diff --git a/examples/COUPLE/lammps_spparks/README b/examples/COUPLE/lammps_spparks/README index 239a8042e3..fc31de5f0b 100644 --- a/examples/COUPLE/lammps_spparks/README +++ b/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 -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: +presence of strain. -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 -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 -particles of different types that is larger than the sigma between -particles of the same type (interior to grains). +http://spparks.sandia.gov/doc/app_potts_strain.html. + +The strain is computed by the molecular dynamics code LAMMPS as a +particle displacement where 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 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 diff --git a/python/README b/python/README index 27997582b5..0376fd69ec 100644 --- a/python/README +++ b/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. diff --git a/python/lammps.py b/python/lammps.py index c65e84ced0..0f6e9dc76b 100644 --- a/python/lammps.py +++ b/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 diff --git a/src/USER-PHONON/README b/src/USER-PHONON/README index 67675d31a9..a3cd47fcd7 100644 --- a/src/USER-PHONON/README +++ b/src/USER-PHONON/README @@ -1,18 +1,19 @@ -This package contains a method to measure the dynamical matrices, and -consequently the phonon dispersion, directly from molecular dynamics -simulations. It is implemented as a fix phonon command. +This package contains a fix phonon command that calculates dynamical +matrices, which can then be used to compute phonon dispersion +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 -wrappers from the kspace package of LAMMPS be included as well. +Use of this package requires building LAMMPS with FFT suppport, as +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 -tools/phonon. +There is an auxiliary post-processing tool in tools/phonon that will +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 diff --git a/tools/phonon/README b/tools/phonon/README index 042cc13c7d..f0647a6ff2 100644 --- a/tools/phonon/README +++ b/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 -and helps to analyse the phonon related info. +This program reads the binary file created by fix_phonon and helps to +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 -LAMMPS units "real", "si", "metal", and "cgs"; in these cases, -the 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. +The units of the output frequencies by this code is THz for LAMMPS +units "real", "si", "metal", and "cgs"; in these cases, the +frequencies are $\nu$ instead of $\omega$. Author: Ling-Ti Kong Feb 2013