Added function to select the landmarks indices from a second different collection object

regtest/analysis/rt-reselect-land/Makefile

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

regtest/analysis/rt-reselect-land/config

+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../../trajectories/trajectory.xyz"

regtest/analysis/rt-reselect-land/data.reference

+#! FIELDS dist
+  1.2626 
+  1.3934 

regtest/analysis/rt-reselect-land/mymatrix.dat.reference

+   0.0000   0.0171
+   0.0171   0.0000

regtest/analysis/rt-reselect-land/plumed.dat

+dist: DISTANCE ATOMS=1,2 
+
+ss1: EUCLIDEAN_DISSIMILARITIES ATOMS=1-5 METRIC=OPTIMAL STRIDE=1 USE_ALL_DATA 
+ss2: EUCLIDEAN_DISSIMILARITIES ARG=dist STRIDE=1 USE_ALL_DATA
+
+l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=2
+l2: RESELECT_LANDMARKS USE_OUTPUT_DATA_FROM=ss2 LANDMARKS=l1 
+
+OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=l2 FILE=data FMT=%8.4f
+PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=l2 FILE=mymatrix.dat FMT=%8.4f

src/analysis/AnalysisBase.cpp

@@ -31,7 +31,7 @@ void AnalysisBase::registerKeywords( Keywords& keys ){
   ActionPilot::registerKeywords( keys );
   ActionAtomistic::registerKeywords( keys );
   ActionWithArguments::registerKeywords( keys );
-  ActionWithVessel::registerKeywords( keys ); keys.remove("TOL"); keys.remove("LOWMEM"); keys.remove("TIMINGS"); keys.isAnalysis();  
+  ActionWithVessel::registerKeywords( keys ); keys.remove("TOL"); keys.remove("LOWMEM"); keys.reset_style("TIMINGS","hidden"); keys.isAnalysis();  
   keys.add("atoms-2","USE_OUTPUT_DATA_FROM","use the ouput of the analysis performed by this object as input to your new analysis object");
 }
 

src/analysis/AnalysisBase.h

@@ -46,6 +46,7 @@ class AnalysisBase :
   public ActionWithArguments,
   public vesselbase::ActionWithVessel
   {
+friend class ReselectLandmarks;
 friend class ReadDissimilarityMatrix; 
 friend class AnalysisWithDataCollection;
 private:

src/analysis/EuclideanDissimilarityMatrix.cpp

@@ -55,6 +55,7 @@ PLUMED_REGISTER_ACTION(EuclideanDissimilarityMatrix,"EUCLIDEAN_DISSIMILARITIES")
 
 void EuclideanDissimilarityMatrix::registerKeywords( Keywords& keys ){
   AnalysisWithDataCollection::registerKeywords( keys );
+  keys.reset_style("METRIC","atoms-1");
 }
 
 EuclideanDissimilarityMatrix::EuclideanDissimilarityMatrix( const ActionOptions& ao ):

src/analysis/LandmarkSelectionBase.cpp

@@ -42,7 +42,7 @@ LandmarkSelectionBase::LandmarkSelectionBase( const ActionOptions& ao ):
 Action(ao),
 AnalysisWithDataCollection(ao)
 {
-  parse("NLANDMARKS",nlandmarks); 
+  if( keywords.exists("NLANDMARKS") ) parse("NLANDMARKS",nlandmarks); 
   log.printf("  selecting %d landmark points \n",nlandmarks);
   lweights.resize( nlandmarks );
 
@@ -60,6 +60,7 @@ void LandmarkSelectionBase::selectFrame( const unsigned& iframe ){
 void LandmarkSelectionBase::performAnalysis(){
   landmark_indices.resize(0); selectLandmarks(); 
   plumed_dbg_assert( nlandmarks==getNumberOfDataPoints() );
+  if( lweights.size()!=nlandmarks ) lweights.resize( nlandmarks );
 
   if( !novoronoi ){
       lweights.assign(lweights.size(),0.0);

src/analysis/LandmarkSelectionBase.h

@@ -28,6 +28,7 @@ namespace PLMD {
 namespace analysis {
 
 class LandmarkSelectionBase : public AnalysisWithDataCollection {
+friend class ReselectLandmarks;
 private:
 /// The number of landmarks we are selecting
   unsigned nlandmarks;

src/analysis/ReselectLandmarks.cpp

+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2012-2014 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed-code.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "LandmarkSelectionBase.h"
+#include "core/ActionRegister.h"
+#include "core/PlumedMain.h"
+#include "core/ActionSet.h"
+#include "tools/Random.h"
+
+//+PLUMEDOC LANDMARKS RESELECT_LANDMARKS
+/* 
+This allows us to use one measure in landmark selection and a different measure in dimensionality reduction
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+namespace PLMD {
+namespace analysis {
+
+class ReselectLandmarks : public LandmarkSelectionBase {
+private:
+  LandmarkSelectionBase* mylandmarks;
+public:
+  static void registerKeywords( Keywords& keys );
+  ReselectLandmarks( const ActionOptions& ao );
+  void selectLandmarks();
+};
+
+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");
+}
+
+ReselectLandmarks::ReselectLandmarks( const ActionOptions& ao ):
+Action(ao),
+LandmarkSelectionBase(ao)
+{
+  std::string datastr; parse("LANDMARKS",datastr);
+  mylandmarks = plumed.getActionSet().selectWithLabel<LandmarkSelectionBase*>( datastr );
+  if( !mylandmarks ) error("input to LANDMARKS is not a landmark selection action");
+  nlandmarks = mylandmarks->nlandmarks;
+
+  if( (mylandmarks->mydata)->getNumberOfDataPoints()!=mydata->getNumberOfDataPoints() ||
+      mylandmarks->use_all_data!=mydata->use_all_data ) error("mismatch between ammount of landmark class and base class"); 
+}
+
+void ReselectLandmarks::selectLandmarks(){
+  for(unsigned i=0;i<mylandmarks->getNumberOfDataPoints();++i) selectFrame( mylandmarks->getDataPointIndexInBase(i) );
+}
+
+}
+}