def make_hex_lattice_input(path,
atomic_sep,
kpointdivs,
comment,
forbid_symmetry=True):
pb = hexagonal_unitcell('C', atomic_sep, layersep=25.)
incar = Incar()
incar['SYSTEM'] = comment
incar['ALGO'] = 'Fast'
incar['NSW'] = 1000
incar['IBRION'] = 2
incar['EDIFF'] = 1E-8
if forbid_symmetry:
incar['ISYM'] = 0
kpoints = Kpoints.gamma_automatic(kpointdivs, [0, 0, 0])
metadata = {'atomic_sep': atomic_sep, 'kpointdivs': kpointdivs}
ws = VaspInput(
poscar=pb.poscar(comment=comment),
potcar=pb.potcar(functional='PBE'),
incar=incar,
kpoints=kpoints,
# additional files
metadata=json.dumps(metadata),
)
ws.write_input(path)
def make_hex_lattice_input(path, atomic_sep, kpointdivs, comment, forbid_symmetry=True):
pb = hexagonal_unitcell('C', atomic_sep, layersep=25.)
incar = Incar()
incar['SYSTEM'] = comment
incar['ALGO'] = 'Fast'
incar['NSW'] = 1000
incar['IBRION'] = 2
incar['EDIFF'] = 1E-8
if forbid_symmetry:
incar['ISYM'] = 0
kpoints = Kpoints.gamma_automatic(kpointdivs, [0,0,0])
metadata = {'atomic_sep': atomic_sep, 'kpointdivs': kpointdivs}
ws = VaspInput(
poscar = pb.poscar(comment=comment),
potcar = pb.potcar(functional='PBE'),
incar = incar,
kpoints = kpoints,
# additional files
metadata = json.dumps(metadata),
)
ws.write_input(path)
def make_vasp_input(path, *, kpointdivs, comment, forbid_symmetry, functional, perturb_dist, **kwargs):
assert hasattr(kpointdivs, '__iter__')
assert isinstance(comment, str)
assert isinstance(forbid_symmetry, bool)
assert isinstance(perturb_dist, float)
pb = carbon_chain_poxcar(**kwargs)
incar = Incar()
incar['SYSTEM'] = comment
incar['ALGO'] = 'Fast'
incar['NSW'] = 1000
incar['NPAR'] = 4
incar['IBRION'] = 2
incar['EDIFF'] = 1E-8
incar['EDIFFG'] = -0.001
if forbid_symmetry:
incar['ISYM'] = 0
kpoints = Kpoints.gamma_automatic(kpointdivs, [0,0,0])
metadata = {
'kpointdivs':kpointdivs,
'functional':functional,
'perturb_dist':perturb_dist,
'forbid_symmetry':forbid_symmetry,
}
# FIXME FIXME FIXME
# Here, we insert all structure parameters into the metadata. The purpose is because
# oftentimes those parameters are the ones we're most interested in (such as scale).
#
# However, this is all kinds of bad:
# * Not all structure arguments are necessarily desirable to have in the metadata.
# * What if we want a structure argument to be of a non JSON-encodable type?
# * It creates a dependency between names of function arguments in code, and the output file.
# In other words, madness.
metadata = dict_union(metadata, kwargs)
ws = VaspInput(
poscar = pb.poscar(
perturb_dist=perturb_dist,
comment=comment,
),
potcar = pb.potcar(
functional=functional,
),
incar = incar,
kpoints = kpoints,
# additional files
metadata = json.dumps(metadata),
)
ws.write_input(path)
def make_vasp_input(path, *, kpointdivs, comment, forbid_symmetry, functional,
perturb_dist, **kwargs):
assert hasattr(kpointdivs, '__iter__')
assert isinstance(comment, str)
assert isinstance(forbid_symmetry, bool)
assert isinstance(perturb_dist, float)
pb = carbon_chain_poxcar(**kwargs)
incar = Incar()
incar['SYSTEM'] = comment
incar['ALGO'] = 'Fast'
incar['NSW'] = 1000
incar['NPAR'] = 4
incar['IBRION'] = 2
incar['EDIFF'] = 1E-8
incar['EDIFFG'] = -0.001
if forbid_symmetry:
incar['ISYM'] = 0
kpoints = Kpoints.gamma_automatic(kpointdivs, [0, 0, 0])
metadata = {
'kpointdivs': kpointdivs,
'functional': functional,
'perturb_dist': perturb_dist,
'forbid_symmetry': forbid_symmetry,
}
# FIXME FIXME FIXME
# Here, we insert all structure parameters into the metadata. The purpose is because
# oftentimes those parameters are the ones we're most interested in (such as scale).
#
# However, this is all kinds of bad:
# * Not all structure arguments are necessarily desirable to have in the metadata.
# * What if we want a structure argument to be of a non JSON-encodable type?
# * It creates a dependency between names of function arguments in code, and the output file.
# In other words, madness.
metadata = dict_union(metadata, kwargs)
ws = VaspInput(
poscar=pb.poscar(
perturb_dist=perturb_dist,
comment=comment,
),
potcar=pb.potcar(functional=functional, ),
incar=incar,
kpoints=kpoints,
# additional files
metadata=json.dumps(metadata),
)
ws.write_input(path)
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, "Gamma")
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, "Monkhorst")
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, "Automatic")
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.struct, 500)
self.assertEqual(kpoints.kpts, [[2, 4, 4]])
def _vasp_kpoints_setup(self):
"""Parse mast_kpoints string, which should take the format:
number, number, number designation
examples: "3x3x3 M", "1x1x1 G". If no designation is given,
Monkhorst-Pack is assumed.
"""
name = self.keywords['name']
tryname = os.path.join(name, "KPOINTS")
if os.path.isfile(tryname):
#KPOINTS already exists. Do not overwrite.
my_kpoints = Kpoints.from_file(tryname)
return my_kpoints
if not (self.metafile.read_data('kpoints')==None):
kpoints = self.metafile.read_data('kpoints').split()
kmesh = (int(kpoints[0].split('x')[0]),int(kpoints[0].split('x')[1]),int(kpoints[0].split('x')[2]))
try: desig = kpoints[1].upper()
except IndexError: desig = 'M'
try: kshift = (float(kpoints[2]),float(kpoints[3]),float(kpoints[4]))
except IndexError: kshift = (0.0,0.0,0.0)
else:
if 'mast_kpoints' in self.keywords['program_keys'].keys():
kpoints = self.keywords['program_keys']['mast_kpoints']
else:
raise MASTError(self.__class__.__name__,"k-point instructions need to be set either in ingredients keyword mast_kpoints or scaling section in structure ingredient: No k-point settings for the ingredient %s"% name)
if len(kpoints) == 3:
desig = "M"
elif 'line' in str(kpoints[1]):
desig = 'L'
else:
desig = kpoints[3].upper()
if not desig == 'L':
kmesh = (int(kpoints[0]),int(kpoints[1]),int(kpoints[2]))
kshift = (0,0,0)
if desig == "M":
my_kpoints = Kpoints.monkhorst_automatic(kpts=kmesh,shift=kshift)
elif desig == "G":
my_kpoints = Kpoints.gamma_automatic(kpts=kmesh,shift=kshift)
elif desig == 'L':
my_kpoints='Line Mode\n'+'\n'.join(' '.join(kpoints).split(','))+'\n'
fp=open(name+'/KPOINTS','w')
fp.write(my_kpoints)
else:
raise MASTError(self.__class__.__name__,"kpoint designation " + desig + " not recognized.")
dirutil.lock_directory(name)
if not desig=='L':
my_kpoints.write_file(name + "/KPOINTS")
dirutil.unlock_directory(name)
return my_kpoints
