document extxyz dump style
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Axel Kohlmeyer
committed by
Francois-Xavier Coudert
Francois-Xavier Coudert
parent
f5dbf30965
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2ad0cc1820
@ -19,6 +19,7 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
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* :doc:`custom/gz <dump>`
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* :doc:`custom/zstd <dump>`
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* :doc:`dcd <dump>`
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* :doc:`extxyz <dump>`
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* :doc:`grid <dump>`
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* :doc:`grid/vtk <dump>`
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* :doc:`h5md <dump_h5md>`
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@ -3,6 +3,7 @@
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.. index:: dump cfg
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.. index:: dump custom
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.. index:: dump dcd
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.. index:: dump extxyz
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.. index:: dump grid
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.. index:: dump grid/vtk
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.. index:: dump local
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@ -59,7 +60,7 @@ Syntax
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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 dumped
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* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/adios* or *dcd* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *yaml*
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* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/adios* or *dcd* or *extxyz* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *yaml*
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* N = dump on timesteps which are multiples of N
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* file = name of file to write dump info to
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* attribute1,attribute2,... = list of attributes for a particular style
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@ -77,6 +78,7 @@ Syntax
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*custom*, *custom/gz*, *custom/zstd* attributes = see below
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*custom/adios* attributes = same as *custom* attributes, discussed on :doc:`dump custom/adios <dump_adios>` page
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*dcd* attributes = none
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*extxyz* attributes = none
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*h5md* attributes = discussed on :doc:`dump h5md <dump_h5md>` page
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*grid* attributes = see below
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*grid/vtk* attributes = see below
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@ -242,28 +244,29 @@ all the processors or multiple smaller files.
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frames consistently to the same atom. This can lead to incorrect
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visualizations or results. LAMMPS will print a warning in such cases.
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For the *atom*, *custom*, *cfg*, *grid*, and *local* styles, sorting
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is off by default. For the *dcd*, *grid/vtk*, *xtc*, *xyz*, and
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For the *atom*, *custom*, *cfg*, *grid*, and *local* styles, sorting is
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off by default. For the *dcd*, *extxyz*, *grid/vtk*, *xtc*, *xyz*, and
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*molfile* styles, sorting by atom ID or grid ID is on by default. See
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the :doc:`dump_modify <dump_modify>` page for details.
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The *style* keyword determines what kind of data is written to the
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dump file(s) and in what format.
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Note that *atom*, *custom*, *dcd*, *xtc*, *xyz*, and *yaml* style dump
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files can be read directly by `VMD <https://www.ks.uiuc.edu/Research/vmd>`_,
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a popular tool for visualizing and analyzing trajectories from atomic
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and molecular systems. For reading *netcdf* style dump files, the
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netcdf plugin needs to be recompiled from source using a NetCDF version
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compatible with the one used by LAMMPS. The bundled plugin binary
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uses a very old version of NetCDF that is not compatible with LAMMPS.
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Note that *atom*, *custom*, *dcd*, *extxyz*, *xtc*, *xyz*, and *yaml*
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style dump files can be read directly by `VMD
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<https://www.ks.uiuc.edu/Research/vmd>`_, a popular tool for visualizing
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and analyzing trajectories from atomic and molecular systems. For
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reading *netcdf* style dump files, the netcdf plugin needs to be
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recompiled from source using a NetCDF version compatible with the one
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used by LAMMPS. The bundled plugin binary uses a very old version of
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NetCDF that is not compatible with LAMMPS.
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Likewise the `OVITO visualization package <https://www.ovito.org>`_,
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popular for materials modeling, can read the *atom*, *custom*,
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popular for materials modeling, can read the *atom*, *custom*, *extxyz*,
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*local*, *xtc*, *cfg*, *netcdf*, and *xyz* style atom dump files
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directly. With version 3.8 and above, OVITO can also read and
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visualize *grid* style dump files with grid cell data, including
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iso-surface images of the grid cell values.
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directly. With version 3.8 and above, OVITO can also read and visualize
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*grid* style dump files with grid cell data, including iso-surface
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images of the grid cell values.
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Note that settings made via the :doc:`dump_modify <dump_modify>`
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command can also alter the format of individual values and content of
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@ -475,6 +478,18 @@ label). This option will help many visualization programs to guess bonds
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and colors. You can use the :doc:`dump_modify types labels <dump_modify>`
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option to replace numeric atom types with :doc:`type labels <Howto_type_labels>`.
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.. versionadded:: TBD
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The *extxyz* style writes XYZ files compatible with the Extended XYZ (or
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ExtXYZ) format as defined as defined in `the libAtoms specification
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<https://github.com/libAtoms/extxyz>`_. Specifically, the following
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information will be dumped:
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* timestep
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* time, if enabled with :doc:`dump_modify time yes <dump_modify>`
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* simulation box lattice and pbc conditions
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* atomic velocities and forces
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.. versionadded:: 22Dec2022
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The *grid/vtk* style writes VTK files for grid data on a regular
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@ -607,8 +622,8 @@ with the processor ID from :math:`0` to :math:`P-1`. For example,
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tmp.dump.% becomes tmp.dump.0, tmp.dump.1, ... tmp.dump.:math:`P-1`,
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etc. This creates smaller files and can be a fast mode of output on
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parallel machines that support parallel I/O for output. This option is
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**not** available for the *dcd*, *xtc*, *xyz*, *grid/vtk*, and *yaml*
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styles.
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**not** available for the *dcd*, *extxyz*, *xtc*, *xyz*, *grid/vtk*, and
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*yaml* styles.
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By default, :math:`P` is the the number of processors, meaning one file per
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processor, but :math:`P` can be set to a smaller value via the *nfile* or
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@ -1017,9 +1032,9 @@ the COMPRESS 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 *xtc*, *dcd*, and *yaml* styles are part of the EXTRA-DUMP package.
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They are only enabled if LAMMPS was built with that package. See the
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:doc:`Build package <Build_package>` page for more info.
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The *dcd*, *extxyz*, *xtc*, and *yaml* styles are part of the EXTRA-DUMP
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package. They are only enabled if LAMMPS was built with that package.
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See the :doc:`Build package <Build_package>` page for more info.
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Related commands
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""""""""""""""""
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