testing

diff --git a/src/spirals.cpp b/src/spirals.cpp
index 1bd341a19972296c99f8da8d5f5dc4a11204b754..3078b61b3f8f93291c570d5d9fec0c115ce9bc23 100644 (file)
--- a/src/spirals.cpp
+++ b/src/spirals.cpp
@@ -248,6 +248,7 @@ class Spirals : public TrajectoryAnalysisModule
         int                                     frames      = 0;
         double                                  epsi        = 0.01;
 
+        std::vector< std::vector< RVec > >                  monomers;
         std::vector< kernel_maxima >                        kernel;
         std::vector< std::vector< std::vector< int > > >    circles;
 };
@@ -286,6 +287,7 @@ Spirals::initAnalysis(const TrajectoryAnalysisSettings &settings,
 {
     kernel.resize(0);
     circles.resize(0);
+    monomers.resize(0);
 }
 
 void
@@ -299,6 +301,11 @@ Spirals::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
         copy_rvec(sel[i].position(0).x(), temp[i]);
     }
 
+    monomers.resize(monomers.size() + 1);
+    for (int i = 0; i < sel.size(); i++) {
+        monomers.back().push_back(temp[i]);
+    }
+
     RVec mid, arrow;
 
     mid[0] = 0;
@@ -374,9 +381,15 @@ Spirals::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
 void
 Spirals::finishAnalysis(int /*nframes*/)
 {
+
+
+
     FILE *file;
-    file = std::fopen("linear kernel.txt", "w+");
+    file = std::fopen("linear_kernel.txt", "w+");
     for (int i = 0; i < kernel.size(); i++) {
+        for (int j = 0; j < monomers[i].size(); j++) {
+            std::fprintf(file, "%3.2f %3.2f %3.2f\n", monomers[i][j][0], monomers[i][j][1], monomers[i][j][2]);
+        }
         for (int j = 0; j < kernel[i].krnl.size(); j++) {
             std::fprintf(file, "%3.2f %3.2f %3.2f\n", kernel[i].krnl[j][0], kernel[i].krnl[j][1], kernel[i].krnl[j][2]);
         }
@@ -386,7 +399,9 @@ Spirals::finishAnalysis(int /*nframes*/)
 
 
 
-    /*file = std::fopen("spiral_dist.txt", "w+");
+    /*
+    FILE *file;
+    file = std::fopen("spiral_dist.txt", "w+");
     for (int i = 0; i < spiral_dist.size(); i++) {
         for (int j = 0; j < spiral_dist[i].size(); j++) {
             std::fprintf(file, "%3.2Lf\n", spiral_dist[i][j]);