| 1 |
#define _FILE_OFFSET_BITS 64 |
| 2 |
|
| 3 |
#include <stdio.h> |
| 4 |
#include <stdlib.h> |
| 5 |
#include <sys/types.h> |
| 6 |
#include <sys/stat.h> |
| 7 |
#include <string.h> |
| 8 |
|
| 9 |
#include "params.h" |
| 10 |
#include "tcProps.h" |
| 11 |
#include "readWrite.h" |
| 12 |
|
| 13 |
|
| 14 |
#define BUFFER_SIZE 2000 |
| 15 |
int isScanned; |
| 16 |
int fileOpen; |
| 17 |
int nFrames; |
| 18 |
double *frameTimes; |
| 19 |
FILE* inFile; |
| 20 |
char* inName; |
| 21 |
|
| 22 |
struct linkedPos{ |
| 23 |
|
| 24 |
fpos_t *myPos; |
| 25 |
double timeStamp; |
| 26 |
double Hmat[3][3]; |
| 27 |
struct linkedPos* next; |
| 28 |
}; |
| 29 |
|
| 30 |
struct staticPos{ |
| 31 |
|
| 32 |
fpos_t *myPos; |
| 33 |
double Hmat[3][3]; |
| 34 |
}; |
| 35 |
struct staticPos* posArray; |
| 36 |
|
| 37 |
void parseDumpLine( char readBuffer[BUFFER_SIZE], int index, |
| 38 |
struct atomCoord* atoms ); |
| 39 |
void setU( double q[4], double u[3] ); |
| 40 |
void normalizeQ( double q[4] ); |
| 41 |
|
| 42 |
void openFile( void ){ |
| 43 |
|
| 44 |
inFile = fopen(inName, "r"); |
| 45 |
if(inFile ==NULL){ |
| 46 |
fprintf(stderr, |
| 47 |
"Error opening file \"%s\"\n", |
| 48 |
inName); |
| 49 |
exit(0); |
| 50 |
} |
| 51 |
|
| 52 |
fileOpen = 1; |
| 53 |
} |
| 54 |
|
| 55 |
void closeFile( void ){ |
| 56 |
|
| 57 |
fclose( inFile ); |
| 58 |
|
| 59 |
fileOpen = 0; |
| 60 |
} |
| 61 |
|
| 62 |
void setFrames( void ){ |
| 63 |
|
| 64 |
int i,j,k; |
| 65 |
struct linkedPos* headPos; |
| 66 |
struct linkedPos* currPos; |
| 67 |
fpos_t *currPT; |
| 68 |
char readBuffer[BUFFER_SIZE]; |
| 69 |
char trash[BUFFER_SIZE]; |
| 70 |
char* foo; |
| 71 |
int lineNum = 0; |
| 72 |
|
| 73 |
|
| 74 |
if( !fileOpen ){ |
| 75 |
fprintf(stderr, |
| 76 |
"Attempt to scan the file without first opening the file.\n" ); |
| 77 |
exit(0); |
| 78 |
} |
| 79 |
|
| 80 |
|
| 81 |
nFrames = 0; |
| 82 |
headPos = (struct linkedPos*)malloc(sizeof(struct linkedPos)); |
| 83 |
currPos = headPos; |
| 84 |
|
| 85 |
currPT = (fpos_t *)malloc(sizeof(fpos_t)); |
| 86 |
fgetpos(inFile, currPT); |
| 87 |
|
| 88 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 89 |
lineNum++; |
| 90 |
if( feof( inFile ) ){ |
| 91 |
fprintf( stderr, |
| 92 |
"File \"%s\" ended unexpectedly at line %d\n", |
| 93 |
inName, |
| 94 |
lineNum ); |
| 95 |
exit(0); |
| 96 |
} |
| 97 |
|
| 98 |
while( !feof( inFile ) ){ |
| 99 |
|
| 100 |
currPos->next = (struct linkedPos*)malloc(sizeof(struct linkedPos)); |
| 101 |
currPos = currPos->next; |
| 102 |
currPos->myPos = currPT; |
| 103 |
nFrames++; |
| 104 |
|
| 105 |
i = atoi(readBuffer); |
| 106 |
|
| 107 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 108 |
lineNum++; |
| 109 |
if( feof( inFile ) ){ |
| 110 |
fprintf( stderr, |
| 111 |
"File \"%s\" ended unexpectedly at line %d\n", |
| 112 |
inName, |
| 113 |
lineNum ); |
| 114 |
exit(0); |
| 115 |
} |
| 116 |
|
| 117 |
|
| 118 |
// parse the comment line |
| 119 |
|
| 120 |
foo = strtok(readBuffer, " ,;\t"); |
| 121 |
|
| 122 |
if(foo == NULL){ |
| 123 |
fprintf(stderr, |
| 124 |
"error in reading time from %s at line %d\n", |
| 125 |
inName, lineNum ); |
| 126 |
exit(0); |
| 127 |
} |
| 128 |
currPos->timeStamp = atof( foo ); |
| 129 |
|
| 130 |
// get the Hx vector |
| 131 |
|
| 132 |
foo = strtok(NULL, " ,;\t"); |
| 133 |
if(foo == NULL){ |
| 134 |
fprintf(stderr, |
| 135 |
"error in reading Hx[0] from %s at line %d\n", |
| 136 |
inName, lineNum ); |
| 137 |
exit(0); |
| 138 |
} |
| 139 |
currPos->Hmat[0][0] = atof( foo ); |
| 140 |
|
| 141 |
foo = strtok(NULL, " ,;\t"); |
| 142 |
if(foo == NULL){ |
| 143 |
fprintf(stderr, |
| 144 |
"error in reading Hx[1] from %s at line %d\n", |
| 145 |
inName, lineNum ); |
| 146 |
exit(0); |
| 147 |
} |
| 148 |
currPos->Hmat[1][0] = atof( foo ); |
| 149 |
|
| 150 |
foo = strtok(NULL, " ,;\t"); |
| 151 |
if(foo == NULL){ |
| 152 |
fprintf(stderr, |
| 153 |
"error in reading Hx[2] from %s at line %d\n", |
| 154 |
inName, lineNum ); |
| 155 |
exit(0); |
| 156 |
} |
| 157 |
currPos->Hmat[2][0] = atof( foo ); |
| 158 |
|
| 159 |
// get the Hy vector |
| 160 |
|
| 161 |
foo = strtok(NULL, " ,;\t"); |
| 162 |
if(foo == NULL){ |
| 163 |
fprintf(stderr, |
| 164 |
"error in reading Hy[0] from %s at line %d\n", |
| 165 |
inName, lineNum ); |
| 166 |
exit(0); |
| 167 |
} |
| 168 |
currPos->Hmat[0][1] = atof( foo ); |
| 169 |
|
| 170 |
foo = strtok(NULL, " ,;\t"); |
| 171 |
if(foo == NULL){ |
| 172 |
fprintf(stderr, |
| 173 |
"error in reading Hy[1] from %s at line %d\n", |
| 174 |
inName, lineNum ); |
| 175 |
exit(0); |
| 176 |
} |
| 177 |
currPos->Hmat[1][1] = atof( foo ); |
| 178 |
|
| 179 |
foo = strtok(NULL, " ,;\t"); |
| 180 |
if(foo == NULL){ |
| 181 |
fprintf(stderr, |
| 182 |
"error in reading Hy[2] from %s at line %d\n", |
| 183 |
inName, lineNum ); |
| 184 |
exit(0); |
| 185 |
} |
| 186 |
currPos->Hmat[2][1] = atof( foo ); |
| 187 |
|
| 188 |
// get the Hz vector |
| 189 |
|
| 190 |
foo = strtok(NULL, " ,;\t"); |
| 191 |
if(foo == NULL){ |
| 192 |
fprintf(stderr, |
| 193 |
"error in reading Hz[0] from %s at line %d\n", |
| 194 |
inName, lineNum ); |
| 195 |
exit(0); |
| 196 |
} |
| 197 |
currPos->Hmat[0][2] = atof( foo ); |
| 198 |
|
| 199 |
foo = strtok(NULL, " ,;\t"); |
| 200 |
if(foo == NULL){ |
| 201 |
fprintf(stderr, |
| 202 |
"error in reading Hz[1] from %s at line %d\n", |
| 203 |
inName, lineNum ); |
| 204 |
exit(0); |
| 205 |
} |
| 206 |
currPos->Hmat[1][2] = atof( foo ); |
| 207 |
|
| 208 |
foo = strtok(NULL, " ,;\t"); |
| 209 |
if(foo == NULL){ |
| 210 |
fprintf(stderr, |
| 211 |
"error in reading Hz[2] from %s at line %d\n", |
| 212 |
inName, lineNum ); |
| 213 |
exit(0); |
| 214 |
} |
| 215 |
currPos->Hmat[2][2] = atof( foo ); |
| 216 |
|
| 217 |
// skip the atoms |
| 218 |
|
| 219 |
for(j=0; j<i; j++){ |
| 220 |
|
| 221 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 222 |
lineNum++; |
| 223 |
if( feof( inFile ) ){ |
| 224 |
fprintf( stderr, |
| 225 |
"File \"%s\" ended unexpectedly at line %d," |
| 226 |
" with atom %d\n", |
| 227 |
inName, |
| 228 |
lineNum, |
| 229 |
j ); |
| 230 |
exit(0); |
| 231 |
} |
| 232 |
} |
| 233 |
|
| 234 |
currPT = (fpos_t *)malloc(sizeof(fpos_t)); |
| 235 |
fgetpos(inFile, currPT); |
| 236 |
|
| 237 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 238 |
lineNum++; |
| 239 |
} |
| 240 |
|
| 241 |
// allocate the static position array |
| 242 |
|
| 243 |
posArray = (struct staticPos*)calloc(nFrames, sizeof(struct staticPos)); |
| 244 |
frameTimes = (double *)calloc(nFrames, sizeof(double) ); |
| 245 |
|
| 246 |
i=0; |
| 247 |
currPos = headPos->next; |
| 248 |
while( currPos != NULL ){ |
| 249 |
|
| 250 |
if(i>=nFrames){ |
| 251 |
|
| 252 |
fprintf( stderr, |
| 253 |
"The number of frame pointers exceeded the number of frames.\n" |
| 254 |
" OOPS!\n" ); |
| 255 |
exit(0); |
| 256 |
} |
| 257 |
|
| 258 |
frameTimes[i] = currPos->timeStamp; |
| 259 |
posArray[i].myPos = currPos->myPos; |
| 260 |
for(j=0;j<3;j++){ |
| 261 |
for(k=0;k<3;k++){ |
| 262 |
posArray[i].Hmat[j][k] = currPos->Hmat[j][k]; |
| 263 |
} |
| 264 |
} |
| 265 |
|
| 266 |
i++; |
| 267 |
currPos = currPos->next; |
| 268 |
} |
| 269 |
|
| 270 |
// clean up the linked list |
| 271 |
|
| 272 |
currPos = headPos; |
| 273 |
while( currPos != NULL ){ |
| 274 |
headPos = currPos; |
| 275 |
currPos = headPos->next; |
| 276 |
free(headPos); |
| 277 |
} |
| 278 |
|
| 279 |
|
| 280 |
isScanned = 1; |
| 281 |
} |
| 282 |
|
| 283 |
|
| 284 |
void readFrame(int theFrame, struct atomCoord* atoms, double Hmat[3][3] ){ |
| 285 |
|
| 286 |
// list of 'a priori' constants |
| 287 |
|
| 288 |
const int nLipAtoms = NL_ATOMS; |
| 289 |
const int nBonds = NBONDS; |
| 290 |
const int nLipids = NLIPIDS; |
| 291 |
const int nSSD = NSSD; |
| 292 |
const int nAtoms = nLipAtoms * nLipids + nSSD; |
| 293 |
|
| 294 |
fpos_t *framePos; |
| 295 |
char readBuffer[BUFFER_SIZE]; |
| 296 |
|
| 297 |
int i, j, k; |
| 298 |
|
| 299 |
|
| 300 |
// quick checks |
| 301 |
|
| 302 |
if (theFrame >= nFrames){ |
| 303 |
|
| 304 |
fprintf(stderr, |
| 305 |
"frame %d, is out of range\n", |
| 306 |
theFrame ); |
| 307 |
exit(0); |
| 308 |
} |
| 309 |
|
| 310 |
if( !fileOpen ){ |
| 311 |
|
| 312 |
fprintf( stderr, |
| 313 |
"File is closed, cannot read frame %d.\n", |
| 314 |
theFrame ); |
| 315 |
exit(0); |
| 316 |
} |
| 317 |
|
| 318 |
// access the frame |
| 319 |
|
| 320 |
framePos = posArray[theFrame].myPos; |
| 321 |
fsetpos( inFile, framePos ); |
| 322 |
|
| 323 |
for(j=0;j<3;j++){ |
| 324 |
for(k=0;k<3;k++){ |
| 325 |
Hmat[j][k] = posArray[theFrame].Hmat[j][k]; |
| 326 |
} |
| 327 |
} |
| 328 |
|
| 329 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 330 |
if( feof( inFile ) ){ |
| 331 |
fprintf( stderr, |
| 332 |
"File \"%s\" ended unexpectedly in Frame %d\n", |
| 333 |
inName, |
| 334 |
theFrame ); |
| 335 |
exit(0); |
| 336 |
} |
| 337 |
|
| 338 |
i = atoi( readBuffer ); |
| 339 |
if( i != nAtoms ){ |
| 340 |
fprintf( stderr, |
| 341 |
"Error in frame %d: frame atoms, %d, does not params atoms, %d\n", |
| 342 |
theFrame, |
| 343 |
i, |
| 344 |
nAtoms ); |
| 345 |
exit(0); |
| 346 |
} |
| 347 |
|
| 348 |
// read and toss the comment line |
| 349 |
|
| 350 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 351 |
if( feof( inFile ) ){ |
| 352 |
fprintf( stderr, |
| 353 |
"File \"%s\" ended unexpectedly in Frame %d\n", |
| 354 |
inName, |
| 355 |
theFrame ); |
| 356 |
exit(0); |
| 357 |
} |
| 358 |
|
| 359 |
// read the atoms |
| 360 |
|
| 361 |
for( i=0; i < nAtoms; i++){ |
| 362 |
|
| 363 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 364 |
if( feof( inFile ) ){ |
| 365 |
fprintf( stderr, |
| 366 |
"File \"%s\" ended unexpectedly in Frame %d at atom %d\n", |
| 367 |
inName, |
| 368 |
theFrame, |
| 369 |
i ); |
| 370 |
exit(0); |
| 371 |
} |
| 372 |
|
| 373 |
|
| 374 |
parseDumpLine( readBuffer, i, atoms ); |
| 375 |
} |
| 376 |
} |
| 377 |
|
| 378 |
void parseDumpLine( char readLine[BUFFER_SIZE], int i, |
| 379 |
struct atomCoord* atoms ){ |
| 380 |
|
| 381 |
const int nLipAtoms = NL_ATOMS; |
| 382 |
const int nBonds = NBONDS; |
| 383 |
const int nLipids = NLIPIDS; |
| 384 |
const int nSSD = NSSD; |
| 385 |
const int nAtoms = nLipAtoms * nLipids + nSSD; |
| 386 |
|
| 387 |
char* foo; |
| 388 |
double q[4]; |
| 389 |
|
| 390 |
// set the string tokenizer |
| 391 |
|
| 392 |
foo = strtok(readLine, " ,;\t"); |
| 393 |
|
| 394 |
// check the atom ID |
| 395 |
|
| 396 |
switch( atoms[i].type ){ |
| 397 |
|
| 398 |
case HEAD: |
| 399 |
if( strcmp(foo, "HEAD") ){ |
| 400 |
fprintf( stderr, |
| 401 |
"Atom %s does not match master array type \"HEAD\".\n", |
| 402 |
foo ); |
| 403 |
exit(0); |
| 404 |
} |
| 405 |
break; |
| 406 |
|
| 407 |
case CH: |
| 408 |
if( strcmp(foo, "CH") ){ |
| 409 |
fprintf( stderr, |
| 410 |
"Atom %s does not match master array type \"CH\".\n", |
| 411 |
foo ); |
| 412 |
exit(0); |
| 413 |
} |
| 414 |
break; |
| 415 |
|
| 416 |
case CH2: |
| 417 |
if( strcmp(foo, "CH2") ){ |
| 418 |
fprintf( stderr, |
| 419 |
"Atom %s does not match master array type \"CH2\".\n", |
| 420 |
foo ); |
| 421 |
exit(0); |
| 422 |
} |
| 423 |
break; |
| 424 |
|
| 425 |
case CH3: |
| 426 |
if( strcmp(foo, "CH3") ){ |
| 427 |
fprintf( stderr, |
| 428 |
"Atom %s does not match master array type \"CH3\".\n", |
| 429 |
foo ); |
| 430 |
exit(0); |
| 431 |
} |
| 432 |
break; |
| 433 |
|
| 434 |
case SSD: |
| 435 |
if( strcmp(foo, "SSD") ){ |
| 436 |
fprintf( stderr, |
| 437 |
"Atom %s does not match master array type \"SSD\".\n", |
| 438 |
foo ); |
| 439 |
exit(0); |
| 440 |
} |
| 441 |
break; |
| 442 |
|
| 443 |
default: |
| 444 |
fprintf(stderr, |
| 445 |
"Atom %d is an unrecognized enumeration\n", |
| 446 |
i ); |
| 447 |
exit(0); |
| 448 |
} |
| 449 |
|
| 450 |
// get the positions |
| 451 |
|
| 452 |
foo = strtok(NULL, " ,;\t"); |
| 453 |
if(foo == NULL){ |
| 454 |
fprintf( stderr, |
| 455 |
"error in reading postition x from %s\n" |
| 456 |
"natoms = %d, i = %d\n", |
| 457 |
inName, nAtoms, i ); |
| 458 |
exit(0); |
| 459 |
} |
| 460 |
atoms[i].pos[0] = atof( foo ); |
| 461 |
|
| 462 |
foo = strtok(NULL, " ,;\t"); |
| 463 |
if(foo == NULL){ |
| 464 |
fprintf( stderr, |
| 465 |
"error in reading postition y from %s\n" |
| 466 |
"natoms = %d, i = %d\n", |
| 467 |
inName, nAtoms, i ); |
| 468 |
exit(0); |
| 469 |
} |
| 470 |
atoms[i].pos[1] = atof( foo ); |
| 471 |
|
| 472 |
foo = strtok(NULL, " ,;\t"); |
| 473 |
if(foo == NULL){ |
| 474 |
fprintf( stderr, |
| 475 |
"error in reading postition z from %s\n" |
| 476 |
"natoms = %d, i = %d\n", |
| 477 |
inName, nAtoms, i ); |
| 478 |
exit(0); |
| 479 |
} |
| 480 |
atoms[i].pos[2] = atof( foo ); |
| 481 |
|
| 482 |
|
| 483 |
// get the velocities |
| 484 |
|
| 485 |
foo = strtok(NULL, " ,;\t"); |
| 486 |
if(foo == NULL){ |
| 487 |
fprintf( stderr, |
| 488 |
"error in reading velocity x from %s\n" |
| 489 |
"natoms = %d, i = %d\n", |
| 490 |
inName, nAtoms, i ); |
| 491 |
exit(0); |
| 492 |
} |
| 493 |
atoms[i].vel[0] = atof( foo ); |
| 494 |
|
| 495 |
foo = strtok(NULL, " ,;\t"); |
| 496 |
if(foo == NULL){ |
| 497 |
fprintf( stderr, |
| 498 |
"error in reading velocity y from %s\n" |
| 499 |
"natoms = %d, i = %d\n", |
| 500 |
inName, nAtoms, i ); |
| 501 |
exit(0); |
| 502 |
} |
| 503 |
atoms[i].vel[1] = atof( foo ); |
| 504 |
|
| 505 |
foo = strtok(NULL, " ,;\t"); |
| 506 |
if(foo == NULL){ |
| 507 |
fprintf( stderr, |
| 508 |
"error in reading velocity z from %s\n" |
| 509 |
"natoms = %d, i = %d\n", |
| 510 |
inName, nAtoms, i ); |
| 511 |
exit(0); |
| 512 |
} |
| 513 |
atoms[i].vel[2] = atof( foo ); |
| 514 |
|
| 515 |
|
| 516 |
// get the quaternions |
| 517 |
|
| 518 |
if( (atoms[i].type == HEAD) || (atoms[i].type == SSD) ){ |
| 519 |
|
| 520 |
foo = strtok(NULL, " ,;\t"); |
| 521 |
if(foo == NULL){ |
| 522 |
fprintf( stderr, |
| 523 |
"error in reading quaternion 0 from %s\n" |
| 524 |
"natoms = %d, i = %d\n", |
| 525 |
inName, nAtoms, i ); |
| 526 |
exit(0); |
| 527 |
} |
| 528 |
q[0] = atof( foo ); |
| 529 |
|
| 530 |
foo = strtok(NULL, " ,;\t"); |
| 531 |
if(foo == NULL){ |
| 532 |
fprintf( stderr, |
| 533 |
"error in reading quaternion 1 from %s\n" |
| 534 |
"natoms = %d, i = %d\n", |
| 535 |
inName, nAtoms, i ); |
| 536 |
exit(0); |
| 537 |
} |
| 538 |
q[1] = atof( foo ); |
| 539 |
|
| 540 |
foo = strtok(NULL, " ,;\t"); |
| 541 |
if(foo == NULL){ |
| 542 |
fprintf( stderr, |
| 543 |
"error in reading quaternion 2 from %s\n" |
| 544 |
"natoms = %d, i = %d\n", |
| 545 |
inName, nAtoms, i ); |
| 546 |
exit(0); |
| 547 |
} |
| 548 |
q[2] = atof( foo ); |
| 549 |
|
| 550 |
foo = strtok(NULL, " ,;\t"); |
| 551 |
if(foo == NULL){ |
| 552 |
fprintf( stderr, |
| 553 |
"error in reading quaternion 3 from %s\n" |
| 554 |
"natoms = %d, i = %d\n", |
| 555 |
inName, nAtoms, i ); |
| 556 |
exit(0); |
| 557 |
} |
| 558 |
q[3] = atof( foo ); |
| 559 |
|
| 560 |
normalizeQ( q ); |
| 561 |
|
| 562 |
setU( q, atoms[i].u ); |
| 563 |
} |
| 564 |
} |
| 565 |
|
| 566 |
|
| 567 |
void setU( double the_q[4], double u[3] ){ |
| 568 |
|
| 569 |
double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
| 570 |
double A[3][3]; |
| 571 |
double rb[3]; |
| 572 |
int i,j,k; |
| 573 |
|
| 574 |
// initialize the axis |
| 575 |
|
| 576 |
rb[0] = 0.0; |
| 577 |
rb[1] = 0.0; |
| 578 |
rb[2] = 1.0; |
| 579 |
|
| 580 |
// set the rotation matrix |
| 581 |
|
| 582 |
q0Sqr = the_q[0] * the_q[0]; |
| 583 |
q1Sqr = the_q[1] * the_q[1]; |
| 584 |
q2Sqr = the_q[2] * the_q[2]; |
| 585 |
q3Sqr = the_q[3] * the_q[3]; |
| 586 |
|
| 587 |
A[0][0] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
| 588 |
A[0][1] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
| 589 |
A[0][2] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
| 590 |
|
| 591 |
A[1][0] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
| 592 |
A[1][1] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
| 593 |
A[1][2] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
| 594 |
|
| 595 |
A[2][0] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
| 596 |
A[2][1] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
| 597 |
A[2][2] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
| 598 |
|
| 599 |
// perform the rotation |
| 600 |
|
| 601 |
for( i=0; i<3; i++ ){ |
| 602 |
u[i] = 0.0; |
| 603 |
|
| 604 |
for( j=0; j<3; j++ ){ |
| 605 |
u[i] += A[j][i] * rb[j]; |
| 606 |
} |
| 607 |
} |
| 608 |
} |
| 609 |
|
| 610 |
void normalizeQ( double q[4] ){ |
| 611 |
|
| 612 |
double qSqr, qL; |
| 613 |
int i; |
| 614 |
|
| 615 |
qSqr = 0.0; |
| 616 |
for(i=0;i<4;i++) |
| 617 |
qSqr += q[i] * q[i]; |
| 618 |
|
| 619 |
for(i=0;i<4;i++) |
| 620 |
q[i] /= qSqr; |
| 621 |
} |
| 622 |
|
| 623 |
double scanSmallestZ(int startFrame){ |
| 624 |
double smallest; |
| 625 |
int i; |
| 626 |
|
| 627 |
smallest = posArray[startFrame].Hmat[2][2]; |
| 628 |
for(i=startFrame;i<nFrames;i++) |
| 629 |
smallest = |
| 630 |
(smallest<posArray[i].Hmat[2][2])? smallest : posArray[i].Hmat[2][2]; |
| 631 |
|
| 632 |
return smallest; |
| 633 |
} |
| 634 |
|
| 635 |
double calcAverageXY( double startTime ){ |
| 636 |
|
| 637 |
int i, count, startFrame, startFound; |
| 638 |
double avg; |
| 639 |
|
| 640 |
startFound = 0; |
| 641 |
startFrame = -1; |
| 642 |
while( !startFound ){ |
| 643 |
|
| 644 |
startFrame++; |
| 645 |
|
| 646 |
if(startFrame >= nFrames){ |
| 647 |
|
| 648 |
fprintf( stderr, |
| 649 |
"Start Time, %G, was not found in the dump file.\n", |
| 650 |
startTime ); |
| 651 |
exit(0); |
| 652 |
} |
| 653 |
|
| 654 |
if(startTime <= frameTimes[startFrame]) |
| 655 |
startFound = 1; |
| 656 |
|
| 657 |
|
| 658 |
} |
| 659 |
|
| 660 |
avg = 0.0; |
| 661 |
count = 0; |
| 662 |
for(i=startFrame;i<nFrames;i++){ |
| 663 |
avg += posArray[i].Hmat[0][0] * posArray[i].Hmat[1][1]; |
| 664 |
count++; |
| 665 |
} |
| 666 |
avg /= (double)count; |
| 667 |
|
| 668 |
return avg; |
| 669 |
} |
