147 lines
5.3 KiB
Plaintext
147 lines
5.3 KiB
Plaintext
.. index:: dump molfile
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dump molfile command
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====================
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Syntax
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""""""
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.. parsed-literal::
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dump ID group-ID molfile N file format path
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* ID = user-assigned name for the dump
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* group-ID = ID of the group of atoms to be imaged
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* molfile = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
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* N = dump every this many timesteps
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* file = name of file to write to
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* format = file format to be used
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* path = file path with plugins (optional)
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Examples
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""""""""
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.. parsed-literal::
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dump mf1 all molfile 10 melt1.xml hoomd
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dump mf2 all molfile 10 melt2-*.pdb pdb .
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dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile
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Description
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"""""""""""
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Dump a snapshot of atom coordinates and selected additional quantities
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to one or more files every N timesteps in one of several formats.
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Only information for atoms in the specified group is dumped. This
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specific dump style uses molfile plugins that are bundled with the
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`VMD <http://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
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analysis program. See :ref:`Section tools <vmd>` of the
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manual and the tools/lmp2vmd/README.txt file for more information
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about support in VMD for reading and visualizing native LAMMPS dump
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files.
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Unless the filename contains a * character, the output will be written
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to one single file with the specified format. Otherwise there will be
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one file per snapshot and the * will be replaced by the time step number
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when the snapshot is written.
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.. note::
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Because periodic boundary conditions are enforced only on
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timesteps when neighbor lists are rebuilt, the coordinates of an atom
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written to a dump file may be slightly outside the simulation box.
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The molfile plugin API has a few restrictions that have to be honored
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by this dump style: the number of atoms must not change, the atoms
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must be sorted, outside of the coordinates no change in atom properties
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(like type, mass, charge) will be recorded.
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----------
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The *format* keyword determines what format is used to write out the
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dump. For this to work, LAMMPS must be able to find and load a
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compatible molfile plugin that supports this format. Settings made via
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the :doc:`dump_modify <dump_modify>` command can alter per atom properties
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like element names.
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The *path* keyword determines which in directories. This is a "path"
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like other search paths, i.e. it can contain multiple directories
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separated by a colon (or semi-colon on windows). This keyword is
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optional and default to ".", the current directory.
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The *unwrap* option of the :doc:`dump_modify <dump_modify>` command allows
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coordinates to be written "unwrapped" by the image flags for each atom.
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Unwrapped means that if the atom has passed through a periodic boundary
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one or more times, the value is printed for what the coordinate would be
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if it had not been wrapped back into the periodic box. Note that these
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coordinates may thus be far outside the box size stored with the
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snapshot.
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----------
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Dumps are performed on timesteps that are a multiple of N (including
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timestep 0) and on the last timestep of a minimization if the
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minimization converges. Note that this means a dump will not be
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performed on the initial timestep after the dump command is invoked,
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if the current timestep is not a multiple of N. This behavior can be
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changed via the :doc:`dump_modify first <dump_modify>` command, which can
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be useful if the dump command is invoked after a minimization ended on
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an arbitrary timestep. N can be changed between runs by using the
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:doc:`dump_modify every <dump_modify>` command. The :doc:`dump_modify every <dump_modify>` command also allows a variable to be used to
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determine the sequence of timesteps on which dump files are written.
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----------
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Restrictions
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""""""""""""
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The *molfile* dump style is part of the USER-MOLFILE package. It is
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only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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Molfile plugins provide a consistent programming interface to read and
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write file formats commonly used in molecular simulations. The
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USER-MOLFILE package only provides the interface code, not the plugins.
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These can be obtained from a VMD installation which has to match the
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platform that you are using to compile LAMMPS for. By adding plugins
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to VMD, support for new file formats can be added to LAMMPS (or VMD
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or other programs that use them) without having to recompile the
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application itself. The plugins are installed in the directory:
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<VMDHOME>/plugins/<VMDARCH>/molfile
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.. note::
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while the programming interface (API) to the plugins is backward
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compatible, the binary interface (ABI) has been changing over time, so
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it is necessary to compile this package with the plugin header files
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from VMD that match the binary plugins. These header files in the
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directory: <VMDHOME>/plugins/include For convenience, the package ships
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with a set of header files that are compatible with VMD 1.9 and 1.9.1
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(June 2012)
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----------
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Related commands
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""""""""""""""""
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:doc:`dump <dump>`, :doc:`dump_modify <dump_modify>`, :doc:`undump <undump>`
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Default
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"""""""
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The default path is ".". All other properties have to be specified.
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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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