class MITMPVaspInputSetTest(unittest.TestCase):
def setUp(self):
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.assertEquals(syms, ['Fe_pv', 'P', 'O'])
syms = MPVaspInputSet(sort_structure=False).get_potcar_symbols(struct)
self.assertEquals(syms, ['P', 'Fe_pv', 'O'])
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):
if "VASP_PSP_DIR" not in os.environ:
os.environ["VASP_PSP_DIR"] = test_dir
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.assertEquals(kpoints.kpts, [[4, 4, 6]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mitparamset.get_kpoints(self.struct)
self.assertEquals(kpoints.kpts, [[4, 4, 6]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mpstaticparamset.get_kpoints(self.struct)
self.assertEquals(kpoints.kpts, [[6, 6, 4]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mpnscfparamsetl.get_kpoints(self.struct)
self.assertEquals(kpoints.num_kpts, 140)
self.assertEquals(kpoints.style, 'Reciprocal')
kpoints = self.mpnscfparamsetu.get_kpoints(self.struct)
self.assertEquals(kpoints.num_kpts, 240)
kpoints = self.mpbshseparamsetl.get_kpoints(self.struct)
self.assertAlmostEquals(kpoints.num_kpts, 176)
self.assertAlmostEqual(kpoints.kpts[10][0], 0.25)
self.assertAlmostEqual(kpoints.kpts[10][1], 0.0)
self.assertAlmostEqual(kpoints.kpts[10][2], 0.16666667)
self.assertAlmostEqual(kpoints.kpts[-1][0], 0.66006924)
self.assertAlmostEqual(kpoints.kpts[-1][1], 0.51780182)
self.assertAlmostEqual(kpoints.kpts[-1][2], 0.30173482)
kpoints = self.mpbshseparamsetu.get_kpoints(self.struct)
self.assertAlmostEquals(kpoints.num_kpts, 37)
self.assertAlmostEqual(kpoints.kpts[10][0], 0.25)
self.assertAlmostEqual(kpoints.kpts[10][1], 0.0)
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_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.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 4)
d = self.mitggaparam.to_dict
v = dec.process_decoded(d)
self.assertNotIn("LDAUU", v.incar_settings)
d = self.mithseparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LHFCALC"], True)
d = self.mphseparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LHFCALC"], True)
d = self.paramset.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 5.3)
d = self.userparamset.to_dict
v = dec.process_decoded(d)
#self.assertEqual(type(v), MPVaspInputSet)
self.assertEqual(v.incar_settings["MAGMOM"],
{"Fe": 10, "S": -5, "Mn3+": 100})
from pymatgen.io.vaspio.vasp_input import Kpoints,Incar
from pymatgen.io.vaspio.vasp_output import Outcar, Vasprun
from pymatgen.io.vaspio_set import MPNonSCFVaspInputSet, MPStaticVaspInputSet
import os
if __name__ == '__main__':
mpr = MPRester(api_key="UhlZvcEux2kmJSQx")
id_expgap = open("ids.txt", "r")
for line in id_expgap:
words=line.split()
print words
id_line=words[0]
vasp_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), str(id_line))
vasp_run = Vasprun(os.path.join(vasp_dir,"vasprun.xml")).to_dict
nband = int(vasp_run['input']['parameters']['NBANDS'])
os.chdir(id_line)
user_incar_settings={"EDIFF":1E-4,"NBANDS":nband,"NSW":0}
mpvis = MPNonSCFVaspInputSet(user_incar_settings=user_incar_settings)
s = mpr.get_structure_by_material_id(id_line)
mpvis.get_kpoints(s).write_file('KPOINTS')
mpvis.get_incar(s).write_file('INCAR')
os.chdir('..')
id_expgap.close()
class MITMPVaspInputSetTest(unittest.TestCase):
def setUp(self):
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")
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.assertEquals(syms, ['Fe_pv', 'P', 'O'])
syms = MPVaspInputSet(sort_structure=False).get_potcar_symbols(struct)
self.assertEquals(syms, ['P', 'Fe_pv', 'O'])
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)
si = 14
coords = list()
coords.append(array([0, 0, 0]))
coords.append(array([0.75, 0.5, 0.75]))
#Silicon structure for testing.
latt = Lattice(
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_get_kpoints(self):
kpoints = self.paramset.get_kpoints(self.struct)
self.assertEquals(kpoints.kpts, [[2, 4, 6]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mitparamset.get_kpoints(self.struct)
self.assertEquals(kpoints.kpts, [[2, 4, 6]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mpstaticparamset.get_kpoints(self.struct)
self.assertEquals(kpoints.kpts, [[4, 6, 6]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mpnscfparamsetl.get_kpoints(self.struct)
self.assertEquals(kpoints.num_kpts, 140)
self.assertEquals(kpoints.style, 'Reciprocal')
kpoints = self.mpnscfparamsetu.get_kpoints(self.struct)
self.assertEquals(kpoints.num_kpts, 168)
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.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 4)
d = self.mitggaparam.to_dict
v = dec.process_decoded(d)
self.assertNotIn("LDAUU", v.incar_settings)
d = self.mithseparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LHFCALC"], True)
d = self.paramset.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 5.3)
d = self.userparamset.to_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):
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")
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.assertEquals(syms, ['Fe_pv', 'P', 'O'])
syms = MPVaspInputSet(sort_structure=False).get_potcar_symbols(struct)
self.assertEquals(syms, ['P', 'Fe_pv', 'O'])
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)
si = 14
coords = list()
coords.append(array([0, 0, 0]))
coords.append(array([0.75, 0.5, 0.75]))
#Silicon structure for testing.
latt = Lattice(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_get_kpoints(self):
kpoints = self.paramset.get_kpoints(self.struct)
self.assertEquals(kpoints.kpts, [[2, 4, 6]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mitparamset.get_kpoints(self.struct)
self.assertEquals(kpoints.kpts, [[2, 4, 6]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mpstaticparamset.get_kpoints(self.struct)
self.assertEquals(kpoints.kpts, [[4, 6, 6]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mpnscfparamsetl.get_kpoints(self.struct)
self.assertEquals(kpoints.num_kpts, 140)
self.assertEquals(kpoints.style, 'Reciprocal')
kpoints = self.mpnscfparamsetu.get_kpoints(self.struct)
self.assertEquals(kpoints.num_kpts, 168)
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.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 4)
d = self.mitggaparam.to_dict
v = dec.process_decoded(d)
self.assertNotIn("LDAUU", v.incar_settings)
d = self.mithseparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LHFCALC"], True)
d = self.paramset.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 5.3)
d = self.userparamset.to_dict
v = dec.process_decoded(d)
#self.assertEqual(type(v), MPVaspInputSet)
self.assertEqual(v.incar_settings["MAGMOM"],
{"Fe": 10, "S": -5, "Mn3+": 100})
__author__ = 'Qimin'
from pymatgen.io.vaspio.vasp_output import Vasprun
from pymatgen.io.vaspio.vasp_input import VaspInput
from pymatgen.io.vaspio_set import MPNonSCFVaspInputSet
import os
vasp_dir = os.path.dirname(os.path.abspath(__file__))
vasp_run = Vasprun(os.path.join(vasp_dir, "vasprun.xml")).to_dict
nband = int(vasp_run['input']['parameters']['NBANDS'])
prec = str(vasp_run['input']['incar']['PREC'])
encut = int(vasp_run['input']['incar']['ENCUT'])
user_incar_settings={"PREC":prec,"ENCUT":encut,"EDIFF":1E-4,"NBANDS":nband,"NSW":0}
#user_incar_settings={"EDIFF":1E-4,"NBANDS":nband,"NSW":0}
mpvis = MPNonSCFVaspInputSet(user_incar_settings=user_incar_settings)
vi = VaspInput.from_directory(".") # read the VaspInput from the previous run
mpvis.get_kpoints(vi['POSCAR'].structure).write_file('KPOINTS')
mpvis.get_incar(vi['POSCAR'].structure).write_file('INCAR')
class MITMPVaspInputSetTest(unittest.TestCase):
def setUp(self):
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.assertEquals(syms, ['Fe_pv', 'P', 'O'])
syms = MPVaspInputSet(sort_structure=False).get_potcar_symbols(struct)
self.assertEquals(syms, ['P', 'Fe_pv', 'O'])
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):
if "VASP_PSP_DIR" not in os.environ:
os.environ["VASP_PSP_DIR"] = test_dir
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.assertEquals(kpoints.kpts, [[2, 4, 6]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mitparamset.get_kpoints(self.struct)
self.assertEquals(kpoints.kpts, [[2, 4, 6]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mpstaticparamset.get_kpoints(self.struct)
self.assertEquals(kpoints.kpts, [[6, 6, 4]])
self.assertEquals(kpoints.style, 'Monkhorst')
kpoints = self.mpnscfparamsetl.get_kpoints(self.struct)
self.assertEquals(kpoints.num_kpts, 140)
self.assertEquals(kpoints.style, 'Reciprocal')
kpoints = self.mpnscfparamsetu.get_kpoints(self.struct)
self.assertEquals(kpoints.num_kpts, 168)
kpoints = self.mpbshseparamsetl.get_kpoints(self.struct)
self.assertAlmostEquals(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[-1][0], 0.66006924)
self.assertAlmostEqual(kpoints.kpts[-1][1], 0.51780182)
self.assertAlmostEqual(kpoints.kpts[-1][2], 0.30173482)
kpoints = self.mpbshseparamsetu.get_kpoints(self.struct)
self.assertAlmostEquals(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_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.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 4)
d = self.mitggaparam.to_dict
v = dec.process_decoded(d)
self.assertNotIn("LDAUU", v.incar_settings)
d = self.mithseparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LHFCALC"], True)
d = self.mphseparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LHFCALC"], True)
d = self.paramset.to_dict
v = dec.process_decoded(d)
self.assertEqual(v.incar_settings["LDAUU"]["O"]["Fe"], 5.3)
d = self.userparamset.to_dict
v = dec.process_decoded(d)
#self.assertEqual(type(v), MPVaspInputSet)
self.assertEqual(v.incar_settings["MAGMOM"], {
"Fe": 10,
"S": -5,
"Mn3+": 100
})