1 |
mmeineke |
43 |
#include <math.h> |
2 |
|
|
#include <stdlib.h> |
3 |
|
|
#include <stdio.h> |
4 |
|
|
#include <string.h> |
5 |
|
|
|
6 |
|
|
#include "GofR.h" |
7 |
mmeineke |
45 |
|
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 |
mmeineke |
82 |
struct xyz_frame* frames, int nFrames, |
16 |
|
|
int startFrame, int endFrame ){ |
17 |
mmeineke |
45 |
|
18 |
mmeineke |
46 |
int i,j,k; |
19 |
mmeineke |
45 |
|
20 |
|
|
enum g_types { all_all, atom_all, atom_atom }; |
21 |
|
|
enum g_types the_type; |
22 |
|
|
char* allAtom; |
23 |
|
|
|
24 |
mmeineke |
103 |
double pairDens; |
25 |
|
|
double pairConstant; |
26 |
mmeineke |
45 |
|
27 |
|
|
double nAtom1; |
28 |
|
|
double nAtom2; |
29 |
|
|
double nAtoms; |
30 |
|
|
|
31 |
|
|
double delR; |
32 |
|
|
double boxVol; |
33 |
|
|
double shortBox; |
34 |
|
|
|
35 |
mmeineke |
46 |
double rxj, ryj, rzj; |
36 |
mmeineke |
45 |
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 |
mmeineke |
46 |
if( !strcmp( frames[0].names[i], atom2 ) ) nAtom2++; |
103 |
mmeineke |
45 |
} |
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 |
mmeineke |
103 |
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 |
mmeineke |
45 |
// calculate the histogram |
131 |
|
|
|
132 |
mmeineke |
82 |
for( i=startFrame; i<endFrame; i++){ |
133 |
mmeineke |
45 |
for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
134 |
mmeineke |
46 |
|
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 |
mmeineke |
45 |
|
141 |
mmeineke |
46 |
for( k=j+1; k< frames[i].nAtoms; k++ ){ |
142 |
|
|
|
143 |
mmeineke |
45 |
if( !strcmp( frames[0].names[k], atom2 ) ){ |
144 |
|
|
|
145 |
mmeineke |
46 |
dx = rxj - frames[i].r[k].x; |
146 |
|
|
dy = ryj - frames[i].r[k].y; |
147 |
|
|
dz = rzj - frames[i].r[k].z; |
148 |
mmeineke |
45 |
|
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 |
mmeineke |
46 |
} |
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 |
mmeineke |
45 |
if( !strcmp( frames[0].names[k], atom1 ) ){ |
171 |
|
|
|
172 |
mmeineke |
46 |
dx = rxj - frames[i].r[k].x; |
173 |
|
|
dy = ryj - frames[i].r[k].y; |
174 |
|
|
dz = rzj - frames[i].r[k].z; |
175 |
mmeineke |
45 |
|
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 |
mmeineke |
103 |
nIdeal = volSlice * pairConstant; |
200 |
mmeineke |
45 |
|
201 |
mmeineke |
103 |
the_GofR[i] = histogram[i] / ( nFrames * nIdeal ); |
202 |
mmeineke |
45 |
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 |
mmeineke |
103 |
pairDens = frames[0].nAtoms * (nAtom1 - 1) / boxVol; |
243 |
|
|
pairConstant = ( 4.0 * M_PI * pairDens ) / 3.0; |
244 |
|
|
|
245 |
mmeineke |
45 |
// calculate the histogram |
246 |
|
|
|
247 |
mmeineke |
82 |
for( i=startFrame; i<endFrame; i++){ |
248 |
mmeineke |
45 |
for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
249 |
mmeineke |
46 |
|
250 |
|
|
if( !strcmp( frames[0].names[j], allAtom ) ){ |
251 |
mmeineke |
45 |
|
252 |
mmeineke |
46 |
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 |
mmeineke |
45 |
|
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 |
mmeineke |
46 |
} |
273 |
mmeineke |
45 |
|
274 |
mmeineke |
46 |
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 |
mmeineke |
45 |
|
282 |
mmeineke |
46 |
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 |
mmeineke |
45 |
} |
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 |
mmeineke |
103 |
nIdeal = volSlice * pairConstant; |
312 |
mmeineke |
45 |
|
313 |
mmeineke |
103 |
the_GofR[i] = histogram[i] / ( nFrames * nIdeal ); |
314 |
mmeineke |
45 |
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 |
mmeineke |
103 |
pairDens = frames[0].nAtoms * (frames[0].nAtoms - 1) / boxVol; |
338 |
|
|
pairConstant = ( 4.0 * M_PI * pairDens ) / 3.0; |
339 |
mmeineke |
45 |
|
340 |
|
|
// calculate the histogram |
341 |
|
|
|
342 |
mmeineke |
82 |
for( i=startFrame; i<endFrame; i++){ |
343 |
mmeineke |
45 |
for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
344 |
mmeineke |
46 |
|
345 |
|
|
rxj = frames[i].r[j].x; |
346 |
|
|
ryj = frames[i].r[j].y; |
347 |
|
|
rzj = frames[i].r[j].z; |
348 |
|
|
|
349 |
mmeineke |
45 |
for( k=j+1; k< frames[i].nAtoms; k++ ){ |
350 |
mmeineke |
46 |
|
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 |
mmeineke |
45 |
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 |
mmeineke |
103 |
nIdeal = volSlice * pairConstant; |
377 |
mmeineke |
45 |
|
378 |
mmeineke |
103 |
the_GofR[i] = histogram[i] / ( nFrames * nIdeal ); |
379 |
mmeineke |
45 |
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 |
|
|
|