more updates to the new MESSAGE package

examples/COUPLE/lammps_vasp/README

@@ -5,7 +5,7 @@ See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
 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,
@@ -34,6 +34,40 @@ You can leave off the -z if you do not have ZMQ on your system.
 
 ----------------
 
+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
@@ -76,15 +110,3 @@ ZMQ mode of messaging:
 
 % 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.

examples/COUPLE/lammps_vasp/vasp_wrap.py

@@ -23,13 +23,15 @@
 # could make syntax for launching VASP more flexible
 #   e.g. command-line arg for # of procs
 
-import sys
+import sys,subprocess
-import commands
 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
 
@@ -84,18 +86,18 @@ def poscar_write(poscar,natoms,ntypes,types,coords,box):
 
   # header, including box size
   
-  print >>psnew,psold[0],
+  psnew.write(psold[0])
-  print >>psnew,psold[1],
+  psnew.write(psold[1])
-  print >>psnew,"%g 0.0 0.0" % box[0]
+  psnew.write("%g 0.0 0.0\n" % box[0])
-  print >>psnew,"0.0 %g 0.0" % box[1]
+  psnew.write("0.0 %g 0.0\n" % box[1])
-  print >>psnew,"0.0 0.0 %g" % box[2]
+  psnew.write("0.0 0.0 %g\n" % box[2])
-  print >>psnew,psold[5],
+  psnew.write(psold[5])
-  print >>psnew,psold[6],
+  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):
@@ -103,8 +105,8 @@ def poscar_write(poscar,natoms,ntypes,types,coords,box):
       x = coords[3*i+0]
       y = coords[3*i+1]
       z = coords[3*i+2]
-      aline = "  %g %g %g" % (x,y,z)
+      aline = "  %g %g %g\n" % (x,y,z)
-      print >>psnew,aline
+      psnew.write(aline)
 
   psnew.close()
 
@@ -209,10 +211,9 @@ while 1:
 
   # invoke VASP
   
-  print "Launching VASP ..."
+  print "\nLaunching VASP ..."
   print vaspcmd
-  out = commands.getoutput(vaspcmd)
+  subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True)
-  print out
   
   # process VASP output
     

lib/message/cslib/src/cslib.py

@@ -6,8 +6,8 @@
 #   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
+#   This software is distributed under the modified Berkeley Software
-#   License (LGPL).
+#   Distribution (BSD) License.
 #
 #   See the README file in the top-level CSlib directory.
 # -------------------------------------------------------------------------

src/MESSAGE/message.cpp

@@ -11,7 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring.h>
+#include <cstring>
 #include "message.h"
 #include "error.h"
 

src/MESSAGE/server.cpp

@@ -11,7 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring.h>
+#include <cstring>
 #include "server.h"
 #include "error.h"