Add functionality to calculate the integral of a grid and to use this as a cv

regtest/analysis/rt-integral/Makefile

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

regtest/analysis/rt-integral/colvar.reference

+#! FIELDS time iv b.bias b.force2
+ 0.000000   0.9994   0.3110   6.2200
+ 1.000000   0.9998   0.3121   6.2421
+ 2.000000   0.9959   0.3023   6.0462
+ 3.000000   0.9997   0.3116   6.2327
+ 4.000000   0.9993   0.3108   6.2161

regtest/analysis/rt-integral/config

+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt %8.4f"

regtest/analysis/rt-integral/plumed.dat

+c1: COORDINATIONNUMBER SPECIESA=1-10 SPECIESB=1-200 SWITCH={RATIONAL R_0=1.0} LOWMEM
+h: HISTOGRAM DATA=c1 GRID_BIN=200 GRID_MIN=0 GRID_MAX=10 BANDWIDTH=0.1 
+iv: INTEGRATE_GRID GRID=h 
+
+b: RESTRAINT ARG=iv AT=0.75 KAPPA=10.0 
+PRINT ARG=iv,b.* FILE=colvar FMT=%8.4f

regtest/analysis/rt-uweights-integral/Makefile

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

regtest/analysis/rt-uweights-integral/colvar.reference

+#! FIELDS time iv b.bias b.force2
+ 0.000000   0.3598   0.7614  15.2271
+ 1.000000   0.5437   0.2128   4.2565
+ 2.000000   0.0000   2.8124  56.2470
+ 3.000000   0.0000   2.8122  56.2440
+ 4.000000   2.0008   7.8226 156.4529

regtest/analysis/rt-uweights-integral/config

+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt %8.4f"

regtest/analysis/rt-uweights-integral/plumed.dat

+z1: ZANGLES GROUP=1-5 SWITCH={RATIONAL D_0=2.0 R_0=0.5 D_MAX=5.0}
+z2: ZXTORSIONS GROUP=1-5 SWITCH={RATIONAL D_0=2.0 R_0=0.5 D_MAX=5.0}
+ 
+h: HISTOGRAM DATA=z1,z2 GRID_BIN=20,20 GRID_MIN=0,-pi GRID_MAX=pi,pi BANDWIDTH=0.2,0.2 UNORMALIZED
+iv: INTEGRATE_GRID GRID=h 
+
+b: RESTRAINT ARG=iv AT=0.75 KAPPA=10.0 
+PRINT ARG=iv,b.* FILE=colvar FMT=%8.4f

regtest/analysis/rt-weights-integral/Makefile

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

regtest/analysis/rt-weights-integral/colvar.reference

+#! FIELDS time iv b.bias b.force2
+ 0.000000   1.0002   0.3129   6.2579
+ 1.000000   0.9993   0.3108   6.2163
+ 2.000000   1.0002   0.3130   6.2595
+ 3.000000   0.9888   0.2852   5.7033
+ 4.000000   1.0004   0.3135   6.2703

regtest/analysis/rt-weights-integral/config

+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt %8.4f"

regtest/analysis/rt-weights-integral/plumed.dat

+z1: ZANGLES GROUP=1-5 SWITCH={RATIONAL D_0=2.0 R_0=0.5 D_MAX=5.0}
+z2: ZXTORSIONS GROUP=1-5 SWITCH={RATIONAL D_0=2.0 R_0=0.5 D_MAX=5.0}
+ 
+h: HISTOGRAM DATA=z1,z2 GRID_BIN=20,20 GRID_MIN=0,-pi GRID_MAX=pi,pi BANDWIDTH=0.2,0.2 
+iv: INTEGRATE_GRID GRID=h 
+
+b: RESTRAINT ARG=iv AT=0.75 KAPPA=10.0 
+PRINT ARG=iv,b.* FILE=colvar FMT=%8.4f

src/analysis/Analysis.h

@@ -110,6 +110,8 @@ public:
   static void registerKeywords( Keywords& keys );
   explicit Analysis(const ActionOptions&);
   ~Analysis();
+  void calculate(){}
+  void apply(){}
   void accumulate();
   void performOperations( const bool& from_update );
   virtual void performAnalysis()=0;

src/analysis/Average.cpp

@@ -95,6 +95,8 @@ private:
 public:
   static void registerKeywords( Keywords& keys );
   explicit Average( const ActionOptions& );
+  void calculate(){}
+  void apply(){}
   void performOperations( const bool& from_update );
   void finishAveraging();
   bool isPeriodic(){ return false; }