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