added support for interrupt handling

CMakeLists.txt

@@ -10,6 +10,11 @@ if(NOT ENVSRCDIR)
 	MESSAGE(STATUS $ENV{MYGMX_SRC})
 	MESSAGE(FATAL_ERROR "\nERROR: set the variables MYGMX_SRC  and MYGMX_BUILD to specify a particular path for gromacs source and build directories" )
 endif(NOT ENVSRCDIR)
+
+IF(${UNIX}) 
+ ADD_DEFINITIONS(-DUNIX)
+ENDIF(${UNIX})
+
 #IF(VIRIAL_EXTENSION)
 #	 add_definitions(-DVIRIAL_EXTENSION)
 #ENDIF(VIRIAL_EXTENSION)

README

@@ -11,10 +11,10 @@ website
 
     http://www.gitim.eu 
 
-<<<<<<< HEAD
-=======
+or on the github pages
+
+    http://marcello-sega.github.io/gitim/
 
->>>>>>> cluster-analysis
 Neither the gromacs and kdtree developers nor any other person but
 those listed below are responsible for the changes introduced in
 this derivative work, so please do not ask them for support and do

gmx_density.c

@@ -71,7 +71,12 @@ NOTE: how to acess atom properties
 #include "tpxio.h"
 #include "gmx_ana.h"
 #include <nbsearch.h>
-
+#ifdef UNIX  
+// used for handling signals
+#include<stdio.h>
+#include<signal.h>
+#include<unistd.h>
+#endif //UNIX
 
 #define gmx_ffopen ffopen
 #define gmx_ffclose ffclose
@@ -122,6 +127,9 @@ NOTE: how to acess atom properties
 #endif
 
 #define NORMAL_UNDEFINED -100
+
+int global_interrupt = 0;
+
 typedef	enum { SUPPORT_PHASE=0, INNER_PHASE=1, OUTER_PHASE=2 } PHASE; // These value are not arbitrary and should not be changed.
  /* These value are not arbitrary and should not be changed: 
       OFF_NUMBER    -> for number density profile, used to normalize the order parameter density profile as well.
@@ -1330,16 +1338,17 @@ void collect_statistics_for_layers(ITIM * itim, t_trxframe * fr){
 	}
  	for(i=0;i<itim->n[SUPPORT_PHASE];i++){
 	       atom_index = itim->gmx_index[SUPPORT_PHASE][i];
+               double m = itim->masses[atom_index];
 	       if(itim->mask[i]>0 && itim->mask[i]< itim->maxlayers+1){
 		 layer = itim->mask[i]-1;
 		 n[layer]+=1;
 #ifdef VIRIAL_EXTENSION
                  f[3*layer]   += fr->f[atom_index][0];
                  f[3*layer+1] += fr->f[atom_index][1];
                  f[3*layer+2] += fr->f[atom_index][2];
-                 vir[3*layer]   += fr->vir[atom_index][0];
-                 vir[3*layer+1] += fr->vir[atom_index][1];
-                 vir[3*layer+2] += fr->vir[atom_index][2];
+                 vir[3*layer]   +=  fr->vir[atom_index][0];
+                 vir[3*layer+1] +=  fr->vir[atom_index][1];
+                 vir[3*layer+2] +=  fr->vir[atom_index][2];
 #endif
                }
         }
@@ -2598,12 +2607,12 @@ void compute_layer_profile(matrix box,atom_id ** gmx_index_phase,t_topology * to
 					case 't': 
 						copy_rvec(fr->vir[itim->gmx_alpha_id[i]],tmprvec);
 						tmpreal = itim->box[0]*itim->box[1]*itim->box[2];
-						value = (0.5 * (tmprvec[0]+tmprvec[1]) - tmprvec[2]) / tmpreal;  // TODO: other directions than z ...
+						value = (-0.5 * (tmprvec[0]+tmprvec[1]) + tmprvec[2]) / tmpreal;  
 						break;
 					case 'p': 
 						copy_rvec(fr->vir[itim->gmx_alpha_id[i]],tmprvec);
 						tmpreal = itim->box[0]*itim->box[1]*itim->box[2];
-						value = (tmprvec[2]) / tmpreal;  // TODO: other directions than z ...
+						value = ( tmprvec[2]) / tmpreal; 
 						break;
 #endif
 					default : value =1 ; break;
@@ -3353,6 +3362,17 @@ void flip_atoms_in_box(int natoms, int normal,  rvec * x0){
 	}
 }
 
+#ifdef UNIX
+void sig_handler(int signo)
+{
+  if (signo == SIGINT) { 
+    printf("\n\n === Caught SIGINT, trying to terminate analysis and save all files...\n\n");
+    global_interrupt = 1 ;
+  }
+}
+#endif //UNIX
+
+
 void calc_intrinsic_density(const char *fn, atom_id **index, int gnx[],
 		  real ***slDensity, int *nslices, int maxlayers, t_topology *top, int ePBC,
 		  int axis, int nr_grps, real *slWidth, const output_env_t oenv,
@@ -3378,7 +3398,7 @@ void calc_intrinsic_density(const char *fn, atom_id **index, int gnx[],
 	radii = load_radii(top);
 //        if ((natoms = read_first_x(oenv,&status,fn,&t,&x0,box)) == 0)
 //          gmx_fatal(FARGS,"Could not read coordinates from statusfile\n");
-	flags = TRX_READ_X |  TRX_READ_F ;
+	flags = TRX_READ_X | TRX_READ_V |  TRX_READ_F ;
 	if (!read_first_frame(oenv, &status,  fn , &fr, flags))
           gmx_fatal(FARGS,"Error loading the trajectory\n");
 	for(int i=0;i<3;i++) for(int j=0;j<3;j++) box[i][j] = fr.box[i][j];
@@ -3410,6 +3430,12 @@ void calc_intrinsic_density(const char *fn, atom_id **index, int gnx[],
 	if(bInclusive) check_inclusive_conditions(index, gnx);
 	do { 
 // (SAW) BUG : when no pbc are defined, it loops forever... 
+#ifdef UNIX
+		if (signal(SIGINT, sig_handler) == SIG_ERR) {
+			printf("Error handling SIGINT");
+			// sets global_interrupt to 1 when catching SIGINT
+		}
+#endif //UNIX
 		x0 = fr.x;	
         	natoms = fr.natoms;
 		for(int i=0;i<3;i++) for(int j=0;j<3;j++) box[i][j] = fr.box[i][j];
@@ -3454,7 +3480,7 @@ void calc_intrinsic_density(const char *fn, atom_id **index, int gnx[],
  		   compute_intrinsic_profile(box, index, top,dens_opt, & fr); 
                 }
 
-  	} while (read_next_frame(oenv,status,&fr));
+  	} while (read_next_frame(oenv,status,&fr) &&  (global_interrupt == 0) );
 
         if(surf_cid  !=NULL)fclose(surf_cid);
         if(surfmol_cid!=NULL)fclose(surfmol_cid);