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 |
|
|
struct xyz_frame* frames, int nFrames ){ |
16 |
|
|
|
17 |
|
|
int i,j,k,l; |
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 dx, dy, dz; |
40 |
|
|
double distSqr; |
41 |
|
|
double dist; |
42 |
|
|
|
43 |
|
|
double rLower, rUpper; |
44 |
|
|
double nIdeal; |
45 |
|
|
double volSlice; |
46 |
|
|
|
47 |
|
|
int bin; |
48 |
|
|
int histogram[GofRBins]; |
49 |
|
|
double the_GofR[GofRBins]; |
50 |
|
|
double rValue[GofRBins]; |
51 |
|
|
|
52 |
|
|
char out_name[500]; |
53 |
|
|
char tempString[100]; |
54 |
|
|
FILE *out_file; |
55 |
|
|
|
56 |
|
|
|
57 |
|
|
// figure out the type of GofR we are calculating |
58 |
|
|
|
59 |
|
|
if( !strcmp( atom1, "all" ) ){ |
60 |
|
|
|
61 |
|
|
if( !strcmp( atom2, "all" ) ) the_type = all_all; |
62 |
|
|
else{ |
63 |
|
|
the_type = atom_all; |
64 |
|
|
allAtom = atom2; |
65 |
|
|
} |
66 |
|
|
} |
67 |
|
|
else{ |
68 |
|
|
|
69 |
|
|
if( !strcmp( atom2, "all" ) ){ |
70 |
|
|
the_type = atom_all; |
71 |
|
|
allAtom = atom1; |
72 |
|
|
} |
73 |
|
|
else the_type = atom_atom; |
74 |
|
|
} |
75 |
|
|
|
76 |
|
|
// find the box size and delR; |
77 |
|
|
|
78 |
|
|
shortBox = frames[0].boxX; |
79 |
|
|
if( shortBox > frames[0].boxY ) shortBox = frames[0].boxY; |
80 |
|
|
if( shortBox > frames[0].boxZ ) shortBox = frames[0].boxZ; |
81 |
|
|
|
82 |
|
|
delR = ( shortBox / 2.0 ) / GofRBins; |
83 |
|
|
boxVol = frames[0].boxX * frames[0].boxY * frames[0].boxZ; |
84 |
|
|
|
85 |
|
|
// zero the histograms; |
86 |
|
|
|
87 |
|
|
for(i=0; i<GofRBins; i++ ){ |
88 |
|
|
|
89 |
|
|
rValue[i] = 0.0; |
90 |
|
|
the_GofR[i] = 0.0; |
91 |
|
|
histogram[i] = 0; |
92 |
|
|
} |
93 |
|
|
|
94 |
|
|
switch( the_type ){ |
95 |
|
|
|
96 |
|
|
case atom_atom: |
97 |
|
|
|
98 |
|
|
// find the number of each type; |
99 |
|
|
|
100 |
|
|
nAtom1 = 0; |
101 |
|
|
nAtom2 = 0; |
102 |
|
|
for( i=0; i<frames[0].nAtoms; i++ ){ |
103 |
|
|
|
104 |
|
|
if( !strcmp( frames[0].names[i], atom1 ) ) nAtom1++; |
105 |
|
|
else if( !strcmp( frames[0].names[i], atom2 ) ) nAtom2++; |
106 |
|
|
} |
107 |
|
|
|
108 |
|
|
if( !nAtom1 ){ |
109 |
|
|
|
110 |
|
|
fprintf( stderr, |
111 |
|
|
"\n" |
112 |
|
|
"GofR error, \"%s\" was not found in the trajectory.\n", |
113 |
|
|
atom1 ); |
114 |
|
|
exit(8); |
115 |
|
|
} |
116 |
|
|
|
117 |
|
|
if( !nAtom2 ){ |
118 |
|
|
|
119 |
|
|
fprintf( stderr, |
120 |
|
|
"\n" |
121 |
|
|
"GofR error, \"%s\" was not found in the trajectory.\n", |
122 |
|
|
atom2 ); |
123 |
|
|
exit(8); |
124 |
|
|
} |
125 |
|
|
|
126 |
|
|
// calculate some of the constants; |
127 |
|
|
|
128 |
|
|
atom1Dens = nAtom1 / boxVol; |
129 |
|
|
atom2Dens = nAtom2 / boxVol; |
130 |
|
|
|
131 |
|
|
atom1Constant = ( 4.0 * M_PI * atom1Dens ) / 3.0; |
132 |
|
|
atom2Constant = ( 4.0 * M_PI * atom2Dens ) / 3.0; |
133 |
|
|
|
134 |
|
|
// calculate the histogram |
135 |
|
|
|
136 |
|
|
for( i=0; i<nFrames; i++){ |
137 |
|
|
for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
138 |
|
|
for( k=j+1; k< frames[i].nAtoms; k++ ){ |
139 |
|
|
|
140 |
|
|
if( !strcmp( frames[0].names[j], atom1 ) ){ |
141 |
|
|
if( !strcmp( frames[0].names[k], atom2 ) ){ |
142 |
|
|
|
143 |
|
|
dx = frames[i].r[j].x - frames[i].r[k].x; |
144 |
|
|
dy = frames[i].r[j].y - frames[i].r[k].y; |
145 |
|
|
dz = frames[i].r[j].z - frames[i].r[k].z; |
146 |
|
|
|
147 |
|
|
map( &dx, &dy, &dz, |
148 |
|
|
frames[i].boxX, frames[i].boxY, frames[i].boxZ ); |
149 |
|
|
|
150 |
|
|
distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
151 |
|
|
dist = sqrt( distSqr ); |
152 |
|
|
|
153 |
|
|
// add to the appropriate bin |
154 |
|
|
bin = (int)( dist / delR ); |
155 |
|
|
if( bin < GofRBins ) histogram[bin] += 2; |
156 |
|
|
} |
157 |
|
|
} |
158 |
|
|
|
159 |
|
|
else if( !strcmp( frames[0].names[j], atom2 ) ){ |
160 |
|
|
if( !strcmp( frames[0].names[k], atom1 ) ){ |
161 |
|
|
|
162 |
|
|
dx = frames[i].r[j].x - frames[i].r[k].x; |
163 |
|
|
dy = frames[i].r[j].y - frames[i].r[k].y; |
164 |
|
|
dz = frames[i].r[j].z - frames[i].r[k].z; |
165 |
|
|
|
166 |
|
|
map( &dx, &dy, &dz, |
167 |
|
|
frames[i].boxX, frames[i].boxY, frames[i].boxZ ); |
168 |
|
|
|
169 |
|
|
distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
170 |
|
|
dist = sqrt( distSqr ); |
171 |
|
|
|
172 |
|
|
// add to the appropriate bin |
173 |
|
|
bin = (int)( dist / delR ); |
174 |
|
|
if( bin < GofRBins ) histogram[bin] += 2; |
175 |
|
|
} |
176 |
|
|
} |
177 |
|
|
} |
178 |
|
|
} |
179 |
|
|
} |
180 |
|
|
|
181 |
|
|
// calculate the GofR |
182 |
|
|
|
183 |
|
|
for( i=0; i<GofRBins; i++ ){ |
184 |
|
|
|
185 |
|
|
rLower = i * delR; |
186 |
|
|
rUpper = rLower + delR; |
187 |
|
|
|
188 |
|
|
volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
189 |
|
|
nIdeal = volSlice * ( atom1Constant + atom2Constant ); |
190 |
|
|
|
191 |
|
|
the_GofR[i] = histogram[i] / ( nFrames * ( nAtom1 + nAtom2 ) * nIdeal ); |
192 |
|
|
rValue[i] = rLower + ( delR / 2.0 ); |
193 |
|
|
} |
194 |
|
|
|
195 |
|
|
// make the out_name; |
196 |
|
|
|
197 |
|
|
strcpy( out_name, out_prefix ); |
198 |
|
|
sprintf( tempString, "-%s-%s.GofR", atom1, atom2 ); |
199 |
|
|
strcat( out_name, tempString ); |
200 |
|
|
|
201 |
|
|
out_file = fopen( out_name, "w" ); |
202 |
|
|
if( out_file == NULL ){ |
203 |
|
|
fprintf( stderr, |
204 |
|
|
"\n" |
205 |
|
|
"GofR error, unable to open \"%s\" for writing.\n", |
206 |
|
|
out_name ); |
207 |
|
|
exit(8); |
208 |
|
|
} |
209 |
|
|
break; |
210 |
|
|
|
211 |
|
|
case atom_all: |
212 |
|
|
|
213 |
|
|
// find the number of AllAtoms; |
214 |
|
|
|
215 |
|
|
nAtom1 = 0; |
216 |
|
|
for( i=0; i<frames[0].nAtoms; i++ ){ |
217 |
|
|
|
218 |
|
|
if( !strcmp( frames[0].names[i], allAtom ) ) nAtom1++; |
219 |
|
|
} |
220 |
|
|
|
221 |
|
|
if( !nAtom1 ){ |
222 |
|
|
|
223 |
|
|
fprintf( stderr, |
224 |
|
|
"\n" |
225 |
|
|
"GofR error, \"%s\" was not found in the trajectory.\n", |
226 |
|
|
atom1 ); |
227 |
|
|
exit(8); |
228 |
|
|
} |
229 |
|
|
|
230 |
|
|
// calculate some of the constants; |
231 |
|
|
|
232 |
|
|
atom1Dens = nAtom1 / boxVol; |
233 |
|
|
allDens = frames[0].nAtoms / boxVol; |
234 |
|
|
|
235 |
|
|
atom1Constant = ( 4.0 * M_PI * atom1Dens ) / 3.0; |
236 |
|
|
allConstant = ( 4.0 * M_PI * allDens ) / 3.0; |
237 |
|
|
|
238 |
|
|
// calculate the histogram |
239 |
|
|
|
240 |
|
|
for( i=0; i<nFrames; i++){ |
241 |
|
|
for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
242 |
|
|
for( k=j+1; k< frames[i].nAtoms; k++ ){ |
243 |
|
|
|
244 |
|
|
if( !strcmp( frames[0].names[j], allAtom ) ){ |
245 |
|
|
|
246 |
|
|
dx = frames[i].r[j].x - frames[i].r[k].x; |
247 |
|
|
dy = frames[i].r[j].y - frames[i].r[k].y; |
248 |
|
|
dz = frames[i].r[j].z - frames[i].r[k].z; |
249 |
|
|
|
250 |
|
|
map( &dx, &dy, &dz, |
251 |
|
|
frames[i].boxX, frames[i].boxY, frames[i].boxZ ); |
252 |
|
|
|
253 |
|
|
distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
254 |
|
|
dist = sqrt( distSqr ); |
255 |
|
|
|
256 |
|
|
// add to the appropriate bin |
257 |
|
|
bin = (int)( dist / delR ); |
258 |
|
|
if( bin < GofRBins ) histogram[bin] += 2; |
259 |
|
|
} |
260 |
|
|
|
261 |
|
|
else if( !strcmp( frames[0].names[k], allAtom ) ){ |
262 |
|
|
|
263 |
|
|
dx = frames[i].r[j].x - frames[i].r[k].x; |
264 |
|
|
dy = frames[i].r[j].y - frames[i].r[k].y; |
265 |
|
|
dz = frames[i].r[j].z - frames[i].r[k].z; |
266 |
|
|
|
267 |
|
|
map( &dx, &dy, &dz, |
268 |
|
|
frames[i].boxX, frames[i].boxY, frames[i].boxZ ); |
269 |
|
|
|
270 |
|
|
distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
271 |
|
|
dist = sqrt( distSqr ); |
272 |
|
|
|
273 |
|
|
// add to the appropriate bin |
274 |
|
|
bin = (int)( dist / delR ); |
275 |
|
|
if( bin < GofRBins ) histogram[bin] += 2; |
276 |
|
|
} |
277 |
|
|
} |
278 |
|
|
} |
279 |
|
|
} |
280 |
|
|
|
281 |
|
|
// calculate the GofR |
282 |
|
|
|
283 |
|
|
for( i=0; i<GofRBins; i++ ){ |
284 |
|
|
|
285 |
|
|
rLower = i * delR; |
286 |
|
|
rUpper = rLower + delR; |
287 |
|
|
|
288 |
|
|
volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
289 |
|
|
nIdeal = volSlice * ( allConstant ); |
290 |
|
|
|
291 |
|
|
the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal ); |
292 |
|
|
rValue[i] = rLower + ( delR / 2.0 ); |
293 |
|
|
} |
294 |
|
|
|
295 |
|
|
// make the out_name; |
296 |
|
|
|
297 |
|
|
strcpy( out_name, out_prefix ); |
298 |
|
|
sprintf( tempString, "-%s-%s.GofR", allAtom, "all" ); |
299 |
|
|
strcat( out_name, tempString ); |
300 |
|
|
|
301 |
|
|
out_file = fopen( out_name, "w" ); |
302 |
|
|
if( out_file == NULL ){ |
303 |
|
|
fprintf( stderr, |
304 |
|
|
"\n" |
305 |
|
|
"GofR error, unable to open \"%s\" for writing.\n", |
306 |
|
|
out_name ); |
307 |
|
|
exit(8); |
308 |
|
|
} |
309 |
|
|
break; |
310 |
|
|
|
311 |
|
|
case all_all: |
312 |
|
|
|
313 |
|
|
// calculate some of the constants; |
314 |
|
|
|
315 |
|
|
allDens = frames[0].nAtoms / boxVol; |
316 |
|
|
|
317 |
|
|
allConstant = ( 4.0 * M_PI * allDens ) / 3.0; |
318 |
|
|
|
319 |
|
|
// calculate the histogram |
320 |
|
|
|
321 |
|
|
for( i=0; i<nFrames; i++){ |
322 |
|
|
for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
323 |
|
|
for( k=j+1; k< frames[i].nAtoms; k++ ){ |
324 |
|
|
|
325 |
|
|
dx = frames[i].r[j].x - frames[i].r[k].x; |
326 |
|
|
dy = frames[i].r[j].y - frames[i].r[k].y; |
327 |
|
|
dz = frames[i].r[j].z - frames[i].r[k].z; |
328 |
|
|
|
329 |
|
|
map( &dx, &dy, &dz, |
330 |
|
|
frames[i].boxX, frames[i].boxY, frames[i].boxZ ); |
331 |
|
|
|
332 |
|
|
distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
333 |
|
|
dist = sqrt( distSqr ); |
334 |
|
|
|
335 |
|
|
// add to the appropriate bin |
336 |
|
|
bin = (int)( dist / delR ); |
337 |
|
|
if( bin < GofRBins ) histogram[bin] += 2; |
338 |
|
|
} |
339 |
|
|
} |
340 |
|
|
} |
341 |
|
|
|
342 |
|
|
// calculate the GofR |
343 |
|
|
|
344 |
|
|
for( i=0; i<GofRBins; i++ ){ |
345 |
|
|
|
346 |
|
|
rLower = i * delR; |
347 |
|
|
rUpper = rLower + delR; |
348 |
|
|
|
349 |
|
|
volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
350 |
|
|
nIdeal = volSlice * ( allConstant ); |
351 |
|
|
|
352 |
|
|
the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal ); |
353 |
|
|
rValue[i] = rLower + ( delR / 2.0 ); |
354 |
|
|
} |
355 |
|
|
|
356 |
|
|
// make the out_name; |
357 |
|
|
|
358 |
|
|
strcpy( out_name, out_prefix ); |
359 |
|
|
sprintf( tempString, "-%s-%s.GofR", "all", "all" ); |
360 |
|
|
strcat( out_name, tempString ); |
361 |
|
|
|
362 |
|
|
out_file = fopen( out_name, "w" ); |
363 |
|
|
if( out_file == NULL ){ |
364 |
|
|
fprintf( stderr, |
365 |
|
|
"\n" |
366 |
|
|
"GofR error, unable to open \"%s\" for writing.\n", |
367 |
|
|
out_name ); |
368 |
|
|
exit(8); |
369 |
|
|
} |
370 |
|
|
break; |
371 |
|
|
} |
372 |
|
|
|
373 |
|
|
for( i=0; i<GofRBins; i++ ){ |
374 |
|
|
fprintf( out_file, |
375 |
|
|
"%lf\t%lf\n", |
376 |
|
|
rValue[i], the_GofR[i] ); |
377 |
|
|
} |
378 |
|
|
|
379 |
|
|
fclose( out_file ); |
380 |
|
|
} |
381 |
|
|
|
382 |
|
|
|
383 |
|
|
void map( double *x, double *y, double *z, |
384 |
|
|
double boxX, double boxY, double boxZ ){ |
385 |
|
|
|
386 |
|
|
*x -= boxX * copysign(1.0,*x) * floor( fabs( *x/boxX ) + 0.5 ); |
387 |
|
|
*y -= boxY * copysign(1.0,*y) * floor( fabs( *y/boxY ) + 0.5 ); |
388 |
|
|
*z -= boxZ * copysign(1.0,*z) * floor( fabs( *z/boxZ ) + 0.5 ); |
389 |
|
|
|
390 |
|
|
} |