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