Use a single pointer for offsets storage

it's cleaner and easier to handle in the cython wrapper. I also reworded
the comments to be better understandable.

Author: kain88-de

package/MDAnalysis/lib/formats/include/xdrfile_xtc.h

@@ -50,7 +50,7 @@ extern "C" {
 extern int read_xtc_natoms(char *fn, int *natoms);
 
 /* Seek through trajectory counting and indexing frames */
-extern int read_xtc_n_frames(char *fn, int *n_frames, int64_t **offsets);
+extern int read_xtc_n_frames(char *fn, int *n_frames, int64_t *offsets);
 
 /* Read one frame of an open xtc file */
 extern int read_xtc(XDRFILE *xd, int natoms, int *step, float *time, matrix box,
@@ -66,11 +66,17 @@ extern int write_xtc(XDRFILE *xd, int natoms, int step, float time, matrix box,
 #define XTC_SHORTHEADER_SIZE (20 + DIM * DIM * 4)
 /* Short XTCs store each coordinate as a 32-bit float. */
 #define XTC_SHORT_BYTESPERATOM 12
-/* XTC header fields until frame bytes: *** only for trajectories of more than 9
- * atoms! ***  */
-/* magic natoms step time DIM*DIM_box_vecs natoms prec DIM_min_xyz DIM_max_xyz
- * smallidx */
-#define XTC_HEADER_SIZE (DIM * DIM * 4 + DIM * 2 + 46)
+/* Number of bytes until we can read the frame bytes in a frame, for frames
+ * containing more then 9 atoms.
+ *
+ * This header is composed of the read header and the coordinate section header.
+ * The 'real' header contains the following entries: magic, natoms, step, time.
+ * The coordinate section header contains: 3x3 box, natoms, prec, 3 min_xyz, 3
+ * max_xyz, smallidx.
+ * Each of these entries is 4 byte long. In total that is 22
+ * entries. So we need to skip 88 bytes.
+ */
+#define XTC_HEADER_SIZE 88
 
 #ifdef __cplusplus
 }

package/MDAnalysis/lib/formats/src/xdrfile_xtc.c

@@ -113,7 +113,7 @@ int read_xtc(XDRFILE *xd, int natoms, int *step, float *time, matrix box,
   return exdrOK;
 }
 
-int read_xtc_n_frames(char *fn, int *n_frames, int64_t **offsets) {
+int read_xtc_n_frames(char *fn, int *n_frames, int64_t *offsets) {
   XDRFILE *xd;
   int framebytes, natoms, step;
   float time;
@@ -141,10 +141,10 @@ int read_xtc_n_frames(char *fn, int *n_frames, int64_t **offsets) {
     *n_frames = filesize / framebytes; /* Should we complain if framesize
                                           doesn't divide filesize? */
     /* Allocate memory for the frame index array */
-    if ((*offsets = (int64_t *)malloc(sizeof(int64_t) * (*n_frames))) == NULL)
+    if ((offsets = malloc(sizeof(int64_t) * (*n_frames))) == NULL)
       return exdrNOMEM;
     for (i = 0; i < *n_frames; i++) {
-      (*offsets)[i] = i * framebytes;
+      offsets[i] = i * framebytes;
     }
     return exdrOK;
   } else /* No easy way out. We must iterate. */
@@ -167,16 +167,16 @@ int read_xtc_n_frames(char *fn, int *n_frames, int64_t **offsets) {
     est_nframes += est_nframes / 5;
 
     /* Allocate memory for the frame index array */
-    if ((*offsets = (int64_t *)malloc(sizeof(int64_t) * est_nframes)) == NULL) {
+    if ((offsets = malloc(sizeof(int64_t) * est_nframes)) == NULL) {
       xdrfile_close(xd);
       return exdrNOMEM;
     }
-    (*offsets)[0] = 0L;
+    offsets[0] = 0L;
     *n_frames = 1;
     while (1) {
       if (xdr_seek(xd, (int64_t)(framebytes + XTC_HEADER_SIZE), SEEK_CUR) !=
           exdrOK) {
-        free(*offsets);
+        free(offsets);
         xdrfile_close(xd);
         return exdrNR;
       }
@@ -186,14 +186,14 @@ int read_xtc_n_frames(char *fn, int *n_frames, int64_t **offsets) {
       /* Check if we need to enlarge array */
       if (*n_frames == est_nframes) {
         est_nframes += est_nframes / 5 + 1; // Increase in 20% stretches
-        if ((*offsets = realloc(*offsets, sizeof(int64_t) * est_nframes)) ==
+        if ((offsets = realloc(offsets, sizeof(int64_t) * est_nframes)) ==
             NULL) {
-          free(*offsets);
+          free(offsets);
           xdrfile_close(xd);
           return exdrNOMEM;
         }
       }
-      (*offsets)[*n_frames] =
+      offsets[*n_frames] =
           xdr_tell(xd) - 4L - (int64_t)(XTC_HEADER_SIZE); // Account for the
                                                           // header and the
                                                           // nbytes bytes we