Added mapping module for paths

regtest/.gitignore

@@ -7,6 +7,7 @@
 !/analysis
 !/basic
 !/crystallization
+!/mapping
 !/multicolvar
 !/secondarystructure
 !/trajectories

regtest/mapping/Makefile

+include ../scripts/module.make
+

regtest/mapping/rt39-mpi/Makefile

+include ../../scripts/test.make

regtest/mapping/rt39-mpi/config

+mpiprocs=2
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../../trajectories/diala_traj_nm.xyz  ../trajectories/path_msd/all.pdb "

regtest/mapping/rt39-mpi/plumed.dat

+p2: PATH_GT REFERENCE=all.pdb LAMBDA=69087    
+p3: PATHMSD REFERENCE=all.pdb LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=5
+PRINT ARG=p2.sss,p2.zzz,p3.sss,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
+DUMPDERIVATIVES ARG=p2.sss,p2.zzz,p3.sss,p3.zzz STRIDE=1 FILE=deriv FMT=%8.4f

regtest/mapping/rt39-mpi/test_distances.tcl

+mol new diala_traj_nm.xyz  type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+set nn1 [  molinfo top get numframes ] 
+mol new all.pdb  type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+set nn2 [  molinfo 1 get numframes ] 
+set sel1 "index 0 4 5 6 7 8 9 10 14 15 16 17 18  "
+set sel2 " all   "
+#for { set i 0 } { $i < $nn1 } { incr i } {
+for { set i 0 } { $i < 1 } { incr i } {
+puts "FRAME $i"
+ #scale all traj 
+ set runsel_all [  atomselect 0 "all" frame $i ]
+ set c  [ $runsel_all get { x y z } ]
+ set ci [ $runsel_all get index ]
+ for  { set j 0 } { $j < [llength $c ]} { incr j } {
+         set idx [ lindex $ci $j  ]
+         set aa [ atomselect 0 "index $idx"  frame $i ]
+         $aa set x [ expr [ lindex [ lindex $c $j ] 0 ] *10. ]
+         $aa set y [ expr [ lindex [ lindex $c $j ] 1 ] *10. ]
+         $aa set z [ expr [ lindex [ lindex $c $j ] 2 ] *10. ]
+ } 
+ set runsel [ atomselect 0 $sel1 frame $i    ]
+ for { set j 0 } { $j < $nn2  } { incr j } {
+	set refsel [ atomselect 1 $sel2 frame $j   ]
+        set mymat  [ measure fit  $runsel $refsel ]
+        [ atomselect 1 "all " ]  move $mymat
+        puts  "[expr pow([measure rmsd $runsel $refsel],1)/100.]" 
+ } 
+}
+puts "END"

regtest/mapping/rt39/Makefile

+include ../../scripts/test.make

regtest/mapping/rt39/config

+type=driver
+arg="--plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../../trajectories/diala_traj_nm.xyz  ../../trajectories/path_msd/all.pdb "

regtest/mapping/rt39/plumed.dat

+p2: PATH_GT REFERENCE=all.pdb LAMBDA=69087    
+p3: PATHMSD REFERENCE=all.pdb LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=5
+PRINT ARG=p2.sss,p2.zzz,p3.sss,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
+DUMPDERIVATIVES ARG=p2.sss,p2.zzz,p3.sss,p3.zzz STRIDE=1 FILE=deriv FMT=%8.4f

regtest/mapping/rt39/test_distances.tcl

+mol new diala_traj_nm.xyz  type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+set nn1 [  molinfo top get numframes ] 
+mol new all.pdb  type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+set nn2 [  molinfo 1 get numframes ] 
+set sel1 "index 0 4 5 6 7 8 9 10 14 15 16 17 18  "
+set sel2 " all   "
+#for { set i 0 } { $i < $nn1 } { incr i } {
+for { set i 0 } { $i < 1 } { incr i } {
+puts "FRAME $i"
+ #scale all traj 
+ set runsel_all [  atomselect 0 "all" frame $i ]
+ set c  [ $runsel_all get { x y z } ]
+ set ci [ $runsel_all get index ]
+ for  { set j 0 } { $j < [llength $c ]} { incr j } {
+         set idx [ lindex $ci $j  ]
+         set aa [ atomselect 0 "index $idx"  frame $i ]
+         $aa set x [ expr [ lindex [ lindex $c $j ] 0 ] *10. ]
+         $aa set y [ expr [ lindex [ lindex $c $j ] 1 ] *10. ]
+         $aa set z [ expr [ lindex [ lindex $c $j ] 2 ] *10. ]
+ } 
+ set runsel [ atomselect 0 $sel1 frame $i    ]
+ for { set j 0 } { $j < $nn2  } { incr j } {
+	set refsel [ atomselect 1 $sel2 frame $j   ]
+        set mymat  [ measure fit  $runsel $refsel ]
+        [ atomselect 1 "all " ]  move $mymat
+        puts  "[expr pow([measure rmsd $runsel $refsel],1)/100.]" 
+ } 
+}
+puts "END"

regtest/mapping/rt40-mpi/Makefile

+include ../../scripts/test.make