USER-NETCDF

This package provides the netcdf and netcdf/mpiio dump styles. See the doc page for dump netcdf or dump netcdf/mpiio command for how to use them. Compiling these dump styles requires having the netCDF library installed on your system. See lib/netcdf/README for additional details.

PACKAGE DESCRIPTION

This is a LAMMPS (http://lammps.sandia.gov/) dump style for output into a NetCDF database. The database format follows the AMBER NetCDF trajectory convention (http://ambermd.org/netcdf/nctraj.xhtml), but includes extensions to this convention. These extension are:

• A variable "cell_origin" (of dimension "frame", "cell_spatial") that contains the bottom left corner of the simulation cell.
• Any number of additional variables corresponding to per atom scalar, vector or tensor quantities available within LAMMPS. Tensor quantities are written in Voigt notation. An additional dimension "Voigt" of length 6 is created for this purpose.
• Possibility to output to an HDF5 database.

NetCDF files can be directly visualized with the following tools:

• Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and all of the above extensions.
• VMD (http://www.ks.uiuc.edu/Research/vmd/).
• AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains a NetCDF reader that is not present in the standard distribution of AtomEye.

The person who created these files is Lars Pastewka at the University of Freiburg (lars.pastewka@imtek.uni-freiburg.de). Contact him directly if you have questions.

Lars Pastewka University of Freiburg Department of Microsystems Engineering Georges-Köhler-Allee 103, 79110 Freiburg, Germany e-mail: lars.pastewka@imtek.uni-freiburg.de