #Test chemsys search data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula') self.assertTrue(len(data) > 1) elements = {Element("Li"), Element("Fe"), Element("O")} for d in data: self.assertTrue( set(Composition(d['unit_cell_formula']).elements).issubset( elements)) self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3", "badmethod") def test_get_entries_in_chemsys(self): syms = ["Li", "Fe", "O"] all_entries = self.rester.get_entries_in_chemsys(syms, False) entries = self.rester.get_entries_in_chemsys(syms) self.assertTrue(len(entries) <= len(all_entries)) elements = set([Element(sym) for sym in syms]) for e in entries: self.assertIsInstance(e, ComputedEntry) self.assertTrue(set(e.composition.elements).issubset(elements)) def test_get_structure_by_material_id(self): s1 = self.rester.get_structure_by_material_id("mp-1") self.assertEqual(s1.formula, "Cs1") def test_get_entry_by_material_id(self): e = self.rester.get_entry_by_material_id("mp-540081") self.assertIsInstance(e, ComputedEntry) self.assertTrue(e.composition.reduced_formula, "LiFePO4") def test_mpquery(self): criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}} props = ['formula', 'energy'] data = self.rester.mpquery(criteria=criteria, properties=props) self.assertTrue(len(data) > 6) def test_get_exp_thermo_data(self): data = self.rester.get_exp_thermo_data("Fe2O3") self.assertTrue(len(data) > 0) for d in data: self.assertEqual(d.formula, "Fe2O3") def test_get_dos_by_id(self): dos = self.rester.get_dos_by_material_id("mp-555389") self.assertIsInstance(dos, CompleteDos) def test_get_bandstructure_by_material_id(self): bs = self.rester.get_bandstructure_by_material_id("mp-555389") self.assertIsInstance(bs, BandStructureSymmLine) def test_get_structures(self): structs = self.rester.get_structures("Mn3O4") self.assertTrue(len(structs) > 0) for s in structs: self.assertEqual(s.composition.reduced_formula, "Mn3O4") def test_get_entries(self): entries = self.rester.get_entries("TiO2") self.assertTrue(len(entries) > 1) for e in entries: self.assertEqual(e.composition.reduced_formula, "TiO2") entries = self.rester.get_entries("TiO2", inc_structure="final") self.assertTrue(len(entries) > 1) for e in entries: self.assertEqual(e.structure.composition.reduced_formula, "TiO2") def test_get_exp_entry(self): entry = self.rester.get_exp_entry("Fe2O3") self.assertEqual(entry.energy, -825.5) def test_submit_query_delete_snl(self): s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]]) # d = self.rester.submit_snl( # [s, s], remarks=["unittest"], # authors="Test User <*****@*****.**>") # self.assertEqual(len(d), 2) # data = self.rester.query_snl({"about.remarks": "unittest"}) # self.assertEqual(len(data), 2) # snlids = [d["_id"] for d in data] # self.rester.delete_snl(snlids) # data = self.rester.query_snl({"about.remarks": "unittest"}) # self.assertEqual(len(data), 0) def test_get_stability(self): entries = self.rester.get_entries("Fe-O") modified_entries = [] for entry in entries: # Create modified entries with energies that are 0.01eV higher # than the corresponding entries. if entry.composition.reduced_formula == "Fe2O3": modified_entries.append( ComputedEntry(entry.composition, entry.uncorrected_energy + 0.01, parameters=entry.parameters, entry_id="mod_{}".format(entry.entry_id))) rest_ehulls = self.rester.get_stability(modified_entries) all_entries = entries + modified_entries compat = MaterialsProjectCompatibility() all_entries = compat.process_entries(all_entries) pd = PhaseDiagram(all_entries) a = PDAnalyzer(pd) for e in all_entries: if str(e.entry_id).startswith("mod"): for d in rest_ehulls: if d["entry_id"] == e.entry_id: data = d break self.assertAlmostEqual(a.get_e_above_hull(e), data["e_above_hull"])
def main(api="", queryid=""): """Get VASP inputs for Materials Project structure Args: api <str>: Materials Project API key queryid <str>: Materials Project ID of the structure Returns: creates a folder named with that mpid, and including some VASP input files. """ if api == "": print "Must have an API key from materialsproject.org" return None if queryid == "": print "No MP structure ID given. Exiting." return None rest_adapter = MPRester(api) entries = list() proplist = list() proplist.append('pretty_formula') proplist.append('structure') proplist.append('potcar') proplist.append('material_id') myentry = rest_adapter.mpquery(criteria={'material_id': queryid}, properties=proplist) if len(myentry) == 0: print "Could not find entry for %s as material_id. Trying entry_id." % queryid myentry = rest_adapter.mpquery(criteria={'entry_id': queryid}, properties=proplist) if len(myentry) == 0: print "Could not find entry for %s" % queryid return None entries.extend(myentry) workdir = os.getcwd() from pymatgen.io.vaspio_set import MITVaspInputSet, MPVaspInputSet for entry in entries: mpvis = MPVaspInputSet() myname = str(entry['pretty_formula']) #print entry['structure'].composition #print entry['structure'].formula #myname = entry['pretty_formula'] myname = myname.replace("(", "_").replace(")", "_") myname = myname + "_" + entry['material_id'] os.mkdir(myname) os.chdir(myname) mystructure = entry['structure'] if mystructure.num_sites <= 10: mystructure.make_supercell([2, 2, 2]) #mystructure.perturb(0.01) incar = mpvis.get_incar(mystructure) incar.write_file("INCAR") potcar = mpvis.get_potcar(mystructure) potcar.write_file("POTCAR") #potcar_symbols = mpvis.get_potcar_symbols(mystructure) myposcar = Poscar(mystructure) mykpoints = mpvis.get_kpoints(mystructure) mykpoints.write_file("KPOINTS") myposcar.write_file("POSCAR") os.chdir(workdir)