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update docs for noremap option to read_restart

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Axel Kohlmeyer
2022-06-21 20:19:13 -04:00
parent 7d49ad5924
commit b0f4ef8a39
2 changed files with 34 additions and 34 deletions
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67
doc/src/read_restart.rst
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@ -11,7 +11,7 @@ Syntax
read_restart file flag
* file = name of binary restart file to read in
* flag = remap (optional)
* flag = noremap (optional)
Examples
""""""""
@ -19,39 +19,36 @@ Examples
.. code-block:: LAMMPS
read_restart save.10000
read_restart save.10000 remap
read_restart save.10000 noremap
read_restart restart.*
read_restart restart.*.mpiio
read_restart poly.*.% remap
read_restart poly.*.% noremap
Description
"""""""""""
Read in a previously saved system configuration from a restart file.
This allows continuation of a previous run. Details about what
information is stored (and not stored) in a restart file is given
below. Basically this operation will re-create the simulation box
with all its atoms and their attributes as well as some related global
settings, at the point in time it was written to the restart file by a
previous simulation. The simulation box will be partitioned into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors in the current simulation and the settings of the
information is stored (and not stored) in a restart file is given below.
Basically this operation will re-create the simulation box with all its
atoms and their attributes as well as some related global settings, at
the point in time it was written to the restart file by a previous
simulation. The simulation box will be partitioned into a regular 3d
grid of rectangular bricks, one per processor, based on the number of
processors in the current simulation and the settings of the
:doc:`processors <processors>` command. The partitioning can later be
changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
changed by the :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands.
.. note::
Normally, restart files are written by the
:doc:`restart <restart>` or :doc:`write_restart <write_restart>` commands
so that all atoms in the restart file are inside the simulation box.
If this is not the case, the read_restart command will print an error
that atoms were "lost" when the file is read. This error should be
reported to the LAMMPS developers so the invalid writing of the
restart file can be fixed. If you still wish to use the restart file,
the optional *remap* flag can be appended to the read_restart command.
This should avoid the error, by explicitly remapping each atom back
into the simulation box, updating image flags for the atom
appropriately.
When restart files are read, atoms are explicitly remapped back into
the simulation box and image flags updated accordingly. In most
cases this will not make a difference since writing a restart file
will also trigger a rebuild of the neighbor lists and remapping of
atoms into the simulation box. This extra remap results in some
overhead that can be avoided by appending the optional *noremap* flag
to the read_restart command.
Restart files are saved in binary format to enable exact restarts,
meaning that the trajectories of a restarted run will precisely match
@ -65,7 +62,8 @@ certain settings such as those set by the :doc:`newton <newton>` or
these cases.
Certain fixes will not restart exactly, though they should provide
statistically similar results. These include :doc:`fix shake <fix_shake>` and :doc:`fix langevin <fix_langevin>`.
statistically similar results. These include :doc:`fix shake
<fix_shake>` and :doc:`fix langevin <fix_langevin>`.
Certain pair styles will not restart exactly, though they should
provide statistically similar results. This is because the forces
@ -81,18 +79,19 @@ produced the restart file, it could be a LAMMPS bug, so consider
:doc:`reporting it <Errors_bugs>` if you think the behavior is a bug.
Because restart files are binary, they may not be portable to other
machines. In this case, you can use the :doc:`-restart command-line switch <Run_options>` to convert a restart file to a data file.
machines. In this case, you can use the :doc:`-restart command-line
switch <Run_options>` to convert a restart file to a data file.
Similar to how restart files are written (see the
:doc:`write_restart <write_restart>` and :doc:`restart <restart>`
commands), the restart filename can contain two wild-card characters.
If a "\*" appears in the filename, the directory is searched for all
filenames that match the pattern where "\*" is replaced with a timestep
value. The file with the largest timestep value is read in. Thus,
this effectively means, read the latest restart file. It's useful if
you want your script to continue a run from where it left off. See
the :doc:`run <run>` command and its "upto" option for how to specify
the run command so it does not need to be changed either.
Similar to how restart files are written (see the :doc:`write_restart
<write_restart>` and :doc:`restart <restart>` commands), the restart
filename can contain two wild-card characters. If a "\*" appears in the
filename, the directory is searched for all filenames that match the
pattern where "\*" is replaced with a timestep value. The file with the
largest timestep value is read in. Thus, this effectively means, read
the latest restart file. It's useful if you want your script to
continue a run from where it left off. See the :doc:`run <run>` command
and its "upto" option for how to specify the run command so it does not
need to be changed either.
If a "%" character appears in the restart filename, LAMMPS expects a
set of multiple files to exist. The :doc:`restart <restart>` and

1
doc/utils/sphinx-config/false_positives.txt
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@ -2369,6 +2369,7 @@ nopreliminary
Nord
norder
Nordlund
noremap
normals
normx
normy