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clarify dump doc page meaning Nevery = N

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This commit is contained in:
Steve Plimpton
2022-09-01 09:53:57 -06:00
parent ced73080b8
commit 4cff211a5e
1 changed files with 30 additions and 21 deletions
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doc/src/dump.rst
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@ -62,7 +62,7 @@ Syntax
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped
* 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*
* N = dump every this many timesteps
* N = dump on timesteps which are a multiple of N
* file = name of file to write dump info to
* args = list of arguments for a particular style
@ -176,14 +176,15 @@ Examples
Description
"""""""""""
Dump a snapshot of atom quantities to one or more files every :math:`N`
timesteps in one of several styles. The *image* and *movie* styles are
the exception: the *image* style renders a JPG, PNG, or PPM image file
of the atom configuration every :math:`N` timesteps while the *movie* style
combines and compresses them into a movie file; both are discussed in
detail on the :doc:`dump image <dump_image>` page. The timesteps on
which dump output is written can also be controlled by a variable.
See the :doc:`dump_modify every <dump_modify>` command.
Dump a snapshot of atom quantities to one or more files once every
:math:`N` timesteps in one of several styles. The *image* and *movie*
styles are the exception: the *image* style renders a JPG, PNG, or PPM
image file of the atom configuration every :math:`N` timesteps while
the *movie* style combines and compresses them into a movie file; both
are discussed in detail on the :doc:`dump image <dump_image>` page.
The timesteps on which dump output is written can also be controlled
by a variable. See the :doc:`dump_modify every <dump_modify>`
command.
Only information for atoms in the specified group is dumped. The
:doc:`dump_modify thresh and region and refresh <dump_modify>` commands
@ -485,21 +486,29 @@ popular molecular viewing program.
----------
Dumps are performed on timesteps that are a multiple of :math:`N` (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
Dumps are performed on timesteps that are a multiple of :math:`N`
(including timestep 0) and on the last timestep of a minimization if
the minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of :math:`N`. This behavior can be
changed via the :doc:`dump_modify first <dump_modify>` command, which
can also be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. :math:`N` can be changed between runs by
using the :doc:`dump_modify every <dump_modify>` command (not allowed
for *dcd* style). The :doc:`dump_modify every <dump_modify>` command
also allows a variable to be used to determine the sequence of
timesteps on which dump files are written. In this mode a dump on the
first timestep of a run will also not be written unless the
if the current timestep is not a multiple of :math:`N`. This behavior
can be changed via the :doc:`dump_modify first <dump_modify>` command,
which can also be useful if the dump command is invoked after a
minimization ended on an arbitrary timestep.
The value of :math:`N` can be changed between runs by using the
:doc:`dump_modify every <dump_modify>` command (not allowed for *dcd*
style). The :doc:`dump_modify every <dump_modify>` command also
allows a variable to be used to determine the sequence of timesteps on
which dump files are written. In this mode a dump on the first
timestep of a run will also not be written unless the
:doc:`dump_modify first <dump_modify>` command is used.
If you instead want to dump snapshots based on simulation time (in
time units of the :doc:`units` command), the :doc:`dump_modify
every/time <dump_modify>` command can be used. This can be useful
when the timestep size varies during a simulation run, e.g. by use of
the :doc:`fix dt/reset <fix_dt_reset>` command.
The specified filename determines how the dump file(s) is written.
The default is to write one large text file, which is opened when the
dump command is invoked and closed when an :doc:`undump <undump>`