[Swift-commit] r5908 - in SwiftApps/CMTS/dimers: . bin

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2012-08-27 11:36:20 -0500 (Mon, 27 Aug 2012)
New Revision: 5908

Modified:
   SwiftApps/CMTS/dimers/README
   SwiftApps/CMTS/dimers/bin/dimers.sh
Log:
Use MPI


Modified: SwiftApps/CMTS/dimers/README
===================================================================
--- SwiftApps/CMTS/dimers/README	2012-08-27 07:14:42 UTC (rev 5907)
+++ SwiftApps/CMTS/dimers/README	2012-08-27 16:36:20 UTC (rev 5908)
@@ -46,7 +46,7 @@
 Usage: rundimers.sh [-s sitename] 
 
 The sitename option determines where a run will take place. Currently, the
-only tested options are "makena" and "grotthuss".
+only tested option is "makena".
 
 Example:
 

Modified: SwiftApps/CMTS/dimers/bin/dimers.sh
===================================================================
--- SwiftApps/CMTS/dimers/bin/dimers.sh	2012-08-27 07:14:42 UTC (rev 5907)
+++ SwiftApps/CMTS/dimers/bin/dimers.sh	2012-08-27 16:36:20 UTC (rev 5908)
@@ -6,9 +6,11 @@
 virion_radius=$4
 ndimers=$5
 
+lmp_john=`which lmp_john`
+
 insert_molecules ${prev_ndimers_file} ${dimer_file} ${n_dimers_to_add} ${virion_radius} 0 25.0 start_${ndimers}.lammps_config
 
-lmp_john -in lammps_new_spherical.in -var CONFIG start_${ndimers}.lammps_config -var NTDNTD_LJEPS 5.0 -var NTDCTD_LJEPS 5.0 -var RANDOMSEED 666 -var SPHERE_RADIUS ${virion_radius} -var NDIMERS ${ndimers}
+mpiexec -machinefile $PBS_NODEFILE ${lmp_john} -in lammps_new_spherical.in -var CONFIG start_${ndimers}.lammps_config -var NTDNTD_LJEPS 5.0 -var NTDCTD_LJEPS 5.0 -var RANDOMSEED 666 -var SPHERE_RADIUS ${virion_radius} -var NDIMERS ${ndimers}
 
 restart2data end_${ndimers}.restart end_${ndimers}.lammps_config