forked from lijiext/lammps
77 lines
2.7 KiB
Plaintext
77 lines
2.7 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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dump netcdf command :h3
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dump netcdf/mpiio command :h3
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[Syntax:]
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dump ID group-ID netcdf N file args
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dump ID group-ID netcdf/mpiio N file args :pre
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ID = user-assigned name for the dump :ulb,l
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group-ID = ID of the group of atoms to be imaged :l
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{netcdf} or {netcdf/mpiio} = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
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N = dump every this many timesteps :l
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file = name of file to write dump info to :l
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args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
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[Examples:]
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dump 1 all netcdf 100 traj.nc type x y z vx vy vz
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dump_modify 1 append yes at -1 thermo yes
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dump 1 all netcdf/mpiio 1000 traj.nc id type x y z
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dump 1 all netcdf 1000 traj.*.nc id type x y z :pre
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[Description:]
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Dump a snapshot of atom coordinates every N timesteps in Amber-style
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NetCDF file format. NetCDF files are binary, portable and
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self-describing. This dump style will write only one file on the root
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node. The dump style {netcdf} uses the "standard NetCDF
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library"_netcdf-home. All data is collected on one processor and then
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written to the dump file. Dump style {netcdf/mpiio} uses the
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"parallel NetCDF library"_pnetcdf-home and MPI-IO to write to the dump
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file in parallel; it has better performance on a larger number of
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processors. Note that style {netcdf} outputs all atoms sorted by atom
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tag while style {netcdf/mpiio} outputs atoms in order of their MPI
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rank.
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NetCDF files can be directly visualized via the following tools:
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Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
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all extensions of this dump style. :ule,b
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VMD (http://www.ks.uiuc.edu/Research/vmd/). :l
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AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
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contains a NetCDF reader that is not present in the standard
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distribution of AtomEye. :l,ule
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In addition to per-atom data, "thermo"_thermo.html data can be included in the
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dump file. The data included in the dump file is identical to the data specified
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by "thermo_style"_thermo_style.html.
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:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
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:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
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:line
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[Restrictions:]
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The {netcdf} and {netcdf/mpiio} dump styles are part of the
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USER-NETCDF package. They are only enabled if LAMMPS was built with
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that package. See the "Build package"_Build_package.html doc page for
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more info.
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:line
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[Related commands:]
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"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
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