trunk/madProps/madProps.c

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>


#include "madProps.h"
#include "frameCount.h"

char *program_name; /*the name of the program */

void usage(void);

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


  struct xyz_frame *dumpArray;
  int nFrames; // the nu8mvber of frames
  int lineNum = 0; // keeps track of the line number
  int n_atoms; // the number of atoms
  int i,j; // loop counters
  int isFirst;

  char read_buffer[2000]; /*the line buffer for reading */
  char *foo; /*the pointer to the current string token */
  FILE *in_file; /* the input file */
  char *in_name = NULL; /*the name of the input file */
  char *out_prefix; // the output prefix
  char current_flag; // used in parseing the flags


  int done = 0; // multipurpose boolean
  int have_prefix = 0; // prefix boolean
  int calcRMSD = 0;

  int calcGofR = 0;
  char gofR1[30];
  char gofR2[30];

  int calcMuCorr = 0;
  char muCorr[30];

  int calcCosCorr = 0;
  char cosCorr1[30];
  char cosCorr2[30];

  int startFrame = 0;
  int haveStartFrame = 0;
  int endFrame = 0;
  int haveEndFrame = 0;

  program_name = argv[0]; /*save the program name in case we need it*/
  
  for( i = 1; i < argc; i++){
    
    if(argv[i][0] =='-'){

      // parse the option
      
      if(argv[i][1] == '-' ){

        // parse long word options
        
        if( !strcmp( argv[i], "--GofR" ) ){
          calcGofR = 1;
          i++;
          strcpy( gofR1, argv[i] );
          i++;
          strcpy( gofR2, argv[i] );
        }

        else if( !strcmp( argv[i], "--MuCorr") ){
          calcMuCorr = 1;
          i++;
          strcpy( muCorr, argv[i] );
        }
        
        else if( !strcmp( argv[i], "--startFrame" ) ){
          haveStartFrame = 1;
          i++;
          startFrame = atoi(argv[i]);
        }

        else if( !strcmp( argv[i], "--endFrame" ) ){
          haveEndFrame = 1;
          i++;
          endFrame = 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 prefix.

            i++;
            out_prefix = argv[i];
            have_prefix = 1;
            done = 1;
            break;

          case 'h':
            // -h => give the usage
            
            usage();
            break;
        
          case 'r':
            // calculates the rmsd

            calcRMSD = 1;
            break;

          case 'g':
            // calculate all to all g(r)

            calcGofR = 1;
            strcpy( gofR1, "all" );
            strcpy( gofR2, "all" );
            break;

          default:

            fprintf( stderr, "about to print bad option\n" );

            (void)fprintf(stderr, "Bad option \"-%s\"\n", current_flag);
            usage();
          }
          j++;
          current_flag = argv[i][j];
        }
      }
    }

    else{
      
      if( in_name != NULL ){
        fprintf( stderr, 
                 "Error at \"%s\", program does not currently support\n"
                 "more than one input file.\n"
                 "\n",
                 argv[i]);
        usage();
      }

      in_name = argv[i];
    }
  }

  if(in_name == NULL){
    usage();
  }

  if( !have_prefix ) out_prefix = in_name;
  
  printf( "Counting number of frames..." );
  fflush( stdout );
  
  nFrames = frameCount( in_name );
  if( !haveEndFrame ) endFrame = nFrames;

  printf( "done.\n"
          "nframes = %d\n"
          "\n",
          nFrames );
  fflush( stdout );

  in_file = fopen(in_name, "r");
  if(in_file == NULL){
    printf("Cannot open file: %s\n", in_name);
    exit(8);
  }

  // create and initialize the array of frames

  dumpArray = (struct xyz_frame*)calloc( nFrames,
                                         sizeof( struct xyz_frame ) );
  for( i=0; i<nFrames; i++ ){
    dumpArray[i].nAtoms = 0;
    dumpArray[i].time   = 0.0;
    dumpArray[i].boxX   = 0.0;
    dumpArray[i].boxY   = 0.0;
    dumpArray[i].boxZ   = 0.0;
    dumpArray[i].r      = NULL;
    dumpArray[i].v      = NULL;
    dumpArray[i].names  = NULL;
  }

  // read the frames
  
  printf( "Reading the frames into the coordinate arrays..." );
  fflush( stdout );

  isFirst = 1;
  for(j =0; j<nFrames; j++ ){
    
    // read the number of atoms

    fgets(read_buffer, sizeof(read_buffer), in_file);
    lineNum++;

    n_atoms = atoi( read_buffer );
    dumpArray[j].nAtoms = n_atoms;

    dumpArray[j].r = 
      (struct coords *)calloc(n_atoms, sizeof(struct coords));
    
    if( isFirst ) {
      dumpArray[0].names = 
        (atomID *)calloc( n_atoms, sizeof(atomID) );
      isFirst = 0;
    }

    if( calcMuCorr || calcCosCorr ){
          dumpArray[j].v = 
            (struct vect *)calloc(n_atoms, sizeof(struct vect));
    }

    //read the time and the box sizes

    fgets(read_buffer, sizeof(read_buffer), in_file);
    lineNum++;
    
    foo = strtok(read_buffer, " ,;\t");
    if(foo == NULL){
      printf("error in reading time at line %d\n", lineNum);
      exit(8);
    }
    
    dumpArray[j].time = atof( foo );
    
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading boxX at line %d\n", lineNum);
      exit(8);
    }
    
    dumpArray[j].boxX = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading boxY at line %d\n", lineNum);
      exit(8);
    }
    
    dumpArray[j].boxY = atof( foo );
    
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      printf("error in reading boxZ at line %d\n", lineNum);
      exit(8);
    }
    
    dumpArray[j].boxZ = atof( foo );


    for( i=0; i < n_atoms; i++){
      
      fgets(read_buffer, sizeof(read_buffer), in_file);
      lineNum++;
      
      // get the name and positions

      foo = strtok(read_buffer, " ,;\t");
      if(foo == NULL){
        printf("error in reading atom name at line %d\n", lineNum );
        exit(8);
      }
      
      strcpy(dumpArray[0].names[i], foo); /*copy the atom name */

      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading position x at line %d\n", lineNum);
        exit(8);
      }
      
      dumpArray[j].r[i].x = atof( foo );

      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading position y at line %d\n", lineNum);
        exit(8);
      }
      
      dumpArray[j].r[i].y = atof( foo );

      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        printf("error in reading position z at line %d\n", lineNum);
        exit(8);
      }
      
      dumpArray[j].r[i].z = atof( foo );

      if( calcCosCorr || calcMuCorr ){
        
        foo = strtok(NULL, " ,;\t");
        if(foo == NULL){
                  
          dumpArray[j].v[i].x = 0.0;
          dumpArray[j].v[i].y = 0.0;
          dumpArray[j].v[i].z = 0.0;
        }
        else{

          dumpArray[j].v[i].x = atof( foo );
          
          foo = strtok(NULL, " ,;\t");
          if(foo == NULL){
            printf("error in reading vector y at line %d\n", lineNum);
            exit(8);
          }
          
          dumpArray[j].v[i].y = atof( foo );
          
          foo = strtok(NULL, " ,;\t");
          if(foo == NULL){
            printf("error in reading vector z at line %d\n", lineNum);
            exit(8);
          }
          
          dumpArray[j].v[i].z = atof( foo );
        }
      }
      
    }
  }
  
  (void)fclose(in_file);
  
  printf( "done\n"
          "\n" );
  fflush( stdout );
  
  
  // do calculations here.

  if( calcGofR ){
    
    fprintf( stdout,
             "Calculating the g(r) between atoms \"%s\" and \"%s\"...",
             gofR1, gofR2 );
    fflush( stdout );
    
    // gofr call
    GofR( out_prefix, gofR1, gofR2, dumpArray, nFrames, startFrame, endFrame );
    
    fprintf( stdout, 
             " done.\n"
             "\n");
    fflush(stdout);
  }

  if( calcRMSD ){
    
    fprintf( stdout,
             "Calculating the RMSD..." );
    fflush( stdout );
    
    // RMSD call

    
    fprintf( stdout, 
             " done.\n"
             "\n");
    fflush(stdout);
  }

  if( calcMuCorr ){
    
    fprintf( stdout,
             "Calculating the mu correlation for \"%s\"...",
             muCorr);
    fflush( stdout );
    
    // muCorr call

    
    fprintf( stdout, 
             " done.\n"
             "\n");
    fflush(stdout);
  }

  if( calcCosCorr ){
    
    fprintf( stdout,
             "Calculating the cos correlation between \"%s\" and \"%s\"...",
             cosCorr1, cosCorr2 );
    fflush( stdout );
    
    cosCorr( out_prefix, cosCorr1, cosCorr2, dumpArray, nFrames, startFrame, 
             endFrame );
    
    fprintf( stdout, 
             " done.\n"
             "\n");
    fflush(stdout);
  }
  
  return 0;
  
}


void map( double *x, double *y, double *z, 
          double boxX, double boxY, double boxZ ){ 
  
  *x -= boxX * copysign(1.0,*x) * floor( fabs( *x/boxX ) + 0.5  );
  *y -= boxY * copysign(1.0,*y) * floor( fabs( *y/boxY ) + 0.5  );
  *z -= boxZ * copysign(1.0,*z) * floor( fabs( *z/boxZ ) + 0.5  );

}


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

void usage(){
  (void)fprintf(stdout, 
                "The proper usage is: %s [options] <xyz_file>\n"
                "\n"
                "Options:\n"
                "\n"
                "   short:\n"
                "   ------\n"
                "   -h              Display this message\n"
                "   -o <prefix>     The output prefix\n"
                "   -r              Calculate the RMSD\n"
                "   -g              Calculate all to all g(r)\n"
                
                "\n"
                "   long:\n"
                "   -----\n"
                "   --GofR <atom1> <atom2>    Calculates g(r) between atom1 and atom 2\n"
                "                               -note: \"all\" will do all atoms\n"
                "   --MuCorr <atom>           Calculate mu correlation of atom\n"
                "   --CosCorr <atom1> <atom2> Calculate the cos correlation between atom1 and atom2\n"
                "  --startFrame <frame#>      Specifies a frame to start correlating\n"
                "  --endFrame <frame#>        Specifies a frame to stop correlating.\n"
                
                "\n"
                "\n",
                program_name);
  exit(8);
}
Revision:	82
Committed:	Fri Aug 16 04:05:45 2002 UTC (21 years, 11 months ago) by mmeineke
Content type:	text/plain
File size:	9569 byte(s)
Log Message:	added the capability to specify a start and end frame for cosCorr and GofR
#	User	Rev	Content
1	mmeineke	38	#include <stdio.h>
2			#include <stdlib.h>
3			#include <string.h>
4			#include <math.h>
5
6	mmeineke	43
7			#include "madProps.h"
8	mmeineke	38	#include "frameCount.h"
9
10			char program_name; /the name of the program */
11
12			void usage(void);
13
14			int main(argc, argv)
15			int argc;
16			char *argv[];
17			{
18
19
20			struct xyz_frame *dumpArray;
21			int nFrames; // the nu8mvber of frames
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	mmeineke	45	int isFirst;
26	mmeineke	38
27			char read_buffer[2000]; /the line buffer for reading /
28			char foo; /the pointer to the current string token */
29			FILE in_file; / the input file */
30			char in_name = NULL; /the name of the input file */
31	mmeineke	43	char *out_prefix; // the output prefix
32			char current_flag; // used in parseing the flags
33	mmeineke	38
34
35	mmeineke	43
36			int done = 0; // multipurpose boolean
37			int have_prefix = 0; // prefix boolean
38			int calcRMSD = 0;
39
40			int calcGofR = 0;
41			char gofR1[30];
42			char gofR2[30];
43
44			int calcMuCorr = 0;
45			char muCorr[30];
46
47			int calcCosCorr = 0;
48			char cosCorr1[30];
49			char cosCorr2[30];
50
51	mmeineke	82	int startFrame = 0;
52			int haveStartFrame = 0;
53			int endFrame = 0;
54			int haveEndFrame = 0;
55
56	mmeineke	38	program_name = argv[0]; /save the program name in case we need it/
57
58	mmeineke	43	for( i = 1; i < argc; i++){
59	mmeineke	38
60			if(argv[i][0] =='-'){
61	mmeineke	43
62			// parse the option
63	mmeineke	38
64	mmeineke	43	if(argv[i][1] == '-' ){
65
66			// parse long word options
67
68			if( !strcmp( argv[i], "--GofR" ) ){
69			calcGofR = 1;
70			i++;
71			strcpy( gofR1, argv[i] );
72			i++;
73			strcpy( gofR2, argv[i] );
74			}
75
76			else if( !strcmp( argv[i], "--MuCorr") ){
77			calcMuCorr = 1;
78			i++;
79			strcpy( muCorr, argv[i] );
80			}
81
82	mmeineke	82	else if( !strcmp( argv[i], "--startFrame" ) ){
83			haveStartFrame = 1;
84	mmeineke	43	i++;
85	mmeineke	82	startFrame = atoi(argv[i]);
86			}
87
88			else if( !strcmp( argv[i], "--endFrame" ) ){
89			haveEndFrame = 1;
90	mmeineke	43	i++;
91	mmeineke	82	endFrame = atoi(argv[i]);
92	mmeineke	43	}
93
94			else{
95			fprintf( stderr,
96			"Invalid option \"%s\"\n", argv[i] );
97			usage();
98			}
99			}
100	mmeineke	38
101	mmeineke	43	else{
102	mmeineke	38
103	mmeineke	43	// parse single character options
104
105			done =0;
106			j = 1;
107			current_flag = argv[i][j];
108			while( (current_flag != '\0') && (!done) ){
109
110			switch(current_flag){
111	mmeineke	38
112	mmeineke	43	case 'o':
113			// -o <prefix> => the output prefix.
114	mmeineke	38
115	mmeineke	43	i++;
116			out_prefix = argv[i];
117			have_prefix = 1;
118			done = 1;
119			break;
120
121			case 'h':
122			// -h => give the usage
123
124			usage();
125			break;
126
127			case 'r':
128			// calculates the rmsd
129
130			calcRMSD = 1;
131			break;
132
133			case 'g':
134			// calculate all to all g(r)
135
136			calcGofR = 1;
137			strcpy( gofR1, "all" );
138			strcpy( gofR2, "all" );
139			break;
140
141			default:
142
143			fprintf( stderr, "about to print bad option\n" );
144
145			(void)fprintf(stderr, "Bad option \"-%s\"\n", current_flag);
146			usage();
147			}
148			j++;
149			current_flag = argv[i][j];
150			}
151			}
152			}
153
154			else{
155
156			if( in_name != NULL ){
157			fprintf( stderr,
158			"Error at \"%s\", program does not currently support\n"
159			"more than one input file.\n"
160			"\n",
161			argv[i]);
162	mmeineke	38	usage();
163			}
164	mmeineke	43
165			in_name = argv[i];
166	mmeineke	38	}
167			}
168
169			if(in_name == NULL){
170			usage();
171			}
172	mmeineke	43
173			if( !have_prefix ) out_prefix = in_name;
174	mmeineke	38
175			printf( "Counting number of frames..." );
176			fflush( stdout );
177
178			nFrames = frameCount( in_name );
179	mmeineke	82	if( !haveEndFrame ) endFrame = nFrames;
180	mmeineke	38
181			printf( "done.\n"
182			"nframes = %d\n"
183			"\n",
184			nFrames );
185			fflush( stdout );
186
187			in_file = fopen(in_name, "r");
188			if(in_file == NULL){
189			printf("Cannot open file: %s\n", in_name);
190			exit(8);
191			}
192
193	mmeineke	45	// create and initialize the array of frames
194	mmeineke	38
195			dumpArray = (struct xyz_frame*)calloc( nFrames,
196			sizeof( struct xyz_frame ) );
197	mmeineke	45	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	mmeineke	38
208			// read the frames
209
210			printf( "Reading the frames into the coordinate arrays..." );
211			fflush( stdout );
212
213	mmeineke	45	isFirst = 1;
214	mmeineke	38	for(j =0; j<nFrames; j++ ){
215
216			// read the number of atoms
217
218			fgets(read_buffer, sizeof(read_buffer), in_file);
219			lineNum++;
220
221			n_atoms = atoi( read_buffer );
222			dumpArray[j].nAtoms = n_atoms;
223
224			dumpArray[j].r =
225			(struct coords *)calloc(n_atoms, sizeof(struct coords));
226	mmeineke	45
227			if( isFirst ) {
228			dumpArray[0].names =
229			(atomID *)calloc( n_atoms, sizeof(atomID) );
230			isFirst = 0;
231			}
232	mmeineke	38
233	mmeineke	43	if( calcMuCorr \|\| calcCosCorr ){
234			dumpArray[j].v =
235			(struct vect *)calloc(n_atoms, sizeof(struct vect));
236			}
237
238	mmeineke	38	//read the time and the box sizes
239
240			fgets(read_buffer, sizeof(read_buffer), in_file);
241			lineNum++;
242
243			foo = strtok(read_buffer, " ,;\t");
244			if(foo == NULL){
245			printf("error in reading time at line %d\n", lineNum);
246			exit(8);
247			}
248
249			dumpArray[j].time = atof( foo );
250
251			foo = strtok(NULL, " ,;\t");
252			if(foo == NULL){
253			printf("error in reading boxX at line %d\n", lineNum);
254			exit(8);
255			}
256
257			dumpArray[j].boxX = atof( foo );
258
259			foo = strtok(NULL, " ,;\t");
260			if(foo == NULL){
261			printf("error in reading boxY at line %d\n", lineNum);
262			exit(8);
263			}
264
265			dumpArray[j].boxY = atof( foo );
266
267			foo = strtok(NULL, " ,;\t");
268			if(foo == NULL){
269			printf("error in reading boxZ at line %d\n", lineNum);
270			exit(8);
271			}
272
273			dumpArray[j].boxZ = atof( foo );
274
275
276			for( i=0; i < n_atoms; i++){
277
278			fgets(read_buffer, sizeof(read_buffer), in_file);
279			lineNum++;
280
281			// get the name and positions
282
283			foo = strtok(read_buffer, " ,;\t");
284			if(foo == NULL){
285			printf("error in reading atom name at line %d\n", lineNum );
286			exit(8);
287			}
288
289	mmeineke	45	strcpy(dumpArray[0].names[i], foo); /copy the atom name /
290	mmeineke	38
291			foo = strtok(NULL, " ,;\t");
292			if(foo == NULL){
293			printf("error in reading position x at line %d\n", lineNum);
294			exit(8);
295			}
296
297			dumpArray[j].r[i].x = atof( foo );
298
299			foo = strtok(NULL, " ,;\t");
300			if(foo == NULL){
301			printf("error in reading position y at line %d\n", lineNum);
302			exit(8);
303			}
304
305			dumpArray[j].r[i].y = atof( foo );
306
307			foo = strtok(NULL, " ,;\t");
308			if(foo == NULL){
309			printf("error in reading position z at line %d\n", lineNum);
310			exit(8);
311			}
312
313			dumpArray[j].r[i].z = atof( foo );
314	mmeineke	43
315			if( calcCosCorr \|\| calcMuCorr ){
316
317			foo = strtok(NULL, " ,;\t");
318			if(foo == NULL){
319
320			dumpArray[j].v[i].x = 0.0;
321			dumpArray[j].v[i].y = 0.0;
322			dumpArray[j].v[i].z = 0.0;
323			}
324			else{
325
326			dumpArray[j].v[i].x = atof( foo );
327
328			foo = strtok(NULL, " ,;\t");
329			if(foo == NULL){
330			printf("error in reading vector y at line %d\n", lineNum);
331			exit(8);
332			}
333
334			dumpArray[j].v[i].y = atof( foo );
335
336			foo = strtok(NULL, " ,;\t");
337			if(foo == NULL){
338			printf("error in reading vector z at line %d\n", lineNum);
339			exit(8);
340			}
341
342			dumpArray[j].v[i].z = atof( foo );
343			}
344			}
345
346	mmeineke	38	}
347			}
348
349			(void)fclose(in_file);
350
351			printf( "done\n"
352			"\n" );
353			fflush( stdout );
354
355
356
357			// do calculations here.
358
359	mmeineke	43	if( calcGofR ){
360
361			fprintf( stdout,
362			"Calculating the g(r) between atoms \"%s\" and \"%s\"...",
363			gofR1, gofR2 );
364			fflush( stdout );
365
366			// gofr call
367	mmeineke	82	GofR( out_prefix, gofR1, gofR2, dumpArray, nFrames, startFrame, endFrame );
368	mmeineke	43
369			fprintf( stdout,
370			" done.\n"
371			"\n");
372			fflush(stdout);
373			}
374	mmeineke	38
375	mmeineke	43	if( calcRMSD ){
376
377			fprintf( stdout,
378			"Calculating the RMSD..." );
379			fflush( stdout );
380
381			// RMSD call
382	mmeineke	38
383	mmeineke	43
384			fprintf( stdout,
385			" done.\n"
386			"\n");
387			fflush(stdout);
388			}
389	mmeineke	38
390	mmeineke	43	if( calcMuCorr ){
391
392			fprintf( stdout,
393			"Calculating the mu correlation for \"%s\"...",
394			muCorr);
395			fflush( stdout );
396
397			// muCorr call
398	mmeineke	38
399	mmeineke	43
400			fprintf( stdout,
401			" done.\n"
402			"\n");
403			fflush(stdout);
404			}
405
406			if( calcCosCorr ){
407
408			fprintf( stdout,
409			"Calculating the cos correlation between \"%s\" and \"%s\"...",
410			cosCorr1, cosCorr2 );
411			fflush( stdout );
412
413	mmeineke	82	cosCorr( out_prefix, cosCorr1, cosCorr2, dumpArray, nFrames, startFrame,
414			endFrame );
415	mmeineke	43
416			fprintf( stdout,
417			" done.\n"
418			"\n");
419			fflush(stdout);
420			}
421	mmeineke	38
422			return 0;
423
424			}
425
426
427	mmeineke	46	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	mmeineke	38
434	mmeineke	46	}
435
436
437	mmeineke	38	/***************************************************************************
438			* prints out the usage for the command line arguments, then exits.
439			***************************************************************************/
440
441			void usage(){
442	mmeineke	43	(void)fprintf(stdout,
443			"The proper usage is: %s [options] <xyz_file>\n"
444			"\n"
445			"Options:\n"
446			"\n"
447			" short:\n"
448			" ------\n"
449			" -h Display this message\n"
450			" -o <prefix> The output prefix\n"
451			" -r Calculate the RMSD\n"
452			" -g Calculate all to all g(r)\n"
453
454			"\n"
455			" long:\n"
456			" -----\n"
457			" --GofR <atom1> <atom2> Calculates g(r) between atom1 and atom 2\n"
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	mmeineke	82	" --startFrame <frame#> Specifies a frame to start correlating\n"
462			" --endFrame <frame#> Specifies a frame to stop correlating.\n"
463	mmeineke	43
464			"\n"
465			"\n",
466	mmeineke	38	program_name);
467			exit(8);
468			}