lattice_example

from pprint import pprint

import logging
logging.basicConfig(filename='lattice_example.log',level=logging.DEBUG)

The lattice object keeps track of the lattice used in Structure object

import pymatgen_core.core.lattice as lattice

lat = lattice.Lattice()

print(lat)
print(lat.unit_conf['length'])

The default size of the lattice is 100.0 angstroms

The lattice also has lattice constants

print(lat.constants)
print(lat.unit_conf['length'])

Which are returned as [a,b,c,alpha,beta,gamma]

We can calculate the distance between two points in the lattice

Let’s turn on periodic boundary conditions

lat.pbcs = [True,True,True]

pos_i = [25.0,25.0,25.0]
pos_j = [-50.0,25.0,25.0]

dr_ij = lat.d_pos(pos_i,pos_j)
print(dr_ij)

If we want a tuple of the vector and the magnitude we can use

dr_ij,mag_dr_ij =  lat.delta_pos(pos_i,pos_j)
print(dr_ij,mag_dr_ij)

We can also turn pbcs off and calculate the distance

lat.pbcs = [False,False,False]

print(lat.delta_pos(pos_i,pos_j))

The size of the lattice can be changed using the matrix or the constants setter

lat.matrix = [ 12,0,0,0,12,0,0,0,12 ]

print(lat.matrix)
print(lat.constants)
print(lat.unit_conf['length'])

To set to a triclinic lattice

lat.constants = [ 12,8,15,60.0,120.0,80.0 ]

print(lat.matrix)
print(lat.constants)
print(lat.unit_conf['length'])

Let’s turn pbcs’s back on and calculate the distance

lat.pbcs = [True,True,True]

print(pos_i,pos_j)

dr_ij,mag_dr_ij =  lat.delta_pos(pos_i,pos_j)
print(dr_ij,mag_dr_ij)

Change the units to nm

lat.update_units({'length':'nm'})

print(lat.matrix)
print(lat.constants)
print(lat.unit_conf['length'])

If you need your angles in radians

lat.update_units({'angle':'radian'})

print(lat.matrix)
print(lat.constants)
print(lat.unit_conf['length'],lat.unit_conf['angle'])

We can export the lattice object as json object and dump it into a file

lat_json = lat.export_json('lat_ex',write_file=True)

Delete the lattice object

del lat

Create a new blank object

lat = lattice.Lattice()

And read in the file to get the properties of the lattice back

lat.import_json('lat_ex',read_file=True)

Handy for saving or exporting to javascript

print(lat.matrix)
print(lat.constants)
print(lat.unit_conf['length'],lat.unit_conf['angle'])