From 76a2202f9325bca140f76bfd8f73ef127a335ce9 Mon Sep 17 00:00:00 2001
From: Alexey Shvetsov <alexxy@gentoo.org>
Date: Wed, 11 Jul 2018 10:15:10 +0300
Subject: [PATCH] NS enable

Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
---
 .gitignore   |  2 +-
 src/sans.cpp | 21 ++++++++++++++++++---
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index 8c730ba..fa89576 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,4 @@
 *.creator.user
 *.files
 *.includes
-
+*.user
diff --git a/src/sans.cpp b/src/sans.cpp
index b738de9..bfd4d0e 100644
--- a/src/sans.cpp
+++ b/src/sans.cpp
@@ -66,13 +66,15 @@ class SANS : public TrajectoryAnalysisModule
 
         std::string                      fnNdx_;
         double                           cutoff_;
+        double                           grid_;
 
         AnalysisNeighborhood             nb_;
+        const TopologyInformation          *top_;
 
 };
 
 SANS::SANS()
-    : cutoff_(1.0)
+    : cutoff_(1.0), grid_(0.05)
 {
 }
 
@@ -97,14 +99,27 @@ void
 SANS::initAnalysis(const TrajectoryAnalysisSettings &settings,
                                const TopologyInformation         & top)
 {
+    nb_.setCutoff(cutoff_);
+    top_ = &top;
 }
 
 void
 SANS::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
                                TrajectoryAnalysisModuleData *pdata)
 {
-	RVec GridSpacing(0.1, 0.1, 0.1);
-	
+    RVec GridSpacing(0.1, 0.1, 0.1);
+    AnalysisNeighborhoodSearch nbsearch = nb_.initSearch(pbc, AnalysisNeighborhoodPositions(fr.x, fr.natoms));
+    AnalysisNeighborhoodPairSearch pairSearch = nbsearch.startPairSearch(GridSpacing.as_vec());
+    AnalysisNeighborhoodPair pair;
+    t_topology *top = top_->topology();
+    while (pairSearch.findNextPair(&pair))
+      {
+          fprintf(stderr,"Index %d\n", pair.refIndex());
+          fprintf(stderr,"dx =  (%f, %f, %f)\n", pair.dx()[XX], pair.dx()[YY], pair.dx()[ZZ] );
+          fprintf(stderr,"ref =  (%f, %f, %f)\n", fr.x[pair.refIndex()][XX], fr.x[pair.refIndex()][YY], fr.x[pair.refIndex()][ZZ]);
+          fprintf(stderr,"ref_dx =  (%f, %f, %f)\n", GridSpacing[XX]+pair.dx()[XX], GridSpacing[YY]+pair.dx()[YY], GridSpacing[ZZ]+pair.dx()[ZZ] );
+
+      }
 }
 
 void
-- 
2.22.0