Added new functionality for output pdb in analysis

You can now use COLLECT_FRAMES to collect pdb data from the trajectory
and output a pdb file that contains the underlying atomic coordinates
in pdb format even if you are not using the rmsd distance to measure
the dissimilarity matrix for dimensionality reduction.  Also fixed
a number of bugs.

regtest/analysis/rt-calc-dissims2/Makefile

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

regtest/analysis/rt-calc-dissims2/config

+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+extra_files="../../trajectories/trajectory.xyz"

regtest/analysis/rt-calc-dissims2/plumed.dat

+d1: DISTANCE ATOMS=1,2 
+d2: DISTANCE ATOMS=3,4
+
+c1: COLLECT_FRAMES ATOMS=1-20 STRIDE=1 
+r1: EUCLIDEAN_DISSIMILARITIES FRAMES=c1 ARG=d1,d2
+l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=r1 NLANDMARKS=5
+OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=l1 FILE=configs-stride.pdb FMT=%8.4f

regtest/analysis/rt-read-dissims2/plumed.dat

-c1: READ_ANALYSIS_FRAMES ATOMS=1-20 STRIDE=1 
+c1: COLLECT_FRAMES ATOMS=1-20 STRIDE=1 
 
-r1: READ_DISSIMILARITY_MATRIX TRAJ=c1 FILE=mymatrix.dat 
+r1: READ_DISSIMILARITY_MATRIX FRAMES=c1 FILE=mymatrix.dat 
 PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=r1 FILE=mymatrix_out.dat FMT=%8.4f
 
 l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=r1 NLANDMARKS=5

regtest/dimred/Makefile

+include ../scripts/module.make
+

regtest/dimred/rt-mds2/Makefile

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

regtest/dimred/rt-mds2/analysis.0.list_embed.reference

+#! FIELDS mds.1 mds.2
+  0.0873   0.0013 
+  0.0535   0.0044 
+  0.0150   0.0044 
+ -0.0136   0.0019 
+ -0.0308  -0.0012 
+ -0.0355  -0.0018 
+ -0.0090  -0.0015 
+  0.0145   0.0004 
+  0.0191   0.0022 
+  0.0278   0.0015 
+  0.0091  -0.0004 
+ -0.0359  -0.0012 
+ -0.0540   0.0004 
+ -0.0322  -0.0034 
+ -0.0205  -0.0150 
+ -0.0282  -0.0289 
+ -0.0530  -0.0358 
+ -0.0769  -0.0312 
+ -0.0893  -0.0259 
+ -0.0697  -0.0246 
+ -0.0302  -0.0196 
+  0.0093  -0.0072 
+  0.0274   0.0009 
+  0.0301   0.0016 
+  0.0265  -0.0033 
+  0.0433  -0.0053 
+  0.0514  -0.0019 
+  0.0222   0.0031 
+ -0.0129   0.0061 
+ -0.0322   0.0084 
+ -0.0355   0.0080 
+ -0.0337   0.0067 
+ -0.0308   0.0047 
+ -0.0253   0.0016 
+ -0.0132  -0.0021 
+  0.0040  -0.0031 
+  0.0107   0.0011 
+  0.0299   0.0060 
+  0.0540   0.0070 
+  0.0650   0.0039 
+  0.0415   0.0025 
+  0.0074   0.0033 
+ -0.0185   0.0059 
+ -0.0413   0.0073 
+ -0.0548   0.0074 
+ -0.0385   0.0041 
+ -0.0383  -0.0006 
+ -0.0584  -0.0008 
+ -0.0584   0.0023 
+ -0.0553   0.0090 
+ -0.0772   0.0146 
+ -0.0757   0.0157 
+ -0.0644   0.0144 
+ -0.0816   0.0141 
+ -0.1045   0.0148 
+ -0.0867   0.0111 
+ -0.0365   0.0014 
+  0.0113  -0.0067 
+  0.0272  -0.0074 
+  0.0381  -0.0012 
+  0.0548   0.0021 
+  0.0470   0.0012 
+  0.0227  -0.0019 
+  0.0132  -0.0022 
+  0.0040   0.0004 
+ -0.0045   0.0008 
+ -0.0145   0.0006 
+ -0.0116   0.0025 
+ -0.0031   0.0044 
+ -0.0148   0.0086 
+ -0.0318   0.0109 
+ -0.0166   0.0078 
+  0.0154   0.0036 
+  0.0451   0.0018 
+  0.0364   0.0021 
+  0.0125   0.0036 
+  0.0330   0.0045 
+  0.0605   0.0048 
+  0.0417   0.0041 
+  0.0115   0.0011 
+  0.0257  -0.0018 
+  0.0451  -0.0029 
+  0.0387  -0.0032 
+  0.0254  -0.0017 
+  0.0311  -0.0001 
+  0.0448   0.0006 
+  0.0499   0.0020 
+  0.0543   0.0037 
+  0.0486   0.0054 
+  0.0459   0.0051 
+  0.0715  -0.0001 
+  0.0764  -0.0063 
+  0.0603  -0.0119 
+  0.0378  -0.0153 
+  0.0214  -0.0124 
+  0.0063  -0.0091 
+ -0.0095  -0.0016 
+ -0.0259   0.0036 
+ -0.0234   0.0061 
+  0.0012   0.0060 

regtest/dimred/rt-mds2/config

+type=simplemd
+

regtest/dimred/rt-mds2/in

+inputfile input.xyz
+outputfile output.xyz
+temperature 0.2
+tstep 0.005
+friction 1
+forcecutoff 2.5
+listcutoff  3.0
+ndim 2
+nstep 2000
+nconfig 1000 trajectory.xyz
+nstat   1000 energies.dat

regtest/dimred/rt-mds2/input.xyz

+7  
+100. 100. 100.       
+Ar 7.3933470660       -2.6986483924        0.0000000000
+Ar 7.8226765198       -0.7390907295        0.0000000000
+Ar 7.1014969839       -1.6164766614        0.0000000000
+Ar 8.2357184242       -1.7097824975        0.0000000000
+Ar 6.7372520842       -0.5111536183        0.0000000000
+Ar 6.3777119489       -2.4640437401        0.0000000000
+Ar 5.9900631495       -1.3385375043        0.0000000000

regtest/dimred/rt-mds2/list_embed.reference

+#! FIELDS mds.1 mds.2
+  0.0594   0.0053 
+  0.0683   0.0034 
+  0.0705   0.0006 
+  0.0729  -0.0019 
+  0.0874  -0.0069 
+  0.0961  -0.0095 
+  0.0867  -0.0062 
+  0.0719  -0.0008 
+  0.0575   0.0031 
+  0.0552   0.0034 
+  0.0682  -0.0002 
+  0.0781  -0.0024 
+  0.0785  -0.0025 
+  0.0763  -0.0027 
+  0.0755  -0.0041 
+  0.0792  -0.0069 
+  0.0778  -0.0062 
+  0.0727  -0.0025 
+  0.0726   0.0014 
+  0.0756   0.0030 
+  0.0821   0.0017 
+  0.0816   0.0001 
+  0.0774   0.0008 
+  0.0766   0.0008 
+  0.0838  -0.0005 
+  0.0931  -0.0016 
+  0.0936  -0.0010 
+  0.0923  -0.0009 
+  0.0906  -0.0008 
+  0.0706   0.0025 
+  0.0664   0.0050 
+  0.0901   0.0019 
+  0.1059  -0.0015 
+  0.0917   0.0006 
+  0.0876   0.0021 
+  0.1008  -0.0001 
+  0.0955  -0.0014 
+  0.0858  -0.0018 
+  0.0894  -0.0005 
+  0.0922   0.0014 
+  0.0917   0.0010 
+  0.0925  -0.0043 
+  0.0967  -0.0102 
+  0.1073  -0.0096 
+  0.1065  -0.0047 
+  0.0935  -0.0003 
+  0.0668   0.0049 
+  0.0410   0.0086 
+  0.0264   0.0110 
+  0.0254   0.0125 
+  0.0503   0.0085 
+  0.0855   0.0007 
+  0.0975  -0.0028 
+  0.0983  -0.0035 
+  0.0997  -0.0044 
+  0.0877  -0.0021 
+  0.0501   0.0053 
+  0.0104   0.0140 
+ -0.0199   0.0221 
+ -0.0416   0.0277 
+ -0.0688   0.0338 
+ -0.0858   0.0354 
+ -0.0897   0.0313 
+ -0.0920   0.0254 
+ -0.1168   0.0227 
+ -0.1447   0.0227 
+ -0.1636   0.0221 
+ -0.1461   0.0182 
+ -0.1212   0.0139 
+ -0.0775   0.0056 
+ -0.0008  -0.0041 
+  0.0469  -0.0038 
+  0.0771  -0.0004 
+  0.0917   0.0005 
+  0.0656   0.0042 
+ -0.0034   0.0115 
+ -0.0901   0.0141 
+ -0.1784   0.0069 
+ -0.2253  -0.0077 
+ -0.2372  -0.0248 
+ -0.2415  -0.0448 
+ -0.2562  -0.0539 
+ -0.2901  -0.0433 
+ -0.3173  -0.0215 
+ -0.3117   0.0096 
+ -0.2787   0.0317 
+ -0.2319   0.0372 
+ -0.1897   0.0305 
+ -0.1592   0.0142 
+ -0.1212  -0.0049 
+ -0.0960  -0.0150 
+ -0.0842  -0.0162 
+ -0.0813  -0.0187 
+ -0.0823  -0.0193 
+ -0.0773  -0.0179 
+ -0.0621  -0.0202 
+ -0.0449  -0.0215 
+ -0.0269  -0.0307 
+ -0.0075  -0.0368 
+  0.0266  -0.0342 

regtest/dimred/rt-mds2/plumed.dat

+UNITS NATURAL
+COM ATOMS=1-7 LABEL=com
+DISTANCE ATOMS=1,com LABEL=d1
+UPPER_WALLS ARG=d1 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=2,com LABEL=d2
+UPPER_WALLS ARG=d2 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=3,com LABEL=d3
+UPPER_WALLS ARG=d3 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=4,com LABEL=d4
+UPPER_WALLS ARG=d4 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=5,com LABEL=d5
+UPPER_WALLS ARG=d5 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=6,com LABEL=d6
+UPPER_WALLS ARG=d6 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=7,com LABEL=d7
+UPPER_WALLS ARG=d7 AT=2.0 KAPPA=100.
+
+COORDINATIONNUMBER SPECIES=1-7 MOMENTS=2-3 SWITCH={RATIONAL R_0=1.5 NN=8 MM=16} LABEL=c1
+
+ff: COLLECT_FRAMES ATOMS=1-7 STRIDE=10 RUN=1000
+oo: EUCLIDEAN_DISSIMILARITIES ARG=c1.moment-2,c1.moment-3 FRAMES=ff
+
+CLASSICAL_MDS ... 
+  USE_OUTPUT_DATA_FROM=oo
+  NLOW_DIM=2
+  LABEL=mds
+... CLASSICAL_MDS
+
+OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=mds FILE=list_embed FMT=%8.4f 
+OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=mds FILE=embed FMT=%8.4f

src/analysis/AnalysisBase.cpp

@@ -52,7 +52,7 @@ mydata(NULL)
   if( datastr.length()>0 ){
       mydata=plumed.getActionSet().selectWithLabel<AnalysisBase*>( datastr );
       ReadAnalysisFrames* checkt = dynamic_cast<ReadAnalysisFrames*>( mydata );
-      if( checkt ) error("READ_ANALYSIS_FRAMES should only be used in association with READ_DISSSIMILARITY_MATRIX"); 
+      if( checkt ) error("READ_ANALYSIS_FRAMES should only be used in input to the FRAMES keyword"); 
       log.printf("  performing analysis on output from %s \n",datastr.c_str() );
       if( !mydata ) error("could not find analysis action named " + datastr );
       freq=mydata->freq; use_all_data=mydata->use_all_data;

src/analysis/AnalysisBase.h

@@ -85,8 +85,6 @@ public:
   virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
 /// Get a reference configuration (in dimensionality reduction this returns the projection)
   virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata  );
-/// Get the input configuration (in dimensionality reduction this returns the high dimensional configuration)
-  virtual ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
 /// This actually performs the analysis
   virtual void performAnalysis()=0;
 /// These overwrite things from inherited classes (this is a bit of a fudge)
@@ -170,11 +168,6 @@ ReferenceConfiguration* AnalysisBase::getReferenceConfiguration( const unsigned&
   return mydata->getReferenceConfiguration( idata );
 }
 
-inline
-ReferenceConfiguration* AnalysisBase::getInputReferenceConfiguration( const unsigned& idata ){
-  return mydata->getInputReferenceConfiguration( idata );
-}
-
 }
 }
 

src/analysis/AnalysisWithDataCollection.cpp

@@ -46,6 +46,9 @@ void AnalysisWithDataCollection::registerKeywords( Keywords& keys ){
   keys.addFlag("USE_ALL_DATA",false,"just analyse all the data in the trajectory.  This option should be used in tandem with ATOMS/ARG + STRIDE");
   keys.addFlag("REWEIGHT_BIAS",false,"reweight the data using all the biases acting on the dynamics.  This option must be used in tandem with ATOMS/ARG + STRIDE + RUN/USE_ALL_DATA. " 
                                      "For more information see \\ref analysisbas");
+  keys.reserve("optional","FRAMES","with this keyword you can specify the atomic configurations that you would like to store using "
+                                   "an COLLECT_FRAMES action.  When the projection is output in dimensionality reduction you will then "
+                                   "print the underlying atoms and their projection");
   keys.add("optional","REWEIGHT_TEMP","reweight data from a trajectory at one temperature and output the probability distribution at a second temperature.  This option must be used in tandem with ATOMS/ARG + STRIDE + RUN/USE_ALL_DATA. "
                                       "For more information see \\ref analysisbas");
   keys.add("optional","TEMP","the system temperature. This is required if you are reweighting (REWEIGHT_BIAS/REWEIGHT_TEMP) or if you are calculating free energies. You are not required to specify the temperature if this is passed by the underlying MD code.");
@@ -63,13 +66,25 @@ write_chq(false),
 rtemp(0),
 idata(0),
 firstAnalysisDone(false),
-old_norm(0.0)
+old_norm(0.0),
+myframes(NULL)
 {
   if( !mydata ){
+      // Check for FRAMES keyword that allows us to read reference configurations from elsewhere
+      std::string instring; if( keywords.exists("FRAMES") ) parse("FRAMES",instring);
+      if( instring.length()>0 ){
+          if( mydata ) error("frames keyword is not compatible with USE_OUTPUT_DATA_FROM");
+          myframes=plumed.getActionSet().selectWithLabel<ReadAnalysisFrames*>( instring );
+          if( !myframes ) error( instring + " is not the name of an object that collects trajectory data");
+          log.printf("  frames are stored by object with label %s \n",instring.c_str() );
+          freq=myframes->freq; use_all_data=myframes->use_all_data; setStride( myframes->getStride() );
+      }
+
       // Check if we are using the input data from another action
       std::string datastr; 
       if( keywords.exists("REUSE_INPUT_DATA_FROM") ) parse("REUSE_INPUT_DATA_FROM",datastr);
       if( datastr.length()>0 ) {
+         if( myframes ) error("FRAMES command is incompatible with REUSE_INPUT_DATA_FROM");
          AnalysisWithDataCollection* checkd = plumed.getActionSet().selectWithLabel<AnalysisWithDataCollection*>( datastr );       
          if( !checkd) error("cannot reuse input data from action with label " + datastr + " as this does not store data");
          ReadAnalysisFrames* checkt = dynamic_cast<ReadAnalysisFrames*>( checkd );
@@ -129,31 +144,49 @@ old_norm(0.0)
              metricname="";
          }
 
-         // Read in the information about how often to run the analysis (storage is read in in ActionPilot.cpp)
-         if( keywords.exists("USE_ALL_DATA") ){
-             if( !keywords.exists("RUN") ) use_all_data=true;
-             else parseFlag("USE_ALL_DATA",use_all_data);
-         }
-         if(!use_all_data){
-             if( keywords.exists("RUN") ) parse("RUN",freq); 
-             // Setup everything given the ammount of data that we will have in each analysis 
-             if( freq%getStride()!= 0 ) error("Frequncy of running is not a multiple of the stride");
-             unsigned ndata=freq/getStride(); data.resize(ndata); logweights.resize( ndata );
-             for(unsigned i=0;i<ndata;++i) data[i]=metricRegister().create<ReferenceConfiguration>( metricname );
-             log.printf("  running analysis every %u steps\n",freq);
-             // Check if we are doing block averaging
-             nomemory=false;
-             if( keywords.exists("NOMEMORY") ) parseFlag("NOMEMORY",nomemory);
-             if(nomemory) log.printf("  doing block averaging and analysing each portion of trajectory separately\n");
+         bool dobias;
+         if( !myframes ){
+             // Read in the information about how often to run the analysis (storage is read in in ActionPilot.cpp)
+             if( keywords.exists("USE_ALL_DATA") ){
+                 if( !keywords.exists("RUN") ) use_all_data=true;
+                 else parseFlag("USE_ALL_DATA",use_all_data);
+             }
+             if(!use_all_data){
+                 if( keywords.exists("RUN") ) parse("RUN",freq); 
+                 // Setup everything given the ammount of data that we will have in each analysis 
+                 if( freq%getStride()!= 0 ) error("Frequncy of running is not a multiple of the stride");
+                 // Check if we are doing block averaging
+                 nomemory=false;
+                 if( keywords.exists("NOMEMORY") ) parseFlag("NOMEMORY",nomemory);
+                 if(nomemory) log.printf("  doing block averaging and analysing each portion of trajectory separately\n");
+             } else {
+                 log.printf("  analysing all data in trajectory\n");
+             }
+
+             // Read in stuff for reweighting of trajectories
+
+             // Reweighting for biases
+             if( keywords.exists("REWEIGHT_BIAS") ) parseFlag("REWEIGHT_BIAS",dobias);
+
+             // Reweighting for temperatures
+             rtemp=0; 
+             if( keywords.exists("REWEIGHT_TEMP") ) parse("REWEIGHT_TEMP",rtemp);
+             if( rtemp!=0 ){ 
+                 rtemp*=plumed.getAtoms().getKBoltzmann(); 
+                 log.printf("  reweighting simulation to probabilities at temperature %f\n",rtemp);
+             }
+             // Now retrieve the temperature in the simulation
+             simtemp=0; 
+             if( keywords.exists("TEMP") ) parse("TEMP",simtemp); 
+             if(simtemp>0) simtemp*=plumed.getAtoms().getKBoltzmann();
+             else simtemp=plumed.getAtoms().getKbT();
+             if(simtemp==0 && (rtemp!=0 || !biases.empty()) ) error("The MD engine does not pass the temperature to plumed so you have to specify it using TEMP");
          } else {
-             log.printf("  analysing all data in trajectory\n");
+             nomemory = myframes->nomemory; dobias = (myframes->biases.size()>0);
+             rtemp = myframes->rtemp; simtemp = myframes->simtemp;
          }
 
-         // Read in stuff for reweighting of trajectories
-
-         // Reweighting for biases
-         bool dobias; 
-         if( keywords.exists("REWEIGHT_BIAS") ) parseFlag("REWEIGHT_BIAS",dobias);
+         // Setup bias reweighting
          if( dobias ){
              std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
              if( all.empty() ) error("your input file is not telling plumed to calculate anything");
@@ -171,20 +204,13 @@ old_norm(0.0)
              if( biases.empty() ) error("you are asking to reweight bias but there does not appear to be a bias acting on your system");
              requestArguments( arg );
          }
-
-         // Reweighting for temperatures
-         rtemp=0; 
-         if( keywords.exists("REWEIGHT_TEMP") ) parse("REWEIGHT_TEMP",rtemp);
-         if( rtemp!=0 ){ 
-            rtemp*=plumed.getAtoms().getKBoltzmann(); 
-            log.printf("  reweighting simulation to probabilities at temperature %f\n",rtemp);
+         // Setup reference configuration objects to store data
+         if( !use_all_data ){
+             plumed_assert( !mydata );
+             log.printf("  running analysis every %u steps\n",freq);
+             unsigned ndata=freq/getStride(); data.resize(ndata); logweights.resize( ndata );
+             for(unsigned i=0;i<ndata;++i) data[i]=metricRegister().create<ReferenceConfiguration>( metricname );
          }
-         // Now retrieve the temperature in the simulation
-         simtemp=0; 
-         if( keywords.exists("TEMP") ) parse("TEMP",simtemp); 
-         if(simtemp>0) simtemp*=plumed.getAtoms().getKBoltzmann();
-         else simtemp=plumed.getAtoms().getKbT();
-         if(simtemp==0 && (rtemp!=0 || !biases.empty()) ) error("The MD engine does not pass the temperature to plumed so you have to specify it using TEMP");
 
          // Check if a check point is required   (this should be got rid of at some point when we have proper checkpointing) GAT
          if( keywords.exists("WRITE_CHECKPOINT") ) parseFlag("WRITE_CHECKPOINT",write_chq);
@@ -207,8 +233,8 @@ old_norm(0.0)
             for(unsigned i=0;i<getNumberOfArguments();++i) rfile.setupPrintValue( getPntrToArgument(i) );
          }
          // This is the end of the stuff for the checkpoint file - hopefully get rid of all this in not too distant future  GAT
-      }
-  }
+     }
+     }
 }
 
 AnalysisWithDataCollection::~AnalysisWithDataCollection(){
@@ -264,15 +290,14 @@ void AnalysisWithDataCollection::getDataPoint( const unsigned& idat, std::vector
 }
 
 ReferenceConfiguration* AnalysisWithDataCollection::getReferenceConfiguration( const unsigned& idat ){
-  if( !mydata ){ plumed_dbg_assert( idat<data.size() ); return data[idat]; }
+  if( !mydata ){ 
+     plumed_dbg_assert( idat<data.size() ); 
+     if( myframes ) return myframes->getReferenceConfiguration( idat );
+     return data[idat]; 
+  }
   return AnalysisBase::getReferenceConfiguration( idat );
 }
 
-ReferenceConfiguration* AnalysisWithDataCollection::getInputReferenceConfiguration( const unsigned& idat ){
-  if( !mydata ){ plumed_dbg_assert( idat<data.size() ); return data[idat]; }
-  return AnalysisBase::getInputReferenceConfiguration( idat );
-}
-
 void AnalysisWithDataCollection::update(){
   if( mydata ){ AnalysisBase::update(); return; }
   // Ignore first bit of data if we are not using all data - this is a weird choice - I am not sure I understand GAT (perhaps this should be changed)?

src/analysis/AnalysisWithDataCollection.h

@@ -31,7 +31,11 @@ class ReferenceConfiguration;
 
 namespace analysis {
 
+class ReadAnalysisFrames;
+
 class AnalysisWithDataCollection : public AnalysisBase {
+friend class EuclideanDissimilarityMatrix;
+friend class ReadDissimilarityMatrix;
 private:
 /// Are we treating each block of data separately
   bool nomemory;
@@ -53,6 +57,9 @@ private:
   bool firstAnalysisDone;
 /// The value of the old normalization constant
   double norm, old_norm;
+/// This allows you to output trajectory data with the projections
+/// in EUCLIDEAN_DISSIMLAIRITIES and READ_DISSIMILARITY_MATRIX
+  ReadAnalysisFrames* myframes;
 /// Data is collected from the trajectory by passing it to this pdb.  These pdb
 /// files are then read by the ReferenceConfigurations in data
   PDB mypdb;
@@ -93,8 +100,6 @@ public:
   virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
 /// Get a reference configuration (in dimensionality reduction this returns the projection)
   virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
-/// Get the underlying reference configuration (in dimensionality reduction this return the high dimensional point)
-  ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idat );
 /// This ensures that the energy is stored if we are reweighting
   void prepare();
 /// This stores the data and calls the analysis to be performed

src/analysis/EuclideanDissimilarityMatrix.cpp

@@ -55,7 +55,7 @@ PLUMED_REGISTER_ACTION(EuclideanDissimilarityMatrix,"EUCLIDEAN_DISSIMILARITIES")
 
 void EuclideanDissimilarityMatrix::registerKeywords( Keywords& keys ){
   AnalysisWithDataCollection::registerKeywords( keys );
-  keys.reset_style("METRIC","atoms-1");
+  keys.reset_style("METRIC","atoms-1"); keys.use("FRAMES");
 }
 
 EuclideanDissimilarityMatrix::EuclideanDissimilarityMatrix( const ActionOptions& ao ):
@@ -72,8 +72,15 @@ void EuclideanDissimilarityMatrix::performAnalysis(){
 double EuclideanDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const unsigned& jframe ){
   plumed_dbg_assert( iframe<dissimilarities.nrows() && jframe<dissimilarities.ncols() );
   if( dissimilarities(iframe,jframe)>0. ){ return dissimilarities(iframe,jframe); }
-  if( iframe!=jframe ){ 
-     dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = distance( getPbc(), getArguments(), getReferenceConfiguration(iframe), getReferenceConfiguration(jframe), true ); 
+  if( iframe!=jframe ){
+     ReferenceConfiguration* myref1; ReferenceConfiguration* myref2; 
+     if( mydata ){ myref1=AnalysisBase::getReferenceConfiguration(iframe); myref2=AnalysisBase::getReferenceConfiguration(jframe); }
+     else { myref1 = data[iframe]; myref2 = data[jframe]; }
+     if( myref1->getNumberOfProperties()>0 ){
+        dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = property_distance( myref1, myref2, true );
+     } else {
+        dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = distance( getPbc(), getArguments(), myref1, myref2, true ); 
+     }
      return dissimilarities(iframe,jframe);
   }
   return 0.0;

src/analysis/ReadAnalysisFrames.cpp

@@ -24,7 +24,7 @@
 #include "core/ActionSet.h"
 #include "core/ActionRegister.h"
 
-//+PLUMEDOC ANALYSIS READ_ANALYSIS_FRAMES
+//+PLUMEDOC ANALYSIS COLLECT_FRAMES
 /* 
 This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object
 
@@ -36,21 +36,17 @@ This allows you to convert a trajectory and a dissimilarity matrix into a dissim
 namespace PLMD {
 namespace analysis {
 
-PLUMED_REGISTER_ACTION(ReadAnalysisFrames,"READ_ANALYSIS_FRAMES")
+PLUMED_REGISTER_ACTION(ReadAnalysisFrames,"COLLECT_FRAMES")
 
 void ReadAnalysisFrames::registerKeywords( Keywords& keys ){
   AnalysisWithDataCollection::registerKeywords( keys ); 
-  keys.reset_style("USE_ALL_DATA","hidden"); keys.remove("RUN"); keys.remove("REWEIGHT_BIAS"); keys.remove("REWEIGHT_TEMP"); 
-  keys.remove("TEMP"); keys.remove("WRITE_CHECKPOINT"); keys.remove("NOMEMORY"); keys.remove("RESTART"); 
-  keys.remove("UPDATE_FROM"); keys.remove("UPDATE_UNTIL"); keys.remove("USE_OUTPUT_DATA_FROM");
-  keys.remove("ARG"); keys.remove("SERIAL"); keys.remove("REUSE_INPUT_DATA_FROM");
+  keys.remove("ARG"); keys.remove("SERIAL"); keys.remove("USE_OUTPUT_DATA_FROM");
 }
 
 ReadAnalysisFrames::ReadAnalysisFrames( const ActionOptions& ao ):
 Action(ao),
 AnalysisWithDataCollection(ao)
 {
-  if( plumed.getActionSet().size()!=0 ) error("read analysis frames command must be at top of input file");
 }
 
 }