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 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=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 * ( 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=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 * ( 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=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 * ( 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:	82
Committed:	Fri Aug 16 04:05:45 2002 UTC (21 years, 11 months ago) by mmeineke
Content type:	text/plain
File size:	9338 byte(s)
Log Message:	added the capability to specify a start and end frame for cosCorr and GofR
#	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 atom1Dens;
25	double atom2Dens;
26	double allDens;
27
28	double atom1Constant;
29	double atom2Constant;
30	double allConstant;
31
32	double nAtom1;
33	double nAtom2;
34	double nAtoms;
35
36	double delR;
37	double boxVol;
38	double shortBox;
39
40	double rxj, ryj, rzj;
41	double dx, dy, dz;
42	double distSqr;
43	double dist;
44
45	double rLower, rUpper;
46	double nIdeal;
47	double volSlice;
48
49	int bin;
50	int histogram[GofRBins];
51	double the_GofR[GofRBins];
52	double rValue[GofRBins];
53
54	char out_name[500];
55	char tempString[100];
56	FILE *out_file;
57
58
59	// figure out the type of GofR we are calculating
60
61	if( !strcmp( atom1, "all" ) ){
62
63	if( !strcmp( atom2, "all" ) ) the_type = all_all;
64	else{
65	the_type = atom_all;
66	allAtom = atom2;
67	}
68	}
69	else{
70
71	if( !strcmp( atom2, "all" ) ){
72	the_type = atom_all;
73	allAtom = atom1;
74	}
75	else the_type = atom_atom;
76	}
77
78	// find the box size and delR;
79
80	shortBox = frames[0].boxX;
81	if( shortBox > frames[0].boxY ) shortBox = frames[0].boxY;
82	if( shortBox > frames[0].boxZ ) shortBox = frames[0].boxZ;
83
84	delR = ( shortBox / 2.0 ) / GofRBins;
85	boxVol = frames[0].boxX * frames[0].boxY * frames[0].boxZ;
86
87	// zero the histograms;
88
89	for(i=0; i<GofRBins; i++ ){
90
91	rValue[i] = 0.0;
92	the_GofR[i] = 0.0;
93	histogram[i] = 0;
94	}
95
96	switch( the_type ){
97
98	case atom_atom:
99
100	// find the number of each type;
101
102	nAtom1 = 0;
103	nAtom2 = 0;
104	for( i=0; i<frames[0].nAtoms; i++ ){
105
106	if( !strcmp( frames[0].names[i], atom1 ) ) nAtom1++;
107	if( !strcmp( frames[0].names[i], atom2 ) ) nAtom2++;
108	}
109
110	if( !nAtom1 ){
111
112	fprintf( stderr,
113	"\n"
114	"GofR error, \"%s\" was not found in the trajectory.\n",
115	atom1 );
116	exit(8);
117	}
118
119	if( !nAtom2 ){
120
121	fprintf( stderr,
122	"\n"
123	"GofR error, \"%s\" was not found in the trajectory.\n",
124	atom2 );
125	exit(8);
126	}
127
128	// calculate some of the constants;
129
130	atom1Dens = nAtom1 / boxVol;
131	atom2Dens = nAtom2 / boxVol;
132
133	atom1Constant = ( 4.0 * M_PI * atom1Dens ) / 3.0;
134	atom2Constant = ( 4.0 * M_PI * atom2Dens ) / 3.0;
135
136	// calculate the histogram
137
138	for( i=startFrame; i<endFrame; i++){
139	for( j=0; j<(frames[i].nAtoms-1); j++ ){
140
141	if( !strcmp( frames[0].names[j], atom1 ) ){
142
143	rxj = frames[i].r[j].x;
144	ryj = frames[i].r[j].y;
145	rzj = frames[i].r[j].z;
146
147	for( k=j+1; k< frames[i].nAtoms; k++ ){
148
149	if( !strcmp( frames[0].names[k], atom2 ) ){
150
151	dx = rxj - frames[i].r[k].x;
152	dy = ryj - frames[i].r[k].y;
153	dz = rzj - frames[i].r[k].z;
154
155	map( &dx, &dy, &dz,
156	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
157
158	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
159	dist = sqrt( distSqr );
160
161	// add to the appropriate bin
162	bin = (int)( dist / delR );
163	if( bin < GofRBins ) histogram[bin] += 2;
164	}
165	}
166	}
167
168	else if( !strcmp( frames[0].names[j], atom2 ) ){
169
170	rxj = frames[i].r[j].x;
171	ryj = frames[i].r[j].y;
172	rzj = frames[i].r[j].z;
173
174	for( k=j+1; k< frames[i].nAtoms; k++ ){
175
176	if( !strcmp( frames[0].names[k], atom1 ) ){
177
178	dx = rxj - frames[i].r[k].x;
179	dy = ryj - frames[i].r[k].y;
180	dz = rzj - frames[i].r[k].z;
181
182	map( &dx, &dy, &dz,
183	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
184
185	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
186	dist = sqrt( distSqr );
187
188	// add to the appropriate bin
189	bin = (int)( dist / delR );
190	if( bin < GofRBins ) histogram[bin] += 2;
191	}
192	}
193	}
194	}
195	}
196
197	// calculate the GofR
198
199	for( i=0; i<GofRBins; i++ ){
200
201	rLower = i * delR;
202	rUpper = rLower + delR;
203
204	volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
205	nIdeal = volSlice * ( atom1Constant + atom2Constant );
206
207	the_GofR[i] = histogram[i] / ( nFrames * ( nAtom1 + nAtom2 ) * nIdeal );
208	rValue[i] = rLower + ( delR / 2.0 );
209	}
210
211	// make the out_name;
212
213	strcpy( out_name, out_prefix );
214	sprintf( tempString, "-%s-%s.GofR", atom1, atom2 );
215	strcat( out_name, tempString );
216
217	out_file = fopen( out_name, "w" );
218	if( out_file == NULL ){
219	fprintf( stderr,
220	"\n"
221	"GofR error, unable to open \"%s\" for writing.\n",
222	out_name );
223	exit(8);
224	}
225	break;
226
227	case atom_all:
228
229	// find the number of AllAtoms;
230
231	nAtom1 = 0;
232	for( i=0; i<frames[0].nAtoms; i++ ){
233
234	if( !strcmp( frames[0].names[i], allAtom ) ) nAtom1++;
235	}
236
237	if( !nAtom1 ){
238
239	fprintf( stderr,
240	"\n"
241	"GofR error, \"%s\" was not found in the trajectory.\n",
242	atom1 );
243	exit(8);
244	}
245
246	// calculate some of the constants;
247
248	atom1Dens = nAtom1 / boxVol;
249	allDens = frames[0].nAtoms / boxVol;
250
251	atom1Constant = ( 4.0 * M_PI * atom1Dens ) / 3.0;
252	allConstant = ( 4.0 * M_PI * allDens ) / 3.0;
253
254	// calculate the histogram
255
256	for( i=startFrame; i<endFrame; i++){
257	for( j=0; j<(frames[i].nAtoms-1); j++ ){
258
259	if( !strcmp( frames[0].names[j], allAtom ) ){
260
261	rxj = frames[i].r[j].x;
262	ryj = frames[i].r[j].y;
263	rzj = frames[i].r[j].z;
264
265	for( k=j+1; k< frames[i].nAtoms; k++ ){
266
267	dx = rxj - frames[i].r[k].x;
268	dy = ryj - frames[i].r[k].y;
269	dz = rzj - frames[i].r[k].z;
270
271	map( &dx, &dy, &dz,
272	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
273
274	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
275	dist = sqrt( distSqr );
276
277	// add to the appropriate bin
278	bin = (int)( dist / delR );
279	if( bin < GofRBins ) histogram[bin] += 2;
280	}
281	}
282
283	else{
284
285	rxj = frames[i].r[j].x;
286	ryj = frames[i].r[j].y;
287	rzj = frames[i].r[j].z;
288
289	for( k=j+1; k< frames[i].nAtoms; k++ ){
290
291	if( !strcmp( frames[0].names[k], allAtom ) ){
292
293	dx = rxj - frames[i].r[k].x;
294	dy = ryj - frames[i].r[k].y;
295	dz = rzj - frames[i].r[k].z;
296
297	map( &dx, &dy, &dz,
298	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
299
300	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
301	dist = sqrt( distSqr );
302
303	// add to the appropriate bin
304	bin = (int)( dist / delR );
305	if( bin < GofRBins ) histogram[bin] += 2;
306	}
307	}
308	}
309	}
310	}
311
312	// calculate the GofR
313
314	for( i=0; i<GofRBins; i++ ){
315
316	rLower = i * delR;
317	rUpper = rLower + delR;
318
319	volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
320	nIdeal = volSlice * ( allConstant );
321
322	the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal );
323	rValue[i] = rLower + ( delR / 2.0 );
324	}
325
326	// make the out_name;
327
328	strcpy( out_name, out_prefix );
329	sprintf( tempString, "-%s-%s.GofR", allAtom, "all" );
330	strcat( out_name, tempString );
331
332	out_file = fopen( out_name, "w" );
333	if( out_file == NULL ){
334	fprintf( stderr,
335	"\n"
336	"GofR error, unable to open \"%s\" for writing.\n",
337	out_name );
338	exit(8);
339	}
340	break;
341
342	case all_all:
343
344	// calculate some of the constants;
345
346	allDens = frames[0].nAtoms / boxVol;
347
348	allConstant = ( 4.0 * M_PI * allDens ) / 3.0;
349
350	// calculate the histogram
351
352	for( i=startFrame; i<endFrame; i++){
353	for( j=0; j<(frames[i].nAtoms-1); j++ ){
354
355	rxj = frames[i].r[j].x;
356	ryj = frames[i].r[j].y;
357	rzj = frames[i].r[j].z;
358
359	for( k=j+1; k< frames[i].nAtoms; k++ ){
360
361	dx = rxj - frames[i].r[k].x;
362	dy = ryj - frames[i].r[k].y;
363	dz = rzj - frames[i].r[k].z;
364
365	map( &dx, &dy, &dz,
366	frames[i].boxX, frames[i].boxY, frames[i].boxZ );
367
368	distSqr = (dx * dx) + (dy * dy) + (dz * dz);
369	dist = sqrt( distSqr );
370
371	// add to the appropriate bin
372	bin = (int)( dist / delR );
373	if( bin < GofRBins ) histogram[bin] += 2;
374	}
375	}
376	}
377
378	// calculate the GofR
379
380	for( i=0; i<GofRBins; i++ ){
381
382	rLower = i * delR;
383	rUpper = rLower + delR;
384
385	volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 );
386	nIdeal = volSlice * ( allConstant );
387
388	the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal );
389	rValue[i] = rLower + ( delR / 2.0 );
390	}
391
392	// make the out_name;
393
394	strcpy( out_name, out_prefix );
395	sprintf( tempString, "-%s-%s.GofR", "all", "all" );
396	strcat( out_name, tempString );
397
398	out_file = fopen( out_name, "w" );
399	if( out_file == NULL ){
400	fprintf( stderr,
401	"\n"
402	"GofR error, unable to open \"%s\" for writing.\n",
403	out_name );
404	exit(8);
405	}
406	break;
407	}
408
409	for( i=0; i<GofRBins; i++ ){
410	fprintf( out_file,
411	"%lf\t%lf\n",
412	rValue[i], the_GofR[i] );
413	}
414
415	fclose( out_file );
416	}
417