def plot_images(self, outfile):
"""
Generates a POSCAR with the calculated diffusion path with respect to the first endpoint.
:param outfile: Output file for the POSCAR
"""
sum_struct = self.__images[0].sites
for image in self.__images:
for site_i in self.__relax_sites:
sum_struct.append(PeriodicSite(image.sites[site_i].specie, image.sites[site_i].frac_coords,
self.__images[0].lattice, to_unit_cell=True, coords_are_cartesian=False))
sum_struct = Structure.from_sites(sum_struct, validate_proximity=False)
p = Poscar(sum_struct)
p.write_file(outfile)
def plot_images(self, outfile):
"""
Generates a POSCAR with the calculated diffusion path with respect to the first endpoint.
:param outfile: Output file for the POSCAR
"""
sum_struct = self.__images[0].sites
for image in self.__images:
for site_i in self.__relax_sites:
sum_struct.append(
PeriodicSite(image.sites[site_i].specie,
image.sites[site_i].frac_coords,
self.__images[0].lattice,
to_unit_cell=True,
coords_are_cartesian=False))
sum_struct = Structure.from_sites(sum_struct, validate_proximity=False)
p = Poscar(sum_struct)
p.write_file(outfile)
sd_flag_iface= []
j= 0
sd_flag_slab= []
for i in iface.sites:
sd_flag_iface.append(false_site)
for i in iface_slab.sites:
sd_flag_slab.append(false_site)
#POSCAR and POTCAR construction, pending setting of exact flags for POSCAR
interface_poscar = Poscar(iface, selective_dynamics= sd_flag_iface)
interface_potcar= Potcar(interface_poscar.site_symbols)
slab_poscar = Poscar(iface_slab, selective_dynamics= sd_flag_slab)
slab_potcar= Potcar(slab_poscar.site_symbols)
#write the files in appropriate directories
interface_poscar.write_file("./Interface/POSCAR_PbS100DMF_interface_with_sd.vasp")
slab_poscar.write_file("./Slab/POSCAR_PbS100_slab_with_sd.vasp")
interface_potcar.write_file("./Interface_with_vdw/POTCAR")
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,
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
