dump molfile command

Syntax

dump ID group-ID molfile N file format path
  • ID = user-assigned name for the dump
  • group-ID = ID of the group of atoms to be imaged
  • molfile = style of dump command (other styles atom or cfg or dcd or xtc or xyz or local or custom are discussed on the dump doc page)
  • N = dump every this many timesteps
  • file = name of file to write to
  • format = file format to be used
  • path = file path with plugins (optional)

Examples

dump mf1 all molfile 10 melt1.xml hoomd
dump mf2 all molfile 10 melt2-*.pdb pdb .
dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile

Description

Dump a snapshot of atom coordinates and selected additional quantities to one or more files every N timesteps in one of several formats. Only information for atoms in the specified group is dumped. This specific dump style uses molfile plugins that are bundled with the VMD molecular visualization and analysis program.

Unless the filename contains a * character, the output will be written to one single file with the specified format. Otherwise there will be one file per snapshot and the * will be replaced by the time step number when the snapshot is written.

Note

Because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box.

The molfile plugin API has a few restrictions that have to be honored by this dump style: the number of atoms must not change, the atoms must be sorted, outside of the coordinates no change in atom properties (like type, mass, charge) will be recorded.


The format keyword determines what format is used to write out the dump. For this to work, LAMMPS must be able to find and load a compatible molfile plugin that supports this format. Settings made via the dump_modify command can alter per atom properties like element names.

The path keyword determines which in directories. This is a “path” like other search paths, i.e. it can contain multiple directories separated by a colon (or semi-colon on windows). This keyword is optional and default to “.”, the current directory.

The unwrap option of the dump_modify command allows coordinates to be written “unwrapped” by the image flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what the coordinate would be if it had not been wrapped back into the periodic box. Note that these coordinates may thus be far outside the box size stored with the snapshot.


Dumps are performed on timesteps that are a multiple of N (including timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be changed via the dump_modify first command, which can be useful if the dump command is invoked after a minimization ended on an arbitrary timestep. N can be changed between runs by using the dump_modify every command. The dump_modify every command also allows a variable to be used to determine the sequence of timesteps on which dump files are written.


Restrictions

The molfile dump style is part of the USER-MOLFILE package. It is only enabled if LAMMPS was built with that package. See the Build package doc page for more info.

Molfile plugins provide a consistent programming interface to read and write file formats commonly used in molecular simulations. The USER-MOLFILE package only provides the interface code, not the plugins. These can be obtained from a VMD installation which has to match the platform that you are using to compile LAMMPS for. By adding plugins to VMD, support for new file formats can be added to LAMMPS (or VMD or other programs that use them) without having to recompile the application itself. The plugins are installed in the directory: <VMDHOME>/plugins/<VMDARCH>/molfile

Note

while the programming interface (API) to the plugins is backward compatible, the binary interface (ABI) has been changing over time, so it is necessary to compile this package with the plugin header files from VMD that match the binary plugins. These header files in the directory: <VMDHOME>/plugins/include For convenience, the package ships with a set of header files that are compatible with VMD 1.9 and 1.9.1 (June 2012)


Default

The default path is “.”. All other properties have to be specified.