def test_to_dict_and_from_dict(self):
file_name = os.path.join(test_dir, "INCAR")
incar = Incar.from_file(file_name)
d = incar.to_dict
incar2 = Incar.from_dict(d)
self.assertEqual(incar, incar2)
def run_task(self, fw_spec):
Incar.from_dict(fw_spec['vasp']['incar']).write_file('INCAR')
Poscar.from_dict(fw_spec['vasp']['poscar']).write_file('POSCAR')
Potcar.from_dict(fw_spec['vasp']['potcar']).write_file('POTCAR')
Kpoints.from_dict(fw_spec['vasp']['kpoints']).write_file('KPOINTS')
def test_to_dict_and_from_dict(self):
file_name = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(file_name)
d = incar.to_dict
incar2 = Incar.from_dict(d)
self.assertEqual(incar, incar2)
def test_as_dict_and_from_dict(self):
d = self.incar.as_dict()
incar2 = Incar.from_dict(d)
self.assertEqual(self.incar, incar2)
slab_potcar.write_file("./Slab_with_vdw/POTCAR")
#set the common INCAR file and KPOINTS
incar_dict = {
'SYSTEM': 'ligand_PbS',
'ENCUT': 600,
'ISIF': 2,
'IBRION': 2,
'ALGO': 'Normal',
'ISMEAR': 1,
'ISPIN': 1,
'EDIFF': 1e-06,
'EDIFFG': -0.005,
'NPAR': 8,
'SIGMA': 0.1,
'PREC': 'Accurate',
'IVDW': 2,
'NSW': 1000
}
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts= (8, 8, 1), shift= (0, 0, 0))
#write the files in appropriate directory
incar.write_file("./Interface_with_vdw/INCAR")
incar.write_file("./Slab_with_vdw/INCAR")
kpoints.write_file("./Interface_with_vdw/KPOINTS")
kpoints.write_file("./Slab_with_vdw/KPOINTS")
shu.copy("./submit_job", "./Interface_with_vdw/")
shu.copy("./submit_job", "./Slab_with_vdw")
def get_VASP_inputs(structure, workdir, job_name, nproc=64, kppa=500, extra_incar_dict = None):
if os.path.exists(workdir):
print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB'
return -1
poscar = Poscar(structure)
list_potcar_singles, potcar= get_POTCAR(poscar)
kpoints = Kpoints.automatic_density(structure, kppa=kppa)
# Default values
incar_dict = dict( SYSTEM = structure.formula, # Name of job
LREAL = 'Auto', # Should projections be done in real space? Let VASP decide
ENCUT = 520., # 520. eV, just like Ceder
IBRION = 2, # Controls ionic relataxion: 1-> DISS, 2 -> CG, 3-> MD
EDIFF = 1E-7, # criterion to stop SCF loop, in eV
EDIFFG = -1E-3, # criterion to stop ionic relaxations. Negative means FORCES < |EDIFFG|
PREC = 'HIGH', # level of precision
AMIX = 0.2,
AMIX_MAG= 0.8,
BMIX = 0.001,
BMIX_MAG= 0.001,
NSW = 150, # Maximum number of ionic steps
ISMEAR = 0, # smearing scheme. Use 0 for insulators, as suggested by VASPWIKI
ISPIN = 2, # spin polarized
NPAR = 8, # VASPWIKI recommends sqrt(ncore)
LSCALU = False, # Don't use scalapack. Probably a can of worms.
ALGO = 'NORMAL', # what ionic relaxation scheme to use?
LORBIT = 11, # 11 prints out the DOS
ISIF = 3, # Controls the computation of stress tensor. 3 computes everything
NSIM = 4, # how many bands to treat in parallel? Default is 4, probably fine.
SIGMA = 0.025, # smearing in eV
LMAXMIX = 4, # Description: LMAXMIX controls up to which l-quantum number the one-center PAW charge densities are passed through the charge density mixer. MaterialsProject uses 4.
LCHARG = False, # Write charge densities?
LWAVE = False, # write out the wavefunctions?
LPLANE = True, # Plane distribution of FFT coefficients. Reduces communications in FFT.
NELM = 100, # maximum number of SCF cycles.
NELMDL = -10, # since initial orbitals may be random, fixes hamiltonian for |NELM| SCF cycles to give wf a chance to simmer down.
ISTART = 0, # begin from scratch!
ISYM = 2) # use symmetry
if extra_incar_dict != None:
incar_dict.update( extra_incar_dict )
incar = Incar.from_dict(incar_dict )
incar.write_file(workdir+'INCAR')
poscar.write_file(workdir+'POSCAR', vasp4_compatible = True)
kpoints.write_file(workdir+'KPOINTS')
potcar.write_file(workdir+'POTCAR')
potcar.sort()
hack_potcar_file(workdir,list_potcar_singles)
with open(workdir+'job.sh','w') as f:
f.write(submit_template.format(job_name,nproc))
with open(workdir+'clean.sh','w') as f:
f.write(clean_template)
return 0
def get_calibration_task(structure, phase="CalibrateBulk", \
slab_interface_params={'hkl':[1,0,0], 'ligand': None},\
turn_knobs={}, incar_params={}, other_params={}):
"""
returns general calibration task for a structure
Args:
structure : pymatgen structure to be calibrated (can be a bulk, ligand, slab
or interface)
phase : calibration type, viz. CalibrateBulk, CalibrateMolecule,
CalibrateSlab, CalibrateInterface
hkl : in case of Slab and Interface miller indices of facet
turn_knobs : specifies the parameters to be calibrated
incar_params : dictionary of additional incar parameters, refer defined
incar_dict for defaults
other_params : other parameters for calibration, viz. job_dir, is_matrix, etc.
described in the calibrate module
"""
#structure definition
poscar = Poscar(structure)
incar_dict = { 'SYSTEM': 'slab',
'ENCUT': 500,
'ISIF': 2,
'IBRION': 2,
'ISMEAR': 1,
'EDIFF': 1e-05,
'NPAR': 4,
'SIGMA': 0.1,
'PREC': 'Accurate'
}
if incar_params:
incar_dict.update(incar_params)
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts=(8, 8, 1))
que = { 'nnodes':1,
'nprocs':16,
'walltime':'48:00:00',
'job_bin': '/home/km468/Software/VASP/vaspsol_kappa.5.3.5/vasp'
}
# calibration task: relax hkl
calparams = {}
calparams['calibrate'] = phase
calparams['incar'] = incar.as_dict()
calparams['poscar'] = poscar.as_dict()
calparams['kpoints'] = kpoints.as_dict()
calparams['que_params'] = que
calparams['turn_knobs'] = turn_knobs
if phase == 'CalibrateSlab':
calparams['system'] = {'hkl':slab_interface_params['hkl'],
'ligand':slab_interface_params['ligand']
}
elif phase == 'CalibrateInterface':
calparams['system'] = {'hkl':hkl,
'ligand':structure.ligand.reduced_formula
}
calparams['other_params'] = {
'is_matrix':False,
'from_ase':True,
'Grid_type':'M'
}
if other_params:
calparams['other_params'].update(other_params)
return MPINTCalibrateTask(calparams)
def run_task(self, fw_spec):
Incar.from_dict(fw_spec['vasp']['incar']).write_file('INCAR')
Poscar.from_dict(fw_spec['vasp']['poscar']).write_file('POSCAR')
Potcar.from_dict(fw_spec['vasp']['potcar']).write_file('POTCAR')
Kpoints.from_dict(fw_spec['vasp']['kpoints']).write_file('KPOINTS')
def get_calibration_task(structure, phase="CalibrateBulk", \
slab_interface_params={'hkl':[1,0,0], 'ligand': None},\
turn_knobs={}, incar_params={}, other_params={}):
"""
returns general calibration task for a structure
Args:
structure : pymatgen structure to be calibrated (can be a bulk, ligand, slab
or interface)
phase : calibration type, viz. CalibrateBulk, CalibrateMolecule,
CalibrateSlab, CalibrateInterface
hkl : in case of Slab and Interface miller indices of facet
turn_knobs : specifies the parameters to be calibrated
incar_params : dictionary of additional incar parameters, refer defined
incar_dict for defaults
other_params : other parameters for calibration, viz. job_dir, is_matrix, etc.
described in the calibrate module
"""
#structure definition
poscar = Poscar(structure)
incar_dict = {
'SYSTEM': 'slab',
'ENCUT': 500,
'ISIF': 2,
'IBRION': 2,
'ISMEAR': 1,
'EDIFF': 1e-05,
'NPAR': 4,
'SIGMA': 0.1,
'PREC': 'Accurate'
}
if incar_params:
incar_dict.update(incar_params)
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts=(8, 8, 1))
que = {
'nnodes': 1,
'nprocs': 16,
'walltime': '48:00:00',
'job_bin': '/home/km468/Software/VASP/vaspsol_kappa.5.3.5/vasp'
}
# calibration task: relax hkl
calparams = {}
calparams['calibrate'] = phase
calparams['incar'] = incar.as_dict()
calparams['poscar'] = poscar.as_dict()
calparams['kpoints'] = kpoints.as_dict()
calparams['que_params'] = que
calparams['turn_knobs'] = turn_knobs
if phase == 'CalibrateSlab':
calparams['system'] = {
'hkl': slab_interface_params['hkl'],
'ligand': slab_interface_params['ligand']
}
elif phase == 'CalibrateInterface':
calparams['system'] = {
'hkl': hkl,
'ligand': structure.ligand.reduced_formula
}
calparams['other_params'] = {
'is_matrix': False,
'from_ase': True,
'Grid_type': 'M'
}
if other_params:
calparams['other_params'].update(other_params)
return MPINTCalibrateTask(calparams)
def test_as_dict_and_from_dict(self):
d = self.incar.as_dict()
incar2 = Incar.from_dict(d)
self.assertEqual(self.incar, incar2)
