cleaned up for diploma

diff --git a/src/domains.cpp b/src/domains.cpp
index cf88944ae9581987703872248876a5ade2248d70..31709a7da946c9a37133f44e020e2848f04f51ce 100644 (file)
--- a/src/domains.cpp
+++ b/src/domains.cpp
@@ -43,15 +43,10 @@
 #include <iostream>
 #include <chrono>
 #include <omp.h>
-#include <thread>
-#include <string>
 
 #include <gromacs/trajectoryanalysis.h>
 #include <gromacs/pbcutil/pbc.h>
-#include <gromacs/pbcutil/rmpbc.h>
 #include <gromacs/utility/smalloc.h>
-#include <gromacs/math/vectypes.h>
-#include <gromacs/math/vec.h>
 #include <gromacs/math/do_fit.h>
 
 #define MAX_NTRICVEC 12
@@ -203,12 +198,12 @@ bool check_domsizes(std::vector< std::vector< int > > cd_domsizes, int cd_domain
     return false;
 }
 
-void print_domains(std::vector< std::vector< int > > pd_domains, std::vector< int > index, std::string fnNdx_) {
+void print_domains(std::vector< std::vector< int > > pd_domains, std::vector< int > index, std::string fnNdx_, int dms, double epsi, double delta) {
     FILE               *fpNdx_;
     fpNdx_ = std::fopen(fnNdx_.c_str(), "w+");
     int write_count;
     for (int i = 0; i < pd_domains.size(); i++) {
-        std::fprintf(fpNdx_, "[domain_%d]\n", i + 1);
+        std::fprintf(fpNdx_, "[domain_№_%3d_%3d_%4.3f_%4.3f]\n", i + 1, dms, epsi, delta);
         write_count = 0;
         for (int j = 0; j < pd_domains[i].size(); j++) {
             write_count++;
@@ -224,13 +219,7 @@ void print_domains(std::vector< std::vector< int > > pd_domains, std::vector< in
     std::fclose(fpNdx_);
 }
 
-
 /*! \brief
- * Class used to compute free volume in a simulations box.
- *
- * Inherits TrajectoryAnalysisModule and all functions from there.
- * Does not implement any new functionality.
- *
  * \ingroup module_trajectoryanalysis
  */
 class Domains : public TrajectoryAnalysisModule
@@ -282,11 +271,10 @@ class Domains : public TrajectoryAnalysisModule
 
         real                                                        **w_rls;
         int                                                         bone;
-        double                                                      delta               = 0.90; //0.95 // selectable
-        double                                                      epsi                = 0.15; //0.30 // selectable
+        double                                                      delta               = 0.90; // selectable
+        double                                                      epsi                = 0.15; // selectable
 
         int                                                         domains_ePBC;
-
         int                                                         DomainSearchingAlgorythm = 0; // selectable
         // Copy and assign disallowed by base.
 };
@@ -424,10 +412,6 @@ Domains::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
     std::cout << "frame: " << frames << " analyzed\n";
 }
 
-//domains -s '/home/toluk/Develop/samples/reca_rd/reca_rd.mono.tpr' -f '/home/toluk/Develop/samples/reca_rd/reca_rd.mono.xtc' -select 'name CA'
-//domains -s '/home/toluk/Develop/samples/banana_phone/pgk.md.non-sol.tpr' -f '/home/toluk/Develop/samples/banana_phone/pgk.md.non-sol.10th.xtc' -select 'name CA'
-//domains -s '/home/toluk/Data/reca_rd/reca_rd.mono.tpr' -f '/home/toluk/Data/reca_rd/reca_rd.mono.xtc' - select 'name CA'
-
 void
 Domains::finishAnalysis(int nframes)
 {
@@ -464,11 +448,10 @@ void
 Domains::writeOutput()
 {
     std::cout << "making output file\n";
-    print_domains(domains, index, fnNdx_); // see function for details | numbers from index
+    print_domains(domains, index, fnNdx_, domain_min_size, epsi, delta); // see function for details | numbers from index
     std::cout << "\n END \n";
 }
 
-
 /*! \brief
  * The main function for the analysis template.
  */