Run uncrustify

Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>

diff --git a/src/rcore.cpp b/src/rcore.cpp
index 56b3874005dd68358f5ca936444d86789d375934..95735b38deb765a8952eef0646df642d547c0048 100644 (file)
--- a/src/rcore.cpp
+++ b/src/rcore.cpp
@@ -76,15 +76,15 @@ class AnalysisTemplate : public TrajectoryAnalysisModule
 
         AnalysisData                     data_;
         AnalysisDataAverageModulePointer avem_;
-        
-        
+
+
         Selection                                           selec;
         std::vector< std::vector < RVec > >                 trajectory;
         std::vector< double >                               noise;
         std::vector< int >                                  index;
-        double                                              epsi = 0.1; // should be selectable
-        int                                                 etalon_frame = 0; // should be selectable
-        int                                                 frames = 0;
+        double                                              epsi         = 0.1; // should be selectable
+        int                                                 etalon_frame = 0;   // should be selectable
+        int                                                 frames       = 0;
 };
 
 
@@ -122,16 +122,16 @@ AnalysisTemplate::initOptions(IOptionsContainer          *options,
                            .store(&fnDist_).defaultBasename("avedist")
                            .description("Average distances from reference group"));
 
-    options->addOption(SelectionOption("reference")
+       options->addOption(SelectionOption("reference")
                            .store(&refsel_).required()
                            .description("Reference group to calculate distances from"));*/
     options->addOption(SelectionOption("select")
                            .store(&selec).required()
                            .description("Atoms that are considered as part of the excluded volume"));
-   /* options->addOption(DoubleOption("cutoff").store(&cutoff_)
-                           .description("Cutoff for distance calculation (0 = no cutoff)"));
+    /* options->addOption(DoubleOption("cutoff").store(&cutoff_)
+                            .description("Cutoff for distance calculation (0 = no cutoff)"));
 
-    settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);*/
+       settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);*/
 }
 
 void
@@ -140,7 +140,8 @@ AnalysisTemplate::initAnalysis(const TrajectoryAnalysisSettings &settings,
 {
     index.resize(0);
     ConstArrayRef< int > atomind = selec.atomIndices();
-    for (ConstArrayRef< int >::iterator ai = atomind.begin(); (ai < atomind.end()); ai++) {
+    for (ConstArrayRef< int >::iterator ai = atomind.begin(); (ai < atomind.end()); ai++)
+    {
         index.push_back(*ai);
     }
 }
@@ -152,7 +153,8 @@ AnalysisTemplate::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
 {
     trajectory.resize(frames + 1);
     trajectory[frames].resize(index.size());
-    for (int i = 0; i < index.size(); i++) {
+    for (int i = 0; i < index.size(); i++)
+    {
         trajectory[frames][i] = fr.x[index[i]];
     }
     frames++;
@@ -162,11 +164,11 @@ AnalysisTemplate::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
 void
 AnalysisTemplate::finishAnalysis(int /*nframes*/)
 {
-    real *w_rls;
-    rvec *x1, *x2, temp;
+    real               *w_rls;
+    rvec               *x1, *x2, temp;
     std::vector< bool > flag;
-    double noise_mid = 9999;
-    int count = 0;
+    double              noise_mid = 9999;
+    int                 count     = 0;
 
     snew(x1, index.size());
     snew(x2, index.size());
@@ -174,57 +176,73 @@ AnalysisTemplate::finishAnalysis(int /*nframes*/)
     flag.resize(index.size(), true);
     noise.resize(index.size(), 0);
 
-    while (noise_mid > epsi) {
+    while (noise_mid > epsi)
+    {
         noise_mid = 0;
-        count = 0;
+        count     = 0;
         noise.assign(index.size(), 0);
 
-        for (int i = 0; i < index.size(); i++) {
-            if (flag[i]) {
+        for (int i = 0; i < index.size(); i++)
+        {
+            if (flag[i])
+            {
                 w_rls[i] = 1;
-            } else {
+            }
+            else
+            {
                 w_rls[i] = 0;
             }
         }
 
-        for (int i = 0; i < frames; i++) {
-            for (int j = 0; j < trajectory[i].size(); j++) {
+        for (int i = 0; i < frames; i++)
+        {
+            for (int j = 0; j < trajectory[i].size(); j++)
+            {
                 copy_rvec(trajectory[i][j].as_vec(), x2[j]);
                 copy_rvec(trajectory[etalon_frame][j].as_vec(), x1[j]); // i think its nessesary to do because of lots of reset_x
             }
             reset_x(index.size(), NULL, index.size(), NULL, x1, w_rls);
             reset_x(index.size(), NULL, index.size(), NULL, x2, w_rls);
             do_fit(index.size(), w_rls, x1, x2);
-            if (i % 100 == 0) {
+            if (i % 100 == 0)
+            {
                 std::cout << i << " / " << frames << "\n";
             }
-            for (int j = 0; j < index.size(); j++) {
+            for (int j = 0; j < index.size(); j++)
+            {
                 rvec_sub(x1[j], x2[j], temp);
                 noise[j] += norm(temp);
             }
         }
 
-        for (int i = 0; i < index.size(); i++) {
+        for (int i = 0; i < index.size(); i++)
+        {
             noise[i] /= frames;
         }
 
-        for (int i = 0; i < index.size(); i++) {
-            if (flag[i]) {
+        for (int i = 0; i < index.size(); i++)
+        {
+            if (flag[i])
+            {
                 count++;
                 noise_mid += noise[i];
             }
         }
         noise_mid /= count;
 
-        for (int i = 0; i < index.size(); i++) {
-            if (noise[i] > noise_mid) {
+        for (int i = 0; i < index.size(); i++)
+        {
+            if (noise[i] > noise_mid)
+            {
                 flag[i] = false;
             }
         }
     }
 
-    for (int i = 0; i < noise.size(); i++) {
-        if (noise[i] <= epsi) {
+    for (int i = 0; i < noise.size(); i++)
+    {
+        if (noise[i] <= epsi)
+        {
             //fprintf(pFile, "%d ", i + 1);
             // numbers from index, +1 for starting from 1 not 0
         }