Update bonds when atoms moved individually

src/analysis.c

@@ -482,7 +482,7 @@ for (n=0 ; n<analysis->num_frames ; n++)
 */
 
 /* CURRENT - loop over all atoms - even duplicates so that we can record */
-/* distance between an atom and it's periodic images (NB: correct for double counting) */
+/* distance between an atom and its periodic images (NB: correct for double counting) */
   for (i=0 ; i<analysis->num_atoms ; i++)
     {
     corei = g_slist_nth_data(model->cores, i);

src/coords.c

@@ -47,6 +47,32 @@ The GNU GPL can also be found at http://www.gnu.org
 extern struct sysenv_pak sysenv;
 extern struct elem_pak elements[];
 
+#define DEBUG_CALC_CENTROID 0
+/*************************************/
+/* return centroid of selected atoms */
+/*************************************/
+void calc_centroid(gdouble *centroid, GSList *input)
+{
+GSList *list=NULL;
+struct core_pak *core;
+
+if (!input)
+  return;
+
+VEC3SET(centroid, 0.0, 0.0, 0.0);
+for (list=input ; list ; list=g_slist_next(list))
+  {
+  core = list->data;
+  ARR3ADD(centroid, core->x);
+  }
+
+VEC3MUL(centroid, 1.0 / (gdouble) g_slist_length(input));
+
+#if DEBUG_CALC_CENTROID
+   P3VEC("Centroid = ", centroid);
+#endif
+}
+
 /**********************/
 /* debugging routines */
 /**********************/

src/coords.h

@@ -291,3 +291,4 @@ GSList *connect_fragment_get(struct core_pak *,
                              struct model_pak *);
 GSList *connect_neighbours(struct core_pak *) ;
 
+void calc_centroid(gdouble *, GSList *);

src/file.c

@@ -33,6 +33,12 @@ The GNU GPL can also be found at http://www.gnu.org
 #include <sys/stat.h>
 #include <sys/types.h>
 
+#define GLIB_VERSION(major, minor, micro) \
+    (GLIB_MAJOR_VERSION > (major) || \
+    (GLIB_MAJOR_VERSION == (major) && GLIB_MINOR_VERSION > (minor)) || \
+    (GLIB_MAJOR_VERSION == (major) && GLIB_MINOR_VERSION == (minor) && \
+     GLIB_MICRO_VERSION >= (micro)))
+
 #include "gdis.h"
 #include "coords.h"
 #include "error.h"
@@ -56,9 +62,9 @@ The GNU GPL can also be found at http://www.gnu.org
 extern struct sysenv_pak sysenv;
 extern struct elem_pak elements[];
 
-/***************************************/
-/* setup the recognized file type list */
-/***************************************/
+/****************************************/
+/* set up the recognized file type list */
+/****************************************/
 #define DEBUG_FILE_INIT 0
 void file_init(void)
 {
@@ -346,7 +352,7 @@ file_data = g_malloc(sizeof(struct file_pak));
 file_data->id = QE;
 file_data->group = QE;
 file_data->menu = TRUE;
-file_data->label = g_strdup("QE");
+file_data->label = g_strdup("Quantum Espresso");
 file_data->ext = NULL;
 file_data->ext = g_slist_append(file_data->ext, "qein");
 file_data->write_file = write_qe;
@@ -801,7 +807,11 @@ while (list)
   name = list->data;
   list = g_slist_next(list);
 
+#if GLIB_VERSION(2, 7, 0)
+  if (!g_pattern_spec_match_string(ps, name))
+#else
   if (!g_pattern_match_string(ps, name))
+#endif
     {
     files = g_slist_remove(files, name);
     g_free(name);

src/file.h

@@ -101,6 +101,7 @@ gint write_gmf(gchar *, struct model_pak *);
 gint write_planes(gchar *, struct model_pak *);
 gint write_marvin(gchar *, struct model_pak *);
 gint write_xml(gchar *, struct model_pak *);
+gint write_xsf(gchar *, struct model_pak *);
 gint write_xtl(gchar *, struct model_pak *);
 gint write_xyz(gchar *, struct model_pak *);
 gint write_gms(gchar *, struct model_pak *);
@@ -142,6 +143,7 @@ gint read_marvin(gchar *, struct model_pak *);
 gint read_mvnout(gchar *, struct model_pak *);
 gint read_sout(gchar *, struct model_pak *);
 gint read_xml(gchar *, struct model_pak *);
+gint read_xsf(gchar *, struct model_pak *);
 gint read_xtl(gchar *, struct model_pak *);
 gint read_xyz(gchar *, struct model_pak *);
 gint read_using_babel(gchar *, struct model_pak *);
@@ -189,6 +191,7 @@ gint read_qe_out_frame(FILE *, struct model_pak *);
 gint read_xyz_frame(FILE *, struct model_pak *);
 gint read_dlpoly_frame(FILE *, struct model_pak *);
 gint read_dmol_frame(FILE *, struct model_pak *);
+gint read_xsf_frame(FILE *, struct model_pak *);
 
 /*NEW: track/update frames (TODO)*/
 gint update_frame_uspex(gint idx,struct model_pak *model);

src/file_cif.c

@@ -776,7 +776,7 @@ else
     return(-1);
     }
 #if DEBUG_LOAD_CIF
-printf("Found %d atom%c.\n", natom, (natom != 1?'s':''));
+printf("Found %d atom%s\n", natom, (natom != 1 ? "s.":"."));
 printf("Found %d symmetry matrices.\n", data->sginfo.order);
 printf("Found %d model(s)\n", new);
 printf("Periodicity is %d\n", data->periodic);

src/file_meta.c

@@ -35,21 +35,21 @@ extern struct elem_pak elements[];
 
 /* meta data for computational chemistry archiving */
 
-/*****************************************************************/
-/* split a string containing units into it's raw value and units */
-/*****************************************************************/
+/****************************************************************/
+/* split a string containing units into its raw value and units */
+/****************************************************************/
 void meta_parse_units(gchar **value, gchar **units, gchar *source)
 {
 gchar **buff;
 
 buff = g_strsplit(source, " ", 2);
 
-if (*buff+0)
-  *value = g_strdup(*(buff+0));
+if (*buff)
+  *value = g_strdup(*(buff));
 else
   *value = NULL;
 
-if (*buff+1)
+if (g_strv_length(buff) == 2)
   *units = g_strdup(*(buff+1));
 else
   *units = NULL;