82 lines
2.6 KiB
ReStructuredText
82 lines
2.6 KiB
ReStructuredText
.. index:: dump netcdf
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.. index:: dump netcdf/mpiio
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dump netcdf command
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===================
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dump netcdf/mpiio command
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=========================
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Syntax
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""""""
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.. code-block:: LAMMPS
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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
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* ID = user-assigned name for the dump
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* group-ID = ID of the group of atoms to be imaged
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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 :doc:`dump <dump>` doc page)
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* N = dump every this many timesteps
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* file = name of file to write dump info to
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* args = list of atom attributes, same as for :doc:`dump_style custom <dump>`
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Examples
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""""""""
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.. code-block:: LAMMPS
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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
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Description
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"""""""""""
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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 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 (https://www.ovito.org/). Ovito supports the AMBER convention and
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all extensions of this dump style.
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* VMD (https://www.ks.uiuc.edu/Research/vmd/).
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In addition to per-atom data, :doc:`thermo <thermo>` 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 :doc:`thermo_style <thermo_style>`.
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.. _netcdf-home: https://www.unidata.ucar.edu/software/netcdf/
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.. _pnetcdf-home: https://trac.mcs.anl.gov/projects/parallel-netcdf/
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----------
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Restrictions
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""""""""""""
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The *netcdf* and *netcdf/mpiio* dump styles are part of the
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NETCDF package. They are only enabled if LAMMPS was built with
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that package. See the :doc:`Build package <Build_package>` page for
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more info.
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The *netcdf* and *netcdf/mpiio* dump styles currently cannot dump
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string properties or properties from variables.
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----------
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Related commands
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""""""""""""""""
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:doc:`dump <dump>`, :doc:`dump_modify <dump_modify>`, :doc:`undump <undump>`
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