| 1 |
#define _FILE_OFFSET_BITS 64 |
| 2 |
|
| 3 |
#include <iostream> |
| 4 |
#include <cmath> |
| 5 |
#include <vector> |
| 6 |
|
| 7 |
#include <stdio.h> |
| 8 |
#include <stdlib.h> |
| 9 |
#include <string.h> |
| 10 |
#include <unistd.h> |
| 11 |
#include <sys/types.h> |
| 12 |
#include <sys/stat.h> |
| 13 |
|
| 14 |
#include "ReadWrite.hpp" |
| 15 |
#include "simError.h" |
| 16 |
|
| 17 |
#ifdef IS_MPI |
| 18 |
#include <mpi.h> |
| 19 |
#include "mpiSimulation.hpp" |
| 20 |
#define TAKE_THIS_TAG_CHAR 0 |
| 21 |
#define TAKE_THIS_TAG_INT 1 |
| 22 |
|
| 23 |
namespace dumpRead{ |
| 24 |
void nodeZeroError( void ); |
| 25 |
void anonymousNodeDie( void ); |
| 26 |
|
| 27 |
|
| 28 |
class FilePos{ |
| 29 |
public: |
| 30 |
|
| 31 |
|
| 32 |
private: |
| 33 |
|
| 34 |
|
| 35 |
}; |
| 36 |
|
| 37 |
vector<FilePos> frameStart; |
| 38 |
} |
| 39 |
|
| 40 |
using namespace dumpRead; |
| 41 |
|
| 42 |
#endif // is_mpi |
| 43 |
|
| 44 |
DumpReader :: DumpReader( char *in_name ){ |
| 45 |
#ifdef IS_MPI |
| 46 |
if (worldRank == 0) { |
| 47 |
#endif |
| 48 |
|
| 49 |
c_in_file = fopen(in_name, "r"); |
| 50 |
if(c_in_file == NULL){ |
| 51 |
sprintf(painCave.errMsg, |
| 52 |
"Cannot open file: %s\n", in_name); |
| 53 |
painCave.isFatal = 1; |
| 54 |
simError(); |
| 55 |
} |
| 56 |
|
| 57 |
strcpy( c_in_name, in_name); |
| 58 |
#ifdef IS_MPI |
| 59 |
} |
| 60 |
strcpy( checkPointMsg, "Dump file opened for reading successfully." ); |
| 61 |
MPIcheckPoint(); |
| 62 |
#endif |
| 63 |
return; |
| 64 |
} |
| 65 |
|
| 66 |
DumpReader :: ~DumpReader( ){ |
| 67 |
#ifdef IS_MPI |
| 68 |
if (worldRank == 0) { |
| 69 |
#endif |
| 70 |
int error; |
| 71 |
error = fclose( c_in_file ); |
| 72 |
if( error ){ |
| 73 |
sprintf( painCave.errMsg, |
| 74 |
"Error closing %s\n", c_in_name ); |
| 75 |
simError(); |
| 76 |
} |
| 77 |
#ifdef IS_MPI |
| 78 |
} |
| 79 |
strcpy( checkPointMsg, "Dump file closed successfully." ); |
| 80 |
MPIcheckPoint(); |
| 81 |
#endif |
| 82 |
|
| 83 |
return; |
| 84 |
} |
| 85 |
|
| 86 |
|
| 87 |
|
| 88 |
void DumpReader :: getFrame( SimInfo* the_simnfo, int whichFrame){ |
| 89 |
|
| 90 |
int i, j, done, which_node, which_atom; // loop counter |
| 91 |
|
| 92 |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 93 |
int n_atoms; // the number of atoms |
| 94 |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
| 95 |
#ifdef IS_MPI |
| 96 |
char send_buffer[BUFFERSIZE]; |
| 97 |
#endif |
| 98 |
|
| 99 |
char *eof_test; // ptr to see when we reach the end of the file |
| 100 |
char *parseErr; |
| 101 |
int procIndex; |
| 102 |
double boxMat[9]; |
| 103 |
double theBoxMat3[3][3]; |
| 104 |
|
| 105 |
simnfo = the_simnfo; |
| 106 |
|
| 107 |
#ifndef IS_MPI |
| 108 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 109 |
if( eof_test == NULL ){ |
| 110 |
sprintf( painCave.errMsg, |
| 111 |
"DumpReader error: error reading 1st line of \"%s\"\n", |
| 112 |
c_in_name ); |
| 113 |
painCave.isFatal = 1; |
| 114 |
simError(); |
| 115 |
} |
| 116 |
|
| 117 |
n_atoms = atoi( read_buffer ); |
| 118 |
|
| 119 |
Atom **atoms = simnfo->atoms; |
| 120 |
DirectionalAtom* dAtom; |
| 121 |
|
| 122 |
if( n_atoms != simnfo->n_atoms ){ |
| 123 |
sprintf( painCave.errMsg, |
| 124 |
"DumpReader error. %s n_atoms, %d, " |
| 125 |
"does not match the BASS file's n_atoms, %d.\n", |
| 126 |
c_in_name, n_atoms, simnfo->n_atoms ); |
| 127 |
painCave.isFatal = 1; |
| 128 |
simError(); |
| 129 |
} |
| 130 |
|
| 131 |
//read the box mat from the comment line |
| 132 |
|
| 133 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 134 |
if(eof_test == NULL){ |
| 135 |
sprintf( painCave.errMsg, |
| 136 |
"error in reading commment in %s\n", c_in_name); |
| 137 |
painCave.isFatal = 1; |
| 138 |
simError(); |
| 139 |
} |
| 140 |
|
| 141 |
parseErr = parseCommentLine( read_buffer, time, boxMat ); |
| 142 |
if( parseErr != NULL ){ |
| 143 |
strcpy( painCave.errMsg, parseErr ); |
| 144 |
painCave.isFatal = 1; |
| 145 |
simError(); |
| 146 |
} |
| 147 |
|
| 148 |
simnfo->setTime( time ); |
| 149 |
|
| 150 |
for(i=0;i<3;i++) |
| 151 |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
| 152 |
|
| 153 |
|
| 154 |
simnfo->setBoxM( theBoxMat3 ); |
| 155 |
|
| 156 |
|
| 157 |
for( i=0; i < n_atoms; i++){ |
| 158 |
|
| 159 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 160 |
if(eof_test == NULL){ |
| 161 |
sprintf(painCave.errMsg, |
| 162 |
"error in reading file %s\n" |
| 163 |
"natoms = %d; index = %d\n" |
| 164 |
"error reading the line from the file.\n", |
| 165 |
c_in_name, n_atoms, i ); |
| 166 |
painCave.isFatal = 1; |
| 167 |
simError(); |
| 168 |
} |
| 169 |
|
| 170 |
|
| 171 |
parseErr = parseDumpLine( read_buffer, i ); |
| 172 |
if( parseErr != NULL ){ |
| 173 |
strcpy( painCave.errMsg, parseErr ); |
| 174 |
painCave.isFatal = 1; |
| 175 |
simError(); |
| 176 |
} |
| 177 |
} |
| 178 |
|
| 179 |
|
| 180 |
// MPI Section of code.......... |
| 181 |
#else //IS_MPI |
| 182 |
|
| 183 |
// first thing first, suspend fatalities. |
| 184 |
painCave.isEventLoop = 1; |
| 185 |
|
| 186 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
| 187 |
int haveError; |
| 188 |
|
| 189 |
MPI_Status istatus; |
| 190 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
| 191 |
|
| 192 |
|
| 193 |
haveError = 0; |
| 194 |
if (worldRank == 0) { |
| 195 |
|
| 196 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 197 |
if( eof_test == NULL ){ |
| 198 |
sprintf( painCave.errMsg, |
| 199 |
"Error reading 1st line of %d \n ",c_in_name); |
| 200 |
haveError = 1; |
| 201 |
simError(); |
| 202 |
} |
| 203 |
|
| 204 |
n_atoms = atoi( read_buffer ); |
| 205 |
|
| 206 |
Atom **atoms = simnfo->atoms; |
| 207 |
DirectionalAtom* dAtom; |
| 208 |
|
| 209 |
// Check to see that the number of atoms in the intial configuration file is the |
| 210 |
// same as declared in simBass. |
| 211 |
|
| 212 |
if( n_atoms != mpiSim->getTotAtoms() ){ |
| 213 |
sprintf( painCave.errMsg, |
| 214 |
"Initialize from File error. %s n_atoms, %d, " |
| 215 |
"does not match the BASS file's n_atoms, %d.\n", |
| 216 |
c_in_name, n_atoms, simnfo->n_atoms ); |
| 217 |
haveError= 1; |
| 218 |
simError(); |
| 219 |
} |
| 220 |
|
| 221 |
//read the time and boxMat from the comment line |
| 222 |
|
| 223 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 224 |
if(eof_test == NULL){ |
| 225 |
sprintf( painCave.errMsg, |
| 226 |
"error in reading commment in %s\n", c_in_name); |
| 227 |
haveError = 1; |
| 228 |
simError(); |
| 229 |
} |
| 230 |
|
| 231 |
parseErr = parseCommentLine( read_buffer, time, boxMat ); |
| 232 |
if( parseErr != NULL ){ |
| 233 |
strcpy( painCave.errMsg, parseErr ); |
| 234 |
haveError = 1; |
| 235 |
simError(); |
| 236 |
} |
| 237 |
|
| 238 |
MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
| 239 |
|
| 240 |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
| 241 |
|
| 242 |
if(haveError) nodeZeroError(); |
| 243 |
|
| 244 |
for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
| 245 |
|
| 246 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 247 |
if(eof_test == NULL){ |
| 248 |
sprintf(painCave.errMsg, |
| 249 |
"error in reading file %s\n" |
| 250 |
"natoms = %d; index = %d\n" |
| 251 |
"error reading the line from the file.\n", |
| 252 |
c_in_name, n_atoms, i ); |
| 253 |
haveError= 1; |
| 254 |
simError(); |
| 255 |
} |
| 256 |
|
| 257 |
if(haveError) nodeZeroError(); |
| 258 |
|
| 259 |
// Get the Node number which wants this atom: |
| 260 |
which_node = AtomToProcMap[i]; |
| 261 |
if (which_node == 0) { |
| 262 |
parseErr = parseDumpLine( read_buffer, i ); |
| 263 |
if( parseErr != NULL ){ |
| 264 |
strcpy( painCave.errMsg, parseErr ); |
| 265 |
haveError = 1; |
| 266 |
simError(); |
| 267 |
} |
| 268 |
if(haveError) nodeZeroError(); |
| 269 |
} |
| 270 |
|
| 271 |
else { |
| 272 |
|
| 273 |
myStatus = 1; |
| 274 |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
| 275 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 276 |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
| 277 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
| 278 |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
| 279 |
MPI_COMM_WORLD); |
| 280 |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
| 281 |
MPI_COMM_WORLD, &istatus); |
| 282 |
|
| 283 |
if(!myStatus) nodeZeroError(); |
| 284 |
} |
| 285 |
} |
| 286 |
myStatus = -1; |
| 287 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
| 288 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
| 289 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 290 |
} |
| 291 |
|
| 292 |
} else { |
| 293 |
|
| 294 |
MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
| 295 |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
| 296 |
|
| 297 |
done = 0; |
| 298 |
while (!done) { |
| 299 |
|
| 300 |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
| 301 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
| 302 |
|
| 303 |
if(!myStatus) anonymousNodeDie(); |
| 304 |
|
| 305 |
if(myStatus < 0) break; |
| 306 |
|
| 307 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
| 308 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
| 309 |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
| 310 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
| 311 |
|
| 312 |
myStatus = 1; |
| 313 |
parseErr = parseDumpLine( read_buffer, which_atom ); |
| 314 |
if( parseErr != NULL ){ |
| 315 |
strcpy( painCave.errMsg, parseErr ); |
| 316 |
myStatus = 0;; |
| 317 |
simError(); |
| 318 |
} |
| 319 |
|
| 320 |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
| 321 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 322 |
|
| 323 |
} |
| 324 |
} |
| 325 |
|
| 326 |
// last thing last, enable fatalities. |
| 327 |
painCave.isEventLoop = 0; |
| 328 |
|
| 329 |
simnfo->setTime( time ); |
| 330 |
|
| 331 |
for(i=0;i<3;i++) |
| 332 |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
| 333 |
|
| 334 |
simnfo->setBoxM( theBoxMat3 ); |
| 335 |
|
| 336 |
|
| 337 |
#endif |
| 338 |
} |
| 339 |
|
| 340 |
char* DumpReader::parseDumpLine(char* readLine, int globalIndex){ |
| 341 |
|
| 342 |
char *foo; // the pointer to the current string token |
| 343 |
|
| 344 |
double rx, ry, rz; // position place holders |
| 345 |
double vx, vy, vz; // velocity placeholders |
| 346 |
double q[4]; // the quaternions |
| 347 |
double jx, jy, jz; // angular velocity placeholders; |
| 348 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
| 349 |
|
| 350 |
Atom **atoms = simnfo->atoms; |
| 351 |
DirectionalAtom* dAtom; |
| 352 |
|
| 353 |
int j, n_atoms, atomIndex; |
| 354 |
|
| 355 |
#ifdef IS_MPI |
| 356 |
n_atoms = mpiSim->getTotAtoms(); |
| 357 |
atomIndex=-1; |
| 358 |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
| 359 |
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
| 360 |
} |
| 361 |
if (atomIndex == -1) { |
| 362 |
sprintf( painCave.errMsg, |
| 363 |
"Initialize from file error. Atom at index %d " |
| 364 |
"in file %s does not exist on processor %d .\n", |
| 365 |
globalIndex, c_in_name, mpiSim->getMyNode() ); |
| 366 |
return strdup( painCave.errMsg ); |
| 367 |
} |
| 368 |
#else |
| 369 |
n_atoms = simnfo->n_atoms; |
| 370 |
atomIndex = globalIndex; |
| 371 |
#endif // is_mpi |
| 372 |
|
| 373 |
// set the string tokenizer |
| 374 |
|
| 375 |
foo = strtok(readLine, " ,;\t"); |
| 376 |
|
| 377 |
// check the atom name to the current atom |
| 378 |
|
| 379 |
if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
| 380 |
sprintf( painCave.errMsg, |
| 381 |
"Initialize from file error. Atom %s at index %d " |
| 382 |
"in file %s does not" |
| 383 |
" match the BASS atom %s.\n", |
| 384 |
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
| 385 |
return strdup( painCave.errMsg ); |
| 386 |
} |
| 387 |
|
| 388 |
// get the positions |
| 389 |
|
| 390 |
foo = strtok(NULL, " ,;\t"); |
| 391 |
if(foo == NULL){ |
| 392 |
sprintf( painCave.errMsg, |
| 393 |
"error in reading postition x from %s\n" |
| 394 |
"natoms = %d, index = %d\n", |
| 395 |
c_in_name, n_atoms, atomIndex ); |
| 396 |
return strdup( painCave.errMsg ); |
| 397 |
} |
| 398 |
rx = atof( foo ); |
| 399 |
|
| 400 |
foo = strtok(NULL, " ,;\t"); |
| 401 |
if(foo == NULL){ |
| 402 |
sprintf( painCave.errMsg, |
| 403 |
"error in reading postition y from %s\n" |
| 404 |
"natoms = %d, index = %d\n", |
| 405 |
c_in_name, n_atoms, atomIndex ); |
| 406 |
return strdup( painCave.errMsg ); |
| 407 |
} |
| 408 |
ry = atof( foo ); |
| 409 |
|
| 410 |
foo = strtok(NULL, " ,;\t"); |
| 411 |
if(foo == NULL){ |
| 412 |
sprintf( painCave.errMsg, |
| 413 |
"error in reading postition z from %s\n" |
| 414 |
"natoms = %d, index = %d\n", |
| 415 |
c_in_name, n_atoms, atomIndex ); |
| 416 |
return strdup( painCave.errMsg ); |
| 417 |
} |
| 418 |
rz = atof( foo ); |
| 419 |
|
| 420 |
|
| 421 |
// get the velocities |
| 422 |
|
| 423 |
foo = strtok(NULL, " ,;\t"); |
| 424 |
if(foo == NULL){ |
| 425 |
sprintf( painCave.errMsg, |
| 426 |
"error in reading velocity x from %s\n" |
| 427 |
"natoms = %d, index = %d\n", |
| 428 |
c_in_name, n_atoms, atomIndex ); |
| 429 |
return strdup( painCave.errMsg ); |
| 430 |
} |
| 431 |
vx = atof( foo ); |
| 432 |
|
| 433 |
foo = strtok(NULL, " ,;\t"); |
| 434 |
if(foo == NULL){ |
| 435 |
sprintf( painCave.errMsg, |
| 436 |
"error in reading velocity y from %s\n" |
| 437 |
"natoms = %d, index = %d\n", |
| 438 |
c_in_name, n_atoms, atomIndex ); |
| 439 |
return strdup( painCave.errMsg ); |
| 440 |
} |
| 441 |
vy = atof( foo ); |
| 442 |
|
| 443 |
foo = strtok(NULL, " ,;\t"); |
| 444 |
if(foo == NULL){ |
| 445 |
sprintf( painCave.errMsg, |
| 446 |
"error in reading velocity z from %s\n" |
| 447 |
"natoms = %d, index = %d\n", |
| 448 |
c_in_name, n_atoms, atomIndex ); |
| 449 |
return strdup( painCave.errMsg ); |
| 450 |
} |
| 451 |
vz = atof( foo ); |
| 452 |
|
| 453 |
|
| 454 |
// get the quaternions |
| 455 |
|
| 456 |
if( atoms[atomIndex]->isDirectional() ){ |
| 457 |
|
| 458 |
foo = strtok(NULL, " ,;\t"); |
| 459 |
if(foo == NULL){ |
| 460 |
sprintf(painCave.errMsg, |
| 461 |
"error in reading quaternion 0 from %s\n" |
| 462 |
"natoms = %d, index = %d\n", |
| 463 |
c_in_name, n_atoms, atomIndex ); |
| 464 |
return strdup( painCave.errMsg ); |
| 465 |
} |
| 466 |
q[0] = atof( foo ); |
| 467 |
|
| 468 |
foo = strtok(NULL, " ,;\t"); |
| 469 |
if(foo == NULL){ |
| 470 |
sprintf( painCave.errMsg, |
| 471 |
"error in reading quaternion 1 from %s\n" |
| 472 |
"natoms = %d, index = %d\n", |
| 473 |
c_in_name, n_atoms, atomIndex ); |
| 474 |
return strdup( painCave.errMsg ); |
| 475 |
} |
| 476 |
q[1] = atof( foo ); |
| 477 |
|
| 478 |
foo = strtok(NULL, " ,;\t"); |
| 479 |
if(foo == NULL){ |
| 480 |
sprintf( painCave.errMsg, |
| 481 |
"error in reading quaternion 2 from %s\n" |
| 482 |
"natoms = %d, index = %d\n", |
| 483 |
c_in_name, n_atoms, atomIndex ); |
| 484 |
return strdup( painCave.errMsg ); |
| 485 |
} |
| 486 |
q[2] = atof( foo ); |
| 487 |
|
| 488 |
foo = strtok(NULL, " ,;\t"); |
| 489 |
if(foo == NULL){ |
| 490 |
sprintf( painCave.errMsg, |
| 491 |
"error in reading quaternion 3 from %s\n" |
| 492 |
"natoms = %d, index = %d\n", |
| 493 |
c_in_name, n_atoms, atomIndex ); |
| 494 |
return strdup( painCave.errMsg ); |
| 495 |
} |
| 496 |
q[3] = atof( foo ); |
| 497 |
|
| 498 |
// get the angular velocities |
| 499 |
|
| 500 |
foo = strtok(NULL, " ,;\t"); |
| 501 |
if(foo == NULL){ |
| 502 |
sprintf( painCave.errMsg, |
| 503 |
"error in reading angular momentum jx from %s\n" |
| 504 |
"natoms = %d, index = %d\n", |
| 505 |
c_in_name, n_atoms, atomIndex ); |
| 506 |
return strdup( painCave.errMsg ); |
| 507 |
} |
| 508 |
jx = atof( foo ); |
| 509 |
|
| 510 |
foo = strtok(NULL, " ,;\t"); |
| 511 |
if(foo == NULL){ |
| 512 |
sprintf( painCave.errMsg, |
| 513 |
"error in reading angular momentum jy from %s\n" |
| 514 |
"natoms = %d, index = %d\n", |
| 515 |
c_in_name, n_atoms, atomIndex ); |
| 516 |
return strdup( painCave.errMsg ); |
| 517 |
} |
| 518 |
jy = atof(foo ); |
| 519 |
|
| 520 |
foo = strtok(NULL, " ,;\t"); |
| 521 |
if(foo == NULL){ |
| 522 |
sprintf( painCave.errMsg, |
| 523 |
"error in reading angular momentum jz from %s\n" |
| 524 |
"natoms = %d, index = %d\n", |
| 525 |
c_in_name, n_atoms, atomIndex ); |
| 526 |
return strdup( painCave.errMsg ); |
| 527 |
} |
| 528 |
jz = atof( foo ); |
| 529 |
|
| 530 |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
| 531 |
|
| 532 |
// check that the quaternion vector is normalized |
| 533 |
|
| 534 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
| 535 |
|
| 536 |
qLength = sqrt( qSqr ); |
| 537 |
q[0] = q[0] / qLength; |
| 538 |
q[1] = q[1] / qLength; |
| 539 |
q[2] = q[2] / qLength; |
| 540 |
q[3] = q[3] / qLength; |
| 541 |
|
| 542 |
dAtom->setQ( q ); |
| 543 |
|
| 544 |
// add the angular velocities |
| 545 |
|
| 546 |
dAtom->setJx( jx ); |
| 547 |
dAtom->setJy( jy ); |
| 548 |
dAtom->setJz( jz ); |
| 549 |
} |
| 550 |
|
| 551 |
// add the positions and velocities to the atom |
| 552 |
|
| 553 |
atoms[atomIndex]->setX( rx ); |
| 554 |
atoms[atomIndex]->setY( ry ); |
| 555 |
atoms[atomIndex]->setZ( rz ); |
| 556 |
|
| 557 |
atoms[atomIndex]->set_vx( vx ); |
| 558 |
atoms[atomIndex]->set_vy( vy ); |
| 559 |
atoms[atomIndex]->set_vz( vz ); |
| 560 |
|
| 561 |
return NULL; |
| 562 |
} |
| 563 |
|
| 564 |
|
| 565 |
char* DumpReader::parseCommentLine(char* readLine, double time, |
| 566 |
double boxMat[9]){ |
| 567 |
|
| 568 |
char *foo; // the pointer to the current string token |
| 569 |
int j; |
| 570 |
|
| 571 |
// set the string tokenizer |
| 572 |
|
| 573 |
foo = strtok(readLine, " ,;\t"); |
| 574 |
if(foo == NULL){ |
| 575 |
sprintf( painCave.errMsg, |
| 576 |
"error in reading time from %s\n", |
| 577 |
c_in_name ); |
| 578 |
return strdup( painCave.errMsg ); |
| 579 |
} |
| 580 |
time = atof( foo ); |
| 581 |
|
| 582 |
// get the Hx vector |
| 583 |
|
| 584 |
foo = strtok(NULL, " ,;\t"); |
| 585 |
if(foo == NULL){ |
| 586 |
sprintf( painCave.errMsg, |
| 587 |
"error in reading Hx[0] from %s\n", |
| 588 |
c_in_name ); |
| 589 |
return strdup( painCave.errMsg ); |
| 590 |
} |
| 591 |
boxMat[0] = atof( foo ); |
| 592 |
|
| 593 |
foo = strtok(NULL, " ,;\t"); |
| 594 |
if(foo == NULL){ |
| 595 |
sprintf( painCave.errMsg, |
| 596 |
"error in reading Hx[1] from %s\n", |
| 597 |
c_in_name ); |
| 598 |
return strdup( painCave.errMsg ); |
| 599 |
} |
| 600 |
boxMat[1] = atof( foo ); |
| 601 |
|
| 602 |
foo = strtok(NULL, " ,;\t"); |
| 603 |
if(foo == NULL){ |
| 604 |
sprintf( painCave.errMsg, |
| 605 |
"error in reading Hx[2] from %s\n", |
| 606 |
c_in_name ); |
| 607 |
return strdup( painCave.errMsg ); |
| 608 |
} |
| 609 |
boxMat[2] = atof( foo ); |
| 610 |
|
| 611 |
// get the Hy vector |
| 612 |
|
| 613 |
foo = strtok(NULL, " ,;\t"); |
| 614 |
if(foo == NULL){ |
| 615 |
sprintf( painCave.errMsg, |
| 616 |
"error in reading Hy[0] from %s\n", |
| 617 |
c_in_name ); |
| 618 |
return strdup( painCave.errMsg ); |
| 619 |
} |
| 620 |
boxMat[3] = atof( foo ); |
| 621 |
|
| 622 |
foo = strtok(NULL, " ,;\t"); |
| 623 |
if(foo == NULL){ |
| 624 |
sprintf( painCave.errMsg, |
| 625 |
"error in reading Hy[1] from %s\n", |
| 626 |
c_in_name ); |
| 627 |
return strdup( painCave.errMsg ); |
| 628 |
} |
| 629 |
boxMat[4] = atof( foo ); |
| 630 |
|
| 631 |
foo = strtok(NULL, " ,;\t"); |
| 632 |
if(foo == NULL){ |
| 633 |
sprintf( painCave.errMsg, |
| 634 |
"error in reading Hy[2] from %s\n", |
| 635 |
c_in_name ); |
| 636 |
return strdup( painCave.errMsg ); |
| 637 |
} |
| 638 |
boxMat[5] = atof( foo ); |
| 639 |
|
| 640 |
// get the Hz vector |
| 641 |
|
| 642 |
foo = strtok(NULL, " ,;\t"); |
| 643 |
if(foo == NULL){ |
| 644 |
sprintf( painCave.errMsg, |
| 645 |
"error in reading Hz[0] from %s\n", |
| 646 |
c_in_name ); |
| 647 |
return strdup( painCave.errMsg ); |
| 648 |
} |
| 649 |
boxMat[6] = atof( foo ); |
| 650 |
|
| 651 |
foo = strtok(NULL, " ,;\t"); |
| 652 |
if(foo == NULL){ |
| 653 |
sprintf( painCave.errMsg, |
| 654 |
"error in reading Hz[1] from %s\n", |
| 655 |
c_in_name ); |
| 656 |
return strdup( painCave.errMsg ); |
| 657 |
} |
| 658 |
boxMat[7] = atof( foo ); |
| 659 |
|
| 660 |
foo = strtok(NULL, " ,;\t"); |
| 661 |
if(foo == NULL){ |
| 662 |
sprintf( painCave.errMsg, |
| 663 |
"error in reading Hz[2] from %s\n", |
| 664 |
c_in_name ); |
| 665 |
return strdup( painCave.errMsg ); |
| 666 |
} |
| 667 |
boxMat[8] = atof( foo ); |
| 668 |
|
| 669 |
return NULL; |
| 670 |
} |
| 671 |
|
| 672 |
|
| 673 |
#ifdef IS_MPI |
| 674 |
|
| 675 |
// a couple of functions to let us escape the read loop |
| 676 |
|
| 677 |
void initFile::nodeZeroError( void ){ |
| 678 |
int j, myStatus; |
| 679 |
|
| 680 |
myStatus = 0; |
| 681 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
| 682 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
| 683 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 684 |
} |
| 685 |
|
| 686 |
|
| 687 |
MPI_Finalize(); |
| 688 |
exit (0); |
| 689 |
|
| 690 |
} |
| 691 |
|
| 692 |
void initFile::anonymousNodeDie( void ){ |
| 693 |
|
| 694 |
MPI_Finalize(); |
| 695 |
exit (0); |
| 696 |
} |
| 697 |
|
| 698 |
#endif //is_mpi |
