more updates to the new MESSAGE package

Section_howto.html#howto10 for more details on how client/server

coupling works in LAMMPS.

In this dir, the vasp_warp.py is a wrapper on the VASP quantum DFT

In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT

code so it can work as a "server" code which LAMMPS drives as a

"client" code to perform ab initio MD.  LAMMPS performs the MD

timestepping, sends VASP a current set of coordinates each timestep,

----------------

Prepare to use VASP and the vasp_wrapper.py script

You can run the vasp_wrap.py script as-is to test that the

coupling between it and LAMMPS is functional.  But the as-is

version will not attempt to run VASP.

To do this, you must edit the 1st vaspcmd line at the top of

vasp_wrapper.py to be the launch command needed to run VASP on your

system.  It can be a command to run VASP in serial or in parallel,

e.g. an mpirun command.  Then comment out the 2nd vaspcmd line

immediately following it.

Insure you have the necessary VASP input files in this

directory, suitable for the VASP calculation you want to perform:

INCAR

KPOINTS

POSCAR_template

POTCAR

Examples of all but the POTCAR file are provided.  As explained below,

POSCAR_W is an input file for a 2-atom unit cell of tungsten and can

be used to test the LAMMPS/VASP coupling.  The POTCAR file is a

proprietary VASP file, so use one from your VASP installation.

Note that the POSCAR_template file should be matched to the LAMMPS

input script (# of atoms and atom types, box size, etc).  The provided

POSCAR_W matches in.client.W.

NOTE: explain how vasp_wrapper.py finds the cslib.py wrapper on the

CSlib to import.

----------------

To run in client/server mode:

Both the client (LAMMPS) and server (vasp_wrap.py) must use the same

% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W

% python vasp_wrap.py zmq POSCAR_W

--------------

The provided data.W file (for LAMMPS) and POSCAR_W file (for VASP) are

for a simple 2-atom unit cell of bcc tungsten (W).  You could

replicate this with LAMMPS to create a larger system.  The

vasp_wrap.py script needs to be generalized to create an appropriate

POSCAR_W file for a larger box.

VASP input file include the sample INCAR and KPOINTS files provided.

A POTCAR file is also needed, which should come from your VASP package

installation.

# could make syntax for launching VASP more flexible

#   e.g. command-line arg for # of procs

import sys

import commands

import sys,subprocess

import xml.etree.ElementTree as ET  

from cslib import CSlib

# comment out 2nd line once 1st line is correct for your system

vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \

          "-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"

vaspcmd = "touch tmp"

# enums matching FixClientMD class in LAMMPS

  # header, including box size

  print >>psnew,psold[0],

  print >>psnew,psold[1],

  print >>psnew,"%g 0.0 0.0" % box[0]

  print >>psnew,"0.0 %g 0.0" % box[1]

  print >>psnew,"0.0 0.0 %g" % box[2]

  print >>psnew,psold[5],

  print >>psnew,psold[6],

  psnew.write(psold[0])

  psnew.write(psold[1])

  psnew.write("%g 0.0 0.0\n" % box[0])

  psnew.write("0.0 %g 0.0\n" % box[1])

  psnew.write("0.0 0.0 %g\n" % box[2])

  psnew.write(psold[5])

  psnew.write(psold[6])

  # per-atom coords

  # grouped by types

  print >>psnew,"Cartesian"

  psnew.write("Cartesian\n")

  for itype in range(1,ntypes+1):

    for i in range(natoms):

      x = coords[3*i+0]

      y = coords[3*i+1]

      z = coords[3*i+2]

      aline = "  %g %g %g" % (x,y,z)

      print >>psnew,aline

      aline = "  %g %g %g\n" % (x,y,z)

      psnew.write(aline)

  psnew.close()

  # invoke VASP

  print "Launching VASP ..."

  print "\nLaunching VASP ..."

  print vaspcmd

  out = commands.getoutput(vaspcmd)

  print out

  subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True)

  # process VASP output

#   Copyright 2018 National Technology & Engineering Solutions of

#   Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with

#   NTESS, the U.S. Government retains certain rights in this software.

#   This software is distributed under the GNU Lesser General Public

#   License (LGPL).

#   This software is distributed under the modified Berkeley Software

#   Distribution (BSD) License.

#

#   See the README file in the top-level CSlib directory.

# -------------------------------------------------------------------------

   See the README file in the top-level LAMMPS directory.

------------------------------------------------------------------------- */

#include <cstring.h>

#include <cstring>

#include "message.h"

#include "error.h"