diff --git a/src/analysis/ReadDissimilarityMatrix.cpp b/src/analysis/ReadDissimilarityMatrix.cpp index 052b33f6e9b3f42d4d1114a120606771e51f5221..324a177a9bae3697e730fb9089d6c5dd3bb0d816 100644 --- a/src/analysis/ReadDissimilarityMatrix.cpp +++ b/src/analysis/ReadDissimilarityMatrix.cpp @@ -53,6 +53,8 @@ public: static void registerKeywords( Keywords& keys ); ReadDissimilarityMatrix( const ActionOptions& ao ); unsigned getNumberOfDataPoints() const ; +// Return the index of the data point in the base class + unsigned getDataPointIndexInBase( const unsigned& idata ) const ; /// This gives an error as if we read in the matrix we dont have the coordinates DataCollectionObject& getStoredData( const unsigned& idata, const bool& calcdist ); /// Tell everyone we have dissimilarities @@ -141,6 +143,10 @@ unsigned ReadDissimilarityMatrix::getNumberOfDataPoints() const { return dissimilarities.size(); } +unsigned ReadDissimilarityMatrix::getDataPointIndexInBase( const unsigned& idata ) const { + return idata; +} + double ReadDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const unsigned& jframe ) { return dissimilarities[iframe][jframe]*dissimilarities[iframe][jframe]; } diff --git a/src/dimred/SketchMap.cpp b/src/dimred/SketchMap.cpp index 70a068ed715c2e3c2f2436ec6bc8e241c0950f68..b1cc7043d13e7c784b09066d09eb8473ea1d87e5 100644 --- a/src/dimred/SketchMap.cpp +++ b/src/dimred/SketchMap.cpp @@ -82,7 +82,7 @@ ActionShortcut(ao) std::string imds_line_pw = getShortcutLabel() + "_smap1_pw: SKETCHMAP_POINTWISE USE_OUTPUT_DATA_FROM=" + getShortcutLabel() + "_smap1_cg"; imds_line_pw += pw_step_input + " MIXPARAM=1.0"; readInputLine( imds_line_pw ); // Now sketch-map - unsigned asteps; parse("ANNEAL_STEPS",asteps); std::string psmap = getShortcutLabel() + "_smap1.0_pw"; + unsigned asteps; parse("ANNEAL_STEPS",asteps); std::string psmap = getShortcutLabel() + "_smap1_pw"; if( asteps>1 ) { double smear; parse("ANNEAL_RATE", smear); double old_mix = 1.0; double new_mix = old_mix*smear; for(unsigned i=0;i<asteps;++i) {