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LAMMPS (view source)

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Combinations of potentials can be used for hybrid systems, e.g. water on metal, polymer/semiconductor interfaces, colloids in solution, ...
Combinations of potentials can be used for hybrid systems, e.g. water on metal, polymer/semiconductor interfaces, colloids in solution, ...


= Modules =
= Versions and packages =


Several versions of [http://lammps.sandia.gov/ LAMMPS] were installed on cvmfs and accessible on Compute Canada systems through [[Using modules|modules]]. To find the modules, use:
To see which versions of LAMMPS are installed on Compute Canada systems, run <code>module spider lammps</code>. See [[Using modules]] for more about <code>module</code> subcommands.
<code> module spider lammps</code> or <code>module -r spider '.*lammps.*'</code>  


The version of each module gives the date of the release of each version in the format: YYYYMMDD. The name of the module contains an attribute depending on the accelerators included in the module.
LAMMPS version numbers are based on their release dates, and have the format YYYYMMDD.
For each release installed, one or more modules are are available.
For example, the release of 31 March 2017 has three modules: 


For each release installed, one or more modules are are available. For example, the release of 31 March 2017 has 3 modules:   
* Built with MPI: <code>lammps/20170331</code>
* Built with USER-OMP support:  <code>lammps-omp/20170331</code>
* Built with USER-INTEL support: <code>lammps-user-intel/20170331</code>


* Version built with MPI: <code>lammps/20170331</code>
These versions are also available with GPU support.
* Version built with USER-OMP support:  <code>lmmps-omp/20170331</code>
In order to use the GPU-enabled version, load the [[CUDA]] module before loading the LAMMPS module:
* Version built with USER-INTEL support: <code>lammps-user-intel/20170331</code>


These versions are also available with GPU support. In order to load the GPU enabled version of LAMMPS, the <code>[[CUDA|cuda]]</code> module needs to be loaded first before loading the LAMMPS module:
$ module load cuda
$ module load lammps-omp/20170331


$ module load cuda
The name of the executable may differ from one version to another. All prebuilt versions on Compute Canada clusters have a symbolic link called <code>lmp</code>. It means that no matter which module you pick, you can execute LAMMPS by calling <code>lmp</code>.
$ module load lmmps-omp/20170331


The name of the executable may differ from one version to another. To figure out what is the name of the executable that correspond to a given module, do the following (example for lammps-omp/20170331):
If you wish to see the original name of the executable for a given module, list the files in the <code>${EBROOTLAMMPS}/bin</code> directory. For example:


  $ module load lmmps-omp/20170331
  $ module load lammps-omp/20170331
  $ ls ${EBROOTLAMMPS}/bin/
  $ ls ${EBROOTLAMMPS}/bin/
  lmp lmp_icc_openmpi
  lmp lmp_icc_openmpi


From this output, the executable is: '''lmp_icc_openmpi'''. Note that '''lmp''' is a symbolic link to the executable. For all versions installed on cvmfs, a symbolic link was added to each LAMMPS executable and it is called '''lmp'''. It means that no matter which module you pick, '''lmp''' will work as the executable for that module.
In this example the executable is <code>lmp_icc_openmpi</code>, and <code>lmp</code> is the symbolic link to it.  
 
The reason behind different versions for the same release is the difference in the packages included. The recent versions of  [http://lammps.sandia.gov/ LAMMPS] contain about 60 different packages that can be enabled when compiling the program. All the [http://lammps.sandia.gov/doc/Section_packages.html packages] are documented on the official web page of [http://lammps.sandia.gov/ LAMMPS] .
 
For each module installed on cvmfs, a file ''list-packages.txt '' is provided and gives a list of supported and non-supported packages for that particular module. The different versions for one release mentioned above come from the fact one can not put all available packages in one binary. If for some reason, your simulation does not work with one module, it is more likely related to the fact that the corresponding package was not included.


To see or know more about the supported packages on a given module , do the following:
The reason there are different modules for the same release is the difference in the ''packages'' included. Recent versions of LAMMPS contain about 60 different packages that can be enabled or disabled when compiling the program. Not all packages can be enabled in a single executable. All [https://lammps.sandia.gov/doc/Packages.html packages] are documented on the official web page.


* First load a particular module of LAMMPS (use <code>module -r spider '.*lammps.*'</code> to see how to load a particular module).
For each LAMMPS module we provide a file <code>list-packages.txt</code> listing the enabled ("Supported") and disabled ("Not Supported") packages. Once you have loaded a particular module, run <code>cat ${EBROOTLAMMPS}/list-packages.txt</code> to see the contents.
* Then, execute the command: <code>cat ${EBROOTLAMMPS}/list-packages.txt</code>  


For more information on Environment Modules, please refer to the [[Using modules]] page.
If your simulation does not work with one module, it may be related to the fact that the necessary package was not included.


= Scripts for running LAMMPS =
= Scripts for running LAMMPS =
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