src/applications/quickLate.c

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>

struct coords{
  double pos[3]; // cartesian coords
  double q[4];  // the quanternions
  char name[30];
};

struct linked_xyz{
  struct coords *r;
  double time;
  double Hmat[3][3];
  double HmatI[3][3];
  struct linked_xyz *next;
};

char *program_name; /*the name of the program */
int printWater = 0;
int printDipole = 0;

void usage(void);

void rotWrite( FILE* out_file, struct coords* theSSD );

void setRot( double A[3][3], double q[4] );

void rotMe( double A[3][3], double r[3] );
void wrapVector( double thePos[3], double Hmat[3][3], double HmatI[3][3]);
double matDet3(double a[3][3]);
void invertMat3(double a[3][3], double b[3][3]);
void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
double roundMe(double x);

int main(argc, argv)
     int argc;
     char *argv[];
{


  struct coords *out_coords;

  int i, j, k, l, m; /* loop counters */
  mode_t dir_mode = S_IRWXU;

  int lineCount = 0;  //the line number
  int newN; // the new number of atoms
  int nSSD=0; // the number of SSD per frame

  unsigned int nAtoms; /*the number of atoms in each time step */
  char read_buffer[1000]; /*the line buffer for reading */
  char *eof_test; /*ptr to see when we reach the end of the file */
  char *foo; /*the pointer to the current string token */
  FILE *in_file; /* the input file */
  FILE *out_file; /*the output file */
  char *out_prefix = NULL; /*the prefix of the output file */
  char out_name[500]; /*the output name */
  int have_outName =0;
  char in_name[500]; // the input file name
  char temp_name[500];
  char *root_name = NULL; /*the root name of the input file */
  unsigned int n_out = 0; /*keeps track of which output file is being written*/


  int skipFrames = 1;

  struct linked_xyz *current_frame;
  struct linked_xyz *temp_frame;

  int nframes =0;

  int wrap = 0;

  double cX = 0.0;
  double cY = 0.0;
  double cZ = 0.0;

  double mcX, mcY, mcZ;
  double newCX, newCY, newCZ;
  double dx, dy, dz;
  int mcount;

  int repeatX = 0;
  int repeatY = 0;
  int repeatZ = 0;

  int nRepeatX = 0;
  int nRepeatY = 0;
  int nRepeatZ = 0;

  struct coords* rCopy;
  
  int done;
  char current_flag;

  program_name = argv[0]; /*save the program name in case we need it*/
  
  for( i = 1; i < argc; i++){
    
    if(argv[i][0] =='-'){
      
      if(argv[i][1] == '-' ){
        
        // parse long word options
        
        if( !strcmp( argv[i], "--repeatX" ) ){
          repeatX = 1;
          i++;
          nRepeatX = atoi( argv[i] );
        }

        else if( !strcmp( argv[i], "--repeatY" ) ){
          repeatY = 1;
          i++;
          nRepeatY = atoi( argv[i] );
        }

        else if( !strcmp( argv[i], "--repeatZ" ) ){
          repeatZ = 1;
          i++;
          nRepeatZ = atoi( argv[i] );
        }

        else{
          fprintf( stderr, 
                   "Invalid option \"%s\"\n", argv[i] );
          usage();
        }
      }
      
      else{

        // parse single character options
        
        done =0;
        j = 1;
        current_flag = argv[i][j];
        while( (current_flag != '\0') && (!done) ){
          
          switch(current_flag){
            
          case 'o':
            // -o <prefix> => the output
            
            i++;
            strcpy( out_name, argv[i] );
            have_outName = 1;
            done = 1;
            break;
            
          case 'n':
            // -n <#> => print every <#> frames
            
            i++;
            skipFrames = atoi(argv[i]);
            done = 1;
            break;
            
          case 'h':
            // -h => give the usage
            
            usage();
            break;
            
          case 'd':
            // print the dipoles
            
            printDipole = 1;
            break;
            
          case 'w':
            // print the waters
            
            printWater = 1;
            break;
            
          case 'm':
            // map to a periodic box
            
            wrap = 1;
            break;
            
          default:
            
            fprintf(stderr, "Bad option \"-%c\"\n", current_flag);
            usage();
          }
          j++;
          current_flag = argv[i][j];
        }
      }
    }
    
    else{
      
      if( root_name != NULL ){
        fprintf( stderr, 
                 "Error at \"%s\", program does not currently support\n"
                 "more than one input file.\n"
                 "\n",
                 argv[i]);
        usage();
      }
      
      root_name = argv[i];
    }
  }
  
  if(root_name == NULL){
    usage();
  }

  sprintf( in_name, "%s", root_name );
  if( !have_outName ) sprintf( out_name, "%s.xyz", root_name );

  in_file = fopen(in_name, "r");
  if(in_file == NULL){
    printf("Cannot open file \"%s\" for reading.\n", in_name);
    exit(8);
  }
  
  out_file = fopen( out_name, "w" );
  if( out_file == NULL ){
    printf("Cannot open file \"%s\" for writing.\n", out_name);
    exit(8);
  }

  // start reading the first frame

  eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
  lineCount++;
  
  current_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz));
  current_frame->next = NULL;
  

  while(eof_test != NULL){
    
    (void)sscanf(read_buffer, "%d", &nAtoms);
    current_frame->r = 
      (struct coords *)calloc(nAtoms, sizeof(struct coords));

    // read and the comment line and grab the time and box dimensions

    eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
    lineCount++;
    if(eof_test == NULL){
      printf("error in reading file at line: %d\n", lineCount);
      exit(8);
    }

    foo = strtok( read_buffer, " ,;\t" );
    sscanf( read_buffer, "%lf", &current_frame->time );
    
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading file at line: %d\n", lineCount);
      exit(8);
    }
    (void)sscanf(foo, "%lf",&current_frame->Hmat[0][0]);

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading file at line: %d\n", lineCount);
      exit(8);
    }
    (void)sscanf(foo, "%lf",&current_frame->Hmat[1][0]);

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading file at line: %d\n", lineCount);
      exit(8);
    }
    (void)sscanf(foo, "%lf",&current_frame->Hmat[2][0]);

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading file at line: %d\n", lineCount);
      exit(8);
    }
    (void)sscanf(foo, "%lf",&current_frame->Hmat[0][1]);

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading file at line: %d\n", lineCount);
      exit(8);
    }
    (void)sscanf(foo, "%lf",&current_frame->Hmat[1][1]);

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading file at line: %d\n", lineCount);
      exit(8);
    }
    (void)sscanf(foo, "%lf",&current_frame->Hmat[2][1]);

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading file at line: %d\n", lineCount);
      exit(8);
    }
    (void)sscanf(foo, "%lf",&current_frame->Hmat[0][2]);

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading file at line: %d\n", lineCount);
      exit(8);
    }
    (void)sscanf(foo, "%lf",&current_frame->Hmat[1][2]);

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading file at line: %d\n", lineCount);
      exit(8);
    }
    (void)sscanf(foo, "%lf",&current_frame->Hmat[2][2]);


    // Find HmatI:

    invertMat3(current_frame->Hmat, current_frame->HmatI);


    for( i=0; i < nAtoms; i++){
      
      eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
      lineCount++;
      if(eof_test == NULL){
        printf("error in reading file at line: %d\n", lineCount);
        exit(8);
      }

      foo = strtok(read_buffer, " ,;\t");
      if ( !strcmp( "SSD", foo ) ) nSSD++;
      (void)strcpy(current_frame->r[i].name, foo); //copy the atom name 
                          
      // next we grab the positions 
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading postition x from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      (void)sscanf( foo, "%lf", &current_frame->r[i].pos[0] );
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading postition y from %s\n"
             "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      (void)sscanf( foo, "%lf", &current_frame->r[i].pos[1] );
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading postition z from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      (void)sscanf( foo, "%lf", &current_frame->r[i].pos[2] );
    
      // get the velocities
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading velocity x from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      
    
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading velocity y from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading velocity z from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      
      // get the quaternions
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading quaternion 0 from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      (void)sscanf( foo, "%lf", &current_frame->r[i].q[0] );
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading quaternion 1 from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      (void)sscanf( foo, "%lf", &current_frame->r[i].q[1] );
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading quaternion 2 from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      (void)sscanf( foo, "%lf", &current_frame->r[i].q[2] );

      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading quaternion 3 from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      (void)sscanf( foo, "%lf", &current_frame->r[i].q[3] );
      
      // get the angular velocities
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading angular momentum jx from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading angular momentum jy from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading angular momentum jz from %s\n"
               "natoms  = %d, line = %d\n",
               in_name, nAtoms, lineCount );
        exit(8);
      }
    }

    // if necassary, wrap into the periodic image
    
    if(wrap){
      
      for( i=0; i<nAtoms; i++ ){
        
        /*
        if( !strcmp( current_frame->r[i].name, "HEAD" ) ){
          
          // find the center of the lipid
          
          mcX = 0.0;
          mcY = 0.0;
          mcZ = 0.0;
          mcount = 0;

          mcX += current_frame->r[i].x;
          mcY += current_frame->r[i].y;
          mcZ += current_frame->r[i].z;
          mcount++;
          i++;

          while( strcmp( current_frame->r[i].name, "HEAD" ) &&
                 strcmp( current_frame->r[i].name, "SSD" ) ){
            
            mcX += current_frame->r[i].x;
            mcY += current_frame->r[i].y;
            mcZ += current_frame->r[i].z;
            mcount++;
            i++;
          }
          
          mcX /= mcount;
          mcY /= mcount;
          mcZ /= mcount;

          newCX = mcX;
          newCY = mcY;
          newCZ = mcZ;
          
          map( &newCX, &newCY, &newCZ,
               cX, cY, cZ,
               current_frame->boxX,
               current_frame->boxY,
               current_frame->boxZ );
          
          dx = mcX - newCX;
          dy = mcY - newCY;
          dz = mcZ - newCZ;

          for(j=(i-mcount); j<mcount; j++ ){
            
            current_frame->r[j].x -= dx;
            current_frame->r[j].y -= dy;
            current_frame->r[j].z -= dz;
          }
          
          i--; // so we don't skip the next atom
        }
        */
        // else 
        
        wrapVector(current_frame->r[i].pos, 
                   current_frame->Hmat, 
                   current_frame->HmatI);
        
      }
    }   

    nframes++; 
    
    // write out here    
    
    if(printWater) newN = nAtoms + ( nSSD * 3 ); 
    else newN = nAtoms - nSSD;
    
    newN *= (nRepeatX+1);
    newN *= (nRepeatY+1);
    newN *= (nRepeatZ+1);

    if( !(nframes%skipFrames) ){
      fprintf( out_file,        
               "%d\n"
               "%lf;\t%lf\t%lf\t%lf;\t%lf\t%lf\t%lf;\t%lf\t%lf\t%lf;\n",
               newN, current_frame->time,
               current_frame->Hmat[0][0], current_frame->Hmat[1][0],
               current_frame->Hmat[2][0],
               current_frame->Hmat[0][1], current_frame->Hmat[1][1],
               current_frame->Hmat[2][1],
               current_frame->Hmat[0][2], current_frame->Hmat[1][2],
               current_frame->Hmat[2][2] );
    
      rCopy = (struct coords*)
        calloc( nAtoms, sizeof( struct coords ));

      for(i=0; i<nAtoms; i++){
        rCopy[i].q[0] = current_frame->r[i].q[0];
        rCopy[i].q[1] = current_frame->r[i].q[1];
        rCopy[i].q[2] = current_frame->r[i].q[2];
        rCopy[i].q[3] = current_frame->r[i].q[3];

        strcpy(rCopy[i].name, current_frame->r[i].name);
      }

      for(j=0; j<(nRepeatX+1); j++){
        for(k=0; k<(nRepeatY+1); k++){
          for(l=0; l<(nRepeatZ+1); l++){

            for(i=0; i<nAtoms; i++){

              for(m = 0; m < 3; m++) {
                rCopy[i].pos[m] = current_frame->r[i].pos[m] +
                  j * current_frame->Hmat[m][0] + 
                  k * current_frame->Hmat[m][1] + 
                  l * current_frame->Hmat[m][2];
              }
              
              if( !strcmp( "SSD", rCopy[i].name ) ){
                
                rotWrite( out_file, &rCopy[i] );
              }
              
              else if( !strcmp( "HEAD", rCopy[i].name ) ){
                
                rotWrite( out_file, &rCopy[i] );
              }
              else{
                //modify
                fprintf( out_file,
                         "%s\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
                         rCopy[i].name,
                         rCopy[i].pos[0],
                         rCopy[i].pos[1],
                         rCopy[i].pos[2] );
              }
            }
          }
        }
      }
      
      free( rCopy );
    }
    
    /*free up memory */
    
    temp_frame = current_frame->next;
    current_frame->next = NULL;
    
    if(temp_frame != NULL){
      
      free(temp_frame->r);
      free(temp_frame);
    }
    
    /* make a new frame */
    
    temp_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz));
    temp_frame->next = current_frame;
    current_frame = temp_frame;
    
    nSSD = 0;

    eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
    lineCount++;
  }
  
  (void)fclose(in_file);
  
  return 0;
  
}


void rotWrite( FILE* out_file, struct coords* theDipole ){

  double u[3];
  double h1[3];
  double h2[3];
  double ox[3];
  
  double A[3][3];
  
 
  u[0] = 0.0; u[1] = 0.0; u[2] = 1.0;

  h1[0] = 0.0; h1[1] = -0.75695; h1[2] = 0.5206;

  h2[0] = 0.0; h2[1] = 0.75695;  h2[2] = 0.5206;

  ox[0] = 0.0; ox[1] = 0.0;      ox[2] = -0.0654;

  
  setRot( A, theDipole->q );
  rotMe( A, u );

  if( !strcmp( "SSD", theDipole->name )){
    
    rotMe( A, h1 );
    rotMe( A, h2 );
    rotMe( A, ox );

    if( printWater ){
      
      if(printDipole) {
        
        fprintf( out_file,
                 "X\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
                 theDipole->pos[0],
                 theDipole->pos[1],
                 theDipole->pos[2],
                 u[0], u[1], u[2] );

        fprintf( out_file,
                 "O\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
                 theDipole->pos[0] + ox[0],
                 theDipole->pos[1] + ox[1],
                 theDipole->pos[2] + ox[2] );
        
        fprintf( out_file,
                 "H\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
                 theDipole->pos[0] + h1[0],
                 theDipole->pos[1] + h1[1],
                 theDipole->pos[2] + h1[2] );
        
        fprintf( out_file,
                 "H\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
                 theDipole->pos[0] + h2[0],
                 theDipole->pos[1] + h2[1],
                 theDipole->pos[2] + h2[2] );
        }
      else{
        
        fprintf( out_file,
                 "X\t%lf\t%lf\t%lf\n",
                 theDipole->pos[0],
                 theDipole->pos[1],
                 theDipole->pos[2] );

        fprintf( out_file,
                 "O\t%lf\t%lf\t%lf\n",
                 theDipole->pos[0] + ox[0],
                 theDipole->pos[1] + ox[1],
                 theDipole->pos[2] + ox[2] );
        
        fprintf( out_file,
                 "H\t%lf\t%lf\t%lf\n",
                 theDipole->pos[0] + h1[0],
                 theDipole->pos[1] + h1[1],
                 theDipole->pos[2] + h1[2] );
        
        fprintf( out_file,
                 "H\t%lf\t%lf\t%lf\n",
                 theDipole->pos[0] + h2[0],
                 theDipole->pos[1] + h2[1],
                 theDipole->pos[2] + h2[2] );
      }     
    }
  }
  
  else if( !strcmp( "HEAD", theDipole->name )) {
    
    if( printDipole ){
      
      fprintf( out_file,
               "HEAD\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
               theDipole->pos[0],
               theDipole->pos[1],
               theDipole->pos[2],
               u[0], u[1], u[2] );
    }
    else{
     
      fprintf( out_file,
               "HEAD\t%lf\t%lf\t%lf\n",
               theDipole->pos[0],
               theDipole->pos[1],
               theDipole->pos[2] );
    }
  }
}


void setRot( double A[3][3], double the_q[4] ){

  double q0Sqr, q1Sqr, q2Sqr, q3Sqr;
  
  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;
}


void rotMe( double A[3][3], double r[3] ){
  
  int i,j;
  double rb[3]; // the body frame vector 
 
  for(i=0; i<3; i++ ){
    rb[i] = r[i];
  }
  
  for( i=0; i<3; i++ ){
    r[i] = 0.0;
    
    for( j=0; j<3; j++ ){
      r[i] += A[j][i] * rb[j];
    }
  }
}


/***************************************************************************
 * prints out the usage for the command line arguments, then exits.
 ***************************************************************************/

void usage(){
  (void)fprintf(stderr, 
                "The proper usage is: %s [options] <dumpfile>\n"
                "\n"
                "Options:\n"
                "\n"
                "   -h              Display this message\n"
                "   -o <out_name>   The output file (Defaults to <dumpfile>.xyz)\n"
                "   -d              print the dipole moments\n"
                "   -w              print the waters\n"
                "   -m              map to the periodic box\n"
                "   -n <#>          print every <#> frames\n" 
                "\n"
                "  --repeatX <#>    The number of images to repeat in the x direction\n"
                "  --repeatY <#>    The number of images to repeat in the y direction\n"
                "  --repeatZ <#>    The number of images to repeat in the z direction\n"
                
                "\n",
                
                program_name);
  exit(8);
}

void wrapVector( double thePos[3], double Hmat[3][3], double HmatInv[3][3]){

  int i;
  double scaled[3];

  // calc the scaled coordinates.
  
  matVecMul3(HmatInv, thePos, scaled);
  
  for(i=0; i<3; i++)
    scaled[i] -= roundMe(scaled[i]);
  
  // calc the wrapped real coordinates from the wrapped scaled coordinates
  
  matVecMul3(Hmat, scaled, thePos);
    
}

double matDet3(double a[3][3]) {
  int i, j, k;
  double determinant;

  determinant = 0.0;

  for(i = 0; i < 3; i++) {
    j = (i+1)%3;
    k = (i+2)%3;

    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
  }
  return determinant;
}

void invertMat3(double a[3][3], double b[3][3]) {

  int  i, j, k, l, m, n;
  double determinant;

  determinant = matDet3( a );

  if (determinant == 0.0) {
    printf("Can't invert a matrix with a zero determinant!\n");
  }

  for (i=0; i < 3; i++) {
    j = (i+1)%3;
    k = (i+2)%3;
    for(l = 0; l < 3; l++) {
      m = (l+1)%3;
      n = (l+2)%3;

      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
    }
  }
}


void matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
  double a0, a1, a2;

  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];

  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
}

double roundMe( double x ){
  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
}
Revision:	2
Committed:	Fri Sep 24 04:16:43 2004 UTC (20 years, 7 months ago) by gezelter
Content type:	text/plain
File size:	20567 byte(s)
Log Message:	Import of OOPSE v. 2.0
#	User	Rev	Content
1	gezelter	2	#include <stdio.h>
2			#include <stdlib.h>
3			#include <string.h>
4			#include <math.h>
5			#include <unistd.h>
6			#include <sys/types.h>
7			#include <sys/stat.h>
8
9			struct coords{
10			double pos[3]; // cartesian coords
11			double q[4]; // the quanternions
12			char name[30];
13			};
14
15			struct linked_xyz{
16			struct coords *r;
17			double time;
18			double Hmat[3][3];
19			double HmatI[3][3];
20			struct linked_xyz *next;
21			};
22
23			char program_name; /the name of the program */
24			int printWater = 0;
25			int printDipole = 0;
26
27			void usage(void);
28
29			void rotWrite( FILE* out_file, struct coords* theSSD );
30
31			void setRot( double A[3][3], double q[4] );
32
33			void rotMe( double A[3][3], double r[3] );
34			void wrapVector( double thePos[3], double Hmat[3][3], double HmatI[3][3]);
35			double matDet3(double a[3][3]);
36			void invertMat3(double a[3][3], double b[3][3]);
37			void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
38			double roundMe(double x);
39
40			int main(argc, argv)
41			int argc;
42			char *argv[];
43			{
44
45
46			struct coords *out_coords;
47
48			int i, j, k, l, m; /* loop counters */
49			mode_t dir_mode = S_IRWXU;
50
51			int lineCount = 0; //the line number
52			int newN; // the new number of atoms
53			int nSSD=0; // the number of SSD per frame
54
55			unsigned int nAtoms; /the number of atoms in each time step /
56			char read_buffer[1000]; /the line buffer for reading /
57			char eof_test; /ptr to see when we reach the end of the file */
58			char foo; /the pointer to the current string token */
59			FILE in_file; / the input file */
60			FILE out_file; /the output file */
61			char out_prefix = NULL; /the prefix of the output file */
62			char out_name[500]; /the output name /
63			int have_outName =0;
64			char in_name[500]; // the input file name
65			char temp_name[500];
66			char root_name = NULL; /the root name of the input file */
67			unsigned int n_out = 0; /keeps track of which output file is being written/
68
69
70			int skipFrames = 1;
71
72			struct linked_xyz *current_frame;
73			struct linked_xyz *temp_frame;
74
75			int nframes =0;
76
77			int wrap = 0;
78
79			double cX = 0.0;
80			double cY = 0.0;
81			double cZ = 0.0;
82
83			double mcX, mcY, mcZ;
84			double newCX, newCY, newCZ;
85			double dx, dy, dz;
86			int mcount;
87
88			int repeatX = 0;
89			int repeatY = 0;
90			int repeatZ = 0;
91
92			int nRepeatX = 0;
93			int nRepeatY = 0;
94			int nRepeatZ = 0;
95
96			struct coords* rCopy;
97
98			int done;
99			char current_flag;
100
101			program_name = argv[0]; /save the program name in case we need it/
102
103			for( i = 1; i < argc; i++){
104
105			if(argv[i][0] =='-'){
106
107			if(argv[i][1] == '-' ){
108
109			// parse long word options
110
111			if( !strcmp( argv[i], "--repeatX" ) ){
112			repeatX = 1;
113			i++;
114			nRepeatX = atoi( argv[i] );
115			}
116
117			else if( !strcmp( argv[i], "--repeatY" ) ){
118			repeatY = 1;
119			i++;
120			nRepeatY = atoi( argv[i] );
121			}
122
123			else if( !strcmp( argv[i], "--repeatZ" ) ){
124			repeatZ = 1;
125			i++;
126			nRepeatZ = atoi( argv[i] );
127			}
128
129			else{
130			fprintf( stderr,
131			"Invalid option \"%s\"\n", argv[i] );
132			usage();
133			}
134			}
135
136			else{
137
138			// parse single character options
139
140			done =0;
141			j = 1;
142			current_flag = argv[i][j];
143			while( (current_flag != '\0') && (!done) ){
144
145			switch(current_flag){
146
147			case 'o':
148			// -o <prefix> => the output
149
150			i++;
151			strcpy( out_name, argv[i] );
152			have_outName = 1;
153			done = 1;
154			break;
155
156			case 'n':
157			// -n <#> => print every <#> frames
158
159			i++;
160			skipFrames = atoi(argv[i]);
161			done = 1;
162			break;
163
164			case 'h':
165			// -h => give the usage
166
167			usage();
168			break;
169
170			case 'd':
171			// print the dipoles
172
173			printDipole = 1;
174			break;
175
176			case 'w':
177			// print the waters
178
179			printWater = 1;
180			break;
181
182			case 'm':
183			// map to a periodic box
184
185			wrap = 1;
186			break;
187
188			default:
189
190			fprintf(stderr, "Bad option \"-%c\"\n", current_flag);
191			usage();
192			}
193			j++;
194			current_flag = argv[i][j];
195			}
196			}
197			}
198
199			else{
200
201			if( root_name != NULL ){
202			fprintf( stderr,
203			"Error at \"%s\", program does not currently support\n"
204			"more than one input file.\n"
205			"\n",
206			argv[i]);
207			usage();
208			}
209
210			root_name = argv[i];
211			}
212			}
213
214			if(root_name == NULL){
215			usage();
216			}
217
218			sprintf( in_name, "%s", root_name );
219			if( !have_outName ) sprintf( out_name, "%s.xyz", root_name );
220
221			in_file = fopen(in_name, "r");
222			if(in_file == NULL){
223			printf("Cannot open file \"%s\" for reading.\n", in_name);
224			exit(8);
225			}
226
227			out_file = fopen( out_name, "w" );
228			if( out_file == NULL ){
229			printf("Cannot open file \"%s\" for writing.\n", out_name);
230			exit(8);
231			}
232
233			// start reading the first frame
234
235			eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
236			lineCount++;
237
238			current_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz));
239			current_frame->next = NULL;
240
241
242			while(eof_test != NULL){
243
244			(void)sscanf(read_buffer, "%d", &nAtoms);
245			current_frame->r =
246			(struct coords *)calloc(nAtoms, sizeof(struct coords));
247
248			// read and the comment line and grab the time and box dimensions
249
250			eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
251			lineCount++;
252			if(eof_test == NULL){
253			printf("error in reading file at line: %d\n", lineCount);
254			exit(8);
255			}
256
257			foo = strtok( read_buffer, " ,;\t" );
258			sscanf( read_buffer, "%lf", &current_frame->time );
259
260			foo = strtok(NULL, " ,;\t");
261			if(foo == NULL){
262			printf("error in reading file at line: %d\n", lineCount);
263			exit(8);
264			}
265			(void)sscanf(foo, "%lf",&current_frame->Hmat[0][0]);
266
267			foo = strtok(NULL, " ,;\t");
268			if(foo == NULL){
269			printf("error in reading file at line: %d\n", lineCount);
270			exit(8);
271			}
272			(void)sscanf(foo, "%lf",&current_frame->Hmat[1][0]);
273
274			foo = strtok(NULL, " ,;\t");
275			if(foo == NULL){
276			printf("error in reading file at line: %d\n", lineCount);
277			exit(8);
278			}
279			(void)sscanf(foo, "%lf",&current_frame->Hmat[2][0]);
280
281			foo = strtok(NULL, " ,;\t");
282			if(foo == NULL){
283			printf("error in reading file at line: %d\n", lineCount);
284			exit(8);
285			}
286			(void)sscanf(foo, "%lf",&current_frame->Hmat[0][1]);
287
288			foo = strtok(NULL, " ,;\t");
289			if(foo == NULL){
290			printf("error in reading file at line: %d\n", lineCount);
291			exit(8);
292			}
293			(void)sscanf(foo, "%lf",&current_frame->Hmat[1][1]);
294
295			foo = strtok(NULL, " ,;\t");
296			if(foo == NULL){
297			printf("error in reading file at line: %d\n", lineCount);
298			exit(8);
299			}
300			(void)sscanf(foo, "%lf",&current_frame->Hmat[2][1]);
301
302			foo = strtok(NULL, " ,;\t");
303			if(foo == NULL){
304			printf("error in reading file at line: %d\n", lineCount);
305			exit(8);
306			}
307			(void)sscanf(foo, "%lf",&current_frame->Hmat[0][2]);
308
309			foo = strtok(NULL, " ,;\t");
310			if(foo == NULL){
311			printf("error in reading file at line: %d\n", lineCount);
312			exit(8);
313			}
314			(void)sscanf(foo, "%lf",&current_frame->Hmat[1][2]);
315
316			foo = strtok(NULL, " ,;\t");
317			if(foo == NULL){
318			printf("error in reading file at line: %d\n", lineCount);
319			exit(8);
320			}
321			(void)sscanf(foo, "%lf",&current_frame->Hmat[2][2]);
322
323
324			// Find HmatI:
325
326			invertMat3(current_frame->Hmat, current_frame->HmatI);
327
328
329			for( i=0; i < nAtoms; i++){
330
331			eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
332			lineCount++;
333			if(eof_test == NULL){
334			printf("error in reading file at line: %d\n", lineCount);
335			exit(8);
336			}
337
338			foo = strtok(read_buffer, " ,;\t");
339			if ( !strcmp( "SSD", foo ) ) nSSD++;
340			(void)strcpy(current_frame->r[i].name, foo); //copy the atom name
341
342			// next we grab the positions
343
344			foo = strtok(NULL, " ,;\t");
345			if(foo == NULL){
346			printf("error in reading postition x from %s\n"
347			"natoms = %d, line = %d\n",
348			in_name, nAtoms, lineCount );
349			exit(8);
350			}
351			(void)sscanf( foo, "%lf", &current_frame->r[i].pos[0] );
352
353			foo = strtok(NULL, " ,;\t");
354			if(foo == NULL){
355			printf("error in reading postition y from %s\n"
356			"natoms = %d, line = %d\n",
357			in_name, nAtoms, lineCount );
358			exit(8);
359			}
360			(void)sscanf( foo, "%lf", &current_frame->r[i].pos[1] );
361
362			foo = strtok(NULL, " ,;\t");
363			if(foo == NULL){
364			printf("error in reading postition z from %s\n"
365			"natoms = %d, line = %d\n",
366			in_name, nAtoms, lineCount );
367			exit(8);
368			}
369			(void)sscanf( foo, "%lf", &current_frame->r[i].pos[2] );
370
371			// get the velocities
372
373			foo = strtok(NULL, " ,;\t");
374			if(foo == NULL){
375			printf("error in reading velocity x from %s\n"
376			"natoms = %d, line = %d\n",
377			in_name, nAtoms, lineCount );
378			exit(8);
379			}
380
381
382			foo = strtok(NULL, " ,;\t");
383			if(foo == NULL){
384			printf("error in reading velocity y from %s\n"
385			"natoms = %d, line = %d\n",
386			in_name, nAtoms, lineCount );
387			exit(8);
388			}
389
390
391			foo = strtok(NULL, " ,;\t");
392			if(foo == NULL){
393			printf("error in reading velocity z from %s\n"
394			"natoms = %d, line = %d\n",
395			in_name, nAtoms, lineCount );
396			exit(8);
397			}
398
399			// get the quaternions
400
401			foo = strtok(NULL, " ,;\t");
402			if(foo == NULL){
403			printf("error in reading quaternion 0 from %s\n"
404			"natoms = %d, line = %d\n",
405			in_name, nAtoms, lineCount );
406			exit(8);
407			}
408			(void)sscanf( foo, "%lf", &current_frame->r[i].q[0] );
409
410			foo = strtok(NULL, " ,;\t");
411			if(foo == NULL){
412			printf("error in reading quaternion 1 from %s\n"
413			"natoms = %d, line = %d\n",
414			in_name, nAtoms, lineCount );
415			exit(8);
416			}
417			(void)sscanf( foo, "%lf", &current_frame->r[i].q[1] );
418
419			foo = strtok(NULL, " ,;\t");
420			if(foo == NULL){
421			printf("error in reading quaternion 2 from %s\n"
422			"natoms = %d, line = %d\n",
423			in_name, nAtoms, lineCount );
424			exit(8);
425			}
426			(void)sscanf( foo, "%lf", &current_frame->r[i].q[2] );
427
428			foo = strtok(NULL, " ,;\t");
429			if(foo == NULL){
430			printf("error in reading quaternion 3 from %s\n"
431			"natoms = %d, line = %d\n",
432			in_name, nAtoms, lineCount );
433			exit(8);
434			}
435			(void)sscanf( foo, "%lf", &current_frame->r[i].q[3] );
436
437			// get the angular velocities
438
439			foo = strtok(NULL, " ,;\t");
440			if(foo == NULL){
441			printf("error in reading angular momentum jx from %s\n"
442			"natoms = %d, line = %d\n",
443			in_name, nAtoms, lineCount );
444			exit(8);
445			}
446
447			foo = strtok(NULL, " ,;\t");
448			if(foo == NULL){
449			printf("error in reading angular momentum jy from %s\n"
450			"natoms = %d, line = %d\n",
451			in_name, nAtoms, lineCount );
452			exit(8);
453			}
454
455			foo = strtok(NULL, " ,;\t");
456			if(foo == NULL){
457			printf("error in reading angular momentum jz from %s\n"
458			"natoms = %d, line = %d\n",
459			in_name, nAtoms, lineCount );
460			exit(8);
461			}
462			}
463
464			// if necassary, wrap into the periodic image
465
466			if(wrap){
467
468			for( i=0; i<nAtoms; i++ ){
469
470			/*
471			if( !strcmp( current_frame->r[i].name, "HEAD" ) ){
472
473			// find the center of the lipid
474
475			mcX = 0.0;
476			mcY = 0.0;
477			mcZ = 0.0;
478			mcount = 0;
479
480			mcX += current_frame->r[i].x;
481			mcY += current_frame->r[i].y;
482			mcZ += current_frame->r[i].z;
483			mcount++;
484			i++;
485
486			while( strcmp( current_frame->r[i].name, "HEAD" ) &&
487			strcmp( current_frame->r[i].name, "SSD" ) ){
488
489			mcX += current_frame->r[i].x;
490			mcY += current_frame->r[i].y;
491			mcZ += current_frame->r[i].z;
492			mcount++;
493			i++;
494			}
495
496			mcX /= mcount;
497			mcY /= mcount;
498			mcZ /= mcount;
499
500			newCX = mcX;
501			newCY = mcY;
502			newCZ = mcZ;
503
504			map( &newCX, &newCY, &newCZ,
505			cX, cY, cZ,
506			current_frame->boxX,
507			current_frame->boxY,
508			current_frame->boxZ );
509
510			dx = mcX - newCX;
511			dy = mcY - newCY;
512			dz = mcZ - newCZ;
513
514			for(j=(i-mcount); j<mcount; j++ ){
515
516			current_frame->r[j].x -= dx;
517			current_frame->r[j].y -= dy;
518			current_frame->r[j].z -= dz;
519			}
520
521			i--; // so we don't skip the next atom
522			}
523			*/
524			// else
525
526			wrapVector(current_frame->r[i].pos,
527			current_frame->Hmat,
528			current_frame->HmatI);
529
530			}
531			}
532
533			nframes++;
534
535			// write out here
536
537			if(printWater) newN = nAtoms + ( nSSD * 3 );
538			else newN = nAtoms - nSSD;
539
540			newN *= (nRepeatX+1);
541			newN *= (nRepeatY+1);
542			newN *= (nRepeatZ+1);
543
544			if( !(nframes%skipFrames) ){
545			fprintf( out_file,
546			"%d\n"
547			"%lf;\t%lf\t%lf\t%lf;\t%lf\t%lf\t%lf;\t%lf\t%lf\t%lf;\n",
548			newN, current_frame->time,
549			current_frame->Hmat[0][0], current_frame->Hmat[1][0],
550			current_frame->Hmat[2][0],
551			current_frame->Hmat[0][1], current_frame->Hmat[1][1],
552			current_frame->Hmat[2][1],
553			current_frame->Hmat[0][2], current_frame->Hmat[1][2],
554			current_frame->Hmat[2][2] );
555
556			rCopy = (struct coords*)
557			calloc( nAtoms, sizeof( struct coords ));
558
559			for(i=0; i<nAtoms; i++){
560			rCopy[i].q[0] = current_frame->r[i].q[0];
561			rCopy[i].q[1] = current_frame->r[i].q[1];
562			rCopy[i].q[2] = current_frame->r[i].q[2];
563			rCopy[i].q[3] = current_frame->r[i].q[3];
564
565			strcpy(rCopy[i].name, current_frame->r[i].name);
566			}
567
568			for(j=0; j<(nRepeatX+1); j++){
569			for(k=0; k<(nRepeatY+1); k++){
570			for(l=0; l<(nRepeatZ+1); l++){
571
572			for(i=0; i<nAtoms; i++){
573
574			for(m = 0; m < 3; m++) {
575			rCopy[i].pos[m] = current_frame->r[i].pos[m] +
576			j * current_frame->Hmat[m][0] +
577			k * current_frame->Hmat[m][1] +
578			l * current_frame->Hmat[m][2];
579			}
580
581			if( !strcmp( "SSD", rCopy[i].name ) ){
582
583			rotWrite( out_file, &rCopy[i] );
584			}
585
586			else if( !strcmp( "HEAD", rCopy[i].name ) ){
587
588			rotWrite( out_file, &rCopy[i] );
589			}
590			else{
591			//modify
592			fprintf( out_file,
593			"%s\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
594			rCopy[i].name,
595			rCopy[i].pos[0],
596			rCopy[i].pos[1],
597			rCopy[i].pos[2] );
598			}
599			}
600			}
601			}
602			}
603
604			free( rCopy );
605			}
606
607			/free up memory /
608
609			temp_frame = current_frame->next;
610			current_frame->next = NULL;
611
612			if(temp_frame != NULL){
613
614			free(temp_frame->r);
615			free(temp_frame);
616			}
617
618			/* make a new frame */
619
620			temp_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz));
621			temp_frame->next = current_frame;
622			current_frame = temp_frame;
623
624			nSSD = 0;
625
626			eof_test = fgets(read_buffer, sizeof(read_buffer), in_file);
627			lineCount++;
628			}
629
630			(void)fclose(in_file);
631
632			return 0;
633
634			}
635
636
637
638			void rotWrite( FILE* out_file, struct coords* theDipole ){
639
640			double u[3];
641			double h1[3];
642			double h2[3];
643			double ox[3];
644
645			double A[3][3];
646
647
648			u[0] = 0.0; u[1] = 0.0; u[2] = 1.0;
649
650			h1[0] = 0.0; h1[1] = -0.75695; h1[2] = 0.5206;
651
652			h2[0] = 0.0; h2[1] = 0.75695; h2[2] = 0.5206;
653
654			ox[0] = 0.0; ox[1] = 0.0; ox[2] = -0.0654;
655
656
657			setRot( A, theDipole->q );
658			rotMe( A, u );
659
660			if( !strcmp( "SSD", theDipole->name )){
661
662			rotMe( A, h1 );
663			rotMe( A, h2 );
664			rotMe( A, ox );
665
666			if( printWater ){
667
668			if(printDipole) {
669
670			fprintf( out_file,
671			"X\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
672			theDipole->pos[0],
673			theDipole->pos[1],
674			theDipole->pos[2],
675			u[0], u[1], u[2] );
676
677			fprintf( out_file,
678			"O\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
679			theDipole->pos[0] + ox[0],
680			theDipole->pos[1] + ox[1],
681			theDipole->pos[2] + ox[2] );
682
683			fprintf( out_file,
684			"H\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
685			theDipole->pos[0] + h1[0],
686			theDipole->pos[1] + h1[1],
687			theDipole->pos[2] + h1[2] );
688
689			fprintf( out_file,
690			"H\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
691			theDipole->pos[0] + h2[0],
692			theDipole->pos[1] + h2[1],
693			theDipole->pos[2] + h2[2] );
694			}
695			else{
696
697			fprintf( out_file,
698			"X\t%lf\t%lf\t%lf\n",
699			theDipole->pos[0],
700			theDipole->pos[1],
701			theDipole->pos[2] );
702
703			fprintf( out_file,
704			"O\t%lf\t%lf\t%lf\n",
705			theDipole->pos[0] + ox[0],
706			theDipole->pos[1] + ox[1],
707			theDipole->pos[2] + ox[2] );
708
709			fprintf( out_file,
710			"H\t%lf\t%lf\t%lf\n",
711			theDipole->pos[0] + h1[0],
712			theDipole->pos[1] + h1[1],
713			theDipole->pos[2] + h1[2] );
714
715			fprintf( out_file,
716			"H\t%lf\t%lf\t%lf\n",
717			theDipole->pos[0] + h2[0],
718			theDipole->pos[1] + h2[1],
719			theDipole->pos[2] + h2[2] );
720			}
721			}
722			}
723
724			else if( !strcmp( "HEAD", theDipole->name )) {
725
726			if( printDipole ){
727
728			fprintf( out_file,
729			"HEAD\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
730			theDipole->pos[0],
731			theDipole->pos[1],
732			theDipole->pos[2],
733			u[0], u[1], u[2] );
734			}
735			else{
736
737			fprintf( out_file,
738			"HEAD\t%lf\t%lf\t%lf\n",
739			theDipole->pos[0],
740			theDipole->pos[1],
741			theDipole->pos[2] );
742			}
743			}
744			}
745
746
747			void setRot( double A[3][3], double the_q[4] ){
748
749			double q0Sqr, q1Sqr, q2Sqr, q3Sqr;
750
751			q0Sqr = the_q[0] * the_q[0];
752			q1Sqr = the_q[1] * the_q[1];
753			q2Sqr = the_q[2] * the_q[2];
754			q3Sqr = the_q[3] * the_q[3];
755
756			A[0][0] = q0Sqr + q1Sqr - q2Sqr - q3Sqr;
757			A[0][1] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] );
758			A[0][2] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] );
759
760			A[1][0] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] );
761			A[1][1] = q0Sqr - q1Sqr + q2Sqr - q3Sqr;
762			A[1][2] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] );
763
764			A[2][0] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] );
765			A[2][1] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] );
766			A[2][2] = q0Sqr - q1Sqr -q2Sqr +q3Sqr;
767			}
768
769
770
771			void rotMe( double A[3][3], double r[3] ){
772
773			int i,j;
774			double rb[3]; // the body frame vector
775
776			for(i=0; i<3; i++ ){
777			rb[i] = r[i];
778			}
779
780			for( i=0; i<3; i++ ){
781			r[i] = 0.0;
782
783			for( j=0; j<3; j++ ){
784			r[i] += A[j][i] * rb[j];
785			}
786			}
787			}
788
789
790
791			/***************************************************************************
792			* prints out the usage for the command line arguments, then exits.
793			***************************************************************************/
794
795			void usage(){
796			(void)fprintf(stderr,
797			"The proper usage is: %s [options] <dumpfile>\n"
798			"\n"
799			"Options:\n"
800			"\n"
801			" -h Display this message\n"
802			" -o <out_name> The output file (Defaults to <dumpfile>.xyz)\n"
803			" -d print the dipole moments\n"
804			" -w print the waters\n"
805			" -m map to the periodic box\n"
806			" -n <#> print every <#> frames\n"
807			"\n"
808			" --repeatX <#> The number of images to repeat in the x direction\n"
809			" --repeatY <#> The number of images to repeat in the y direction\n"
810			" --repeatZ <#> The number of images to repeat in the z direction\n"
811
812			"\n",
813
814			program_name);
815			exit(8);
816			}
817
818			void wrapVector( double thePos[3], double Hmat[3][3], double HmatInv[3][3]){
819
820			int i;
821			double scaled[3];
822
823			// calc the scaled coordinates.
824
825			matVecMul3(HmatInv, thePos, scaled);
826
827			for(i=0; i<3; i++)
828			scaled[i] -= roundMe(scaled[i]);
829
830			// calc the wrapped real coordinates from the wrapped scaled coordinates
831
832			matVecMul3(Hmat, scaled, thePos);
833
834			}
835
836			double matDet3(double a[3][3]) {
837			int i, j, k;
838			double determinant;
839
840			determinant = 0.0;
841
842			for(i = 0; i < 3; i++) {
843			j = (i+1)%3;
844			k = (i+2)%3;
845
846			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
847			}
848			return determinant;
849			}
850
851			void invertMat3(double a[3][3], double b[3][3]) {
852
853			int i, j, k, l, m, n;
854			double determinant;
855
856			determinant = matDet3( a );
857
858			if (determinant == 0.0) {
859			printf("Can't invert a matrix with a zero determinant!\n");
860			}
861
862			for (i=0; i < 3; i++) {
863			j = (i+1)%3;
864			k = (i+2)%3;
865			for(l = 0; l < 3; l++) {
866			m = (l+1)%3;
867			n = (l+2)%3;
868
869			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
870			}
871			}
872			}
873
874
875			void matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
876			double a0, a1, a2;
877
878			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
879
880			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
881			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
882			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
883			}
884
885			double roundMe( double x ){
886			return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
887			}