Difference between revisions of "LAMMPS"
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[[Category:Software]][[Category:Molecular Dynamics]] | [[Category:Software]][[Category:Molecular Dynamics]] | ||
{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
| − | |{{#vardefine:app| | + | |{{#vardefine:app|LAMMPS}} |
|{{#vardefine:url|http://lammps.sandia.gov}} | |{{#vardefine:url|http://lammps.sandia.gov}} | ||
| − | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> |
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
|{{#vardefine:pbs|1}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|1}} <!--Enable PBS script wiki page link--> | ||
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<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_LAMMPS_BIN - executable directory | * HPC_LAMMPS_BIN - executable directory | ||
* HPC_LAMMPS_LIB - library directory | * HPC_LAMMPS_LIB - library directory | ||
<!--Additional--> | <!--Additional--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | To execute lammps binaries set up the appropriate environment variables and execute them with srun using the pmix level corresponding to the openmpi version used to build the binary. E.g. the command will look similar to | |
| + | srun --mpi=pmix_v3 $LAMMPS -sf gpu -pk gpu 2 -var x 2 -var y 7 -var z 7 < in.$job | ||
| + | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| − | {{#if: {{#var: pbs}}|== | + | {{#if: {{#var: pbs}}|==Job Script Examples== |
| − | See the [[{{PAGENAME}} | + | See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} job script examples.|}} |
{{#if: {{#var: policy}}|==Usage Policy== | {{#if: {{#var: policy}}|==Usage Policy== | ||
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
Revision as of 21:21, 6 December 2019
Description
LAMMPS , Large-scale Atomic/Molecular Massively Parallel Simulator, is a molecular dynamic simulator that models an ensemble of particles in liquid, solid, or gaseous state. It is a open source software, written in C++ and developed at Sandia laboratory. It can be used to model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using various force fields and boundary conditions.
Environment Modules
Run module spider LAMMPS to find out what environment modules are available for this application.
System Variables
- HPC_LAMMPS_DIR - installation directory
- HPC_LAMMPS_BIN - executable directory
- HPC_LAMMPS_LIB - library directory
Additional Information
To execute lammps binaries set up the appropriate environment variables and execute them with srun using the pmix level corresponding to the openmpi version used to build the binary. E.g. the command will look similar to
srun --mpi=pmix_v3 $LAMMPS -sf gpu -pk gpu 2 -var x 2 -var y 7 -var z 7 < in.$job
Job Script Examples
See the LAMMPS_Job_Scripts page for LAMMPS job script examples.