From 99157504bbdedb51b0369a703791604936849f02 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 13 Jun 2012 16:42:24 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8281 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/dump_molfile.html | 137 ++++++++++++++++++++++++++++++++++++++++++ doc/dump_molfile.txt | 126 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 263 insertions(+) create mode 100644 doc/dump_molfile.html create mode 100644 doc/dump_molfile.txt diff --git a/doc/dump_molfile.html b/doc/dump_molfile.html new file mode 100644 index 0000000000..daa53a41aa --- /dev/null +++ b/doc/dump_molfile.html @@ -0,0 +1,137 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

dump molfile command +

+

Syntax: +

+
dump ID group-ID molfile N file format path 
+
+ +

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. See Section tools of the +manual and the tools/lmp2vmd/README.txt file for more information about +support in VMD for reading and visualizing native LAMMPS dump files. +

+

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. +

+

IMPORTANT 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 Making +LAMMPS section 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: +/plugins//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: /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) +

+
+ +

Related commands: +

+

dump, dump_modify, undump +

+

Default: +

+

The default path is ".". All other properties have to be specified. +

+ diff --git a/doc/dump_molfile.txt b/doc/dump_molfile.txt new file mode 100644 index 0000000000..65f055f1e2 --- /dev/null +++ b/doc/dump_molfile.txt @@ -0,0 +1,126 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +dump molfile command :h3 + +[Syntax:] + +dump ID group-ID molfile N file format path :pre + +ID = user-assigned name for the dump :ulb,l +group-ID = ID of the group of atoms to be imaged :l +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"_dump.html doc page) :l +N = dump every this many timesteps :l +file = name of file to write to :l +format = file format to be used :l +path = file path with plugins (optional) :l +:ule + +[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 :pre + +[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"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and +analysis program. See "Section tools"_Section_tools.html#vmd of the +manual and the tools/lmp2vmd/README.txt file for more information about +support in VMD for reading and visualizing native LAMMPS dump files. + +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. + +IMPORTANT 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. + +:line + +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"_dump_modify.html 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"_dump_modify.html 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. + +:line + +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"_dump_modify.html 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"_dump_modify.html command. The "dump_modify +every"_dump_modify.html command also allows a variable to be used to +determine the sequence of timesteps on which dump files are written. + +:line + +[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 "Making +LAMMPS"_Section_start.html#start_3 section 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: +/plugins//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: /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) + +:line + +[Related commands:] + +"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html + +[Default:] + +The default path is ".". All other properties have to be specified. +