From bb4bee8899e83ca9365e550fdb1f3f3e79ef250a Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Wed, 11 Jul 2018 12:08:55 +0100
Subject: [PATCH] Fixed small bug in reading of dissimilarity matrices
---
src/analysis/ReadDissimilarityMatrix.cpp | 6 ++++++
src/dimred/SketchMap.cpp | 2 +-
2 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/src/analysis/ReadDissimilarityMatrix.cpp b/src/analysis/ReadDissimilarityMatrix.cpp
index 052b33f6e..324a177a9 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 70a068ed7..b1cc7043d 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) {
--
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