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.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 4, 4]])
self.assertEqual(kpoints.style, "Monkhorst")
kpoints = Kpoints.automatic_density(poscar.structure, 500, True)
self.assertEqual(kpoints.style, "Gamma")
kpoints = Kpoints.automatic_density_by_vol(poscar.structure, 1000)
self.assertEqual(kpoints.kpts, [[6, 11, 13]])
self.assertEqual(kpoints.style, "Gamma")
s = poscar.structure
s.make_supercell(3)
kpoints = Kpoints.automatic_density(s, 500)
self.assertEqual(kpoints.kpts, [[1, 1, 1]])
self.assertEqual(kpoints.style, "Gamma")
def get_kpoints(self, structure):
"""
Writes out a KPOINTS file using the automated gamma grid method.
VASP crashes GW calculations on none gamma centered meshes.
"""
if self.sort_structure:
structure = structure.get_sorted_structure()
dens = int(self.kpoints_settings['grid_density'])
if dens == 1:
return Kpoints.gamma_automatic()
else:
return Kpoints.automatic_gamma_density(structure, dens)
def get_kpoints(self, structure):
"""
Writes out a KPOINTS file using the automated gamma grid method.
VASP crashes GW calculations on none gamma centered meshes.
"""
if self.sort_structure:
structure = structure.get_sorted_structure()
dens = int(self.kpoints_settings['grid_density'])
if dens == 1:
return Kpoints.gamma_automatic()
else:
return Kpoints.automatic_gamma_density(structure, dens)
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.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 3, 4]])
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.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 3, 4]])
def get_kpoints(self, structure):
return Kpoints.gamma_automatic()
def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
user_incar_settings=None,
make_dir_if_not_present=True):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
previous_vasp_dir:
The directory contains the outputs(vasprun.xml and OUTCAR) of
previous vasp run.
output_dir:
The directory to write the VASP input files for the static
calculations. Default to write in the current directory.
make_dir_if_not_present:
Set to True if you want the directory (and the whole path) to
be created if it is not present.
"""
try:
vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
parse_dos=False, parse_eigen=None)
outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
previous_incar = vasp_run.incar
previous_kpoints = vasp_run.kpoints
previous_final_structure = vasp_run.final_structure
except:
traceback.format_exc()
raise RuntimeError("Can't get valid results from previous run")
structure = MPStaticVaspInputSet.get_structure(vasp_run, outcar)
mpsvip = MPStaticVaspInputSet()
mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
#new_incar = Incar.from_file(os.path.join(output_dir, "INCAR"))
new_incar = mpsvip.get_incar(structure)
# Use previous run INCAR and override necessary parameters
previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
"LCHARG": True, "LORBIT": 11, "LVHAR": True,
"LWAVE": False, "NSW": 0, "ICHARG": 0})
for incar_key in ["MAGMOM", "NUPDOWN"]:
if new_incar.get(incar_key, None):
previous_incar.update({incar_key: new_incar[incar_key]})
else:
previous_incar.pop(incar_key, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if previous_incar.get('LDAU'):
u = previous_incar.get('LDAUU', [])
j = previous_incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
previous_incar.update({tag: new_incar[tag]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
previous_incar.update({"EDIFF": min(previous_incar.get("EDIFF", 1),
new_incar["EDIFF"])})
# add user settings
if user_incar_settings:
previous_incar.update(user_incar_settings)
previous_incar.write_file(os.path.join(output_dir, "INCAR"))
# Prefer to use k-point scheme from previous run
previous_kpoints_density = np.prod(previous_kpoints.kpts[0]) / \
previous_final_structure.lattice.reciprocal_lattice.volume
new_kpoints_density = max(previous_kpoints_density, 90)
new_kpoints = mpsvip.get_kpoints(structure,
kpoints_density=new_kpoints_density)
if previous_kpoints.style[0] != new_kpoints.style[0]:
if previous_kpoints.style[0] == "M" and \
SymmetryFinder(structure, 0.01).get_lattice_type() != \
"hexagonal":
k_div = (kp + 1 if kp % 2 == 1 else kp
for kp in new_kpoints.kpts[0])
Kpoints.monkhorst_automatic(k_div). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
Kpoints.gamma_automatic(new_kpoints.kpts[0]). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
new_kpoints.write_file(os.path.join(output_dir, "KPOINTS"))
def get_kpoints(self, structure):
return Kpoints.gamma_automatic()
def from_previous_vasp_run(previous_vasp_dir,
output_dir='.',
user_incar_settings=None,
make_dir_if_not_present=True):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
previous_vasp_dir:
The directory contains the outputs(vasprun.xml and OUTCAR) of
previous vasp run.
output_dir:
The directory to write the VASP input files for the static
calculations. Default to write in the current directory.
make_dir_if_not_present:
Set to True if you want the directory (and the whole path) to
be created if it is not present.
"""
try:
vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
parse_dos=False,
parse_eigen=None)
outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
previous_incar = vasp_run.incar
previous_kpoints = vasp_run.kpoints
previous_final_structure = vasp_run.final_structure
except:
traceback.format_exc()
raise RuntimeError("Can't get valid results from previous run")
structure = MPStaticVaspInputSet.get_structure(vasp_run, outcar)
mpsvip = MPStaticVaspInputSet()
mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
#new_incar = Incar.from_file(os.path.join(output_dir, "INCAR"))
new_incar = mpsvip.get_incar(structure)
# Use previous run INCAR and override necessary parameters
previous_incar.update({
"IBRION": -1,
"ISMEAR": -5,
"LAECHG": True,
"LCHARG": True,
"LORBIT": 11,
"LVHAR": True,
"LWAVE": False,
"NSW": 0,
"ICHARG": 0
})
for incar_key in ["MAGMOM", "NUPDOWN"]:
if new_incar.get(incar_key, None):
previous_incar.update({incar_key: new_incar[incar_key]})
else:
previous_incar.pop(incar_key, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if previous_incar.get('LDAU'):
u = previous_incar.get('LDAUU', [])
j = previous_incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
previous_incar.update({tag: new_incar[tag]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
previous_incar.update(
{"EDIFF": min(previous_incar.get("EDIFF", 1), new_incar["EDIFF"])})
# add user settings
if user_incar_settings:
previous_incar.update(user_incar_settings)
previous_incar.write_file(os.path.join(output_dir, "INCAR"))
# Prefer to use k-point scheme from previous run
previous_kpoints_density = np.prod(previous_kpoints.kpts[0]) / \
previous_final_structure.lattice.reciprocal_lattice.volume
new_kpoints_density = max(previous_kpoints_density, 90)
new_kpoints = mpsvip.get_kpoints(structure,
kpoints_density=new_kpoints_density)
if previous_kpoints.style[0] != new_kpoints.style[0]:
if previous_kpoints.style[0] == "M" and \
SymmetryFinder(structure, 0.01).get_lattice_type() != \
"hexagonal":
k_div = (kp + 1 if kp % 2 == 1 else kp
for kp in new_kpoints.kpts[0])
Kpoints.monkhorst_automatic(k_div). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
Kpoints.gamma_automatic(new_kpoints.kpts[0]). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
new_kpoints.write_file(os.path.join(output_dir, "KPOINTS"))
def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
user_incar_settings=None,
make_dir_if_not_present=True,
kpoints_density=90, sym_prec=0.1):
"""
Generate a set of Vasp input files for static calculations from a
directory of previous Vasp run.
Args:
previous_vasp_dir (str): Directory containing the outputs(
vasprun.xml and OUTCAR) of previous vasp run.
output_dir (str): Directory to write the VASP input files for
the static calculations. Defaults to current directory.
make_dir_if_not_present (bool): Set to True if you want the
directory (and the whole path) to be created if it is not
present.
kpoints_density (int): kpoints density for the reciprocal cell
of structure. Might need to increase the default value when
calculating metallic materials.
sym_prec (float): Tolerance for symmetry finding
"""
# Read input and output from previous run
try:
vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
parse_dos=False, parse_eigen=None)
outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
previous_incar = vasp_run.incar
previous_kpoints = vasp_run.kpoints
except:
traceback.format_exc()
raise RuntimeError("Can't get valid results from previous run")
mpsvip = MPStaticVaspInputSet(kpoints_density=kpoints_density,
sym_prec=sym_prec)
structure = mpsvip.get_structure(vasp_run, outcar)
mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
new_incar = mpsvip.get_incar(structure)
# Use previous run INCAR and override necessary parameters
previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
"LCHARG": True, "LORBIT": 11, "LVHAR": True,
"LWAVE": False, "NSW": 0, "ICHARG": 0})
for incar_key in ["MAGMOM", "NUPDOWN"]:
if new_incar.get(incar_key, None):
previous_incar.update({incar_key: new_incar[incar_key]})
else:
previous_incar.pop(incar_key, None)
# use new LDAUU when possible b/c the Poscar might have changed
# representation
if previous_incar.get('LDAU'):
u = previous_incar.get('LDAUU', [])
j = previous_incar.get('LDAUJ', [])
if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
previous_incar.update({tag: new_incar[tag]})
# ensure to have LMAXMIX for GGA+U static run
if "LMAXMIX" not in previous_incar:
previous_incar.update({"LMAXMIX": new_incar["LMAXMIX"]})
# Compare ediff between previous and staticinputset values,
# choose the tighter ediff
previous_incar.update({"EDIFF": min(previous_incar.get("EDIFF", 1),
new_incar["EDIFF"])})
# add user settings
if user_incar_settings:
previous_incar.update(user_incar_settings)
previous_incar.write_file(os.path.join(output_dir, "INCAR"))
# Perform checking on INCAR parameters
if any([previous_incar.get("NSW", 0) != 0, previous_incar["IBRION"] != -1,
previous_incar["LCHARG"] != True,
any([sum(previous_incar["LDAUU"])<=0, previous_incar["LMAXMIX"]<4])
if previous_incar.get("LDAU") else False]):
raise ValueError("Incompatible INCAR parameters!")
# Prefer to use k-point scheme from previous run
new_kpoints = mpsvip.get_kpoints(structure)
if previous_kpoints.style[0] != new_kpoints.style[0]:
if previous_kpoints.style[0] == "M" and \
SymmetryFinder(structure, 0.1).get_lattice_type() != \
"hexagonal":
k_div = (kp + 1 if kp % 2 == 1 else kp
for kp in new_kpoints.kpts[0])
Kpoints.monkhorst_automatic(k_div). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
Kpoints.gamma_automatic(new_kpoints.kpts[0]). \
write_file(os.path.join(output_dir, "KPOINTS"))
else:
new_kpoints.write_file(os.path.join(output_dir, "KPOINTS"))
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
os.chdir('..')
id_expgap.close()
