Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases.
General Information
Towhee serves as a useful tool for the molecular simulation community and allows science to move forward more quickly by eliminating the need for individual research groups to rewrite routines that already exist and instead allows them to focus on algorithm advancement, force field development, and application to interesting systems.
Towhee may use different type of ensembles and Monte Carlo moves implemented into Towhee and can alos used different force fields included with the distribution. (See here for more information )
How to Use
send_towhee
- To send Towhee to the queue system use the send_gulp utility. When executed,
shows the command syntax, which is summarized below: - send_towhee JOBNAME NODES PROCS_PER_NODE TIME [ MEM ] [``Other queue options'' ]
| JOBNAME: | Is the name of the Output. |
| 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 a Towhee job1 to 1 node, 4 processors on that node, with a requested time of 4 hours . The results will be in the OUT file.
send_towhee OUT 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_towhee OUT 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_towhee OUT 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''
send_towhee 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 Towhee calculations, you can use remote_vi
remote_vi JOBID
It show us the *.out file (only if it was sent using send_towhee).