merge fixes

benchmarks/opencl/cutcp/readatom.c

@@ -0,0 +1,139 @@
+/***************************************************************************
+ *cr
+ *cr            (C) Copyright 2008-2010 The Board of Trustees of the
+ *cr                        University of Illinois
+ *cr                         All Rights Reserved
+ *cr
+ ***************************************************************************/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "atom.h"
+
+
+#define LINELEN 96
+#define INITLEN 20
+
+
+Atoms *read_atom_file(const char *fname)
+{
+  FILE *file;
+  char line[LINELEN];
+
+  Atom *atom;			/* Atom array */
+  int len = INITLEN;		/* Size of atom array */
+  int cnt = 0;			/* Number of atoms read */
+
+  /* allocate initial atom array */
+  atom = (Atom *) malloc(len * sizeof(Atom));
+  if (NULL==atom) {
+    fprintf(stderr, "can't allocate memory\n");
+    return NULL;
+  }
+
+  int i;
+  for (i = 0; i < len; ++i) {
+    atom[i].x = i+0;
+    atom[i].y = i+1;
+    atom[i].z = i+2;
+    atom[i].q = 1;
+  }
+
+#if 0
+  /* open atom "pqr" file */
+  file = fopen(fname, "r");
+  if (NULL==file) {
+    fprintf(stderr, "can't open file \"%s\" for reading\n", fname);
+    return NULL;
+  }
+
+  /* loop to read pqr file line by line */
+  while (fgets(line, LINELEN, file) != NULL) {
+
+    if (strncmp(line, "ATOM  ", 6) != 0 && strncmp(line, "HETATM", 6) != 0) {
+      continue;  /* skip anything that isn't an atom record */
+    }
+
+    if (cnt==len) {  /* extend atom array */
+      void *tmp = realloc(atom, 2*len*sizeof(Atom));
+      if (NULL==tmp) {
+        fprintf(stderr, "can't allocate more memory\n");
+        return NULL;
+      }
+      atom = (Atom *) tmp;
+      len *= 2;
+    }
+
+    /* read position coordinates and charge from atom record */
+    if (sscanf(line, "%*s %*d %*s %*s %*d %f %f %f %f", &(atom[cnt].x),
+          &(atom[cnt].y), &(atom[cnt].z), &(atom[cnt].q)) != 4) {
+      fprintf(stderr, "atom record %d does not have expected format\n", cnt+1);
+      return NULL;
+    }
+
+    cnt++;  /* count atoms as we store them */
+  }
+
+  /* verify EOF and close file */
+  if ( !feof(file) ) {
+    fprintf(stderr, "did not find EOF\n");
+    return NULL;
+  }
+  if (fclose(file)) {
+    fprintf(stderr, "can't close file\n");
+    return NULL;
+  }
+#endif
+
+  /* Build the output data structure */
+  {
+    Atoms *out = (Atoms *)malloc(sizeof(Atoms));
+
+    if (NULL == out) {
+      fprintf(stderr, "can't allocate memory\n");
+      return NULL;
+    }
+
+    out->size = cnt;
+    out->atoms = atom;
+
+    return out;
+  }
+}
+
+
+void free_atom(Atoms *atom)
+{
+  if (atom) {
+    free(atom->atoms);
+    free(atom);
+  }
+}
+
+void
+get_atom_extent(Vec3 *out_lo, Vec3 *out_hi, Atoms *atom)
+{
+  Atom *atoms = atom->atoms;
+  int natoms = atom->size;
+  Vec3 lo;
+  Vec3 hi;
+  int n;
+
+  hi.x = lo.x = atoms[0].x;
+  hi.y = lo.y = atoms[0].y;
+  hi.z = lo.z = atoms[0].z;
+
+  for (n = 1; n < natoms; n++) {
+    lo.x = fminf(lo.x, atoms[n].x);
+    hi.x = fmaxf(hi.x, atoms[n].x);
+    lo.y = fminf(lo.y, atoms[n].y);
+    hi.y = fmaxf(hi.y, atoms[n].y);
+    lo.z = fminf(lo.z, atoms[n].z);
+    hi.z = fmaxf(hi.z, atoms[n].z);
+  }
+
+  *out_lo = lo;
+  *out_hi = hi;
+}