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mc.py
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Sat, Nov 16, 04:50

mc.py
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#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# mc.py
# Purpose: mimic operation of example/MC/in.mc via Python
# Syntax: mc.py in.mc
# in.mc = LAMMPS input script
import sys,random,math
# set these parameters
# make sure neigh skin (in in.mc) > 2*deltamove
nloop = 3000
deltaperturb = 0.2
deltamove = 0.1
kT = 0.05
random.seed(27848)
# parse command line
argv = sys.argv
if len(argv) != 2:
print "Syntax: mc.py in.mc"
sys.exit()
infile = sys.argv[1]
from lammps import lammps
lmp = lammps()
# run infile one line at a time
# just sets up MC problem
lines = open(infile,'r').readlines()
for line in lines: lmp.command(line)
lmp.command("variable e equal pe")
# run 0 to get energy of perfect lattice
# emin = minimum energy
lmp.command("run 0")
natoms = lmp.extract_global("natoms",0)
emin = lmp.extract_compute("thermo_pe",0,0) / natoms
lmp.command("variable emin equal $e")
# disorder the system
# estart = initial energy
x = lmp.extract_atom("x",3)
for i in xrange(natoms):
x[i][0] += deltaperturb * (2*random.random()-1)
x[i][1] += deltaperturb * (2*random.random()-1)
lmp.command("variable elast equal $e")
lmp.command("thermo_style custom step v_emin v_elast pe")
lmp.command("run 0")
x = lmp.extract_atom("x",3)
lmp.command("variable elast equal $e")
estart = lmp.extract_compute("thermo_pe",0,0) / natoms
# loop over Monte Carlo moves
# extract x after every run, in case reneighboring changed ptr in LAMMPS
elast = estart
naccept = 0
for i in xrange(nloop):
iatom = random.randrange(0,natoms)
x0 = x[iatom][0]
y0 = x[iatom][1]
x[iatom][0] += deltamove * (2*random.random()-1)
x[iatom][1] += deltamove * (2*random.random()-1)
lmp.command("run 1 pre no post no")
x = lmp.extract_atom("x",3)
e = lmp.extract_compute("thermo_pe",0,0) / natoms
if e <= elast:
elast = e
lmp.command("variable elast equal $e")
naccept += 1
elif random.random() <= math.exp(natoms*(elast-e)/kT):
elast = e
lmp.command("variable elast equal $e")
naccept += 1
else:
x[iatom][0] = x0
x[iatom][1] = y0
# final energy and stats
lmp.command("variable nbuild equal nbuild")
nbuild = lmp.extract_variable("nbuild",None,0)
lmp.command("run 0")
estop = lmp.extract_compute("thermo_pe",0,0) / natoms
print "MC stats:"
print " starting energy =",estart
print " final energy =",estop
print " minimum energy of perfect lattice =",emin
print " accepted MC moves =",naccept
print " neighbor list rebuilds =",nbuild

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