| 1 |
#include <iostream> |
| 2 |
#include <cmath> |
| 3 |
|
| 4 |
#include <stdio.h> |
| 5 |
#include <stdlib.h> |
| 6 |
#include <string.h> |
| 7 |
#include <unistd.h> |
| 8 |
#include <sys/types.h> |
| 9 |
#include <sys/stat.h> |
| 10 |
|
| 11 |
#include "ReadWrite.hpp" |
| 12 |
#include "simError.h" |
| 13 |
|
| 14 |
|
| 15 |
InitializeFromFile :: InitializeFromFile( char *in_name ){ |
| 16 |
#ifdef IS_MPI |
| 17 |
if (worldRank == 0) { |
| 18 |
#endif |
| 19 |
|
| 20 |
c_in_file = fopen(in_name, "r"); |
| 21 |
if(c_in_file == NULL){ |
| 22 |
sprintf(painCave.errMsg, |
| 23 |
"Cannot open file: %s\n", in_name); |
| 24 |
painCave.isFatal = 1; |
| 25 |
simError(); |
| 26 |
} |
| 27 |
|
| 28 |
strcpy( c_in_name, in_name); |
| 29 |
#ifdef IS_MPI |
| 30 |
} |
| 31 |
strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
| 32 |
MPIcheckPoint(); |
| 33 |
#endif |
| 34 |
return; |
| 35 |
} |
| 36 |
|
| 37 |
InitializeFromFile :: ~InitializeFromFile( ){ |
| 38 |
#ifdef IS_MPI |
| 39 |
if (worldRank == 0) { |
| 40 |
#endif |
| 41 |
int error; |
| 42 |
error = fclose( c_in_file ); |
| 43 |
if( error ){ |
| 44 |
sprintf( painCave.errMsg, |
| 45 |
"Error closing %s\n", c_in_name ); |
| 46 |
simError(); |
| 47 |
} |
| 48 |
#ifdef IS_MPI |
| 49 |
} |
| 50 |
strcpy( checkPointMsg, "Infile closed successfully." ); |
| 51 |
MPIcheckPoint(); |
| 52 |
#endif |
| 53 |
|
| 54 |
return; |
| 55 |
} |
| 56 |
|
| 57 |
|
| 58 |
void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
| 59 |
|
| 60 |
int i; // loop counter |
| 61 |
|
| 62 |
int n_atoms; // the number of atoms |
| 63 |
char read_buffer[2000]; //the line buffer for reading |
| 64 |
#ifdef IS_MPI |
| 65 |
char send_buffer[2000]; |
| 66 |
#endif |
| 67 |
|
| 68 |
char *eof_test; // ptr to see when we reach the end of the file |
| 69 |
char *foo; // the pointer to the current string token |
| 70 |
|
| 71 |
double rx, ry, rz; // position place holders |
| 72 |
double vx, vy, vz; // velocity placeholders |
| 73 |
double q[4]; // the quaternions |
| 74 |
double jx, jy, jz; // angular velocity placeholders; |
| 75 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
| 76 |
|
| 77 |
entry_plug = the_entry_plug |
| 78 |
|
| 79 |
|
| 80 |
#ifndef IS_MPI |
| 81 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 82 |
if( eof_test == NULL ){ |
| 83 |
std::cerr << "error reading 1st line of" << c_in_name << "\n"; |
| 84 |
} |
| 85 |
|
| 86 |
(void)sscanf(read_buffer, "%d", &n_atoms); |
| 87 |
|
| 88 |
Atom **atoms = entry_plug->atoms; |
| 89 |
DirectionalAtom* dAtom; |
| 90 |
|
| 91 |
if( n_atoms != entry_plug->n_atoms ){ |
| 92 |
sprintf( painCave.errMsg, |
| 93 |
"Initialize from File error. %s n_atoms, %d, " |
| 94 |
"does not match the BASS file's n_atoms, %d.\n", |
| 95 |
c_in_name, n_atoms, entry_plug->n_atoms ); |
| 96 |
painCave.isFatal = 1; |
| 97 |
simError(); |
| 98 |
} |
| 99 |
|
| 100 |
//read and toss the comment line |
| 101 |
|
| 102 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 103 |
if(eof_test == NULL){ |
| 104 |
sprintf( painCave.errMsg, |
| 105 |
"error in reading commment in %s\n", c_in_name); |
| 106 |
painCave.isFatal = 1; |
| 107 |
simError(); |
| 108 |
} |
| 109 |
|
| 110 |
for( i=0; i < n_atoms; i++){ |
| 111 |
|
| 112 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 113 |
if(eof_test == NULL){ |
| 114 |
sprintf(painCave.errMsg, |
| 115 |
"error in reading file %s\n" |
| 116 |
"natoms = %d; index = %d\n" |
| 117 |
"error reading the line from the file.\n", |
| 118 |
c_in_name, n_atoms, i ); |
| 119 |
painCave.isFatal = 1; |
| 120 |
simError(); |
| 121 |
} |
| 122 |
|
| 123 |
foo = strtok(read_buffer, " ,;\t"); |
| 124 |
|
| 125 |
// check the atom name to the current atom |
| 126 |
|
| 127 |
if( strcmp( foo, atoms[i]->getType() ) ){ |
| 128 |
sprintf( painCave.errMsg, |
| 129 |
"Initialize from file error. Atom %s at index %d " |
| 130 |
"in file %s does not" |
| 131 |
" match the BASS atom %s.\n", |
| 132 |
foo, i, c_in_name, atoms[i]->getType() ); |
| 133 |
painCave.isFatal = 1; |
| 134 |
simError(); |
| 135 |
} |
| 136 |
|
| 137 |
// get the positions |
| 138 |
|
| 139 |
foo = strtok(NULL, " ,;\t"); |
| 140 |
if(foo == NULL){ |
| 141 |
sprintf( painCave.errMsg, |
| 142 |
"error in reading postition x from %s\n" |
| 143 |
"natoms = %d, index = %d\n", |
| 144 |
c_in_name, n_atoms, i ); |
| 145 |
painCave.isFatal = 1; |
| 146 |
simError(); |
| 147 |
} |
| 148 |
(void)sscanf( foo, "%lf", &rx ); |
| 149 |
|
| 150 |
foo = strtok(NULL, " ,;\t"); |
| 151 |
if(foo == NULL){ |
| 152 |
sprintf( painCave.errMsg, |
| 153 |
"error in reading postition y from %s\n" |
| 154 |
"natoms = %d, index = %d\n", |
| 155 |
c_in_name, n_atoms, i ); |
| 156 |
painCave.isFatal = 1; |
| 157 |
simError(); |
| 158 |
} |
| 159 |
(void)sscanf( foo, "%lf", &ry ); |
| 160 |
|
| 161 |
foo = strtok(NULL, " ,;\t"); |
| 162 |
if(foo == NULL){ |
| 163 |
sprintf( painCave.errMsg, |
| 164 |
"error in reading postition z from %s\n" |
| 165 |
"natoms = %d, index = %d\n", |
| 166 |
c_in_name, n_atoms, i ); |
| 167 |
painCave.isFatal = 1; |
| 168 |
simError(); |
| 169 |
} |
| 170 |
(void)sscanf( foo, "%lf", &rz ); |
| 171 |
|
| 172 |
// get the velocities |
| 173 |
|
| 174 |
foo = strtok(NULL, " ,;\t"); |
| 175 |
if(foo == NULL){ |
| 176 |
sprintf( painCave.errMsg, |
| 177 |
"error in reading velocity x from %s\n" |
| 178 |
"natoms = %d, index = %d\n", |
| 179 |
c_in_name, n_atoms, i ); |
| 180 |
painCave.isFatal = 1; |
| 181 |
simError(); |
| 182 |
} |
| 183 |
(void)sscanf( foo, "%lf", &vx ); |
| 184 |
|
| 185 |
foo = strtok(NULL, " ,;\t"); |
| 186 |
if(foo == NULL){ |
| 187 |
sprintf( painCave.errMsg, |
| 188 |
"error in reading velocity y from %s\n" |
| 189 |
"natoms = %d, index = %d\n", |
| 190 |
c_in_name, n_atoms, i ); |
| 191 |
painCave.isFatal = 1; |
| 192 |
simError(); |
| 193 |
} |
| 194 |
(void)sscanf( foo, "%lf", &vy ); |
| 195 |
|
| 196 |
foo = strtok(NULL, " ,;\t"); |
| 197 |
if(foo == NULL){ |
| 198 |
sprintf( painCave.errMsg, |
| 199 |
"error in reading velocity z from %s\n" |
| 200 |
"natoms = %d, index = %d\n", |
| 201 |
c_in_name, n_atoms, i ); |
| 202 |
painCave.isFatal = 1; |
| 203 |
simError(); |
| 204 |
} |
| 205 |
(void)sscanf( foo, "%lf", &vz ); |
| 206 |
|
| 207 |
|
| 208 |
// get the quaternions |
| 209 |
|
| 210 |
if( atoms[i]->isDirectional() ){ |
| 211 |
|
| 212 |
foo = strtok(NULL, " ,;\t"); |
| 213 |
if(foo == NULL){ |
| 214 |
sprintf(painCave.errMsg, |
| 215 |
"error in reading quaternion 0 from %s\n" |
| 216 |
"natoms = %d, index = %d\n", |
| 217 |
c_in_name, n_atoms, i ); |
| 218 |
painCave.isFatal = 1; |
| 219 |
simError(); |
| 220 |
} |
| 221 |
(void)sscanf( foo, "%lf", &q[0] ); |
| 222 |
|
| 223 |
foo = strtok(NULL, " ,;\t"); |
| 224 |
if(foo == NULL){ |
| 225 |
sprintf( painCave.errMsg, |
| 226 |
"error in reading quaternion 1 from %s\n" |
| 227 |
"natoms = %d, index = %d\n", |
| 228 |
c_in_name, n_atoms, i ); |
| 229 |
painCave.isFatal = 1; |
| 230 |
simError(); |
| 231 |
} |
| 232 |
(void)sscanf( foo, "%lf", &q[1] ); |
| 233 |
|
| 234 |
foo = strtok(NULL, " ,;\t"); |
| 235 |
if(foo == NULL){ |
| 236 |
sprintf( painCave.errMsg, |
| 237 |
"error in reading quaternion 2 from %s\n" |
| 238 |
"natoms = %d, index = %d\n", |
| 239 |
c_in_name, n_atoms, i ); |
| 240 |
painCave.isFatal = 1; |
| 241 |
simError(); |
| 242 |
} |
| 243 |
(void)sscanf( foo, "%lf", &q[2] ); |
| 244 |
|
| 245 |
foo = strtok(NULL, " ,;\t"); |
| 246 |
if(foo == NULL){ |
| 247 |
sprintf( painCave.errMsg, |
| 248 |
"error in reading quaternion 3 from %s\n" |
| 249 |
"natoms = %d, index = %d\n", |
| 250 |
c_in_name, n_atoms, i ); |
| 251 |
painCave.isFatal = 1; |
| 252 |
simError(); |
| 253 |
} |
| 254 |
(void)sscanf( foo, "%lf", &q[3] ); |
| 255 |
|
| 256 |
// get the angular velocities |
| 257 |
|
| 258 |
foo = strtok(NULL, " ,;\t"); |
| 259 |
if(foo == NULL){ |
| 260 |
sprintf( painCave.errMsg, |
| 261 |
"error in reading angular momentum jx from %s\n" |
| 262 |
"natoms = %d, index = %d\n", |
| 263 |
c_in_name, n_atoms, i ); |
| 264 |
painCave.isFatal = 1; |
| 265 |
simError(); |
| 266 |
} |
| 267 |
(void)sscanf( foo, "%lf", &jx ); |
| 268 |
|
| 269 |
foo = strtok(NULL, " ,;\t"); |
| 270 |
if(foo == NULL){ |
| 271 |
sprintf( painCave.errMsg, |
| 272 |
"error in reading angular momentum jy from %s\n" |
| 273 |
"natoms = %d, index = %d\n", |
| 274 |
c_in_name, n_atoms, i ); |
| 275 |
painCave.isFatal = 1; |
| 276 |
simError(); |
| 277 |
} |
| 278 |
(void)sscanf( foo, "%lf", &jy ); |
| 279 |
|
| 280 |
foo = strtok(NULL, " ,;\t"); |
| 281 |
if(foo == NULL){ |
| 282 |
sprintf( painCave.errMsg, |
| 283 |
"error in reading angular momentum jz from %s\n" |
| 284 |
"natoms = %d, index = %d\n", |
| 285 |
c_in_name, n_atoms, i ); |
| 286 |
painCave.isFatal = 1; |
| 287 |
simError(); |
| 288 |
} |
| 289 |
(void)sscanf( foo, "%lf", &jz ); |
| 290 |
|
| 291 |
dAtom = ( DirectionalAtom* )atoms[i]; |
| 292 |
|
| 293 |
// check that the quaternion vector is normalized |
| 294 |
|
| 295 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
| 296 |
|
| 297 |
qLength = sqrt( qSqr ); |
| 298 |
q[0] = q[0] / qLength; |
| 299 |
q[1] = q[1] / qLength; |
| 300 |
q[2] = q[2] / qLength; |
| 301 |
q[3] = q[3] / qLength; |
| 302 |
|
| 303 |
dAtom->setQ( q ); |
| 304 |
|
| 305 |
// add the angular velocities |
| 306 |
|
| 307 |
dAtom->setJx( jx ); |
| 308 |
dAtom->setJy( jy ); |
| 309 |
dAtom->setJz( jz ); |
| 310 |
} |
| 311 |
|
| 312 |
// add the positions and velocities to the atom |
| 313 |
|
| 314 |
atoms[i]->setX( rx ); |
| 315 |
atoms[i]->setY( ry ); |
| 316 |
atoms[i]->setZ( rz ); |
| 317 |
|
| 318 |
atoms[i]->set_vx( vx ); |
| 319 |
atoms[i]->set_vy( vy ); |
| 320 |
atoms[i]->set_vz( vz ); |
| 321 |
|
| 322 |
} |
| 323 |
|
| 324 |
|
| 325 |
// MPI Section of code.......... |
| 326 |
#else //IS_MPI |
| 327 |
|
| 328 |
|
| 329 |
|
| 330 |
|
| 331 |
if (worldRank == 0) { |
| 332 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 333 |
if( eof_test == NULL ){ |
| 334 |
sprintf( painCave.errMsg, |
| 335 |
"Error reading 1st line of %d \n ",c_in_name); |
| 336 |
painCave.isFatal = 1; |
| 337 |
simError(); |
| 338 |
} |
| 339 |
|
| 340 |
(void)sscanf(read_buffer, "%d", &n_atoms); |
| 341 |
|
| 342 |
Atom **atoms = entry_plug->atoms; |
| 343 |
DirectionalAtom* dAtom; |
| 344 |
|
| 345 |
if( n_atoms != entry_plug->n_atoms ){ |
| 346 |
sprintf( painCave.errMsg, |
| 347 |
"Initialize from File error. %s n_atoms, %d, " |
| 348 |
"does not match the BASS file's n_atoms, %d.\n", |
| 349 |
c_in_name, n_atoms, entry_plug->n_atoms ); |
| 350 |
painCave.isFatal = 1; |
| 351 |
simError(); |
| 352 |
} |
| 353 |
|
| 354 |
//read and toss the comment line |
| 355 |
|
| 356 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 357 |
if(eof_test == NULL){ |
| 358 |
sprintf( painCave.errMsg, |
| 359 |
"error in reading commment in %s\n", c_in_name); |
| 360 |
painCave.isFatal = 1; |
| 361 |
simError(); |
| 362 |
} |
| 363 |
} |
| 364 |
for( i=0; i < n_atoms; i++){ |
| 365 |
|
| 366 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 367 |
if(eof_test == NULL){ |
| 368 |
sprintf(painCave.errMsg, |
| 369 |
"error in reading file %s\n" |
| 370 |
"natoms = %d; index = %d\n" |
| 371 |
"error reading the line from the file.\n", |
| 372 |
c_in_name, n_atoms, i ); |
| 373 |
painCave.isFatal = 1; |
| 374 |
simError(); |
| 375 |
} |
| 376 |
|
| 377 |
foo = strtok(read_buffer, " ,;\t"); |
| 378 |
|
| 379 |
// check the atom name to the current atom |
| 380 |
|
| 381 |
if( strcmp( foo, atoms[i]->getType() ) ){ |
| 382 |
sprintf( painCave.errMsg, |
| 383 |
"Initialize from file error. Atom %s at index %d " |
| 384 |
"in file %s does not" |
| 385 |
" match the BASS atom %s.\n", |
| 386 |
foo, i, c_in_name, atoms[i]->getType() ); |
| 387 |
painCave.isFatal = 1; |
| 388 |
simError(); |
| 389 |
} |
| 390 |
|
| 391 |
// get the positions |
| 392 |
|
| 393 |
foo = strtok(NULL, " ,;\t"); |
| 394 |
if(foo == NULL){ |
| 395 |
sprintf( painCave.errMsg, |
| 396 |
"error in reading postition x from %s\n" |
| 397 |
"natoms = %d, index = %d\n", |
| 398 |
c_in_name, n_atoms, i ); |
| 399 |
painCave.isFatal = 1; |
| 400 |
simError(); |
| 401 |
} |
| 402 |
(void)sscanf( foo, "%lf", &rx ); |
| 403 |
|
| 404 |
foo = strtok(NULL, " ,;\t"); |
| 405 |
if(foo == NULL){ |
| 406 |
sprintf( painCave.errMsg, |
| 407 |
"error in reading postition y from %s\n" |
| 408 |
"natoms = %d, index = %d\n", |
| 409 |
c_in_name, n_atoms, i ); |
| 410 |
painCave.isFatal = 1; |
| 411 |
simError(); |
| 412 |
} |
| 413 |
(void)sscanf( foo, "%lf", &ry ); |
| 414 |
|
| 415 |
foo = strtok(NULL, " ,;\t"); |
| 416 |
if(foo == NULL){ |
| 417 |
sprintf( painCave.errMsg, |
| 418 |
"error in reading postition z from %s\n" |
| 419 |
"natoms = %d, index = %d\n", |
| 420 |
c_in_name, n_atoms, i ); |
| 421 |
painCave.isFatal = 1; |
| 422 |
simError(); |
| 423 |
} |
| 424 |
(void)sscanf( foo, "%lf", &rz ); |
| 425 |
|
| 426 |
// get the velocities |
| 427 |
|
| 428 |
foo = strtok(NULL, " ,;\t"); |
| 429 |
if(foo == NULL){ |
| 430 |
sprintf( painCave.errMsg, |
| 431 |
"error in reading velocity x from %s\n" |
| 432 |
"natoms = %d, index = %d\n", |
| 433 |
c_in_name, n_atoms, i ); |
| 434 |
painCave.isFatal = 1; |
| 435 |
simError(); |
| 436 |
} |
| 437 |
(void)sscanf( foo, "%lf", &vx ); |
| 438 |
|
| 439 |
foo = strtok(NULL, " ,;\t"); |
| 440 |
if(foo == NULL){ |
| 441 |
sprintf( painCave.errMsg, |
| 442 |
"error in reading velocity y from %s\n" |
| 443 |
"natoms = %d, index = %d\n", |
| 444 |
c_in_name, n_atoms, i ); |
| 445 |
painCave.isFatal = 1; |
| 446 |
simError(); |
| 447 |
} |
| 448 |
(void)sscanf( foo, "%lf", &vy ); |
| 449 |
|
| 450 |
foo = strtok(NULL, " ,;\t"); |
| 451 |
if(foo == NULL){ |
| 452 |
sprintf( painCave.errMsg, |
| 453 |
"error in reading velocity z from %s\n" |
| 454 |
"natoms = %d, index = %d\n", |
| 455 |
c_in_name, n_atoms, i ); |
| 456 |
painCave.isFatal = 1; |
| 457 |
simError(); |
| 458 |
} |
| 459 |
(void)sscanf( foo, "%lf", &vz ); |
| 460 |
|
| 461 |
|
| 462 |
// get the quaternions |
| 463 |
|
| 464 |
if( atoms[i]->isDirectional() ){ |
| 465 |
|
| 466 |
foo = strtok(NULL, " ,;\t"); |
| 467 |
if(foo == NULL){ |
| 468 |
sprintf(painCave.errMsg, |
| 469 |
"error in reading quaternion 0 from %s\n" |
| 470 |
"natoms = %d, index = %d\n", |
| 471 |
c_in_name, n_atoms, i ); |
| 472 |
painCave.isFatal = 1; |
| 473 |
simError(); |
| 474 |
} |
| 475 |
(void)sscanf( foo, "%lf", &q[0] ); |
| 476 |
|
| 477 |
foo = strtok(NULL, " ,;\t"); |
| 478 |
if(foo == NULL){ |
| 479 |
sprintf( painCave.errMsg, |
| 480 |
"error in reading quaternion 1 from %s\n" |
| 481 |
"natoms = %d, index = %d\n", |
| 482 |
c_in_name, n_atoms, i ); |
| 483 |
painCave.isFatal = 1; |
| 484 |
simError(); |
| 485 |
} |
| 486 |
(void)sscanf( foo, "%lf", &q[1] ); |
| 487 |
|
| 488 |
foo = strtok(NULL, " ,;\t"); |
| 489 |
if(foo == NULL){ |
| 490 |
sprintf( painCave.errMsg, |
| 491 |
"error in reading quaternion 2 from %s\n" |
| 492 |
"natoms = %d, index = %d\n", |
| 493 |
c_in_name, n_atoms, i ); |
| 494 |
painCave.isFatal = 1; |
| 495 |
simError(); |
| 496 |
} |
| 497 |
(void)sscanf( foo, "%lf", &q[2] ); |
| 498 |
|
| 499 |
foo = strtok(NULL, " ,;\t"); |
| 500 |
if(foo == NULL){ |
| 501 |
sprintf( painCave.errMsg, |
| 502 |
"error in reading quaternion 3 from %s\n" |
| 503 |
"natoms = %d, index = %d\n", |
| 504 |
c_in_name, n_atoms, i ); |
| 505 |
painCave.isFatal = 1; |
| 506 |
simError(); |
| 507 |
} |
| 508 |
(void)sscanf( foo, "%lf", &q[3] ); |
| 509 |
|
| 510 |
// get the angular velocities |
| 511 |
|
| 512 |
foo = strtok(NULL, " ,;\t"); |
| 513 |
if(foo == NULL){ |
| 514 |
sprintf( painCave.errMsg, |
| 515 |
"error in reading angular momentum jx from %s\n" |
| 516 |
"natoms = %d, index = %d\n", |
| 517 |
c_in_name, n_atoms, i ); |
| 518 |
painCave.isFatal = 1; |
| 519 |
simError(); |
| 520 |
} |
| 521 |
(void)sscanf( foo, "%lf", &jx ); |
| 522 |
|
| 523 |
foo = strtok(NULL, " ,;\t"); |
| 524 |
if(foo == NULL){ |
| 525 |
sprintf( painCave.errMsg, |
| 526 |
"error in reading angular momentum jy from %s\n" |
| 527 |
"natoms = %d, index = %d\n", |
| 528 |
c_in_name, n_atoms, i ); |
| 529 |
painCave.isFatal = 1; |
| 530 |
simError(); |
| 531 |
} |
| 532 |
(void)sscanf( foo, "%lf", &jy ); |
| 533 |
|
| 534 |
foo = strtok(NULL, " ,;\t"); |
| 535 |
if(foo == NULL){ |
| 536 |
sprintf( painCave.errMsg, |
| 537 |
"error in reading angular momentum jz from %s\n" |
| 538 |
"natoms = %d, index = %d\n", |
| 539 |
c_in_name, n_atoms, i ); |
| 540 |
painCave.isFatal = 1; |
| 541 |
simError(); |
| 542 |
} |
| 543 |
(void)sscanf( foo, "%lf", &jz ); |
| 544 |
|
| 545 |
dAtom = ( DirectionalAtom* )atoms[i]; |
| 546 |
|
| 547 |
// check that the quaternion vector is normalized |
| 548 |
|
| 549 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
| 550 |
|
| 551 |
qLength = sqrt( qSqr ); |
| 552 |
q[0] = q[0] / qLength; |
| 553 |
q[1] = q[1] / qLength; |
| 554 |
q[2] = q[2] / qLength; |
| 555 |
q[3] = q[3] / qLength; |
| 556 |
|
| 557 |
dAtom->setQ( q ); |
| 558 |
|
| 559 |
// add the angular velocities |
| 560 |
|
| 561 |
dAtom->setJx( jx ); |
| 562 |
dAtom->setJy( jy ); |
| 563 |
dAtom->setJz( jz ); |
| 564 |
} |
| 565 |
|
| 566 |
// add the positions and velocities to the atom |
| 567 |
|
| 568 |
atoms[i]->setX( rx ); |
| 569 |
atoms[i]->setY( ry ); |
| 570 |
atoms[i]->setZ( rz ); |
| 571 |
|
| 572 |
atoms[i]->set_vx( vx ); |
| 573 |
atoms[i]->set_vy( vy ); |
| 574 |
atoms[i]->set_vz( vz ); |
| 575 |
|
| 576 |
} |
| 577 |
#endif |
| 578 |
} |
| 579 |
|
| 580 |
char* IntitializeFromFile::parseDumpLine(char* readLine); |
