def main(api="", queryid=""):
"""Get VASP inputs for Materials Project structure
Args:
api <str>: Materials Project API key
queryid <str>: Materials Project ID of the structure
Returns:
creates a folder named with that mpid, and including
some VASP input files.
"""
if api == "":
print "Must have an API key from materialsproject.org"
return None
if queryid == "":
print "No MP structure ID given. Exiting."
return None
rest_adapter = MPRester(api)
entries=list()
proplist=list()
proplist.append('pretty_formula')
proplist.append('structure')
proplist.append('potcar')
proplist.append('material_id')
myentry = rest_adapter.mpquery(criteria={'material_id':queryid}, properties=proplist)
if len(myentry) == 0:
print "Could not find entry for %s as material_id. Trying entry_id." % queryid
myentry = rest_adapter.mpquery(criteria={'entry_id':queryid}, properties=proplist)
if len(myentry) == 0:
print "Could not find entry for %s" % queryid
return None
entries.extend(myentry)
workdir = os.getcwd()
from pymatgen.io.vaspio_set import MITVaspInputSet, MPVaspInputSet
for entry in entries:
mpvis = MPVaspInputSet()
myname = str(entry['pretty_formula'])
#print entry['structure'].composition
#print entry['structure'].formula
#myname = entry['pretty_formula']
myname = myname.replace("(","_").replace(")","_")
myname = myname + "_" + entry['material_id']
os.mkdir(myname)
os.chdir(myname)
mystructure = entry['structure']
if mystructure.num_sites <= 10:
mystructure.make_supercell([2,2,2])
#mystructure.perturb(0.01)
incar = mpvis.get_incar(mystructure)
incar.write_file("INCAR")
potcar = mpvis.get_potcar(mystructure)
potcar.write_file("POTCAR")
#potcar_symbols = mpvis.get_potcar_symbols(mystructure)
myposcar=Poscar(mystructure)
mykpoints=mpvis.get_kpoints(mystructure)
mykpoints.write_file("KPOINTS")
myposcar.write_file("POSCAR")
os.chdir(workdir)
def test_to_from_dict(self):
self.mitparamset = MITVaspInputSet()
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MPVaspInputSet()
self.userparamset = MPVaspInputSet(
{'MAGMOM': {"Fe": 10, "S": -5, "Mn3+": 100}}
)
d = self.mitparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MITVaspInputSet)
d = self.mitggaparam.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MITGGAVaspInputSet)
d = self.mithseparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MITHSEVaspInputSet)
d = self.paramset.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MPVaspInputSet)
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})
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).to_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 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).to_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 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
})
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_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})
def test_to_from_dict(self):
self.mitparamset = MITVaspInputSet()
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MPVaspInputSet()
self.userparamset = MPVaspInputSet(
{'MAGMOM': {
"Fe": 10,
"S": -5,
"Mn3+": 100
}})
d = self.mitparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MITVaspInputSet)
d = self.mitggaparam.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MITGGAVaspInputSet)
d = self.mithseparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MITHSEVaspInputSet)
d = self.paramset.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MPVaspInputSet)
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
})
def __init__(self,save_old_file=False):
# read in what is there
json_filename = 'run_data.json'
try:
with open(json_filename,'r') as f:
data =json.load(f)
except:
print("CANNOT FIND run_data.json: CLASS MUST BE CALLED IN DIRECTORY WHERE FILE IS")
return
last_step = data['relaxation'][-1]
structure = pymatgen.Structure.from_dict(last_step['structure'])
composition = structure.composition
energy = last_step['electronic']['e_0_energy']
set = MPVaspInputSet()
incar = set.get_incar(structure)
poscar = set.get_poscar(structure)
potcar = set.get_potcar(structure)
parameters = self.parse_pseudo_inputs(poscar,incar,potcar)
entry = pymatgen.entries.computed_entries.ComputedEntry(composition, energy, parameters=parameters )
data['ComputedEntry'] = entry
if save_old_file:
shutil.move('run_data.json','run_data_OLD.json')
pmg_dump(data, 'run_data.json')
return
def setUp(self):
filepath = os.path.join(test_dir, "POSCAR")
poscar = Poscar.from_file(filepath)
self.struct = poscar.structure
self.mitparamset = MITVaspInputSet()
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MPVaspInputSet()
self.userparamset = MPVaspInputSet({"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 __init__(self, compat_type="Advanced", correct_peroxide=True):
module_dir = os.path.dirname(os.path.abspath(__file__))
fp = os.path.join(module_dir, "MPCompatibility.yaml")
i_s = MPVaspInputSet()
Compatibility.__init__(
self, [PotcarCorrection(i_s),
GasCorrection(fp, correct_peroxide=correct_peroxide),
UCorrection(fp, i_s, compat_type), AqueousCorrection(fp)])
def convert_fmt(args):
iformat = args.input_format[0]
oformat = args.output_format[0]
filename = args.input_filename[0]
out_filename = args.output_filename[0]
try:
if iformat == "smart":
structure = read_structure(filename)
if iformat == "POSCAR":
p = Poscar.from_file(filename)
structure = p.structure
elif iformat == "CIF":
r = CifParser(filename)
structure = r.get_structures()[0]
elif iformat == "CSSR":
structure = Cssr.from_file(filename).structure
if oformat == "smart":
write_structure(structure, out_filename)
elif oformat == "POSCAR":
p = Poscar(structure)
p.write_file(out_filename)
elif oformat == "CIF":
w = CifWriter(structure)
w.write_file(out_filename)
elif oformat == "CSSR":
c = Cssr(structure)
c.write_file(out_filename)
elif oformat == "VASP":
input_set = MPVaspInputSet()
ts = TransformedStructure(structure, [],
history=[{
"source":
"file",
"datetime":
str(datetime.datetime.now()),
"original_file":
open(filename).read()
}])
ts.write_vasp_input(input_set, output_dir=out_filename)
elif oformat == "MITVASP":
input_set = MITVaspInputSet()
ts = TransformedStructure(structure, [],
history=[{
"source":
"file",
"datetime":
str(datetime.datetime.now()),
"original_file":
open(filename).read()
}])
ts.write_vasp_input(input_set, output_dir=out_filename)
except Exception as ex:
print "Error converting file. Are they in the right format?"
print str(ex)
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 _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 run_task(self, fw_spec):
chgcar_start = False
vi = VaspInput.from_directory(".") # read the VaspInput from the previous run
# figure out what GGA+U values to use and override them
mpvis = MPVaspInputSet()
incar = mpvis.get_incar(vi['POSCAR'].structure).to_dict
incar_updates = {k: incar[k] for k in incar.keys() if 'LDAU' in k} # LDAU values to use
vi['INCAR'].update(incar_updates) # override the +U keys
# start from the CHGCAR of previous run
if os.path.exists('CHGCAR'):
vi['INCAR']['ICHARG'] = 1
chgcar_start = True
vi['INCAR'].write_file('INCAR') # write back the new INCAR to the current directory
return FWAction(stored_data={'chgcar_start': chgcar_start})
def run_task(self, fw_spec):
chgcar_start = False
# read the VaspInput from the previous run
vi = VaspInput.from_directory(".")
# figure out what GGA+U values to use and override them
# LDAU values to use
mpvis = MPVaspInputSet()
incar = mpvis.get_incar(vi['POSCAR'].structure).to_dict
incar_updates = {k: incar[k] for k in incar.keys() if 'LDAU' in k}
vi['INCAR'].update(incar_updates) # override the +U keys
# start from the CHGCAR of previous run
if os.path.exists('CHGCAR'):
vi['INCAR']['ICHARG'] = 1
chgcar_start = True
# write back the new INCAR to the current directory
vi['INCAR'].write_file('INCAR')
return FWAction(stored_data={'chgcar_start': chgcar_start})
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
self.struct = poscar.structure
self.mitparamset = MITVaspInputSet()
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MPVaspInputSet()
self.userparamset = MPVaspInputSet(
{'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 get_LDAU(self):
""" Produce LDAU related variables, to be passed to VASP as strings """
# let's simply use the Materials Project results as default.
self.check_structure_is_read()
dummy_input_set = MPVaspInputSet()
dummy_incar = dummy_input_set.get_incar(self.structure)
LDAU_dict = {}
for key in self._LDAU_KEYS:
if key in dummy_incar:
LDAU_dict[key] = dummy_incar[key]
# no need to hack the poscar or potcar
poscar_need_hack = False
potcar_need_hack = False
return LDAU_dict, poscar_need_hack, potcar_need_hack
def __init__(self, save_old_file=False):
# read in what is there
json_filename = 'run_data.json'
try:
with open(json_filename, 'r') as f:
data = json.load(f)
except:
print(
"CANNOT FIND run_data.json: CLASS MUST BE CALLED IN DIRECTORY WHERE FILE IS"
)
return
last_step = data['relaxation'][-1]
structure = pymatgen.Structure.from_dict(last_step['structure'])
composition = structure.composition
energy = last_step['electronic']['e_0_energy']
set = MPVaspInputSet()
incar = set.get_incar(structure)
poscar = set.get_poscar(structure)
potcar = set.get_potcar(structure)
parameters = self.parse_pseudo_inputs(poscar, incar, potcar)
entry = pymatgen.entries.computed_entries.ComputedEntry(
composition, energy, parameters=parameters)
data['ComputedEntry'] = entry
if save_old_file:
shutil.move('run_data.json', 'run_data_OLD.json')
pmg_dump(data, 'run_data.json')
return
def __init__(self, input_set_name, compat_type):
"""
Args:
input_set_name:
The name of the input set to use. Can be either
MaterialsProject or MITMatgen.
compat_type:
Two options, GGA or Advanced. GGA means all GGA+U entries are
excluded. Advanced means mixing scheme is implemented to make
entries compatible with each other, but entries which are
supposed to be done in GGA+U will have the equivalent GGA
entries excluded. For example, Fe oxides should have a U value
under the Advanced scheme. A GGA Fe oxide run will therefore be
excluded under the scheme.
"""
self.compat_type = compat_type
self.input_set_name = input_set_name
if input_set_name == "MaterialsProject":
self.input_set = MPVaspInputSet()
elif input_set_name == "MITMatgen":
self.input_set = MITVaspInputSet()
else:
raise ValueError(
"Invalid input set name {}".format(input_set_name))
module_dir = os.path.dirname(os.path.abspath(__file__))
self._config = ConfigParser.SafeConfigParser()
self._config.optionxform = str
self._config.readfp(open(os.path.join(module_dir,
"Compatibility.cfg")))
u_corrections = {}
for el in self.input_set.incar_settings["LDAUU"].keys():
name = "{}{}UCorrections{}".format(input_set_name, compat_type, el)
if name in self._config.sections():
corr = dict(self._config.items(name))
u_corrections[el] = {k: float(v) for k, v in corr.items()}
cpd_energies = dict(
self._config.items("{}{}CompoundEnergies".format(
input_set_name, compat_type)))
self.u_corrections = u_corrections
self.cpd_energies = {k: float(v) for k, v in cpd_energies.items()}
self.valid_potcars = set(self.input_set.potcar_settings.values())
self.u_settings = self.input_set.incar_settings["LDAUU"]
if compat_type == "GGA":
self.u_corrections = {}
self.u_settings = {}
def get_LDAU(self):
""" Produce LDAU related variables, to be passed to VASP as strings """
# let's simply use the Materials Project results as default.
self.check_structure_is_read()
dummy_input_set = MPVaspInputSet()
dict = dummy_input_set.as_dict()
# Spoof the input set to throw in the values of U we want!
for symbol, U_value in self.new_U_dict.iteritems():
dict['config_dict']['INCAR']['LDAUU']['O'][symbol] = U_value
input_set = pymatgen.io.vaspio_set.DictVaspInputSet.from_dict(dict)
incar = input_set.get_incar(self.structure)
LDAU_dict = {}
for key in self._LDAU_KEYS:
if key in incar:
if key == 'MAGMOM':
magn_array = np.array(incar[key])
# add randomness to large values, corresponding to TM
new_magn_array = np.where(magn_array > 1, magn_array+0.01*np.random.random(len(magn_array)), magn_array)
LDAU_dict[key] = list(new_magn_array)
else:
LDAU_dict[key] = incar[key]
# no need to hack the poscar or potcar
poscar_need_hack = False
potcar_need_hack = False
return LDAU_dict, poscar_need_hack, potcar_need_hack
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 __init__(self, name):
"""
Args:
name:
Name of settings to use. Current valid settings are MP or
MIT, which is the relevant settings based on the MP or MIT
VaspInputSets.
Raises:
ValueError if entry do not contain "potcar_symbols" key.
"""
if name == "MP":
input_set = MPVaspInputSet()
elif name == "MIT":
input_set = MITVaspInputSet()
else:
raise ValueError("Only MIT and MP POTCAR corrections are "
"supported currently.")
self.valid_potcars = set(input_set.potcar_settings.values())
def __init__(self, name, compat_type):
"""
Args:
name:
Name of settings to use. Current valid settings are MP or
MIT, which is the relevant settings based on the MP or MIT
VaspInputSets.
compat_type:
Two options, GGA or Advanced. GGA means all GGA+U entries are
excluded. Advanced means mixing scheme is implemented to make
entries compatible with each other, but entries which are
supposed to be done in GGA+U will have the equivalent GGA
entries excluded. For example, Fe oxides should have a U value
under the Advanced scheme. A GGA Fe oxide run will therefore be
excluded under the scheme.
"""
module_dir = os.path.dirname(os.path.abspath(__file__))
config = ConfigParser.SafeConfigParser()
config.optionxform = str
config.readfp(open(os.path.join(module_dir, "Compatibility.cfg")))
if name == "MP":
self.input_set = MPVaspInputSet()
elif name == "MIT":
self.input_set = MITVaspInputSet()
else:
raise ValueError("Invalid input set name {}".format(name))
u_corrections = {}
for el in self.input_set.incar_settings["LDAUU"].keys():
sect_name = "{}{}UCorrections{}".format(name, compat_type, el)
if sect_name in config.sections():
corr = dict(config.items(sect_name))
u_corrections[el] = {k: float(v) for k, v in corr.items()}
self.u_corrections = u_corrections
self.u_settings = self.input_set.incar_settings["LDAUU"]
if compat_type == "GGA":
self.u_corrections = {}
self.u_settings = {}
def _snl_to_spec(snl, enforce_gga=False):
spec = {}
incar_enforce = {'NPAR': 2}
structure = snl.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.to_dict
spec['vasp']['poscar'] = poscar.to_dict
spec['vasp']['kpoints'] = kpoints.to_dict
spec['vasp']['potcar'] = potcar.to_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)
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 get_MaterialsProject_VASP_inputs(structure, workdir, job_name, nproc=16, supplementary_incar_dict=None):
if os.path.exists(workdir):
print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB'
return -1
os.mkdir(workdir)
input_set = MPVaspInputSet()
incar = input_set.get_incar(structure)
# set the number of parallel processors to sqrt(nproc),
# as recommended in manual.
incar.update({'NPAR':int(np.sqrt(nproc))})
if supplementary_incar_dict != None:
incar.update(supplementary_incar_dict)
poscar = input_set.get_poscar(structure)
kpoints = input_set.get_kpoints(structure)
potcar = input_set.get_potcar(structure)
incar.write_file(workdir+'INCAR')
poscar.write_file(workdir+'POSCAR', vasp4_compatible = True)
kpoints.write_file(workdir+'KPOINTS')
potcar.write_file(workdir+'POTCAR')
with open(workdir+'job.sh','w') as f:
f.write(submit_template.format(job_name,nproc))
with open(workdir+'clean.sh','w') as f:
f.write(clean_template)
return 0
def main(api="", queryid=""):
"""Get VASP inputs for Materials Project structure
Args:
api <str>: Materials Project API key
queryid <str>: Materials Project ID of the structure
Returns:
creates a folder named with that mpid, and including
some VASP input files.
"""
if api == "":
print "Must have an API key from materialsproject.org"
return None
if queryid == "":
print "No MP structure ID given. Exiting."
return None
rest_adapter = MPRester(api)
entries = list()
proplist = list()
proplist.append('pretty_formula')
proplist.append('structure')
proplist.append('potcar')
proplist.append('material_id')
myentry = rest_adapter.mpquery(criteria={'material_id': queryid},
properties=proplist)
if len(myentry) == 0:
print "Could not find entry for %s as material_id. Trying entry_id." % queryid
myentry = rest_adapter.mpquery(criteria={'entry_id': queryid},
properties=proplist)
if len(myentry) == 0:
print "Could not find entry for %s" % queryid
return None
entries.extend(myentry)
workdir = os.getcwd()
from pymatgen.io.vaspio_set import MITVaspInputSet, MPVaspInputSet
for entry in entries:
mpvis = MPVaspInputSet()
myname = str(entry['pretty_formula'])
#print entry['structure'].composition
#print entry['structure'].formula
#myname = entry['pretty_formula']
myname = myname.replace("(", "_").replace(")", "_")
myname = myname + "_" + entry['material_id']
os.mkdir(myname)
os.chdir(myname)
mystructure = entry['structure']
if mystructure.num_sites <= 10:
mystructure.make_supercell([2, 2, 2])
#mystructure.perturb(0.01)
incar = mpvis.get_incar(mystructure)
incar.write_file("INCAR")
potcar = mpvis.get_potcar(mystructure)
potcar.write_file("POTCAR")
#potcar_symbols = mpvis.get_potcar_symbols(mystructure)
myposcar = Poscar(mystructure)
mykpoints = mpvis.get_kpoints(mystructure)
mykpoints.write_file("KPOINTS")
myposcar.write_file("POSCAR")
os.chdir(workdir)
# print os.environ['VASP_PSP_DIR']
id_expgap = open("ids.txt", "r")
for line in id_expgap:
words=line.split()
print words
id_line=words[0]
os.mkdir(id_line)
os.chdir(id_line)
s = mpr.get_structure_by_material_id(id_line)
# obtain structural information from Materials Project database
#print json.dumps(s.to_dict)
# convert structural infomation into a dictionary and then dump to a json file
user_incar_settings={"ALGO":'Normal',"EDIFF":1E-8,"ENCUT":500,"NSW":0,"LWAVE":True}
mpvis = MPVaspInputSet(user_incar_settings=user_incar_settings)
mpvis.get_incar(s).write_file('INCAR')
# from the GW input set, get the incar parameters, generate INCAR
print mpvis.get_incar(s)
#
kp_density = mpvis.get_kpoints(s).kpts[0]
# from the GW input set, get the k-point density
kpoints = Kpoints.gamma_automatic(kp_density)
# generate Gamma centered k-point mesh
kpoints.write_file('KPOINTS')
# generate KPOINTS file
mpvis.get_poscar(s).write_file('POSCAR')
# generate POSCAR file
mpvis.get_potcar(s).write_file('POTCAR')
# generate POTCAR file
def snl_to_wf(snl, parameters=None):
fws = []
connections = {}
parameters = parameters if parameters else {}
snl_priority = parameters.get('priority', 1)
priority = snl_priority * 2 # once we start a job, keep going!
f = Composition.from_formula(
snl.structure.composition.reduced_formula).alphabetical_formula
# add the SNL to the SNL DB and figure out duplicate group
tasks = [AddSNLTask()]
spec = {
'task_type': 'Add to SNL database',
'snl': snl.to_dict,
'_queueadapter': QA_DB,
'_priority': snl_priority
}
if 'snlgroup_id' in parameters and isinstance(snl, MPStructureNL):
spec['force_mpsnl'] = snl.to_dict
spec['force_snlgroup_id'] = parameters['snlgroup_id']
del spec['snl']
fws.append(
FireWork(tasks,
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=0))
connections[0] = [1]
# run GGA structure optimization
spec = _snl_to_spec(snl, enforce_gga=True)
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
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,
'_allow_fizzled_parents': True,
'_queueadapter': QA_DB
}
fws.append(
FireWork([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=2))
connections[1] = [2]
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=3))
connections[2] = [3]
# determine if GGA+U FW is needed
incar = MPVaspInputSet().get_incar(snl.structure).to_dict
if 'LDAU' in incar and incar['LDAU']:
spec = _snl_to_spec(snl, enforce_gga=False)
del spec[
'vasp'] # we are stealing all VASP params and such from previous run
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
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
}
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)'
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.from_formula(
snl.structure.composition.reduced_formula).alphabetical_formula,
metadata=wf_meta)
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")
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})
def get_ModifiedMaterialsProject_VASP_inputs(structure, workdir, job_name, nproc=16,
U_strategy_instance = None, supplementary_incar_dict = None):
"""
Inputs will be inspired by MaterialsProject, but this function is appropriate
when we are seriously modifying the inputs such that they no longer conform to Materials Project.
"""
if os.path.exists(workdir):
print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB'
return -1
os.mkdir(workdir)
# let's start with MP
input_set = MPVaspInputSet()
incar = input_set.get_incar(structure)
if U_strategy_instance != None:
# reading the structure here insures consistency, rather
# than having the strategy read the structure outside this driver.
U_strategy_instance.read_structure(structure)
# Generate all LDAU-related variables according to specified strategy.
LDAU_dict, poscar_need_hack, potcar_need_hack = U_strategy_instance.get_LDAU()
incar.update(LDAU_dict)
# set the number of parallel processors to sqrt(nproc),
# as recommended in manual.
incar.update({'NPAR':int(np.sqrt(nproc))})
if supplementary_incar_dict != None:
incar.update(supplementary_incar_dict)
poscar = input_set.get_poscar(structure)
kpoints = input_set.get_kpoints(structure)
potcar = input_set.get_potcar(structure)
incar.write_file(workdir+'INCAR')
poscar.write_file(workdir+'POSCAR', vasp4_compatible = True)
kpoints.write_file(workdir+'KPOINTS')
potcar.write_file(workdir+'POTCAR')
if poscar_need_hack:
# do we need specialized hacking of the poscar because of the U strategy?
new_poscar_lines = U_strategy_instance.get_new_poscar_lines()
with open(workdir+'POSCAR','w') as f:
for line in new_poscar_lines:
print >>f, line.strip()
if potcar_need_hack:
# do we need specialized hacking of the potcar because of the U strategy?
new_potcar_symbols = U_strategy_instance.get_new_potcar_symbols(potcar)
new_potcar = Potcar(new_potcar_symbols)
# overwrite the previous potcar
new_potcar.write_file(workdir+'POTCAR')
with open(workdir+'job.sh','w') as f:
f.write(submit_template.format(job_name,nproc))
with open(workdir+'clean.sh','w') as f:
f.write(clean_template)
return 0
def test_get_vasp_input(self):
vaspis = MPVaspInputSet()
self.assertEqual(
"Na_pv\nO\nP\nFe_pv",
self.trans.get_vasp_input(vaspis, False)['POTCAR.spec'])
self.assertEqual(len(self.trans.structures), 2)
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)'
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)
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")
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
})
