forked from lijiext/lammps
200 lines
7.4 KiB
Plaintext
200 lines
7.4 KiB
Plaintext
.. index:: restart
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restart command
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===============
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Syntax
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""""""
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.. parsed-literal::
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restart 0
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restart N root keyword value ...
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restart N file1 file2 keyword value ...
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* N = write a restart file every this many timesteps
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* N can be a variable (see below)
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* root = filename to which timestep # is appended
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* file1,file2 = two full filenames, toggle between them when writing file
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* zero or more keyword/value pairs may be appended
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* keyword = *fileper* or *nfile*
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.. parsed-literal::
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*fileper* arg = Np
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Np = write one file for every this many processors
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*nfile* arg = Nf
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Nf = write this many files, one from each of Nf processors
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Examples
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""""""""
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.. parsed-literal::
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restart 0
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restart 1000 poly.restart
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restart 1000 poly.restart.mpiio
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restart 1000 restart.*.equil
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restart 10000 poly.%.1 poly.%.2 nfile 10
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restart v_mystep poly.restart
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Description
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"""""""""""
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Write out a binary restart file with the current state of the
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simulation every so many timesteps, in either or both of two modes, as
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a run proceeds. A value of 0 means do not write out any restart
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files. The two modes are as follows. If one filename is specified, a
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series of filenames will be created which include the timestep in the
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filename. If two filenames are specified, only 2 restart files will
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be created, with those names. LAMMPS will toggle between the 2 names
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as it writes successive restart files.
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Note that you can specify the restart command twice, once with a
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single filename and once with two filenames. This would allow you,
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for example, to write out archival restart files every 100000 steps
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using a single filenname, and more frequent temporary restart files
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every 1000 steps, using two filenames. Using restart 0 will turn off
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both modes of output.
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Similar to :doc:`dump <dump>` files, the restart filename(s) can contain
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two wild-card characters.
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If a "*" appears in the single filename, it is replaced with the
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current timestep value. This is only recognized when a single
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filename is used (not when toggling back and forth). Thus, the 3rd
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example above creates restart files as follows: restart.1000.equil,
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restart.2000.equil, etc. If a single filename is used with no "*",
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then the timestep value is appended. E.g. the 2nd example above
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creates restart files as follows: poly.restart.1000,
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poly.restart.2000, etc.
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If a "%" character appears in the restart filename(s), then one file
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is written for each processor and the "%" character is replaced with
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the processor ID from 0 to P-1. An additional file with the "%"
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replaced by "base" is also written, which contains global information.
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For example, the files written on step 1000 for filename restart.%
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would be restart.base.1000, restart.0.1000, restart.1.1000, ...,
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restart.P-1.1000. This creates smaller files and can be a fast mode
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of output and subsequent input on parallel machines that support
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parallel I/O. The optional *fileper* and *nfile* keywords discussed
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below can alter the number of files written.
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The restart file can also be written in parallel as one large binary
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file via the MPI-IO library, which is part of the MPI standard for
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versions 2.0 and above. Using MPI-IO requires two steps. First,
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build LAMMPS with its MPIIO package installed, e.g.
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.. parsed-literal::
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make yes-mpiio # installs the MPIIO package
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make g++ # build LAMMPS for your platform
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Second, use a restart filename which contains ".mpiio". Note that it
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does not have to end in ".mpiio", just contain those characters.
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Unlike MPI-IO dump files, a particular restart file must be both
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written and read using MPI-IO.
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Restart files are written on timesteps that are a multiple of N but
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not on the first timestep of a run or minimization. You can use the
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:doc:`write_restart <write_restart>` command to write a restart file
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before a run begins. A restart file is not written on the last
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timestep of a run unless it is a multiple of N. A restart file is
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written on the last timestep of a minimization if N > 0 and the
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minimization converges.
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Instead of a numeric value, N can be specifed as an :doc:`equal-style variable <variable>`, which should be specified as v_name, where
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name is the variable name. In this case, the variable is evaluated at
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the beginning of a run to determine the next timestep at which a
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restart file will be written out. On that timestep, the variable will
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be evaluated again to determine the next timestep, etc. Thus the
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variable should return timestep values. See the stagger() and
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logfreq() and stride() math functions for :doc:`equal-style variables <variable>`, as examples of useful functions to use in
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this context. Other similar math functions could easily be added as
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options for :doc:`equal-style variables <variable>`.
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For example, the following commands will write restart files
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every step from 1100 to 1200, and could be useful for debugging
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a simulation where something goes wrong at step 1163:
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.. parsed-literal::
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variable s equal stride(1100,1200,1)
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restart v_s tmp.restart
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----------
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See the :doc:`read_restart <read_restart>` command for information about
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what is stored in a restart file.
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Restart files can be read by a :doc:`read_restart <read_restart>`
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command to restart a simulation from a particular state. Because the
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file is binary (to enable exact restarts), it may not be readable on
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another machine. In this case, you can use the :ref:`-r command-line switch <start_7>` to convert a restart file to a data
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file.
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.. note::
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Although the purpose of restart files is to enable restarting a
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simulation from where it left off, not all information about a
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simulation is stored in the file. For example, the list of fixes that
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were specified during the initial run is not stored, which means the
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new input script must specify any fixes you want to use. Even when
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restart information is stored in the file, as it is for some fixes,
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commands may need to be re-specified in the new input script, in order
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to re-use that information. See the :doc:`read_restart <read_restart>`
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command for information about what is stored in a restart file.
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----------
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The optional *nfile* or *fileper* keywords can be used in conjunction
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with the "%" wildcard character in the specified restart file name(s).
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As explained above, the "%" character causes the restart file to be
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written in pieces, one piece for each of P processors. By default P =
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the number of processors the simulation is running on. The *nfile* or
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*fileper* keyword can be used to set P to a smaller value, which can
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be more efficient when running on a large number of processors.
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The *nfile* keyword sets P to the specified Nf value. For example, if
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Nf = 4, and the simulation is running on 100 processors, 4 files will
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be written, by processors 0,25,50,75. Each will collect information
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from itself and the next 24 processors and write it to a restart file.
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For the *fileper* keyword, the specified value of Np means write one
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file for every Np processors. For example, if Np = 4, every 4th
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processor (0,4,8,12,etc) will collect information from itself and the
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next 3 processors and write it to a restart file.
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----------
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Restrictions
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""""""""""""
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To write and read restart files in parallel with MPI-IO, the MPIIO
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package must be installed.
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Related commands
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""""""""""""""""
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:doc:`write_restart <write_restart>`, :doc:`read_restart <read_restart>`
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Default
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"""""""
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.. parsed-literal::
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restart 0
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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