class VaspBulk(object):
def __init__(self,
struct,
struct_type='insulator',
ggaU=False,
base_param_set=None):
self.struct = Structure.from_sites(struct.get_sorted_structure().sites,
to_unit_cell=False,
validate_proximity=True)
if base_param_set:
self.base_params = base_param_set
else:
self.base_params = MITGGAVaspInputSet(hubbard_off=(not ggaU))
self.ggaU = ggaU
self.struct_type = struct_type
def get_incar(self, cg_algo=False, relax=False):
incar = self.base_params.get_incar(self.struct)
#---------------------------------------------------------------------------------------------------------------
# Basic setup
#---------------------------------------------------------------------------------------------------------------
incar['ISYM'] = 0 # Symmetry bad, symmetry go away
incar["SYMPREC"] = 1e-8
incar['ISIF'] = 3
incar['ISMEAR'] = 0
if self.struct_type == 'insulator':
incar['SIGMA'] = 0.05
elif self.struct_type == 'metal':
incar['SIGMA'] = 0.2
incar['LREAL'] = 'Auto'
incar['LVTOT'] = False
incar['LVHAR'] = False
incar['LWAVE'] = False
incar['LCHARG'] = True
#incar['GGA'] = 'PS' # For turning on PBEsol - here just use normal PBE
incar['ICHARG'] = 2
incar['ISTART'] = 0
incar['LVTOT'] = True
incar['LVHAR'] = True
#---------------------------------------------------------------------------------------------------------------
# Convergence changes
#---------------------------------------------------------------------------------------------------------------
if not cg_algo:
incar['ALGO'] = 'Fast'
else:
incar['ALGO'] = 'A'
incar['LSUBROT'] = False
incar['TIME'] = 0.2
incar['AMIX'] = 0.2
incar['AMIN'] = 0.01
incar['BMIX'] = 0.0001
incar['AMIX_MAG'] = 0.8
incar['BMIX_MAG'] = 0.0001
incar['LMAXMIX'] = 4
#incar['LASPH'] = True # Generally should be set as it fixes lots of problems but its inconsistent with the
# runs in MP and Matgen so keep it off
incar['EDIFF'] = 1e-6 * len(self.struct.sites)
incar['NELMDL'] = -6
incar['NELMIN'] = 8
incar['ISIF'] = 2
# For Vesta
incar['NPAR'] = 8
# For Vesta end
#---------------------------------------------------------------------------------------------------------------
# Relaxation
#---------------------------------------------------------------------------------------------------------------
if relax:
incar['IBRION'] = 2
incar['NSW'] = 100
incar['POTIM'] = 0.25
else:
incar["IBRION"] = -1
incar["NSW"] = 0
#---------------------------------------------------------------------------------------------------------------
# Make sure +U is turned off if necessary
#---------------------------------------------------------------------------------------------------------------
if not self.ggaU:
delete_keys = ["LDAU", "LDAUJ", "LDAUL", "LDAUTYPE", "LDAUU"]
for key in delete_keys:
if key in incar.keys():
del incar[key]
return incar
def get_potcar(self):
potcar = self.base_params.get_potcar(self.struct)
return potcar
def get_kpoints(self):
kpoints = Kpoints.gamma_automatic((1, 1, 1), shift=(0, 0, 0))
return kpoints
def get_poscar(self):
structure = self.struct.get_sorted_structure()
selective_dynamics = np.zeros((structure.num_sites, 3), dtype=bool)
selective_dynamics = list(selective_dynamics)
poscar = Poscar(structure, selective_dynamics=selective_dynamics)
return poscar
class PointRunInput(object):
def __init__(self, struct, struct_type='insulator', ggaU=False, base_param_set=None):
self.struct = Structure.from_sites(struct.get_sorted_structure().sites,
to_unit_cell=False, validate_proximity=True)
if base_param_set:
self.base_params = base_param_set
else:
self.base_params = MITGGAVaspInputSet(hubbard_off=(not ggaU))
self.ggaU = ggaU
self.struct_type = struct_type
def get_incar(self, cg_algo=False, relax=True):
incar = self.base_params.get_incar(self.struct)
#---------------------------------------------------------------------------------------------------------------
# Basic setup
#---------------------------------------------------------------------------------------------------------------
incar['ISYM'] = 0 # Symmetry bad, symmetry go away
incar['ISIF'] = 2
incar['ISPIN'] = 2
incar['ISPIND'] = 2
#incar['ISIF'] = 2 #This should be changed back to 2 in production phase
incar['ISMEAR'] = 0
if self.struct_type == 'insulator':
incar['SIGMA'] = 0.05
elif self.struct_type == 'metal':
incar['SIGMA'] = 0.2
incar['LREAL'] = 'Auto'
#incar['LREAL'] = False #This setting needs to be changed back to Auto in production phase
#incar['LVTOT'] = False
#incar['LVHAR'] = False
incar['LWAVE'] = False
incar['LCHARG'] = True
incar['LPLANE'] = True
#incar['GGA'] = 'PS' For turning on PBEsol - here just use normal PBE
incar['ICHARG'] = 2
incar['ISTART'] = 0
incar['LORBIT'] = 0
incar['LSCALU'] = False
#---------------------------------------------------------------------------------------------------------------
# Convergence changes
#---------------------------------------------------------------------------------------------------------------
if not cg_algo:
incar['ALGO'] = 'Fast'
else:
incar['ALGO'] = 'A'
incar['LSUBROT'] = False
incar['TIME'] = 0.2
#incar['AMIX'] = 0.2
#incar['AMIN'] = 0.01
#incar['BMIX'] = 0.0001
#incar['AMIX_MAG'] = 0.8
#incar['BMIX_MAG'] = 0.0001
#incar['LMAXMIX'] = 4
#incar['LASPH'] = True # Generally should be set as it fixes lots of problems but its inconsistent with the
# runs in MP and Matgen so keep it off
incar['EDIFF'] = 1e-5 * len(self.struct.sites)
#incar['NELMDL'] = -6
incar['NELMIN'] = 4
incar['NELM'] = 100
# For Vesta
incar['NPAR'] = 8
# For Vesta end
incar['NSIM'] = 4
incar['PREC'] = 'High'
#---------------------------------------------------------------------------------------------------------------
# Relaxation
#---------------------------------------------------------------------------------------------------------------
if relax:
incar['IBRION'] = 1
incar['NSW'] = 200
incar['POTIM'] = 0.25
else:
incar["IBRION"] = -1
incar["NSW"] = 0
#---------------------------------------------------------------------------------------------------------------
# Make sure +U is turned off if necessary
#---------------------------------------------------------------------------------------------------------------
if not self.ggaU:
delete_keys = ["LDAU", "LDAUJ", "LDAUL", "LDAUTYPE", "LDAUU"]
for key in delete_keys:
if key in incar.keys():
del incar[key]
return incar
def get_potcar(self):
potcar = self.base_params.get_potcar(self.struct)
return potcar
def get_kpoints(self):
kpoints = Kpoints.automatic_density(self.struct, kppa=1000)
return kpoints
def get_poscar(self, e):
structure = self.struct.get_sorted_structure()
index = 0
for i, site in enumerate(structure.sites):
if site.specie == e:
index = i
selective_dynamics = np.ones((structure.num_sites, 3), dtype=bool)
selective_dynamics[index, :] = np.zeros(3, dtype=bool)
#Fix Furthest atom from moving cation
dis_from_cation = 0
fix_index = index
for i, site in enumerate(structure.sites):
if site.distance(structure.sites[index]) > dis_from_cation:
dis_from_cation = site.distance(structure.sites[index])
fix_index = i
selective_dynamics[fix_index, :] = np.zeros(3, dtype=bool)
selective_dynamics = list(selective_dynamics)
poscar = Poscar(structure, selective_dynamics=selective_dynamics)
return poscar
