| 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, sum2_orderpar, ave_orderpar, ave2_orderpar, err_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 |
sum2_orderpar = 0.0; |
| 176 |
ave_orderpar = 0.0; |
| 177 |
ave2_orderpar = 0.0; |
| 178 |
|
| 179 |
for(i = 0; i < 3; i++){ |
| 180 |
for(j = 0; j < 1000; j++){ |
| 181 |
director[i][j] = 0.0; |
| 182 |
vr[i][j] = 0.0; |
| 183 |
} |
| 184 |
} |
| 185 |
|
| 186 |
for(i = 0; i < 1000; i++){ |
| 187 |
sum_vrhist[i] = 0.0; |
| 188 |
ave_vrhist[i] = 0.0; |
| 189 |
} |
| 190 |
|
| 191 |
for(i = 0; i < 3; i++){ |
| 192 |
sum_director[i] = 0.0; |
| 193 |
ave_director[i] = 0.0; |
| 194 |
sum_vr[i] = 0.0; |
| 195 |
ave_vr[i] = 0.0; |
| 196 |
} |
| 197 |
|
| 198 |
for (i = 0; i < nbins; i++) { |
| 199 |
for (j = 0; j < nbins; j++) { |
| 200 |
corrhist[nbins * i + j] = 0.0; |
| 201 |
h2hist[nbins * i + j] = 0.0; |
| 202 |
} |
| 203 |
} |
| 204 |
|
| 205 |
for (i = 0; i < 100; i++) { |
| 206 |
for (j = 0; j < 500; j++) { |
| 207 |
vrhist[i][j] = 0.0; |
| 208 |
} |
| 209 |
} |
| 210 |
|
| 211 |
for(i = 0; i < nbins2; i++){ |
| 212 |
ophist[i] = 0; |
| 213 |
} |
| 214 |
|
| 215 |
t = 300; |
| 216 |
|
| 217 |
in_file = fopen(in_name, "r"); |
| 218 |
if(in_file == NULL){ |
| 219 |
printf("Cannot open file \"%s\" for reading.\n", in_name); |
| 220 |
exit(8); |
| 221 |
} |
| 222 |
|
| 223 |
nframes = 0; |
| 224 |
n1 = 0; |
| 225 |
n2 = 0; |
| 226 |
n3 = 0; |
| 227 |
n4 = 0; |
| 228 |
|
| 229 |
// start reading the first frame |
| 230 |
|
| 231 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
| 232 |
nAtoms = atoi(read_buffer); |
| 233 |
ux = (double *) calloc(nAtoms, sizeof(double)); |
| 234 |
uy = (double *) calloc(nAtoms, sizeof(double)); |
| 235 |
uz = (double *) calloc(nAtoms, sizeof(double)); |
| 236 |
lineCount++; |
| 237 |
|
| 238 |
for(i = 0; i < nAtoms; i++){ |
| 239 |
ux[i] = 0.0; |
| 240 |
uy[i] = 0.0; |
| 241 |
uz[i] = 0.0; |
| 242 |
} |
| 243 |
|
| 244 |
state = (struct system *) malloc(sizeof(struct system)); |
| 245 |
state->next = NULL; |
| 246 |
state->strength = 7.0; |
| 247 |
|
| 248 |
while(eof_test != NULL){ |
| 249 |
|
| 250 |
nframes++; |
| 251 |
(void)sscanf(read_buffer, "%d", &state->nAtoms); |
| 252 |
N = 2 * state->nAtoms; |
| 253 |
|
| 254 |
state->r = (struct coords *)calloc(N, sizeof(struct coords)); |
| 255 |
|
| 256 |
for(i = 0; i < 3; i++){ |
| 257 |
for(j = 0; j < 3; j++){ |
| 258 |
omat[i][j] = 0.0; |
| 259 |
} |
| 260 |
} |
| 261 |
|
| 262 |
// read and the comment line and grab the time and box dimensions |
| 263 |
|
| 264 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
| 265 |
lineCount++; |
| 266 |
if(eof_test == NULL){ |
| 267 |
printf("error in reading file at line: %d\n", lineCount); |
| 268 |
exit(8); |
| 269 |
} |
| 270 |
|
| 271 |
foo = strtok( read_buffer, " ,;\t\n" ); |
| 272 |
(void)sscanf( read_buffer, "%d", &state->iCycle ); |
| 273 |
|
| 274 |
foo = strtok(NULL, " ,;\t\0"); |
| 275 |
if(foo == NULL){ |
| 276 |
printf("error in reading file at line: %d\n", lineCount); |
| 277 |
exit(8); |
| 278 |
} |
| 279 |
(void)sscanf(foo, "%d", &state->nx); |
| 280 |
|
| 281 |
nx = state->nx; |
| 282 |
|
| 283 |
foo = strtok(NULL, " ,;\t\0"); |
| 284 |
if(foo == NULL){ |
| 285 |
printf("error in reading file at line: %d\n", lineCount); |
| 286 |
exit(8); |
| 287 |
} |
| 288 |
(void)sscanf(foo, "%d", &state->ny); |
| 289 |
|
| 290 |
ny = state->ny; |
| 291 |
|
| 292 |
foo = strtok(NULL, " ,;\t\0"); |
| 293 |
if(foo == NULL){ |
| 294 |
printf("error in reading file at line: %d\n", lineCount); |
| 295 |
exit(8); |
| 296 |
} |
| 297 |
(void)sscanf(foo, "%lf",&state->Hmat[0][0]); |
| 298 |
|
| 299 |
foo = strtok(NULL, " ,;\t\0"); |
| 300 |
if(foo == NULL){ |
| 301 |
printf("error in reading file at line: %d\n", lineCount); |
| 302 |
exit(8); |
| 303 |
} |
| 304 |
(void)sscanf(foo, "%lf",&state->Hmat[1][0]); |
| 305 |
|
| 306 |
foo = strtok(NULL, " ,;\t\0"); |
| 307 |
if(foo == NULL){ |
| 308 |
printf("error in reading file at line: %d\n", lineCount); |
| 309 |
exit(8); |
| 310 |
} |
| 311 |
(void)sscanf(foo, "%lf",&state->Hmat[0][1]); |
| 312 |
|
| 313 |
foo = strtok(NULL, " ,;\t\0"); |
| 314 |
if(foo == NULL){ |
| 315 |
printf("error in reading file at line: %d\n", lineCount); |
| 316 |
exit(8); |
| 317 |
} |
| 318 |
(void)sscanf(foo, "%lf",&state->Hmat[1][1]); |
| 319 |
|
| 320 |
//Find HmatI: |
| 321 |
|
| 322 |
invertMat2(state->Hmat, state->HmatI); |
| 323 |
|
| 324 |
// Length of the two box vectors: |
| 325 |
|
| 326 |
dx = sqrt(pow(state->Hmat[0][0], 2) + pow(state->Hmat[1][0], 2)); |
| 327 |
dy = sqrt(pow(state->Hmat[0][1], 2) + pow(state->Hmat[1][1], 2)); |
| 328 |
|
| 329 |
aLat = dx / (double)(state->nx); |
| 330 |
bLat = dy / (double)(state->ny); |
| 331 |
|
| 332 |
// FFT stuff depends on nx and ny, so delay allocation until we have |
| 333 |
// that information |
| 334 |
|
| 335 |
for (i=0;i<state->nAtoms;i++){ |
| 336 |
|
| 337 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
| 338 |
lineCount++; |
| 339 |
if(eof_test == NULL){ |
| 340 |
printf("error in reading file at line: %d\n", lineCount); |
| 341 |
exit(8); |
| 342 |
} |
| 343 |
|
| 344 |
foo = strtok(read_buffer, " ,;\t\0"); |
| 345 |
(void)strcpy(state->r[i].name, foo); //copy the atom name |
| 346 |
|
| 347 |
// next we grab the positions |
| 348 |
|
| 349 |
foo = strtok(NULL, " ,;\t\0"); |
| 350 |
if(foo == NULL){ |
| 351 |
printf("error in reading postition x from %s\n" |
| 352 |
"natoms = %d, line = %d\n", |
| 353 |
in_name, state->nAtoms, lineCount ); |
| 354 |
exit(8); |
| 355 |
} |
| 356 |
(void)sscanf( foo, "%lf", &state->r[i].pos[0] ); |
| 357 |
|
| 358 |
foo = strtok(NULL, " ,;\t\0"); |
| 359 |
if(foo == NULL){ |
| 360 |
printf("error in reading postition y from %s\n" |
| 361 |
"natoms = %d, line = %d\n", |
| 362 |
in_name, state->nAtoms, lineCount ); |
| 363 |
exit(8); |
| 364 |
} |
| 365 |
(void)sscanf( foo, "%lf", &state->r[i].pos[1] ); |
| 366 |
|
| 367 |
foo = strtok(NULL, " ,;\t\0"); |
| 368 |
if(foo == NULL){ |
| 369 |
printf("error in reading postition z from %s\n" |
| 370 |
"natoms = %d, line = %d\n", |
| 371 |
in_name, state->nAtoms, lineCount ); |
| 372 |
exit(8); |
| 373 |
} |
| 374 |
(void)sscanf( foo, "%lf", &state->r[i].pos[2] ); |
| 375 |
|
| 376 |
foo = strtok(NULL, " ,;\t\0"); |
| 377 |
if(foo == NULL){ |
| 378 |
printf("error in reading angle phi from %s\n" |
| 379 |
"natoms = %d, line = %d\n", |
| 380 |
in_name, state->nAtoms, lineCount ); |
| 381 |
exit(8); |
| 382 |
} |
| 383 |
(void)sscanf( foo, "%lf", &state->r[i].phi ); |
| 384 |
|
| 385 |
foo = strtok(NULL, " ,;\t\0"); |
| 386 |
if(foo == NULL){ |
| 387 |
printf("error in reading unit vector x from %s\n" |
| 388 |
"natoms = %d, line = %d\n", |
| 389 |
in_name, state->nAtoms, lineCount ); |
| 390 |
exit(8); |
| 391 |
} |
| 392 |
(void)sscanf( foo, "%lf", &ux[i] ); |
| 393 |
|
| 394 |
foo = strtok(NULL, " ,;\t\0"); |
| 395 |
if(foo == NULL){ |
| 396 |
printf("error in reading unit vector y from %s\n" |
| 397 |
"natoms = %d, line = %d\n", |
| 398 |
in_name, state->nAtoms, lineCount ); |
| 399 |
exit(8); |
| 400 |
} |
| 401 |
(void)sscanf( foo, "%lf", &uy[i] ); |
| 402 |
|
| 403 |
foo = strtok(NULL, " ,;\t\0"); |
| 404 |
if(foo == NULL){ |
| 405 |
printf("error in reading unit vector z from %s\n" |
| 406 |
"natoms = %d, line = %d\n", |
| 407 |
in_name, state->nAtoms, lineCount ); |
| 408 |
exit(8); |
| 409 |
} |
| 410 |
(void)sscanf( foo, "%lf", &uz[i] ); |
| 411 |
|
| 412 |
state->r[i].theta = acos(uz[i]); |
| 413 |
|
| 414 |
// The one parameter not stored in the dump file is the dipole strength |
| 415 |
state->r[i].mu = state->strength; |
| 416 |
} |
| 417 |
|
| 418 |
hsum_temp = 0.0; |
| 419 |
for (i = 0; i < state->nAtoms; i++) { |
| 420 |
|
| 421 |
h = state->r[i].pos[2]; |
| 422 |
h2 = pow(h,2); |
| 423 |
|
| 424 |
hsum_temp += h; |
| 425 |
hsum += h; |
| 426 |
h2sum += h2; |
| 427 |
|
| 428 |
n1++; |
| 429 |
} |
| 430 |
|
| 431 |
for(i = 0; i < state->nAtoms; i++){ |
| 432 |
|
| 433 |
omat[0][0] += ux[i] * ux[i] - onethird; |
| 434 |
omat[0][1] += ux[i] * uy[i]; |
| 435 |
omat[0][2] += ux[i] * uz[i]; |
| 436 |
omat[1][0] += uy[i] * ux[i]; |
| 437 |
omat[1][1] += uy[i] * uy[i] - onethird; |
| 438 |
omat[1][2] += uy[i] * uz[i]; |
| 439 |
omat[2][0] += uz[i] * ux[i]; |
| 440 |
omat[2][1] += uz[i] * uy[i]; |
| 441 |
omat[2][2] += uz[i] * uz[i] - onethird; |
| 442 |
|
| 443 |
} |
| 444 |
|
| 445 |
for(i = 0; i < 3; i++){ |
| 446 |
for(j = 0; j < 3; j++){ |
| 447 |
omat[i][j] /= (double) state->nAtoms; |
| 448 |
} |
| 449 |
} |
| 450 |
|
| 451 |
// temp_array = dsyev_ctof(omat, nfilled, nfilled); |
| 452 |
|
| 453 |
for(j=0;j<3;j++) |
| 454 |
for(i=0;i<3;i++) |
| 455 |
wrapMat[i+j*3] = omat[i][j]; |
| 456 |
|
| 457 |
ifail = 0; |
| 458 |
dsyev(&job, &uplo, &nfilled, wrapMat, &ndiag, evals, work, &lwork, &ifail); |
| 459 |
|
| 460 |
for(j=0;j<3;j++) |
| 461 |
for(i=0;i<3;i++) |
| 462 |
omat[i][j] = wrapMat[i+j*3]; |
| 463 |
|
| 464 |
//dsyev_ftoc2(temp_array, omat, nfilled, nfilled); |
| 465 |
|
| 466 |
//free(temp_array); |
| 467 |
|
| 468 |
max = 0.0; |
| 469 |
for(j = 0; j < 3; j++){ |
| 470 |
if(fabs(evals[j]) > max){ |
| 471 |
which = j; |
| 472 |
max = fabs(evals[j]); |
| 473 |
} |
| 474 |
} |
| 475 |
|
| 476 |
director[0][nframes-1] = omat[0][which]; |
| 477 |
director[1][nframes-1] = omat[1][which]; |
| 478 |
director[2][nframes-1] = omat[2][which]; |
| 479 |
|
| 480 |
vr[0][nframes-1] = fabs(director[1][nframes-1]); |
| 481 |
vr[1][nframes-1] = fabs(-director[0][nframes-1]); |
| 482 |
vr[2][nframes-1] = 0; |
| 483 |
|
| 484 |
orderpar[nframes-1] = 1.5 * max; |
| 485 |
|
| 486 |
opbin = (int) (orderpar[nframes-1] / delr); |
| 487 |
if(opbin < nbins2) ophist[opbin] += 1; |
| 488 |
|
| 489 |
for(i = 0; i < state->nAtoms; i++){ |
| 490 |
proj = vr[0][nframes-1] * state->r[i].pos[0] + vr[1][nframes-1] * state->r[i].pos[1]; |
| 491 |
hi = state->r[i].pos[2] - hsum_temp / (double) state->nAtoms; |
| 492 |
|
| 493 |
whichbin2 = (int) ((proj / (vr[0][nframes-1] * dx + vr[1][nframes-1] * dy)) * nbins2); |
| 494 |
vrhist[whichbin2][nframes-1] += hi; |
| 495 |
vrsamp[whichbin2][nframes-1]++; |
| 496 |
} |
| 497 |
|
| 498 |
for(i = 0; i < state->nAtoms; i++){ |
| 499 |
for(j = 0; j < state->nAtoms; j++){ |
| 500 |
|
| 501 |
d[0] = state->r[j].pos[0] - state->r[i].pos[0]; |
| 502 |
d[1] = state->r[j].pos[1] - state->r[i].pos[1]; |
| 503 |
|
| 504 |
wrapVector(d, state->Hmat, state->HmatI); |
| 505 |
|
| 506 |
whichbinx = (int) ((nbins-1) * (dx/2.0 + d[0]) / dx); |
| 507 |
whichbiny = (int) ((nbins-1) * (dy/2.0 + d[1]) / dy); |
| 508 |
|
| 509 |
//if (i == j) { |
| 510 |
//printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); |
| 511 |
//} |
| 512 |
|
| 513 |
//printf("d0 = %lf, d1 = %lf\n", d[0], d[1]); |
| 514 |
//printf("wx = %d, wy = %d\n", whichbinx, whichbiny); |
| 515 |
|
| 516 |
if (whichbinx >= nbins || whichbiny >= nbins) { |
| 517 |
printf("off by one error\n"); |
| 518 |
printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); |
| 519 |
exit(0); |
| 520 |
} |
| 521 |
if (whichbinx < 0 || whichbiny < 0) { |
| 522 |
printf("off by one error\n"); |
| 523 |
printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); |
| 524 |
exit(0); |
| 525 |
} |
| 526 |
|
| 527 |
hcorr = state->r[j].pos[2] * state->r[i].pos[2]; |
| 528 |
|
| 529 |
corrhist[nbins * whichbinx + whichbiny] += hcorr; |
| 530 |
|
| 531 |
dh = state->r[j].pos[2] - state->r[i].pos[2]; |
| 532 |
dh2 = pow(dh, 2); |
| 533 |
|
| 534 |
h2hist[nbins * whichbinx + whichbiny] += dh2; |
| 535 |
|
| 536 |
n2++; |
| 537 |
} |
| 538 |
} |
| 539 |
|
| 540 |
temp_state = state->next; |
| 541 |
state->next = NULL; |
| 542 |
|
| 543 |
if (temp_state != NULL) { |
| 544 |
free(temp_state->r); |
| 545 |
free(temp_state); |
| 546 |
} |
| 547 |
|
| 548 |
// Make a new frame |
| 549 |
|
| 550 |
temp_state = (struct system *) malloc(sizeof(struct system)); |
| 551 |
temp_state->next = state; |
| 552 |
state = temp_state; |
| 553 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
| 554 |
lineCount++; |
| 555 |
} |
| 556 |
|
| 557 |
|
| 558 |
have = hsum / (double) n1; |
| 559 |
h2ave = h2sum / (double) n1; |
| 560 |
fluc = h2ave - pow(have, 2); |
| 561 |
|
| 562 |
printf("# <h> = %lf\n", have); |
| 563 |
printf("# <h2> = %lf\n", h2ave); |
| 564 |
printf("# sigma(h) = %lf\n", sqrt(h2ave - have * have)); |
| 565 |
printf("# fluctuation = %lf\n", fluc); |
| 566 |
|
| 567 |
for(i = 0; i < nframes; i++){ |
| 568 |
sum_orderpar += orderpar[i]; |
| 569 |
sum2_orderpar += pow(orderpar[i], 2); |
| 570 |
} |
| 571 |
ave_orderpar = sum_orderpar / (double) nframes; |
| 572 |
ave2_orderpar = sum2_orderpar / (double) nframes; |
| 573 |
err_orderpar = ave2_orderpar - pow(ave_orderpar, 2); |
| 574 |
|
| 575 |
for(i = 0; i < nframes; i++){ |
| 576 |
sum_director[0] += director[0][i]; |
| 577 |
sum_director[1] += director[1][i]; |
| 578 |
sum_director[2] += director[2][i]; |
| 579 |
} |
| 580 |
ave_director[0] = sum_director[0] / (double) nframes; |
| 581 |
ave_director[1] = sum_director[1] / (double) nframes; |
| 582 |
ave_director[2] = sum_director[2] / (double) nframes; |
| 583 |
|
| 584 |
for(i = 0; i < nframes; i++){ |
| 585 |
sum_vr[0] += vr[0][i]; |
| 586 |
sum_vr[1] += vr[1][i]; |
| 587 |
sum_vr[2] += vr[2][i]; |
| 588 |
} |
| 589 |
ave_vr[0] = sum_vr[0] / (double) nframes; |
| 590 |
ave_vr[1] = sum_vr[1] / (double) nframes; |
| 591 |
ave_vr[2] = sum_vr[2] / (double) nframes; |
| 592 |
|
| 593 |
printf("# orderparameter = %lf\n", ave_orderpar); |
| 594 |
printf("# error = %lf\n", err_orderpar); |
| 595 |
printf("# director axis is ( %lf\t%lf\t%lf )\n", |
| 596 |
ave_director[0], ave_director[1], ave_director[2]); |
| 597 |
printf("# vr axis is ( %lf\t%lf\t%lf )\n", ave_vr[0], ave_vr[1], ave_vr[2]); |
| 598 |
|
| 599 |
for(i = 0; i < nbins2; i++){ |
| 600 |
for(j = 0; j < nframes; j++){ |
| 601 |
sum_vrhist[i] += vrhist[i][j]; |
| 602 |
} |
| 603 |
} |
| 604 |
|
| 605 |
dx = sqrt(pow(state->Hmat[0][0], 2) + pow(state->Hmat[1][0], 2)); |
| 606 |
dy = sqrt(pow(state->Hmat[0][1], 2) + pow(state->Hmat[1][1], 2)); |
| 607 |
|
| 608 |
area = dx * dy; |
| 609 |
|
| 610 |
bigL = sqrt(area); |
| 611 |
|
| 612 |
areaPerMolecule = area / (double) state->nAtoms; |
| 613 |
|
| 614 |
smallA = sqrt(areaPerMolecule); |
| 615 |
|
| 616 |
gamma = t * log(bigL / smallA) / (2.0 * M_PI * fluc); |
| 617 |
|
| 618 |
printf("# first gamma estimate = %lf\n", gamma); |
| 619 |
|
| 620 |
printf("# \n"); |
| 621 |
|
| 622 |
for(i = 0; i < nbins2; i++){ |
| 623 |
ave_vrhist[i] = sum_vrhist[i] / (double) nframes; |
| 624 |
printf("%lf\t%lf\n", (double) i * (ave_vr[0] * dx + ave_vr[1] * dy) / (double) nbins2, |
| 625 |
ave_vrhist[i]); |
| 626 |
} |
| 627 |
|
| 628 |
selfx = (int) ((double)nbins / 2.0); |
| 629 |
selfy = (int) ((double)nbins / 2.0); |
| 630 |
|
| 631 |
/* for (i = 0; i < nbins; i++) { */ |
| 632 |
/* for (j = 0; j < nbins; j++) { */ |
| 633 |
/* printf("%lf\t", h2hist[nbins * i + j] / (double) n2); */ |
| 634 |
/* } */ |
| 635 |
/* printf("\n"); */ |
| 636 |
/* } */ |
| 637 |
|
| 638 |
free(work); |
| 639 |
free(corrhist); |
| 640 |
free(h2hist); |
| 641 |
free(ux); |
| 642 |
free(uy); |
| 643 |
free(uz); |
| 644 |
return 1; |
| 645 |
|
| 646 |
} |
| 647 |
|
| 648 |
double matDet2(double a[2][2]) { |
| 649 |
|
| 650 |
double determinant; |
| 651 |
|
| 652 |
determinant = (a[0][0] * a[1][1]) - (a[0][1] * a[1][0]); |
| 653 |
|
| 654 |
return determinant; |
| 655 |
} |
| 656 |
|
| 657 |
|
| 658 |
void invertMat2(double a[2][2], double b[2][2]) { |
| 659 |
|
| 660 |
double determinant; |
| 661 |
|
| 662 |
determinant = matDet2( a ); |
| 663 |
|
| 664 |
if (determinant == 0.0) { |
| 665 |
printf("Can't invert a matrix with a zero determinant!\n"); |
| 666 |
} |
| 667 |
|
| 668 |
b[0][0] = a[1][1] / determinant; |
| 669 |
b[0][1] = -a[0][1] / determinant; |
| 670 |
b[1][0] = -a[1][0] / determinant; |
| 671 |
b[1][1] = a[0][0] / determinant; |
| 672 |
} |
| 673 |
|
| 674 |
void matVecMul2(double m[2][2], double inVec[2], double outVec[2]) { |
| 675 |
double a0, a1, a2; |
| 676 |
|
| 677 |
a0 = inVec[0]; a1 = inVec[1]; |
| 678 |
|
| 679 |
outVec[0] = m[0][0]*a0 + m[0][1]*a1; |
| 680 |
outVec[1] = m[1][0]*a0 + m[1][1]*a1; |
| 681 |
} |
| 682 |
|
| 683 |
void wrapVector( double thePos[2], double Hmat[2][2], double HmatInv[2][2]){ |
| 684 |
|
| 685 |
int i; |
| 686 |
double scaled[2]; |
| 687 |
|
| 688 |
// calc the scaled coordinates. |
| 689 |
|
| 690 |
matVecMul2(HmatInv, thePos, scaled); |
| 691 |
|
| 692 |
for(i=0; i<2; i++) |
| 693 |
scaled[i] -= roundMe(scaled[i]); |
| 694 |
|
| 695 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 696 |
|
| 697 |
matVecMul2(Hmat, scaled, thePos); |
| 698 |
|
| 699 |
} |
| 700 |
|
| 701 |
/* double* dsyev_ctof(double **in, int rows, int cols) */ |
| 702 |
/* { */ |
| 703 |
/* double *out; */ |
| 704 |
/* int i, j; */ |
| 705 |
|
| 706 |
/* out = (double *) calloc(rows * cols, sizeof(double)); */ |
| 707 |
|
| 708 |
/* if (!out){ */ |
| 709 |
/* printf("Fail to allocate memory\n"); */ |
| 710 |
/* exit(1); */ |
| 711 |
/* } */ |
| 712 |
|
| 713 |
/* for (i = 0; i < rows; i++) */ |
| 714 |
/* for (j = 0; j < cols; j++) */ |
| 715 |
/* out[i+j*cols] = in[i][j]; */ |
| 716 |
|
| 717 |
/* return(out); */ |
| 718 |
/* } */ |
| 719 |
|
| 720 |
/* void dsyev_ftoc2(double *in, double **out, int rows, int cols) */ |
| 721 |
/* { */ |
| 722 |
/* int i, j; */ |
| 723 |
|
| 724 |
/* for (i = 0; i < rows; i++) */ |
| 725 |
/* for (j = 0; j < cols; j++) */ |
| 726 |
/* out[i][j] = in[i+j*cols]; */ |
| 727 |
/* } */ |
| 728 |
/* void direct(double rcut, double box, int n, int nstep, int maxbin){ */ |
| 729 |
|
| 730 |
/* int bin, maxbin, nbins, i, j, k, n, bind, which; */ |
| 731 |
/* int hist[maxbin], histd[maxbin], startstep; */ |
| 732 |
/* int nstep, stopstep, ndiag, nfilled, ifail, lwork; */ |
| 733 |
/* double delr, rijsp, rxij, ryij, rzij, rij; */ |
| 734 |
/* double delrd, rijsqd, rijd, orderpar[1000], nideal; */ |
| 735 |
/* double omat[3][3], evals[100], cons, rlower; */ |
| 736 |
/* double rcut, box, dens, director[3][1000], rupper; */ |
| 737 |
/* double rx[1000][1000], ry[1000][1000], rz[1000][1000]; */ |
| 738 |
/* double ux[1000][1000], uy[1000][1000], uz[1000][1000]; */ |
| 739 |
/* double vx[1000][1000], vy[1000][1000], vz[1000][1000]; */ |
| 740 |
/* double jx[1000][1000], jy[1000][1000], jz[1000][1000]; */ |
| 741 |
/* double grd[5000], gr[5000], max, binmin, binmax; */ |
| 742 |
/* double onethird, ordvals[5000]; */ |
| 743 |
/* char job, uplo; */ |
| 744 |
/* int ndiag; */ |
| 745 |
/* int nfilled; */ |
| 746 |
/* double omat[3][3]; */ |
| 747 |
/* double evals[100]; */ |
| 748 |
/* double work[]; */ |
| 749 |
/* int lwork; */ |
| 750 |
/* int ifail; */ |
| 751 |
|
| 752 |
/* lwork = 9; */ |
| 753 |
/* work = (double *)calloc(lwork, sizeof(double)); */ |
| 754 |
|
| 755 |
/* onethird = 1.0 / 3.0; */ |
| 756 |
/* ndiag = 3; */ |
| 757 |
/* nfilled = 3; */ |
| 758 |
/* job = 'V'; */ |
| 759 |
/* uplo = 'U'; */ |
| 760 |
/* ifail = 0; */ |
| 761 |
|
| 762 |
/* binmin = 0.0; */ |
| 763 |
/* binmax = 1.0; */ |
| 764 |
/* delr = (binmax - binmin) / (double) maxbin; */ |
| 765 |
|
| 766 |
/* for(i = 0; i < maxbin; i++){ */ |
| 767 |
|
| 768 |
/* ordvals(i) = 0.0; */ |
| 769 |
/* hist(i) = 0.0; */ |
| 770 |
|
| 771 |
/* } */ |
| 772 |
|
| 773 |
/* for(i = 0; i < stopstep; i++){ */ |
| 774 |
|
| 775 |
/* for(j = 0; j < 3; j++){ */ |
| 776 |
/* for(k = 0; k < 3; k++){ */ |
| 777 |
/* omat[j][k] = 0.0; */ |
| 778 |
/* } */ |
| 779 |
/* } */ |
| 780 |
|
| 781 |
/* for(j = 0; j < n; j++){ */ |
| 782 |
|
| 783 |
/* omat[1][1] = omat[1][1] + ux[j][i] * ux[j][i] - onethird; */ |
| 784 |
/* omat[1][2] = omat[1][2] + ux[j][i] * uy[j][i]; */ |
| 785 |
/* omat[1][3] = omat[1][3] + ux[j][i] * uz[j][i]; */ |
| 786 |
/* omat[2][1] = omat[2][1] + uy[j][i] * ux[j][i]; */ |
| 787 |
/* omat[2][2] = omat[2][2] + uy[j][i] * uy[j][i] - onethird; */ |
| 788 |
/* omat[2][3] = omat[2][3] + uy[j][i] * uz[j][i]; */ |
| 789 |
/* omat[3][1] = omat[3][1] + uz[j][i] * ux[j][i]; */ |
| 790 |
/* omat[3][2] = omat[3][2] + uz[j][i] * uy[j][i]; */ |
| 791 |
/* omat[3][3] = omat[3][3] + uz[j][i] * uz[j][i] - onethird; */ |
| 792 |
|
| 793 |
/* } */ |
| 794 |
|
| 795 |
|
| 796 |
/* for(j = 0; j < 3; j++){ */ |
| 797 |
/* for(k = 0; k < 3; k++){ */ |
| 798 |
/* omat[j][k] = omat[j][k] / (double) n; */ |
| 799 |
/* } */ |
| 800 |
/* } */ |
| 801 |
|
| 802 |
/* dsyev_(job, uplo, nfilled, omat, ndiag, evals, work, lwork, ifail); */ |
| 803 |
|
| 804 |
/* max = 0.0; */ |
| 805 |
/* for(j = 0; j < 3; j++){ */ |
| 806 |
/* if(fabs(evals(j)) > max){ */ |
| 807 |
/* which = j; */ |
| 808 |
/* max = fabs(evals(j)); */ |
| 809 |
/* } */ |
| 810 |
/* } */ |
| 811 |
|
| 812 |
/* director[1][i] = omat[1][which]; */ |
| 813 |
/* director[2][i] = omat[2][which]; */ |
| 814 |
/* director[3][i] = omat[3][which]; */ |
| 815 |
|
| 816 |
/* orderpar(i) = 1.5 * max; */ |
| 817 |
|
| 818 |
/* bin = (int) (orderpar(i) / delr) + 1; */ |
| 819 |
|
| 820 |
/* if(bin < maxbin) */ |
| 821 |
/* hist(bin) = hist(bin) + 1; */ |
| 822 |
/* } */ |
| 823 |
|
| 824 |
/* cons = 1.0; */ |
| 825 |
/* for(bin = 0; bin < maxbin; bin++){ */ |
| 826 |
|
| 827 |
/* rlower = (double) (bin - 1) * delr; */ |
| 828 |
/* rupper = rlower + delr; */ |
| 829 |
/* ordvals(bin) = rlower + (delr / 2.0); */ |
| 830 |
/* nideal = cons * (pow(rupper, 3) - pow(rlower, 3)); */ |
| 831 |
/* gr(bin) = (double) (hist(bin)) / (double) nstep /nideal; */ |
| 832 |
|
| 833 |
/* } */ |
| 834 |
/* } */ |
