Gsfe curve

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Purpose

  • Generates a POSCAR file or input file for each point for a stacking fault curve
  • Executes VASP or Quantum Espresso
  • Extracts energy per stacking fault area for a static system
  • Two stacking fault types are implemented for FCC, and three for BCC
    • For FCC, users can choose either (111)[1-10] (full) or (111)[11-2] (partial).
    • For BCC, users can choose from (110)[-111] (full), (110)[001] (partial), or (110) [-110] (longpartial).

Usage

Copy the text under "Source" into a text file and save with a *.py extension. This section assumes it has been saved as gsfe_curve.py .

Edit the script, gsfe_curve.py , to reflect the DFT code you will be using.

#
### EDIT THIS PARAMETER FOR CODE IN USE
# 'qe' - Quantum Espresso
# 'vasp' - VASP
dft = 'qe' 

If using VASP, the INCAR, KPOINTS, and POTCAR files must be in the same directory. The script should be edited with the path to your vasp executable.

If using Quantum Espresso, modify the script with the correct pseudopotential directory, element name, psuedopotential file name, and atomic weight.

##### MATERIAL SETTINGS - USER EDIT REQUIRED #####

# vvv These parameters are for QE only, VASP will use the available POTCAR file vvv
# Directory containing your pseudopotentials
pp_dir = '/cavs/users/bradley/software/qe-6.0/pseudo/'
# Element name
el = 'Ta'
# Potential file name
potential = 'Ta.pbesol-spn-kjpaw_psl.0.2.UPF'
# Element weight
el_weight = 180.94788
# ^^^

The script will also have to be edited if the Quantum Espresso executable, pw.x , is not on the path. For example, if pw.x was in the /scratch/ICME_2019/, the script would be changed as follows.

# Run quantum espresso
		os.system('mpirun -np {} /scratch/ICME_2019/pw.x < gsfe.in > gsfe.out'.format(num_proc))

Change the energy cutoff (eV) and number of K-points as desired.

##### DFT PARAMETERS - USER EDIT IF DESIRED #####
# Energy cutoff value (eV) (qe only)
energy_cutoff = 290.0
# The below energy cutoff setting works for most materials.
# Check your pseudopotential file to see the suggested value for your material
energy_cutoff_rho = energy_cutoff * 4.0
# K-points specification
kpoints = 15

Modify the python script, gsfe_curve.py , to control how many points are generated.

##### STACKING FAULT PARAMETERS - USER EDIT IF NEEDED #####
# Number or location of simulated points. It MUST start with 0.
#fault_points = [0.0, 1./4., 1./2.]
fault_points = np.linspace(0,1,16)

Use the commented line to specify specific points. The displacement is normalized here - points should range from 0 to 1, and start with 0. Otherwise, use the line below it ( fault_points = np.linspace(0,1,16) ) to create evenly spaced points.

This script should be run with python 2.7.8. To run the python script on the HPC cluster at Mississippi State University, prepare a PBS script including the modules needed to run the simulation. A sample PBS script with the details needed to run a gsfe_curve calculation is posted here for convenience; this script loads the modules python/2.7.8 and openmpi-intel:

#!/bin/bash
#PBS -N Cr.gsfe.f.16pt
#PBS -l nodes=1:ppn=12
#PBS -l walltime=192:00:00
#PBS -q q48p192h
#PBS -A 193000-990015
#PBS -m ae
#PBS -r n
#PBS -V

cd $PBS_O_WORKDIR

ml python/2.7.8
ml openmpi-intel

#Run gsfe python script
/work/path_to_files/gsfefull12/gsfe_curve.py BCC 2.8497783 full

The arguments after gsfe_curve.py can be changed as per the requirements:

gsfe_curve.py fcc 3.63 partial

The first argument, fcc is the reference structure. Only fcc and bcc are currently implemented. The second, 3.63 is the ground state lattice parameter. The third, partial specifies the kind of dislocation. For more explanation on the types, run the script with no inputs, or look in the create_stackingfault function.


The script generates an output file called "GSFE_SUMMARY" containing three data columns. From left to right, these columns are the upper atom displacement normalized by the lattice parameter, the change in energy in mJ/m², and the wall time in seconds.

Source

#!/usr/bin/env python

import numpy as np
import os
import re
from time import time
from subprocess import Popen, PIPE


#
### EDIT THIS PARAMETER FOR CODE IN USE
# 'qe' - Quantum Espresso
# 'vasp' - VASP
dft = 'vasp'

# Number of processors
num_proc = 16

##### MATERIAL SETTINGS - USER EDIT REQUIRED #####

# vvv These parameters are for QE only, VASP will use the available POTCAR file vvv
# Directory containing your pseudopotentials
pp_dir = '/cavs/users/bradley/software/qe-6.0/pseudo/'
# Element name
el = 'Ta'
# Potential file name
potential = 'Ta.pbesol-spn-kjpaw_psl.0.2.UPF'
# Element weight
el_weight = 180.94788
# ^^^


##### DFT PARAMETERS - USER EDIT IF DESIRED #####
# Energy cutoff value (eV) (qe only)
energy_cutoff = 290.0
# The below energy cutoff setting works for most materials.
# Check your pseudopotential file to see the suggested value for your material
energy_cutoff_rho = energy_cutoff * 4.0
# K-points specification
kpoints = 15
# Smearing parameter (QE only)
smear = 0.06
# Relax the ions in the z direction? (vasp only right now)
relax = False


##### STACKING FAULT PARAMETERS - USER EDIT IF NEEDED #####
# Number or location of simulated points. It MUST start with 0.
#fault_points = [0.0, 1./4., 1./2.]
fault_points = np.linspace(0,1,16)
# Size of vacuum in Ang.
vacuum = 20.0
# Number of stacking layers - CAREFUL, DFT scales very poorly with more atoms
stacking_layers = 10


##### Unit conversions #####
ry_to_ev = 13.6056849587
au_to_ang = 0.52917721092

##### Below this line should not require user edits #####

# Function that creates the geometry and writes the input file
def create_stackingfault( struct, lp, layers, slip, system=None ):
	# struct : reference structure
	# lp : lattice parameter\
	# layers : number of layers of atoms to generate
	# slip : normalized displacement in slip direction
	# system : the type of stacking fault to create

	if struct.lower() == 'fcc':
		basis = np.array( [[ np.sqrt(2.)/4., np.sqrt(6.)/4., 0.0 ],
				   [ -np.sqrt(2.)/4., np.sqrt(6.)/4., 0.0 ],
				   [ 0.0, np.sqrt(6.)/6., np.sqrt(3.)/3.]] )
		base_atoms = np.array( [[ 0.0, 0.0, 0.0]] )
		if not system or system == 'partial' or system == 'shockley':
			# Assume the partial dislocation is desired (most common)
			slip_vector = np.array([0.0, np.sqrt(6.)/2., 0.0]) # Partial dislocation line
		elif system == 'full' or system == 'burgers':
			slip_vector = basis[0,:] # burgers vector direction

	elif struct.lower() == 'bcc':
		basis = np.array( [[ (np.sqrt(2.)/4. + 0.5), -(0.5 - np.sqrt(2.)/4.), 0.0 ],
				   [ -(0.5 - np.sqrt(2.)/4.), (np.sqrt(2.)/4. + 0.5), 0.0 ],
				   [ np.sqrt(2.)/4., np.sqrt(2.)/4., np.sqrt(2.)/2.]] )
		base_atoms = np.array( [[ 0.0, 0.0, 0.0]] )
		if not system or system == 'partial':
			# Assume the partial dislocation is desired (most common)
			slip_vector = np.array([np.sqrt(2.)/2.,np.sqrt(2.)/2., 0.0]) # Partial dislocation line?
		elif system == 'longpartial':
			# or?
			slip_vector = np.array([0.5,-0.5,0.0])
		elif system == 'full' or system == 'burgers':
			slip_vector = basis[0,:] # burgers vector directionn

	# Create atoms
	atoms = []
	threshold = np.cross(basis[0,0:2],basis[1,0:2])
	if threshold < 0:
		threshold = np.cross(basis[1,0:2],basis[0,0:2])
		d1 = lambda x : -basis[1,1]*x[0] + basis[1,0]*x[1]
		d2 = lambda x : -basis[0,1]*x[0] + basis[0,0]*x[1]
		b1 = basis[1,:]
		b2 = basis[0,:]
	else:
		d1 = lambda x : -basis[0,1]*x[0] + basis[0,0]*x[1]
		d2 = lambda x : -basis[1,1]*x[0] + basis[1,0]*x[1]
		b1 = basis[0,:]
		b2 = basis[1,:]

	for i in range(layers):
		if i == 0:
			old_atom = np.zeros(3)
			atoms.append(old_atom)
			continue

		new_atom = old_atom + basis[2,:]

		# Check if atom is within cell boundaries
		in_cellx, in_celly = False, False
		while not in_cellx or not in_celly:
			if d1(new_atom) < 0:
				new_atom += b2
			elif d1(new_atom) > threshold:
				new_atom -= b2
			else:
				in_cellx = True

			if d2(new_atom) > 0:
				new_atom += b1
			elif d2(new_atom) < -threshold:
				new_atom -= b1
			else:
				in_celly = True

		old_atom = new_atom.copy()

		if i >= int(layers/2):
			new_atom += slip*slip_vector

			# Check if atom is within cell boundaries
			in_cellx, in_celly = False, False
			while not in_cellx or not in_celly:
				if d1(new_atom) < 0:
					new_atom += b2
				elif d1(new_atom) > threshold:
					new_atom -= b2
				else:
					in_cellx = True

				if d2(new_atom) > 0:
					new_atom += b1
				elif d2(new_atom) < -threshold:
					new_atom -= b1
				else:
					in_celly = True

		atoms.append(new_atom)

	if dft == 'vasp':
		write_vasp_inputs(lp, basis, layers, atoms)
	elif dft == 'qe':
		write_qe_inputs(lp, basis, layers, atoms)

	# Returns the stacking fault area
	return [np.linalg.norm(np.cross(basis[0,:],basis[1,:])), np.linalg.norm(slip_vector), len(atoms)]
# end create_stackingfault

def write_qe_inputs(lp, basis, layers, atoms):

	# Write the input file
	with open('gsfe.in','w') as f:
		# Control section
		f.write(' &control' + os.linesep)
		f.write("\tprefix=''" + os.linesep)
    		f.write("\toutdir='temp'" + os.linesep)
		f.write("\tpseudo_dir = '{}',".format(pp_dir) + os.linesep)
 		f.write(' /' + os.linesep)
 		# System section
		f.write(' &system' + os.linesep)
		f.write('\tibrav= 0, nat= {}, ntyp= 1,'.format(layers) + os.linesep)
		f.write('\tcelldm(1) ={0}, '.format(lp/au_to_ang) + os.linesep)  # Convert lattice parameter to a.u.
		f.write('\tecutwfc ={},ecutrho ={}, '.format(energy_cutoff/ry_to_ev,\
		 	energy_cutoff_rho/ry_to_ev) + os.linesep)  # Convert energy to Rydberg
		f.write("\toccupations='smearing', smearing='mp', degauss={} ".format(smear)\
		 	+ os.linesep)
		f.write(' / ' + os.linesep)
		# Electrons section
		f.write(' &electrons ' + os.linesep)
		f.write("mixing_mode ='local-TF', " + os.linesep)
		f.write(' / ' + os.linesep)
		# Atomic species - pseudopotential specification
		f.write('ATOMIC_SPECIES ' + os.linesep)
		f.write(' {}  {} {} '.format(el,el_weight,potential) + os.linesep)
		# Atomic positions
		f.write('ATOMIC_POSITIONS alat ' + os.linesep)
		for a in atoms:
			f.write(' {1}\t{0[0]}\t{0[1]}\t{0[2]} '.format(a, el) + os.linesep)
		# K-points
		f.write('K_POINTS automatic ' + os.linesep)
		f.write(' {0} {0} 1 0 0 0 '.format(kpoints) + os.linesep)
		# Basis vectors
		f.write('CELL_PARAMETERS alat ' + os.linesep)
		f.write('{0[0]}\t{0[1]}\t{0[2]} '.format(basis[0,:]) + os.linesep)
		f.write('{0[0]}\t{0[1]}\t{0[2]} '.format(basis[1,:]) + os.linesep)
		f.write('0.0\t0.0\t{} '.format(basis[2,2]*10. + vacuum/lp) + os.linesep) # Adds vacuum.
# end write_qe_inputs

def write_vasp_inputs(lp, basis, layers, atoms):

	# Write the POSCAR file
	with open('POSCAR','w') as f:
		f.write(el + os.linesep)
		f.write('%f '%lp + os.linesep)
		f.write('{0[0]}\t{0[1]}\t0.0 '.format(basis[0,:]) + os.linesep)
		f.write('{0[0]}\t{0[1]}\t0.0 '.format(basis[1,:]) + os.linesep)
		f.write('0.0\t0.0\t{0} '.format(basis[2,2]*layers + 20.0/lp) + os.linesep)
		f.write('%i '%layers + os.linesep)
		f.write('Cartesian ' + os.linesep)
		for a in atoms:
			f.write('{0[0]}\t{0[1]}\t{0[2]}\tF\tF\tT '.format(a) + os.linesep)

	# Write the KPOINTS file
	with open('KPOINTS', 'w') as f:
		f.write(el + os.linesep)
		f.write('0 ' + os.linesep)
		f.write('Monkhorst-Pack ' + os.linesep)
		f.write('{0} {0} 1 '.format(kpoints) + os.linesep)
		f.write('0 0 0 ' + os.linesep)
# end write_vasp_inputs

def gsfe( struct, lp, slip_system=None ):

	# Creates the summary file
	with open('GSFE_SUMMARY','w') as f:
		pass
		#f.write("Generalized Stacking Fault Energy for {} {}\n".format(struct,el))
		#f.write("=============================================\n")

	# Initialize the lists for the energy values
	energy = []
	for d in fault_points:
		# Create the stacking fault structure
		[area, fault_length, natoms] = create_stackingfault( struct, lp, stacking_layers, d, slip_system )

		if dft == 'qe':
			E, walltime = run_qe()
			E = E*ry_to_ev
		elif dft == 'vasp':
			if len(energy) == 0:
				try:
					os.remove('IBZKPT CHG CONTCAR DOSCAR EIGENVAL OSZICAR OUTCAR'\
				+ ' PCDAT XDATCAR EIGENVAL vasprun.xml cellvol PROCAR CHGCAR WAVECAR')
				except Exception:
					pass
			start_time = time()
			E = run_vasp()
			walltime = time() - start_time

		energy.append(E)

		with open('GSFE_SUMMARY','a') as f:
			# Write the normalized displacement and the relaxed and static energies in mJ/m**2
			f.write('{}\t{}\t{} '.format(d*fault_length,
					(energy[-1] - energy[0]) * 1.60217733e-19 * 1e23 / area,
					walltime) + os.linesep)
# end gsfe

def run_qe():

		# Run quantum espresso
		os.system('mpirun -np {} pw.x < gsfe.in > gsfe.out'.format(num_proc))

		# Get energy
		p1 = Popen(['grep','! *[ ] total energy','gsfe.out'], stdout=PIPE)
		p2 = Popen(['awk','{print $5}'], stdin=p1.stdout, stdout=PIPE)

		# Get walltime
		try:
			p3 = Popen(['grep','PWSCF','gsfe.out'],stdout=PIPE)
			p4 = Popen(['tail','-n1'],stdin=p3.stdout,stdout=PIPE)

			time_str = p4.communicate()[0]
			time_arr = re.findall('(\d+)m[ ]*(\d+).(\d+)s', time_str)[-1]
			time_arr = [int(i) for i in time_arr]

			if len(time_arr) == 3:
				time = 60*time_arr[0] + time_arr[1] + 0.01*time_arr[2]
			else:
				time = time_arr[0] + 0.01*time_arr[1]
		except:
			time = 0.0

		return [float(p2.communicate()[0]), time]
# end run_qe

def run_vasp():

		# Run vasp - Static run first.
		tries = 0
		has_run = False
		while tries < 2 and not has_run:
			try:
				if relax:
					# Run vasp - first a relaxation, then a static run
					os.system('cp relax.INCAR INCAR')
					msg = os.system('mpirun -np {} ./vasp'.format(num_proc))
					os.system('cp CONTCAR POSCAR')
				os.system('rm WAVECAR CHGCAR')
				os.system('cp gsfe.INCAR INCAR')
				msg = os.system('mpirun -np {} ./vasp'.format(num_proc))
				p1 = Popen(['tail','-n1','OSZICAR'], stdout=PIPE)
				p2 = Popen(['awk','{print $5}'], stdin=p1.stdout, stdout=PIPE)
				E = float(p2.communicate()[0])
				has_run = True
			except Exception:
				print "VASP run failed, trying again after deleting output files."
				try:
					os.remove('IBZKPT CHG CONTCAR DOSCAR EIGENVAL OSZICAR OUTCAR'\
				+ ' PCDAT XDATCAR EIGENVAL vasprun.xml cellvol PROCAR CHGCAR WAVECAR')
				except Exception:
					pass
				tries += 1
		# Get energy
		p1 = Popen(['tail','-n1','OSZICAR'], stdout=PIPE)
		p2 = Popen(['awk','{print $5}'], stdin=p1.stdout, stdout=PIPE)

		return float(p2.communicate()[0])


		#if msg != 0:
		#	print("VASP exited with an error. It may only be able to run on the CAVS cluster machines.")
# end run_vasp


if __name__ == "__main__":
	import sys
	argc = len(sys.argv)

	# Get inputs from the command line
	struct = sys.argv[1] if argc > 1 else None
	latp = float(sys.argv[2]) if argc > 2 else None
	slip = sys.argv[3] if argc > 3 else None
	extent = float(sys.argv[4]) if argc > 4 else None

	# If the inputs are not specified, prompt for them.
	#if not element:
	#	print("Enter the element name:")
	#	element = raw_input("> ")
	if not struct:
		i_struct = None
		while not i_struct:
			print("== Enter the desired structure ==")
			print("= 1) FCC                        =")
			print("= 2) BCC                        =")
			print("=================================")
			i_struct = int(raw_input("> "))
			if i_struct == 1:
				struct = 'fcc'
				print("Structure type: FCC")
			elif i_struct == 2:
				struct = 'bcc'
				print("Structure type: BCC")
			else:
				print(" Only FCC and BCC systems are implemented currently ")
				i_struct = None
	if struct.lower() == 'fcc':
		slip_choices = ['(111)[1-10] (full)','(111)[11-2] (partial)']
	elif struct.lower() == 'bcc':
		slip_choices = ['(110)[-111] (full)','(110)[001] (partial)','(110)[-110] (longpartial)']
	else:
		print("Structures other than FCC and BCC are not currently supported")
		sys.exit(1)
	if not latp:
		print("Enter the equilibrium lattice parameter for your element:")
		latp = float(raw_input("> "))
	if not slip:
		i_slip = None
		while not i_slip:
			print("====== Enter the desired slip system ======")
			for i,sc in enumerate(slip_choices):
				print("= {0}) {1:<36} =".format(i+1,sc))
			print("===========================================")
			i_slip = int(raw_input("> "))
			if i_slip == 1:
				slip = 'full'
				print("Using burgers vector direction")
			elif i_slip == 2:
				slip = 'partial'
				print("Using partial dislocation direction")
			elif i_slip == 3 and struct == 'bcc':
				slip = 'longpartial'
				print("Using longer partial dislocation direction")
			else:
				print(os.linesep + "Choice not recognized" + os.linesep)
				i_slip = None
	if not extent:
		extent = 1.0

	gsfe(struct, latp, slip)
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