[Swift-commit] r5864 - in SwiftApps/rmsd: . conf input_files

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2012-07-19 13:02:19 -0500 (Thu, 19 Jul 2012)
New Revision: 5864

Modified:
   SwiftApps/rmsd/conf/makena.cf
   SwiftApps/rmsd/conf/makena.xml
   SwiftApps/rmsd/input_files/cg_clath_cage.temp.conf
   SwiftApps/rmsd/rmsd.sh
   SwiftApps/rmsd/rmsd.swift
Log:
Do the full runs
Use gensites variables for makena
Replace data directory within the namd config file


Modified: SwiftApps/rmsd/conf/makena.cf
===================================================================
--- SwiftApps/rmsd/conf/makena.cf	2012-07-19 17:12:04 UTC (rev 5863)
+++ SwiftApps/rmsd/conf/makena.cf	2012-07-19 18:02:19 UTC (rev 5864)
@@ -7,32 +7,5 @@
 provider.staging.pin.swiftfiles=false
 use.wrapper.staging=false
 
-#app vmd=/state/partition1/apps/vmd-1.9/bin/vmd
-#app generate_cgk=/state/partition1/apps/code/energylandscape/generate_cgk_pfENM-6.pl
-#app read_masses=/state/partition1/apps/code/energylandscape/aamasses.pl
-#app eigenvectors_from_heteroENM=$PWD/../bin/eigen
-#app stretch_geometry=$PWD/../bin/generate_distorted_geometry_ev
-#app stretch_geometry_pdb=$PWD/../bin/generate_distorted_pdb_ev
-#app project_onto_eigenvector=$PWD/../bin/project_onto_eigenvector
-#app forces_onto_eigenvector=$PWD/../bin/forces_onto_eigenvector
-#app diagonalize=$PWD/../bin/eigenvalues
-#app average_column=/scratch/sinitskiy/energy_landscape_test/working/src_averaging/averaging.x
-#app process_xf_from_NAMDlog=$PWD/../bin/process_xf_from_NAMDlog
-#app shortest_distance_between_mirror_images=$PWD/../bin/shortest_distance_between_mirror_images
-#app grompp=g_grompp
-#app mdrun=g_mdrun
-#app pdb2gmx=g_pdb2gmx
-#app editconf=g_editconf
-#app genbox=g_genbox
-#app genion=g_genion
-#app g_energy=g_energy
-#app g_rms=g_rms
-#app gmxdump=g_gmxdump
-#app namd=/state/partition1/apps/namd/namd_2.8-intel-openmpi/namd2
-#app namd_multiproc=/scratch/polaris/namd/2.7b3-openmpi-g++/namd2
-#app wget_pdb=$PWD/../src/scripts/wget_pdb.sh
-#app gen_xyz=$PWD/../src/scripts/gen_xyz.sh
-#app build_pf=$PWD/../src/scripts/build_pf.sh
-#app pre_equilibration=$PWD/../src/scripts/pre_equilibration.sh
-#app nonstretched_simulation=$PWD/../src/scripts/nonstretched_simulation.sh
-#app stretched_simulation=$PWD/../src/scripts/stretched_simulation.sh
+#app rmsd=$PWD/../rmsd.sh
+

Modified: SwiftApps/rmsd/conf/makena.xml
===================================================================
--- SwiftApps/rmsd/conf/makena.xml	2012-07-19 17:12:04 UTC (rev 5863)
+++ SwiftApps/rmsd/conf/makena.xml	2012-07-19 18:02:19 UTC (rev 5864)
@@ -11,7 +11,7 @@
   <profile key="queue" namespace="globus">devel</profile>
   <profile key="jobThrottle" namespace="karajan">5.99</profile>
   <profile key="initialScore" namespace="karajan">10000</profile>
-  <workdirectory>/scratch/davidk/work</workdirectory>
+  <workdirectory>_WORK_</workdirectory>
 </pool>
 </config>
 

Modified: SwiftApps/rmsd/input_files/cg_clath_cage.temp.conf
===================================================================
--- SwiftApps/rmsd/input_files/cg_clath_cage.temp.conf	2012-07-19 17:12:04 UTC (rev 5863)
+++ SwiftApps/rmsd/input_files/cg_clath_cage.temp.conf	2012-07-19 18:02:19 UTC (rev 5864)
@@ -1,7 +1,7 @@
 # NAMD Config file - autogenerated by NAMDgui plugin
 # Author: Jan Saam,  saam at charite.de
 
-set DIR			/lustre/beagle/fxv/CLATH/CG_MODEL/OPT/CAGE/PSWEEP
+set DIR			__DIR__			
 
 # input
 coordinates             $DIR/cg_clath_cage.pdb

Modified: SwiftApps/rmsd/rmsd.sh
===================================================================
--- SwiftApps/rmsd/rmsd.sh	2012-07-19 17:12:04 UTC (rev 5863)
+++ SwiftApps/rmsd/rmsd.sh	2012-07-19 18:02:19 UTC (rev 5864)
@@ -8,7 +8,7 @@
 namd_parameters=$6
 vmd_script=$7
 
-sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ $namd_input
+sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
 sed -i -e s/HBEPS/0.01/ -e s/PXEPS/-$b1/ -e s/DTEPS/-$b2/ -e s/AKEPS/0.01/ -e s/LTEPS/0.01/ $namd_parameters
 sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s/B1/$b1/ -e s/B2/$b2/ $vmd_script
 

Modified: SwiftApps/rmsd/rmsd.swift
===================================================================
--- SwiftApps/rmsd/rmsd.swift	2012-07-19 17:12:04 UTC (rev 5863)
+++ SwiftApps/rmsd/rmsd.swift	2012-07-19 18:02:19 UTC (rev 5864)
@@ -22,15 +22,13 @@
 file namd_params <"par_cg_clath.temp.inp">;
 file namd_input <"cg_clath_cage.temp.conf">;
 file vmd_script <"rmsd.temp.tcl">;
-file output <"output.txt">;
-file error <"error.txt">;
 
-(output, error) = rmsd(0.0, 0.0, b1name, b2name, namd_input, namd_params, vmd_script);
+foreach b1 in [b1min:b1max:delta] {
+   foreach b2 in [b2min:b2max:delta] {
+      file output <single_file_mapper; file=@strcat("logs/output-", b1, "-", b2, ".txt")>;
+      file error <single_file_mapper; file=@strcat("logs/error-", b1, "-", b2, ".txt")>;
+      (output, error) = rmsd(b1, b2, b1name, b2name, namd_input, namd_params, vmd_script);
+   }
+}
 
-#foreach b1 in [b1min:b1max:delta] {
-#   foreach b2 in [b2min:b2max:delta] {
-#      tracef("b1:%f, b2:%f\n", b1, b2);
-#   }
-#}
 
-