intergrate references to dump cfg/uef into the dump command docs
This commit is contained in:
Axel Kohlmeyer
@ -27,6 +27,9 @@ dump command
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:doc:`dump custom/adios <dump_adios>` command
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=============================================
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:doc:`dump cfg/uef <dump_cfg_uef>` command
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==========================================
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Syntax
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""""""
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@ -36,7 +39,7 @@ 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/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* 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 *xyz/mpiio* or *yaml*
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* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* 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 *xyz/mpiio* or *yaml*
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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 arguments for a particular style
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@ -47,22 +50,23 @@ Syntax
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*atom/gz* args = none
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*atom/zstd* args = none
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*atom/mpiio* args = none
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*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` doc page
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*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` page
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*cfg* args = same as *custom* args, see below
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*cfg/gz* args = same as *custom* args, see below
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*cfg/zstd* args = same as *custom* args, see below
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*cfg/mpiio* args = same as *custom* args, see below
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*cfg/uef* args = same as *custom* args, discussed on :doc:`dump cfg/uef <dump_cfg_uef>` page
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*custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* args = see below
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*custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios <dump_adios>` doc page
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*custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios <dump_adios>` page
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*dcd* args = none
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*h5md* args = discussed on :doc:`dump h5md <dump_h5md>` doc page
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*image* args = discussed on :doc:`dump image <dump_image>` doc page
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*h5md* args = discussed on :doc:`dump h5md <dump_h5md>` page
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*image* args = discussed on :doc:`dump image <dump_image>` page
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*local*, *local/gz*, *local/zstd* args = see below
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*molfile* args = discussed on :doc:`dump molfile <dump_molfile>` doc page
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*movie* args = discussed on :doc:`dump image <dump_image>` doc page
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*netcdf* args = discussed on :doc:`dump netcdf <dump_netcdf>` doc page
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*netcdf/mpiio* args = discussed on :doc:`dump netcdf <dump_netcdf>` doc page
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*vtk* args = same as *custom* args, see below, also :doc:`dump vtk <dump_vtk>` doc page
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*molfile* args = discussed on :doc:`dump molfile <dump_molfile>` page
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*movie* args = discussed on :doc:`dump image <dump_image>` page
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*netcdf* args = discussed on :doc:`dump netcdf <dump_netcdf>` page
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*netcdf/mpiio* args = discussed on :doc:`dump netcdf <dump_netcdf>` page
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*vtk* args = same as *custom* args, see below, also :doc:`dump vtk <dump_vtk>` page
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*xtc* args = none
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*xyz* args = none
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*xyz/gz* args = none
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@ -155,7 +159,7 @@ timesteps in one of several styles. The *image* and *movie* styles are
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the exception: the *image* style renders a JPG, PNG, or PPM image file
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of the atom configuration every N timesteps while the *movie* style
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combines and compresses them into a movie file; both are discussed in
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detail on the :doc:`dump image <dump_image>` doc page. The timesteps on
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detail on the :doc:`dump image <dump_image>` page. The timesteps on
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which dump output is written can also be controlled by a variable.
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See the :doc:`dump_modify every <dump_modify>` command.
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@ -194,7 +198,7 @@ or multiple smaller files).
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For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by
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default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting
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by atom ID is on by default. See the :doc:`dump_modify <dump_modify>`
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doc page for details.
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page for details.
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The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
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are identical in command syntax to the corresponding styles without
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@ -204,7 +208,7 @@ alternative approach to writing compressed files via a pipe, as done
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by the regular dump styles, which may be required on clusters where
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the interface to the high-speed network disallows using the fork()
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library call (which is needed for a pipe). For the remainder of this
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doc page, you should thus consider the *atom* and *atom/gz* styles
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page, you should thus consider the *atom* and *atom/gz* styles
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(etc) to be inter-changeable, with the exception of the required
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filename suffix.
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@ -218,7 +222,7 @@ As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and
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*xyz/mpiio* styles are identical in command syntax and in the format
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of the dump files they create, to the corresponding styles without
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"mpiio", except the single dump file they produce is written in
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parallel via the MPI-IO library. For the remainder of this doc page,
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parallel via the MPI-IO library. For the remainder of this page,
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you should thus consider the *atom* and *atom/mpiio* styles (etc) to
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be inter-changeable. The one exception is how the filename is
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specified for the MPI-IO styles, as explained below.
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@ -664,7 +668,7 @@ so that each value is 0.0 to 1.0. If the simulation box is triclinic
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(tilted), then all atom coords will still be between 0.0 and 1.0.
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I.e. actual unscaled (x,y,z) = xs\*A + ys\*B + zs\*C, where (A,B,C) are
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the non-orthogonal vectors of the simulation box edges, as discussed
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on the :doc:`Howto triclinic <Howto_triclinic>` doc page.
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on the :doc:`Howto triclinic <Howto_triclinic>` page.
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Use *xu*, *yu*, *zu* if you want the coordinates "unwrapped" by the
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image flags for each atom. Unwrapped means that if the atom has
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@ -787,7 +791,7 @@ more info.
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The *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles
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are part of the MPIIO package. They are only enabled if LAMMPS was
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built with that package. See the :doc:`Build package <Build_package>`
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doc page for more info.
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page for 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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@ -797,12 +801,12 @@ Related commands
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""""""""""""""""
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:doc:`dump atom/adios <dump_adios>`, :doc:`dump custom/adios <dump_adios>`,
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:doc:`dump h5md <dump_h5md>`, :doc:`dump image <dump_image>`,
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:doc:`dump molfile <dump_molfile>`, :doc:`dump_modify <dump_modify>`,
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:doc:`undump <undump>`
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:doc:`dump cfg/uef <dump_cfg_uef>`, :doc:`dump h5md <dump_h5md>`,
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:doc:`dump image <dump_image>`, :doc:`dump molfile <dump_molfile>`,
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:doc:`dump_modify <dump_modify>`, :doc:`undump <undump>`, :doc:`write_dump <write_dump>`
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Default
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"""""""
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The defaults for the *image* and *movie* styles are listed on the
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:doc:`dump image <dump_image>` doc page.
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:doc:`dump image <dump_image>` page.
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