calc = vasp_calculator.Vasp(
encut=500,
xc='PBE',
#setups={'O': '_s', 'C': '_s'},
gga='PE',
#kpts = (2,2,1),
# kpts=(6, 6, 1),
# For typical 2x2 cell IrO2 110 with 2 cusp sites and 2 bridge sites
kpts=(4, 4, 1),
kpar=10,
npar=4,
gamma=True, # Gamma-centered (defaults to Monkhorst-Pack)
ismear=0,
inimix=0,
amix=0.2,
bmix=0.0001,
amix_mag=0.1,
bmix_mag=0.0001,
# Conservative Mixing Paramters
# amix=0.05,
# bmix=0.00001,
# amix_mag=0.05,
# bmix_mag=0.00001,
#nupdown= 0,
nelm=250,
sigma=0.05,
algo=algo,
# algo='Very_Fast', # algorithm: Normal (Davidson) | Fast | Very_Fast (RMM-DIIS)
# algo='normal',
ibrion=ibrion,
potim=potim,
isif=2,
ediffg=-0.02, # forces
ediff=1e-5, # energy conv.
#nedos=2001,
prec='Normal',
nsw=int(200 /
potim), # don't use the VASP internal relaxation, only use ASE
lvtot=False,
ispin=2,
ldau=u_corr,
ldautype=2,
lreal='auto',
lasph=True,
ldau_luj={
'Ni': {
'L': 2,
'U': 6.45,
'J': 0.0
},
'Co': {
'L': 2,
'U': 3.32,
'J': 0.0
},
'Cr': {
'L': 2,
'U': 3.5,
'J': 0.0
},
'Fe': {
'L': 2,
'U': 5.3,
'J': 0.0
},
'Ce': {
'L': 3,
'U': 4.50,
'J': 0.0
},
'V': {
'L': 2,
'U': 3.25,
'J': 0.0
},
'Mn': {
'L': 2,
'U': 3.75,
'J': 0.0
},
'Ti': {
'L': 2,
'U': 3.00,
'J': 0.0
},
'W': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'O': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'C': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Au': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Ir': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Cu': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'H': {
'L': -1,
'U': 0.0,
'J': 0.0
},
},
ldauprint=2,
# lmaxmix=4,
lmaxmix=6,
lorbit=11,
idipol=3,
dipol=(0, 0, 0.5),
ldipol=dipole_corr,
# ldipol=True,
# addgrid=True,
# isym=0,
)
# Reading VASP parameters from file and merging with params in script
from ase_modules.dft_params import VASP_Params
VP = VASP_Params(load_defaults=False)
VP.load_params()
dft_calc_settings.update(VP.params)
# ########################################################
if easy_params:
dft_calc_settings.update(easy_dft_calc_settings)
# Setting NSW to 1, just need to create Charge files
dft_calc_settings.update(dict(nsw=1))
# ########################################################
calc = vasp_calculator.Vasp(**dft_calc_settings)
# ########################################################
# Writing all calculator parameters to json
with open("out_data/calc_params.json", "w") as outfile:
json.dump(calc.todict(), outfile, indent=2)
#__|
# Setting magmoms to 0 if not running spin-polarized calculation
if dft_calc_settings.get("ispin", None) == 1:
print(30 * "*")
print("Setting magnetic moments to 0 since ispin=1")
print(30 * "*")
calc = vasp_calculator.Vasp(
encut=500,
xc='PBE',
gga='PS',
kpts=(3, 3, 3),
kpar=10,
npar=4,
gamma=True, # Gamma-centered (defaults to Monkhorst-Pack)
#ICHARG =1 ,
#ISTART = 2,
#isym = 0,
ismear=0,
inimix=0,
amix=0.1,
bmix=0.00001,
amix_mag=0.1,
bmix_mag=0.00001,
#NUPDOWN= 0,
nelm=250,
sigma=0.05,
algo='normal',
#algo = 'fast',
ibrion=2,
isif=2,
ediffg=-0.02, # forces
ediff=1e-5, #energy conv.
nedos=2001,
prec='Normal',
#prec='Accurate',
#nsw=130, # don't use the VASP internal relaxation, only use ASE
nsw=0, # don't use the VASP internal relaxation, only use ASE
lvtot=False,
ispin=1,
ldau=False,
ldautype=2,
lreal=False,
lwave=True,
lasph=True,
#ldipol = True,
#idipol = 3,
ldau_luj={
'Ni': {
'L': 2,
'U': 6.45,
'J': 0.0
},
#ldau_luj={'Ni':{'L':2, 'U':8, 'J':0.0},
'Co': {
'L': 2,
'U': 3.32,
'J': 0.0
},
'Fe': {
'L': 2,
'U': 5.3,
'J': 0.0
},
'Ce': {
'L': 3,
'U': 5.5,
'J': 1.0
},
'Sm': {
'L': 3,
'U': 4.5,
'J': 0.0
},
'W': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'O': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'C': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Au': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Cu': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'H': {
'L': -1,
'U': 0.0,
'J': 0.0
}
},
ldauprint=2,
lmaxmix=6,
lorbit=11,
)
# new calculation
atoms = read('init.traj')
calc = vasp_calculator.Vasp(
encut=500,
xc='BEEF',
luse_vdw=True,
zab_vdw=True,
zab_vdw=-1.8867,
gga='BF',
kpts=(4, 3, 1),
npar=2,
gamma=True, # Gamma-centered (defaults to Monkhorst-Pack)
ismear=0,
algo='fast',
nelm=250,
sigma=0.05,
ibrion=2,
ediffg=-0.05, # forces
ediff=
1e-4, #energy conv. both of these are for the internal relaxation, ie nsw
prec='Accurate',
nsw=0, # don't use the VASP internal relaxation, only use ASE
ispin=1,
ldipol=True,
lvhar=True,
dipol=(0.5, 0.5, 0.5),
idipol=3,
icharg=1) #start from CHGCAR if icharg = 1
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc = vasp_calculator.Vasp(
encut=500,
xc='PBE',
gga='BF',
luse_vdw=True,
zab_vdw=-1.8867,
kpts=(4, 3, 1),
kpar=
7, # use this if you run on one node (most calculations). see suncat confluence page for optimal setting
npar=
1, # use this if you run on one node (most calculations). see suncat confluence page for optimal setting
gamma=True, # Gamma-centered (defaults to Monkhorst-Pack)
ismear=0,
algo='all',
nelm=250,
sigma=0.05,
ibrion=2,
nelmdl=-9,
#isif = 3, # 3 for vc-relax, otherwise delete the flag
ediffg=-0.05, # forces
ediff=
1e-4, # energy conv. both of these are for the internal relaxation, ie nsw
prec='Accurate',
nsw=0, # don't use the VASP internal relaxation, only use ASE
ispin=1,
lreal='auto', # automatically decide to do real vs recip space calc
ldipol=True,
lvhar=True,
dipol=(0.0, 0.0, 0.0),
idipol=3,
icharg=1) # start from CHGCAR if icharg = 1
'L': -1,
'U': 0.0,
'J': 0.0
},
},
ldauprint=2,
#lmaxmix=4,
lmaxmix=6,
lorbit=11,
#idipol=3,
#dipol=(0, 0, 0.5),
#ldipol=True
)
# Reading VASP parameters from file and merging with params in script
from ase_modules.dft_params import VASP_Params
VP = VASP_Params(load_defaults=False)
VP.load_params()
calc_params.update(VP.params)
calc = vasp_calculator.Vasp(**calc_params)
#__|
atoms.set_calculator(calc)
atoms.get_potential_energy()
io.write('out.traj', atoms)
io.write('out.traj', atoms)
clean_up_dft()
def vasp_script():
import ase.calculators.vasp as vasp_calculator
import json, multiprocessing, time, os, subprocess
params, atoms = initialize(
) # Remove old .out/.err files, load from fw_spec, and write 'init.traj'
#############################################
print "Initializing VASP calculator..."
#-----------------------------------------
calc = vasp_calculator.Vasp(
encut=params['pw'],
setups=json.loads(params['psp']) # dictionary {'Cu':'_s'}
,
xc=params['xc'],
gga=params['gga'] # 'BF'
,
luse_vdw=params['luse_vdw'] # True
,
zab_vdw=params.get('zab_vdw'),
kpts=json.loads(params['kpts']),
npar=
1 # use this if you run on one node (most calculations). see suncat confluence page for optimal setting
,
kpar=1,
gamma=params[
'gamma'] # True, # Gamma-centered (defaults to Monkhorst-Pack)
,
ismear=
0 # assume gaussian smearing, we can make this parameter if necessary
,
algo=params['algo'] #'fast',
,
nelm=params['maxstep'],
sigma=params['sigma'],
ibrion=params['ibrion'] #2
,
nelmdl=params['nelmdl'],
isif=3 if params['jobkind'] == 'vcrelax' else 2,
ediffg=-params['fmax'] # forces
,
ediff=params[
'econv'] # energy conv. both of these are for the internal relaxation, ie nsw
,
prec=params['prec'] #'Accurate'
,
nsw=params['ionic_steps'] # use ASE ?
,
ispin=2 if params['spinpol'] else 1,
lreal=params[
'lreal'] # automatically decide to do real vs recip space calc
,
ldipol=params['dipole'] #True,
,
lvhar=params['lvhar'] #True,
,
dipol=params.get('dipol') #(0.5,0.5,0.5),
,
idipol=3 if params['dipole'] else None,
icharg=1) # start from CHGCAR if icharg = 1
atoms.set_calculator(calc)
############################################
print "Generating VASP Input files with ASE"
#------------------------------------------
try:
proc = multiprocessing.Process(target=atoms.get_potential_energy)
proc.start()
time.sleep(10)
if proc.is_alive(): proc.terminate()
except IOError:
pass #on nersc, we get io error
#######################
print "Running VASP natively..."
#----------------------
loader = {
'sherlock': "ml vasp/5.4.1.intel.gpu",
'sherlock2': "ml chemistry vasp/5.4.1",
'nersc': "module load vasp-tpc/5.4.1"
}
vaspout, vasperr = subprocess.Popen(loader[get_cluster()] +
';which vasp_std;srun -n 32 vasp_std',
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True).communicate()
print 'VASP output:\n', vaspout
with open('OUTCAR', 'r') as f:
if 'General timing and accounting informations for this job' in f.read(
):
if rank() == 0: log(params)
return 0
raise ValueError, vasperr
calc = vasp_calculator.Vasp(
encut=500,
xc='PBE',
#setups={'O': '_s', 'C': '_s'},
gga='PE',
kpts=(5, 5, 1),
kpar=5,
npar=8,
gamma=True, # Gamma-centered (defaults to Monkhorst-Pack)
ismear=0,
INIMIX=0,
AMIX=0.2,
BMIX=0.0001,
AMIX_MAG=0.4,
BMIX_MAG=0.0001,
#NUPDOWN= 0,
nelm=250,
sigma=0.05,
algo='normal',
ibrion=2,
ediffg=-0.02, # forces
ediff=1e-6, #energy conv.
nedos=2001,
prec='Normal',
#prec='Accurate',
nsw=0, # don't use the VASP internal relaxation, only use ASE
#nsw=200, # don't use the VASP internal relaxation, only use ASE
lvtot=False,
ispin=2,
ldau=True,
ldautype=2,
LREAL='auto',
LASPH=True,
LWAVE=False,
LDIPOL=True,
IDIPOL=3,
dipol=(0, 0, 0),
#ldau_luj={'Ni':{'L':2, 'U':6.45, 'J':0.0},
ldau_luj={
'Ni': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Co': {
'L': 2,
'U': 3.32,
'J': 0.0
},
'Fe': {
'L': 2,
'U': 5.3,
'J': 0.0
},
'Ce': {
'L': 3,
'U': 5.5,
'J': 1.0
},
'W': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'O': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'C': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Au': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Cu': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'H': {
'L': -1,
'U': 0.0,
'J': 0.0
}
},
ldauprint=2,
lmaxmix=6,
lorbit=11)
calc = vasp_calculator.Vasp(
encut=500,
xc='PBE',
gga='BF',
luse_vdw=True,
zab_vdw=-1.8867,
kpts=(4, 3, 1),
kpar=
1 # use this if you run on one node (most calculations). see suncat confluence page for optimal setting
,
npar=
4 # use this if you run on one node (most calculations). see suncat confluence page for optimal setting
,
lhfcalc=True # HSE parameter
,
hfscreen=0.3 # HSE parameter
,
setups={
'K': '_pv',
'Nb': '_pv',
'Zr': '_sv'
} # don't use default for these, _sv = include semi-core electrons too, _h and _s (hard vs soft)?
,
gamma=True # Gamma-centered (defaults to Monkhorst-Pack)
,
ismear=0
#,inimix = 0 # density mixing
,
amix=0.2 # etc.
,
bmix=0.00001 #
,
amix_mag=0.1 # magnetic mixing
,
bmix_mag=0.00001
#NUPDOWN= 0,
,
nelm=250 # max electronic steps
,
sigma=0.05 # fermi temp
,
algo='Normal' # diagonalization
,
ibrion=2 # conjugate gradient descent
#POTIM=1.0,
,
ediffg=-0.02 # force cutoff (IF NEGATIVE)
,
ediff=1e-4 # energy conv.
,
nedos=2001 # # gridpoints in dos
,
prec='Normal' # precision
#,nsw=0, # don't use the VASP internal relaxation, only use ASE
,
nsw=300 # don't use the VASP internal relaxation, only use ASE
,
lvtot=
False # never want this to be true (if you want work function, use lvhar=True to write locpot)
,
ispin=2 # turns on spin polarization (1 = false 2 = true)
,
ldau=True # turns on + U
,
ldautype=2 # parameter ?
,
lreal='auto' # automatically decide to do real vs recip space calc
,
lasph=
True # "also includes non-spherical contributions from the gradient corrections inside the PAW spheres. "
,
lwave=False # don't write out wf
,
ldau_luj={
'Ni': {
'L': 2,
'U': 6.45,
'J': 0.0
}, # how to apply U correction (what shell, how much, etc.)
'Co': {
'L': 2,
'U': 3.32,
'J': 0.0
},
'Cr': {
'L': 2,
'U': 3.5,
'J': 0.0
},
'Fe': {
'L': 2,
'U': 5.3,
'J': 0.0
},
'V': {
'L': 2,
'U': 3.10,
'J': 0.0
},
'Mn': {
'L': 2,
'U': 3.75,
'J': 0.0
},
'Ti': {
'L': 2,
'U': 3.00,
'J': 0.0
},
'W': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'O': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'C': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Au': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Cu': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Ce': {
'L': 3,
'U': 5.5,
'J': 1.0
},
'H': {
'L': -1,
'U': 0.0,
'J': 0.0
}
},
ldauprint=2 # prints u values to outcar
,
idipol=3 # what direction (z)
,
dipol=(0, 0, 0.5) # location
,
ldipol=True # turns it on
,
lmaxmix=4,
lorbit=11) # prints magnetic moments in outcar
calc = vasp_calculator.Vasp(
encut=600,
xc='PBE',
#setups={'O': '_s', 'C': '_s'},
gga='PE',
#kpts = (2,2,1),
kpts=(kpoints[0], kpoints[1], kpoints[2]),
kpar=kpar,
npar=4,
gamma=True, # Gamma-centered (defaults to Monkhorst-Pack)
ismear=0,
inimix=0,
amix=0.2,
bmix=0.0001,
amix_mag=0.1,
bmix_mag=0.0001,
#nupdown= 0,
nelm=120,
sigma=0.05,
algo='normal',
ibrion=2,
isif=3,
ediffg=-0.02, # forces
ediff=1e-5, #energy conv.
#nedos=2001,
prec='Normal',
nsw=150, # don't use the VASP internal relaxation, only use ASE
lvtot=False,
ispin=2,
ldau=False,
ldautype=2,
#lreal = 'False',#more accuratre volume
lreal='auto',
lasph=True,
ldau_luj={
'Ni': {
'L': 2,
'U': 6.45,
'J': 0.0
},
'Co': {
'L': 2,
'U': 3.32,
'J': 0.0
},
'Cr': {
'L': 2,
'U': 3.5,
'J': 0.0
},
'Fe': {
'L': 2,
'U': 5.3,
'J': 0.0
},
'Ce': {
'L': 3,
'U': 4.50,
'J': 0.0
},
'V': {
'L': 2,
'U': 3.25,
'J': 0.0
},
'Mn': {
'L': 2,
'U': 3.75,
'J': 0.0
},
'Ti': {
'L': 2,
'U': 3.00,
'J': 0.0
},
'W': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'O': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'C': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Au': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'Cu': {
'L': -1,
'U': 0.0,
'J': 0.0
},
'H': {
'L': -1,
'U': 0.0,
'J': 0.0
}
},
ldauprint=2,
#lmaxmix=4,
lmaxmix=6,
lorbit=11,
#idipol=3,
#dipol=(0, 0, 0.5),
#ldipol=True
)
# 'Fe':{'L':2, 'U':5.3, 'J':0.0},
# 'Ce':{'L':3, 'U':5.5, 'J':1.0},
# 'Sm':{'L':3, 'U':4.5, 'J':0.0},
# 'W':{'L':-1, 'U':0.0, 'J':0.0},
# 'O':{'L':-1, 'U':0.0, 'J':0.0},
# 'C':{'L':-1, 'U':0.0, 'J':0.0},
# 'Au':{'L':-1, 'U':0.0, 'J':0.0},
# 'Cu':{'L':-1, 'U':0.0, 'J':0.0},
# 'H':{'L':-1, 'U':0.0, 'J':0.0},
# },
ldauprint=2,
lmaxmix=6,
lorbit=11,
)
calc = vasp_calculator.Vasp(kpar=10, lwave=True, **shared_calc_settings)
new_atoms.set_calculator(calc)
new_atoms.get_potential_energy()
calc = vasp_calculator.Vasp(kpar=5, lwave=False, **shared_calc_settings)
#__|
# assert False
#| - Phonon Calculation
from ase.phonons import Phonons
ph = Phonons(new_atoms, calc, supercell=(1, 1, 1))
ph.run()
ph.read(method='frederiksen', acoustic=True)
cc = stretchcombo(initial_value, liste, atoms)
# adjust structure according to the initial value (in this example the initial value is not modified).
atoms.set_positions(cc.return_adjusted_positions())
# set all constraints, keeping old constraints (there are no old constraints in this example).
atoms.set_constraint([cc] + atoms.constraints)
# PBE-D3 (zero damping). should work with any periodic DFT program
calc = vasp_calculator.Vasp(encut=400,
xc='PBE',
ivdw=11,
gga='PE',
kpts=(1, 1, 1),
ncore=2,
gamma=True,
ismear=0,
nelm=250,
algo='fast',
sigma=0.1,
ibrion=-1,
ediffg=-0.01,
ediff=1e-8,
prec='normal',
nsw=50,
lreal='Auto',
ispin=1)
atoms.set_calculator(calc)
dyn = arpess(atoms, scanned_constraint=cc) # minimum: scanned constraint needs to be specified.
dyn.run(fmax=0.01)
atoms.write('final.cif')
