| 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 |
namespace dumpRead{ |
| 26 |
|
| 27 |
#ifdef IS_MPI |
| 28 |
void nodeZeroError( void ); |
| 29 |
void anonymousNodeDie( void ); |
| 30 |
#endif // is_mpi |
| 31 |
|
| 32 |
} |
| 33 |
|
| 34 |
using namespace dumpRead; |
| 35 |
|
| 36 |
|
| 37 |
DumpReader :: DumpReader(const char *in_name ){ |
| 38 |
|
| 39 |
isScanned = false; |
| 40 |
headFP = new FilePos; |
| 41 |
|
| 42 |
#ifdef IS_MPI |
| 43 |
if (worldRank == 0) { |
| 44 |
#endif |
| 45 |
|
| 46 |
inFile = fopen(in_name, "r"); |
| 47 |
if(inFile == NULL){ |
| 48 |
sprintf(painCave.errMsg, |
| 49 |
"Cannot open file: %s\n", in_name); |
| 50 |
painCave.isFatal = 1; |
| 51 |
simError(); |
| 52 |
} |
| 53 |
|
| 54 |
strcpy( inName, in_name); |
| 55 |
#ifdef IS_MPI |
| 56 |
} |
| 57 |
strcpy( checkPointMsg, "Dump file opened for reading successfully." ); |
| 58 |
MPIcheckPoint(); |
| 59 |
#endif |
| 60 |
return; |
| 61 |
} |
| 62 |
|
| 63 |
DumpReader :: ~DumpReader( ){ |
| 64 |
#ifdef IS_MPI |
| 65 |
if (worldRank == 0) { |
| 66 |
#endif |
| 67 |
int error; |
| 68 |
error = fclose( inFile ); |
| 69 |
if( error ){ |
| 70 |
sprintf( painCave.errMsg, |
| 71 |
"Error closing %s\n", inName ); |
| 72 |
simError(); |
| 73 |
} |
| 74 |
#ifdef IS_MPI |
| 75 |
} |
| 76 |
strcpy( checkPointMsg, "Dump file closed successfully." ); |
| 77 |
MPIcheckPoint(); |
| 78 |
#endif |
| 79 |
|
| 80 |
return; |
| 81 |
} |
| 82 |
|
| 83 |
int DumpReader::getNframes( void ){ |
| 84 |
|
| 85 |
if( !isScanned ) scanFile(); |
| 86 |
return nFrames; |
| 87 |
} |
| 88 |
|
| 89 |
void DumpReader::scanFile( void ){ |
| 90 |
|
| 91 |
int vectorSize; |
| 92 |
int i, j, k; |
| 93 |
int lineNum = 0; |
| 94 |
char readBuffer[2000]; |
| 95 |
char* foo; |
| 96 |
fpos_t *currPos; |
| 97 |
double time; |
| 98 |
|
| 99 |
FilePos *currFP; |
| 100 |
|
| 101 |
|
| 102 |
#ifdef IS_MPI |
| 103 |
if( worldRank == 0 ){ |
| 104 |
#endif // is_mpi |
| 105 |
|
| 106 |
rewind( inFile ); |
| 107 |
|
| 108 |
currPos = new fpos_t; |
| 109 |
fgetpos( inFile, currPos ); |
| 110 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 111 |
lineNum++; |
| 112 |
if( feof( inFile ) ){ |
| 113 |
sprintf( painCave.errMsg, |
| 114 |
"File \"%s\" ended unexpectedly at line %d\n", |
| 115 |
inName, |
| 116 |
lineNum ); |
| 117 |
painCave.isFatal = 1; |
| 118 |
simError(); |
| 119 |
} |
| 120 |
|
| 121 |
nFrames = 0; |
| 122 |
while( !feof( inFile ) ){ |
| 123 |
|
| 124 |
headFP->add( currPos ); |
| 125 |
nFrames++; |
| 126 |
|
| 127 |
i = atoi(readBuffer); |
| 128 |
|
| 129 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 130 |
lineNum++; |
| 131 |
if( feof( inFile ) ){ |
| 132 |
sprintf( painCave.errMsg, |
| 133 |
"File \"%s\" ended unexpectedly at line %d\n", |
| 134 |
inName, |
| 135 |
lineNum ); |
| 136 |
painCave.isFatal = 1; |
| 137 |
simError(); |
| 138 |
} |
| 139 |
|
| 140 |
// if(outTime){ |
| 141 |
// foo = strtok( readBuffer, " ,;\t" ); |
| 142 |
// time = atof( foo ); |
| 143 |
// } |
| 144 |
|
| 145 |
for(j=0; j<i; j++){ |
| 146 |
|
| 147 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 148 |
lineNum++; |
| 149 |
if( feof( inFile ) ){ |
| 150 |
sprintf( painCave.errMsg, |
| 151 |
"File \"%s\" ended unexpectedly at line %d," |
| 152 |
" with atom %d\n", |
| 153 |
inName, |
| 154 |
lineNum, |
| 155 |
j ); |
| 156 |
painCave.isFatal = 1; |
| 157 |
simError(); |
| 158 |
} |
| 159 |
|
| 160 |
} |
| 161 |
|
| 162 |
currPos = new fpos_t; |
| 163 |
fgetpos( inFile, currPos ); |
| 164 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
| 165 |
lineNum++; |
| 166 |
} |
| 167 |
|
| 168 |
delete currPos; |
| 169 |
rewind( inFile ); |
| 170 |
|
| 171 |
frameStart = new FilePos*[nFrames]; |
| 172 |
currFP = headFP; |
| 173 |
for(i=0; i<nFrames; i++){ |
| 174 |
|
| 175 |
currFP = currFP->getNext(); |
| 176 |
if( currFP == NULL ){ |
| 177 |
sprintf( painCave.errMsg, |
| 178 |
"DumpReader error: scanFile FilePos mismatch at " |
| 179 |
"nFrames = %d\n", |
| 180 |
i ); |
| 181 |
painCave.isFatal = 1; |
| 182 |
simError(); |
| 183 |
} |
| 184 |
|
| 185 |
frameStart[i] = currFP; |
| 186 |
} |
| 187 |
|
| 188 |
isScanned = true; |
| 189 |
|
| 190 |
#ifdef IS_MPI |
| 191 |
} |
| 192 |
strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
| 193 |
MPIcheckPoint(); |
| 194 |
#endif // is_mpi |
| 195 |
} |
| 196 |
|
| 197 |
void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
| 198 |
|
| 199 |
simnfo = the_simnfo; |
| 200 |
|
| 201 |
this->readSet( whichFrame ); |
| 202 |
} |
| 203 |
|
| 204 |
|
| 205 |
|
| 206 |
void DumpReader :: readSet( int whichFrame ){ |
| 207 |
|
| 208 |
int i, j, done, which_node, which_atom; // loop counter |
| 209 |
|
| 210 |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 211 |
int n_atoms; // the number of atoms |
| 212 |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
| 213 |
#ifdef IS_MPI |
| 214 |
char send_buffer[BUFFERSIZE]; |
| 215 |
#endif |
| 216 |
|
| 217 |
char *eof_test; // ptr to see when we reach the end of the file |
| 218 |
char *parseErr; |
| 219 |
int procIndex; |
| 220 |
double boxMat[9]; |
| 221 |
double theBoxMat3[3][3]; |
| 222 |
double time; |
| 223 |
|
| 224 |
fpos_t *framePos; |
| 225 |
framePos = frameStart[whichFrame]->getPos(); |
| 226 |
|
| 227 |
#ifndef IS_MPI |
| 228 |
|
| 229 |
fsetpos(inFile, framePos); |
| 230 |
|
| 231 |
|
| 232 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 233 |
if( eof_test == NULL ){ |
| 234 |
sprintf( painCave.errMsg, |
| 235 |
"DumpReader error: error reading 1st line of \"%s\"\n", |
| 236 |
inName ); |
| 237 |
painCave.isFatal = 1; |
| 238 |
simError(); |
| 239 |
} |
| 240 |
|
| 241 |
n_atoms = atoi( read_buffer ); |
| 242 |
|
| 243 |
Atom **atoms = simnfo->atoms; |
| 244 |
DirectionalAtom* dAtom; |
| 245 |
|
| 246 |
if( n_atoms != simnfo->n_atoms ){ |
| 247 |
sprintf( painCave.errMsg, |
| 248 |
"DumpReader error. %s n_atoms, %d, " |
| 249 |
"does not match the BASS file's n_atoms, %d.\n", |
| 250 |
inName, n_atoms, simnfo->n_atoms ); |
| 251 |
painCave.isFatal = 1; |
| 252 |
simError(); |
| 253 |
} |
| 254 |
|
| 255 |
//read the box mat from the comment line |
| 256 |
|
| 257 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 258 |
if(eof_test == NULL){ |
| 259 |
sprintf( painCave.errMsg, |
| 260 |
"error in reading commment in %s\n", inName); |
| 261 |
painCave.isFatal = 1; |
| 262 |
simError(); |
| 263 |
} |
| 264 |
|
| 265 |
parseErr = parseCommentLine( read_buffer, time, boxMat ); |
| 266 |
if( parseErr != NULL ){ |
| 267 |
strcpy( painCave.errMsg, parseErr ); |
| 268 |
painCave.isFatal = 1; |
| 269 |
simError(); |
| 270 |
} |
| 271 |
|
| 272 |
simnfo->setTime( time ); |
| 273 |
|
| 274 |
for(i=0;i<3;i++) |
| 275 |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
| 276 |
|
| 277 |
|
| 278 |
simnfo->setBoxM( theBoxMat3 ); |
| 279 |
|
| 280 |
|
| 281 |
for( i=0; i < n_atoms; i++){ |
| 282 |
|
| 283 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 284 |
if(eof_test == NULL){ |
| 285 |
sprintf(painCave.errMsg, |
| 286 |
"error in reading file %s\n" |
| 287 |
"natoms = %d; index = %d\n" |
| 288 |
"error reading the line from the file.\n", |
| 289 |
inName, n_atoms, i ); |
| 290 |
painCave.isFatal = 1; |
| 291 |
simError(); |
| 292 |
} |
| 293 |
|
| 294 |
|
| 295 |
parseErr = parseDumpLine( read_buffer, i ); |
| 296 |
if( parseErr != NULL ){ |
| 297 |
strcpy( painCave.errMsg, parseErr ); |
| 298 |
painCave.isFatal = 1; |
| 299 |
simError(); |
| 300 |
} |
| 301 |
} |
| 302 |
|
| 303 |
|
| 304 |
// MPI Section of code.......... |
| 305 |
#else //IS_MPI |
| 306 |
|
| 307 |
// first thing first, suspend fatalities. |
| 308 |
painCave.isEventLoop = 1; |
| 309 |
|
| 310 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
| 311 |
int haveError; |
| 312 |
|
| 313 |
MPI_Status istatus; |
| 314 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
| 315 |
|
| 316 |
|
| 317 |
haveError = 0; |
| 318 |
if (worldRank == 0) { |
| 319 |
fsetpos(inFile, framePos); |
| 320 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 321 |
if( eof_test == NULL ){ |
| 322 |
sprintf( painCave.errMsg, |
| 323 |
"Error reading 1st line of %d \n ",inName); |
| 324 |
haveError = 1; |
| 325 |
simError(); |
| 326 |
} |
| 327 |
|
| 328 |
n_atoms = atoi( read_buffer ); |
| 329 |
|
| 330 |
Atom **atoms = simnfo->atoms; |
| 331 |
DirectionalAtom* dAtom; |
| 332 |
|
| 333 |
// Check to see that the number of atoms in the intial configuration file is the |
| 334 |
// same as declared in simBass. |
| 335 |
|
| 336 |
if( n_atoms != mpiSim->getTotAtoms() ){ |
| 337 |
sprintf( painCave.errMsg, |
| 338 |
"Initialize from File error. %s n_atoms, %d, " |
| 339 |
"does not match the BASS file's n_atoms, %d.\n", |
| 340 |
inName, n_atoms, simnfo->n_atoms ); |
| 341 |
haveError= 1; |
| 342 |
simError(); |
| 343 |
} |
| 344 |
|
| 345 |
//read the time and boxMat from the comment line |
| 346 |
|
| 347 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
| 348 |
if(eof_test == NULL){ |
| 349 |
sprintf( painCave.errMsg, |
| 350 |
"error in reading commment in %s\n", inName); |
| 351 |
haveError = 1; |
| 352 |
simError(); |
| 353 |
} |
| 354 |
|
| 355 |
parseErr = parseCommentLine( read_buffer, time, boxMat ); |
| 356 |
if( parseErr != NULL ){ |
| 357 |
strcpy( painCave.errMsg, parseErr ); |
| 358 |
haveError = 1; |
| 359 |
simError(); |
| 360 |
} |
| 361 |
|
| 362 |
MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
| 363 |
|
| 364 |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
| 365 |
|
| 366 |
if(haveError) nodeZeroError(); |
| 367 |
|
| 368 |
for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
| 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 |
inName, n_atoms, i ); |
| 377 |
haveError= 1; |
| 378 |
simError(); |
| 379 |
} |
| 380 |
|
| 381 |
if(haveError) nodeZeroError(); |
| 382 |
|
| 383 |
// Get the Node number which wants this atom: |
| 384 |
which_node = AtomToProcMap[i]; |
| 385 |
if (which_node == 0) { |
| 386 |
parseErr = parseDumpLine( read_buffer, i ); |
| 387 |
if( parseErr != NULL ){ |
| 388 |
strcpy( painCave.errMsg, parseErr ); |
| 389 |
haveError = 1; |
| 390 |
simError(); |
| 391 |
} |
| 392 |
if(haveError) nodeZeroError(); |
| 393 |
} |
| 394 |
|
| 395 |
else { |
| 396 |
|
| 397 |
myStatus = 1; |
| 398 |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
| 399 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 400 |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
| 401 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
| 402 |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
| 403 |
MPI_COMM_WORLD); |
| 404 |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
| 405 |
MPI_COMM_WORLD, &istatus); |
| 406 |
|
| 407 |
if(!myStatus) nodeZeroError(); |
| 408 |
} |
| 409 |
} |
| 410 |
myStatus = -1; |
| 411 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
| 412 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
| 413 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 414 |
} |
| 415 |
|
| 416 |
} else { |
| 417 |
|
| 418 |
MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
| 419 |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
| 420 |
|
| 421 |
done = 0; |
| 422 |
while (!done) { |
| 423 |
|
| 424 |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
| 425 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
| 426 |
|
| 427 |
if(!myStatus) anonymousNodeDie(); |
| 428 |
|
| 429 |
if(myStatus < 0) break; |
| 430 |
|
| 431 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
| 432 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
| 433 |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
| 434 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
| 435 |
|
| 436 |
myStatus = 1; |
| 437 |
parseErr = parseDumpLine( read_buffer, which_atom ); |
| 438 |
if( parseErr != NULL ){ |
| 439 |
strcpy( painCave.errMsg, parseErr ); |
| 440 |
myStatus = 0;; |
| 441 |
simError(); |
| 442 |
} |
| 443 |
|
| 444 |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
| 445 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 446 |
|
| 447 |
} |
| 448 |
} |
| 449 |
|
| 450 |
// last thing last, enable fatalities. |
| 451 |
painCave.isEventLoop = 0; |
| 452 |
|
| 453 |
simnfo->setTime( time ); |
| 454 |
|
| 455 |
for(i=0;i<3;i++) |
| 456 |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
| 457 |
|
| 458 |
simnfo->setBoxM( theBoxMat3 ); |
| 459 |
|
| 460 |
|
| 461 |
#endif |
| 462 |
} |
| 463 |
|
| 464 |
char* DumpReader::parseDumpLine(char* readLine, int globalIndex){ |
| 465 |
|
| 466 |
char *foo; // the pointer to the current string token |
| 467 |
|
| 468 |
double pos[3]; // position place holders |
| 469 |
double vel[3]; // velocity placeholders |
| 470 |
double q[4]; // the quaternions |
| 471 |
double ji[3]; // angular velocity placeholders; |
| 472 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
| 473 |
|
| 474 |
Atom **atoms = simnfo->atoms; |
| 475 |
DirectionalAtom* dAtom; |
| 476 |
|
| 477 |
int j, n_atoms, atomIndex; |
| 478 |
|
| 479 |
#ifdef IS_MPI |
| 480 |
n_atoms = mpiSim->getTotAtoms(); |
| 481 |
atomIndex=-1; |
| 482 |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
| 483 |
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
| 484 |
} |
| 485 |
if (atomIndex == -1) { |
| 486 |
sprintf( painCave.errMsg, |
| 487 |
"Initialize from file error. Atom at index %d " |
| 488 |
"in file %s does not exist on processor %d .\n", |
| 489 |
globalIndex, inName, mpiSim->getMyNode() ); |
| 490 |
return strdup( painCave.errMsg ); |
| 491 |
} |
| 492 |
#else |
| 493 |
n_atoms = simnfo->n_atoms; |
| 494 |
atomIndex = globalIndex; |
| 495 |
#endif // is_mpi |
| 496 |
|
| 497 |
// set the string tokenizer |
| 498 |
|
| 499 |
foo = strtok(readLine, " ,;\t"); |
| 500 |
atoms[atomIndex]->setType(foo); |
| 501 |
// check the atom name to the current atom |
| 502 |
|
| 503 |
//if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
| 504 |
// sprintf( painCave.errMsg, |
| 505 |
// "Initialize from file error. Atom %s at index %d " |
| 506 |
// "in file %s does not" |
| 507 |
// " match the BASS atom %s.\n", |
| 508 |
// foo, atomIndex, inName, atoms[atomIndex]->getType() ); |
| 509 |
// return strdup( painCave.errMsg ); |
| 510 |
//} |
| 511 |
|
| 512 |
// get the positions |
| 513 |
|
| 514 |
foo = strtok(NULL, " ,;\t"); |
| 515 |
if(foo == NULL){ |
| 516 |
sprintf( painCave.errMsg, |
| 517 |
"error in reading postition x from %s\n" |
| 518 |
"natoms = %d, index = %d\n", |
| 519 |
inName, n_atoms, atomIndex ); |
| 520 |
return strdup( painCave.errMsg ); |
| 521 |
} |
| 522 |
pos[0] = atof( foo ); |
| 523 |
|
| 524 |
foo = strtok(NULL, " ,;\t"); |
| 525 |
if(foo == NULL){ |
| 526 |
sprintf( painCave.errMsg, |
| 527 |
"error in reading postition y from %s\n" |
| 528 |
"natoms = %d, index = %d\n", |
| 529 |
inName, n_atoms, atomIndex ); |
| 530 |
return strdup( painCave.errMsg ); |
| 531 |
} |
| 532 |
pos[1] = atof( foo ); |
| 533 |
|
| 534 |
foo = strtok(NULL, " ,;\t"); |
| 535 |
if(foo == NULL){ |
| 536 |
sprintf( painCave.errMsg, |
| 537 |
"error in reading postition z from %s\n" |
| 538 |
"natoms = %d, index = %d\n", |
| 539 |
inName, n_atoms, atomIndex ); |
| 540 |
return strdup( painCave.errMsg ); |
| 541 |
} |
| 542 |
pos[2] = atof( foo ); |
| 543 |
|
| 544 |
|
| 545 |
// get the velocities |
| 546 |
|
| 547 |
foo = strtok(NULL, " ,;\t"); |
| 548 |
if(foo == NULL){ |
| 549 |
sprintf( painCave.errMsg, |
| 550 |
"error in reading velocity x from %s\n" |
| 551 |
"natoms = %d, index = %d\n", |
| 552 |
inName, n_atoms, atomIndex ); |
| 553 |
return strdup( painCave.errMsg ); |
| 554 |
} |
| 555 |
vel[0] = atof( foo ); |
| 556 |
|
| 557 |
foo = strtok(NULL, " ,;\t"); |
| 558 |
if(foo == NULL){ |
| 559 |
sprintf( painCave.errMsg, |
| 560 |
"error in reading velocity y from %s\n" |
| 561 |
"natoms = %d, index = %d\n", |
| 562 |
inName, n_atoms, atomIndex ); |
| 563 |
return strdup( painCave.errMsg ); |
| 564 |
} |
| 565 |
vel[1] = atof( foo ); |
| 566 |
|
| 567 |
foo = strtok(NULL, " ,;\t"); |
| 568 |
if(foo == NULL){ |
| 569 |
sprintf( painCave.errMsg, |
| 570 |
"error in reading velocity z from %s\n" |
| 571 |
"natoms = %d, index = %d\n", |
| 572 |
inName, n_atoms, atomIndex ); |
| 573 |
return strdup( painCave.errMsg ); |
| 574 |
} |
| 575 |
vel[2] = atof( foo ); |
| 576 |
|
| 577 |
|
| 578 |
// get the quaternions |
| 579 |
|
| 580 |
if( atoms[atomIndex]->isDirectional() ){ |
| 581 |
|
| 582 |
foo = strtok(NULL, " ,;\t"); |
| 583 |
if(foo == NULL){ |
| 584 |
sprintf(painCave.errMsg, |
| 585 |
"error in reading quaternion 0 from %s\n" |
| 586 |
"natoms = %d, index = %d\n", |
| 587 |
inName, n_atoms, atomIndex ); |
| 588 |
return strdup( painCave.errMsg ); |
| 589 |
} |
| 590 |
q[0] = atof( foo ); |
| 591 |
|
| 592 |
foo = strtok(NULL, " ,;\t"); |
| 593 |
if(foo == NULL){ |
| 594 |
sprintf( painCave.errMsg, |
| 595 |
"error in reading quaternion 1 from %s\n" |
| 596 |
"natoms = %d, index = %d\n", |
| 597 |
inName, n_atoms, atomIndex ); |
| 598 |
return strdup( painCave.errMsg ); |
| 599 |
} |
| 600 |
q[1] = atof( foo ); |
| 601 |
|
| 602 |
foo = strtok(NULL, " ,;\t"); |
| 603 |
if(foo == NULL){ |
| 604 |
sprintf( painCave.errMsg, |
| 605 |
"error in reading quaternion 2 from %s\n" |
| 606 |
"natoms = %d, index = %d\n", |
| 607 |
inName, n_atoms, atomIndex ); |
| 608 |
return strdup( painCave.errMsg ); |
| 609 |
} |
| 610 |
q[2] = atof( foo ); |
| 611 |
|
| 612 |
foo = strtok(NULL, " ,;\t"); |
| 613 |
if(foo == NULL){ |
| 614 |
sprintf( painCave.errMsg, |
| 615 |
"error in reading quaternion 3 from %s\n" |
| 616 |
"natoms = %d, index = %d\n", |
| 617 |
inName, n_atoms, atomIndex ); |
| 618 |
return strdup( painCave.errMsg ); |
| 619 |
} |
| 620 |
q[3] = atof( foo ); |
| 621 |
|
| 622 |
// get the angular velocities |
| 623 |
|
| 624 |
foo = strtok(NULL, " ,;\t"); |
| 625 |
if(foo == NULL){ |
| 626 |
sprintf( painCave.errMsg, |
| 627 |
"error in reading angular momentum jx from %s\n" |
| 628 |
"natoms = %d, index = %d\n", |
| 629 |
inName, n_atoms, atomIndex ); |
| 630 |
return strdup( painCave.errMsg ); |
| 631 |
} |
| 632 |
ji[0] = atof( foo ); |
| 633 |
|
| 634 |
foo = strtok(NULL, " ,;\t"); |
| 635 |
if(foo == NULL){ |
| 636 |
sprintf( painCave.errMsg, |
| 637 |
"error in reading angular momentum jy from %s\n" |
| 638 |
"natoms = %d, index = %d\n", |
| 639 |
inName, n_atoms, atomIndex ); |
| 640 |
return strdup( painCave.errMsg ); |
| 641 |
} |
| 642 |
ji[1] = atof(foo ); |
| 643 |
|
| 644 |
foo = strtok(NULL, " ,;\t"); |
| 645 |
if(foo == NULL){ |
| 646 |
sprintf( painCave.errMsg, |
| 647 |
"error in reading angular momentum jz from %s\n" |
| 648 |
"natoms = %d, index = %d\n", |
| 649 |
inName, n_atoms, atomIndex ); |
| 650 |
return strdup( painCave.errMsg ); |
| 651 |
} |
| 652 |
ji[2] = atof( foo ); |
| 653 |
|
| 654 |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
| 655 |
|
| 656 |
// check that the quaternion vector is normalized |
| 657 |
|
| 658 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
| 659 |
|
| 660 |
qLength = sqrt( qSqr ); |
| 661 |
q[0] = q[0] / qLength; |
| 662 |
q[1] = q[1] / qLength; |
| 663 |
q[2] = q[2] / qLength; |
| 664 |
q[3] = q[3] / qLength; |
| 665 |
|
| 666 |
dAtom->setQ( q ); |
| 667 |
|
| 668 |
// add the angular velocities |
| 669 |
|
| 670 |
dAtom->setJ( ji ); |
| 671 |
} |
| 672 |
|
| 673 |
// add the positions and velocities to the atom |
| 674 |
|
| 675 |
atoms[atomIndex]->setPos( pos ); |
| 676 |
atoms[atomIndex]->setVel( vel ); |
| 677 |
|
| 678 |
return NULL; |
| 679 |
} |
| 680 |
|
| 681 |
|
| 682 |
char* DumpReader::parseCommentLine(char* readLine, double &time, |
| 683 |
double boxMat[9]){ |
| 684 |
|
| 685 |
char *foo; // the pointer to the current string token |
| 686 |
int j; |
| 687 |
double chi, integralOfChidt; |
| 688 |
double eta[9]; |
| 689 |
|
| 690 |
// set the string tokenizer |
| 691 |
|
| 692 |
foo = strtok(readLine, " ,;\t"); |
| 693 |
if(foo == NULL){ |
| 694 |
sprintf( painCave.errMsg, |
| 695 |
"error in reading time from %s\n", |
| 696 |
inName ); |
| 697 |
return strdup( painCave.errMsg ); |
| 698 |
} |
| 699 |
time = atof( foo ); |
| 700 |
|
| 701 |
// get the Hx vector |
| 702 |
|
| 703 |
foo = strtok(NULL, " ,;\t"); |
| 704 |
if(foo == NULL){ |
| 705 |
sprintf( painCave.errMsg, |
| 706 |
"error in reading Hx[0] from %s\n", |
| 707 |
inName ); |
| 708 |
return strdup( painCave.errMsg ); |
| 709 |
} |
| 710 |
boxMat[0] = atof( foo ); |
| 711 |
|
| 712 |
foo = strtok(NULL, " ,;\t"); |
| 713 |
if(foo == NULL){ |
| 714 |
sprintf( painCave.errMsg, |
| 715 |
"error in reading Hx[1] from %s\n", |
| 716 |
inName ); |
| 717 |
return strdup( painCave.errMsg ); |
| 718 |
} |
| 719 |
boxMat[1] = atof( foo ); |
| 720 |
|
| 721 |
foo = strtok(NULL, " ,;\t"); |
| 722 |
if(foo == NULL){ |
| 723 |
sprintf( painCave.errMsg, |
| 724 |
"error in reading Hx[2] from %s\n", |
| 725 |
inName ); |
| 726 |
return strdup( painCave.errMsg ); |
| 727 |
} |
| 728 |
boxMat[2] = atof( foo ); |
| 729 |
|
| 730 |
// get the Hy vector |
| 731 |
|
| 732 |
foo = strtok(NULL, " ,;\t"); |
| 733 |
if(foo == NULL){ |
| 734 |
sprintf( painCave.errMsg, |
| 735 |
"error in reading Hy[0] from %s\n", |
| 736 |
inName ); |
| 737 |
return strdup( painCave.errMsg ); |
| 738 |
} |
| 739 |
boxMat[3] = atof( foo ); |
| 740 |
|
| 741 |
foo = strtok(NULL, " ,;\t"); |
| 742 |
if(foo == NULL){ |
| 743 |
sprintf( painCave.errMsg, |
| 744 |
"error in reading Hy[1] from %s\n", |
| 745 |
inName ); |
| 746 |
return strdup( painCave.errMsg ); |
| 747 |
} |
| 748 |
boxMat[4] = atof( foo ); |
| 749 |
|
| 750 |
foo = strtok(NULL, " ,;\t"); |
| 751 |
if(foo == NULL){ |
| 752 |
sprintf( painCave.errMsg, |
| 753 |
"error in reading Hy[2] from %s\n", |
| 754 |
inName ); |
| 755 |
return strdup( painCave.errMsg ); |
| 756 |
} |
| 757 |
boxMat[5] = atof( foo ); |
| 758 |
|
| 759 |
// get the Hz vector |
| 760 |
|
| 761 |
foo = strtok(NULL, " ,;\t"); |
| 762 |
if(foo == NULL){ |
| 763 |
sprintf( painCave.errMsg, |
| 764 |
"error in reading Hz[0] from %s\n", |
| 765 |
inName ); |
| 766 |
return strdup( painCave.errMsg ); |
| 767 |
} |
| 768 |
boxMat[6] = atof( foo ); |
| 769 |
|
| 770 |
foo = strtok(NULL, " ,;\t"); |
| 771 |
if(foo == NULL){ |
| 772 |
sprintf( painCave.errMsg, |
| 773 |
"error in reading Hz[1] from %s\n", |
| 774 |
inName ); |
| 775 |
return strdup( painCave.errMsg ); |
| 776 |
} |
| 777 |
boxMat[7] = atof( foo ); |
| 778 |
|
| 779 |
foo = strtok(NULL, " ,;\t"); |
| 780 |
if(foo == NULL){ |
| 781 |
sprintf( painCave.errMsg, |
| 782 |
"error in reading Hz[2] from %s\n", |
| 783 |
inName ); |
| 784 |
return strdup( painCave.errMsg ); |
| 785 |
} |
| 786 |
boxMat[8] = atof( foo ); |
| 787 |
|
| 788 |
return NULL; |
| 789 |
|
| 790 |
//get chi and integralOfChidt, they should appear by pair |
| 791 |
foo = strtok(NULL, " ,;\t\n"); |
| 792 |
if(foo != NULL){ |
| 793 |
chi = atof(foo); |
| 794 |
|
| 795 |
foo = strtok(NULL, " ,;\t\n"); |
| 796 |
if(foo == NULL){ |
| 797 |
sprintf( painCave.errMsg, |
| 798 |
"chi and integralOfChidt should appear by pair in %s\n", inName ); |
| 799 |
return strdup( painCave.errMsg ); |
| 800 |
} |
| 801 |
integralOfChidt = atof( foo ); |
| 802 |
|
| 803 |
//push chi and integralOfChidt into SimInfo::properties which can be |
| 804 |
//retrieved by integrator later |
| 805 |
DoubleData* chiValue = new DoubleData(); |
| 806 |
chiValue->setID(CHIVALUE_ID); |
| 807 |
chiValue->setData(chi); |
| 808 |
simnfo->addProperty(chiValue); |
| 809 |
|
| 810 |
DoubleData* integralOfChidtValue = new DoubleData(); |
| 811 |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
| 812 |
integralOfChidtValue->setData(integralOfChidt); |
| 813 |
simnfo->addProperty(integralOfChidtValue); |
| 814 |
|
| 815 |
} |
| 816 |
else |
| 817 |
return NULL; |
| 818 |
|
| 819 |
//get eta |
| 820 |
for(int i = 0 ; i < 9; i++){ |
| 821 |
foo = strtok(NULL, " ,;\t"); |
| 822 |
if(foo == NULL){ |
| 823 |
sprintf( painCave.errMsg, |
| 824 |
"error in reading eta[%d] from %s\n", i, inName ); |
| 825 |
return strdup( painCave.errMsg ); |
| 826 |
} |
| 827 |
eta[i] = atof( foo ); |
| 828 |
} |
| 829 |
|
| 830 |
//push eta into SimInfo::properties which can be |
| 831 |
//retrieved by integrator later |
| 832 |
//simnfo->setBoxM( theBoxMat3 ); |
| 833 |
DoubleArrayData* etaValue = new DoubleArrayData(); |
| 834 |
etaValue->setID(ETAVALUE_ID); |
| 835 |
etaValue->setData(eta, 9); |
| 836 |
simnfo->addProperty(etaValue); |
| 837 |
|
| 838 |
|
| 839 |
return NULL; |
| 840 |
|
| 841 |
|
| 842 |
|
| 843 |
} |
| 844 |
|
| 845 |
|
| 846 |
#ifdef IS_MPI |
| 847 |
|
| 848 |
// a couple of functions to let us escape the read loop |
| 849 |
|
| 850 |
void dumpRead::nodeZeroError( void ){ |
| 851 |
int j, myStatus; |
| 852 |
|
| 853 |
myStatus = 0; |
| 854 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
| 855 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
| 856 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 857 |
} |
| 858 |
|
| 859 |
|
| 860 |
MPI_Finalize(); |
| 861 |
exit (0); |
| 862 |
|
| 863 |
} |
| 864 |
|
| 865 |
void dumpRead::anonymousNodeDie( void ){ |
| 866 |
|
| 867 |
MPI_Finalize(); |
| 868 |
exit (0); |
| 869 |
} |
| 870 |
|
| 871 |
#endif //is_mpi |
