[ViewVC] Diff of: group/trunk/tcProps/readWrite.c

Comparing trunk/tcProps/readWrite.c (file contents):
Revision 1055 by mmeineke, Mon Feb 16 21:50:34 2004 UTC vs.
Revision 1085 by mmeineke, Fri Mar 5 03:10:29 2004 UTC

+#define BUFFER_SIZE 2000
+int isScanned;
-+
+int fileOpen;
-+
+int nFrames;
-+
+double *frameTimes;
+FILE* inFile;
-+
+char* inName;
-–
+struct linkedPos{
+  fpos_t *myPos;
+struct staticPos{
+  fpos_t *myPos;
-–
+  double timeStamp;
+  double Hmat[3][3];
+};
+struct staticPos* posArray;
-+
+void parseDumpLine( char readBuffer[BUFFER_SIZE], int index,
-+
+                    struct atomCoord* atoms );
-+
+void setU( double q[4], double u[3] );
-+
+void normalizeQ( double q[4] );
-+
+void openFile( void ){
-+
-+
+  inFile = fopen(inName, "r");
-+
+  if(inFile ==NULL){
-+
+    fprintf(stderr,
-+
+            "Error opening file \"%s\"\n",
-+
+            inName);
-+
+    exit(0);
-+
+  }
-+
-+
+  fileOpen = 1;
-+
+}
-+
+void closeFile( void ){
+  fclose( inFile );
-+
-+
+  fileOpen = 0;
-<
+int setFrames( char* inFile ){
->
+void setFrames( void ){
-–
+  int nFrames = 0;
+  int i,j,k;
+  struct linkedPos* headPos;
+  struct linkedPos* currPos;
+  int lineNum = 0;
-<
-<
+  inFile = fopen(inName);
-<
+  if(inFile ==NULL){
->
+  if( !fileOpen ){
+    fprintf(stderr,
-<
+            "Error opening file \"%s\"\n",
-<
+            inName);
->
+            "Attempt to scan the file without first opening the file.\n" );
+    exit(0);
-<
->
->
+  nFrames = 0;
+  headPos = (struct linkedPos*)malloc(sizeof(struct linkedPos));
+  currPos = headPos;
-+
-+
+  currPT = (fpos_t *)malloc(sizeof(fpos_t));
-+
+  fgetpos(inFile, currPT);
-+
-+
+  fgets( readBuffer, sizeof( readBuffer ), inFile );
-+
+  lineNum++;
-+
+  if( feof( inFile ) ){
-+
+    fprintf( stderr,
-+
+             "File \"%s\" ended unexpectedly at line %d\n",
-+
+             inName,
-+
+             lineNum );
-+
+    exit(0);
-+
+  }
-+
+  while( !feof( inFile ) ){
-–
+    currPT = (fpos_t *)malloc(sizeof(fpos_t));
-–
+    fgetpos(inFile, currPT);
-–
-–
+    fgets( readBuffer, sizeof( readBuffer ), inFile );
-–
+    lineNum++;
-–
+    if( feof( inFile ) ){
-–
+      fprintf( stderr,
-–
+               "File \"%s\" ended unexpectedly at line %d\n",
-–
+               inName,
-–
+               lineNum );
-–
+      exit(0);
-–
+    }
-–
+    currPos->next = (struct linkedPos*)malloc(sizeof(struct linkedPos));
+    currPos = currPos->next;
+    currPos->myPos = currPT;
+        exit(0);
-+
-+
+    currPT = (fpos_t *)malloc(sizeof(fpos_t));
-+
+    fgetpos(inFile, currPT);
-+
-+
+    fgets( readBuffer, sizeof( readBuffer ), inFile );
-+
+    lineNum++;
-+
-+
+  // allocate the static position array
-+
+  posArray = (struct staticPos*)calloc(nFrames, sizeof(struct staticPos));
-+
+  frameTimes = (double *)calloc(nFrames, sizeof(double) );
-+
-+
+  i=0;
-+
+  currPos = headPos->next;
-+
+  while( currPos != NULL ){
-+
-+
+    if(i>=nFrames){
-+
-+
+      fprintf( stderr,
-+
+               "The number of frame pointers exceeded the number of frames.\n"
-+
+               "  OOPS!\n" );
-+
+      exit(0);
-+
+    }
-+
-+
+    frameTimes[i] = currPos->timeStamp;
-+
+    posArray[i].myPos = currPos->myPos;
-+
+    for(j=0;j<3;j++){
-+
+      for(k=0;k<3;k++){
-+
+        posArray[i].Hmat[j][k] = currPos->Hmat[j][k];
-+
+      }
-+
+    }
-+
-+
+    i++;
-+
+    currPos = currPos->next;
-+
+  }
-+
-+
+  // clean up the linked list
-+
-+
+  currPos = headPos;
-+
+  while( currPos != NULL ){
-+
+    headPos = currPos;
-+
+    currPos = headPos->next;
-+
+    free(headPos);
-+
+  }
-+
-+
+  isScanned = 1;
-–
+  return nFrames;
-+
-+
-+
+void readFrame(int theFrame, struct atomCoord* atoms, double Hmat[3][3] ){
-+
-+
+  // list of 'a priori' constants
-+
-+
+  const int nLipAtoms = NL_ATOMS;
-+
+  const int nBonds    = NBONDS;
-+
+  const int nLipids   = NLIPIDS;
-+
+  const int nSSD      = NSSD;
-+
+  const int nAtoms    = nLipAtoms * nLipids + nSSD;
-+
-+
+  fpos_t *framePos;
-+
+  char readBuffer[BUFFER_SIZE];
-+
-+
+  int i, j, k;
-+
-+
-+
+  // quick checks
-+
-+
+  if (theFrame >= nFrames){
-+
-+
+    fprintf(stderr,
-+
+            "frame %d, is out of range\n",
-+
+            theFrame );
-+
+    exit(0);
-+
+  }
-+
-+
+  if( !fileOpen ){
-+
-+
+    fprintf( stderr,
-+
+             "File is closed, cannot read frame %d.\n",
-+
+             theFrame );
-+
+    exit(0);
-+
+  }
-+
-+
+  // access the frame
-+
-+
+  framePos = posArray[theFrame].myPos;
-+
+  fsetpos( inFile, framePos );
-+
-+
+  for(j=0;j<3;j++){
-+
+    for(k=0;k<3;k++){
-+
+      Hmat[j][k] = posArray[theFrame].Hmat[j][k];
-+
+    }
-+
+  }
-+
-+
+  fgets( readBuffer, sizeof( readBuffer ), inFile );
-+
+  if( feof( inFile ) ){
-+
+    fprintf( stderr,
-+
+             "File \"%s\" ended unexpectedly in Frame %d\n",
-+
+             inName,
-+
+             theFrame );
-+
+    exit(0);
-+
+  }
-+
-+
+  i = atoi( readBuffer );
-+
+  if( i != nAtoms ){
-+
+    fprintf( stderr,
-+
+             "Error in frame %d: frame atoms, %d, does not params atoms, %d\n",
-+
+             theFrame,
-+
+             i,
-+
+             nAtoms );
-+
+    exit(0);
-+
+  }
-+
-+
+  // read and toss the comment line
-+
-+
+  fgets( readBuffer, sizeof( readBuffer ), inFile );
-+
+  if( feof( inFile ) ){
-+
+    fprintf( stderr,
-+
+             "File \"%s\" ended unexpectedly in Frame %d\n",
-+
+             inName,
-+
+             theFrame );
-+
+    exit(0);
-+
+  }
-+
-+
+  // read the atoms
-+
-+
+  for( i=0; i < nAtoms; i++){
-+
-+
+    fgets( readBuffer, sizeof( readBuffer ), inFile );
-+
+    if( feof( inFile ) ){
-+
+      fprintf( stderr,
-+
+               "File \"%s\" ended unexpectedly in Frame %d at atom %d\n",
-+
+               inName,
-+
+               theFrame,
-+
+               i );
-+
+      exit(0);
-+
+    }
-+
-+
-+
+    parseDumpLine( readBuffer, i, atoms );
-+
+  }
-+
+}
-+
-+
+void parseDumpLine( char readLine[BUFFER_SIZE], int i,
-+
+                    struct atomCoord* atoms ){
-+
-+
+  const int nLipAtoms = NL_ATOMS;
-+
+  const int nBonds    = NBONDS;
-+
+  const int nLipids   = NLIPIDS;
-+
+  const int nSSD      = NSSD;
-+
+  const int nAtoms    = nLipAtoms * nLipids + nSSD;
-+
-+
+  char* foo;
-+
+  double q[4];
-+
-+
+  // set the string tokenizer
-+
-+
+  foo = strtok(readLine, " ,;\t");
-+
-+
+  // check the atom ID
-+
-+
+  switch( atoms[i].type ){
-+
-+
+  case HEAD:
-+
+    if( strcmp(foo, "HEAD") ){
-+
+      fprintf( stderr,
-+
+               "Atom %s does not match master array type \"HEAD\".\n",
-+
+               foo );
-+
+      exit(0);
-+
+    }
-+
+    break;
-+
-+
+  case CH:
-+
+    if( strcmp(foo, "CH") ){
-+
+      fprintf( stderr,
-+
+               "Atom %s does not match master array type \"CH\".\n",
-+
+               foo );
-+
+      exit(0);
-+
+    }
-+
+    break;
-+
-+
+  case CH2:
-+
+    if( strcmp(foo, "CH2") ){
-+
+      fprintf( stderr,
-+
+               "Atom %s does not match master array type \"CH2\".\n",
-+
+               foo );
-+
+      exit(0);
-+
+    }
-+
+    break;
-+
-+
+  case CH3:
-+
+    if( strcmp(foo, "CH3") ){
-+
+      fprintf( stderr,
-+
+               "Atom %s does not match master array type \"CH3\".\n",
-+
+               foo );
-+
+      exit(0);
-+
+    }
-+
+    break;
-+
-+
+  case SSD:
-+
+    if( strcmp(foo, "SSD") ){
-+
+      fprintf( stderr,
-+
+               "Atom %s does not match master array type \"SSD\".\n",
-+
+               foo );
-+
+      exit(0);
-+
+    }
-+
+    break;
-+
-+
+  default:
-+
+    fprintf(stderr,
-+
+            "Atom %d is an unrecognized enumeration\n",
-+
+            i );
-+
+    exit(0);
-+
+  }
-+
-+
+  // get the positions
-+
-+
+  foo = strtok(NULL, " ,;\t");
-+
+  if(foo == NULL){
-+
+    fprintf( stderr,
-+
+             "error in reading postition x from %s\n"
-+
+             "natoms  = %d, i = %d\n",
-+
+             inName, nAtoms, i );
-+
+    exit(0);
-+
+  }
-+
+  atoms[i].pos[0] = atof( foo );
-+
-+
+  foo = strtok(NULL, " ,;\t");
-+
+  if(foo == NULL){
-+
+    fprintf( stderr,
-+
+             "error in reading postition y from %s\n"
-+
+             "natoms  = %d, i = %d\n",
-+
+             inName, nAtoms, i );
-+
+    exit(0);
-+
+  }
-+
+  atoms[i].pos[1] = atof( foo );
-+
-+
+  foo = strtok(NULL, " ,;\t");
-+
+  if(foo == NULL){
-+
+    fprintf( stderr,
-+
+             "error in reading postition z from %s\n"
-+
+             "natoms  = %d, i = %d\n",
-+
+             inName, nAtoms, i );
-+
+    exit(0);
-+
+  }
-+
+  atoms[i].pos[2] = atof( foo );
-+
-+
-+
+  // get the velocities
-+
-+
+  foo = strtok(NULL, " ,;\t");
-+
+  if(foo == NULL){
-+
+    fprintf( stderr,
-+
+             "error in reading velocity x from %s\n"
-+
+             "natoms  = %d, i = %d\n",
-+
+             inName, nAtoms, i );
-+
+    exit(0);
-+
+  }
-+
+  atoms[i].vel[0] = atof( foo );
-+
-+
+  foo = strtok(NULL, " ,;\t");
-+
+  if(foo == NULL){
-+
+    fprintf( stderr,
-+
+             "error in reading velocity y from %s\n"
-+
+             "natoms  = %d, i = %d\n",
-+
+             inName, nAtoms, i );
-+
+    exit(0);
-+
+  }
-+
+  atoms[i].vel[1] = atof( foo );
-+
-+
+  foo = strtok(NULL, " ,;\t");
-+
+  if(foo == NULL){
-+
+    fprintf( stderr,
-+
+             "error in reading velocity z from %s\n"
-+
+             "natoms  = %d, i = %d\n",
-+
+             inName, nAtoms, i );
-+
+    exit(0);
-+
+  }
-+
+  atoms[i].vel[2] = atof( foo );
-+
-+
-+
+  // get the quaternions
-+
-+
+  if( (atoms[i].type == HEAD) || (atoms[i].type == SSD) ){
-+
-+
+    foo = strtok(NULL, " ,;\t");
-+
+    if(foo == NULL){
-+
+      fprintf( stderr,
-+
+               "error in reading quaternion 0 from %s\n"
-+
+               "natoms  = %d, i = %d\n",
-+
+               inName, nAtoms, i );
-+
+      exit(0);
-+
+    }
-+
+    q[0] = atof( foo );
-+
-+
+    foo = strtok(NULL, " ,;\t");
-+
+    if(foo == NULL){
-+
+      fprintf( stderr,
-+
+               "error in reading quaternion 1 from %s\n"
-+
+               "natoms  = %d, i = %d\n",
-+
+               inName, nAtoms, i );
-+
+      exit(0);
-+
+    }
-+
+    q[1] = atof( foo );
-+
-+
+    foo = strtok(NULL, " ,;\t");
-+
+    if(foo == NULL){
-+
+      fprintf( stderr,
-+
+               "error in reading quaternion 2 from %s\n"
-+
+               "natoms  = %d, i = %d\n",
-+
+               inName, nAtoms, i );
-+
+      exit(0);
-+
+    }
-+
+    q[2] = atof( foo );
-+
-+
+    foo = strtok(NULL, " ,;\t");
-+
+    if(foo == NULL){
-+
+      fprintf( stderr,
-+
+               "error in reading quaternion 3 from %s\n"
-+
+               "natoms  = %d, i = %d\n",
-+
+               inName, nAtoms, i );
-+
+      exit(0);
-+
+    }
-+
+    q[3] = atof( foo );
-+
-+
+    normalizeQ( q );
-+
-+
+    setU( q, atoms[i].u );
-+
+  }
-+
+}
-+
-+
-+
+void setU( double the_q[4], double u[3] ){
-+
-+
+  double q0Sqr, q1Sqr, q2Sqr, q3Sqr;
-+
+  double A[3][3];
-+
+  double rb[3];
-+
+  int i,j,k;
-+
-+
+  // initialize the axis
-+
-+
+  rb[0] = 0.0;
-+
+  rb[1] = 0.0;
-+
+  rb[2] = 1.0;
-+
-+
+  // set the rotation matrix
-+
-+
+  q0Sqr = the_q[0] * the_q[0];
-+
+  q1Sqr = the_q[1] * the_q[1];
-+
+  q2Sqr = the_q[2] * the_q[2];
-+
+  q3Sqr = the_q[3] * the_q[3];
-+
-+
+  A[0][0] = q0Sqr + q1Sqr - q2Sqr - q3Sqr;
-+
+  A[0][1] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] );
-+
+  A[0][2] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] );
-+
-+
+  A[1][0]  = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] );
-+
+  A[1][1] = q0Sqr - q1Sqr + q2Sqr - q3Sqr;
-+
+  A[1][2] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] );
-+
-+
+  A[2][0] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] );
-+
+  A[2][1] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] );
-+
+  A[2][2] = q0Sqr - q1Sqr -q2Sqr +q3Sqr;
-+
-+
+  // perform the rotation
-+
-+
+  for( i=0; i<3; i++ ){
-+
+    u[i] = 0.0;
-+
-+
+    for( j=0; j<3; j++ ){
-+
+      u[i] += A[j][i] * rb[j];
-+
+    }
-+
+  }
-+
+}
-+
-+
+void normalizeQ( double q[4] ){
-+
-+
+  double qSqr, qL;
-+
+  int i;
-+
-+
+  qSqr = 0.0;
-+
+  for(i=0;i<4;i++)
-+
+    qSqr += q[i] * q[i];
-+
-+
+  for(i=0;i<4;i++)
-+
+    q[i] /= qSqr;
-+
+}
-+
-+
+double scanSmallestZ(int startFrame){
-+
+  double smallest;
-+
+  int i;
-+
-+
+  smallest = posArray[startFrame].Hmat[2][2];
-+
+  for(i=startFrame;i<nFrames;i++)
-+
+    smallest =
-+
+      (smallest<posArray[i].Hmat[2][2])? smallest : posArray[i].Hmat[2][2];
-+
-+
+  return smallest;
-+
+}
-+
-+
+double calcAverageXY( double startTime ){
-+
-+
+  int i, count, startFrame, startFound;
-+
+  double avg;
-+
-+
+  startFound = 0;
-+
+  startFrame = -1;
-+
+  while( !startFound ){
-+
-+
+    startFrame++;
-+
-+
+    if(startFrame >= nFrames){
-+
-+
+      fprintf( stderr,
-+
+               "Start Time, %G, was not found in the dump file.\n",
-+
+               startTime );
-+
+      exit(0);
-+
+    }
-+
-+
+    if(startTime <= frameTimes[startFrame])
-+
+      startFound = 1;
-+
-+
-+
+  }
-+
-+
+  avg = 0.0;
-+
+  count = 0;
-+
+  for(i=startFrame;i<nFrames;i++){
-+
+    avg += posArray[i].Hmat[0][0] * posArray[i].Hmat[1][1];
-+
+    count++;
-+
+  }
-+
+  avg /= (double)count;
-+
-+
+  return avg;
-+
+}

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/tcProps/readWrite.c (file contents): Revision 1055 by mmeineke, Mon Feb 16 21:50:34 2004 UTC vs. Revision 1085 by mmeineke, Fri Mar 5 03:10:29 2004 UTC

Diff Legend

Comparing trunk/tcProps/readWrite.c (file contents):
Revision 1055 by mmeineke, Mon Feb 16 21:50:34 2004 UTC vs.
Revision 1085 by mmeineke, Fri Mar 5 03:10:29 2004 UTC