Generate VASP Inputs for Structure Relaxation



In [1]:

    
from pymatgen import Structure
from pymatgen.io.vasp.sets import MPRelaxSet

s = Structure.from_file("ICSD_182730_Si.cif", primitive=True)
custom_settings = {"NELMIN": 5} # user custom incar settings
relax = MPRelaxSet(s, user_incar_settings=custom_settings)
relax.write_input("Si-relax")

Get total energy and relaxed structure



In [2]:

    
from pymatgen.io.vasp import Vasprun

v = Vasprun("Si-relax/vasprun.xml")
print(v.final_energy) # final total energy
s = v.final_structure
s.to(filename="Si-relax.cif") # save relaxed structure into cif file
print(s) # relaxed structure









    



-10.8485761 eV
Full Formula (Si2)
Reduced Formula: Si
abc   :   3.876799   3.876799   3.876799
angles:  60.000000  60.000000  60.000000
Sites (2)
  #  SP        a      b      c
---  ----  -----  -----  -----
  0  Si     0.75   0.75   0.75
  1  Si    -0     -0     -0

Generate VASP Input for Static Run



In [3]:

    
from pymatgen.io.vasp.sets import MPStaticSet

custom_settings = {"NELM": 60} # user custom incar settings
static = MPStaticSet.from_prev_calc("Si-relax/", standardize=True,
                                    user_incar_settings=custom_settings)
static.write_input("Si-static")

Get total energy from static run



In [4]:

    
from pymatgen.io.vasp import Vasprun

v = Vasprun("Si-static/vasprun.xml")
print(v.final_energy) # final total energy









    



-10.85000555 eV

Generate VASP Input for Density of State(DOS) and Band Structure(BS) calculation



In [5]:

    
from pymatgen.io.vasp.sets import MPNonSCFSet

# generate uniform k-points for DOS calc.
custom_settings = {"LAECHG": "False", "LVHAR": "False"} # user custom incar settings
dos = MPNonSCFSet.from_prev_calc("Si-static/", mode="uniform",reciprocal_density=200,
                                 user_incar_settings=custom_settings)
dos.write_input("Si-dos")

# generate k-points along high symmetry line for band structure calc.
band = MPNonSCFSet.from_prev_calc("Si-static/", mode="line", standardize=True,
                                 user_incar_settings=custom_settings)
band.write_input("Si-band")

Plot Total DOS



In [6]:

    
%matplotlib inline
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter

v = Vasprun('Si-dos/vasprun.xml')
tdos = v.tdos
plotter = DosPlotter()
plotter.add_dos("Total DOS", tdos)
plotter.show(xlim=[-5, 5], ylim=[0, 4])

Plot element-projected DOS



In [7]:

    
%matplotlib inline
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter

v = Vasprun('Si-dos/vasprun.xml')
cdos = v.complete_dos
element_dos = cdos.get_element_dos()
plotter = DosPlotter()
plotter.add_dos_dict(element_dos)
plotter.show(xlim=[-5, 5], ylim=[0, 1])

Plot orbital-projected DOS



In [2]:

    
%matplotlib inline
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter

v = Vasprun('Si-dos/vasprun.xml')
cdos = v.complete_dos
spd_dos = cdos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(spd_dos)
plotter.show(xlim=[-5, 5], ylim=[0, 1])

Plot BS



In [3]:

    
%matplotlib inline
from pymatgen.io.vasp import Vasprun, BSVasprun
from pymatgen.electronic_structure.plotter import BSPlotter

v = BSVasprun("Si-band/vasprun.xml")
bs = v.get_band_structure(kpoints_filename="Si-band/KPOINTS",line_mode=True)
plt = BSPlotter(bs)
plt.get_plot(vbm_cbm_marker=True)









    Out[3]:





<module 'matplotlib.pyplot' from '/Users/wzb/.pyenv/versions/3.5.2/Python.framework/Versions/3.5/lib/python3.5/site-packages/matplotlib/pyplot.py'>



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