Added Python version of Zhou04_create_v2.f: create_eam.py and eamDatabase.py in tools/eam_database
This commit is contained in:
Germain Clavier
173
tools/eam_database/create_eam.py
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173
tools/eam_database/create_eam.py
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@ -0,0 +1,173 @@
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Python version of the code Zhou04_create_v2.f
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original author: X. W. Zhou, xzhou@sandia.gov
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based on updates by: Lucas Hale lucas.hale@nist.gov
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written by: Germain Clavier g.m.g.c.clavier@tue.nl
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This script requires the numpy library.
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"""
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import sys
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import argparse as ap
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import numpy as np
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from eamDatabase import Database
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def prof(at, r):
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atom = Database[at]
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f = np.zeros(r.shape)
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f = atom.fe * np.exp(-atom.beta1 * (r[r >= 0.5] / atom.re - 1.0))
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f = f / (1.0 + (r / atom.re - atom.ramda1) ** 20)
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return f
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def pair(at1, at2, r):
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atom = Database[at1]
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psi1 = atom.A * np.exp(-atom.alpha * (r / atom.re - 1.0))
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psi1 /= 1.0 + (r / atom.re - atom.cai) ** 20
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psi2 = atom.B * np.exp(-atom.beta * (r / atom.re - 1.0))
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psi2 /= 1.0 + (r / atom.re - atom.ramda) ** 20
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if at1 == at2:
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psi = psi1 - psi2
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else:
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psia = psi1 - psi2
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atom2 = Database[at2]
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psi1 = atom2.A * np.exp(-atom2.alpha * (r / atom2.re - 1.0))
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psi1 /= 1.0 + (r / atom2.re - atom2.cai) ** 20
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psi2 = atom2.B * np.exp(-atom2.beta * (r / atom2.re - 1.0))
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psi2 /= 1.0 + (r / atom2.re - atom2.ramda) ** 20
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psib = psi1 - psi2
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prof1 = prof(at1, r)
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prof2 = prof(at2, r)
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psi = 0.5 * (prof2 / prof1 * psia + prof1 / prof2 * psib)
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return psi
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def embed(at, rho):
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atom = Database[at]
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Fm33 = np.zeros(rho.shape)
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Fm33[rho < atom.rhoe] = atom.Fm3
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Fm33[rho >= atom.rhoe] = atom.Fm4
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emb = np.zeros(rho.shape)
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for i, r in enumerate(rho):
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if r == 0:
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emb[i] = 0
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elif r < atom.rhoin:
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dr = r / atom.rhoin - 1
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emb[i] = atom.Fi0 + atom.Fi1 * dr + atom.Fi2 * dr**2 + atom.Fi3 * dr**3
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elif r < atom.rhoout:
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dr = r / atom.rhoe - 1
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emb[i] = atom.Fm0 + atom.Fm1 * dr + atom.Fm2 * dr**2 + Fm33[i] * dr**3
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else:
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dr = r / atom.rhos
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emb[i] = atom.Fn * (1.0 - atom.fnn * np.log(dr)) * dr**atom.fnn
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return emb
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def write_file(attypes, filename, Fr, rhor, z2r, nrho, drho, nr, dr, rc):
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struc = "fcc"
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with open(filename, "w") as f:
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f.write("DATE: 2022-02-11")
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f.write(" CONTRIBUTORS: Xiaowang Zhou xzhou@sandia.gov and")
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f.write(" Lucas Hale lucas.hale@nist.gov")
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f.write(" Germain Clavier g.m.g.c.clavier@tue.nl/germain.clavier@gmail.com\n")
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f.write(" CITATION: X. W. Zhou, R. A. Johnson, H. N. G. Wadley, Phys. Rev. B, 69, 144113(2004)\n")
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f.write("Generated from create_eam.py, Python version of Zhou04_create_v2.f\n")
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f.write("{:<5d} {:<24}\n".format(len(attypes), " ".join(attypes)))
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f.write(
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"{:<5d} {:<24.16e} {:<5d} {:<24.16e} {:<24.16e}\n".format(
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nrho, drho, nr, dr, rc
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)
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)
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for at in attypes:
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atom = Database[at]
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f.write(
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"{:>5d} {:>15.5f} {:>15.5f} {:>8}\n".format(
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atom.ielement, atom.amass, atom.blat, struc
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)
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)
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for i, fr in enumerate(Fr[at]):
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f.write(" {:>24.16E}".format(fr))
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if not (i + 1) % 5:
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f.write("\n")
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for i, rho in enumerate(rhor[at]):
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f.write(" {:>24.16E}".format(rho))
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if not (i + 1) % 5:
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f.write("\n")
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for n1 in range(len(attypes)):
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for n2 in range(n1 + 1):
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for i, z in enumerate(z2r[n1, n2]):
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f.write(" {:>24.16E}".format(z))
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if not (i + 1) % 5:
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f.write("\n")
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return
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def main():
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parser = ap.ArgumentParser(description="Script to make EAM alloy file inputs.")
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parser.add_argument("-n", "--names", dest="names", nargs="+", help="Atom names.")
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parser.add_argument("-nr", dest="nr", type=int, default=2000, help="Number of point in r space [default 2000].")
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parser.add_argument("-nrho", dest="nrho", type=int, default=2000, help="Number of point in rho space [default 2000].")
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args = parser.parse_args()
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atnames = args.names
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nr = args.nr
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nrho = args.nrho
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for n in atnames:
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try:
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Database[n]
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except KeyError:
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output = "Atom {} not found.\n".format(n)
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valid = "Valid inputs are: {}".format(" ".join(Database.keys()))
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sys.exit("".join([output, valid]))
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ntypes = len(atnames)
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outfilename = "".join([*atnames, ".set"])
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rhor = {}
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Fr = {}
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alatmax = max([Database[at].blat for at in atnames])
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rhoemax = max([Database[at].rhoe for at in atnames])
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rc = np.sqrt(10.0) / 2.0 * alatmax
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rst = 0.5
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r = np.linspace(0.0, rc, num=nr, dtype=np.double)
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dr = r[1] - r[0]
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r[r < rst] = rst
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z2r = np.zeros([ntypes, ntypes, nr])
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fmax = -np.inf
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rhomax = -np.inf
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for i, n1 in enumerate(atnames):
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for j, n2 in enumerate(atnames):
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if j > i:
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continue
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elif i == j:
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rhor[n1] = prof(n1, r)
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rhomax = np.max(rhor[n1]) if rhomax < np.max(rhor[n1]) else rhomax
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z2r[i, j, :] = r * pair(n1, n2, r)
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else:
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z2r[i, j, :] = r * pair(n1, n2, r)
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z2r = np.where(z2r, z2r, z2r.transpose((1, 0, 2)))
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if rhomax < 2.0 * rhoemax:
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rhomax = 2.0 * rhoemax
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if rhomax < 100.0:
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rhomax = 100.0
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rho = np.linspace(0.0, rhomax, num=nrho, dtype=np.double)
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drho = rho[1] - rho[0]
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for i, n1 in enumerate(atnames):
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Fr[n1] = embed(n1, rho)
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write_file(atnames, outfilename, Fr, rhor, z2r, nrho, drho, nr, dr, rc)
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return
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if __name__ == "__main__":
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try:
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main()
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except KeyboardInterrupt:
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raise SystemExit("User interruption.")
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610
tools/eam_database/eamDatabase.py
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610
tools/eam_database/eamDatabase.py
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@ -0,0 +1,610 @@
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Python version of the code Zhou04_create_v2.f
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original author: X. W. Zhou, xzhou@sandia.gov
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based on updates by: Lucas Hale lucas.hale@nist.gov
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written by: Germain Clavier g.m.g.c.clavier@tue.nl
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This file contains atom attributes for the EAM model and alloy combination. The
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original file is EAM_code. It is designed to be used with create_eam.py script.
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To add new contribution, just add new AtType instances.
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"""
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import math
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class AtType:
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def __init__(
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self,
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name,
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re,
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fe,
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rhoe,
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rhos,
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alpha,
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beta,
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A,
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B,
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cai,
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ramda,
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Fi0,
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Fi1,
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Fi2,
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Fi3,
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Fm0,
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Fm1,
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Fm2,
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Fm3,
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fnn,
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Fn,
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ielement,
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amass,
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Fm4,
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beta1,
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ramda1,
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rhol,
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rhoh,
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):
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self.name = name
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self.re = re
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self.fe = fe
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self.rhoe = rhoe
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self.rhos = rhos
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self.alpha = alpha
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self.beta = beta
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self.A = A
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self.B = B
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self.cai = cai
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self.ramda = ramda
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self.Fi0 = Fi0
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self.Fi1 = Fi1
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self.Fi2 = Fi2
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self.Fi3 = Fi3
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self.Fm0 = Fm0
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self.Fm1 = Fm1
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self.Fm2 = Fm2
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self.Fm3 = Fm3
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self.fnn = fnn
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self.Fn = Fn
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self.ielement = ielement
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self.amass = amass
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self.Fm4 = Fm4
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self.beta1 = beta1
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self.ramda1 = ramda1
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self.rhol = rhol
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self.rhoh = rhoh
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self.blat = math.sqrt(2.0) * self.re
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self.rhoin = self.rhol * self.rhoe
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self.rhoout = self.rhoh * self.rhoe
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def __repr__(self):
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output = """{}:
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re = {}; fe = {}
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rhoe = {}; rhos = {};
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alpha = {}; beta = {};
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A = {}; B = {}
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cai = {}; ramda = {}
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Fi0 = {}; Fi1 = {}; Fi2 = {}; Fi3 = {}
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Fm0 = {}; Fm1 = {}; Fm2 = {}; Fm3 = {}; Fm4 = {}
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fnn = {}; Fn = {}
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ielement = {}; amass = {}
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beta1 = {}; ramda1 = {}
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rhol = {}; rhoh = {}
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blat = {}; rhoin = {}; rhoout = {}"""
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return output.format(
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self.name,
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self.re,
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self.fe,
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self.rhoe,
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self.rhos,
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self.alpha,
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self.beta,
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self.A,
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self.B,
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self.cai,
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self.ramda,
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self.Fi0,
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self.Fi1,
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self.Fi2,
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self.Fi3,
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self.Fm0,
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self.Fm1,
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self.Fm2,
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self.Fm3,
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self.Fm4,
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self.fnn,
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self.Fn,
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self.ielement,
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self.amass,
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self.beta1,
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self.ramda1,
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self.rhol,
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self.rhoh,
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self.blat,
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self.rhoin,
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self.rhoout,
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)
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Database = {}
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Database["Cu"] = AtType(
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"Cu", # Name
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2.556162, # re
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1.554485, # fe
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21.175871, # rhoe
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21.175395, # rhos
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8.127620, # alpha
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4.334731, # beta
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0.396620, # A
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0.548085, # B
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0.308782, # cai
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0.756515, # ramda
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-2.170269, # Fi0
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-0.263788, # Fi1
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1.088878, # Fi2
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-0.817603, # Fi3
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-2.19, # Fm0
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0.00, # Fm1
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0.561830, # Fm2
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-2.100595, # Fm3
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0.310490, # fnn
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-2.186568, # Fn
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29, # ielement
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63.546, # amass
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-2.100595, # Fm4
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4.334731, # beta1
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0.756515, # ramda1
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0.85, # rhol
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1.15, # rhoh
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)
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Database["Ag"] = AtType(
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"Ag",
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2.891814,
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1.106232,
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14.604100,
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14.604144,
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9.132010,
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4.870405,
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0.277758,
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0.419611,
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0.339710,
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0.750758,
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-1.729364,
|
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-0.255882,
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0.912050,
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-0.561432,
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-1.75,
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0.00,
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0.744561,
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-1.150650,
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0.783924,
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-1.748423,
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47,
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107.8682,
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-1.150650,
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4.870405,
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0.750758,
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0.85,
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1.15,
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)
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Database["Au"] = AtType(
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"Au",
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2.885034,
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1.529021,
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19.991632,
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19.991509,
|
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9.516052,
|
||||
5.075228,
|
||||
0.229762,
|
||||
0.356666,
|
||||
0.356570,
|
||||
0.748798,
|
||||
-2.937772,
|
||||
-0.500288,
|
||||
1.601954,
|
||||
-0.835530,
|
||||
-2.98,
|
||||
0.00,
|
||||
1.706587,
|
||||
-1.134778,
|
||||
1.021095,
|
||||
-2.978815,
|
||||
79,
|
||||
196.96654,
|
||||
-1.134778,
|
||||
5.075228,
|
||||
0.748798,
|
||||
0.85,
|
||||
1.15,
|
||||
)
|
||||
Database["Ni"] = AtType(
|
||||
"Ni",
|
||||
2.488746,
|
||||
2.007018,
|
||||
27.562015,
|
||||
27.562031,
|
||||
8.383453,
|
||||
4.471175,
|
||||
0.429046,
|
||||
0.633531,
|
||||
0.443599,
|
||||
0.820658,
|
||||
-2.693513,
|
||||
-0.076445,
|
||||
0.241442,
|
||||
-2.375626,
|
||||
-2.70,
|
||||
0.00,
|
||||
0.265390,
|
||||
-0.152856,
|
||||
0.445470,
|
||||
-2.7,
|
||||
28,
|
||||
58.6934,
|
||||
-0.152856,
|
||||
4.471175,
|
||||
0.820658,
|
||||
0.85,
|
||||
1.15,
|
||||
)
|
||||
Database["Pd"] = AtType(
|
||||
"Pd",
|
||||
2.750897,
|
||||
1.595417,
|
||||
21.335246,
|
||||
21.940073,
|
||||
8.697397,
|
||||
4.638612,
|
||||
0.406763,
|
||||
0.598880,
|
||||
0.397263,
|
||||
0.754799,
|
||||
-2.321006,
|
||||
-0.473983,
|
||||
1.615343,
|
||||
-0.231681,
|
||||
-2.36,
|
||||
0.00,
|
||||
1.481742,
|
||||
-1.675615,
|
||||
1.130000,
|
||||
-2.352753,
|
||||
46,
|
||||
106.42,
|
||||
-1.675615,
|
||||
4.638612,
|
||||
0.754799,
|
||||
0.85,
|
||||
1.15,
|
||||
)
|
||||
Database["Pt"] = AtType(
|
||||
"Pt",
|
||||
2.771916,
|
||||
2.336509,
|
||||
33.367564,
|
||||
35.205357,
|
||||
7.105782,
|
||||
3.789750,
|
||||
0.556398,
|
||||
0.696037,
|
||||
0.385255,
|
||||
0.770510,
|
||||
-1.455568,
|
||||
-2.149952,
|
||||
0.528491,
|
||||
1.222875,
|
||||
-4.17,
|
||||
0.00,
|
||||
3.010561,
|
||||
-2.420128,
|
||||
1.450000,
|
||||
-4.145597,
|
||||
78,
|
||||
195.08,
|
||||
-2.420128,
|
||||
3.789750,
|
||||
0.770510,
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Database["Ta"] = AtType(
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Database["Mg"] = AtType(
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Database["Co"] = AtType(
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Database["Ti"] = AtType(
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Database["Zr"] = AtType(
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Reference in New Issue
Block a user