This tutorial aims to provide a hands-on tutorial of building crystal structures and cutting surfaces with Pymatgen.

Pymatgen (Python Materials Genomics) is an open-source Python library for materials analysis.

Pre Set-up

Getting Pymatgen

(method 1)

conda install --channel conda-forge pymatgen

(method 2)

pip install pymatgen

Import Structure

From Material Project

from mp_api.client import MPRester

Please check you API code here: https://materialsproject.org/api

Read from local file

from pymatgen.core.structure import Structure

# import structure from local cif file

primitive = Structure.from_file("./primitive.cif")

from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

SGA = SpacegroupAnalyzer(primitive)

conventional = SGA.get_conventional_standard_structure()

Building within Pymatgen

statements

from pymatgen import *

create primitive cell from space group

from pymatgen.core import Structure, Lattice

from pymatgen.core.surface import SlabGenerator, Slab

latt_length = number_1 #lattice length, here a=b=c, in A

latt_angle = number_2 #lattice angle, here alpha=beta=gamma, in degree

latt = Lattice.from_parameters(a=latt_length,b=latt_length,c=latt_length,alpha=latt_angle,beta=latt_angle,gamma=latt_angle)

print(latt)

fractional coordinates

coord = [[x1,y1,z1],

[x2,y2,z2],

[x3,y3,z3],

[x4,y4,z4],

[x5,y5,z5],

[x6,y6,z6]]

cell_name = Structure.from_spacegroup("P1", latt, ["ATOM1","ATOM2","ATOM3","ATOM4","ATOM5","ATOM6"], coord,coords_are_cartesian=False)

print(cell_name)

Visulising Structure

Generate slab from bulk system

Build slab model

Generate slab using slab generator

slabgen = SlabGenerator(conventional,

miller_index=(0,0,1),

min_slab_size=10,

min_vacuum_size=10,

center_slab=False)

Search for all possible terminations

slabs = slabgen.get_slabs()

print("The number of distinct terminations is: {}".format(len(slabs)))

save these slabs in .cif files

for n,slab in enumerate(slabs):

print(n, "writing slab{}.cif".format(n))

slab.to(fmt="cif", filename="slab{}.cif".format(n))

print("Slabs terminated at shift = {}".format(slab.shift))

Search for possible adsorption sites

statements

from pymatgen.analysis.adsorption import AdsorbateSiteFinder, plot_slab

from matplotlib import pyplot as plt

fig = plt.figure()

ax = fig.add_subplot(111)

find adsorbate sites of slab 0 generated in Step 1 will write a for loop to include all slabs

ASF = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0,

put_inside=True,

symm_reduce=0.01,

near_reduce=0.01,

positions=('ontop','hollow','bridge'),

no_obtuse_hollow=True)

Plot slab with adsorption sites

plot_slab(slabs[0],ax,adsorption_sites=True)

save as png

fig.savefig("./slab0.png", dpi=200)

print a list of sites coordinate

sites_dict = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0,

put_inside=True,

symm_reduce=0.01,

near_reduce=0.01,

positions=('ontop','hollow','bridge'),

no_obtuse_hollow=True)

print(sites_dict)

Export Data

statements

from pymatgen.io.cif import CifWriter

from pymatgen.io.xyz import XYZ

Write cif files

wcif = CifWriter(structure)

wcif.write_file("test.cif")

Write xyz files

wxyz = XYZ()

wxyz.write_file("test.xyz")