git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9641 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/COUPLE/lammps_spparks/README

@@ -1,17 +1,20 @@
 This directory has an application that models grain growth in the
-presence of strain.  The grain growth is simulated by a Potts model in
+presence of strain.
-a kinetic Monte Carlo code SPPARKS.  Clusters of like spins on a
-lattice represent grains.  The Hamiltonian for the energy due of a
-collection of spins includes a strain term and is described on this
-page in the SPPARKS documentation:
 
-http://www.sandia.gov/~sjplimp/spparks/doc/app_potts_strain.html.
+The grain growth is simulated by a Potts model in a kinetic Monte
+Carlo code SPPARKS.  Clusters of like spins on a lattice represent
+grains.  The Hamiltonian for the energy due of a collection of spins
+includes a strain term and is described on this page in the SPPARKS
+documentation:
 
-The strain is computed by LAMMPS as a particle displacement where
+http://spparks.sandia.gov/doc/app_potts_strain.html.
-pairs of atoms across a grain boundary are of different types and thus
+
-push off from each other due to a Lennard-Jones sigma between
+The strain is computed by the molecular dynamics code LAMMPS as a
-particles of different types that is larger than the sigma between
+particle displacement where pairs of atoms across a grain boundary are
-particles of the same type (interior to grains).
+of different types and thus push off from each other due to a
+Lennard-Jones sigma between particles of different types that is
+larger than the sigma between particles of the same type (interior to
+grains).
 
 lmpspk.cpp	    main program
 		    it links LAMMPS and SPPARKS as libraries

python/README

@@ -91,7 +91,10 @@ viz_tool.py in.viz 100 5000
 vizplotgui_tool.py in.viz 100 thermo_temp
 
 You can un-comment the Pypar calls if you want to run these in
-parallel.
+parallel.  Then, for example, you can type:
+
+% mpirun -np 4 trivial.py in.trivial
+% mpirun -np 4 python trivial.py in.trivial
 
 Each script has more documentation in the file that explains how to
 use it and what it is doing.

python/lammps.py

@@ -105,7 +105,7 @@ class lammps:
     if type == 0:
       if style > 0: return None
       self.lib.lammps_extract_fix.restype = POINTER(c_double)
-      ptr = self.lib.lammps_extract_bix(self.lmp,id,style,type,i,j)
+      ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
       result = ptr[0]
       self.lib.lammps_free(ptr)
       return result

src/USER-PHONON/README

@@ -1,18 +1,19 @@
-This package contains a method to measure the dynamical matrices, and
+This package contains a fix phonon command that calculates dynamical
-consequently the phonon dispersion, directly from molecular dynamics
+matrices, which can then be used to compute phonon dispersion
-simulations.  It is implemented as a fix phonon command.
+relations, directly from molecular dynamics simulations.
 
 See the doc page for the fix phonon command for detailed usage
 instructions.
 
-The compiling of this package along with LAMMPS requires that the FFT3d
+Use of this package requires building LAMMPS with FFT suppport, as
-wrappers from the kspace package of LAMMPS be included as well.
+described in doc/Section_start.html.
 
 There are example scripts for using this package in
 examples/USER/phonon.
 
-There is an auxiliary post-processing tool for using this package in
+There is an auxiliary post-processing tool in tools/phonon that will
-tools/phonon.
+compute phonon frequencies and dispersion relations from the dynamical
+matrices output by this command.
 
 The person who created this package is Ling-Ti Kong (konglt at
 sjtu.edu.cn) at Shanghai Jiao Tong University.  Contact him directly

tools/phonon/README

@@ -1,7 +1,7 @@
-Phonon post-processing tool
+Phonon dispersion post-processing tool
 
-This program reads the binary file created by fix_phonon
+This program reads the binary file created by fix_phonon and helps to
-and helps to analyse the phonon related info.
+analyse the phonon related info.
 
 The clapack library is needed to solve the eigen problems,
 which could be downloaded from:
@@ -19,13 +19,9 @@ Brillouin zone.
 To compile the code, one needs therefore to install the above
 libraries and set the paths correctly in the Makefile.
 
-The units of the output frequencies by this code is THz for
+The units of the output frequencies by this code is THz for LAMMPS
-LAMMPS units "real", "si", "metal", and "cgs"; in these cases,
+units "real", "si", "metal", and "cgs"; in these cases, the
-the frequencies are $\nu$ instead of $\omega$.
+frequencies are $\nu$ instead of $\omega$.
-
-One is encouraged to visit http://code.google.com/p/fix-phonon/
-to check out the latest revision on fix-phonon and the post-processing
-code.
 
 Author: Ling-Ti Kong
 Feb 2013