def run_task(self, fw_spec):
chgcar_start = False
# read the VaspInput from the previous run
poscar = Poscar.from_file(zpath('POSCAR'))
incar = Incar.from_file(zpath('INCAR'))
# figure out what GGA+U values to use and override them
# LDAU values to use
mpvis = MPVaspInputSet()
ggau_incar = mpvis.get_incar(poscar.structure).as_dict()
incar_updates = {k: ggau_incar[k] for k in ggau_incar.keys() if 'LDAU' in k}
for k in ggau_incar:
# update any parameters not set explicitly in previous INCAR
if k not in incar and k in ggau_incar:
incar_updates[k] = ggau_incar[k]
incar.update(incar_updates) # override the +U keys
# start from the CHGCAR of previous run
if os.path.exists('CHGCAR'):
incar['ICHARG'] = 1
chgcar_start = True
# write back the new INCAR to the current directory
incar.write_file('INCAR')
return FWAction(stored_data={'chgcar_start': chgcar_start})
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 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_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})
def get_INCARs(comp_name, mp_api_key, SOC):
from pymatgen.matproj.rest import MPRester
matproj = MPRester(mp_api_key)
structure = matproj.get_structure_by_material_id(comp_name)
from pymatgen.io.vasp.sets import MPVaspInputSet
from pymatgen.io.vasp.sets import MPGGAVaspInputSet # +U is turned off (if any)
from pymatgen.io.vasp.sets import MPHSEVaspInputSet
from pymatgen.io.vasp.sets import MPStaticVaspInputSet
from pymatgen.io.vasp.sets import MPNonSCFVaspInputSet
from pymatgen.io.vasp.sets import MPStaticDielectricDFPTVaspInputSet
from pymatgen.io.vasp.sets import MPBSHSEVaspInputSet
from pymatgen.io.vasp.sets import MPOpticsNonSCFVaspInputSet
v = MPVaspInputSet()
indic = v.get_incar(structure)
k = v.get_all_vasp_input(structure, generate_potcar=False)
incar_file = open('INCAR', 'w')
# if SOC in ['TRUE', 'True', 'true']:
# indic['LMAXMIX'] = 4
# indic['NBANDS'] = soc_NBANDS
# indic['LSORBIT'] = '.TRUE.'
# indic.pop('MAGMOM', None)
incar_file.write(str(indic))
self = MPStaticVaspInputSet()
indic = self.get_incar(structure)
indic['NEDOS'] = 9001
incar_file = open('INCAR_SELF', 'w')
if SOC in ['TRUE', 'True', 'true']:
indic['LMAXMIX'] = 4
indic['NBANDS'] = soc_NBANDS
indic['LSORBIT'] = '.TRUE.'
indic.pop('MAGMOM', None)
incar_file.write(str(indic))
user_incar_settings = {"NBANDS": 100}
nself = MPNonSCFVaspInputSet(user_incar_settings)
indic = nself.get_incar(structure)
incar_file = open('INCAR_NSELF', 'w')
if SOC in ['TRUE', 'True', 'true']:
indic['LMAXMIX'] = 4
indic['NBANDS'] = soc_NBANDS
indic['LSORBIT'] = '.TRUE.'
indic.pop('MAGMOM', None)
incar_file.write(str(indic))
HSE = MPHSEVaspInputSet()
indic = HSE.get_incar(structure)
incar_file = open('INCAR_HSE', 'w')
if SOC in ['TRUE', 'True', 'true']:
indic['LMAXMIX'] = 4
indic['NBANDS'] = soc_NBANDS
indic['LSORBIT'] = '.TRUE.'
indic.pop('MAGMOM', None)
incar_file.write(str(indic))
def get_INCARs(comp_name, mp_api_key, SOC):
from pymatgen.matproj.rest import MPRester
matproj = MPRester(mp_api_key)
structure = matproj.get_structure_by_material_id(comp_name)
from pymatgen.io.vasp.sets import MPVaspInputSet
from pymatgen.io.vasp.sets import MPGGAVaspInputSet # +U is turned off (if any)
from pymatgen.io.vasp.sets import MPHSEVaspInputSet
from pymatgen.io.vasp.sets import MPStaticVaspInputSet
from pymatgen.io.vasp.sets import MPNonSCFVaspInputSet
from pymatgen.io.vasp.sets import MPStaticDielectricDFPTVaspInputSet
from pymatgen.io.vasp.sets import MPBSHSEVaspInputSet
from pymatgen.io.vasp.sets import MPOpticsNonSCFVaspInputSet
v = MPVaspInputSet()
indic = v.get_incar(structure)
k = v.get_all_vasp_input(structure,generate_potcar = False)
incar_file = open('INCAR','w')
if SOC in ['TRUE', 'True', 'true']:
indic['LMAXMIX'] = 4
indic['NBANDS'] = 128
indic['LSORBIT'] = '.TRUE.'
indic.pop('MAGMOM', None)
incar_file.write(str(indic))
self = MPStaticVaspInputSet()
indic = self.get_incar(structure)
indic['NEDOS'] = 9001
incar_file = open('INCAR_SELF','w')
if SOC in ['TRUE', 'True', 'true']:
indic['LMAXMIX'] = 4
indic['NBANDS'] = 128
indic['LSORBIT'] = '.TRUE.'
indic.pop('MAGMOM', None)
incar_file.write(str(indic))
user_incar_settings = {"NBANDS" : 100}
nself = MPNonSCFVaspInputSet(user_incar_settings)
indic = nself.get_incar(structure)
incar_file = open('INCAR_NSELF','w')
if SOC in ['TRUE', 'True', 'true']:
indic['LMAXMIX'] = 4
indic['NBANDS'] = 128
indic['LSORBIT'] = '.TRUE.'
indic.pop('MAGMOM', None)
incar_file.write(str(indic))
HSE = MPHSEVaspInputSet()
indic = HSE.get_incar(structure)
incar_file = open('INCAR_HSE','w')
if SOC in ['TRUE', 'True', 'true']:
indic['LMAXMIX'] = 4
indic['NBANDS'] = 128
indic['LSORBIT'] = '.TRUE.'
indic.pop('MAGMOM', None)
incar_file.write(str(indic))
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)
recip_paramset = MPVaspInputSet(force_gamma=True)
recip_paramset.kpoints_settings = {"reciprocal_density": 40}
kpoints = recip_paramset.get_kpoints(self.struct)
self.assertEqual(kpoints.kpts, [[2, 4, 6]])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
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)
recip_paramset = MPVaspInputSet(force_gamma=True)
recip_paramset.kpoints_settings = {"reciprocal_density": 40}
kpoints = recip_paramset.get_kpoints(self.struct)
self.assertEqual(kpoints.kpts, [[2, 4, 6]])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
def __init__(self, compat_type="Advanced", correct_peroxide=True,
check_potcar_hash=False):
module_dir = os.path.dirname(os.path.abspath(__file__))
fp = os.path.join(module_dir, "MPCompatibility.yaml")
i_s = MPVaspInputSet()
super(MaterialsProjectAqueousCompatibility, self).__init__(
[PotcarCorrection(i_s, check_hash=check_potcar_hash),
GasCorrection(fp, correct_peroxide=correct_peroxide),
UCorrection(fp, i_s, compat_type), AqueousCorrection(fp)])
def _snl_to_spec(snl, enforce_gga=False, parameters=None):
parameters = parameters if parameters else {}
parameters['boltztrap'] = parameters.get('boltztrap',
True) # by default run boltztrap
spec = {'parameters': parameters}
incar_enforce = {'NPAR': 2}
if 'exact_structure' in parameters and parameters['exact_structure']:
structure = snl.structure
else:
structure = snl.structure.get_primitive_structure()
mpvis = MPGGAVaspInputSet(
user_incar_settings=incar_enforce) if enforce_gga else MPVaspInputSet(
user_incar_settings=incar_enforce)
incar = mpvis.get_incar(structure)
poscar = mpvis.get_poscar(structure)
kpoints = mpvis.get_kpoints(structure)
potcar = mpvis.get_potcar(structure)
spec['vasp'] = {}
spec['vasp']['incar'] = incar.as_dict()
spec['vasp']['poscar'] = poscar.as_dict()
spec['vasp']['kpoints'] = kpoints.as_dict()
spec['vasp']['potcar'] = potcar.as_dict()
# Add run tags of pseudopotential
spec['run_tags'] = spec.get('run_tags', [potcar.functional])
spec['run_tags'].extend(potcar.symbols)
# Add run tags of +U
u_tags = [
'%s=%s' % t
for t in zip(poscar.site_symbols,
incar.get('LDAUU', [0] * len(poscar.site_symbols)))
]
spec['run_tags'].extend(u_tags)
# add user run tags
if 'run_tags' in parameters:
spec['run_tags'].extend(parameters['run_tags'])
del spec['parameters']['run_tags']
# add exact structure run tag automatically if we have a unique situation
if 'exact_structure' in parameters and parameters[
'exact_structure'] and snl.structure != snl.structure.get_primitive_structure(
):
spec['run_tags'].extend('exact_structure')
spec['_dupefinder'] = DupeFinderVasp().to_dict()
spec['vaspinputset_name'] = mpvis.__class__.__name__
spec['task_type'] = 'GGA+U optimize structure (2x)' if spec['vasp'][
'incar'].get('LDAU', False) else 'GGA optimize structure (2x)'
return spec
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
})
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_get_vasp_input(self):
vaspis = MPVaspInputSet()
self.assertEqual(
"Na_pv\nFe_pv\nP\nO",
self.trans.get_vasp_input(vaspis, False)['POTCAR.spec'])
self.assertEqual(len(self.trans.structures), 2)
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
})
def snl_to_wf(snl, parameters=None):
fws = []
connections = defaultdict(list)
parameters = parameters if parameters else {}
snl_priority = parameters.get('priority', 1)
priority = snl_priority * 2 # once we start a job, keep going!
f = Composition(
snl.structure.composition.reduced_formula).alphabetical_formula
snl_spec = {}
if 'snlgroup_id' in parameters:
if 'mpsnl' in parameters:
snl_spec['mpsnl'] = parameters['mpsnl']
elif isinstance(snl, MPStructureNL):
snl_spec['mpsnl'] = snl.as_dict()
else:
raise ValueError("improper use of force SNL")
snl_spec['snlgroup_id'] = parameters['snlgroup_id']
else:
# add the SNL to the SNL DB and figure out duplicate group
tasks = [AddSNLTask()]
spec = {
'task_type': 'Add to SNL database',
'snl': snl.as_dict(),
'_queueadapter': QA_DB,
'_priority': snl_priority
}
fws.append(
Firework(tasks,
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=0))
connections[0] = [1]
trackers = [
Tracker('FW_job.out'),
Tracker('FW_job.error'),
Tracker('vasp.out'),
Tracker('OUTCAR'),
Tracker('OSZICAR'),
Tracker('OUTCAR.relax1'),
Tracker('OUTCAR.relax2')
]
trackers_db = [Tracker('FW_job.out'), Tracker('FW_job.error')]
# run GGA structure optimization
spec = _snl_to_spec(snl, enforce_gga=True, parameters=parameters)
spec.update(snl_spec)
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
spec['_trackers'] = trackers
tasks = [VaspWriterTask(), get_custodian_task(spec)]
fws.append(
Firework(tasks,
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=1))
# insert into DB - GGA structure optimization
spec = {
'task_type': 'VASP db insertion',
'_priority': priority * 2,
'_allow_fizzled_parents': True,
'_queueadapter': QA_DB,
"_dupefinder": DupeFinderDB().to_dict(),
'_trackers': trackers_db
}
fws.append(
Firework([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=2))
connections[1] = [2]
# determine if GGA+U FW is needed
incar = MPVaspInputSet().get_incar(snl.structure).as_dict()
ggau_compound = ('LDAU' in incar and incar['LDAU'])
if not parameters.get('skip_bandstructure', False) and (
not ggau_compound
or parameters.get('force_gga_bandstructure', False)):
spec = {
'task_type': 'Controller: add Electronic Structure v2',
'_priority': priority,
'_queueadapter': QA_CONTROL
}
fws.append(
Firework([AddEStructureTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=3))
connections[2] = [3]
if ggau_compound:
spec = _snl_to_spec(snl, enforce_gga=False, parameters=parameters)
del spec[
'vasp'] # we are stealing all VASP params and such from previous run
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
spec['_trackers'] = trackers
fws.append(
Firework(
[VaspCopyTask(),
SetupGGAUTask(),
get_custodian_task(spec)],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=10))
connections[2].append(10)
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority,
"_dupefinder": DupeFinderDB().to_dict(),
'_trackers': trackers_db
}
fws.append(
Firework([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=11))
connections[10] = [11]
if not parameters.get('skip_bandstructure', False):
spec = {
'task_type': 'Controller: add Electronic Structure v2',
'_priority': priority,
'_queueadapter': QA_CONTROL
}
fws.append(
Firework([AddEStructureTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=12))
connections[11] = [12]
wf_meta = get_meta_from_structure(snl.structure)
wf_meta['run_version'] = 'May 2013 (1)' # not maintained
if '_materialsproject' in snl.data and 'submission_id' in snl.data[
'_materialsproject']:
wf_meta['submission_id'] = snl.data['_materialsproject'][
'submission_id']
return Workflow(
fws,
connections,
name=Composition(
snl.structure.composition.reduced_formula).alphabetical_formula,
metadata=wf_meta)
def __init__(self,
vasp_cmd,
output_file="vasp.out",
suffix="",
final=True,
backup=True,
default_vasp_input_set=MPVaspInputSet(),
auto_npar=True,
auto_gamma=True,
settings_override=None,
gamma_vasp_cmd=None,
copy_magmom=False):
"""
This constructor is necessarily complex due to the need for
flexibility. For standard kinds of runs, it's often better to use one
of the static constructors. The defaults are usually fine too.
Args:
vasp_cmd (str): Command to run vasp as a list of args. For example,
if you are using mpirun, it can be something like
["mpirun", "pvasp.5.2.11"]
output_file (str): Name of file to direct standard out to.
Defaults to "vasp.out".
suffix (str): A suffix to be appended to the final output. E.g.,
to rename all VASP output from say vasp.out to
vasp.out.relax1, provide ".relax1" as the suffix.
final (bool): Indicating whether this is the final vasp job in a
series. Defaults to True.
backup (bool): Whether to backup the initial input files. If True,
the INCAR, KPOINTS, POSCAR and POTCAR will be copied with a
".orig" appended. Defaults to True.
default_vasp_input_set (VaspInputSet): Species the default input
set (see pymatgen's documentation in pymatgen.io.vasp.sets to
use for directories that do not contain full set of VASP
input files. For example, if a directory contains only a
POSCAR or a cif, the vasp input set will be used to generate
the necessary input files for the run. If the directory already
contain a full set of VASP input files,
this input is ignored. Defaults to the MITVaspInputSet.
auto_npar (bool): Whether to automatically tune NPAR to be sqrt(
number of cores) as recommended by VASP for DFT calculations.
Generally, this results in significant speedups. Defaults to
True. Set to False for HF, GW and RPA calculations.
auto_gamma (bool): Whether to automatically check if run is a
Gamma 1x1x1 run, and whether a Gamma optimized version of
VASP exists with ".gamma" appended to the name of the VASP
executable (typical setup in many systems). If so, run the
gamma optimized version of VASP instead of regular VASP. You
can also specify the gamma vasp command using the
gamma_vasp_cmd argument if the command is named differently.
settings_override ([dict]): An ansible style list of dict to
override changes. For example, to set ISTART=1 for subsequent
runs and to copy the CONTCAR to the POSCAR, you will provide::
[{"dict": "INCAR", "action": {"_set": {"ISTART": 1}}},
{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}}]
gamma_vasp_cmd (str): Command for gamma vasp version when
auto_gamma is True. Should follow the list style of
subprocess. Defaults to None, which means ".gamma" is added
to the last argument of the standard vasp_cmd.
copy_magmom (bool): Whether to copy the final magmom from the
OUTCAR to the next INCAR. Useful for multi-relaxation runs
where the CHGCAR and WAVECAR are sometimes deleted (due to
changes in fft grid, etc.). Only applies to non-final runs.
"""
self.vasp_cmd = vasp_cmd
self.output_file = output_file
self.final = final
self.backup = backup
self.default_vis = default_vasp_input_set
self.suffix = suffix
self.settings_override = settings_override
self.auto_npar = auto_npar
self.auto_gamma = auto_gamma
self.gamma_vasp_cmd = gamma_vasp_cmd
self.copy_magmom = copy_magmom