git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12098 f3b2605a-c512-4ea7-a41b-209d697bcdaa

python/examples/in.mc

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+# problem setup for Monte Carlo relaxation of perturbed 2d hex lattice
+# same as example/MC/in.mc
+
+units		lj
+atom_style	atomic
+atom_modify     map array sort 0 0.0
+
+dimension       2
+
+lattice		hex 1.0
+region		box block 0 10 0 5 -0.5 0.5
+
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+pair_modify     shift yes
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes

python/examples/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