write_restart command

Syntax

write_restart file keyword value ...

  • file = name of file to write restart information to

  • zero or more keyword/value pairs may be appended

  • keyword = fileper or nfile

    fileper arg = Np
  Np = write one file for every this many processors
nfile arg = Nf
  Nf = write this many files, one from each of Nf processors

Examples

write_restart restart.equil
write_restart restart.equil.mpiio
write_restart poly.%.* nfile 10

Description

Write a binary restart file of the current state of the simulation.

During a long simulation, the restart command is typically used to output restart files periodically. The write_restart command is useful after a minimization or whenever you wish to write out a single current restart file.

Similar to dump files, the restart filename can contain two wild-card characters. If a “*” appears in the filename, it is replaced with the current timestep value. If a “%” character appears in the filename, then one file is written by each processor and the “%” character is replaced with the processor ID from 0 to P-1. An additional file with the “%” replaced by “base” is also written, which contains global information. For example, the files written for filename restart.% would be restart.base, restart.0, restart.1, … restart.P-1. This creates smaller files and can be a fast mode of output and subsequent input on parallel machines that support parallel I/O. The optional fileper and nfile keywords discussed below can alter the number of files written.

The restart file can also be written in parallel as one large binary file via the MPI-IO library, which 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.

cmake . -DPKG_MPIIO=on  # enables the MPIIO package in the build folder
cmake --build .         # recompiles LAMMPS with the package code included

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.

Restart files can be read by a read_restart command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on another machine. In this case, you can use the -r command-line switch to convert a restart file to a data file.

Note

Although the purpose of restart files is to enable restarting a simulation from where it left off, not all information about a simulation is stored in the file. For example, the list of fixes that were specified during the initial run is not stored, which means the new input script must specify any fixes you want to use. Even when restart information is stored in the file, as it is for some fixes, commands may need to be re-specified in the new input script, in order to re-use that information. Details are usually given in the documentation of the respective command. Also, see the read_restart command for general information about what is stored in a restart file.

The optional nfile or fileper keywords can be used in conjunction with the “%” wildcard character in the specified restart file name. As explained above, the “%” character causes the restart file to be written in pieces, one piece for each of P processors. By default P = the number of processors the simulation is running on. The nfile or fileper keyword can be used to set P to a smaller value, which can be more efficient when running on a large number of processors.

The nfile keyword sets P to the specified Nf value. For example, if Nf = 4, and the simulation is running on 100 processors, 4 files will be written, by processors 0,25,50,75. Each will collect information from itself and the next 24 processors and write it to a restart file.

For the fileper keyword, the specified value of Np means write one file for every Np processors. For example, if Np = 4, every fourth processor (0,4,8,12,etc) will collect information from itself and the next 3 processors and write it to a restart file.

Restrictions

This command requires inter-processor communication to migrate atoms before the restart file is written. This means that your system must be ready to perform a simulation before using this command (force fields setup, atom masses initialized, etc).

To write and read restart files in parallel with MPI-IO, the MPIIO package must be installed.

Default

none