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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Python version of the code Zhou04_create_v2.f
original author: X. W. Zhou, xzhou@sandia.gov
based on updates by: Lucas Hale lucas.hale@nist.gov
written by: Germain Clavier g.m.g.c.clavier@tue.nl
This script requires the numpy library.
"""
import sys
import argparse as ap
from datetime import date
import numpy as np
from eamDatabase import Database
def prof(at, r):
atom = Database[at]
f = np.zeros(r.shape)
f = atom.fe * np.exp(-atom.beta1 * (r[r >= 0.5] / atom.re - 1.0))
f = f / (1.0 + (r / atom.re - atom.ramda1) ** 20)
return f
def pair(at1, at2, r):
atom = Database[at1]
psi1 = atom.A * np.exp(-atom.alpha * (r / atom.re - 1.0))
psi1 /= 1.0 + (r / atom.re - atom.cai) ** 20
psi2 = atom.B * np.exp(-atom.beta * (r / atom.re - 1.0))
psi2 /= 1.0 + (r / atom.re - atom.ramda) ** 20
if at1 == at2:
psi = psi1 - psi2
else:
psia = psi1 - psi2
atom2 = Database[at2]
psi1 = atom2.A * np.exp(-atom2.alpha * (r / atom2.re - 1.0))
psi1 /= 1.0 + (r / atom2.re - atom2.cai) ** 20
psi2 = atom2.B * np.exp(-atom2.beta * (r / atom2.re - 1.0))
psi2 /= 1.0 + (r / atom2.re - atom2.ramda) ** 20
psib = psi1 - psi2
prof1 = prof(at1, r)
prof2 = prof(at2, r)
psi = 0.5 * (prof2 / prof1 * psia + prof1 / prof2 * psib)
return psi
def embed(at, rho):
atom = Database[at]
Fm33 = np.zeros(rho.shape)
Fm33[rho < atom.rhoe] = atom.Fm3
Fm33[rho >= atom.rhoe] = atom.Fm4
emb = np.zeros(rho.shape)
for i, r in enumerate(rho):
if r == 0:
emb[i] = 0
elif r < atom.rhoin:
dr = r / atom.rhoin - 1
emb[i] = atom.Fi0 + atom.Fi1 * dr + atom.Fi2 * dr**2 + atom.Fi3 * dr**3
elif r < atom.rhoout:
dr = r / atom.rhoe - 1
emb[i] = atom.Fm0 + atom.Fm1 * dr + atom.Fm2 * dr**2 + Fm33[i] * dr**3
else:
dr = r / atom.rhos
emb[i] = atom.Fn * (1.0 - atom.fnn * np.log(dr)) * dr**atom.fnn
return emb
def write_file(attypes, filename, Fr, rhor, z2r, nrho, drho, nr, dr, rc):
struc = "fcc"
with open(filename, "w") as f:
f.write("DATE: " + date.today().strftime("%Y-%m-%d") + " UNITS: metal")
f.write(" CONTRIBUTOR: Xiaowang Zhou xzhou@sandia.gov, Lucas Hale lucas.hale@nist.gov,")
f.write(" and Germain Clavier g.m.g.c.clavier@tue.nl/germain.clavier@gmail.com\n")
f.write(" CITATION: X. W. Zhou, R. A. Johnson, H. N. G. Wadley, Phys. Rev. B, 69, 144113(2004)\n")
f.write("Generated by create_eam.py\n")
f.write("{:<5d} {:<24}\n".format(len(attypes), " ".join(attypes)))
f.write("{:<5d} {:<24.16e} {:<5d} {:<24.16e} {:<24.16e}\n".format(nrho, drho, nr, dr, rc))
for at in attypes:
atom = Database[at]
f.write(
"{:>5d} {:>15.5f} {:>15.5f} {:>8}\n".format(
atom.ielement, atom.amass, atom.blat, struc
)
)
for i, fr in enumerate(Fr[at]):
f.write(" {:>24.16E}".format(fr))
if not (i + 1) % 5:
f.write("\n")
for i, rho in enumerate(rhor[at]):
f.write(" {:>24.16E}".format(rho))
if not (i + 1) % 5:
f.write("\n")
for n1 in range(len(attypes)):
for n2 in range(n1 + 1):
for i, z in enumerate(z2r[n1, n2]):
f.write(" {:>24.16E}".format(z))
if not (i + 1) % 5:
f.write("\n")
def create_eam(argv=None):
parser = ap.ArgumentParser(description="Script to create EAM alloy potential files.")
parser.add_argument("-n", "--names", dest="name", nargs="+",
help="Element names")
parser.add_argument("-nr", dest="nr", type=int, default=2000,
help="Number of point in r space [default 2000]")
parser.add_argument("-nrho", dest="nrho", type=int, default=2000,
help="Number of point in rho space [default 2000]")
args = parser.parse_args(argv)
if not args.name:
parser.print_help()
sys.exit("")
atnames = args.name
nr = args.nr
nrho = args.nrho
for n in atnames:
try:
Database[n]
except KeyError:
output = "Element {} not found in database.\n".format(n)
valid = "Supported elements are: {}".format(" ".join(Database.keys()))
sys.exit("".join([output, valid]))
ntypes = len(atnames)
outfilename = "".join([*atnames, ".eam.alloy"])
rhor = {}
Fr = {}
alatmax = max([Database[at].blat for at in atnames])
rhoemax = max([Database[at].rhoe for at in atnames])
rc = np.sqrt(10.0) / 2.0 * alatmax
rst = 0.5
r = np.linspace(0.0, rc, num=nr, dtype=np.double)
dr = r[1] - r[0]
r[r < rst] = rst
z2r = np.zeros([ntypes, ntypes, nr])
rhomax = -np.inf
for i, n1 in enumerate(atnames):
for j, n2 in enumerate(atnames):
if j > i:
continue
if i == j:
rhor[n1] = prof(n1, r)
rhomax = max(rhomax,np.max(rhor[n1]))
z2r[i, j, :] = r * pair(n1, n2, r)
else:
z2r[i, j, :] = r * pair(n1, n2, r)
z2r = np.where(z2r, z2r, z2r.transpose((1, 0, 2)))
rhomax = max(rhomax, 2.0 * rhoemax, 100.0)
rho = np.linspace(0.0, rhomax, num=nrho, dtype=np.double)
drho = rho[1] - rho[0]
for i, n1 in enumerate(atnames):
Fr[n1] = embed(n1, rho)
write_file(atnames, outfilename, Fr, rhor, z2r, nrho, drho, nr, dr, rc)
if __name__ == "__main__":
try:
create_eam(sys.argv[1:])
except KeyboardInterrupt as exc:
raise SystemExit("User interruption.") from exc
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