Using as a Python Module

Script Example for Interfaces

This script will create the interface POSCARs for the first termination in Si and SiC with 3 layers and no vacuum.

from p2ptrans.interfaces import read, readSurface, findMatchingInterfaces, createPoscar

Si = read.poscar("POSCAR_Si") # Create a pylada Structure object for Si
SiC = read.poscar("POSCAR_SiC") # Create a pylada Structure object for SiC

termSi = readSurface(Si, [1,1,0], {"1":{"Si"}}) # Create a list of possible terminations for Si
termSiC = readSurface(SiC, [0,0,1], {"1":{"Si"}}) # Create a list of possible termination for SiC

A, equivTermA = termSi[0]
B, equivTermB = termSiC[0]

ttrans, dispStruc, vec_classes, dmin = findMatchingInterfaces(A, B, 130, 1000) # Run the minimization algorithm with 130 cells and 1000*10 random initializations

createPoscar(A, B, equivTermA[0], equivTermB[0], ttrans[0,:,:], dispStruc[0], layers=3, vacuum=0) # Creates the interface POSCAR for the first variant of termination of A and B

Script Example for Transformations

This script was used to create a transforming martensite plate sandwiched between two austenite slabs for figure 3 of Therrien and Vladan Stevanović. “Minimization of atomic displacements as a guiding principle of the martensitic phase transformation”, Physical Review Letters 125, 125502, (2020).

import p2ptrans as p2p
import numpy as np
from pylada.crystal import write, read, supercell, Structure
import numpy.linalg as la
from copy import deepcopy

layBCC = 6 # Number of BCC (martensite) layers in the final state
layFCC = 4 # Number of FCC (austenite) layers in the final state
dirname = "outdir"
tol = 1e-3

# Read the position files (POSCAR) using the read pylada function
A = read.poscar("POSCAR_FCC")
B = read.poscar("POSCAR_BCC")

# Find best matching between A and B (from A to B)
# Use minimize=False to avoid reoptimizing if there is already a result in "opt_dir"
tmat, dispStruc, vec_classes, dmin = p2p.findMatching(A,B, 600, outdir="opt_dir", minimize=False)

# Find the habit plane (planeHab) using the crystallography function
# tmat transforms B into A, so we use la.inv(tmat) to get strain directions in coordinates of A
eigval, U, P, Q, planeHab = p2p.analysis.crystallography(la.inv(tmat), B, A)

# Find the closest hkl in the basis of the convential cell (cubic)
planeHab = p2p.utils.find_uvw(planeHab[:,0:1], np.eye(3)).reshape(3)

# Using a function from the interfaces submodule find a unit cell of the transformation structure (dispStruc)
# where the cell vectors a and b are in the habit plane
cell2D, cell3D = p2p.interfaces.find_basis(planeHab, dispStruc.cell)

# Replace the atoms in the structure
dispStruc = supercell(dispStruc, cell3D)

# Produce the transition structures with 15 steps
result = p2p.produceTransition(15, tmat, dispStruc, vec_classes, dirname, False, habit=0)
transStruc, spgList, Tpos, color_array, atom_types = result


# The FCC (austenite) structure is the initial state [0]
FCC = transStruc[0]

# Create a supercell with the specified number of layers
FCC = supercell(FCC, FCC.cell.dot(np.array([[1,0,0],[0,1,0],[0,0,layFCC//2]])))


for i, S in enumerate(transStruc):
    # Create a supercell with the specified number of layer for the transforming part of the cell
    S = supercell(S, S.cell.dot(np.array([[1,0,0],[0,1,0],[0,0,layBCC]])))

    # Create cell with inplane dimensions of FCC and z vector of S
    cell = deepcopy(FCC.cell)
    cell[:,2] = S.cell[:,2]

    # Create a structure to contain all the layers
    slab = Structure(FCC.cell)
    slab.cell[:,2] = cell[:,2] + FCC.cell[:,2]*2

    print("Slab thickness is at step %d is:"%i, np.cross(cell[:,0],cell[:,1]).dot(cell[:,2])/la.norm(np.cross(cell[:,0],cell[:,1])))

    # Add the FCC atoms on both sides
    for a in FCC:
        slab.add_atom(*a.pos, a.type)
        slab.add_atom(*(a.pos + cell[:,2] + FCC.cell[:,2]), a.type)

    # Add the S atoms in the middle
    for a in S:
        if 1 - la.inv(S.cell).dot(a.pos)[2] < tol:
            a.pos = a.pos - S.cell[:,2]
        slab.add_atom(*(cell.dot(la.inv(S.cell).dot(a.pos)) + FCC.cell[:,2]), a.type)

    slab = supercell(slab, slab.cell) # Make sure all atoms are inside the cell

    write.poscar(slab, vasp5=True, file= dirname + "/POSCAR_%03d"%i) # Write resulting structure in POSCAR