| 1 |
#define _LARGEFILE_SOURCE64 |
| 2 |
#define _FILE_OFFSET_BITS 64 |
| 3 |
|
| 4 |
#include <sys/types.h> |
| 5 |
#include <sys/stat.h> |
| 6 |
|
| 7 |
#include <iostream> |
| 8 |
#include <math.h> |
| 9 |
|
| 10 |
#include <stdio.h> |
| 11 |
#include <stdlib.h> |
| 12 |
#include <string.h> |
| 13 |
|
| 14 |
|
| 15 |
#include "ReadWrite.hpp" |
| 16 |
#include "simError.h" |
| 17 |
|
| 18 |
#ifdef IS_MPI |
| 19 |
#include <mpi.h> |
| 20 |
#include "mpiSimulation.hpp" |
| 21 |
#define TAKE_THIS_TAG_CHAR 0 |
| 22 |
#define TAKE_THIS_TAG_INT 1 |
| 23 |
#endif // is_mpi |
| 24 |
|
| 25 |
|
| 26 |
DumpReader :: DumpReader(const char *in_name ){ |
| 27 |
|
| 28 |
isScanned = false; |
| 29 |
|
| 30 |
#ifdef IS_MPI |
| 31 |
if (worldRank == 0) { |
| 32 |
#endif |
| 33 |
|
| 34 |
inFile = fopen(in_name, "r"); |
| 35 |
if(inFile == NULL){ |
| 36 |
sprintf(painCave.errMsg, |
| 37 |
"Cannot open file: %s\n", in_name); |
| 38 |
painCave.isFatal = 1; |
| 39 |
simError(); |
| 40 |
} |
| 41 |
|
| 42 |
inFileName = in_name; |
| 43 |
#ifdef IS_MPI |
| 44 |
} |
| 45 |
strcpy( checkPointMsg, "Dump file opened for reading successfully." ); |
| 46 |
MPIcheckPoint(); |
| 47 |
#endif |
| 48 |
return; |
| 49 |
} |
| 50 |
|
| 51 |
DumpReader :: ~DumpReader( ){ |
| 52 |
#ifdef IS_MPI |
| 53 |
if (worldRank == 0) { |
| 54 |
#endif |
| 55 |
vector<fpos_t*>::iterator i; |
| 56 |
|
| 57 |
int error; |
| 58 |
error = fclose( inFile ); |
| 59 |
if( error ){ |
| 60 |
sprintf( painCave.errMsg, |
| 61 |
"Error closing %s\n", inFileName.c_str()); |
| 62 |
simError(); |
| 63 |
} |
| 64 |
|
| 65 |
for(i = framePos.begin(); i != framePos.end(); ++i) |
| 66 |
delete *i; |
| 67 |
framePos.clear(); |
| 68 |
|
| 69 |
#ifdef IS_MPI |
| 70 |
} |
| 71 |
strcpy( checkPointMsg, "Dump file closed successfully." ); |
| 72 |
MPIcheckPoint(); |
| 73 |
#endif |
| 74 |
|
| 75 |
return; |
| 76 |
} |
| 77 |
|
| 78 |
int DumpReader::getNframes( void ){ |
| 79 |
|
| 80 |
if( !isScanned ) |
| 81 |
scanFile(); |
| 82 |
return framePos.size(); |
| 83 |
} |
| 84 |
|
| 85 |
void DumpReader::scanFile( void ){ |
| 86 |
|
| 87 |
int i, j; |
| 88 |
int lineNum = 0; |
| 89 |
char readBuffer[2000]; |
| 90 |
fpos_t *currPos; |
| 91 |
|
| 92 |
#ifdef IS_MPI |
| 93 |
if( worldRank == 0 ){ |
| 94 |
#endif // is_mpi |
| 95 |
|
| 96 |
rewind( inFile ); |
| 97 |
|
| 98 |
currPos = new fpos_t; |
| 99 |
fgetpos( inFile, currPos ); |
| 100 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 101 |
lineNum++; |
| 102 |
if( feof( inFile ) ){ |
| 103 |
sprintf( painCave.errMsg, |
| 104 |
"File \"%s\" ended unexpectedly at line %d\n", |
| 105 |
inFileName.c_str(), |
| 106 |
lineNum ); |
| 107 |
painCave.isFatal = 1; |
| 108 |
simError(); |
| 109 |
} |
| 110 |
|
| 111 |
while( !feof( inFile ) ){ |
| 112 |
|
| 113 |
framePos.push_back(currPos); |
| 114 |
|
| 115 |
i = atoi(readBuffer); |
| 116 |
|
| 117 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 118 |
lineNum++; |
| 119 |
if( feof( inFile ) ){ |
| 120 |
sprintf( painCave.errMsg, |
| 121 |
"File \"%s\" ended unexpectedly at line %d\n", |
| 122 |
inFileName.c_str(), |
| 123 |
lineNum ); |
| 124 |
painCave.isFatal = 1; |
| 125 |
simError(); |
| 126 |
} |
| 127 |
|
| 128 |
for(j=0; j<i; j++){ |
| 129 |
|
| 130 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 131 |
lineNum++; |
| 132 |
if( feof( inFile ) ){ |
| 133 |
sprintf( painCave.errMsg, |
| 134 |
"File \"%s\" ended unexpectedly at line %d," |
| 135 |
" with atom %d\n", |
| 136 |
inFileName.c_str(), |
| 137 |
lineNum, |
| 138 |
j ); |
| 139 |
painCave.isFatal = 1; |
| 140 |
simError(); |
| 141 |
} |
| 142 |
|
| 143 |
} |
| 144 |
|
| 145 |
currPos = new fpos_t; |
| 146 |
fgetpos( inFile, currPos ); |
| 147 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 148 |
lineNum++; |
| 149 |
} |
| 150 |
|
| 151 |
delete currPos; |
| 152 |
rewind( inFile ); |
| 153 |
|
| 154 |
isScanned = true; |
| 155 |
|
| 156 |
#ifdef IS_MPI |
| 157 |
} |
| 158 |
strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
| 159 |
MPIcheckPoint(); |
| 160 |
#endif // is_mpi |
| 161 |
} |
| 162 |
|
| 163 |
void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
| 164 |
|
| 165 |
simnfo = the_simnfo; |
| 166 |
|
| 167 |
this->readSet( whichFrame ); |
| 168 |
} |
| 169 |
|
| 170 |
|
| 171 |
|
| 172 |
void DumpReader :: readSet( int whichFrame ){ |
| 173 |
|
| 174 |
int i; |
| 175 |
unsigned int j; |
| 176 |
|
| 177 |
#ifdef IS_MPI |
| 178 |
int done, which_node, which_atom; // loop counter |
| 179 |
#endif //is_mpi |
| 180 |
|
| 181 |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 182 |
int nTotObjs; // the number of atoms |
| 183 |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
| 184 |
|
| 185 |
char *eof_test; // ptr to see when we reach the end of the file |
| 186 |
char *parseErr; |
| 187 |
|
| 188 |
vector<StuntDouble*> integrableObjects; |
| 189 |
|
| 190 |
|
| 191 |
#ifndef IS_MPI |
| 192 |
|
| 193 |
fsetpos(inFile, framePos[whichFrame]); |
| 194 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 195 |
if( eof_test == NULL ){ |
| 196 |
sprintf( painCave.errMsg, |
| 197 |
"DumpReader error: error reading 1st line of \"%s\"\n", |
| 198 |
inFileName.c_str() ); |
| 199 |
painCave.isFatal = 1; |
| 200 |
simError(); |
| 201 |
} |
| 202 |
|
| 203 |
nTotObjs = atoi( read_buffer ); |
| 204 |
|
| 205 |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
| 206 |
sprintf( painCave.errMsg, |
| 207 |
"DumpReader error. %s nIntegrable, %d, " |
| 208 |
"does not match the meta-data file's nIntegrable, %d.\n", |
| 209 |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
| 210 |
painCave.isFatal = 1; |
| 211 |
simError(); |
| 212 |
} |
| 213 |
|
| 214 |
//read the box mat from the comment line |
| 215 |
|
| 216 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 217 |
if(eof_test == NULL){ |
| 218 |
sprintf( painCave.errMsg, |
| 219 |
"error in reading commment in %s\n", inFileName.c_str()); |
| 220 |
painCave.isFatal = 1; |
| 221 |
simError(); |
| 222 |
} |
| 223 |
|
| 224 |
parseErr = parseCommentLine( read_buffer, simnfo); |
| 225 |
if( parseErr != NULL ){ |
| 226 |
strcpy( painCave.errMsg, parseErr ); |
| 227 |
painCave.isFatal = 1; |
| 228 |
simError(); |
| 229 |
} |
| 230 |
|
| 231 |
//parse dump lines |
| 232 |
|
| 233 |
for( i=0; i < simnfo->n_mol; i++){ |
| 234 |
|
| 235 |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
| 236 |
|
| 237 |
for(j = 0; j < integrableObjects.size(); j++){ |
| 238 |
|
| 239 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 240 |
if(eof_test == NULL){ |
| 241 |
sprintf(painCave.errMsg, |
| 242 |
"error in reading file %s\n" |
| 243 |
"natoms = %d; index = %d\n" |
| 244 |
"error reading the line from the file.\n", |
| 245 |
inFileName.c_str(), nTotObjs, i ); |
| 246 |
painCave.isFatal = 1; |
| 247 |
simError(); |
| 248 |
} |
| 249 |
|
| 250 |
parseErr = parseDumpLine( read_buffer, integrableObjects[j]); |
| 251 |
if( parseErr != NULL ){ |
| 252 |
strcpy( painCave.errMsg, parseErr ); |
| 253 |
painCave.isFatal = 1; |
| 254 |
simError(); |
| 255 |
} |
| 256 |
} |
| 257 |
} |
| 258 |
|
| 259 |
// MPI Section of code.......... |
| 260 |
#else //IS_MPI |
| 261 |
|
| 262 |
// first thing first, suspend fatalities. |
| 263 |
painCave.isEventLoop = 1; |
| 264 |
|
| 265 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
| 266 |
int haveError; |
| 267 |
|
| 268 |
MPI_Status istatus; |
| 269 |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
| 270 |
int localIndex; |
| 271 |
int nCurObj; |
| 272 |
int nitems; |
| 273 |
|
| 274 |
nTotObjs = simnfo->getTotIntegrableObjects(); |
| 275 |
haveError = 0; |
| 276 |
if (worldRank == 0) { |
| 277 |
fsetpos(inFile, framePos[whichFrame]); |
| 278 |
|
| 279 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 280 |
if( eof_test == NULL ){ |
| 281 |
sprintf( painCave.errMsg, |
| 282 |
"Error reading 1st line of %s \n ",inFileName.c_str()); |
| 283 |
haveError = 1; |
| 284 |
simError(); |
| 285 |
} |
| 286 |
|
| 287 |
nitems = atoi( read_buffer ); |
| 288 |
|
| 289 |
// Check to see that the number of integrable objects in the |
| 290 |
// intial configuration file is the same as derived from the |
| 291 |
// meta-data file. |
| 292 |
|
| 293 |
if( nTotObjs != nitems){ |
| 294 |
sprintf( painCave.errMsg, |
| 295 |
"DumpReader Error. %s nIntegrable, %d, " |
| 296 |
"does not match the meta-data file's nIntegrable, %d.\n", |
| 297 |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
| 298 |
haveError= 1; |
| 299 |
simError(); |
| 300 |
} |
| 301 |
|
| 302 |
//read the boxMat from the comment line |
| 303 |
|
| 304 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 305 |
if(eof_test == NULL){ |
| 306 |
sprintf( painCave.errMsg, |
| 307 |
"error in reading commment in %s\n", inFileName.c_str()); |
| 308 |
haveError = 1; |
| 309 |
simError(); |
| 310 |
} |
| 311 |
|
| 312 |
//Every single processor will parse the comment line by itself |
| 313 |
//By using this way, we might lose some efficiency, but if we want to add |
| 314 |
//more parameters into comment line, we only need to modify function |
| 315 |
//parseCommentLine |
| 316 |
|
| 317 |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
| 318 |
|
| 319 |
parseErr = parseCommentLine( read_buffer, simnfo); |
| 320 |
|
| 321 |
if( parseErr != NULL ){ |
| 322 |
strcpy( painCave.errMsg, parseErr ); |
| 323 |
haveError = 1; |
| 324 |
simError(); |
| 325 |
} |
| 326 |
|
| 327 |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
| 328 |
which_node = MolToProcMap[i]; |
| 329 |
if(which_node == 0){ |
| 330 |
//molecules belong to master node |
| 331 |
|
| 332 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
| 333 |
|
| 334 |
if(localIndex == -1) { |
| 335 |
strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
| 336 |
haveError = 1; |
| 337 |
simError(); |
| 338 |
} |
| 339 |
|
| 340 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
| 341 |
for(j=0; j < integrableObjects.size(); j++){ |
| 342 |
|
| 343 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 344 |
if(eof_test == NULL){ |
| 345 |
sprintf(painCave.errMsg, |
| 346 |
"error in reading file %s\n" |
| 347 |
"natoms = %d; index = %d\n" |
| 348 |
"error reading the line from the file.\n", |
| 349 |
inFileName.c_str(), nTotObjs, i ); |
| 350 |
haveError= 1; |
| 351 |
simError(); |
| 352 |
} |
| 353 |
|
| 354 |
if(haveError) nodeZeroError(); |
| 355 |
|
| 356 |
parseDumpLine(read_buffer, integrableObjects[j]); |
| 357 |
|
| 358 |
} |
| 359 |
|
| 360 |
|
| 361 |
} |
| 362 |
else{ |
| 363 |
//molecule belongs to slave nodes |
| 364 |
|
| 365 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
| 366 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
| 367 |
|
| 368 |
for(j=0; j < nCurObj; j++){ |
| 369 |
|
| 370 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 371 |
if(eof_test == NULL){ |
| 372 |
sprintf(painCave.errMsg, |
| 373 |
"error in reading file %s\n" |
| 374 |
"natoms = %d; index = %d\n" |
| 375 |
"error reading the line from the file.\n", |
| 376 |
inFileName.c_str(), nTotObjs, i ); |
| 377 |
haveError= 1; |
| 378 |
simError(); |
| 379 |
} |
| 380 |
|
| 381 |
if(haveError) nodeZeroError(); |
| 382 |
|
| 383 |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
| 384 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
| 385 |
|
| 386 |
} |
| 387 |
|
| 388 |
} |
| 389 |
|
| 390 |
} |
| 391 |
|
| 392 |
} |
| 393 |
else{ |
| 394 |
//actions taken at slave nodes |
| 395 |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
| 396 |
|
| 397 |
parseErr = parseCommentLine( read_buffer, simnfo); |
| 398 |
|
| 399 |
if( parseErr != NULL ){ |
| 400 |
strcpy( painCave.errMsg, parseErr ); |
| 401 |
haveError = 1; |
| 402 |
simError(); |
| 403 |
} |
| 404 |
|
| 405 |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
| 406 |
which_node = MolToProcMap[i]; |
| 407 |
|
| 408 |
if(which_node == worldRank){ |
| 409 |
//molecule with global index i belongs to this processor |
| 410 |
|
| 411 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
| 412 |
|
| 413 |
if(localIndex == -1) { |
| 414 |
sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
| 415 |
haveError = 1; |
| 416 |
simError(); |
| 417 |
} |
| 418 |
|
| 419 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
| 420 |
|
| 421 |
nCurObj = integrableObjects.size(); |
| 422 |
|
| 423 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
| 424 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 425 |
|
| 426 |
for(j = 0; j < integrableObjects.size(); j++){ |
| 427 |
|
| 428 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
| 429 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
| 430 |
|
| 431 |
parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
| 432 |
|
| 433 |
if( parseErr != NULL ){ |
| 434 |
strcpy( painCave.errMsg, parseErr ); |
| 435 |
simError(); |
| 436 |
} |
| 437 |
|
| 438 |
} |
| 439 |
|
| 440 |
} |
| 441 |
|
| 442 |
} |
| 443 |
|
| 444 |
} |
| 445 |
|
| 446 |
#endif |
| 447 |
} |
| 448 |
|
| 449 |
char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){ |
| 450 |
|
| 451 |
char *foo; // the pointer to the current string token |
| 452 |
|
| 453 |
double pos[3]; // position place holders |
| 454 |
double vel[3]; // velocity placeholders |
| 455 |
double q[4]; // the quaternions |
| 456 |
double ji[3]; // angular velocity placeholders; |
| 457 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
| 458 |
|
| 459 |
|
| 460 |
// set the string tokenizer |
| 461 |
|
| 462 |
foo = strtok(readLine, " ,;\t"); |
| 463 |
|
| 464 |
// check the atom name to the current atom |
| 465 |
|
| 466 |
if( strcmp( foo, sd->getType() ) ){ |
| 467 |
sprintf( painCave.errMsg, |
| 468 |
"DumpReader error. Does not" |
| 469 |
" match the meta-data atom %s.\n", |
| 470 |
sd->getType() ); |
| 471 |
return strdup( painCave.errMsg ); |
| 472 |
} |
| 473 |
|
| 474 |
// get the positions |
| 475 |
|
| 476 |
foo = strtok(NULL, " ,;\t"); |
| 477 |
if(foo == NULL){ |
| 478 |
sprintf( painCave.errMsg, |
| 479 |
"error in reading postition x from %s\n", |
| 480 |
inFileName.c_str()); |
| 481 |
return strdup( painCave.errMsg ); |
| 482 |
} |
| 483 |
pos[0] = atof( foo ); |
| 484 |
|
| 485 |
foo = strtok(NULL, " ,;\t"); |
| 486 |
if(foo == NULL){ |
| 487 |
sprintf( painCave.errMsg, |
| 488 |
"error in reading postition y from %s\n", |
| 489 |
inFileName.c_str()); |
| 490 |
return strdup( painCave.errMsg ); |
| 491 |
} |
| 492 |
pos[1] = atof( foo ); |
| 493 |
|
| 494 |
foo = strtok(NULL, " ,;\t"); |
| 495 |
if(foo == NULL){ |
| 496 |
sprintf( painCave.errMsg, |
| 497 |
"error in reading postition z from %s\n", |
| 498 |
inFileName.c_str()); |
| 499 |
return strdup( painCave.errMsg ); |
| 500 |
} |
| 501 |
pos[2] = atof( foo ); |
| 502 |
|
| 503 |
|
| 504 |
// get the velocities |
| 505 |
|
| 506 |
foo = strtok(NULL, " ,;\t"); |
| 507 |
if(foo == NULL){ |
| 508 |
sprintf( painCave.errMsg, |
| 509 |
"error in reading velocity x from %s\n", |
| 510 |
inFileName.c_str() ); |
| 511 |
return strdup( painCave.errMsg ); |
| 512 |
} |
| 513 |
vel[0] = atof( foo ); |
| 514 |
|
| 515 |
foo = strtok(NULL, " ,;\t"); |
| 516 |
if(foo == NULL){ |
| 517 |
sprintf( painCave.errMsg, |
| 518 |
"error in reading velocity x from %s\n", |
| 519 |
inFileName.c_str() ); |
| 520 |
return strdup( painCave.errMsg ); |
| 521 |
} |
| 522 |
vel[1] = atof( foo ); |
| 523 |
|
| 524 |
foo = strtok(NULL, " ,;\t"); |
| 525 |
if(foo == NULL){ |
| 526 |
sprintf( painCave.errMsg, |
| 527 |
"error in reading velocity x from %s\n", |
| 528 |
inFileName.c_str() ); |
| 529 |
return strdup( painCave.errMsg ); |
| 530 |
} |
| 531 |
vel[2] = atof( foo ); |
| 532 |
|
| 533 |
|
| 534 |
// add the positions and velocities to the atom |
| 535 |
|
| 536 |
sd->setPos( pos ); |
| 537 |
sd->setVel( vel ); |
| 538 |
|
| 539 |
if (!sd->isDirectional()) |
| 540 |
return NULL; |
| 541 |
|
| 542 |
// get the quaternions |
| 543 |
|
| 544 |
if( sd->isDirectional() ){ |
| 545 |
|
| 546 |
foo = strtok(NULL, " ,;\t"); |
| 547 |
if(foo == NULL){ |
| 548 |
sprintf( painCave.errMsg, |
| 549 |
"error in reading velocity x from %s\n", |
| 550 |
inFileName.c_str() ); |
| 551 |
return strdup( painCave.errMsg ); |
| 552 |
} |
| 553 |
q[0] = atof( foo ); |
| 554 |
|
| 555 |
foo = strtok(NULL, " ,;\t"); |
| 556 |
if(foo == NULL){ |
| 557 |
sprintf( painCave.errMsg, |
| 558 |
"error in reading velocity x from %s\n", |
| 559 |
inFileName.c_str() ); |
| 560 |
return strdup( painCave.errMsg ); |
| 561 |
} |
| 562 |
q[1] = atof( foo ); |
| 563 |
|
| 564 |
foo = strtok(NULL, " ,;\t"); |
| 565 |
if(foo == NULL){ |
| 566 |
sprintf( painCave.errMsg, |
| 567 |
"error in reading velocity x from %s\n", |
| 568 |
inFileName.c_str() ); |
| 569 |
return strdup( painCave.errMsg ); |
| 570 |
} |
| 571 |
q[2] = atof( foo ); |
| 572 |
|
| 573 |
foo = strtok(NULL, " ,;\t"); |
| 574 |
if(foo == NULL){ |
| 575 |
sprintf( painCave.errMsg, |
| 576 |
"error in reading velocity x from %s\n", |
| 577 |
inFileName.c_str() ); |
| 578 |
return strdup( painCave.errMsg ); |
| 579 |
} |
| 580 |
q[3] = atof( foo ); |
| 581 |
|
| 582 |
// get the angular velocities |
| 583 |
|
| 584 |
foo = strtok(NULL, " ,;\t"); |
| 585 |
if(foo == NULL){ |
| 586 |
sprintf( painCave.errMsg, |
| 587 |
"error in reading velocity x from %s\n", |
| 588 |
inFileName.c_str() ); |
| 589 |
return strdup( painCave.errMsg ); |
| 590 |
} |
| 591 |
ji[0] = atof( foo ); |
| 592 |
|
| 593 |
foo = strtok(NULL, " ,;\t"); |
| 594 |
if(foo == NULL){ |
| 595 |
sprintf( painCave.errMsg, |
| 596 |
"error in reading velocity x from %s\n", |
| 597 |
inFileName.c_str() ); |
| 598 |
return strdup( painCave.errMsg ); |
| 599 |
} |
| 600 |
ji[1] = atof(foo ); |
| 601 |
|
| 602 |
foo = strtok(NULL, " ,;\t"); |
| 603 |
if(foo == NULL){ |
| 604 |
sprintf( painCave.errMsg, |
| 605 |
"error in reading velocity x from %s\n", |
| 606 |
inFileName.c_str() ); |
| 607 |
return strdup( painCave.errMsg ); |
| 608 |
} |
| 609 |
ji[2] = atof( foo ); |
| 610 |
|
| 611 |
|
| 612 |
// check that the quaternion vector is normalized |
| 613 |
|
| 614 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
| 615 |
|
| 616 |
if (fabs(qSqr) < 1e-6) { |
| 617 |
sprintf(painCave.errMsg, |
| 618 |
"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
| 619 |
return strdup(painCave.errMsg); |
| 620 |
} |
| 621 |
|
| 622 |
qLength = sqrt( qSqr ); |
| 623 |
q[0] = q[0] / qLength; |
| 624 |
q[1] = q[1] / qLength; |
| 625 |
q[2] = q[2] / qLength; |
| 626 |
q[3] = q[3] / qLength; |
| 627 |
|
| 628 |
// add quaternion and angular velocities |
| 629 |
|
| 630 |
sd->setQ( q ); |
| 631 |
sd->setJ( ji ); |
| 632 |
} |
| 633 |
|
| 634 |
|
| 635 |
|
| 636 |
return NULL; |
| 637 |
} |
| 638 |
|
| 639 |
|
| 640 |
char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
| 641 |
|
| 642 |
double currTime; |
| 643 |
double boxMat[9]; |
| 644 |
double theBoxMat3[3][3]; |
| 645 |
double chi; |
| 646 |
double integralOfChidt; |
| 647 |
double eta[9]; |
| 648 |
|
| 649 |
char *foo; // the pointer to the current string token |
| 650 |
|
| 651 |
// set the string tokenizer |
| 652 |
|
| 653 |
foo = strtok(readLine, " ,;\t"); |
| 654 |
// set the timeToken. |
| 655 |
|
| 656 |
if(foo == NULL){ |
| 657 |
sprintf( painCave.errMsg, |
| 658 |
"error in reading Time from %s\n", |
| 659 |
inFileName.c_str() ); |
| 660 |
return strdup( painCave.errMsg ); |
| 661 |
} |
| 662 |
|
| 663 |
currTime = atof( foo ); |
| 664 |
entry_plug->setTime( currTime ); |
| 665 |
|
| 666 |
//get H-Matrix |
| 667 |
|
| 668 |
for(int i = 0 ; i < 9; i++){ |
| 669 |
foo = strtok(NULL, " ,;\t"); |
| 670 |
if(foo == NULL){ |
| 671 |
sprintf( painCave.errMsg, |
| 672 |
"error in reading H[%d] from %s\n", i, inFileName.c_str() ); |
| 673 |
return strdup( painCave.errMsg ); |
| 674 |
} |
| 675 |
boxMat[i] = atof( foo ); |
| 676 |
} |
| 677 |
|
| 678 |
for(int i=0;i<3;i++) |
| 679 |
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
| 680 |
|
| 681 |
//set H-Matrix |
| 682 |
entry_plug->setBoxM( theBoxMat3 ); |
| 683 |
|
| 684 |
//get chi and integralOfChidt, they should appear by pair |
| 685 |
|
| 686 |
if( entry_plug->useInitXSstate ){ |
| 687 |
foo = strtok(NULL, " ,;\t\n"); |
| 688 |
if(foo != NULL){ |
| 689 |
chi = atof(foo); |
| 690 |
|
| 691 |
foo = strtok(NULL, " ,;\t\n"); |
| 692 |
if(foo == NULL){ |
| 693 |
sprintf( painCave.errMsg, |
| 694 |
"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() ); |
| 695 |
return strdup( painCave.errMsg ); |
| 696 |
} |
| 697 |
integralOfChidt = atof( foo ); |
| 698 |
|
| 699 |
//push chi and integralOfChidt into SimInfo::properties which can be |
| 700 |
//retrieved by integrator later |
| 701 |
DoubleData* chiValue = new DoubleData(); |
| 702 |
chiValue->setID(CHIVALUE_ID); |
| 703 |
chiValue->setData(chi); |
| 704 |
entry_plug->addProperty(chiValue); |
| 705 |
|
| 706 |
DoubleData* integralOfChidtValue = new DoubleData(); |
| 707 |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
| 708 |
integralOfChidtValue->setData(integralOfChidt); |
| 709 |
entry_plug->addProperty(integralOfChidtValue); |
| 710 |
|
| 711 |
} |
| 712 |
else |
| 713 |
return NULL; |
| 714 |
|
| 715 |
//get eta |
| 716 |
foo = strtok(NULL, " ,;\t\n"); |
| 717 |
if(foo != NULL ){ |
| 718 |
|
| 719 |
for(int i = 0 ; i < 9; i++){ |
| 720 |
|
| 721 |
if(foo == NULL){ |
| 722 |
sprintf( painCave.errMsg, |
| 723 |
"error in reading eta[%d] from %s\n", i, inFileName.c_str() ); |
| 724 |
return strdup( painCave.errMsg ); |
| 725 |
} |
| 726 |
eta[i] = atof( foo ); |
| 727 |
foo = strtok(NULL, " ,;\t\n"); |
| 728 |
} |
| 729 |
} |
| 730 |
else |
| 731 |
return NULL; |
| 732 |
|
| 733 |
//push eta into SimInfo::properties which can be |
| 734 |
//retrieved by integrator later |
| 735 |
//entry_plug->setBoxM( theBoxMat3 ); |
| 736 |
DoubleArrayData* etaValue = new DoubleArrayData(); |
| 737 |
etaValue->setID(ETAVALUE_ID); |
| 738 |
etaValue->setData(eta, 9); |
| 739 |
entry_plug->addProperty(etaValue); |
| 740 |
} |
| 741 |
|
| 742 |
return NULL; |
| 743 |
} |
| 744 |
|
| 745 |
#ifdef IS_MPI |
| 746 |
void DumpReader::nodeZeroError( void ){ |
| 747 |
int j, myStatus; |
| 748 |
|
| 749 |
myStatus = 0; |
| 750 |
for (j = 0; j < mpiSim->getNProcessors(); j++) { |
| 751 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
| 752 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 753 |
} |
| 754 |
|
| 755 |
|
| 756 |
MPI_Finalize(); |
| 757 |
exit (0); |
| 758 |
|
| 759 |
} |
| 760 |
|
| 761 |
void DumpReader::anonymousNodeDie( void ){ |
| 762 |
|
| 763 |
MPI_Finalize(); |
| 764 |
exit (0); |
| 765 |
} |
| 766 |
#endif |
