Made landmarks selction inherit from AnalysisBase as it makes more sense

regtest/analysis/rt-calc-dissims/plumed.dat

@@ -3,7 +3,7 @@ d1: READ FILE=colv_in VALUES=data
 ss1: EUCLIDEAN_DISSIMILARITIES STRIDE=1 USE_ALL_DATA ARG=d1 
 PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ss1 FILE=mymatrix.dat FMT=%8.4f
 
-ll1: LANDMARK_SELECT_STRIDE ARG=d1 USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=5 
+ll1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=5 
 ss2: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=ll1 
 OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=ll1 FILE=output-stride.pdb
 PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ll1 FILE=mymatrix2.dat FMT=%8.4f

regtest/analysis/rt-store-print/plumed.dat

@@ -4,8 +4,8 @@ ss1: OUTPUT_ANALYSIS_DATA_TO_COLVAR STRIDE=1 RUN=6 ARG=d1 FILE=output-half.pdb
 ss2: OUTPUT_ANALYSIS_DATA_TO_COLVAR STRIDE=1 USE_ALL_DATA ARG=d1 FILE=output-all.pdb 
 ss3: OUTPUT_ANALYSIS_DATA_TO_COLVAR REUSE_INPUT_DATA_FROM=ss2 FILE=output-reuse.pdb
 
-ll1: LANDMARK_SELECT_STRIDE ARG=d1 REUSE_INPUT_DATA_FROM=ss3 NLANDMARKS=5 NOVORONOI 
+ll1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss3 NLANDMARKS=5 NOVORONOI 
 OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ll1 FILE=output-stride.pdb
 
-ll2: LANDMARK_SELECT_STRIDE ARG=d1 REUSE_INPUT_DATA_FROM=ss1 NLANDMARKS=3 NOVORONOI
+ll2: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=3 NOVORONOI
 OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ll2 FILE=output-stride2.pdb

src/analysis/FarthestPointSampling.cpp

@@ -48,7 +48,6 @@ PLUMED_REGISTER_ACTION(FarthestPointSampling,"LANDMARK_SELECT_FPS")
 
 void FarthestPointSampling::registerKeywords( Keywords& keys ){
   LandmarkSelectionBase::registerKeywords(keys);
-  LandmarkSelectionBase::removeDataCollectionKeywords( keys );
   keys.add("compulsory","SEED","1234","a random number seed");
 }
 

src/analysis/LandmarkSelectionBase.cpp

@@ -24,15 +24,8 @@
 namespace PLMD {
 namespace analysis {
 
-void LandmarkSelectionBase::removeDataCollectionKeywords( Keywords& keys ){
-  keys.remove("ATOMS"); keys.remove("STRIDE"); keys.remove("RUN"); keys.remove("USE_ALL_DATA");
-  keys.remove("REWEIGHT_BIAS"); keys.remove("REWEIGHT_TEMP"); keys.remove("TEMP"); 
-  keys.remove("REUSE_INPUT_DATA_FROM"); keys.remove("WRITE_CHECKPOINT"); keys.remove("NOMEMORY");
-  keys.remove("RESTART"); keys.remove("UPDATE_FROM"); keys.remove("UPDATE_UNTIL"); keys.remove("ARG");
-}
-
 void LandmarkSelectionBase::registerKeywords( Keywords& keys ){
-  AnalysisWithDataCollection::registerKeywords( keys );
+  AnalysisBase::registerKeywords( keys );
   keys.add("compulsory","NLANDMARKS","the number of landmarks that you would like to select");
   keys.addFlag("NOVORONOI",false,"do not do a Voronoi analysis of the data to determine weights of final points");
   keys.addFlag("IGNORE_WEIGHTS",false,"ignore the weights in the underlying analysis object");
@@ -40,7 +33,7 @@ void LandmarkSelectionBase::registerKeywords( Keywords& keys ){
 
 LandmarkSelectionBase::LandmarkSelectionBase( const ActionOptions& ao ):
 Action(ao),
-AnalysisWithDataCollection(ao)
+AnalysisBase(ao)
 {
   if( keywords.exists("NLANDMARKS") ) parse("NLANDMARKS",nlandmarks); 
   log.printf("  selecting %d landmark points \n",nlandmarks);

src/analysis/LandmarkSelectionBase.h

@@ -22,12 +22,12 @@
 #ifndef __PLUMED_analysis_LandmarkSelectionBase_h
 #define __PLUMED_analysis_LandmarkSelectionBase_h
 
-#include "AnalysisWithDataCollection.h"
+#include "AnalysisBase.h"
 
 namespace PLMD {
 namespace analysis {
 
-class LandmarkSelectionBase : public AnalysisWithDataCollection {
+class LandmarkSelectionBase : public AnalysisBase {
 friend class ReselectLandmarks;
 private:
 /// The number of landmarks we are selecting
@@ -43,7 +43,6 @@ protected:
   void selectFrame( const unsigned& );
 public:
   static void registerKeywords( Keywords& keys );  
-  static void removeDataCollectionKeywords( Keywords& keys );
   LandmarkSelectionBase( const ActionOptions& ao );
 /// Return the number of data points
   unsigned getNumberOfDataPoints() const ;
@@ -71,7 +70,7 @@ unsigned LandmarkSelectionBase::getNumberOfDataPoints() const {
 
 inline
 unsigned LandmarkSelectionBase::getDataPointIndexInBase( const unsigned& idata ) const {
-  return AnalysisWithDataCollection::getDataPointIndexInBase( landmark_indices[idata] );
+  return AnalysisBase::getDataPointIndexInBase( landmark_indices[idata] );
 }
 
 inline
@@ -81,12 +80,12 @@ double LandmarkSelectionBase::getWeight( const unsigned& idata ) const {
 
 inline
 void LandmarkSelectionBase::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
-  AnalysisWithDataCollection::getDataPoint( landmark_indices[idata], point, weight );
+  AnalysisBase::getDataPoint( landmark_indices[idata], point, weight );
 }
 
 inline
 ReferenceConfiguration* LandmarkSelectionBase::getReferenceConfiguration( const unsigned& idat ){
-  return AnalysisWithDataCollection::getReferenceConfiguration( landmark_indices[idat] );
+  return AnalysisBase::getReferenceConfiguration( landmark_indices[idat] );
 }
 
 inline

src/analysis/ReselectLandmarks.cpp

@@ -50,7 +50,6 @@ PLUMED_REGISTER_ACTION(ReselectLandmarks,"RESELECT_LANDMARKS")
 
 void ReselectLandmarks::registerKeywords( Keywords& keys ){
   LandmarkSelectionBase::registerKeywords(keys);
-  LandmarkSelectionBase::removeDataCollectionKeywords( keys );
   keys.remove("NLANDMARKS");
   keys.add("compulsory","LANDMARKS","the action that selects the landmarks that you want to reselect using this action");
 }

user-doc/Analysis.txt

@@ -120,13 +120,12 @@ external file
 
 <table align=center frame=void width=95%% cellpadding=5%%>
 <tr> <td width=5%> \subpage READ_DISSIMILARITY_MATRIX </td> <td> Read a matrix of dissimilarities between a trajectory of atomic configurations from a file. </td> </tr>
+<tr> <td width=5%> \subpage READ_ANALYSIS_FRAMES </td> <td> Store the frames in trajectory to use in tandem with a dissimilarity matrix read using \ref READ_DISSIMILARITY_MATRIX </td> </tr>
 </table>
  
-N.B. You can only use the \ref READ_DISSIMILARITY_MATRIX command when you are doing post-processing.  If you have a 
-trajectory that contains the configurations you read in the configurations from the trajectory using 
-\ref READ_ANALYSIS_FRAMES 
+N.B. You can only use the two commands above when you are doing post-processing.  
 
-\ref landmarks Landmark Selection
+\section landmarks Landmark Selection
 
 Many of the techniques described in the following sections are very computationally expensive to run on large trajectories.
 A common strategy is thus to use a landmark selection algorithm to pick a particularly-reprentative subset of trajectory
@@ -135,8 +134,7 @@ that are available in PLUMED are as follows
 
 @LANDMARKS@
 
-Some of these algorithms (e.g. \ref LANDMARK_SELECT_STRIDE) can collect data from the trajectory themselves.  Others such as
-\ref LANDMARK_SELECT_FPS must take a dissimilarity matrix action as input.  That is to say they must be used as follows:
+In general most of these landmark selection algorithms must be used in tandem with a \ref dissimilaritym "dissimilarity matrix" object as as follows:
 
 \verbatim
 ss1: EUCLIDEAN_DISSIMILARITIES STRIDE=1 USE_ALL_DATA ARG=d1
@@ -196,7 +194,7 @@ a number of different algorithms.  The various algorithms that can be used to op
 
 @DIMRED@
 
-\ref output Outputting the results from analysis algorithms
+\section output Outputting the results from analysis algorithms
 
 The following methods are available for printing the result output by the various analysis algorithms: