Python Potcar.write_file方法代码示例

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Potcar [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Potcar import write_file [as 别名]
def generate_files(args):
    from pymatgen.io.vaspio.vasp_input import Potcar
    if args.symbols:
        try:
            p = Potcar(args.symbols, functional=args.functional)
            p.write_file("POTCAR")
        except Exception as ex:
            print("An error has occurred: {}".format(str(ex)))

    else:
        print("No valid options selected.")

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Potcar [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Potcar import write_file [as 别名]
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, 
                 'NPAR': 8, 
                 'SIGMA': 0.1, 

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Potcar [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Potcar import write_file [as 别名]
def get_ModifiedMaterialsProject_VASP_inputs(structure, workdir, job_name, nproc=16, 
                                U_strategy_instance = None, supplementary_incar_dict = None):
    """
    Inputs will be inspired by MaterialsProject, but this function is appropriate
    when we are seriously modifying the inputs such that they no longer conform to Materials Project.
    """

    if os.path.exists(workdir):
        print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB'
        return -1

    os.mkdir(workdir)

    # let's start with MP
    input_set = MPVaspInputSet()
   
    incar  = input_set.get_incar(structure)

    if U_strategy_instance != None:
        #  reading the structure here insures consistency, rather
        #  than having the strategy read the structure outside this driver.
        U_strategy_instance.read_structure(structure)

        # Generate all LDAU-related variables according to specified strategy.
        LDAU_dict, poscar_need_hack, potcar_need_hack = U_strategy_instance.get_LDAU()

        incar.update(LDAU_dict) 

    # set the number of parallel processors to sqrt(nproc), 
    # as recommended in manual.
    incar.update({'NPAR':int(np.sqrt(nproc))}) 

    if supplementary_incar_dict != None:
        incar.update(supplementary_incar_dict) 

    poscar = input_set.get_poscar(structure)

    kpoints = input_set.get_kpoints(structure)
    potcar = input_set.get_potcar(structure)

    incar.write_file(workdir+'INCAR')
    poscar.write_file(workdir+'POSCAR', vasp4_compatible = True)
    kpoints.write_file(workdir+'KPOINTS')
    potcar.write_file(workdir+'POTCAR')


    if poscar_need_hack:
        # do we need specialized hacking of the poscar because of the U strategy?       
        new_poscar_lines = U_strategy_instance.get_new_poscar_lines()
        with open(workdir+'POSCAR','w') as f:
            for line in new_poscar_lines:
                print >>f, line.strip()

    if potcar_need_hack:
        # do we need specialized hacking of the potcar because of the U strategy?       
        new_potcar_symbols = U_strategy_instance.get_new_potcar_symbols(potcar)
        new_potcar = Potcar(new_potcar_symbols) 
        # overwrite the previous potcar
        new_potcar.write_file(workdir+'POTCAR')

    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