This directory contains Python code which wraps LAMMPS as a library

and allows the library interface to be invoked from a Python, either

from a script or interactively.

Details on how to build and use this Python interface are given in

doc/Section_python.html.

Basically you have to extend the Python on your box to include the

LAMMPS wrappers:

python setup_serial.py build           # for serial LAMMPS and Python

sudo python setup_serial.py install

python setup.py build                  # for parallel LAMMPS and Python

sudo python setuppy install

but there are several issues to be aware of, as discussed in the doc

pages.

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Once you have successfully built and tested the wrappers, you can run

the Python scripts in the examples sub-directory:

trivial.py      read/run a LAMMPS input script thru Python

demo.py		invoke various LAMMPS library interface routines

simple.py	mimic operation of couple/simple/simple.cpp in Python

gui.py		GUI go/stop/temperature-slider to control LAMMPS

plot.py		real-time temeperature plot with GnuPlot via Pizza.py

viz.py		real-time viz from GL tool in Pizza.py

vizplotgui.py   combination of viz.py and plot.py and gui.py

Run them with the following input scripts and arguments:

trivial.py in.trivial

demo.py

simple.py in.simple

gui.py in.gui 100

plot.py in.plot 10 1000 thermo_temp

viz.py in.viz 100 5000

vizplotgui.py in.viz 100 thermo_temp

You can un-comment the Pypar calls if you want to run these in

parallel.

Each script has more documentation at the top of the file that

explains how to use it.

#!/usr/local/bin/python -i

# preceeding line should have path for Python on your machine

# demo.py

# Purpose: illustrate use of many library interface commands

# Syntax:  demo.py

#          uses in.demo as LAMMPS input script

import sys

# parse command line

argv = sys.argv

if len(argv) != 1:

  print "Syntax: demo.py"

  sys.exit()

me = 0

# uncomment if running in parallel via Pypar

#import pypar

#me = pypar.rank()

#nprocs = pypar.size()

from lammps import lammps

from lammps import LMPINT as INT

from lammps import LMPDOUBLE as DOUBLE

from lammps import LMPIPTR as IPTR

from lammps import LMPDPTR as DPTR

from lammps import LMPDPTRPTR as DPTRPTR

lmp = lammps()

# test out various library functions after running in.demo

lmp.file("in.demo")

if me == 0: print "\nPython output:"

natoms = lmp.extract_global("natoms",DOUBLE)

mass = lmp.extract_atom("mass",DPTR)

x = lmp.extract_atom("x",DPTRPTR)

print "Natoms, mass, x[0][0] coord =",natoms,mass[1],x[0][0]

temp = lmp.extract_compute("thermo_temp",0,0)

print "Temperature from compute =",temp

eng = lmp.extract_variable("eng",None,0)

print "Energy from equal-style variable =",eng

vy = lmp.extract_variable("vy","all",1)

print "Velocity component from atom-style variable =",vy[1]

natoms = lmp.get_natoms()

print "Natoms from get_natoms =",natoms

xc = lmp.get_coords()

print "Global coords from get_coords =",xc[0],xc[1],xc[31]

xc[0] = xc[0] + 1.0

lmp.put_coords(xc)

print "Changed x[0][0] via put_coords =",x[0][0]

# uncomment if running in parallel via Pypar

#print "Proc %d out of %d procs has" % (me,nprocs), lmp

#pypar.finalize()

#!/usr/local/bin/python -i

# preceeding line should have path for Python on your machine

# gui.py

# Purpose: control a continuously running LAMMPS simulation via a Tkinter GUI

# Syntax:  gui.py in.lammps Nfreq

#          in.lammps = LAMMPS input script

#          Nfreq = query GUI every this many steps

import sys,time

# methods called by GUI

def go():

  global runflag

  runflag = 1

def stop():

  global runflag

  runflag = 0

def settemp(value):

  global temptarget

  temptarget = slider.get()

def quit():

  global breakflag

  breakflag = 1

# parse command line

argv = sys.argv

if len(argv) != 3:

  print "Syntax: gui.py in.lammps Nfreq"

  sys.exit()

infile = sys.argv[1]

nfreq = int(sys.argv[2])

me = 0

# uncomment if running in parallel via Pypar

#import pypar

#me = pypar.rank()

#nprocs = pypar.size()

from lammps import lammps

lmp = lammps()

# run infile all at once

# assumed to have no run command in it

lmp.file(infile)

lmp.command("thermo %d" % nfreq)

# display GUI with go/stop/quit buttons and slider for temperature

# just proc 0 handles GUI

breakflag = 0

runflag = 0

temptarget = 1.0

if me == 0:

  from Tkinter import *

  tkroot = Tk()

  tkroot.withdraw()

  root = Toplevel(tkroot)

  root.title("LAMMPS GUI")

  frame = Frame(root)

  Button(frame,text="Go",command=go).pack(side=LEFT)

  Button(frame,text="Stop",command=stop).pack(side=LEFT)

  slider = Scale(frame,from_=0.0,to=5.0,resolution=0.1,

                 orient=HORIZONTAL,label="Temperature")

  slider.bind('<ButtonRelease-1>',settemp)

  slider.set(temptarget)

  slider.pack(side=LEFT)

  Button(frame,text="Quit",command=quit).pack(side=RIGHT)

  frame.pack()

  tkroot.update()

# endless loop, checking status of GUI settings every Nfreq steps

# run with pre yes/no and post yes/no depending on go/stop status

# re-invoke fix langevin with new seed when temperature slider changes

# after re-invoke of fix langevin, run with pre yes

running = 0

temp = temptarget

seed = 12345

lmp.command("fix 2 all langevin %g %g 0.1 %d" % (temp,temp,seed))

while 1:

  if me == 0: tkroot.update()

  if temp != temptarget:

    temp = temptarget

    seed += me+1

    lmp.command("fix 2 all langevin %g %g 0.1 %d" % (temp,temp,seed))

    running = 0

  if runflag and running:

    lmp.command("run %d pre no post no" % nfreq)

  elif runflag and not running:

    lmp.command("run %d pre yes post no" % nfreq)

  elif not runflag and running:

    lmp.command("run %d pre no post yes" % nfreq)

  if breakflag: break

  if runflag: running = 1

  else: running = 0

  time.sleep(0.01)

# uncomment if running in parallel via Pypar

#print "Proc %d out of %d procs has" % (me,nprocs), lmp

#pypar.finalize()

# 3d Lennard-Jones melt

units		lj

atom_style	atomic

atom_modify	map hash

lattice		fcc 0.8442

region		box block 0 10 0 10 0 10

create_box	1 box

create_atoms	1 box

mass		1 1.0

velocity	all create 1.44 87287 loop geom

pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5

neighbor	0.3 bin

neigh_modify	delay 0 every 20 check no

fix		1 all nve

variable	eng equal pe

variable	vy atom vy

run		100

# 3d Lennard-Jones melt

units		lj

dimension	2

atom_style	atomic

lattice		sq2 0.8442

region		box block 0 30 0 15 -0.5 0.5

create_box	1 box

create_atoms	1 box

mass		1 1.0

velocity	all create 1.44 87287 loop geom

pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5

neighbor	0.3 bin

neigh_modify	delay 0 every 1 check yes

timestep	0.003

fix		1 all nve

fix		3 all enforce2d