trunk/madProps/GofR.c

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

#include "GofR.h"

void map( double *x, double *y, double *z, 
          double boxX, double boxY, double boxZ );

// this algoritm assumes constant number of atoms between frames, and
// constant boxSize

void GofR( char* out_prefix, char* atom1, char* atom2, 
           struct xyz_frame* frames, int nFrames ){

  int i,j,k;

  enum g_types { all_all, atom_all, atom_atom };
  enum g_types the_type;
  char* allAtom;
  
  double atom1Dens;
  double atom2Dens;
  double allDens;

  double atom1Constant;
  double atom2Constant;
  double allConstant;

  double nAtom1;
  double nAtom2;
  double nAtoms;

  double delR;
  double boxVol;
  double shortBox;

  double rxj, ryj, rzj;
  double dx, dy, dz;
  double distSqr;
  double dist;
  
  double rLower, rUpper;
  double nIdeal;
  double volSlice;

  int bin;
  int histogram[GofRBins];
  double the_GofR[GofRBins];
  double rValue[GofRBins];

  char out_name[500];
  char tempString[100];
  FILE *out_file;

  
   // figure out the type of GofR we are calculating

  if( !strcmp( atom1, "all" ) ){
    
    if( !strcmp( atom2, "all" ) ) the_type = all_all;
    else{
      the_type = atom_all;
      allAtom = atom2;
    }
  }
  else{
    
    if( !strcmp( atom2, "all" ) ){
      the_type = atom_all;
      allAtom = atom1;
    }
    else the_type = atom_atom;
  }

  // find the box size and delR;
  
  shortBox = frames[0].boxX;
  if( shortBox > frames[0].boxY ) shortBox = frames[0].boxY;
  if( shortBox > frames[0].boxZ ) shortBox = frames[0].boxZ;
  
  delR = ( shortBox / 2.0 ) / GofRBins;
  boxVol = frames[0].boxX * frames[0].boxY * frames[0].boxZ;
  
  // zero the histograms;
  
  for(i=0; i<GofRBins; i++ ){
    
    rValue[i]    = 0.0;
    the_GofR[i]  = 0.0;
    histogram[i] = 0;
  }

  switch( the_type ){

  case atom_atom:
    
    // find the number of each type;

    nAtom1 = 0;
    nAtom2 = 0;
    for( i=0; i<frames[0].nAtoms; i++ ){
  
      if( !strcmp( frames[0].names[i], atom1 ) ) nAtom1++;
      if( !strcmp( frames[0].names[i], atom2 ) ) nAtom2++;
    }
    
    if( !nAtom1 ){

      fprintf( stderr, 
               "\n"
               "GofR error, \"%s\" was not found in the trajectory.\n",
               atom1 );
      exit(8);
    }

    if( !nAtom2 ){

      fprintf( stderr, 
               "\n"
               "GofR error, \"%s\" was not found in the trajectory.\n",
               atom2 );
      exit(8);
    }

    // calculate some of the constants;
    
    atom1Dens = nAtom1 / boxVol;
    atom2Dens = nAtom2 / boxVol;
    
    atom1Constant = ( 4.0 * M_PI * atom1Dens ) / 3.0;
    atom2Constant = ( 4.0 * M_PI * atom2Dens ) / 3.0;
    
    // calculate the histogram

    for( i=0; i<nFrames; i++){
      for( j=0; j<(frames[i].nAtoms-1); j++ ){
        
        if( !strcmp( frames[0].names[j], atom1 ) ){

          rxj = frames[i].r[j].x;
          ryj = frames[i].r[j].y;
          rzj = frames[i].r[j].z;
          
          for( k=j+1; k< frames[i].nAtoms; k++ ){
            
            if( !strcmp( frames[0].names[k], atom2 ) ){
          
              dx = rxj - frames[i].r[k].x;
              dy = ryj - frames[i].r[k].y;
              dz = rzj - frames[i].r[k].z;
              
              map( &dx, &dy, &dz, 
                   frames[i].boxX, frames[i].boxY, frames[i].boxZ );
              
              distSqr = (dx * dx) + (dy * dy) + (dz * dz);
              dist = sqrt( distSqr );
              
              // add to the appropriate bin
              bin = (int)( dist / delR );
              if( bin < GofRBins ) histogram[bin] += 2;
            }
          }
        }
        
        else if( !strcmp( frames[0].names[j], atom2 ) ){
          
          rxj = frames[i].r[j].x;
          ryj = frames[i].r[j].y;
          rzj = frames[i].r[j].z;
          
          for( k=j+1; k< frames[i].nAtoms; k++ ){
            
            if( !strcmp( frames[0].names[k], atom1 ) ){
              
              dx = rxj - frames[i].r[k].x;
              dy = ryj - frames[i].r[k].y;
              dz = rzj - frames[i].r[k].z;
              
              map( &dx, &dy, &dz, 
                   frames[i].boxX, frames[i].boxY, frames[i].boxZ );
              
              distSqr = (dx * dx) + (dy * dy) + (dz * dz);
              dist = sqrt( distSqr );
              
              // add to the appropriate bin
              bin = (int)( dist / delR );
              if( bin < GofRBins ) histogram[bin] += 2;
            }
          }
        }         
      }
    }
  
    // calculate the GofR
    
    for( i=0; i<GofRBins; i++ ){

      rLower = i * delR;
      rUpper = rLower + delR;
      
      volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
      nIdeal = volSlice * ( atom1Constant + atom2Constant );
      
      the_GofR[i] = histogram[i] / ( nFrames * ( nAtom1 + nAtom2 ) * nIdeal );
      rValue[i] = rLower + ( delR / 2.0 );
    }

    // make the out_name;

    strcpy( out_name, out_prefix );
    sprintf( tempString, "-%s-%s.GofR", atom1, atom2 );
    strcat( out_name, tempString );

    out_file = fopen( out_name, "w" );
    if( out_file == NULL ){
      fprintf( stderr,
               "\n"
               "GofR error, unable to open \"%s\" for writing.\n",
               out_name );
      exit(8);
    }
    break;

  case atom_all:
    
    // find the number of AllAtoms;

    nAtom1 = 0;
    for( i=0; i<frames[0].nAtoms; i++ ){
      
      if( !strcmp( frames[0].names[i], allAtom ) ) nAtom1++;
    }
    
    if( !nAtom1 ){

      fprintf( stderr, 
               "\n"
               "GofR error, \"%s\" was not found in the trajectory.\n",
               atom1 );
      exit(8);
    }

    // calculate some of the constants;
    
    atom1Dens = nAtom1 / boxVol;
    allDens  = frames[0].nAtoms / boxVol;
    
    atom1Constant = ( 4.0 * M_PI * atom1Dens ) / 3.0;
    allConstant  = ( 4.0 * M_PI * allDens ) / 3.0;
    
    // calculate the histogram

    for( i=0; i<nFrames; i++){
      for( j=0; j<(frames[i].nAtoms-1); j++ ){
        
        if( !strcmp( frames[0].names[j], allAtom ) ){
          
          rxj = frames[i].r[j].x;
          ryj = frames[i].r[j].y;
          rzj = frames[i].r[j].z;
          
          for( k=j+1; k< frames[i].nAtoms; k++ ){
                          
            dx = rxj - frames[i].r[k].x;
            dy = ryj - frames[i].r[k].y;
            dz = rzj - frames[i].r[k].z;
            
            map( &dx, &dy, &dz, 
                 frames[i].boxX, frames[i].boxY, frames[i].boxZ );
            
            distSqr = (dx * dx) + (dy * dy) + (dz * dz);
            dist = sqrt( distSqr );
            
            // add to the appropriate bin
            bin = (int)( dist / delR );
            if( bin < GofRBins ) histogram[bin] += 2;
          }
        }
          
        else{
          
          rxj = frames[i].r[j].x;
          ryj = frames[i].r[j].y;
          rzj = frames[i].r[j].z;
          
          for( k=j+1; k< frames[i].nAtoms; k++ ){
            
            if( !strcmp( frames[0].names[k], allAtom ) ){
              
              dx = rxj - frames[i].r[k].x;
              dy = ryj - frames[i].r[k].y;
              dz = rzj - frames[i].r[k].z;
              
              map( &dx, &dy, &dz, 
                   frames[i].boxX, frames[i].boxY, frames[i].boxZ );
              
              distSqr = (dx * dx) + (dy * dy) + (dz * dz);
              dist = sqrt( distSqr );
              
              // add to the appropriate bin
              bin = (int)( dist / delR );
              if( bin < GofRBins ) histogram[bin] += 2;
            }
          }
        }         
      }
    }
  
    // calculate the GofR
    
    for( i=0; i<GofRBins; i++ ){
      
      rLower = i * delR;
      rUpper = rLower + delR;
      
      volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
      nIdeal = volSlice * ( allConstant );
      
      the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal );
      rValue[i] = rLower + ( delR / 2.0 );
    }

    // make the out_name;

    strcpy( out_name, out_prefix );
    sprintf( tempString, "-%s-%s.GofR", allAtom, "all" );
    strcat( out_name, tempString );

    out_file = fopen( out_name, "w" );
    if( out_file == NULL ){
      fprintf( stderr,
               "\n"
               "GofR error, unable to open \"%s\" for writing.\n",
               out_name );
      exit(8);
    }
    break;
               
  case all_all:
    
    // calculate some of the constants;
    
    allDens  = frames[0].nAtoms / boxVol;
    
    allConstant  = ( 4.0 * M_PI * allDens ) / 3.0;
    
    // calculate the histogram

    for( i=0; i<nFrames; i++){
      for( j=0; j<(frames[i].nAtoms-1); j++ ){
        
        rxj = frames[i].r[j].x;
        ryj = frames[i].r[j].y;
        rzj = frames[i].r[j].z;
        
        for( k=j+1; k< frames[i].nAtoms; k++ ){

          dx = rxj - frames[i].r[k].x;
          dy = ryj - frames[i].r[k].y;
          dz = rzj - frames[i].r[k].z;
                  
          map( &dx, &dy, &dz, 
               frames[i].boxX, frames[i].boxY, frames[i].boxZ );
          
          distSqr = (dx * dx) + (dy * dy) + (dz * dz);
          dist = sqrt( distSqr );
          
          // add to the appropriate bin
          bin = (int)( dist / delR );
          if( bin < GofRBins ) histogram[bin] += 2;
        }         
      }
    }
  
    // calculate the GofR
    
    for( i=0; i<GofRBins; i++ ){
      
      rLower = i * delR;
      rUpper = rLower + delR;
      
      volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
      nIdeal = volSlice * ( allConstant );
      
      the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal );
      rValue[i] = rLower + ( delR / 2.0 );
    }

    // make the out_name;

    strcpy( out_name, out_prefix );
    sprintf( tempString, "-%s-%s.GofR", "all", "all" );
    strcat( out_name, tempString );

    out_file = fopen( out_name, "w" );
    if( out_file == NULL ){
      fprintf( stderr,
               "\n"
               "GofR error, unable to open \"%s\" for writing.\n",
               out_name );
      exit(8);
    }
    break;
  }

  for( i=0; i<GofRBins; i++ ){
    fprintf( out_file,
             "%lf\t%lf\n",
             rValue[i], the_GofR[i] );
  }

  fclose( out_file );
}

Revision:	46
Committed:	Tue Jul 23 20:10:49 2002 UTC (21 years, 11 months ago) by mmeineke
Content type:	text/plain
File size:	9274 byte(s)
Log Message:	added the cos correlation function
#	Content
1	#include <math.h>
2	#include <stdlib.h>
3	#include <stdio.h>
4	#include <string.h>
5
6	#include "GofR.h"
7
8	void map( double x, double y, double *z,
9	double boxX, double boxY, double boxZ );
10
11	// this algoritm assumes constant number of atoms between frames, and
12	// constant boxSize
13
14	void GofR( char* out_prefix, char* atom1, char* atom2,
15	struct xyz_frame* frames, int nFrames ){
16
17	int i,j,k;
18
19	enum g_types { all_all, atom_all, atom_atom };
20	enum g_types the_type;
21	char* allAtom;
22
23	double atom1Dens;
24	double atom2Dens;
25	double allDens;
26
27	double atom1Constant;
28	double atom2Constant;
29	double allConstant;
30
31	double nAtom1;
32	double nAtom2;
33	double nAtoms;
34
35	double delR;
36	double boxVol;
37	double shortBox;
38
39	double rxj, ryj, rzj;
40	double dx, dy, dz;
41	double distSqr;
42	double dist;
43
44	double rLower, rUpper;
45	double nIdeal;
46	double volSlice;
47
48	int bin;
49	int histogram[GofRBins];
50	double the_GofR[GofRBins];
51	double rValue[GofRBins];
52
53	char out_name[500];
54	char tempString[100];
55	FILE *out_file;
56
57
58	// figure out the type of GofR we are calculating
59
60	if( !strcmp( atom1, "all" ) ){
61
62	if( !strcmp( atom2, "all" ) ) the_type = all_all;
63	else{
64	the_type = atom_all;
65	allAtom = atom2;
66	}
67	}
68	else{
69
70	if( !strcmp( atom2, "all" ) ){
71	the_type = atom_all;
72	allAtom = atom1;
73	}
74	else the_type = atom_atom;
75	}
76
77	// find the box size and delR;
78
79	shortBox = frames[0].boxX;
80	if( shortBox > frames[0].boxY ) shortBox = frames[0].boxY;
81	if( shortBox > frames[0].boxZ ) shortBox = frames[0].boxZ;
82
83	delR = ( shortBox / 2.0 ) / GofRBins;
84	boxVol = frames[0].boxX * frames[0].boxY * frames[0].boxZ;
85
86	// zero the histograms;
87
88	for(i=0; i<GofRBins; i++ ){
89
90	rValue[i] = 0.0;
91	the_GofR[i] = 0.0;
92	histogram[i] = 0;
93	}
94
95	switch( the_type ){
96
97	case atom_atom:
98
99	// find the number of each type;
100
101	nAtom1 = 0;
102	nAtom2 = 0;
103	for( i=0; i<frames[0].nAtoms; i++ ){
104
105	if( !strcmp( frames[0].names[i], atom1 ) ) nAtom1++;
106	if( !strcmp( frames[0].names[i], atom2 ) ) nAtom2++;
107	}
108
109	if( !nAtom1 ){
110
111	fprintf( stderr,
112	"\n"
113	"GofR error, \"%s\" was not found in the trajectory.\n",
114	atom1 );
115	exit(8);
116	}
117
118	if( !nAtom2 ){
119
120	fprintf( stderr,
121	"\n"
122	"GofR error, \"%s\" was not found in the trajectory.\n",
123	atom2 );
124	exit(8);
125	}
126
127	// calculate some of the constants;
128
129	atom1Dens = nAtom1 / boxVol;
130	atom2Dens = nAtom2 / boxVol;
131
132	atom1Constant = ( 4.0 * M_PI * atom1Dens ) / 3.0;
133	atom2Constant = ( 4.0 * M_PI * atom2Dens ) / 3.0;
134
135	// calculate the histogram
136
137	for( i=0; i<nFrames; i++){
138	for( j=0; j<(frames[i].nAtoms-1); j++ ){
139
140	if( !strcmp( frames[0].names[j], atom1 ) ){
141
142	rxj = frames[i].r[j].x;
143	ryj = frames[i].r[j].y;
144	rzj = frames[i].r[j].z;
145
146	for( k=j+1; k< frames[i].nAtoms; k++ ){
147
148	if( !strcmp( frames[0].names[k], atom2 ) ){
149
150	dx = rxj - frames[i].r[k].x;
151	dy = ryj - frames[i].r[k].y;
152	dz = rzj - frames[i].r[k].z;
153
154	map( &dx, &dy, &dz,
155	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
156
157	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
158	dist = sqrt( distSqr );
159
160	// add to the appropriate bin
161	bin = (int)( dist / delR );
162	if( bin < GofRBins ) histogram[bin] += 2;
163	}
164	}
165	}
166
167	else if( !strcmp( frames[0].names[j], atom2 ) ){
168
169	rxj = frames[i].r[j].x;
170	ryj = frames[i].r[j].y;
171	rzj = frames[i].r[j].z;
172
173	for( k=j+1; k< frames[i].nAtoms; k++ ){
174
175	if( !strcmp( frames[0].names[k], atom1 ) ){
176
177	dx = rxj - frames[i].r[k].x;
178	dy = ryj - frames[i].r[k].y;
179	dz = rzj - frames[i].r[k].z;
180
181	map( &dx, &dy, &dz,
182	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
183
184	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
185	dist = sqrt( distSqr );
186
187	// add to the appropriate bin
188	bin = (int)( dist / delR );
189	if( bin < GofRBins ) histogram[bin] += 2;
190	}
191	}
192	}
193	}
194	}
195
196	// calculate the GofR
197
198	for( i=0; i<GofRBins; i++ ){
199
200	rLower = i * delR;
201	rUpper = rLower + delR;
202
203	volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
204	nIdeal = volSlice * ( atom1Constant + atom2Constant );
205
206	the_GofR[i] = histogram[i] / ( nFrames * ( nAtom1 + nAtom2 ) * nIdeal );
207	rValue[i] = rLower + ( delR / 2.0 );
208	}
209
210	// make the out_name;
211
212	strcpy( out_name, out_prefix );
213	sprintf( tempString, "-%s-%s.GofR", atom1, atom2 );
214	strcat( out_name, tempString );
215
216	out_file = fopen( out_name, "w" );
217	if( out_file == NULL ){
218	fprintf( stderr,
219	"\n"
220	"GofR error, unable to open \"%s\" for writing.\n",
221	out_name );
222	exit(8);
223	}
224	break;
225
226	case atom_all:
227
228	// find the number of AllAtoms;
229
230	nAtom1 = 0;
231	for( i=0; i<frames[0].nAtoms; i++ ){
232
233	if( !strcmp( frames[0].names[i], allAtom ) ) nAtom1++;
234	}
235
236	if( !nAtom1 ){
237
238	fprintf( stderr,
239	"\n"
240	"GofR error, \"%s\" was not found in the trajectory.\n",
241	atom1 );
242	exit(8);
243	}
244
245	// calculate some of the constants;
246
247	atom1Dens = nAtom1 / boxVol;
248	allDens = frames[0].nAtoms / boxVol;
249
250	atom1Constant = ( 4.0 * M_PI * atom1Dens ) / 3.0;
251	allConstant = ( 4.0 * M_PI * allDens ) / 3.0;
252
253	// calculate the histogram
254
255	for( i=0; i<nFrames; i++){
256	for( j=0; j<(frames[i].nAtoms-1); j++ ){
257
258	if( !strcmp( frames[0].names[j], allAtom ) ){
259
260	rxj = frames[i].r[j].x;
261	ryj = frames[i].r[j].y;
262	rzj = frames[i].r[j].z;
263
264	for( k=j+1; k< frames[i].nAtoms; k++ ){
265
266	dx = rxj - frames[i].r[k].x;
267	dy = ryj - frames[i].r[k].y;
268	dz = rzj - frames[i].r[k].z;
269
270	map( &dx, &dy, &dz,
271	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
272
273	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
274	dist = sqrt( distSqr );
275
276	// add to the appropriate bin
277	bin = (int)( dist / delR );
278	if( bin < GofRBins ) histogram[bin] += 2;
279	}
280	}
281
282	else{
283
284	rxj = frames[i].r[j].x;
285	ryj = frames[i].r[j].y;
286	rzj = frames[i].r[j].z;
287
288	for( k=j+1; k< frames[i].nAtoms; k++ ){
289
290	if( !strcmp( frames[0].names[k], allAtom ) ){
291
292	dx = rxj - frames[i].r[k].x;
293	dy = ryj - frames[i].r[k].y;
294	dz = rzj - frames[i].r[k].z;
295
296	map( &dx, &dy, &dz,
297	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
298
299	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
300	dist = sqrt( distSqr );
301
302	// add to the appropriate bin
303	bin = (int)( dist / delR );
304	if( bin < GofRBins ) histogram[bin] += 2;
305	}
306	}
307	}
308	}
309	}
310
311	// calculate the GofR
312
313	for( i=0; i<GofRBins; i++ ){
314
315	rLower = i * delR;
316	rUpper = rLower + delR;
317
318	volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
319	nIdeal = volSlice * ( allConstant );
320
321	the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal );
322	rValue[i] = rLower + ( delR / 2.0 );
323	}
324
325	// make the out_name;
326
327	strcpy( out_name, out_prefix );
328	sprintf( tempString, "-%s-%s.GofR", allAtom, "all" );
329	strcat( out_name, tempString );
330
331	out_file = fopen( out_name, "w" );
332	if( out_file == NULL ){
333	fprintf( stderr,
334	"\n"
335	"GofR error, unable to open \"%s\" for writing.\n",
336	out_name );
337	exit(8);
338	}
339	break;
340
341	case all_all:
342
343	// calculate some of the constants;
344
345	allDens = frames[0].nAtoms / boxVol;
346
347	allConstant = ( 4.0 * M_PI * allDens ) / 3.0;
348
349	// calculate the histogram
350
351	for( i=0; i<nFrames; i++){
352	for( j=0; j<(frames[i].nAtoms-1); j++ ){
353
354	rxj = frames[i].r[j].x;
355	ryj = frames[i].r[j].y;
356	rzj = frames[i].r[j].z;
357
358	for( k=j+1; k< frames[i].nAtoms; k++ ){
359
360	dx = rxj - frames[i].r[k].x;
361	dy = ryj - frames[i].r[k].y;
362	dz = rzj - frames[i].r[k].z;
363
364	map( &dx, &dy, &dz,
365	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
366
367	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
368	dist = sqrt( distSqr );
369
370	// add to the appropriate bin
371	bin = (int)( dist / delR );
372	if( bin < GofRBins ) histogram[bin] += 2;
373	}
374	}
375	}
376
377	// calculate the GofR
378
379	for( i=0; i<GofRBins; i++ ){
380
381	rLower = i * delR;
382	rUpper = rLower + delR;
383
384	volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
385	nIdeal = volSlice * ( allConstant );
386
387	the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal );
388	rValue[i] = rLower + ( delR / 2.0 );
389	}
390
391	// make the out_name;
392
393	strcpy( out_name, out_prefix );
394	sprintf( tempString, "-%s-%s.GofR", "all", "all" );
395	strcat( out_name, tempString );
396
397	out_file = fopen( out_name, "w" );
398	if( out_file == NULL ){
399	fprintf( stderr,
400	"\n"
401	"GofR error, unable to open \"%s\" for writing.\n",
402	out_name );
403	exit(8);
404	}
405	break;
406	}
407
408	for( i=0; i<GofRBins; i++ ){
409	fprintf( out_file,
410	"%lf\t%lf\n",
411	rValue[i], the_GofR[i] );
412	}
413
414	fclose( out_file );
415	}
416