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 startFrame, int endFrame ){

  int i,j,k;

  enum g_types { all_all, atom_all, atom_atom };
  enum g_types the_type;
  char* allAtom;
  
  double pairDens;
  double pairConstant;

  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;
    
    if( !strcmp( atom1, atom2 ) ) pairDens = nAtom1 * (nAtom1 - 1) / boxVol;
    else pairDens = nAtom1 * nAtom2 / boxVol;

    pairConstant = ( 4.0 * M_PI * pairDens ) / 3.0;
        
    // calculate the histogram

    for( i=startFrame; i<endFrame; 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 * pairConstant;
      
      the_GofR[i] = histogram[i] / ( nFrames * 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;
    
    pairDens = frames[0].nAtoms * (nAtom1 - 1) / boxVol;
    pairConstant =  ( 4.0 * M_PI * pairDens ) / 3.0;

    // calculate the histogram

    for( i=startFrame; i<endFrame; 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 * pairConstant;
      
      the_GofR[i] = histogram[i] / ( nFrames * 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;
    
    pairDens  = frames[0].nAtoms * (frames[0].nAtoms - 1) / boxVol;
    pairConstant  = ( 4.0 * M_PI * pairDens ) / 3.0;
    
    // calculate the histogram

    for( i=startFrame; i<endFrame; 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 * pairConstant;
      
      the_GofR[i] = histogram[i] / ( nFrames * 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:	103
Committed:	Thu Aug 29 17:21:54 2002 UTC (23 years, 2 months ago) by mmeineke
Content type:	text/plain
File size:	9109 byte(s)
Log Message:	fixed a cosCorr and GofR flag bug, as well as the GofR scaling bug.
#	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	int startFrame, int endFrame ){
17
18	int i,j,k;
19
20	enum g_types { all_all, atom_all, atom_atom };
21	enum g_types the_type;
22	char* allAtom;
23
24	double pairDens;
25	double pairConstant;
26
27	double nAtom1;
28	double nAtom2;
29	double nAtoms;
30
31	double delR;
32	double boxVol;
33	double shortBox;
34
35	double rxj, ryj, rzj;
36	double dx, dy, dz;
37	double distSqr;
38	double dist;
39
40	double rLower, rUpper;
41	double nIdeal;
42	double volSlice;
43
44	int bin;
45	int histogram[GofRBins];
46	double the_GofR[GofRBins];
47	double rValue[GofRBins];
48
49	char out_name[500];
50	char tempString[100];
51	FILE *out_file;
52
53
54	// figure out the type of GofR we are calculating
55
56	if( !strcmp( atom1, "all" ) ){
57
58	if( !strcmp( atom2, "all" ) ) the_type = all_all;
59	else{
60	the_type = atom_all;
61	allAtom = atom2;
62	}
63	}
64	else{
65
66	if( !strcmp( atom2, "all" ) ){
67	the_type = atom_all;
68	allAtom = atom1;
69	}
70	else the_type = atom_atom;
71	}
72
73	// find the box size and delR;
74
75	shortBox = frames[0].boxX;
76	if( shortBox > frames[0].boxY ) shortBox = frames[0].boxY;
77	if( shortBox > frames[0].boxZ ) shortBox = frames[0].boxZ;
78
79	delR = ( shortBox / 2.0 ) / GofRBins;
80	boxVol = frames[0].boxX * frames[0].boxY * frames[0].boxZ;
81
82	// zero the histograms;
83
84	for(i=0; i<GofRBins; i++ ){
85
86	rValue[i] = 0.0;
87	the_GofR[i] = 0.0;
88	histogram[i] = 0;
89	}
90
91	switch( the_type ){
92
93	case atom_atom:
94
95	// find the number of each type;
96
97	nAtom1 = 0;
98	nAtom2 = 0;
99	for( i=0; i<frames[0].nAtoms; i++ ){
100
101	if( !strcmp( frames[0].names[i], atom1 ) ) nAtom1++;
102	if( !strcmp( frames[0].names[i], atom2 ) ) nAtom2++;
103	}
104
105	if( !nAtom1 ){
106
107	fprintf( stderr,
108	"\n"
109	"GofR error, \"%s\" was not found in the trajectory.\n",
110	atom1 );
111	exit(8);
112	}
113
114	if( !nAtom2 ){
115
116	fprintf( stderr,
117	"\n"
118	"GofR error, \"%s\" was not found in the trajectory.\n",
119	atom2 );
120	exit(8);
121	}
122
123	// calculate some of the constants;
124
125	if( !strcmp( atom1, atom2 ) ) pairDens = nAtom1 * (nAtom1 - 1) / boxVol;
126	else pairDens = nAtom1 * nAtom2 / boxVol;
127
128	pairConstant = ( 4.0 * M_PI * pairDens ) / 3.0;
129
130	// calculate the histogram
131
132	for( i=startFrame; i<endFrame; i++){
133	for( j=0; j<(frames[i].nAtoms-1); j++ ){
134
135	if( !strcmp( frames[0].names[j], atom1 ) ){
136
137	rxj = frames[i].r[j].x;
138	ryj = frames[i].r[j].y;
139	rzj = frames[i].r[j].z;
140
141	for( k=j+1; k< frames[i].nAtoms; k++ ){
142
143	if( !strcmp( frames[0].names[k], atom2 ) ){
144
145	dx = rxj - frames[i].r[k].x;
146	dy = ryj - frames[i].r[k].y;
147	dz = rzj - frames[i].r[k].z;
148
149	map( &dx, &dy, &dz,
150	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
151
152	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
153	dist = sqrt( distSqr );
154
155	// add to the appropriate bin
156	bin = (int)( dist / delR );
157	if( bin < GofRBins ) histogram[bin] += 2;
158	}
159	}
160	}
161
162	else if( !strcmp( frames[0].names[j], atom2 ) ){
163
164	rxj = frames[i].r[j].x;
165	ryj = frames[i].r[j].y;
166	rzj = frames[i].r[j].z;
167
168	for( k=j+1; k< frames[i].nAtoms; k++ ){
169
170	if( !strcmp( frames[0].names[k], atom1 ) ){
171
172	dx = rxj - frames[i].r[k].x;
173	dy = ryj - frames[i].r[k].y;
174	dz = rzj - frames[i].r[k].z;
175
176	map( &dx, &dy, &dz,
177	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
178
179	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
180	dist = sqrt( distSqr );
181
182	// add to the appropriate bin
183	bin = (int)( dist / delR );
184	if( bin < GofRBins ) histogram[bin] += 2;
185	}
186	}
187	}
188	}
189	}
190
191	// calculate the GofR
192
193	for( i=0; i<GofRBins; i++ ){
194
195	rLower = i * delR;
196	rUpper = rLower + delR;
197
198	volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
199	nIdeal = volSlice * pairConstant;
200
201	the_GofR[i] = histogram[i] / ( nFrames * nIdeal );
202	rValue[i] = rLower + ( delR / 2.0 );
203	}
204
205	// make the out_name;
206
207	strcpy( out_name, out_prefix );
208	sprintf( tempString, "-%s-%s.GofR", atom1, atom2 );
209	strcat( out_name, tempString );
210
211	out_file = fopen( out_name, "w" );
212	if( out_file == NULL ){
213	fprintf( stderr,
214	"\n"
215	"GofR error, unable to open \"%s\" for writing.\n",
216	out_name );
217	exit(8);
218	}
219	break;
220
221	case atom_all:
222
223	// find the number of AllAtoms;
224
225	nAtom1 = 0;
226	for( i=0; i<frames[0].nAtoms; i++ ){
227
228	if( !strcmp( frames[0].names[i], allAtom ) ) nAtom1++;
229	}
230
231	if( !nAtom1 ){
232
233	fprintf( stderr,
234	"\n"
235	"GofR error, \"%s\" was not found in the trajectory.\n",
236	atom1 );
237	exit(8);
238	}
239
240	// calculate some of the constants;
241
242	pairDens = frames[0].nAtoms * (nAtom1 - 1) / boxVol;
243	pairConstant = ( 4.0 * M_PI * pairDens ) / 3.0;
244
245	// calculate the histogram
246
247	for( i=startFrame; i<endFrame; i++){
248	for( j=0; j<(frames[i].nAtoms-1); j++ ){
249
250	if( !strcmp( frames[0].names[j], allAtom ) ){
251
252	rxj = frames[i].r[j].x;
253	ryj = frames[i].r[j].y;
254	rzj = frames[i].r[j].z;
255
256	for( k=j+1; k< frames[i].nAtoms; k++ ){
257
258	dx = rxj - frames[i].r[k].x;
259	dy = ryj - frames[i].r[k].y;
260	dz = rzj - frames[i].r[k].z;
261
262	map( &dx, &dy, &dz,
263	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
264
265	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
266	dist = sqrt( distSqr );
267
268	// add to the appropriate bin
269	bin = (int)( dist / delR );
270	if( bin < GofRBins ) histogram[bin] += 2;
271	}
272	}
273
274	else{
275
276	rxj = frames[i].r[j].x;
277	ryj = frames[i].r[j].y;
278	rzj = frames[i].r[j].z;
279
280	for( k=j+1; k< frames[i].nAtoms; k++ ){
281
282	if( !strcmp( frames[0].names[k], allAtom ) ){
283
284	dx = rxj - frames[i].r[k].x;
285	dy = ryj - frames[i].r[k].y;
286	dz = rzj - frames[i].r[k].z;
287
288	map( &dx, &dy, &dz,
289	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
290
291	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
292	dist = sqrt( distSqr );
293
294	// add to the appropriate bin
295	bin = (int)( dist / delR );
296	if( bin < GofRBins ) histogram[bin] += 2;
297	}
298	}
299	}
300	}
301	}
302
303	// calculate the GofR
304
305	for( i=0; i<GofRBins; i++ ){
306
307	rLower = i * delR;
308	rUpper = rLower + delR;
309
310	volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
311	nIdeal = volSlice * pairConstant;
312
313	the_GofR[i] = histogram[i] / ( nFrames * nIdeal );
314	rValue[i] = rLower + ( delR / 2.0 );
315	}
316
317	// make the out_name;
318
319	strcpy( out_name, out_prefix );
320	sprintf( tempString, "-%s-%s.GofR", allAtom, "all" );
321	strcat( out_name, tempString );
322
323	out_file = fopen( out_name, "w" );
324	if( out_file == NULL ){
325	fprintf( stderr,
326	"\n"
327	"GofR error, unable to open \"%s\" for writing.\n",
328	out_name );
329	exit(8);
330	}
331	break;
332
333	case all_all:
334
335	// calculate some of the constants;
336
337	pairDens = frames[0].nAtoms * (frames[0].nAtoms - 1) / boxVol;
338	pairConstant = ( 4.0 * M_PI * pairDens ) / 3.0;
339
340	// calculate the histogram
341
342	for( i=startFrame; i<endFrame; i++){
343	for( j=0; j<(frames[i].nAtoms-1); j++ ){
344
345	rxj = frames[i].r[j].x;
346	ryj = frames[i].r[j].y;
347	rzj = frames[i].r[j].z;
348
349	for( k=j+1; k< frames[i].nAtoms; k++ ){
350
351	dx = rxj - frames[i].r[k].x;
352	dy = ryj - frames[i].r[k].y;
353	dz = rzj - frames[i].r[k].z;
354
355	map( &dx, &dy, &dz,
356	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
357
358	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
359	dist = sqrt( distSqr );
360
361	// add to the appropriate bin
362	bin = (int)( dist / delR );
363	if( bin < GofRBins ) histogram[bin] += 2;
364	}
365	}
366	}
367
368	// calculate the GofR
369
370	for( i=0; i<GofRBins; i++ ){
371
372	rLower = i * delR;
373	rUpper = rLower + delR;
374
375	volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
376	nIdeal = volSlice * pairConstant;
377
378	the_GofR[i] = histogram[i] / ( nFrames * nIdeal );
379	rValue[i] = rLower + ( delR / 2.0 );
380	}
381
382	// make the out_name;
383
384	strcpy( out_name, out_prefix );
385	sprintf( tempString, "-%s-%s.GofR", "all", "all" );
386	strcat( out_name, tempString );
387
388	out_file = fopen( out_name, "w" );
389	if( out_file == NULL ){
390	fprintf( stderr,
391	"\n"
392	"GofR error, unable to open \"%s\" for writing.\n",
393	out_name );
394	exit(8);
395	}
396	break;
397	}
398
399	for( i=0; i<GofRBins; i++ ){
400	fprintf( out_file,
401	"%lf\t%lf\n",
402	rValue[i], the_GofR[i] );
403	}
404
405	fclose( out_file );
406	}
407