diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 27ab64d50bf0544ef74d31b6e69b4642285abc93..341483d7a7231ef39ca2595ce5d2c4aa6d3d4ac7 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -1153,6 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, - "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, - "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE +"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, - "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, - "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm @@ -1598,6 +1599,29 @@ The person who created this package is Axel Kohlmeyer at Temple U :line +USER-NC-DUMP package :link(USER-NC-DUMP),h5 + +Contents: Dump styles for writing NetCDF format files. NetCDF is a binary, +portable, self-describing file format on top of HDF5. The file format +contents follow the AMBER NetCDF trajectory conventions +(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions to this +convention. This package implements a "dump nc"_dump_nc.html command +and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots +in this format. See src/USER-NC-DUMP/README for more details. + +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. :ulb,l +VMD (http://www.ks.uiuc.edu/Research/vmd/) :l +AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains + a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule + +The person who created these files is Lars Pastewka at +Karlsruhe Institute of Technology (lars.pastewka at kit.edu). +Contact him directly if you have questions. + +:line + USER-OMP package :link(USER-OMP),h5 Supporting info: