The file replicate.c takes a LAMMPS data file and replicates it into a -larger system. The syntax for running the tool is +
The amber2lmp sub-directory contain two Python scripts for converting +files back-and-forth between the AMBER MD code and LAMMPS. See the +README file in amber2lmp for more information.
-replicate options < infile > outfile --
See the top of the replicate.c file for a discussion of the options. -This tool is used by some of the LAMMPS benchmarks -for creating larger systems to run scaled-size problems on multiple -processors. -
-The file restart2data.cpp converts a binary LAMMPS restart file into -an ASCII data file. The syntax for running the tool is -
-restart2data restart-file data-file --
This tool must be compiled on a platform that can read the binary file -created by a LAMMPS run, since binary files are not compatible across -all platforms. -
-Note that a text data file has less precision than a binary restart -file. Hence, continuing a run from a converted data file will -typically not conform as closely to a previous run as will restarting -from a binary restart file. -
-If a "%" appears in the specified restart-file, the tool expects a set -of multiple files to exist. See the restart and -write_restart commands for info on how such sets -of files are written by LAMMPS, and how the files are named. +
These tools were written by Keir Novik while he was at Queen Mary +University of London. Keir is no longer there and cannot support +these tools which are out-of-date with respect to the current LAMMPS +version (and maybe with respect to AMBER as well). Since we don't use +these tools at Sandia, you'll need to experiment with them and make +necessary modifications yourself.
The file data2xmovie.c converts a LAMMPS data file into a snapshot -suitable for visualizing with the xmovie tool, as if it had -been output with a dump command from LAMMPS itself. The syntax for -running the tool is -
-data2xmovie options < infile > outfile --
See the top of the data2xmovie.c file for a discussion of the options. -
-The file chain.f creates a LAMMPS data file containing bead-spring -polymer chains and/or monomer solvent atoms. It uses a text file -containing chain definition parameters as an input. The created -chains and solvent atoms can strongly overlap, so LAMMPS needs to run -the system initially with a "soft" pair potential to un-overlap it. -The syntax for running the tool is -
-chain < def.chain > data.file --
See the def.chain or def.chain.ab files in the tools directory for -examples of definition files. This tool was used to create the -system for the chain benchmark. -
-The file micelle2d.f creates a LAMMPS data file containing short lipid -chains in a monomer solution. It uses a text file containing lipid -definition parameters as an input. The created molecules and solvent -atoms can strongly overlap, so LAMMPS needs to run the system -initially with a "soft" pair potential to un-overlap it. The syntax -for running the tool is -
-micelle2d < def.micelle2d > data.file --
See the def.micelle2d file in the tools directory for an example of a -definition file. This tool was used to create the system for the -micelle example. -
-The xmovie tool is an X-based visualization package that can read -LAMMPS dump files and animate them. It is in its own sub-directory -with the tools directory. You may need to modify its Makefile so that -it can find the appropriate X libraries to link against. -
-The syntax for running xmovie is -
-xmovie options dump.file1 dump.file2 ... --
If you just type "xmovie" you will see a list of options. Note that -by default, LAMMPS dump files are in scaled coordinates, so you -typically need to use the -scale option with xmovie. When xmovie runs -it opens a visualization window and a control window. The control -options are straightforward to use. -
-Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he -spent a summer at Sandia. It displays 2d projections of a 3d domain. -While simple in design, it is an amazingly fast program that can -render large numbers of atoms very quickly. It's a useful tool for -debugging LAMMPS input and output and making sure your simulation is -doing what you think it should. The animations on the Examples page -of the LAMMPS WWW site were created with xmovie. -
-I've lost contact with Mike, so I hope he's comfortable with us -distributing his great tool! -
-The ch2lmp sub-directory contains tools for converting files @@ -204,34 +106,33 @@ and Paul Crozier (pscrozi at sandia.gov) at Sandia.
The msi2lmp sub-directory contains a tool for creating LAMMPS input -data files from Accelrys's Insight MD code (formerly MSI/Biosysm and -its Discover MD code). See the README file for more information. +
The file chain.f creates a LAMMPS data file containing bead-spring +polymer chains and/or monomer solvent atoms. It uses a text file +containing chain definition parameters as an input. The created +chains and solvent atoms can strongly overlap, so LAMMPS needs to run +the system initially with a "soft" pair potential to un-overlap it. +The syntax for running the tool is
-This tool was written by John Carpenter (Cray), Michael Peachey -(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic -(jec at mayo.edu), but still fields questions about the tool. -
-This tool may be out-of-date with respect to the current LAMMPS and -Insight versions. Since we don't use it at Sandia, you'll need to -experiment with it yourself. +
chain < def.chain > data.file ++
See the def.chain or def.chain.ab files in the tools directory for +examples of definition files. This tool was used to create the +system for the chain benchmark.
The amber2lmp sub-directory contain two Python scripts for converting -files back-and-forth between the AMBER MD code and LAMMPS. See the -README file in amber2lmp for more information. +
The file data2xmovie.c converts a LAMMPS data file into a snapshot +suitable for visualizing with the xmovie tool, as if it had +been output with a dump command from LAMMPS itself. The syntax for +running the tool is
-These tools were written by Keir Novik while he was at Queen Mary -University of London. Keir is no longer there and cannot support -these tools which are out-of-date with respect to the current LAMMPS -version (and maybe with respect to AMBER as well). Since we don't use -these tools at Sandia, you'll need to experiment with them and make -necessary modifications yourself. +
data2xmovie options < infile > outfile ++
See the top of the data2xmovie.c file for a discussion of the options.
The matlab sub-directory contains several MATLAB scripts for +post-processing LAMMPS output. The scripts include readers for log +and dump files, a reader for radial distribution output from the fix +rdf command, a reader for EAM potential files, and a +converter that reads LAMMPS dump files and produces CFG files that can +be visualized with the +AtomEye visualizer. +
+See the README.pdf file for more information. +
+These scripts were written by Arun Subramaniyan at Purdue Univ +(asubrama at purdue.edu). +
+ + +The file micelle2d.f creates a LAMMPS data file containing short lipid +chains in a monomer solution. It uses a text file containing lipid +definition parameters as an input. The created molecules and solvent +atoms can strongly overlap, so LAMMPS needs to run the system +initially with a "soft" pair potential to un-overlap it. The syntax +for running the tool is +
+micelle2d < def.micelle2d > data.file ++
See the def.micelle2d file in the tools directory for an example of a +definition file. This tool was used to create the system for the +micelle example. +
+The msi2lmp sub-directory contains a tool for creating LAMMPS input +data files from Accelrys's Insight MD code (formerly MSI/Biosysm and +its Discover MD code). See the README file for more information. +
+This tool was written by John Carpenter (Cray), Michael Peachey +(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic +(jec at mayo.edu), but still fields questions about the tool. +
+This tool may be out-of-date with respect to the current LAMMPS and +Insight versions. Since we don't use it at Sandia, you'll need to +experiment with it yourself. +
+The file replicate.c takes a LAMMPS data file and replicates it into a +larger system. The syntax for running the tool is +
+replicate options < infile > outfile ++
See the top of the replicate.c file for a discussion of the options. +This tool is used by some of the LAMMPS benchmarks +for creating larger systems to run scaled-size problems on multiple +processors. +
+The file restart2data.cpp converts a binary LAMMPS restart file into +an ASCII data file. The syntax for running the tool is +
+restart2data restart-file data-file ++
This tool must be compiled on a platform that can read the binary file +created by a LAMMPS run, since binary files are not compatible across +all platforms. +
+Note that a text data file has less precision than a binary restart +file. Hence, continuing a run from a converted data file will +typically not conform as closely to a previous run as will restarting +from a binary restart file. +
+If a "%" appears in the specified restart-file, the tool expects a set +of multiple files to exist. See the restart and +write_restart commands for info on how such sets +of files are written by LAMMPS, and how the files are named. +
+The thermo_extract tool reads one of more LAMMPS log files and @@ -286,4 +276,34 @@ details.
This tool was written by Vikas Varshney at Wright Patterson AFB (vikas.varshney at gmail.com).
+The xmovie tool is an X-based visualization package that can read +LAMMPS dump files and animate them. It is in its own sub-directory +with the tools directory. You may need to modify its Makefile so that +it can find the appropriate X libraries to link against. +
+The syntax for running xmovie is +
+xmovie options dump.file1 dump.file2 ... ++
If you just type "xmovie" you will see a list of options. Note that +by default, LAMMPS dump files are in scaled coordinates, so you +typically need to use the -scale option with xmovie. When xmovie runs +it opens a visualization window and a control window. The control +options are straightforward to use. +
+Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he +spent a summer at Sandia. It displays 2d projections of a 3d domain. +While simple in design, it is an amazingly fast program that can +render large numbers of atoms very quickly. It's a useful tool for +debugging LAMMPS input and output and making sure your simulation is +doing what you think it should. The animations on the Examples page +of the LAMMPS WWW site were created with xmovie. +
+I've lost contact with Mike, so I hope he's comfortable with us +distributing his great tool! +