1 |
#include<stdio.h> |
2 |
#include<string.h> |
3 |
#include<stdlib.h> |
4 |
#include<math.h> |
5 |
#include<fftw.h> |
6 |
#include<mkl_lapack64.h> |
7 |
|
8 |
//extern void dsyev(char *jobz, char *uplo, int *n, double *a, int *lda, |
9 |
// double *w, double *work, int *lwork,int *info); |
10 |
|
11 |
//void direct(double rcut, double box, int n, int nstep, int maxbin); |
12 |
|
13 |
//double* dsyev_ctof(double **in, int rows, int cols); |
14 |
|
15 |
//void dsyev_ftoc2(double *in, double **out, int rows, int cols); |
16 |
|
17 |
// Structures to store our data: |
18 |
|
19 |
inline double roundMe( double x ){ |
20 |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
21 |
} |
22 |
|
23 |
// coords holds the data for a single tethered dipole: |
24 |
struct coords{ |
25 |
double pos[3]; // cartesian coords |
26 |
double theta; // orientational angle relative to z axis |
27 |
double phi; // orientational angle in x-y plane |
28 |
double mu; // dipole strength |
29 |
char name[30]; // an identifier for the type of atom |
30 |
}; |
31 |
|
32 |
// state holds the current "configuration" of the entire system |
33 |
struct system { |
34 |
int nAtoms; // Number of Atoms in this configuration |
35 |
struct coords *r; // The set of coordinates for all atoms |
36 |
double beta; // beta = 1 /(kb*T) |
37 |
double strength; // strength of the dipoles (Debye) |
38 |
double z0; // default z axis position |
39 |
double theta0; // default theta angle |
40 |
double kz; // force constant for z displacement |
41 |
double ktheta; // force constant for theta displacement |
42 |
int nCycles; // How many cycles to do in total |
43 |
int iCycle; // How many cycles have we done? |
44 |
int nMoves; // How many MC moves in each cycle |
45 |
int nSample; // How many cycles between samples |
46 |
double Hmat[2][2]; // The information about the size of the per. box |
47 |
double HmatI[2][2]; // The inverse box |
48 |
double energy; // The current Energy |
49 |
double dtheta; // maximum size of a theta move |
50 |
double deltaz; // maximum size of a z move |
51 |
double deltaphi; // maximum size of a phi move |
52 |
int nAttempts; // number of MC moves that have been attempted |
53 |
int nAccepts; // number of MC moves that have been accepted |
54 |
int nx; // number of unit cells in x direction |
55 |
int ny; // number of unit cells in y direction |
56 |
struct system *next; // Next frame in the linked list |
57 |
}; |
58 |
|
59 |
char *program_name; /* the name of the program */ |
60 |
|
61 |
// Function prototypes: |
62 |
void usage(void); |
63 |
void invertMat2(double a[2][2], double b[2][2]); |
64 |
void wrapVector( double thePos[2], double Hmat[2][2], double HmatI[2][2]); |
65 |
|
66 |
int main(argc, argv) |
67 |
int argc; |
68 |
char *argv[]; |
69 |
{ |
70 |
FILE *in_file; |
71 |
char in_name[500]; |
72 |
char *eof_test, *foo; |
73 |
char read_buffer[1000]; |
74 |
//int lineCount = 0; |
75 |
int lineCount; |
76 |
int nAtoms; |
77 |
double *mag, *newmag; |
78 |
int *present_in_old; |
79 |
double *ux, *uy, *uz, p1; |
80 |
double aLat, bLat; |
81 |
int cells; |
82 |
double sumZ, sumUx, sumUy, sumUz, sumP; |
83 |
double interpsum, value; |
84 |
int ninterp, px, py, newp; |
85 |
int i, j, k, l, nloops; |
86 |
int newx, newy, newindex, index; |
87 |
int new_i, new_j, new_index; |
88 |
int N, nframes; |
89 |
double freq_x, freq_y, zero_freq_x, zero_freq_y, freq; |
90 |
double maxfreqx, maxfreqy, maxfreq, dfreq; |
91 |
double dx, dy, dx1, dy1, xTemp, yTemp, pt1x, pt1y, pt2x, pt2y; |
92 |
int nx, ny; |
93 |
int *samples; |
94 |
double *bin, binmin, binmax, delr; |
95 |
double *x, *y, *z; |
96 |
double dh2, dh, sumh2, sumh, averh2, averh, t, delta, gamma, hi, proj; |
97 |
double *corrhist, *h2hist; |
98 |
double vrhist[100][500]; |
99 |
double sum_vrhist[1000], ave_vrhist[1000]; |
100 |
int vrsamp[1000][1000]; |
101 |
int *ophist; |
102 |
double d[2], hcorr; |
103 |
double hsum, hsum_temp, h2sum, have, h2ave, fluc, bigL, smallA, areaPerMolecule, area, h, h2; |
104 |
int nbins, nbins2, opbin, whichbinx, whichbiny, whichbin2, n1, n2, n3, n4, m, selfx, selfy; |
105 |
|
106 |
int which; |
107 |
double omat[3][3]; |
108 |
double wrapMat[9]; |
109 |
double onethird, ordvals[5000]; |
110 |
double max; |
111 |
double director[3][1000], vr[3][1000]; |
112 |
double sum_director[3], ave_director[3], sum_vr[3], ave_vr[3]; |
113 |
double orderpar[1000]; |
114 |
double sum_orderpar, ave_orderpar; |
115 |
char job, uplo; |
116 |
int ndiag; |
117 |
int nfilled; |
118 |
double evals[100]; |
119 |
int lwork; |
120 |
double* work; |
121 |
int ifail; |
122 |
int done; |
123 |
char current_flag; |
124 |
|
125 |
lineCount = 0; |
126 |
|
127 |
program_name = argv[0]; |
128 |
if (argc >= 2) |
129 |
strcpy(in_name, argv[1]); |
130 |
/* |
131 |
for(i = 1; i < argc; i++){ |
132 |
if(argv[i][0] == '-'){ |
133 |
done = 0; |
134 |
j = 1; |
135 |
current_flag = argv[i][j]; |
136 |
while( (current_flag != '\0') && ( !done ) ){ |
137 |
switch(current_flag){ |
138 |
case 'i': |
139 |
i++; |
140 |
strcpy( in_name, argv[i] ); |
141 |
done = 1; |
142 |
break; |
143 |
} |
144 |
} |
145 |
} |
146 |
} |
147 |
*/ |
148 |
|
149 |
struct system* state; |
150 |
struct system* temp_state; |
151 |
struct coords* r; |
152 |
|
153 |
lwork = 9; |
154 |
|
155 |
work = (double *) malloc(lwork * sizeof(double)); |
156 |
|
157 |
onethird = 1.0 / 3.0; |
158 |
ndiag = 3; |
159 |
nfilled = 3; |
160 |
job = 'V'; |
161 |
uplo = 'U'; |
162 |
ifail = 0; |
163 |
|
164 |
nbins = 30; |
165 |
nbins2 = 30; |
166 |
binmin = 0.0; |
167 |
binmax = 1.0; |
168 |
delr = (binmax - binmin) / (double) nbins2; |
169 |
corrhist = (double *) calloc(nbins*nbins, sizeof(double)); |
170 |
h2hist = (double *) calloc(nbins*nbins, sizeof(double)); |
171 |
ophist = (int *) calloc(nbins2, sizeof(int)); |
172 |
hsum = 0.0; |
173 |
h2sum = 0.0; |
174 |
sum_orderpar = 0.0; |
175 |
ave_orderpar = 0.0; |
176 |
|
177 |
for(i = 0; i < 3; i++){ |
178 |
for(j = 0; j < 1000; j++){ |
179 |
director[i][j] = 0.0; |
180 |
vr[i][j] = 0.0; |
181 |
} |
182 |
} |
183 |
|
184 |
for(i = 0; i < 1000; i++){ |
185 |
sum_vrhist[i] = 0.0; |
186 |
ave_vrhist[i] = 0.0; |
187 |
} |
188 |
|
189 |
for(i = 0; i < 3; i++){ |
190 |
sum_director[i] = 0.0; |
191 |
ave_director[i] = 0.0; |
192 |
sum_vr[i] = 0.0; |
193 |
ave_vr[i] = 0.0; |
194 |
} |
195 |
|
196 |
for (i = 0; i < nbins; i++) { |
197 |
for (j = 0; j < nbins; j++) { |
198 |
corrhist[nbins * i + j] = 0.0; |
199 |
h2hist[nbins * i + j] = 0.0; |
200 |
} |
201 |
} |
202 |
|
203 |
for (i = 0; i < 100; i++) { |
204 |
for (j = 0; j < 500; j++) { |
205 |
vrhist[i][j] = 0.0; |
206 |
} |
207 |
} |
208 |
|
209 |
for(i = 0; i < nbins2; i++){ |
210 |
ophist[i] = 0; |
211 |
} |
212 |
|
213 |
t = 300; |
214 |
|
215 |
in_file = fopen(in_name, "r"); |
216 |
if(in_file == NULL){ |
217 |
printf("Cannot open file \"%s\" for reading.\n", in_name); |
218 |
exit(8); |
219 |
} |
220 |
|
221 |
nframes = 0; |
222 |
n1 = 0; |
223 |
n2 = 0; |
224 |
n3 = 0; |
225 |
n4 = 0; |
226 |
|
227 |
// start reading the first frame |
228 |
|
229 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
230 |
nAtoms = atoi(read_buffer); |
231 |
ux = (double *) calloc(nAtoms, sizeof(double)); |
232 |
uy = (double *) calloc(nAtoms, sizeof(double)); |
233 |
uz = (double *) calloc(nAtoms, sizeof(double)); |
234 |
lineCount++; |
235 |
|
236 |
for(i = 0; i < nAtoms; i++){ |
237 |
ux[i] = 0.0; |
238 |
uy[i] = 0.0; |
239 |
uz[i] = 0.0; |
240 |
} |
241 |
|
242 |
state = (struct system *) malloc(sizeof(struct system)); |
243 |
state->next = NULL; |
244 |
state->strength = 7.0; |
245 |
|
246 |
while(eof_test != NULL){ |
247 |
|
248 |
nframes++; |
249 |
(void)sscanf(read_buffer, "%d", &state->nAtoms); |
250 |
N = 2 * state->nAtoms; |
251 |
|
252 |
state->r = (struct coords *)calloc(N, sizeof(struct coords)); |
253 |
|
254 |
for(i = 0; i < 3; i++){ |
255 |
for(j = 0; j < 3; j++){ |
256 |
omat[i][j] = 0.0; |
257 |
} |
258 |
} |
259 |
|
260 |
// read and the comment line and grab the time and box dimensions |
261 |
|
262 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
263 |
lineCount++; |
264 |
if(eof_test == NULL){ |
265 |
printf("error in reading file at line: %d\n", lineCount); |
266 |
exit(8); |
267 |
} |
268 |
|
269 |
foo = strtok( read_buffer, " ,;\t\n" ); |
270 |
(void)sscanf( read_buffer, "%d", &state->iCycle ); |
271 |
|
272 |
foo = strtok(NULL, " ,;\t\0"); |
273 |
if(foo == NULL){ |
274 |
printf("error in reading file at line: %d\n", lineCount); |
275 |
exit(8); |
276 |
} |
277 |
(void)sscanf(foo, "%d", &state->nx); |
278 |
|
279 |
nx = state->nx; |
280 |
|
281 |
foo = strtok(NULL, " ,;\t\0"); |
282 |
if(foo == NULL){ |
283 |
printf("error in reading file at line: %d\n", lineCount); |
284 |
exit(8); |
285 |
} |
286 |
(void)sscanf(foo, "%d", &state->ny); |
287 |
|
288 |
ny = state->ny; |
289 |
|
290 |
foo = strtok(NULL, " ,;\t\0"); |
291 |
if(foo == NULL){ |
292 |
printf("error in reading file at line: %d\n", lineCount); |
293 |
exit(8); |
294 |
} |
295 |
(void)sscanf(foo, "%lf",&state->Hmat[0][0]); |
296 |
|
297 |
foo = strtok(NULL, " ,;\t\0"); |
298 |
if(foo == NULL){ |
299 |
printf("error in reading file at line: %d\n", lineCount); |
300 |
exit(8); |
301 |
} |
302 |
(void)sscanf(foo, "%lf",&state->Hmat[1][0]); |
303 |
|
304 |
foo = strtok(NULL, " ,;\t\0"); |
305 |
if(foo == NULL){ |
306 |
printf("error in reading file at line: %d\n", lineCount); |
307 |
exit(8); |
308 |
} |
309 |
(void)sscanf(foo, "%lf",&state->Hmat[0][1]); |
310 |
|
311 |
foo = strtok(NULL, " ,;\t\0"); |
312 |
if(foo == NULL){ |
313 |
printf("error in reading file at line: %d\n", lineCount); |
314 |
exit(8); |
315 |
} |
316 |
(void)sscanf(foo, "%lf",&state->Hmat[1][1]); |
317 |
|
318 |
//Find HmatI: |
319 |
|
320 |
invertMat2(state->Hmat, state->HmatI); |
321 |
|
322 |
// Length of the two box vectors: |
323 |
|
324 |
dx = sqrt(pow(state->Hmat[0][0], 2) + pow(state->Hmat[1][0], 2)); |
325 |
dy = sqrt(pow(state->Hmat[0][1], 2) + pow(state->Hmat[1][1], 2)); |
326 |
|
327 |
aLat = dx / (double)(state->nx); |
328 |
bLat = dy / (double)(state->ny); |
329 |
|
330 |
// FFT stuff depends on nx and ny, so delay allocation until we have |
331 |
// that information |
332 |
|
333 |
for (i=0;i<state->nAtoms;i++){ |
334 |
|
335 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
336 |
lineCount++; |
337 |
if(eof_test == NULL){ |
338 |
printf("error in reading file at line: %d\n", lineCount); |
339 |
exit(8); |
340 |
} |
341 |
|
342 |
foo = strtok(read_buffer, " ,;\t\0"); |
343 |
(void)strcpy(state->r[i].name, foo); //copy the atom name |
344 |
|
345 |
// next we grab the positions |
346 |
|
347 |
foo = strtok(NULL, " ,;\t\0"); |
348 |
if(foo == NULL){ |
349 |
printf("error in reading postition x from %s\n" |
350 |
"natoms = %d, line = %d\n", |
351 |
in_name, state->nAtoms, lineCount ); |
352 |
exit(8); |
353 |
} |
354 |
(void)sscanf( foo, "%lf", &state->r[i].pos[0] ); |
355 |
|
356 |
foo = strtok(NULL, " ,;\t\0"); |
357 |
if(foo == NULL){ |
358 |
printf("error in reading postition y from %s\n" |
359 |
"natoms = %d, line = %d\n", |
360 |
in_name, state->nAtoms, lineCount ); |
361 |
exit(8); |
362 |
} |
363 |
(void)sscanf( foo, "%lf", &state->r[i].pos[1] ); |
364 |
|
365 |
foo = strtok(NULL, " ,;\t\0"); |
366 |
if(foo == NULL){ |
367 |
printf("error in reading postition z from %s\n" |
368 |
"natoms = %d, line = %d\n", |
369 |
in_name, state->nAtoms, lineCount ); |
370 |
exit(8); |
371 |
} |
372 |
(void)sscanf( foo, "%lf", &state->r[i].pos[2] ); |
373 |
|
374 |
foo = strtok(NULL, " ,;\t\0"); |
375 |
if(foo == NULL){ |
376 |
printf("error in reading angle phi from %s\n" |
377 |
"natoms = %d, line = %d\n", |
378 |
in_name, state->nAtoms, lineCount ); |
379 |
exit(8); |
380 |
} |
381 |
(void)sscanf( foo, "%lf", &state->r[i].phi ); |
382 |
|
383 |
foo = strtok(NULL, " ,;\t\0"); |
384 |
if(foo == NULL){ |
385 |
printf("error in reading unit vector x from %s\n" |
386 |
"natoms = %d, line = %d\n", |
387 |
in_name, state->nAtoms, lineCount ); |
388 |
exit(8); |
389 |
} |
390 |
(void)sscanf( foo, "%lf", &ux[i] ); |
391 |
|
392 |
foo = strtok(NULL, " ,;\t\0"); |
393 |
if(foo == NULL){ |
394 |
printf("error in reading unit vector y from %s\n" |
395 |
"natoms = %d, line = %d\n", |
396 |
in_name, state->nAtoms, lineCount ); |
397 |
exit(8); |
398 |
} |
399 |
(void)sscanf( foo, "%lf", &uy[i] ); |
400 |
|
401 |
foo = strtok(NULL, " ,;\t\0"); |
402 |
if(foo == NULL){ |
403 |
printf("error in reading unit vector z from %s\n" |
404 |
"natoms = %d, line = %d\n", |
405 |
in_name, state->nAtoms, lineCount ); |
406 |
exit(8); |
407 |
} |
408 |
(void)sscanf( foo, "%lf", &uz[i] ); |
409 |
|
410 |
state->r[i].theta = acos(uz[i]); |
411 |
|
412 |
// The one parameter not stored in the dump file is the dipole strength |
413 |
state->r[i].mu = state->strength; |
414 |
} |
415 |
|
416 |
hsum_temp = 0.0; |
417 |
for (i = 0; i < state->nAtoms; i++) { |
418 |
|
419 |
h = state->r[i].pos[2]; |
420 |
h2 = pow(h,2); |
421 |
|
422 |
hsum_temp += h; |
423 |
hsum += h; |
424 |
h2sum += h2; |
425 |
|
426 |
n1++; |
427 |
} |
428 |
|
429 |
for(i = 0; i < state->nAtoms; i++){ |
430 |
|
431 |
omat[0][0] += ux[i] * ux[i] - onethird; |
432 |
omat[0][1] += ux[i] * uy[i]; |
433 |
omat[0][2] += ux[i] * uz[i]; |
434 |
omat[1][0] += uy[i] * ux[i]; |
435 |
omat[1][1] += uy[i] * uy[i] - onethird; |
436 |
omat[1][2] += uy[i] * uz[i]; |
437 |
omat[2][0] += uz[i] * ux[i]; |
438 |
omat[2][1] += uz[i] * uy[i]; |
439 |
omat[2][2] += uz[i] * uz[i] - onethird; |
440 |
|
441 |
} |
442 |
|
443 |
for(i = 0; i < 3; i++){ |
444 |
for(j = 0; j < 3; j++){ |
445 |
omat[i][j] /= (double) state->nAtoms; |
446 |
} |
447 |
} |
448 |
|
449 |
// temp_array = dsyev_ctof(omat, nfilled, nfilled); |
450 |
|
451 |
for(j=0;j<3;j++) |
452 |
for(i=0;i<3;i++) |
453 |
wrapMat[i+j*3] = omat[i][j]; |
454 |
|
455 |
ifail = 0; |
456 |
dsyev(&job, &uplo, &nfilled, wrapMat, &ndiag, evals, work, &lwork, &ifail); |
457 |
|
458 |
for(j=0;j<3;j++) |
459 |
for(i=0;i<3;i++) |
460 |
omat[i][j] = wrapMat[i+j*3]; |
461 |
|
462 |
//dsyev_ftoc2(temp_array, omat, nfilled, nfilled); |
463 |
|
464 |
//free(temp_array); |
465 |
|
466 |
max = 0.0; |
467 |
for(j = 0; j < 3; j++){ |
468 |
if(fabs(evals[j]) > max){ |
469 |
which = j; |
470 |
max = fabs(evals[j]); |
471 |
} |
472 |
} |
473 |
|
474 |
director[0][nframes-1] = omat[0][which]; |
475 |
director[1][nframes-1] = omat[1][which]; |
476 |
director[2][nframes-1] = omat[2][which]; |
477 |
|
478 |
vr[0][nframes-1] = fabs(director[1][nframes-1]); |
479 |
vr[1][nframes-1] = fabs(-director[0][nframes-1]); |
480 |
vr[2][nframes-1] = 0; |
481 |
|
482 |
orderpar[nframes-1] = 1.5 * max; |
483 |
printf("%d\t%lf\n", state->iCycle, orderpar[nframes-1]); |
484 |
|
485 |
opbin = (int) (orderpar[nframes-1] / delr); |
486 |
if(opbin < nbins2) ophist[opbin] += 1; |
487 |
|
488 |
/* for(i = 0; i < state->nAtoms; i++){ */ |
489 |
/* proj = vr[0][nframes-1] * state->r[i].pos[0] + vr[1][nframes-1] * state->r[i].pos[1]; */ |
490 |
/* hi = state->r[i].pos[2] - hsum_temp / (double) state->nAtoms; */ |
491 |
|
492 |
/* whichbin2 = (int) ((proj / (vr[0][nframes-1] * dx + vr[1][nframes-1] * dy)) * nbins2); */ |
493 |
/* vrhist[whichbin2][nframes-1] += hi; */ |
494 |
/* vrsamp[whichbin2][nframes-1]++; */ |
495 |
/* } */ |
496 |
|
497 |
/* for(i = 0; i < state->nAtoms; i++){ */ |
498 |
/* for(j = 0; j < state->nAtoms; j++){ */ |
499 |
|
500 |
/* d[0] = state->r[j].pos[0] - state->r[i].pos[0]; */ |
501 |
/* d[1] = state->r[j].pos[1] - state->r[i].pos[1]; */ |
502 |
|
503 |
/* wrapVector(d, state->Hmat, state->HmatI); */ |
504 |
|
505 |
/* whichbinx = (int) ((nbins-1) * (dx/2.0 + d[0]) / dx); */ |
506 |
/* whichbiny = (int) ((nbins-1) * (dy/2.0 + d[1]) / dy); */ |
507 |
|
508 |
/* //if (i == j) { */ |
509 |
/* //printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); */ |
510 |
/* //} */ |
511 |
|
512 |
/* //printf("d0 = %lf, d1 = %lf\n", d[0], d[1]); */ |
513 |
/* //printf("wx = %d, wy = %d\n", whichbinx, whichbiny); */ |
514 |
|
515 |
/* if (whichbinx >= nbins || whichbiny >= nbins) { */ |
516 |
/* printf("off by one error\n"); */ |
517 |
/* printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); */ |
518 |
/* exit(0); */ |
519 |
/* } */ |
520 |
/* if (whichbinx < 0 || whichbiny < 0) { */ |
521 |
/* printf("off by one error\n"); */ |
522 |
/* printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); */ |
523 |
/* exit(0); */ |
524 |
/* } */ |
525 |
|
526 |
/* hcorr = state->r[j].pos[2] * state->r[i].pos[2]; */ |
527 |
|
528 |
/* corrhist[nbins * whichbinx + whichbiny] += hcorr; */ |
529 |
|
530 |
/* dh = state->r[j].pos[2] - state->r[i].pos[2]; */ |
531 |
/* dh2 = pow(dh, 2); */ |
532 |
|
533 |
/* h2hist[nbins * whichbinx + whichbiny] += dh2; */ |
534 |
|
535 |
/* n2++; */ |
536 |
/* } */ |
537 |
/* } */ |
538 |
|
539 |
temp_state = state->next; |
540 |
state->next = NULL; |
541 |
|
542 |
if (temp_state != NULL) { |
543 |
free(temp_state->r); |
544 |
free(temp_state); |
545 |
} |
546 |
|
547 |
// Make a new frame |
548 |
|
549 |
temp_state = (struct system *) malloc(sizeof(struct system)); |
550 |
temp_state->next = state; |
551 |
state = temp_state; |
552 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
553 |
lineCount++; |
554 |
} |
555 |
|
556 |
|
557 |
/* have = hsum / (double) n1; */ |
558 |
/* h2ave = h2sum / (double) n1; */ |
559 |
/* fluc = h2ave - pow(have, 2); */ |
560 |
|
561 |
/* printf("# <h> = %lf\n", have); */ |
562 |
/* printf("# <h2> = %lf\n", h2ave); */ |
563 |
/* printf("# sigma(h) = %lf\n", sqrt(h2ave - have * have)); */ |
564 |
/* printf("# fluctuation = %lf\n", fluc); */ |
565 |
|
566 |
/* for(i = 0; i < nframes; i++){ */ |
567 |
/* sum_orderpar += orderpar[i]; */ |
568 |
/* } */ |
569 |
/* ave_orderpar = sum_orderpar / (double) nframes; */ |
570 |
|
571 |
/* for(i = 0; i < nframes; i++){ */ |
572 |
/* sum_director[0] += director[0][i]; */ |
573 |
/* sum_director[1] += director[1][i]; */ |
574 |
/* sum_director[2] += director[2][i]; */ |
575 |
/* } */ |
576 |
/* ave_director[0] = sum_director[0] / (double) nframes; */ |
577 |
/* ave_director[1] = sum_director[1] / (double) nframes; */ |
578 |
/* ave_director[2] = sum_director[2] / (double) nframes; */ |
579 |
|
580 |
/* for(i = 0; i < nframes; i++){ */ |
581 |
/* sum_vr[0] += vr[0][i]; */ |
582 |
/* sum_vr[1] += vr[1][i]; */ |
583 |
/* sum_vr[2] += vr[2][i]; */ |
584 |
/* } */ |
585 |
/* ave_vr[0] = sum_vr[0] / (double) nframes; */ |
586 |
/* ave_vr[1] = sum_vr[1] / (double) nframes; */ |
587 |
/* ave_vr[2] = sum_vr[2] / (double) nframes; */ |
588 |
|
589 |
/* printf("# orderparameter = %lf\n", ave_orderpar); */ |
590 |
/* printf("# director axis is ( %lf\t%lf\t%lf )\n", */ |
591 |
/* ave_director[0], ave_director[1], ave_director[2]); */ |
592 |
/* printf("# vr axis is ( %lf\t%lf\t%lf )\n", ave_vr[0], ave_vr[1], ave_vr[2]); */ |
593 |
|
594 |
/* for(i = 0; i < nbins2; i++){ */ |
595 |
/* for(j = 0; j < nframes; j++){ */ |
596 |
/* sum_vrhist[i] += vrhist[i][j]; */ |
597 |
/* } */ |
598 |
/* } */ |
599 |
|
600 |
/* dx = sqrt(pow(state->Hmat[0][0], 2) + pow(state->Hmat[1][0], 2)); */ |
601 |
/* dy = sqrt(pow(state->Hmat[0][1], 2) + pow(state->Hmat[1][1], 2)); */ |
602 |
|
603 |
/* area = dx * dy; */ |
604 |
|
605 |
/* bigL = sqrt(area); */ |
606 |
|
607 |
/* areaPerMolecule = area / (double) state->nAtoms; */ |
608 |
|
609 |
/* smallA = sqrt(areaPerMolecule); */ |
610 |
|
611 |
/* gamma = t * log(bigL / smallA) / (2.0 * M_PI * fluc); */ |
612 |
|
613 |
/* printf("# first gamma estimate = %lf\n", gamma); */ |
614 |
|
615 |
/* printf("# \n"); */ |
616 |
|
617 |
/* for(i = 0; i < nbins2; i++){ */ |
618 |
/* ave_vrhist[i] = sum_vrhist[i] / (double) nframes; */ |
619 |
/* printf("%lf\t%lf\n", (double) i * (ave_vr[0] * dx + ave_vr[1] * dy) / (double) nbins2, */ |
620 |
/* ave_vrhist[i]); */ |
621 |
/* } */ |
622 |
|
623 |
/* selfx = (int) ((double)nbins / 2.0); */ |
624 |
/* selfy = (int) ((double)nbins / 2.0); */ |
625 |
|
626 |
/* for (i = 0; i < nbins; i++) { */ |
627 |
/* for (j = 0; j < nbins; j++) { */ |
628 |
/* printf("%lf\t", h2hist[nbins * i + j] / (double) n2); */ |
629 |
/* } */ |
630 |
/* printf("\n"); */ |
631 |
/* } */ |
632 |
|
633 |
free(work); |
634 |
free(corrhist); |
635 |
free(h2hist); |
636 |
free(ux); |
637 |
free(uy); |
638 |
free(uz); |
639 |
return 1; |
640 |
|
641 |
} |
642 |
|
643 |
double matDet2(double a[2][2]) { |
644 |
|
645 |
double determinant; |
646 |
|
647 |
determinant = (a[0][0] * a[1][1]) - (a[0][1] * a[1][0]); |
648 |
|
649 |
return determinant; |
650 |
} |
651 |
|
652 |
|
653 |
void invertMat2(double a[2][2], double b[2][2]) { |
654 |
|
655 |
double determinant; |
656 |
|
657 |
determinant = matDet2( a ); |
658 |
|
659 |
if (determinant == 0.0) { |
660 |
printf("Can't invert a matrix with a zero determinant!\n"); |
661 |
} |
662 |
|
663 |
b[0][0] = a[1][1] / determinant; |
664 |
b[0][1] = -a[0][1] / determinant; |
665 |
b[1][0] = -a[1][0] / determinant; |
666 |
b[1][1] = a[0][0] / determinant; |
667 |
} |
668 |
|
669 |
void matVecMul2(double m[2][2], double inVec[2], double outVec[2]) { |
670 |
double a0, a1, a2; |
671 |
|
672 |
a0 = inVec[0]; a1 = inVec[1]; |
673 |
|
674 |
outVec[0] = m[0][0]*a0 + m[0][1]*a1; |
675 |
outVec[1] = m[1][0]*a0 + m[1][1]*a1; |
676 |
} |
677 |
|
678 |
void wrapVector( double thePos[2], double Hmat[2][2], double HmatInv[2][2]){ |
679 |
|
680 |
int i; |
681 |
double scaled[2]; |
682 |
|
683 |
// calc the scaled coordinates. |
684 |
|
685 |
matVecMul2(HmatInv, thePos, scaled); |
686 |
|
687 |
for(i=0; i<2; i++) |
688 |
scaled[i] -= roundMe(scaled[i]); |
689 |
|
690 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
691 |
|
692 |
matVecMul2(Hmat, scaled, thePos); |
693 |
|
694 |
} |
695 |
|
696 |
/* double* dsyev_ctof(double **in, int rows, int cols) */ |
697 |
/* { */ |
698 |
/* double *out; */ |
699 |
/* int i, j; */ |
700 |
|
701 |
/* out = (double *) calloc(rows * cols, sizeof(double)); */ |
702 |
|
703 |
/* if (!out){ */ |
704 |
/* printf("Fail to allocate memory\n"); */ |
705 |
/* exit(1); */ |
706 |
/* } */ |
707 |
|
708 |
/* for (i = 0; i < rows; i++) */ |
709 |
/* for (j = 0; j < cols; j++) */ |
710 |
/* out[i+j*cols] = in[i][j]; */ |
711 |
|
712 |
/* return(out); */ |
713 |
/* } */ |
714 |
|
715 |
/* void dsyev_ftoc2(double *in, double **out, int rows, int cols) */ |
716 |
/* { */ |
717 |
/* int i, j; */ |
718 |
|
719 |
/* for (i = 0; i < rows; i++) */ |
720 |
/* for (j = 0; j < cols; j++) */ |
721 |
/* out[i][j] = in[i+j*cols]; */ |
722 |
/* } */ |
723 |
/* void direct(double rcut, double box, int n, int nstep, int maxbin){ */ |
724 |
|
725 |
/* int bin, maxbin, nbins, i, j, k, n, bind, which; */ |
726 |
/* int hist[maxbin], histd[maxbin], startstep; */ |
727 |
/* int nstep, stopstep, ndiag, nfilled, ifail, lwork; */ |
728 |
/* double delr, rijsp, rxij, ryij, rzij, rij; */ |
729 |
/* double delrd, rijsqd, rijd, orderpar[1000], nideal; */ |
730 |
/* double omat[3][3], evals[100], cons, rlower; */ |
731 |
/* double rcut, box, dens, director[3][1000], rupper; */ |
732 |
/* double rx[1000][1000], ry[1000][1000], rz[1000][1000]; */ |
733 |
/* double ux[1000][1000], uy[1000][1000], uz[1000][1000]; */ |
734 |
/* double vx[1000][1000], vy[1000][1000], vz[1000][1000]; */ |
735 |
/* double jx[1000][1000], jy[1000][1000], jz[1000][1000]; */ |
736 |
/* double grd[5000], gr[5000], max, binmin, binmax; */ |
737 |
/* double onethird, ordvals[5000]; */ |
738 |
/* char job, uplo; */ |
739 |
/* int ndiag; */ |
740 |
/* int nfilled; */ |
741 |
/* double omat[3][3]; */ |
742 |
/* double evals[100]; */ |
743 |
/* double work[]; */ |
744 |
/* int lwork; */ |
745 |
/* int ifail; */ |
746 |
|
747 |
/* lwork = 9; */ |
748 |
/* work = (double *)calloc(lwork, sizeof(double)); */ |
749 |
|
750 |
/* onethird = 1.0 / 3.0; */ |
751 |
/* ndiag = 3; */ |
752 |
/* nfilled = 3; */ |
753 |
/* job = 'V'; */ |
754 |
/* uplo = 'U'; */ |
755 |
/* ifail = 0; */ |
756 |
|
757 |
/* binmin = 0.0; */ |
758 |
/* binmax = 1.0; */ |
759 |
/* delr = (binmax - binmin) / (double) maxbin; */ |
760 |
|
761 |
/* for(i = 0; i < maxbin; i++){ */ |
762 |
|
763 |
/* ordvals(i) = 0.0; */ |
764 |
/* hist(i) = 0.0; */ |
765 |
|
766 |
/* } */ |
767 |
|
768 |
/* for(i = 0; i < stopstep; i++){ */ |
769 |
|
770 |
/* for(j = 0; j < 3; j++){ */ |
771 |
/* for(k = 0; k < 3; k++){ */ |
772 |
/* omat[j][k] = 0.0; */ |
773 |
/* } */ |
774 |
/* } */ |
775 |
|
776 |
/* for(j = 0; j < n; j++){ */ |
777 |
|
778 |
/* omat[1][1] = omat[1][1] + ux[j][i] * ux[j][i] - onethird; */ |
779 |
/* omat[1][2] = omat[1][2] + ux[j][i] * uy[j][i]; */ |
780 |
/* omat[1][3] = omat[1][3] + ux[j][i] * uz[j][i]; */ |
781 |
/* omat[2][1] = omat[2][1] + uy[j][i] * ux[j][i]; */ |
782 |
/* omat[2][2] = omat[2][2] + uy[j][i] * uy[j][i] - onethird; */ |
783 |
/* omat[2][3] = omat[2][3] + uy[j][i] * uz[j][i]; */ |
784 |
/* omat[3][1] = omat[3][1] + uz[j][i] * ux[j][i]; */ |
785 |
/* omat[3][2] = omat[3][2] + uz[j][i] * uy[j][i]; */ |
786 |
/* omat[3][3] = omat[3][3] + uz[j][i] * uz[j][i] - onethird; */ |
787 |
|
788 |
/* } */ |
789 |
|
790 |
|
791 |
/* for(j = 0; j < 3; j++){ */ |
792 |
/* for(k = 0; k < 3; k++){ */ |
793 |
/* omat[j][k] = omat[j][k] / (double) n; */ |
794 |
/* } */ |
795 |
/* } */ |
796 |
|
797 |
/* dsyev_(job, uplo, nfilled, omat, ndiag, evals, work, lwork, ifail); */ |
798 |
|
799 |
/* max = 0.0; */ |
800 |
/* for(j = 0; j < 3; j++){ */ |
801 |
/* if(fabs(evals(j)) > max){ */ |
802 |
/* which = j; */ |
803 |
/* max = fabs(evals(j)); */ |
804 |
/* } */ |
805 |
/* } */ |
806 |
|
807 |
/* director[1][i] = omat[1][which]; */ |
808 |
/* director[2][i] = omat[2][which]; */ |
809 |
/* director[3][i] = omat[3][which]; */ |
810 |
|
811 |
/* orderpar(i) = 1.5 * max; */ |
812 |
|
813 |
/* bin = (int) (orderpar(i) / delr) + 1; */ |
814 |
|
815 |
/* if(bin < maxbin) */ |
816 |
/* hist(bin) = hist(bin) + 1; */ |
817 |
/* } */ |
818 |
|
819 |
/* cons = 1.0; */ |
820 |
/* for(bin = 0; bin < maxbin; bin++){ */ |
821 |
|
822 |
/* rlower = (double) (bin - 1) * delr; */ |
823 |
/* rupper = rlower + delr; */ |
824 |
/* ordvals(bin) = rlower + (delr / 2.0); */ |
825 |
/* nideal = cons * (pow(rupper, 3) - pow(rlower, 3)); */ |
826 |
/* gr(bin) = (double) (hist(bin)) / (double) nstep /nideal; */ |
827 |
|
828 |
/* } */ |
829 |
/* } */ |