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root/group/trunk/madProps/madProps.c
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Comparing trunk/madProps/madProps.c (file contents):
Revision 43 by mmeineke, Fri Jul 19 19:05:59 2002 UTC vs.
Revision 82 by mmeineke, Fri Aug 16 04:05:45 2002 UTC

# Line 22 | Line 22 | int main(argc, argv)
22    int lineNum = 0; // keeps track of the line number
23    int n_atoms; // the number of atoms
24    int i,j; // loop counters
25 +  int isFirst;
26  
27    char read_buffer[2000]; /*the line buffer for reading */
28    char *foo; /*the pointer to the current string token */
# Line 47 | Line 48 | int main(argc, argv)
48    char cosCorr1[30];
49    char cosCorr2[30];
50  
51 +  int startFrame = 0;
52 +  int haveStartFrame = 0;
53 +  int endFrame = 0;
54 +  int haveEndFrame = 0;
55  
51 –
56    program_name = argv[0]; /*save the program name in case we need it*/
57    
58    for( i = 1; i < argc; i++){
# Line 75 | Line 79 | int main(argc, argv)
79            strcpy( muCorr, argv[i] );
80          }
81          
82 <        else if( !strcmp( argv[i], "--CosCorr" ) ){
83 <          calcCosCorr = 1;
82 >        else if( !strcmp( argv[i], "--startFrame" ) ){
83 >          haveStartFrame = 1;
84            i++;
85 <          strcpy( cosCorr1, argv[i] );
85 >          startFrame = atoi(argv[i]);
86 >        }
87 >
88 >        else if( !strcmp( argv[i], "--endFrame" ) ){
89 >          haveEndFrame = 1;
90            i++;
91 <          strcpy( cosCorr2, argv[i] );
91 >          endFrame = atoi(argv[i]);
92          }
93  
94          else{
# Line 168 | Line 176 | int main(argc, argv)
176    fflush( stdout );
177    
178    nFrames = frameCount( in_name );
179 +  if( !haveEndFrame ) endFrame = nFrames;
180  
181    printf( "done.\n"
182            "nframes = %d\n"
# Line 181 | Line 190 | int main(argc, argv)
190      exit(8);
191    }
192  
193 <  // create the array of frames
193 >  // create and initialize the array of frames
194  
195    dumpArray = (struct xyz_frame*)calloc( nFrames,
196                                           sizeof( struct xyz_frame ) );
197 +  for( i=0; i<nFrames; i++ ){
198 +    dumpArray[i].nAtoms = 0;
199 +    dumpArray[i].time   = 0.0;
200 +    dumpArray[i].boxX   = 0.0;
201 +    dumpArray[i].boxY   = 0.0;
202 +    dumpArray[i].boxZ   = 0.0;
203 +    dumpArray[i].r      = NULL;
204 +    dumpArray[i].v      = NULL;
205 +    dumpArray[i].names  = NULL;
206 +  }
207  
208    // read the frames
209    
210    printf( "Reading the frames into the coordinate arrays..." );
211    fflush( stdout );
212  
213 +  isFirst = 1;
214    for(j =0; j<nFrames; j++ ){
215      
216      // read the number of atoms
# Line 203 | Line 223 | int main(argc, argv)
223  
224      dumpArray[j].r =
225        (struct coords *)calloc(n_atoms, sizeof(struct coords));
226 +    
227 +    if( isFirst ) {
228 +      dumpArray[0].names =
229 +        (atomID *)calloc( n_atoms, sizeof(atomID) );
230 +      isFirst = 0;
231 +    }
232  
233      if( calcMuCorr || calcCosCorr ){
234            dumpArray[j].v =
# Line 260 | Line 286 | int main(argc, argv)
286          exit(8);
287        }
288        
289 <      strcpy(dumpArray[j].r[i].name, foo); /*copy the atom name */
289 >      strcpy(dumpArray[0].names[i], foo); /*copy the atom name */
290  
291        foo = strtok(NULL, " ,;\t");
292        if(foo == NULL){
# Line 338 | Line 364 | int main(argc, argv)
364      fflush( stdout );
365      
366      // gofr call
367 <    GofR( out_prefix, gofR1, gofR2, dumpArray, nFrames );
367 >    GofR( out_prefix, gofR1, gofR2, dumpArray, nFrames, startFrame, endFrame );
368      
369      fprintf( stdout,
370               " done.\n"
# Line 384 | Line 410 | int main(argc, argv)
410               cosCorr1, cosCorr2 );
411      fflush( stdout );
412      
413 <    // cosCorr call
414 <
413 >    cosCorr( out_prefix, cosCorr1, cosCorr2, dumpArray, nFrames, startFrame,
414 >             endFrame );
415      
416      fprintf( stdout,
417               " done.\n"
# Line 393 | Line 419 | int main(argc, argv)
419      fflush(stdout);
420    }
421    
396 –  
422    return 0;
423    
424   }
425  
426  
427 + void map( double *x, double *y, double *z,
428 +          double boxX, double boxY, double boxZ ){
429 +  
430 +  *x -= boxX * copysign(1.0,*x) * floor( fabs( *x/boxX ) + 0.5  );
431 +  *y -= boxY * copysign(1.0,*y) * floor( fabs( *y/boxY ) + 0.5  );
432 +  *z -= boxZ * copysign(1.0,*z) * floor( fabs( *z/boxZ ) + 0.5  );
433  
434 + }
435 +
436 +
437   /***************************************************************************
438   * prints out the usage for the command line arguments, then exits.
439   ***************************************************************************/
# Line 424 | Line 458 | void usage(){
458                  "                               -note: \"all\" will do all atoms\n"
459                  "   --MuCorr <atom>           Calculate mu correlation of atom\n"
460                  "   --CosCorr <atom1> <atom2> Calculate the cos correlation between atom1 and atom2\n"
461 +                "  --startFrame <frame#>      Specifies a frame to start correlating\n"
462 +                "  --endFrame <frame#>        Specifies a frame to stop correlating.\n"
463                  
428 –                
464                  "\n"
465                  "\n",
466                  program_name);

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