Merge branch 'v2.4'

# Conflicts:
#	regtest/basic/rt-maxent-4/config
#	regtest/basic/rt-maxent-5/config
#	regtest/basic/rt63c-mpi/config
#	src/cltools/Driver.cpp

CHANGES/v2.3.md

@@ -233,3 +233,6 @@ For developers:
 For users:
 - Fixed a problem leading to NaN derivatives of \ref switchingfunction `Q` when distance between two atoms is large.
 
+For developers:
+- Fixed small issue in debug options of \ref driver (see \issue{245}).
+

regtest/basic/rt-drift-2/config

 mpiprocs=4
 type=driver
 # this is to test a different name
-arg="--plumed plumed.dat --timestep=0.005  --initial-step=1 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --debug-dd"
+arg="--plumed plumed.dat --timestep=0.005  --initial-step=1 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --debug-dd yes"
 

regtest/basic/rt-drift-3/config

 mpiprocs=4
 type=driver
 # this is to test a different name
-arg="--plumed plumed.dat --timestep=0.005  --initial-step=1 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --debug-pd"
+arg="--plumed plumed.dat --timestep=0.005  --initial-step=1 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --debug-pd yes"
 

regtest/basic/rt-maxent-4/config

 mpiprocs=6
 type=driver
-arg="--plumed plumed.dat --mf_xtc traj.xtc --dump-forces forces --dump-forces-fmt=%8.4f --debug-dd"
+arg="--plumed plumed.dat --mf_xtc traj.xtc --dump-forces forces --dump-forces-fmt=%8.4f --debug-dd yes"

regtest/basic/rt-maxent-5/config

 mpiprocs=6
 type=driver
-arg="--plumed plumed.dat --mf_xtc traj.xtc --dump-forces forces --multi 3 --dump-forces-fmt=%8.4f --debug-dd"
+arg="--plumed plumed.dat --mf_xtc traj.xtc --dump-forces forces --multi 3 --dump-forces-fmt=%8.4f --debug-dd yes"

regtest/basic/rt-mpi1/config

 mpiprocs=4
 type=driver
 # this is to test a different name
-arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff  --debug-pd"
+arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff  --debug-pd yes"
 extra_files="../../trajectories/trajectory.xyz"

regtest/basic/rt-mpi10/config

 mpiprocs=6
 type=driver
-arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --multi 3 --debug-dd --debug-grex 6 --debug-grex-log log.grex --initial-step 3"
+arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --multi 3 --debug-dd yes --debug-grex 6 --debug-grex-log log.grex --initial-step 3"

regtest/basic/rt-mpi2/config

 mpiprocs=4
 type=driver
 # this is to test a different name
-arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --debug-dd"
+arg="--debug-dd yes --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb"
 extra_files="../../trajectories/trajectory.xyz"

regtest/basic/rt-mpi2sync/config

 mpiprocs=4
 type=driver
 # this is to test a different name
-arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --debug-dd"
+arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --debug-dd yes"
 extra_files="../../trajectories/trajectory.xyz"
 export PLUMED_ASYNC_SHARE=no

regtest/basic/rt-mpi3/config

@@ -2,4 +2,4 @@ mpiprocs=6
 type=driver
 # this is to test a different name
 arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --multi 3
-     --debug-dd --debug-grex 2 --debug-grex-log log.grex"
+     --debug-dd yes --debug-grex 2 --debug-grex-log log.grex"

regtest/basic/rt-mpi4/config

@@ -2,4 +2,4 @@ mpiprocs=6
 type=driver
 # this is to test a different name
 arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --multi 3
-      --debug-dd --debug-grex 2 --debug-grex-log log.grex"
+      --debug-dd yes --debug-grex 2 --debug-grex-log log.grex"

regtest/basic/rt-mpi8/config

@@ -2,4 +2,4 @@ mpiprocs=6
 type=driver
 # this is to test a different name
 arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --multi 3
-      --debug-dd --debug-grex 2 --debug-grex-log log.grex"
+      --debug-dd yes --debug-grex 2 --debug-grex-log log.grex"

regtest/basic/rt63-mpi/config

 type=driver
 mpiprocs=2
-arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --igro helix.input.gro --dump-forces ff --dump-full-virial --debug-dd"
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --igro helix.input.gro --dump-forces ff --dump-full-virial --debug-dd yes"

regtest/basic/rt63c-mpi/config

 type=driver
 mpiprocs=2
-arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --igro helix.input.gro --dump-forces ff --dump-full-virial --dump-forces-fmt=%7.4f --debug-dd"
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --igro helix.input.gro --dump-forces ff --dump-full-virial --dump-forces-fmt=%7.4f --debug-dd yes"

src/cltools/Driver.cpp

@@ -241,9 +241,9 @@ void Driver<real>::registerKeywords( Keywords& keys ) {
   keys.add("optional","--initial-step","provides a number for the initial step, default is 0");
   keys.add("optional","--debug-forces","output a file containing the forces due to the bias evaluated using numerical derivatives "
            "and using the analytical derivatives implemented in plumed");
-  keys.add("hidden","--debug-float","turns on the single precision version (to check float interface)");
-  keys.add("hidden","--debug-dd","use a fake domain decomposition");
-  keys.add("hidden","--debug-pd","use a fake particle decomposition");
+  keys.add("hidden","--debug-float","[yes/no] turns on the single precision version (to check float interface)");
+  keys.add("hidden","--debug-dd","[yes/no] use a fake domain decomposition");
+  keys.add("hidden","--debug-pd","[yes/no] use a fake particle decomposition");
   keys.add("hidden","--debug-grex","use a fake gromacs-like replica exchange, specify exchange stride");
   keys.add("hidden","--debug-grex-log","log file for debug=grex");
 #ifdef __PLUMED_HAS_MOLFILE_PLUGINS
@@ -277,9 +277,9 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
   if( printhelpdebug ) {
     fprintf(out,"%s",
             "Additional options for debug (only to be used in regtest):\n"
-            "  [--debug-float]         : turns on the single precision version (to check float interface)\n"
-            "  [--debug-dd]            : use a fake domain decomposition\n"
-            "  [--debug-pd]            : use a fake particle decomposition\n"
+            "  [--debug-float yes]     : turns on the single precision version (to check float interface)\n"
+            "  [--debug-dd yes]        : use a fake domain decomposition\n"
+            "  [--debug-pd yes]        : use a fake particle decomposition\n"
            );
     return 0;
   }
@@ -287,16 +287,39 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
   bool noatoms; parseFlag("--noatoms",noatoms);
 
   std::string fakein;
-  bool debugfloat=parse("--debug-float",fakein);
-  if(debugfloat && sizeof(real)!=sizeof(float)) {
+  bool debug_float=false;
+  fakein="";
+  if(parse("--debug-float",fakein)) {
+    if(fakein=="yes") debug_float=true;
+    else if(fakein=="no") debug_float=false;
+    else error("--debug-float should have argument yes or no");
+  }
+
+  if(debug_float && sizeof(real)!=sizeof(float)) {
     std::unique_ptr<CLTool> cl(cltoolRegister().create(CLToolOptions("driver-float")));
     cl->setInputData(this->getInputData());
     int ret=cl->main(in,out,pc);
     return ret;
   }
 
-  bool debug_pd=parse("--debug-pd",fakein);
-  bool debug_dd=parse("--debug-dd",fakein);
+  bool debug_pd=false;
+  fakein="";
+  if(parse("--debug-pd",fakein)) {
+    if(fakein=="yes") debug_pd=true;
+    else if(fakein=="no") debug_pd=false;
+    else error("--debug-pd should have argument yes or no");
+  }
+  if(debug_pd) fprintf(out,"DEBUGGING PARTICLE DECOMPOSITION\n");
+
+  bool debug_dd=false;
+  fakein="";
+  if(parse("--debug-dd",fakein)) {
+    if(fakein=="yes") debug_dd=true;
+    else if(fakein=="no") debug_dd=false;
+    else error("--debug-dd should have argument yes or no");
+  }
+  if(debug_dd) fprintf(out,"DEBUGGING DOMAIN DECOMPOSITION\n");
+
   if( debug_pd || debug_dd ) {
     if(noatoms) error("cannot debug without atoms");
   }