def setUp(self): if "VASP_PSP_DIR" not in os.environ: os.environ["VASP_PSP_DIR"] = test_dir filepath = os.path.join(test_dir, 'POSCAR') poscar = Poscar.from_file(filepath) self.struct = poscar.structure self.mitparamset = MITVaspInputSet() self.mitparamset_unsorted = MITVaspInputSet(sort_structure=False) self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': { "Fe": 10, "S": -5, "Mn3+": 100 }}) self.mitggaparam = MITGGAVaspInputSet() self.mpstaticparamset = MPStaticVaspInputSet() self.mpnscfparamsetu = MPNonSCFVaspInputSet({"NBANDS": 50}, mode="Uniform") self.mpnscfparamsetl = MPNonSCFVaspInputSet({"NBANDS": 60}, mode="Line") self.mphseparamset = MPHSEVaspInputSet() self.mpbshseparamsetl = MPBSHSEVaspInputSet(mode="Line") self.mpbshseparamsetu = MPBSHSEVaspInputSet( mode="Uniform", added_kpoints=[[0.5, 0.5, 0.0]]) self.mpdielparamset = MPStaticDielectricDFPTVaspInputSet()
def __init__(self, struct, struct_type='insulator', ggaU=False, base_param_set=None): self.struct = Structure.from_sites(struct.get_sorted_structure().sites, to_unit_cell=False, validate_proximity=True) if base_param_set: self.base_params = base_param_set else: self.base_params = MITGGAVaspInputSet(hubbard_off=(not ggaU)) self.ggaU = ggaU self.struct_type = struct_type
def setUp(self): if "VASP_PSP_DIR" not in os.environ: os.environ["VASP_PSP_DIR"] = test_dir filepath = os.path.join(test_dir, 'POSCAR') poscar = Poscar.from_file(filepath) self.struct = poscar.structure self.mitparamset = MITVaspInputSet() self.mitparamset_unsorted = MITVaspInputSet(sort_structure=False) self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': {"Fe": 10, "S": -5, "Mn3+": 100}} ) self.mitggaparam = MITGGAVaspInputSet() self.mpstaticparamset = MPStaticVaspInputSet() self.mpnscfparamsetu = MPNonSCFVaspInputSet( {"NBANDS": 50}, mode="Uniform") self.mpnscfparamsetl = MPNonSCFVaspInputSet( {"NBANDS": 60}, mode="Line") self.mphseparamset = MPHSEVaspInputSet() self.mpbshseparamsetl = MPBSHSEVaspInputSet(mode="Line") self.mpbshseparamsetu = MPBSHSEVaspInputSet( mode="Uniform", added_kpoints=[[0.5, 0.5, 0.0]]) self.mpdielparamset = MPStaticDielectricDFPTVaspInputSet()
class MITMPVaspInputSetTest(unittest.TestCase): def setUp(self): if "VASP_PSP_DIR" not in os.environ: os.environ["VASP_PSP_DIR"] = test_dir filepath = os.path.join(test_dir, 'POSCAR') poscar = Poscar.from_file(filepath) self.struct = poscar.structure self.mitparamset = MITVaspInputSet() self.mitparamset_unsorted = MITVaspInputSet(sort_structure=False) self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': {"Fe": 10, "S": -5, "Mn3+": 100}} ) self.mitggaparam = MITGGAVaspInputSet() self.mpstaticparamset = MPStaticVaspInputSet() self.mpnscfparamsetu = MPNonSCFVaspInputSet( {"NBANDS": 50}, mode="Uniform") self.mpnscfparamsetl = MPNonSCFVaspInputSet( {"NBANDS": 60}, mode="Line") self.mphseparamset = MPHSEVaspInputSet() self.mpbshseparamsetl = MPBSHSEVaspInputSet(mode="Line") self.mpbshseparamsetu = MPBSHSEVaspInputSet( mode="Uniform", added_kpoints=[[0.5, 0.5, 0.0]]) self.mpdielparamset = MPStaticDielectricDFPTVaspInputSet() def test_get_poscar(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) s_unsorted = self.mitparamset_unsorted.get_poscar(struct).structure s_sorted = self.mitparamset.get_poscar(struct).structure self.assertEqual(s_unsorted[0].specie.symbol, 'Fe') self.assertEqual(s_sorted[0].specie.symbol, 'Mn') def test_get_potcar_symbols(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.75, 0.25, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe", "O"], coords) syms = self.paramset.get_potcar_symbols(struct) self.assertEqual(syms, ['Fe_pv', 'P', 'O']) syms = MPVaspInputSet(sort_structure=False).get_potcar_symbols(struct) self.assertEqual(syms, ['P', 'Fe_pv', 'O']) def test_false_potcar_hash(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.75, 0.25, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe", "O"], coords) self.mitparamset.potcar_settings['Fe']['symbol'] = 'Fe_pv' self.assertRaises(ValueError, self.mitparamset.get_potcar, struct, check_hash=True) self.mitparamset.potcar_settings['Fe']['symbol'] = 'Fe' def test_lda_potcar(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe"], coords) p = MITVaspInputSet(potcar_functional="LDA").get_potcar(struct) self.assertEqual(p.functional, 'LDA') def test_get_nelect(self): coords = [[0]*3, [0.5]*3, [0.75]*3] lattice = Lattice.cubic(4) s = Structure(lattice, ['Si', 'Si', 'Fe'], coords) self.assertAlmostEqual(MITVaspInputSet().get_nelect(s), 16) def test_get_incar(self): incar = self.paramset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [5.3, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar = self.mitparamset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar_gga = self.mitggaparam.get_incar(self.struct) self.assertNotIn("LDAU", incar_gga) incar_static = self.mpstaticparamset.get_incar(self.struct) self.assertEqual(incar_static["NSW"], 0) incar_nscfl = self.mpnscfparamsetl.get_incar(self.struct) self.assertEqual(incar_nscfl["NBANDS"], 60) incar_nscfu = self.mpnscfparamsetu.get_incar(self.struct) self.assertEqual(incar_nscfu["ISYM"], 0) incar_hse = self.mphseparamset.get_incar(self.struct) self.assertEqual(incar_hse['LHFCALC'], True) self.assertEqual(incar_hse['HFSCREEN'], 0.2) incar_hse_bsl = self.mpbshseparamsetl.get_incar(self.struct) self.assertEqual(incar_hse_bsl['LHFCALC'], True) self.assertEqual(incar_hse_bsl['HFSCREEN'], 0.2) self.assertEqual(incar_hse_bsl['NSW'], 0) incar_hse_bsu = self.mpbshseparamsetu.get_incar(self.struct) self.assertEqual(incar_hse_bsu['LHFCALC'], True) self.assertEqual(incar_hse_bsu['HFSCREEN'], 0.2) self.assertEqual(incar_hse_bsu['NSW'], 0) incar_diel = self.mpdielparamset.get_incar(self.struct) self.assertEqual(incar_diel['IBRION'], 8) self.assertEqual(incar_diel['LEPSILON'], True) si = 14 coords = list() coords.append(np.array([0, 0, 0])) coords.append(np.array([0.75, 0.5, 0.75])) #Silicon structure for testing. latt = Lattice(np.array([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]])) struct = Structure(latt, [si, si], coords) incar = self.paramset.get_incar(struct) self.assertNotIn("LDAU", incar) incar = self.mithseparamset.get_incar(self.struct) self.assertTrue(incar['LHFCALC']) coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertNotIn('LDAU', incar) #check fluorides struct = Structure(lattice, ["Fe", "F"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) self.assertEqual(incar['MAGMOM'], [5, 0.6]) struct = Structure(lattice, ["Fe", "F"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0]) #Make sure this works with species. struct = Structure(lattice, ["Fe2+", "O2-"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) struct = Structure(lattice, ["Fe", "Mn"], coords, site_properties={'magmom': (5.2, -4.5)}) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mpstaticparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mitparamset_unsorted.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5.2, -4.5]) struct = Structure(lattice, [Specie("Fe", 2, {'spin': 4.1}), "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5, 4.1]) incar = self.mpnscfparamsetl.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) struct = Structure(lattice, ["Mn3+", "Mn4+"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [4, 3]) incar = self.mpnscfparamsetu.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) self.assertEqual(self.userparamset.get_incar(struct)['MAGMOM'], [100, 0.6]) #sulfide vs sulfate test coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.25, 0.5, 0]) struct = Structure(lattice, ["Fe", "Fe", "S"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [1.9, 0]) #Make sure Matproject sulfides are ok. self.assertNotIn('LDAUU', self.paramset.get_incar(struct)) self.assertNotIn('LDAUU', self.mpstaticparamset.get_incar(struct)) struct = Structure(lattice, ["Fe", "S", "O"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) #Make sure Matproject sulfates are ok. self.assertEqual(self.paramset.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual(self.mpnscfparamsetl.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual(self.userparamset.get_incar(struct)['MAGMOM'], [10, -5, 0.6]) def test_optics(self): self.mpopticsparamset = MPOpticsNonSCFVaspInputSet.from_previous_vasp_run( '{}/static_silicon'.format(test_dir), output_dir='optics_test_dir', nedos=1145) self.assertTrue(os.path.exists('optics_test_dir/CHGCAR')) incar = Incar.from_file('optics_test_dir/INCAR') self.assertTrue(incar['LOPTICS']) self.assertEqual(incar['NEDOS'], 1145) #Remove the directory in which the inputs have been created shutil.rmtree('optics_test_dir') def test_get_kpoints(self): kpoints = self.paramset.get_kpoints(self.struct) self.assertEqual(kpoints.kpts, [[2, 4, 6]]) self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst) kpoints = self.mitparamset.get_kpoints(self.struct) self.assertEqual(kpoints.kpts, [[2, 4, 6]]) self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst) kpoints = self.mpstaticparamset.get_kpoints(self.struct) self.assertEqual(kpoints.kpts, [[6, 6, 4]]) self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst) kpoints = self.mpnscfparamsetl.get_kpoints(self.struct) self.assertEqual(kpoints.num_kpts, 140) self.assertEqual(kpoints.style, Kpoints.supported_modes.Reciprocal) kpoints = self.mpnscfparamsetu.get_kpoints(self.struct) self.assertEqual(kpoints.num_kpts, 168) kpoints = self.mpbshseparamsetl.get_kpoints(self.struct) self.assertAlmostEqual(kpoints.num_kpts, 164) self.assertAlmostEqual(kpoints.kpts[10][0], 0.0) self.assertAlmostEqual(kpoints.kpts[10][1], 0.5) self.assertAlmostEqual(kpoints.kpts[10][2], 0.16666667) self.assertAlmostEqual(kpoints.kpts[26][0], 0.0714285714286) self.assertAlmostEqual(kpoints.kpts[26][1], 0.0) self.assertAlmostEqual(kpoints.kpts[26][2], 0.0) self.assertAlmostEqual(kpoints.kpts[-1][0], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][1], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][2], 0.5) kpoints = self.mpbshseparamsetu.get_kpoints(self.struct) self.assertAlmostEqual(kpoints.num_kpts, 25) self.assertAlmostEqual(kpoints.kpts[10][0], 0.0) self.assertAlmostEqual(kpoints.kpts[10][1], 0.5) self.assertAlmostEqual(kpoints.kpts[10][2], 0.16666667) self.assertAlmostEqual(kpoints.kpts[-1][0], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][1], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][2], 0.0) def test_get_all_vasp_input(self): d = self.mitparamset.get_all_vasp_input(self.struct) self.assertEqual(d["INCAR"]["ISMEAR"], -5) self.struct.make_supercell(4) d = self.mitparamset.get_all_vasp_input(self.struct) self.assertEqual(d["INCAR"]["ISMEAR"], 0) def test_to_from_dict(self): self.mitparamset = MITVaspInputSet() self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': {"Fe": 10, "S": -5, "Mn3+": 100}} ) d = self.mitparamset.as_dict() v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 4) d = self.mitggaparam.as_dict() v = dec.process_decoded(d) self.assertNotIn("LDAUU", v.incar_settings) d = self.mithseparamset.as_dict() v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LHFCALC"], True) d = self.mphseparamset.as_dict() v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LHFCALC"], True) d = self.paramset.as_dict() v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 5.3) d = self.userparamset.as_dict() v = dec.process_decoded(d) #self.assertEqual(type(v), MPVaspInputSet) self.assertEqual(v.incar_settings["MAGMOM"], {"Fe": 10, "S": -5, "Mn3+": 100})
class MITMPVaspInputSetTest(unittest.TestCase): def setUp(self): if "VASP_PSP_DIR" not in os.environ: os.environ["VASP_PSP_DIR"] = test_dir filepath = os.path.join(test_dir, 'POSCAR') poscar = Poscar.from_file(filepath) self.struct = poscar.structure self.mitparamset = MITVaspInputSet() self.mitparamset_unsorted = MITVaspInputSet(sort_structure=False) self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': { "Fe": 10, "S": -5, "Mn3+": 100 }}) self.mitggaparam = MITGGAVaspInputSet() self.mpstaticparamset = MPStaticVaspInputSet() self.mpnscfparamsetu = MPNonSCFVaspInputSet({"NBANDS": 50}, mode="Uniform") self.mpnscfparamsetl = MPNonSCFVaspInputSet({"NBANDS": 60}, mode="Line") self.mphseparamset = MPHSEVaspInputSet() self.mpbshseparamsetl = MPBSHSEVaspInputSet(mode="Line") self.mpbshseparamsetu = MPBSHSEVaspInputSet( mode="Uniform", added_kpoints=[[0.5, 0.5, 0.0]]) self.mpdielparamset = MPStaticDielectricDFPTVaspInputSet() def test_get_poscar(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) s_unsorted = self.mitparamset_unsorted.get_poscar(struct).structure s_sorted = self.mitparamset.get_poscar(struct).structure self.assertEqual(s_unsorted[0].specie.symbol, 'Fe') self.assertEqual(s_sorted[0].specie.symbol, 'Mn') def test_get_potcar_symbols(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.75, 0.25, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe", "O"], coords) syms = self.paramset.get_potcar_symbols(struct) self.assertEqual(syms, ['Fe_pv', 'P', 'O']) syms = MPVaspInputSet(sort_structure=False).get_potcar_symbols(struct) self.assertEqual(syms, ['P', 'Fe_pv', 'O']) def test_false_potcar_hash(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.75, 0.25, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe", "O"], coords) self.mitparamset.potcar_settings['Fe']['symbol'] = 'Fe_pv' self.assertRaises(ValueError, self.mitparamset.get_potcar, struct, check_hash=True) self.mitparamset.potcar_settings['Fe']['symbol'] = 'Fe' def test_lda_potcar(self): coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["P", "Fe"], coords) p = MITVaspInputSet(potcar_functional="LDA").get_potcar(struct) self.assertEqual(p.functional, 'LDA') def test_get_nelect(self): coords = [[0] * 3, [0.5] * 3, [0.75] * 3] lattice = Lattice.cubic(4) s = Structure(lattice, ['Si', 'Si', 'Fe'], coords) self.assertAlmostEqual(MITVaspInputSet().get_nelect(s), 16) def test_get_incar(self): incar = self.paramset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [5.3, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar = self.mitparamset.get_incar(self.struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) self.assertAlmostEqual(incar['EDIFF'], 0.0012) incar_gga = self.mitggaparam.get_incar(self.struct) self.assertNotIn("LDAU", incar_gga) incar_static = self.mpstaticparamset.get_incar(self.struct) self.assertEqual(incar_static["NSW"], 0) incar_nscfl = self.mpnscfparamsetl.get_incar(self.struct) self.assertEqual(incar_nscfl["NBANDS"], 60) incar_nscfu = self.mpnscfparamsetu.get_incar(self.struct) self.assertEqual(incar_nscfu["ISYM"], 0) incar_hse = self.mphseparamset.get_incar(self.struct) self.assertEqual(incar_hse['LHFCALC'], True) self.assertEqual(incar_hse['HFSCREEN'], 0.2) incar_hse_bsl = self.mpbshseparamsetl.get_incar(self.struct) self.assertEqual(incar_hse_bsl['LHFCALC'], True) self.assertEqual(incar_hse_bsl['HFSCREEN'], 0.2) self.assertEqual(incar_hse_bsl['NSW'], 0) incar_hse_bsu = self.mpbshseparamsetu.get_incar(self.struct) self.assertEqual(incar_hse_bsu['LHFCALC'], True) self.assertEqual(incar_hse_bsu['HFSCREEN'], 0.2) self.assertEqual(incar_hse_bsu['NSW'], 0) incar_diel = self.mpdielparamset.get_incar(self.struct) self.assertEqual(incar_diel['IBRION'], 8) self.assertEqual(incar_diel['LEPSILON'], True) si = 14 coords = list() coords.append(np.array([0, 0, 0])) coords.append(np.array([0.75, 0.5, 0.75])) #Silicon structure for testing. latt = Lattice( np.array([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]])) struct = Structure(latt, [si, si], coords) incar = self.paramset.get_incar(struct) self.assertNotIn("LDAU", incar) incar = self.mithseparamset.get_incar(self.struct) self.assertTrue(incar['LHFCALC']) coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice([[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]) struct = Structure(lattice, ["Fe", "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertNotIn('LDAU', incar) #check fluorides struct = Structure(lattice, ["Fe", "F"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) self.assertEqual(incar['MAGMOM'], [5, 0.6]) struct = Structure(lattice, ["Fe", "F"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0]) #Make sure this works with species. struct = Structure(lattice, ["Fe2+", "O2-"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['LDAUU'], [5.3, 0]) struct = Structure(lattice, ["Fe", "Mn"], coords, site_properties={'magmom': (5.2, -4.5)}) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mpstaticparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [-4.5, 5.2]) incar = self.mitparamset_unsorted.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5.2, -4.5]) struct = Structure(lattice, [Specie("Fe", 2, {'spin': 4.1}), "Mn"], coords) incar = self.paramset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [5, 4.1]) incar = self.mpnscfparamsetl.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) struct = Structure(lattice, ["Mn3+", "Mn4+"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['MAGMOM'], [4, 3]) incar = self.mpnscfparamsetu.get_incar(struct) self.assertEqual(incar.get('MAGMOM', None), None) self.assertEqual( self.userparamset.get_incar(struct)['MAGMOM'], [100, 0.6]) #sulfide vs sulfate test coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) coords.append([0.25, 0.5, 0]) struct = Structure(lattice, ["Fe", "Fe", "S"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [1.9, 0]) #Make sure Matproject sulfides are ok. self.assertNotIn('LDAUU', self.paramset.get_incar(struct)) self.assertNotIn('LDAUU', self.mpstaticparamset.get_incar(struct)) struct = Structure(lattice, ["Fe", "S", "O"], coords) incar = self.mitparamset.get_incar(struct) self.assertEqual(incar['LDAUU'], [4.0, 0, 0]) #Make sure Matproject sulfates are ok. self.assertEqual(self.paramset.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual( self.mpnscfparamsetl.get_incar(struct)['LDAUU'], [5.3, 0, 0]) self.assertEqual( self.userparamset.get_incar(struct)['MAGMOM'], [10, -5, 0.6]) def test_optics(self): self.mpopticsparamset = MPOpticsNonSCFVaspInputSet.from_previous_vasp_run( '{}/static_silicon'.format(test_dir), output_dir='optics_test_dir', nedos=1145) self.assertTrue(os.path.exists('optics_test_dir/CHGCAR')) incar = Incar.from_file('optics_test_dir/INCAR') self.assertTrue(incar['LOPTICS']) self.assertEqual(incar['NEDOS'], 1145) #Remove the directory in which the inputs have been created shutil.rmtree('optics_test_dir') def test_get_kpoints(self): kpoints = self.paramset.get_kpoints(self.struct) self.assertEqual(kpoints.kpts, [[2, 4, 6]]) self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst) kpoints = self.mitparamset.get_kpoints(self.struct) self.assertEqual(kpoints.kpts, [[2, 4, 6]]) self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst) kpoints = self.mpstaticparamset.get_kpoints(self.struct) self.assertEqual(kpoints.kpts, [[6, 6, 4]]) self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst) kpoints = self.mpnscfparamsetl.get_kpoints(self.struct) self.assertEqual(kpoints.num_kpts, 140) self.assertEqual(kpoints.style, Kpoints.supported_modes.Reciprocal) kpoints = self.mpnscfparamsetu.get_kpoints(self.struct) self.assertEqual(kpoints.num_kpts, 168) kpoints = self.mpbshseparamsetl.get_kpoints(self.struct) self.assertAlmostEqual(kpoints.num_kpts, 164) self.assertAlmostEqual(kpoints.kpts[10][0], 0.0) self.assertAlmostEqual(kpoints.kpts[10][1], 0.5) self.assertAlmostEqual(kpoints.kpts[10][2], 0.16666667) self.assertAlmostEqual(kpoints.kpts[26][0], 0.0714285714286) self.assertAlmostEqual(kpoints.kpts[26][1], 0.0) self.assertAlmostEqual(kpoints.kpts[26][2], 0.0) self.assertAlmostEqual(kpoints.kpts[-1][0], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][1], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][2], 0.5) kpoints = self.mpbshseparamsetu.get_kpoints(self.struct) self.assertAlmostEqual(kpoints.num_kpts, 25) self.assertAlmostEqual(kpoints.kpts[10][0], 0.0) self.assertAlmostEqual(kpoints.kpts[10][1], 0.5) self.assertAlmostEqual(kpoints.kpts[10][2], 0.16666667) self.assertAlmostEqual(kpoints.kpts[-1][0], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][1], 0.5) self.assertAlmostEqual(kpoints.kpts[-1][2], 0.0) def test_get_all_vasp_input(self): d = self.mitparamset.get_all_vasp_input(self.struct) self.assertEqual(d["INCAR"]["ISMEAR"], -5) self.struct.make_supercell(4) d = self.mitparamset.get_all_vasp_input(self.struct) self.assertEqual(d["INCAR"]["ISMEAR"], 0) def test_to_from_dict(self): self.mitparamset = MITVaspInputSet() self.mithseparamset = MITHSEVaspInputSet() self.paramset = MPVaspInputSet() self.userparamset = MPVaspInputSet( user_incar_settings={'MAGMOM': { "Fe": 10, "S": -5, "Mn3+": 100 }}) d = self.mitparamset.as_dict() v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 4) d = self.mitggaparam.as_dict() v = dec.process_decoded(d) self.assertNotIn("LDAUU", v.incar_settings) d = self.mithseparamset.as_dict() v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LHFCALC"], True) d = self.mphseparamset.as_dict() v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LHFCALC"], True) d = self.paramset.as_dict() v = dec.process_decoded(d) self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 5.3) d = self.userparamset.as_dict() v = dec.process_decoded(d) #self.assertEqual(type(v), MPVaspInputSet) self.assertEqual(v.incar_settings["MAGMOM"], { "Fe": 10, "S": -5, "Mn3+": 100 })
class VaspBulk(object): def __init__(self, struct, struct_type='insulator', ggaU=False, base_param_set=None): self.struct = Structure.from_sites(struct.get_sorted_structure().sites, to_unit_cell=False, validate_proximity=True) if base_param_set: self.base_params = base_param_set else: self.base_params = MITGGAVaspInputSet(hubbard_off=(not ggaU)) self.ggaU = ggaU self.struct_type = struct_type def get_incar(self, cg_algo=False, relax=False): incar = self.base_params.get_incar(self.struct) #--------------------------------------------------------------------------------------------------------------- # Basic setup #--------------------------------------------------------------------------------------------------------------- incar['ISYM'] = 0 # Symmetry bad, symmetry go away incar["SYMPREC"] = 1e-8 incar['ISIF'] = 3 incar['ISMEAR'] = 0 if self.struct_type == 'insulator': incar['SIGMA'] = 0.05 elif self.struct_type == 'metal': incar['SIGMA'] = 0.2 incar['LREAL'] = 'Auto' incar['LVTOT'] = False incar['LVHAR'] = False incar['LWAVE'] = False incar['LCHARG'] = True #incar['GGA'] = 'PS' # For turning on PBEsol - here just use normal PBE incar['ICHARG'] = 2 incar['ISTART'] = 0 incar['LVTOT'] = True incar['LVHAR'] = True #--------------------------------------------------------------------------------------------------------------- # Convergence changes #--------------------------------------------------------------------------------------------------------------- if not cg_algo: incar['ALGO'] = 'Fast' else: incar['ALGO'] = 'A' incar['LSUBROT'] = False incar['TIME'] = 0.2 incar['AMIX'] = 0.2 incar['AMIN'] = 0.01 incar['BMIX'] = 0.0001 incar['AMIX_MAG'] = 0.8 incar['BMIX_MAG'] = 0.0001 incar['LMAXMIX'] = 4 #incar['LASPH'] = True # Generally should be set as it fixes lots of problems but its inconsistent with the # runs in MP and Matgen so keep it off incar['EDIFF'] = 1e-6 * len(self.struct.sites) incar['NELMDL'] = -6 incar['NELMIN'] = 8 incar['ISIF'] = 2 # For Vesta incar['NPAR'] = 8 # For Vesta end #--------------------------------------------------------------------------------------------------------------- # Relaxation #--------------------------------------------------------------------------------------------------------------- if relax: incar['IBRION'] = 2 incar['NSW'] = 100 incar['POTIM'] = 0.25 else: incar["IBRION"] = -1 incar["NSW"] = 0 #--------------------------------------------------------------------------------------------------------------- # Make sure +U is turned off if necessary #--------------------------------------------------------------------------------------------------------------- if not self.ggaU: delete_keys = ["LDAU", "LDAUJ", "LDAUL", "LDAUTYPE", "LDAUU"] for key in delete_keys: if key in incar.keys(): del incar[key] return incar def get_potcar(self): potcar = self.base_params.get_potcar(self.struct) return potcar def get_kpoints(self): kpoints = Kpoints.gamma_automatic((1, 1, 1), shift=(0, 0, 0)) return kpoints def get_poscar(self): structure = self.struct.get_sorted_structure() selective_dynamics = np.zeros((structure.num_sites, 3), dtype=bool) selective_dynamics = list(selective_dynamics) poscar = Poscar(structure, selective_dynamics=selective_dynamics) return poscar
class PointRunInput(object): def __init__(self, struct, struct_type='insulator', ggaU=False, base_param_set=None): self.struct = Structure.from_sites(struct.get_sorted_structure().sites, to_unit_cell=False, validate_proximity=True) if base_param_set: self.base_params = base_param_set else: self.base_params = MITGGAVaspInputSet(hubbard_off=(not ggaU)) self.ggaU = ggaU self.struct_type = struct_type def get_incar(self, cg_algo=False, relax=True): incar = self.base_params.get_incar(self.struct) #--------------------------------------------------------------------------------------------------------------- # Basic setup #--------------------------------------------------------------------------------------------------------------- incar['ISYM'] = 0 # Symmetry bad, symmetry go away incar['ISIF'] = 2 incar['ISPIN'] = 2 incar['ISPIND'] = 2 #incar['ISIF'] = 2 #This should be changed back to 2 in production phase incar['ISMEAR'] = 0 if self.struct_type == 'insulator': incar['SIGMA'] = 0.05 elif self.struct_type == 'metal': incar['SIGMA'] = 0.2 incar['LREAL'] = 'Auto' #incar['LREAL'] = False #This setting needs to be changed back to Auto in production phase #incar['LVTOT'] = False #incar['LVHAR'] = False incar['LWAVE'] = False incar['LCHARG'] = True incar['LPLANE'] = True #incar['GGA'] = 'PS' For turning on PBEsol - here just use normal PBE incar['ICHARG'] = 2 incar['ISTART'] = 0 incar['LORBIT'] = 0 incar['LSCALU'] = False #--------------------------------------------------------------------------------------------------------------- # Convergence changes #--------------------------------------------------------------------------------------------------------------- if not cg_algo: incar['ALGO'] = 'Fast' else: incar['ALGO'] = 'A' incar['LSUBROT'] = False incar['TIME'] = 0.2 #incar['AMIX'] = 0.2 #incar['AMIN'] = 0.01 #incar['BMIX'] = 0.0001 #incar['AMIX_MAG'] = 0.8 #incar['BMIX_MAG'] = 0.0001 #incar['LMAXMIX'] = 4 #incar['LASPH'] = True # Generally should be set as it fixes lots of problems but its inconsistent with the # runs in MP and Matgen so keep it off incar['EDIFF'] = 1e-5 * len(self.struct.sites) #incar['NELMDL'] = -6 incar['NELMIN'] = 4 incar['NELM'] = 100 # For Vesta incar['NPAR'] = 8 # For Vesta end incar['NSIM'] = 4 incar['PREC'] = 'High' #--------------------------------------------------------------------------------------------------------------- # Relaxation #--------------------------------------------------------------------------------------------------------------- if relax: incar['IBRION'] = 1 incar['NSW'] = 200 incar['POTIM'] = 0.25 else: incar["IBRION"] = -1 incar["NSW"] = 0 #--------------------------------------------------------------------------------------------------------------- # Make sure +U is turned off if necessary #--------------------------------------------------------------------------------------------------------------- if not self.ggaU: delete_keys = ["LDAU", "LDAUJ", "LDAUL", "LDAUTYPE", "LDAUU"] for key in delete_keys: if key in incar.keys(): del incar[key] return incar def get_potcar(self): potcar = self.base_params.get_potcar(self.struct) return potcar def get_kpoints(self): kpoints = Kpoints.automatic_density(self.struct, kppa=1000) return kpoints def get_poscar(self, e): structure = self.struct.get_sorted_structure() index = 0 for i, site in enumerate(structure.sites): if site.specie == e: index = i selective_dynamics = np.ones((structure.num_sites, 3), dtype=bool) selective_dynamics[index, :] = np.zeros(3, dtype=bool) #Fix Furthest atom from moving cation dis_from_cation = 0 fix_index = index for i, site in enumerate(structure.sites): if site.distance(structure.sites[index]) > dis_from_cation: dis_from_cation = site.distance(structure.sites[index]) fix_index = i selective_dynamics[fix_index, :] = np.zeros(3, dtype=bool) selective_dynamics = list(selective_dynamics) poscar = Poscar(structure, selective_dynamics=selective_dynamics) return poscar