def load_species_mnte_dummy_fe(vasp : Vasp, structure):
# See vasp/functional.py: elementName, fileName, max or min oxidation state
pseudoDir = '$PSEUDO_DIR'
vasp.add_specie = "Te", pseudoDir + "/Te"
vasp.add_specie = "Mn", pseudoDir + "/Mn_pv"
vasp.add_specie = "Fe", pseudoDir + "/Mn_pv"
return(vasp)
def set_ncore_auto(vasp: Vasp, structure=None):
vasp.npar = None
try:
vasp.add_keyword('ncore', int(os.environ['PBS_NUM_PPN']))
except:
vasp.add_keyword('ncore', int(os.environ['SLURM_CPUS_ON_NODE']))
return vasp
def set_kpar_per_node(vasp: Vasp, structure=None):
try:
nodes = int(os.environ['PBS_NUM_NODES'])
except:
nodes = int(os.environ['SLURM_JOB_NUM_NODES'])
vasp.add_keyword('kpar', nodes)
return vasp
def set_333(vasp: Vasp, structure=None):
x = 3
y = 3
z = 3
packing = 'Gamma'
vasp.kpoints = "Gamma_Mesh\n0\n{}\n{} {} {}".format(packing, x, y, z)
vasp.add_keyword('auto_gamma', False)
return vasp
def set_gamma(vasp: Vasp, structure=None):
x = 1
y = 1
z = 1
packing = 'Gamma'
vasp.kpoints = "Gamma_Mesh\n0\n{}\n{} {} {}".format(packing, x, y, z)
vasp.ismear = 0
vasp.add_keyword('kpar', 1)
return vasp
def set_algo_normal_optimal_converge(vasp: Vasp, structure=None):
'''
:param vasp: Vasp
:param structure:
:return:
'''
vasp.algo = "Normal"
vasp.add_keyword('nsim', 1)
return vasp
def set_kpoint(vasp: Vasp, structure):
lengths = [
sum([x**2 for x in structure.cell.transpose()[i]])**(1 / 2)
for i in range(3)
] # using distance formula to get vector lengths
kpoints = [math.ceil(min(lengths) / x * kpoint) for x in lengths
] # scaling number of kpoints for shorter vectors
packing = 'Gamma'
vasp.kpoints = "Gamma_Mesh\n0\n{}\n{} {} {}".format(
packing, kpoints[0], kpoints[1], kpoints[2])
vasp.ediff = convergence_value / 1000
return vasp
def vibrations_disp(vasp: Vasp, structure: Structure):
vasp.ibrion = 5
vasp.istart = 1
vasp.icharg = 1
vasp.nelmin = 3
vasp.nsw = 1
vasp.potim = 0.015
vasp.ediff = 1e-8
vasp.add_keyword('iopt', 0)
return vasp
def get_eigen(vasp: Vasp, structure=None):
# Start
vasp.istart = 1
vasp.icharg = 1
# Electronic
vasp.prec = "Accurate"
vasp.nelm = 200
vasp.ediff = 1e-5
vasp.nelmdl = 0
# Ionic
vasp.nsw = 5000
vasp.ediffg = -0.05
# Output
vasp.lwave = True
vasp.lcharg = True
return vasp
def set_441(vasp: Vasp, structure=None):
x = 4
y = 4
z = 1
packing = 'Gamma'
vasp.kpoints = "Gamma_Mesh\n0\n{}\n{} {} {}".format(packing, x, y, z)
return vasp
def full_converge(vasp: Vasp, structure=None):
# Start
vasp.istart = 1
vasp.icharg = 1
# Electronic
vasp.prec = "Accurate"
vasp.nelm = 200
vasp.ediff = 1e-6
vasp.nelmdl = 0
# Ionic
vasp.nsw = 5000
vasp.ediffg = -0.02
# Output
vasp.lwave = True
vasp.lcharg = True
return vasp
def set_kpoints_auto_20(vasp: Vasp, structure=None):
x = 20
packing = 'Auto'
vasp.kpoints = "Automatic\n0\n{}\n{}".format(packing, x)
kpoint_str = vasp.kpoints.split('\n')[3]
kpoints = [int(x) for x in kpoint_str.split()]
if len(kpoints) > 1:
num_kpoints = kpoints[0] * kpoints[1] * kpoints[2]
else:
density = kpoints[0]
num_kpoints = math.ceil(
density / np.linalg.norm(structure.cell[:, 0])) * math.ceil(
density / np.linalg.norm(structure.cell[:, 1])) * math.ceil(
density / np.linalg.norm(structure.cell[:, 2]))
if num_kpoints < 4:
vasp.ismear = 0
return vasp
def set_algo_normal(vasp: Vasp, structure=None):
'''
:param vasp: Vasp
:param structure:
:return:
'''
vasp.algo = "Normal"
return vasp
def set_nospin(vasp: Vasp, structure=None):
'''
:param vasp: Vasp
:param structure:
:return:
'''
vasp.ispin = 1
return vasp
def cell_relax(vasp: Vasp, structure=None):
vasp.isif = 3
vasp.ibrion = 1
vasp.potim = 0.4
vasp.ediffg = -0.005
vasp.add_keyword('iopt', 0)
return vasp
def scan(vasp: Vasp, structure=None):
vasp.add_keyword('metagga', 'SCAN')
vasp.add_keyword('lhfcalc', False)
vasp.algo = 'Normal'
vasp.ldau = False
no_U(vasp, structure)
return vasp
def set_kpar_by_core(vasp: Vasp, structure=None):
try:
np = int(os.environ['PBS_NP'])
except:
np = int(os.environ['SLURM_NTASKS'])
atoms = len(structure)
if np / atoms > 1:
kpar = math.ceil(np / math.sqrt(atoms))
print(vasp.kpoints)
print(vasp.kpoints)
print(vasp.kpoints)
print(vasp.kpoints)
print(vasp.kpoints)
kpoint_str = vasp.kpoints.split('\n')[3]
kpoints = [int(x) for x in kpoint_str.split()]
num_kpoints = kpoints[0] * kpoints[1] * kpoints[2]
while kpar > 1:
if (num_kpoints % kpar == 0) and (np % kpar == 0):
vasp.add_keyword('kpar', kpar)
return vasp
else:
kpar = kpar - 1
vasp.add_keyword('kpar', 1)
return vasp
def load_species(vasp : Vasp, structure):
# See vasp/functional.py: elementName, fileName, max or min oxidation state
pseudoDir = '$PSEUDO_DIR'
vasp.add_specie = "Zn", pseudoDir + "/Zn"
vasp.add_specie = "O", pseudoDir + "/O"
vasp.add_specie = "Al", pseudoDir + "/Al"
vasp.add_specie = "Cd", pseudoDir + "/Cd"
vasp.add_specie = "Te", pseudoDir + "/Te"
vasp.add_specie = "Ga", pseudoDir + "/Ga"
vasp.add_specie = "As", pseudoDir + "/As"
vasp.add_specie = "In", pseudoDir + "/In"
vasp.add_specie = "P", pseudoDir + "/P"
vasp.add_specie = "Te", pseudoDir + "/Te"
vasp.add_specie = "Bi", pseudoDir + "/Bi_d"
vasp.add_specie = "Mn_+", pseudoDir + "/Mn_pv"
vasp.add_specie = "Mn_-", pseudoDir + "/Mn_pv"
return(vasp)
def set_kpar_auto(vasp: Vasp, structure=None):
try:
nodes = int(os.environ['PBS_NUM_NODES'])
procs = int(os.environ['PBS_NP'])
except:
nodes = int(os.environ['SLURM_JOB_NUM_NODES'])
procs = int(os.environ['SLURM_NTASKS'])
atoms = len(structure)
if procs / atoms > 1:
kpar = math.ceil(procs / atoms) * 2
print(vasp.kpoints)
print(vasp.kpoints)
print(vasp.kpoints)
print(vasp.kpoints)
print(vasp.kpoints)
kpoint_str = vasp.kpoints.split('\n')[3]
kpoints = [int(x) for x in kpoint_str.split()]
if len(kpoints) > 1:
num_kpoints = kpoints[0] * kpoints[1] * kpoints[2]
else:
density = kpoints[0]
num_kpoints = math.ceil(
density / np.linalg.norm(structure.cell[:, 0])) * math.ceil(
density /
np.linalg.norm(structure.cell[:, 1])) * math.ceil(
density / np.linalg.norm(structure.cell[:, 2]))
while kpar > 1:
if num_kpoints % kpar == 0 and nodes % kpar == 0:
vasp.add_keyword('kpar', kpar)
vasp.npar = int(nodes / kpar)
return vasp
else:
kpar = kpar - 1
vasp.add_keyword('kpar', 1)
vasp.npar = int(nodes)
return vasp
def set_900(vasp: Vasp, structure=None):
vasp.encut = 900
return vasp
def set_850(vasp: Vasp, structure=None):
vasp.encut = 850
return vasp
def set_npar_1(vasp: Vasp, structure=None):
vasp.npar = 1
return vasp
def set_ncore_12(vasp: Vasp, structure=None):
vasp.npar = None
vasp.add_keyword('ncore', 12)
return vasp
def tetrahedron(vasp: Vasp, structure=None):
vasp.ismear = -5
return vasp
def set_npar_2(vasp: Vasp, structure=None):
vasp.npar = 2
return vasp
def set_dos(vasp: Vasp, structure=None):
vasp.algo = 'None'
return vasp
def ggau(vasp: Vasp, structure=None):
vasp.add_keyword('metagga', None)
vasp.add_keyword('lhfcalc', False)
vasp.algo = 'Normal'
vasp.ldau = True
return vasp
def set_algo_damp025(vasp: Vasp, structure=None):
vasp.algo = "Damped"
vasp.add_keyword('time', 0.25)
return vasp
def no_hse06(vasp: Vasp, structure=None):
vasp.add_keyword('lhfcalc', False)
vasp.algo = 'Normal'
vasp.ldau = True
return vasp
def hse06(vasp: Vasp, structure=None):
vasp.nelmdl = 0
vasp.nelm = 1000
vasp.add_keyword('lhfcalc', True)
vasp.precfock = 'Fast'
vasp.add_keyword('hfscreen', 0.2)
vasp.algo = 'All'
vasp.npar = None
vasp.ldau = False
vasp.lwave = True
vasp.lcharg = True
vasp.ismear = 0
vasp.add_keyword('metagga', False)
vasp.add_keyword('ncore', 8)
return vasp