40 lines
1.7 KiB
Plaintext
40 lines
1.7 KiB
Plaintext
NETCDF
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============
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This package provides the netcdf and netcdf/mpiio dump styles.
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See the doc page for dump netcdf or dump netcdf/mpiio command for how to use
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them. Compiling these dump styles requires having the netCDF library installed
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on your system. See lib/netcdf/README for additional details.
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PACKAGE DESCRIPTION
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-------------------
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This is a LAMMPS (https://www.lammps.org/) dump style for output into a NetCDF
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database. The database format follows the AMBER NetCDF trajectory convention
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(http://ambermd.org/netcdf/nctraj.xhtml), but includes extensions to this
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convention. These extension are:
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* A variable "cell_origin" (of dimension "frame", "cell_spatial") that contains
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the bottom left corner of the simulation cell.
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* Any number of additional variables corresponding to per atom scalar, vector
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or tensor quantities available within LAMMPS. Tensor quantities are written in
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Voigt notation. An additional dimension "Voigt" of length 6 is created for
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this purpose.
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* Possibility to output to an HDF5 database.
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NetCDF files can be directly visualized with the following tools:
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* Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and all of
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the above extensions.
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* VMD (http://www.ks.uiuc.edu/Research/vmd/).
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* AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
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a NetCDF reader that is not present in the standard distribution of AtomEye.
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The person who created these files is Lars Pastewka at
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the University of Freiburg (lars.pastewka@imtek.uni-freiburg.de).
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Contact him directly if you have questions.
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Lars Pastewka
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University of Freiburg
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Department of Microsystems Engineering
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Georges-Köhler-Allee 103, 79110 Freiburg, Germany
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e-mail: lars.pastewka@imtek.uni-freiburg.de
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