ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/madProps/madProps.c
(Generate patch)

Comparing trunk/madProps/madProps.c (file contents):
Revision 43 by mmeineke, Fri Jul 19 19:05:59 2002 UTC vs.
Revision 85 by mmeineke, Fri Aug 16 16:55:46 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 64 | Line 68 | int main(argc, argv)
68          if( !strcmp( argv[i], "--GofR" ) ){
69            calcGofR = 1;
70            i++;
71 +          strcpy( cosCorr1, argv[i] );
72 +          i++;
73 +          strcpy( cosCorr2, argv[i] );
74 +        }
75 +
76 +        else if( !strcmp( argv[i], "--CosCorr" ) ){
77 +          calcCosCorr = 1;
78 +          i++;
79            strcpy( gofR1, argv[i] );
80            i++;
81            strcpy( gofR2, argv[i] );
# Line 75 | Line 87 | int main(argc, argv)
87            strcpy( muCorr, argv[i] );
88          }
89          
90 <        else if( !strcmp( argv[i], "--CosCorr" ) ){
91 <          calcCosCorr = 1;
90 >        else if( !strcmp( argv[i], "--startFrame" ) ){
91 >          haveStartFrame = 1;
92            i++;
93 <          strcpy( cosCorr1, argv[i] );
93 >          startFrame = atoi(argv[i]);
94 >          startFrame--;
95 >        }
96 >
97 >        else if( !strcmp( argv[i], "--endFrame" ) ){
98 >          haveEndFrame = 1;
99            i++;
100 <          strcpy( cosCorr2, argv[i] );
100 >          endFrame = atoi(argv[i]);
101          }
102  
103          else{
# Line 168 | Line 185 | int main(argc, argv)
185    fflush( stdout );
186    
187    nFrames = frameCount( in_name );
188 +  if( !haveEndFrame ) endFrame = nFrames;
189  
190    printf( "done.\n"
191            "nframes = %d\n"
# Line 181 | Line 199 | int main(argc, argv)
199      exit(8);
200    }
201  
202 <  // create the array of frames
202 >  // create and initialize the array of frames
203  
204    dumpArray = (struct xyz_frame*)calloc( nFrames,
205                                           sizeof( struct xyz_frame ) );
206 +  for( i=0; i<nFrames; i++ ){
207 +    dumpArray[i].nAtoms = 0;
208 +    dumpArray[i].time   = 0.0;
209 +    dumpArray[i].boxX   = 0.0;
210 +    dumpArray[i].boxY   = 0.0;
211 +    dumpArray[i].boxZ   = 0.0;
212 +    dumpArray[i].r      = NULL;
213 +    dumpArray[i].v      = NULL;
214 +    dumpArray[i].names  = NULL;
215 +  }
216  
217    // read the frames
218    
219    printf( "Reading the frames into the coordinate arrays..." );
220    fflush( stdout );
221  
222 +  isFirst = 1;
223    for(j =0; j<nFrames; j++ ){
224      
225      // read the number of atoms
# Line 203 | Line 232 | int main(argc, argv)
232  
233      dumpArray[j].r =
234        (struct coords *)calloc(n_atoms, sizeof(struct coords));
235 +    
236 +    if( isFirst ) {
237 +      dumpArray[0].names =
238 +        (atomID *)calloc( n_atoms, sizeof(atomID) );
239 +      isFirst = 0;
240 +    }
241  
242      if( calcMuCorr || calcCosCorr ){
243            dumpArray[j].v =
# Line 260 | Line 295 | int main(argc, argv)
295          exit(8);
296        }
297        
298 <      strcpy(dumpArray[j].r[i].name, foo); /*copy the atom name */
298 >      strcpy(dumpArray[0].names[i], foo); /*copy the atom name */
299  
300        foo = strtok(NULL, " ,;\t");
301        if(foo == NULL){
# Line 338 | Line 373 | int main(argc, argv)
373      fflush( stdout );
374      
375      // gofr call
376 <    GofR( out_prefix, gofR1, gofR2, dumpArray, nFrames );
376 >    GofR( out_prefix, gofR1, gofR2, dumpArray, nFrames, startFrame, endFrame );
377      
378      fprintf( stdout,
379               " done.\n"
# Line 384 | Line 419 | int main(argc, argv)
419               cosCorr1, cosCorr2 );
420      fflush( stdout );
421      
422 <    // cosCorr call
423 <
422 >    cosCorr( out_prefix, cosCorr1, cosCorr2, dumpArray, nFrames, startFrame,
423 >             endFrame );
424      
425      fprintf( stdout,
426               " done.\n"
# Line 393 | Line 428 | int main(argc, argv)
428      fflush(stdout);
429    }
430    
396 –  
431    return 0;
432    
433   }
434  
435  
436 + void map( double *x, double *y, double *z,
437 +          double boxX, double boxY, double boxZ ){
438 +  
439 +  *x -= boxX * copysign(1.0,*x) * floor( fabs( *x/boxX ) + 0.5  );
440 +  *y -= boxY * copysign(1.0,*y) * floor( fabs( *y/boxY ) + 0.5  );
441 +  *z -= boxZ * copysign(1.0,*z) * floor( fabs( *z/boxZ ) + 0.5  );
442  
443 + }
444 +
445 +
446   /***************************************************************************
447   * prints out the usage for the command line arguments, then exits.
448   ***************************************************************************/
# Line 424 | Line 467 | void usage(){
467                  "                               -note: \"all\" will do all atoms\n"
468                  "   --MuCorr <atom>           Calculate mu correlation of atom\n"
469                  "   --CosCorr <atom1> <atom2> Calculate the cos correlation between atom1 and atom2\n"
470 +                "   --startFrame <frame#>     Specifies a frame to start correlating\n"
471 +                "   --endFrame <frame#>       Specifies a frame to stop correlating.\n"
472                  
428 –                
473                  "\n"
474                  "\n",
475                  program_name);

Diff Legend

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