Daily Archives: January 24, 2012

Gulp 4.0

Biochemistry

General Information

GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons. Analytic derivatives are included up to at least second order for most force fields, and to third order for many.

How to Use

First, before you use it, be aware of its usage conditions.

send_gulp

  • To send GULP to the queue system  use the send_gulp utility. When executed,
    shows the command syntax, which is summarized below:
  • send_gulp JOBNAME NODES PROCS_PER_NODE TIME [ MEM ] [``Other queue options'' ]
JOBNAME: Is the  name of the input with extension.
NODES: Number of nodes.
PROCS: Number of  processors.
TIME: Time requested to the queue system, format hh:mm:ss.
MEM: Optional. Memory in Gb ( It will used 1GB/core if not set).
[``Other Torque Options'' ] Optional. There is the possibility to pass more variables to the queuing system.
See examples below.   More information about this options

Examples

We send the GULP input job1 to 1 node, 4 processors on that node, with a requested time of 4 hours :

send_gulp job1.gin 1 4 04:00:00

We send job2  to 2 compuation nodes, 8 processors on each node, with a requested time of 192 hours, 8 GB of RAM and to start running after work 1234.arinab is finished:

send_gulp job2.gin 2 8 192:00:00 8 ``-W depend=afterany:1234'

We  send the input job3 to 4 nodes and 4 processors on each node, with arequested time of 200:00:00 hours, 2 GB of RAM and we request to be send an email at the beginning and end of the calculation to the direction specified.

send_gulp job.gin 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''

send_gulp command copies the contents of the directory from which the job is sent to /scratch or / gscratch, if we use 2 or more nodes. And there is where the calculation is done.

Jobs Monitoring

To facilitate monitoring and/or control of the GULP calculations, you can use remote_vi

remote_vi JOBID

It show us the *.out file  (only if it was sent using send_lmp).

More information

http://projects.ivec.org/gulp/

LAMMPS

Biochemistry, MM/MD @en, Software @en

LAMMPS (“Large-scale Atomic/Molecular Massively Parallel Simulator”) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of MPI for parallel communication and is a free open-source code, distributed under the terms of the GNU General Public License.
LAMMPS was originally developed under a Cooperative Research and Development Agreement (CRADA) between two laboratories from United States Department of Energy and three other laboratories from private sector firms. It is currently maintained and distributed by researchers at the Sandia National Laboratories. (Taken from Wikipedia). Jun-05-2019 version.

General Information

LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions.

In the most general sense, LAMMPS integrates Newton’s equations of motion for collections of atoms, molecules, or macroscopic particles that interact via short- or long-range forces with a variety of initial and/or boundary conditions. For computational efficiency LAMMPS uses neighbor lists to keep track of nearby particles. The lists are optimized for systems with particles that are repulsive at short distances, so that the local density of particles never becomes too large. On parallel machines, LAMMPS uses spatial-decomposition techniques to partition the simulation domain into small 3d sub-domains, one of which is assigned to each processor. Processors communicate and store “ghost” atom information for atoms that border their sub-domain. LAMMPS is most efficient (in a parallel sense) for systems whose particles fill a 3d rectangular box with roughly uniform density. Papers with technical details of the algorithms used in LAMMPS are listed in this section.

How to Use

send_lmp

  • To send LAMMPS to the queue system  use the send_lmp utility. When executed,
    shows the command syntax, which is summarized below:
  • send_lmp JOBNAME NODES PROCS_PER_NODE TIME [ MEM ] [``Other queue options'' ]
    JOBNAME: Is the  name of the input with extension.
    NODES: Number of nodes.
    PROCS: Number of  processors.
    TIME: Time requested to the queue system, format hh:mm:ss.
    MEM: Optional. Memory in Gb ( It will used 1GB/core if not set).
    [``Other Torque Options'' ] Optional. There is the possibility to pass more variables to the queuing system.
    See examples below.   More information about this options

Examples

We send the lammps input job1 to 1 node, 4 processors on that node, with a requested time of 4 hours:

send_lmp job1.in 1 4 04:00:00

We send job2  to 2 compuation nodes, 8 processors on each node, with a requested time of 192 hours, 8 GB of RAM and to start running after work 1234.arinab is finished:

send_lmp job2.inp 2 8 192:00:00 8 ``-W depend=afterany:1234'

We  send the input job3 to 4 nodes and 4 processors on each node, with arequested time of 200:00:00 hours, 2 GB of RAM and we request to be send an email at the beginning and end of the calculation to the direction specified.

send_lmp job.tpr 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''

send_lmp command copies the contents of the directory from which the job is sent to /scratch or / gscratch, if we use 2 or more nodes. And there is where the calculation is done.

Jobs Monitoring

To facilitate monitoring and/or control of the LAMMPS calculations, you can use remote_vi

remote_vi JOBID

It show us the *.out file  (only if it was sent using send_lmp).

More information

http://lammps.sandia.gov