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md_software [2016/02/25 18:51]
sjabbari [LAMMPS]
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-====== Molecular Dynamics Simulation Sofware ====== 
  
-LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. 
- 
-LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. 
- 
-LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.  
- 
-For further information, please visit LAMMPS website. 
-==== LAMMPS ==== 
- 
-    * Module:  
-           
-          * ''intel/composer/2013_4_183'' 
-          * ''fftw/3.3.4/intel/composer2013-4.183/interlagos'' 
-          * ''mpi/intelmpi/5.1.0.079'' 
-          * ''software/lammps/7Dec15'' 
-    * Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.  
- 
-For further information, please visit LAMMPS website. 
-    * Binaries: ''lmp_mpi'' and ''lmp_serial'' plus those in the module's ''tools'' directory. 
-    * URL(s): [[http://lammps.sandia.gov/|lammps]] 
-    * Docs: 
-    * Example call(s): 
- 
- 
-     # To run lammps, you need to provide an input script for example "in.script" and also a a data file that your input script needs to read to start the simulation. In the following example, "16" is the number of cores requested. 
-  
-     mpirun  -n 16  -envall lmp_mpi < in.script 
-  <code bash> 
-   
-</code> 
- 
-    * LSF considerations (e.g. ''bsub'' example): an example of a script for job submission 
-      
-    *''#!/bin/bash'' 
-    * '' #BSUB -J lammps-test      #jobname '' 
-    * '' #BSUB -o test.log '' 
-    * ''#BSUB -e  test.err '' 
-    * '' #BSUB -q nodeshort '' 
-    * ''  #BSUB -W 300      #runtime in min '' 
-    * '' #BSUB -n  64 '' 
-    * ''mpirun  -n 64  -envall lmp_mpi <in.fene1000x10 '' 
- 
- 
- 
- 
-you can submit the job as ''bsub < lammps_job.sh '' 
-  
-    * Please download all the required modules, before starting to run lammps. 
- 
- 
- 
- 
- 
- 
-    * contact: ''sjabbari'' (Institut für Physik) 
- 
-==== HOOMD ==== 
- 
-    * Modules:    
-          * ''software/hoomd/1.0.5/gcc-4.6.2_cuda-6.5.14/nompi'' 
-          * ''software/hoomd/1.0.5/gcc-4.6.2_cuda-6.5.14/openmpi-1.8.7'' 
-          * ''software/hoomd/1.3.2/gcc-4.6.2_cuda-6.5.14/nompi'' 
-    * Description:  
-    * Binaries: ''hoomd'' and ''hoomd-config.sh'' plus those in the module's ''tools'' directory. 
-    * URL(s): [[https://codeblue.umich.edu/hoomd-blue/doc/index.html|HOOMD]] 
-    * Docs: [[https://codeblue.umich.edu/hoomd-blue/doc/page_quick_start.html|HOOMD-Tutorial]] 
-    * Example call(s): 
-  <code bash> 
-   
-</code> 
- 
-    * LSF considerations (e.g. ''bsub'' example): 
-    * contact: ''milchev'' (Institut für Physik) 
  • md_software.1456422700.txt.gz
  • Last modified: 2016/02/25 18:51
  • by sjabbari