diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst index 4d68167560..b593fd51ae 100644 --- a/doc/src/read_restart.rst +++ b/doc/src/read_restart.rst @@ -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 ` command. The partitioning can later be -changed by the :doc:`balance ` or :doc:`fix balance ` commands. +changed by the :doc:`balance ` or :doc:`fix balance +` commands. .. note:: - Normally, restart files are written by the - :doc:`restart ` or :doc:`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 ` or these cases. Certain fixes will not restart exactly, though they should provide -statistically similar results. These include :doc:`fix shake ` and :doc:`fix langevin `. +statistically similar results. These include :doc:`fix shake +` and :doc:`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 ` 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 ` to convert a restart file to a data file. +machines. In this case, you can use the :doc:`-restart command-line +switch ` to convert a restart file to a data file. -Similar to how restart files are written (see the -:doc:`write_restart ` and :doc:`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 ` 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 +` and :doc:`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 ` 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 ` and diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index b42cff262a..cce6e92d05 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2369,6 +2369,7 @@ nopreliminary Nord norder Nordlund +noremap normals normx normy