Added documentation to many actions to fix problems higlighted by ccp…

…check

src/adjmat/AdjacencyMatrixBase.cpp

@@ -49,7 +49,8 @@ AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions& ao):
   read_one_group(false),
   neighbour_list_updated(false),
   linkcells(comm),
-  threecells(comm)
+  threecells(comm),
+  natoms_per_list(0)
 {
   std::vector<unsigned> shape(2); std::vector<AtomNumber> t; parseAtomList("GROUP", t );
   if( t.size()==0 ) {

src/adjmat/Bridge.cpp

@@ -22,6 +22,15 @@
 #include "core/ActionShortcut.h"
 #include "core/ActionRegister.h"
 
+//+PLUMEDOC MCOLVAR BRIDGE
+/*
+Calculate a matrix with elements equal to one if there is a bridging atom between the two atoms
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/Determinent.cpp

@@ -22,6 +22,15 @@
 #include "core/ActionRegister.h"
 #include "core/ActionShortcut.h"
 
+//+PLUMEDOC MCOLVAR DETERMINANT
+/*
+Calculate the determinant of a matrix
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/DiagonalizeMatrix.cpp

@@ -22,6 +22,15 @@
 #include "MatrixOperationBase.h"
 #include "core/ActionRegister.h"
 
+//+PLUMEDOC ANALYSIS DIAGONALIZE
+/*
+Calculate the eigenvalues and eigenvectors of a square matrix
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/FunctionOfMatrix.cpp

@@ -28,6 +28,69 @@
 #include "function/Custom.h"
 #include "function/Combine.h"
 
+//+PLUMEDOC COLVAR SUM_MATRIX
+/*
+Sum all the elements in a matrix
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+//+PLUMEDOC COLVAR LESS_THAN_MATRIX
+/*
+Transform all the elements of a matrix using a switching function that is one when the input value is smaller than a threshold
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+//+PLUMEDOC COLVAR MORE_THAN_MATRIX
+/*
+Transform all the elements of a matrix using a switching function that is one when the input value is larger than a threshold
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+//+PLUMEDOC COLVAR BETWEEN_MATRIX
+/*
+Transform all the elements of a matrix using a switching function that is oen when the input value is within a particular range
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+//+PLUMEDOC COLVAR CUSTOM_MATRIX
+/*
+Calculate an arbitrary function piecewise for one or multiple input matrices.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+//+PLUMEDOC COLVAR MATHEVAL_MATRIX
+/*
+Calculate an arbitrary function piecewise for one or multiple input matrices.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+//+PLUMEDOC COLVAR COMBINE_MATRIX
+/*
+Calculate the sum of a number of matrices
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/InvertMatrix.cpp

@@ -23,6 +23,15 @@
 #include "core/ActionSetup.h"
 #include "core/ActionRegister.h"
 
+//+PLUMEDOC MCOLVAR INVERT_MATRIX
+/*
+Calculate the inverse of the input matrix
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/MatrixTimesMatrix.cpp

@@ -23,6 +23,15 @@
 #include "AdjacencyMatrixBase.h"
 #include "core/ActionRegister.h"
 
+//+PLUMEDOC MCOLVAR MATRIX_PRODUCT
+/*
+Calculate the product of two matrices
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/MatrixTimesVector.cpp

@@ -22,6 +22,15 @@
 #include "ActionWithMatrix.h"
 #include "core/ActionRegister.h"
 
+//+PLUMEDOC MCOLVAR MATRIX_VECTOR_PRODUCT
+/*
+Calculate the product of the matrix and the vector
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/Neighbors.cpp

@@ -22,6 +22,15 @@
 #include "ActionWithMatrix.h"
 #include "core/ActionRegister.h"
 
+//+PLUMEDOC MCOLVAR NEIGHBORS
+/*
+Build a matrix with ones in for the N nearest neighbours of an atom
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/OuterProduct.cpp

@@ -23,6 +23,15 @@
 #include "core/ActionRegister.h"
 #include "tools/LeptonCall.h"
 
+//+PLUMEDOC COLVAR OUTER_PRODUCT
+/*
+Calculate the outer product matrix of two vectors
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/TopologyMatrix.cpp

@@ -57,7 +57,7 @@ class TopologyMatrix : public AdjacencyMatrixBase {
   SwitchingFunction switchingFunction;
   SwitchingFunction cylinder_sw;
   SwitchingFunction low_sf;
-  double beadrad, lsfmax, binw_mat;
+  double binw_mat;
   SwitchingFunction threshold_switch;
 public:
   static void registerKeywords( Keywords& keys );

src/adjmat/TorsionsMatrix.cpp

@@ -23,6 +23,15 @@
 #include "core/ActionRegister.h"
 #include "tools/Torsion.h"
 
+//+PLUMEDOC MCOLVAR TORSIONS_MATRIX
+/*
+Calculate the matrix of torsions between two vectors of molecules
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/TransposeMatrix.cpp

@@ -22,6 +22,15 @@
 #include "MatrixOperationBase.h"
 #include "core/ActionRegister.h"
 
+//+PLUMEDOC MCOLVAR TRANSPOSE
+/*
+Calculate the transpose of a matrix
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/adjmat/VStack.cpp

@@ -22,6 +22,15 @@
 #include "ActionWithMatrix.h"
 #include "core/ActionRegister.h"
 
+//+PLUMEDOC MCOLVAR VSTACK
+/*
+Create a matrix by stacking vectors together
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace adjmat {
 

src/analysis/Accumulate.cpp

@@ -27,6 +27,15 @@
 #include "core/ActionSet.h"
 #include "gridtools/ActionWithGrid.h"
 
+//+PLUMEDOC GRIDCALC ACCUMULATE
+/*
+Sum the elements of this value over the course of the trajectory
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace analysis {
 

src/analysis/Collect.cpp

@@ -27,6 +27,15 @@
 #include "core/ActionSet.h"
 #include "gridtools/ActionWithGrid.h"
 
+//+PLUMEDOC ANALYSIS COLLECT
+/*
+Collect data from the trajectory for later analysis
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace analysis {
 

src/analysis/GatherReplicas.cpp

@@ -24,6 +24,16 @@
 #include "core/ActionRegister.h"
 #include "tools/Communicator.h"
 
+//+PLUMEDOC ANALYSIS GATHER_REPLICAS
+/*
+Create a vector that contains the copies of the input quantities from all replicas
+
+\par Examples
+
+
+*/
+//+ENDPLUMEDOC
+
 namespace PLMD {
 namespace analysis {
 

src/bias/LWalls.cpp

@@ -61,6 +61,16 @@ PRINT ARG=uwall.bias,lwall.bias
 */
 //+ENDPLUMEDOC
 
+//+PLUMEDOC BIAS LOWER_WALLS_SCALAR
+/*
+Defines a wall for the value of one or more collective variables,
+ which limits the region of the phase space accessible during the simulation.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 class LWalls : public Bias {
   std::vector<double> at;
   std::vector<double> kappa;

src/bias/Restraint.cpp

@@ -56,6 +56,15 @@ PRINT ARG=restraint.bias
 */
 //+ENDPLUMEDOC
 
+//+PLUMEDOC BIAS RESTRAINT_SCALAR
+/*
+Adds harmonic and/or linear restraints on one or more scalar variables.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 class Restraint : public Bias {
   std::vector<double> at;
   std::vector<double> kappa;

src/bias/UWalls.cpp

@@ -60,6 +60,16 @@ PRINT ARG=uwall.bias,lwall.bias
 */
 //+ENDPLUMEDOC
 
+//+PLUMEDOC BIAS UPPER_WALLS_SCALAR
+/*
+Defines a wall for the value of one or more collective variables,
+ which limits the region of the phase space accessible during the simulation.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 class UWalls : public Bias {
   std::vector<double> at;
   std::vector<double> kappa;

src/clusters/ClusterDistribution.cpp

@@ -62,16 +62,24 @@ PRINT ARG=nclust.* FILE=colvar
 */
 //+ENDPLUMEDOC
 
+//+PLUMEDOC CONCOMP CLUSTER_DISTRIBUTION_CALC
+/*
+Calculate functions of the distribution of properties in your connected components.
+
+See \ref CLUSTER_DISTRIBUTION
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
 
 namespace PLMD {
 namespace clusters {
 
 class ClusterDistribution :
   public ActionWithArguments,
   public ActionWithValue {
-private:
-/// The cluster we are looking for
-  unsigned clustr;
 public:
 /// Create manual
   static void registerKeywords( Keywords& keys );