Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/read_restart.html
979c5746a06cefficient_neuronet

Last Change
Raw File

read_restart.html
View Options

<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>read_restart command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>read_restart file
</PRE>
<UL><LI>file = name of binary restart file to read in
</UL>
<P><B>Examples:</B>
</P>
<PRE>read_restart save.10000
read_restart restart.*
read_restart restart.*.mpiio
read_restart poly.*.%
</PRE>
<PRE>
</PRE>
<P><B>Description:</B>
</P>
<P>Read in a previously saved simulation from a restart file. This
allows continuation of a previous run. Information about what is
stored in a restart file is given below.
</P>
<P>Restart files are saved in binary format to enable exact restarts,
meaning that the trajectories of a restarted run will precisely match
those produced by the original run had it continued on.
</P>
<P>Several things can prevent exact restarts due to round-off effects, in
which case the trajectories in the 2 runs will slowly diverge. These
include running on a different number of processors or changing
certain settings such as those set by the <A HREF = "newton.html">newton</A> or
<A HREF = "processors.html">processors</A> commands. LAMMPS will issue a warning in
these cases.
</P>
<P>Certain fixes will not restart exactly, though they should provide
statistically similar results. These include <A HREF = "fix_shake.html">fix
shake</A> and <A HREF = "fix_langevin.html">fix langevin</A>.
</P>
<P>Certain pair styles will not restart exactly, though they should
provide statistically similar results. This is because the forces
they compute depend on atom velocities, which are used at half-step
values every timestep when forces are computed. When a run restarts,
forces are initially evaluated with a full-step velocity, which is
different than if the run had continued. These pair styles include
<A HREF = "pair_gran.html">granular pair styles</A>, <A HREF = "pair_dpd.html">pair dpd</A>, and
<A HREF = "pair_lubricate.html">pair lubricate</A>.
</P>
<P>If a restarted run is immediately different than the run which
produced the restart file, it could be a LAMMPS bug, so consider
<A HREF = "Section_errors.html#err_2">reporting it</A> if you think the behavior is
wrong.
</P>
<P>Because restart files are binary, they may not be portable to other
machines. In this case, you can use the <A HREF = "Section_start.html#start_7">-r command-line
switch</A> to convert a restart file to a data
file.
</P>
<P>Similar to how restart files are written (see the
<A HREF = "write_restart.html">write_restart</A> and <A HREF = "restart.html">restart</A>
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 <A HREF = "run.html">run</A> command and its "upto" option for how to specify
the run command so it doesn't need to be changed either.
</P>
<P>If a "%" character appears in the restart filename, LAMMPS expects a
set of multiple files to exist. The <A HREF = "restart.html">restart</A> and
<A HREF = "write_restart.html">write_restart</A> commands explain how such sets are
created. Read_restart will first read a filename where "%" is
replaced by "base". This file tells LAMMPS how many processors
created the set and how many files are in it. Read_restart then reads
the additional files. For example, if the restart file was specified
as save.% when it was written, then read_restart reads the files
save.base, save.0, save.1, ... save.P-1, where P is the number of
processors that created the restart file.
</P>
<P>Note that P could be the total number of processors in the previous
simulation, or some subset of those processors, if the <I>fileper</I> or
<I>nfile</I> options were used when the restart file was written; see the
<A HREF = "restart.html">restart</A> and <A HREF = "write_restart.html">write_restart</A> commands
for details. The processors in the current LAMMPS simulation share
the work of reading these files; each reads a roughly equal subset of
the files. The number of processors which created the set can be
different the number of processors in the current LAMMPS simulation.
This can be a fast mode of input on parallel machines that support
parallel I/O.
</P>
<P>A restart file can also be read in parallel as one large binary file
via the MPI-IO library, assuming it was also written with MPI-IO.
MPI-IO is part of the MPI standard for versions 2.0 and above. Using
MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
installed, e.g.
</P>
<PRE>make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform
</PRE>
<P>Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters.
Unlike MPI-IO dump files, a particular restart file must be both
written and read using MPI-IO.
</P>
<HR>
<P>A restart file stores the following information about a simulation:
units and atom style, simulation box size and shape and boundary
settings, group definitions, per-type atom settings such as mass,
per-atom attributes including their group assignments and molecular
topology attributes, force field styles and coefficients, and
<A HREF = "special_bonds.html">special_bonds</A> settings. This means that commands
for these quantities do not need to be re-specified in the input
script that reads the restart file, though you can redefine settings
after the restart file is read.
</P>
<P>One exception is that some pair styles do not store their info in
restart files. Typically these are many-body potentials which read
their parameters from separate files; you need to re-specify the <A HREF = "pair_style.html">pair
style</A> and <A HREF = "pair_coeff.html">pair coeff</A> commands in
your restart input script. The doc pages for individual pair styles
note if this is the case. This is also true of bond_style hybrid (and
angle_style, dihedral_style, improper_style hybrid).
</P>
<P>All settings made by the <A HREF = "pair_modify.html">pair_modify</A> command, such
as the shift and tail settings, are stored in the restart file with
the pair style. The one exception is the <A HREF = "pair_modify.html">pair_modify
compute</A> setting is not stored, since it is typically
only used for debugging purposes.
</P>
<P>Information about <A HREF = "kspace_style.html">kspace_style</A> settings are not
stored in the restart file. Hence if you wish to use an Ewald or PPPM
solver, these commands must be re-issued after the restart file is
read.
</P>
<P>The list of <A HREF = "fix.html">fixes</A> used for a simulation is not stored in
the restart file. This means the new input script should specify all
fixes it will use. Note that some fixes store an internal "state"
which is written to the restart file. This allows the fix to continue
on with its calculations in a restarted simulation. To re-enable such
a fix, the fix command in the new input script must use the same
fix-ID and group-ID as was used in the input script that wrote the
restart file. If a match is found, LAMMPS prints a message indicating
that the fix is being re-enabled. If no match is found before the
first run or minimization is performed by the new script, the "state"
information for the saved fix is discarded. See the doc pages for
individual fixes for info on which ones can be restarted in this
manner.
</P>
<P>Bond interactions (angle, etc) that have been turned off by the <A HREF = "fix_shake.html">fix
shake</A> or <A HREF = "delete_bonds.html">delete_bonds</A> command will
be written to a restart file as if they are turned on. This means
they will need to be turned off again in a new run after the restart
file is read.
</P>
<P>Bonds that are broken (e.g. by a bond-breaking potential) are written
to the restart file as broken bonds with a type of 0. Thus these
bonds will still be broken when the restart file is read.
</P>
<P>IMPORTANT NOTE: No other information is stored in the restart file.
This means that an input script that reads a restart file should
specify settings for quantities like <A HREF = "timestep.html">timestep size</A>,
<A HREF = "thermo_style.html">thermodynamic</A>, <A HREF = "neighbor.html">neighbor list</A>
criteria including settings made via the
<A HREF = "neigh_modify.html">neigh_modify</A> comand, <A HREF = "dump.html">dump</A> file
output, <A HREF = "region.html">geometric regions</A>, etc.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>To write and read restart files in parallel with MPI-IO, the MPIIO
package must be installed.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "read_data.html">read_data</A>, <A HREF = "read_dump.html">read_dump</A>,
<A HREF = "write_restart.html">write_restart</A>, <A HREF = "restart.html">restart</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
c4science · Help