update tools/eam_database from upstream
This commit is contained in:
Axel Kohlmeyer
@ -1,9 +1,11 @@
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EAM database tool
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Xiaowang Zhou (Sandia), xzhou at sandia.gov
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Revised version including fixes from https://www.ctcms.nist.gov/potentials/entry/2004--Zhou-X-W-Johnson-R-A-Wadley-H-N-G--Al/
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Fortran version (create.f) by Xiaowang Zhou (Sandia), xzhou at sandia.gov
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with revisions by Lucas Hale lucas.hale at nist.gov from https://www.ctcms.nist.gov/potentials/entry/2004--Zhou-X-W-Johnson-R-A-Wadley-H-N-G--Al/
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based on this paper:
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Python version (create_eam.py) by Germain Clavier germain.clavier at gmail.com
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Most parameters based on this paper:
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X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
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144113 (2004).
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@ -26,10 +28,25 @@ alloys. Thus any potential files created with this tool should be used
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with care and test calculations (e.g. on multiple binary mixtures) performed
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to gauge the error.
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Steps:
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Steps (create.f):
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1) compile create.f -> a.out (e.g. gfortran create.f)
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2) edit the input file EAM.input to list 2 or more desired elements to include
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3) a.out < EAM.input will create an *.eam.alloy potential file
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4) in DYNAMO or LAMMPS context this file is referred to as a setfl file
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that can be used with the LAMMPS pair_style eam/alloy command
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Steps (create_eam.py):
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Usage: create_eam.py [-h] [-n NAME [NAME ...]] [-nr NR] [-nrho NRHO]
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options:
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-n NAME [NAME ...], --names NAME [NAME ...]
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Element names
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-nr NR Number of point in r space [default 2000]
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-nrho NRHO Number of point in rho space [default 2000]
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1) you must have numpy installed
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2) run "python create_eam.py -n Ta Cu" with the list of desired elements
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3) this will create an *.eam.alloy potential file
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in DYNAMO or LAMMPS context the created file is referred to as a setfl file
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that can be used with the LAMMPS pair_style eam/alloy command
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@ -243,11 +243,12 @@ ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
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outfile = outfile(1:index(outfile,' ')-1)//'.eam.alloy'
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open(unit=1,file=outfile)
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call date_and_time(DATE=date)
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write(1,*) ' DATE: ',date(1:4),'-',date(5:6),'-',date(7:8),' ',
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* 'CONTRIBUTOR: Xiaowang Zhou xzhou@sandia.gov and ',
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* 'Lucas Hale lucas.hale@nist.gov ',
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* 'CITATION: X. W. Zhou, R. A. Johnson, ',
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write(1,*) 'DATE: ',date(1:4),'-',date(5:6),'-',date(7:8),
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* ' UNITS: metal CONTRIBUTOR: Xiaowang Zhou xzhou@sandia.gov and ',
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* 'Lucas Hale lucas.hale@nist.gov '
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write(1,*) 'CITATION: X. W. Zhou, R. A. Johnson, ',
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* 'H. N. G. Wadley, Phys. Rev. B, 69, 144113(2004)'
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write(1,*) 'Generated by create.f'
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write(1,8)ntypes,outelem
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8 format(i5,' ',a24)
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write(1,9)nrho,drho,nr,dr,rc
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165
tools/eam_database/create_eam.py
Normal file
165
tools/eam_database/create_eam.py
Normal file
@ -0,0 +1,165 @@
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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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from datetime import date
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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: " + date.today().strftime("%Y-%m-%d") + " UNITS: metal")
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f.write(" CONTRIBUTOR: Xiaowang Zhou xzhou@sandia.gov, Lucas Hale lucas.hale@nist.gov,")
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f.write(" and 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 by create_eam.py\n")
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f.write("{:<5d} {:<24}\n".format(len(attypes), " ".join(attypes)))
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f.write("{:<5d} {:<24.16e} {:<5d} {:<24.16e} {:<24.16e}\n".format(nrho, drho, nr, dr, rc))
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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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def create_eam(argv=None):
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parser = ap.ArgumentParser(description="Script to create EAM alloy potential files.")
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parser.add_argument("-n", "--names", dest="name", nargs="+",
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help="Element names")
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parser.add_argument("-nr", dest="nr", type=int, default=2000,
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help="Number of point in r space [default 2000]")
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parser.add_argument("-nrho", dest="nrho", type=int, default=2000,
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help="Number of point in rho space [default 2000]")
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args = parser.parse_args(argv)
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if not args.name:
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parser.print_help()
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sys.exit("")
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atnames = args.name
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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 = "Element {} not found in database.\n".format(n)
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valid = "Supported elements 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, ".eam.alloy"])
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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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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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if i == j:
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rhor[n1] = prof(n1, r)
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rhomax = max(rhomax,np.max(rhor[n1]))
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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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rhomax = max(rhomax, 2.0 * rhoemax, 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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if __name__ == "__main__":
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try:
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create_eam(sys.argv[1:])
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except KeyboardInterrupt as exc:
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raise SystemExit("User interruption.") from exc
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640
tools/eam_database/eamDatabase.py
Normal file
640
tools/eam_database/eamDatabase.py
Normal file
@ -0,0 +1,640 @@
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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
|
||||
0.308782, # cai
|
||||
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,
|
||||
14.604144,
|
||||
9.132010,
|
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4.870405,
|
||||
0.277758,
|
||||
0.419611,
|
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0.339710,
|
||||
0.750758,
|
||||
-1.729364,
|
||||
-0.255882,
|
||||
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,
|
||||
-1.150650,
|
||||
0.783924,
|
||||
-1.748423,
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47,
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107.8682,
|
||||
-1.150650,
|
||||
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,
|
||||
19.991632,
|
||||
19.991509,
|
||||
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,
|
||||
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Reference in New Issue
Block a user