piv regtest (plumed#390)

* PIV metric coupled with PathCV and added input example for doxygen.

* Line CRYST1 of a PDB file is read and box vectors, axis and angles are
computed. Functions are added to get box parameters.

* Added function getClosePairAtomNumber to get pairs in AtomNumber format
for piv construction.

* Added function set_r0 to set the R_0 value from piv class once the
scaling factor has been defined.

* piv module added

* Added piv module regtests on distance and derivatives/virial

* PIV.cpp Astyled

* Files astyled using plumed astyle

* solved Travis warnings on non-initialized member variables

* Solved the R_0 issue without adding any new function in
SwitchingFunction.cpp, but by substituting its value in the string read as
in PIV.cpp.

* Fixed format in reading box parmaters (CRYST1) in pdb.cpp

* Changed the construction of the box vectors from length and angle
parameters in pdb.cpp

* fixed update_piv

* Better timing part2

* Fixed problems in Makefiles for regtests

* Fixed details from a resolved conflict

* Added Makefile for regtests

* Deleted tmp directories in regtests

* Revert "Deleted tmp directories in regtests"

This reverts commit 1fd9813.

* Revert "Added Makefile for regtests"

This reverts commit 552cb52.

* Reverted commit and Makefile added

* using the "serial" path for distance tests. This fixes the MPI errors in
regtests

* Fixed problems in regtests with debug flags for compiler

* PIV.cpp astyled

regtest/piv/Makefile

@@ -0,0 +1,2 @@
+include ../scripts/module.make
+

regtest/piv/rt-piv-derivatives/Makefile

@@ -1 +1 @@
-include ../scripts/test.make
+include ../../scripts/test.make

regtest/piv/rt-piv-derivatives_onlycross/Makefile

@@ -1 +1 @@
-include ../scripts/test.make
+include ../../scripts/test.make

regtest/piv/rt-piv-derivatives_onlydirect/Makefile

@@ -1 +1 @@
-include ../scripts/test.make
+include ../../scripts/test.make

regtest/piv/rt-piv-distance/Makefile

@@ -1 +1 @@
-include ../scripts/test.make
+include ../../scripts/test.make

regtest/piv/rt-piv-distance/plumed.dat

@@ -7,6 +7,7 @@ NLIST
 REF_FILE=Liq.pdb
 PIVATOMS=2
 ATOMTYPES=OW1,HW
+SFACTOR=1.,1.,1.
 SORT=1,1,1  
 SWITCH1={RATIONAL R_0=0.7 MM=12 NN=4}
 SWITCH2={RATIONAL R_0=0.7 MM=12 NN=6}
@@ -23,6 +24,7 @@ NLIST
 REF_FILE=Ice.pdb
 PIVATOMS=2
 ATOMTYPES=OW1,HW
+SFACTOR=1.,1.,1.
 SORT=1,1,1  
 SWITCH1={RATIONAL R_0=0.7 MM=12 NN=4}
 SWITCH2={RATIONAL R_0=0.7 MM=12 NN=6}

regtest/piv/rt-piv-distance_onlycross/Makefile

@@ -1 +1 @@
-include ../scripts/test.make
+include ../../scripts/test.make

regtest/piv/rt-piv-distance_onlycross/plumed.dat

@@ -7,6 +7,7 @@ ONLYCROSS
 REF_FILE=Liq.pdb
 PIVATOMS=2
 ATOMTYPES=OW1,HW
+SFACTOR=1.
 SORT=1  
 SWITCH1={RATIONAL R_0=0.5 MM=12 NN=4}
 NL_CUTOFF=3.
@@ -22,6 +23,7 @@ ONLYCROSS
 REF_FILE=Ice.pdb
 PIVATOMS=2
 ATOMTYPES=OW1,HW
+SFACTOR=1.
 SORT=1  
 SWITCH1={RATIONAL R_0=0.5 MM=12 NN=4}
 NL_CUTOFF=3.

regtest/piv/rt-piv-distance_onlydirect/Makefile

@@ -1 +1 @@
-include ../scripts/test.make
+include ../../scripts/test.make

regtest/piv/rt-piv-distance_onlydirect/plumed.dat

@@ -7,6 +7,7 @@ REF_FILE=Liq.pdb
 PIVATOMS=2
 ATOMTYPES=OW1,HW
 ONLYDIRECT
+SFACTOR=1.,1.
 SORT=1,1  
 SWITCH1={RATIONAL R_0=0.7 MM=12 NN=4}
 SWITCH2={RATIONAL R_0=0.7 MM=12 NN=6}
@@ -23,6 +24,7 @@ REF_FILE=Ice.pdb
 PIVATOMS=2
 ATOMTYPES=OW1,HW
 ONLYDIRECT
+SFACTOR=1.,1.
 SORT=1,1  
 SWITCH1={RATIONAL R_0=0.7 MM=12 NN=4}
 SWITCH2={RATIONAL R_0=0.7 MM=12 NN=6}

src/piv/PIV.cpp

@@ -281,7 +281,6 @@ PIV::PIV(const ActionOptions&ao):
 //com2atoms(std:: vector<std:: vector<unsigned> >(Nlist))
 {
   log << "Starting PIV Constructor\n";
-  unsigned rank=comm.Get_rank();
 
   // Precision on the real-to-integer transformation for the sorting
   parse("PRECISION",Nprec);
@@ -303,6 +302,7 @@ PIV::PIV(const ActionOptions&ao):
     log << "Serial PIV construction\n";
   } else     {
     log << "Parallel PIV construction\n";
+    unsigned rank=comm.Get_rank();
   }
 
   // Derivatives
@@ -496,7 +496,6 @@ PIV::PIV(const ActionOptions&ao):
     parseVector("SFACTOR",scaling);
     //if(scaling.size()!=getNumberOfArguments() && scaling.size()!=0) error("not enough values for SFACTOR");
   }
-
   // Neighbour Lists option
   parseFlag("NLIST",doneigh);
   nl.resize(Nlist);
@@ -737,7 +736,6 @@ void PIV::calculate()
   static std:: vector<std:: vector<double> > cPIV(Nlist);
   static std:: vector<std:: vector<int> > Atom0(Nlist);
   static std:: vector<std:: vector<int> > Atom1(Nlist);
-  //
   std:: vector<std:: vector<int> > A0(Nprec);
   std:: vector<std:: vector<int> > A1(Nprec);
   unsigned stride=1;
@@ -754,7 +752,6 @@ void PIV::calculate()
   // Transform (and sort) the rPIV before starting the dynamics
   if (((prev_stp==-1) || (init_stp==1)) &&!CompDer) {
     if(prev_stp!=-1) {init_stp=0;}
-    log << "Debug " << prev_stp << " " << init_stp << "\n";
     // Calculate the volume scaling factor
     if(Svol) {
       Fvol=cbrt(Vol0/getBox().determinant());
@@ -925,7 +922,7 @@ void PIV::calculate()
         }
         if(timer) stopwatch.stop("1 Build cPIV");
         if(timer) stopwatch.start("2 Sort cPIV");
-        if(!doserial) {
+        if(!doserial && comm.initialized()) {
           // Vectors keeping track of the dimension and the starting-position of the rank-specific pair vector in the big pair vector.
           std:: vector<int> Vdim(stride,0);
           std:: vector<int> Vpos(stride,0);
@@ -987,6 +984,8 @@ void PIV::calculate()
           // Loop on blocks
           //for(unsigned m=0;m<Nlist;m++) {
           // Loop on Ordering Vector size excluding zeros (i=1)
+          if(timer) stopwatch.stop("2 Sort cPIV");
+          if(timer) stopwatch.start("3 Reconstruct cPIV");
           for(unsigned i=1; i<Nprec; i++) {
             // Loop on the ranks
             for(unsigned l=0; l<stride; l++) {
@@ -1000,7 +999,7 @@ void PIV::calculate()
               }
             }
           }
-          if(timer) stopwatch.stop("2 Sort cPIV");
+          if(timer) stopwatch.stop("3 Reconstruct cPIV");
         } else {
           for(unsigned i=1; i<Nprec; i++) {
             for(unsigned m=0; m<OrdVec[i]; m++) {
@@ -1013,7 +1012,6 @@ void PIV::calculate()
       }
     }
   }
-
   Vector distance;
   double dfunc=0.;
   // Calculate volume scaling factor
@@ -1072,7 +1070,7 @@ void PIV::calculate()
     exit();
   }
 
-  if(timer) stopwatch.start("3 Build For Derivatives");
+  if(timer) stopwatch.start("4 Build For Derivatives");
   // non-global variables Nder and Scalevol defined to speedup if structures in cycles
   bool Nder=CompDer;
   bool Scalevol=Svol;
@@ -1206,18 +1204,17 @@ void PIV::calculate()
       }
     }
 
-    if (!serial) {
+    if (!serial && comm.initialized()) {
       comm.Barrier();
       comm.Sum(&m_PIVdistance,1);
       if(!m_deriv.empty()) comm.Sum(&m_deriv[0][0],3*m_deriv.size());
       comm.Sum(&m_virial[0][0],9);
     }
-
   }
   prev_stp=getStep();
 
   //Timing
-  if(timer) stopwatch.stop("3 Build For Derivatives");
+  if(timer) stopwatch.stop("4 Build For Derivatives");
   if(timer) {
     log.printf("Timings for action %s with label %s \n", getName().c_str(), getLabel().c_str() );
     log<<stopwatch;

src/tools/SwitchingFunction.cpp

@@ -503,7 +503,6 @@ double SwitchingFunction::get_dmax2() const {
   return dmax_2;
 }
 
-
 }