| 1 |
#define _FILE_OFFSET_BITS 64 |
| 2 |
|
| 3 |
#include <string.h> |
| 4 |
#include <iostream> |
| 5 |
#include <fstream> |
| 6 |
|
| 7 |
#ifdef IS_MPI |
| 8 |
#include <mpi.h> |
| 9 |
#include "mpiSimulation.hpp" |
| 10 |
|
| 11 |
namespace dWrite{ |
| 12 |
void DieDieDie( void ); |
| 13 |
} |
| 14 |
|
| 15 |
using namespace dWrite; |
| 16 |
#endif //is_mpi |
| 17 |
|
| 18 |
#include "ReadWrite.hpp" |
| 19 |
#include "simError.h" |
| 20 |
|
| 21 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
| 22 |
|
| 23 |
entry_plug = the_entry_plug; |
| 24 |
|
| 25 |
#ifdef IS_MPI |
| 26 |
if(worldRank == 0 ){ |
| 27 |
#endif // is_mpi |
| 28 |
|
| 29 |
strcpy( outName, entry_plug->sampleName ); |
| 30 |
|
| 31 |
outFile.open(outName, ios::out | ios::trunc ); |
| 32 |
|
| 33 |
if( !outFile ){ |
| 34 |
|
| 35 |
sprintf( painCave.errMsg, |
| 36 |
"Could not open \"%s\" for dump output.\n", |
| 37 |
outName); |
| 38 |
painCave.isFatal = 1; |
| 39 |
simError(); |
| 40 |
} |
| 41 |
|
| 42 |
//outFile.setf( ios::scientific ); |
| 43 |
|
| 44 |
#ifdef IS_MPI |
| 45 |
} |
| 46 |
|
| 47 |
sprintf( checkPointMsg, |
| 48 |
"Sucessfully opened output file for dumping.\n"); |
| 49 |
MPIcheckPoint(); |
| 50 |
#endif // is_mpi |
| 51 |
} |
| 52 |
|
| 53 |
DumpWriter::~DumpWriter( ){ |
| 54 |
|
| 55 |
#ifdef IS_MPI |
| 56 |
if(worldRank == 0 ){ |
| 57 |
#endif // is_mpi |
| 58 |
|
| 59 |
outFile.close(); |
| 60 |
|
| 61 |
#ifdef IS_MPI |
| 62 |
} |
| 63 |
#endif // is_mpi |
| 64 |
} |
| 65 |
|
| 66 |
void DumpWriter::writeDump( double currentTime ){ |
| 67 |
|
| 68 |
const int BUFFERSIZE = 2000; |
| 69 |
const int MINIBUFFERSIZE = 100; |
| 70 |
|
| 71 |
char tempBuffer[BUFFERSIZE]; |
| 72 |
char writeLine[BUFFERSIZE]; |
| 73 |
|
| 74 |
int i; |
| 75 |
|
| 76 |
#ifdef IS_MPI |
| 77 |
|
| 78 |
int *potatoes; |
| 79 |
int myPotato; |
| 80 |
|
| 81 |
int nProc; |
| 82 |
int j, which_node, done, which_atom, local_index; |
| 83 |
double atomData6[6]; |
| 84 |
double atomData13[13]; |
| 85 |
int isDirectional; |
| 86 |
char* atomTypeString; |
| 87 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
| 88 |
|
| 89 |
#else //is_mpi |
| 90 |
int nAtoms = entry_plug->n_atoms; |
| 91 |
#endif //is_mpi |
| 92 |
|
| 93 |
double q[4]; |
| 94 |
DirectionalAtom* dAtom; |
| 95 |
Atom** atoms = entry_plug->atoms; |
| 96 |
double pos[3], vel[3]; |
| 97 |
|
| 98 |
// write current frame to the eor file |
| 99 |
|
| 100 |
this->writeFinal( currentTime ); |
| 101 |
|
| 102 |
#ifndef IS_MPI |
| 103 |
|
| 104 |
outFile << nAtoms << "\n"; |
| 105 |
|
| 106 |
outFile << currentTime << ";\t" |
| 107 |
<< entry_plug->Hmat[0][0] << "\t" |
| 108 |
<< entry_plug->Hmat[1][0] << "\t" |
| 109 |
<< entry_plug->Hmat[2][0] << ";\t" |
| 110 |
|
| 111 |
<< entry_plug->Hmat[0][1] << "\t" |
| 112 |
<< entry_plug->Hmat[1][1] << "\t" |
| 113 |
<< entry_plug->Hmat[2][1] << ";\t" |
| 114 |
|
| 115 |
<< entry_plug->Hmat[0][2] << "\t" |
| 116 |
<< entry_plug->Hmat[1][2] << "\t" |
| 117 |
<< entry_plug->Hmat[2][2] << ";"; |
| 118 |
//write out additional parameters, such as chi and eta |
| 119 |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
| 120 |
outFile << endl; |
| 121 |
|
| 122 |
for( i=0; i<nAtoms; i++ ){ |
| 123 |
|
| 124 |
atoms[i]->getPos(pos); |
| 125 |
atoms[i]->getVel(vel); |
| 126 |
|
| 127 |
sprintf( tempBuffer, |
| 128 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 129 |
atoms[i]->getType(), |
| 130 |
pos[0], |
| 131 |
pos[1], |
| 132 |
pos[2], |
| 133 |
vel[0], |
| 134 |
vel[1], |
| 135 |
vel[2]); |
| 136 |
strcpy( writeLine, tempBuffer ); |
| 137 |
|
| 138 |
if( atoms[i]->isDirectional() ){ |
| 139 |
|
| 140 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 141 |
dAtom->getQ( q ); |
| 142 |
|
| 143 |
sprintf( tempBuffer, |
| 144 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 145 |
q[0], |
| 146 |
q[1], |
| 147 |
q[2], |
| 148 |
q[3], |
| 149 |
dAtom->getJx(), |
| 150 |
dAtom->getJy(), |
| 151 |
dAtom->getJz()); |
| 152 |
strcat( writeLine, tempBuffer ); |
| 153 |
} |
| 154 |
else |
| 155 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 156 |
|
| 157 |
outFile << writeLine; |
| 158 |
} |
| 159 |
outFile.flush(); |
| 160 |
|
| 161 |
#else // is_mpi |
| 162 |
|
| 163 |
/* code to find maximum tag value */ |
| 164 |
|
| 165 |
int *tagub, flag, MAXTAG; |
| 166 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
| 167 |
if (flag) { |
| 168 |
MAXTAG = *tagub; |
| 169 |
} else { |
| 170 |
MAXTAG = 32767; |
| 171 |
} |
| 172 |
|
| 173 |
int haveError; |
| 174 |
|
| 175 |
MPI_Status istatus; |
| 176 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
| 177 |
|
| 178 |
// write out header and node 0's coordinates |
| 179 |
|
| 180 |
if( worldRank == 0 ){ |
| 181 |
|
| 182 |
// Node 0 needs a list of the magic potatoes for each processor; |
| 183 |
|
| 184 |
nProc = mpiSim->getNumberProcessors(); |
| 185 |
potatoes = new int[nProc]; |
| 186 |
|
| 187 |
for (i = 0; i < nProc; i++) |
| 188 |
potatoes[i] = 0; |
| 189 |
|
| 190 |
outFile << mpiSim->getTotAtoms() << "\n"; |
| 191 |
|
| 192 |
outFile << currentTime << ";\t" |
| 193 |
<< entry_plug->Hmat[0][0] << "\t" |
| 194 |
<< entry_plug->Hmat[1][0] << "\t" |
| 195 |
<< entry_plug->Hmat[2][0] << ";\t" |
| 196 |
|
| 197 |
<< entry_plug->Hmat[0][1] << "\t" |
| 198 |
<< entry_plug->Hmat[1][1] << "\t" |
| 199 |
<< entry_plug->Hmat[2][1] << ";\t" |
| 200 |
|
| 201 |
<< entry_plug->Hmat[0][2] << "\t" |
| 202 |
<< entry_plug->Hmat[1][2] << "\t" |
| 203 |
<< entry_plug->Hmat[2][2] << ";"; |
| 204 |
|
| 205 |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
| 206 |
outFile << endl; |
| 207 |
outFile.flush(); |
| 208 |
|
| 209 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
| 210 |
|
| 211 |
// Get the Node number which has this atom; |
| 212 |
|
| 213 |
which_node = AtomToProcMap[i]; |
| 214 |
|
| 215 |
if (which_node != 0) { |
| 216 |
|
| 217 |
if (potatoes[which_node] + 3 >= MAXTAG) { |
| 218 |
// The potato was going to exceed the maximum value, |
| 219 |
// so wrap this processor potato back to 0: |
| 220 |
|
| 221 |
potatoes[which_node] = 0; |
| 222 |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
| 223 |
|
| 224 |
} |
| 225 |
|
| 226 |
myPotato = potatoes[which_node]; |
| 227 |
|
| 228 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
| 229 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 230 |
|
| 231 |
//strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
| 232 |
|
| 233 |
// Null terminate the atomTypeString just in case: |
| 234 |
|
| 235 |
//atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
| 236 |
atomTypeString = MPIatomTypeString; |
| 237 |
|
| 238 |
myPotato++; |
| 239 |
|
| 240 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
| 241 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 242 |
|
| 243 |
myPotato++; |
| 244 |
|
| 245 |
if (isDirectional) { |
| 246 |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
| 247 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 248 |
} else { |
| 249 |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
| 250 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 251 |
} |
| 252 |
|
| 253 |
myPotato++; |
| 254 |
potatoes[which_node] = myPotato; |
| 255 |
|
| 256 |
} else { |
| 257 |
|
| 258 |
haveError = 0; |
| 259 |
which_atom = i; |
| 260 |
local_index=-1; |
| 261 |
|
| 262 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
| 263 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
| 264 |
} |
| 265 |
|
| 266 |
if (local_index != -1) { |
| 267 |
|
| 268 |
atomTypeString = atoms[local_index]->getType(); |
| 269 |
|
| 270 |
atoms[local_index]->getPos(pos); |
| 271 |
atoms[local_index]->getVel(vel); |
| 272 |
|
| 273 |
atomData6[0] = pos[0]; |
| 274 |
atomData6[1] = pos[1]; |
| 275 |
atomData6[2] = pos[2]; |
| 276 |
|
| 277 |
atomData6[3] = vel[0]; |
| 278 |
atomData6[4] = vel[1]; |
| 279 |
atomData6[5] = vel[2]; |
| 280 |
|
| 281 |
isDirectional = 0; |
| 282 |
|
| 283 |
if( atoms[local_index]->isDirectional() ){ |
| 284 |
|
| 285 |
isDirectional = 1; |
| 286 |
|
| 287 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
| 288 |
dAtom->getQ( q ); |
| 289 |
|
| 290 |
for (int j = 0; j < 6 ; j++) |
| 291 |
atomData13[j] = atomData6[j]; |
| 292 |
|
| 293 |
atomData13[6] = q[0]; |
| 294 |
atomData13[7] = q[1]; |
| 295 |
atomData13[8] = q[2]; |
| 296 |
atomData13[9] = q[3]; |
| 297 |
|
| 298 |
atomData13[10] = dAtom->getJx(); |
| 299 |
atomData13[11] = dAtom->getJy(); |
| 300 |
atomData13[12] = dAtom->getJz(); |
| 301 |
} |
| 302 |
|
| 303 |
} else { |
| 304 |
sprintf(painCave.errMsg, |
| 305 |
"Atom %d not found on processor %d\n", |
| 306 |
i, worldRank ); |
| 307 |
haveError= 1; |
| 308 |
simError(); |
| 309 |
} |
| 310 |
|
| 311 |
if(haveError) DieDieDie(); |
| 312 |
|
| 313 |
} |
| 314 |
// If we've survived to here, format the line: |
| 315 |
|
| 316 |
if (!isDirectional) { |
| 317 |
|
| 318 |
sprintf( tempBuffer, |
| 319 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 320 |
atomTypeString, |
| 321 |
atomData6[0], |
| 322 |
atomData6[1], |
| 323 |
atomData6[2], |
| 324 |
atomData6[3], |
| 325 |
atomData6[4], |
| 326 |
atomData6[5]); |
| 327 |
|
| 328 |
strcpy( writeLine, tempBuffer ); |
| 329 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 330 |
|
| 331 |
} else { |
| 332 |
|
| 333 |
sprintf( tempBuffer, |
| 334 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 335 |
atomTypeString, |
| 336 |
atomData13[0], |
| 337 |
atomData13[1], |
| 338 |
atomData13[2], |
| 339 |
atomData13[3], |
| 340 |
atomData13[4], |
| 341 |
atomData13[5], |
| 342 |
atomData13[6], |
| 343 |
atomData13[7], |
| 344 |
atomData13[8], |
| 345 |
atomData13[9], |
| 346 |
atomData13[10], |
| 347 |
atomData13[11], |
| 348 |
atomData13[12]); |
| 349 |
|
| 350 |
strcpy( writeLine, tempBuffer ); |
| 351 |
|
| 352 |
} |
| 353 |
|
| 354 |
outFile << writeLine; |
| 355 |
outFile.flush(); |
| 356 |
} |
| 357 |
|
| 358 |
|
| 359 |
outFile.flush(); |
| 360 |
sprintf( checkPointMsg, |
| 361 |
"Sucessfully took a dump.\n"); |
| 362 |
MPIcheckPoint(); |
| 363 |
delete[] potatoes; |
| 364 |
} else { |
| 365 |
|
| 366 |
// worldRank != 0, so I'm a remote node. |
| 367 |
|
| 368 |
// Set my magic potato to 0: |
| 369 |
|
| 370 |
myPotato = 0; |
| 371 |
|
| 372 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
| 373 |
|
| 374 |
// Am I the node which has this atom? |
| 375 |
|
| 376 |
if (AtomToProcMap[i] == worldRank) { |
| 377 |
|
| 378 |
if (myPotato + 3 >= MAXTAG) { |
| 379 |
|
| 380 |
// The potato was going to exceed the maximum value, |
| 381 |
// so wrap this processor potato back to 0 (and block until |
| 382 |
// node 0 says we can go: |
| 383 |
|
| 384 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
| 385 |
|
| 386 |
} |
| 387 |
which_atom = i; |
| 388 |
local_index=-1; |
| 389 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
| 390 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
| 391 |
} |
| 392 |
if (local_index != -1) { |
| 393 |
|
| 394 |
atomTypeString = atoms[local_index]->getType(); |
| 395 |
|
| 396 |
atoms[local_index]->getPos(pos); |
| 397 |
atoms[local_index]->getVel(vel); |
| 398 |
|
| 399 |
atomData6[0] = pos[0]; |
| 400 |
atomData6[1] = pos[1]; |
| 401 |
atomData6[2] = pos[2]; |
| 402 |
|
| 403 |
atomData6[3] = vel[0]; |
| 404 |
atomData6[4] = vel[1]; |
| 405 |
atomData6[5] = vel[2]; |
| 406 |
|
| 407 |
isDirectional = 0; |
| 408 |
|
| 409 |
if( atoms[local_index]->isDirectional() ){ |
| 410 |
|
| 411 |
isDirectional = 1; |
| 412 |
|
| 413 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
| 414 |
dAtom->getQ( q ); |
| 415 |
|
| 416 |
for (int j = 0; j < 6 ; j++) |
| 417 |
atomData13[j] = atomData6[j]; |
| 418 |
|
| 419 |
atomData13[6] = q[0]; |
| 420 |
atomData13[7] = q[1]; |
| 421 |
atomData13[8] = q[2]; |
| 422 |
atomData13[9] = q[3]; |
| 423 |
|
| 424 |
atomData13[10] = dAtom->getJx(); |
| 425 |
atomData13[11] = dAtom->getJy(); |
| 426 |
atomData13[12] = dAtom->getJz(); |
| 427 |
} |
| 428 |
|
| 429 |
} else { |
| 430 |
sprintf(painCave.errMsg, |
| 431 |
"Atom %d not found on processor %d\n", |
| 432 |
i, worldRank ); |
| 433 |
haveError= 1; |
| 434 |
simError(); |
| 435 |
} |
| 436 |
|
| 437 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
| 438 |
|
| 439 |
// null terminate the string before sending (just in case): |
| 440 |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
| 441 |
|
| 442 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
| 443 |
myPotato, MPI_COMM_WORLD); |
| 444 |
|
| 445 |
myPotato++; |
| 446 |
|
| 447 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
| 448 |
myPotato, MPI_COMM_WORLD); |
| 449 |
|
| 450 |
myPotato++; |
| 451 |
|
| 452 |
if (isDirectional) { |
| 453 |
|
| 454 |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
| 455 |
myPotato, MPI_COMM_WORLD); |
| 456 |
|
| 457 |
} else { |
| 458 |
|
| 459 |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
| 460 |
myPotato, MPI_COMM_WORLD); |
| 461 |
} |
| 462 |
|
| 463 |
myPotato++; |
| 464 |
} |
| 465 |
} |
| 466 |
|
| 467 |
sprintf( checkPointMsg, |
| 468 |
"Sucessfully took a dump.\n"); |
| 469 |
MPIcheckPoint(); |
| 470 |
|
| 471 |
} |
| 472 |
|
| 473 |
#endif // is_mpi |
| 474 |
} |
| 475 |
|
| 476 |
void DumpWriter::writeFinal(double finalTime){ |
| 477 |
|
| 478 |
char finalName[500]; |
| 479 |
ofstream finalOut; |
| 480 |
|
| 481 |
const int BUFFERSIZE = 2000; |
| 482 |
const int MINIBUFFERSIZE = 100; |
| 483 |
char tempBuffer[BUFFERSIZE]; |
| 484 |
char writeLine[BUFFERSIZE]; |
| 485 |
|
| 486 |
double q[4]; |
| 487 |
DirectionalAtom* dAtom; |
| 488 |
Atom** atoms = entry_plug->atoms; |
| 489 |
int i; |
| 490 |
#ifdef IS_MPI |
| 491 |
|
| 492 |
int *potatoes; |
| 493 |
int myPotato; |
| 494 |
|
| 495 |
int nProc; |
| 496 |
int j, which_node, done, which_atom, local_index; |
| 497 |
double atomData6[6]; |
| 498 |
double atomData13[13]; |
| 499 |
int isDirectional; |
| 500 |
char* atomTypeString; |
| 501 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
| 502 |
|
| 503 |
#else //is_mpi |
| 504 |
int nAtoms = entry_plug->n_atoms; |
| 505 |
#endif //is_mpi |
| 506 |
|
| 507 |
double pos[3], vel[3]; |
| 508 |
|
| 509 |
#ifdef IS_MPI |
| 510 |
if(worldRank == 0 ){ |
| 511 |
#endif // is_mpi |
| 512 |
|
| 513 |
strcpy( finalName, entry_plug->finalName ); |
| 514 |
|
| 515 |
finalOut.open( finalName, ios::out | ios::trunc ); |
| 516 |
if( !finalOut ){ |
| 517 |
sprintf( painCave.errMsg, |
| 518 |
"Could not open \"%s\" for final dump output.\n", |
| 519 |
finalName ); |
| 520 |
painCave.isFatal = 1; |
| 521 |
simError(); |
| 522 |
} |
| 523 |
|
| 524 |
// finalOut.setf( ios::scientific ); |
| 525 |
|
| 526 |
#ifdef IS_MPI |
| 527 |
} |
| 528 |
|
| 529 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
| 530 |
MPIcheckPoint(); |
| 531 |
|
| 532 |
#endif //is_mpi |
| 533 |
|
| 534 |
|
| 535 |
#ifndef IS_MPI |
| 536 |
|
| 537 |
finalOut << nAtoms << "\n"; |
| 538 |
|
| 539 |
finalOut << finalTime << ";\t" |
| 540 |
<< entry_plug->Hmat[0][0] << "\t" |
| 541 |
<< entry_plug->Hmat[1][0] << "\t" |
| 542 |
<< entry_plug->Hmat[2][0] << ";\t" |
| 543 |
|
| 544 |
<< entry_plug->Hmat[0][1] << "\t" |
| 545 |
<< entry_plug->Hmat[1][1] << "\t" |
| 546 |
<< entry_plug->Hmat[2][1] << ";\t" |
| 547 |
|
| 548 |
<< entry_plug->Hmat[0][2] << "\t" |
| 549 |
<< entry_plug->Hmat[1][2] << "\t" |
| 550 |
<< entry_plug->Hmat[2][2] << ";"; |
| 551 |
|
| 552 |
//write out additional parameters, such as chi and eta |
| 553 |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
| 554 |
finalOut << endl; |
| 555 |
|
| 556 |
for( i=0; i<nAtoms; i++ ){ |
| 557 |
|
| 558 |
atoms[i]->getPos(pos); |
| 559 |
atoms[i]->getVel(vel); |
| 560 |
|
| 561 |
sprintf( tempBuffer, |
| 562 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 563 |
atoms[i]->getType(), |
| 564 |
pos[0], |
| 565 |
pos[1], |
| 566 |
pos[2], |
| 567 |
vel[0], |
| 568 |
vel[1], |
| 569 |
vel[2]); |
| 570 |
strcpy( writeLine, tempBuffer ); |
| 571 |
|
| 572 |
if( atoms[i]->isDirectional() ){ |
| 573 |
|
| 574 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 575 |
dAtom->getQ( q ); |
| 576 |
|
| 577 |
sprintf( tempBuffer, |
| 578 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 579 |
q[0], |
| 580 |
q[1], |
| 581 |
q[2], |
| 582 |
q[3], |
| 583 |
dAtom->getJx(), |
| 584 |
dAtom->getJy(), |
| 585 |
dAtom->getJz()); |
| 586 |
strcat( writeLine, tempBuffer ); |
| 587 |
} |
| 588 |
else |
| 589 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 590 |
|
| 591 |
finalOut << writeLine; |
| 592 |
} |
| 593 |
finalOut.flush(); |
| 594 |
finalOut.close(); |
| 595 |
|
| 596 |
#else // is_mpi |
| 597 |
|
| 598 |
/* code to find maximum tag value */ |
| 599 |
int *tagub, flag, MAXTAG; |
| 600 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
| 601 |
if (flag) { |
| 602 |
MAXTAG = *tagub; |
| 603 |
} else { |
| 604 |
MAXTAG = 32767; |
| 605 |
} |
| 606 |
|
| 607 |
int haveError; |
| 608 |
|
| 609 |
MPI_Status istatus; |
| 610 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
| 611 |
|
| 612 |
// write out header and node 0's coordinates |
| 613 |
|
| 614 |
if( worldRank == 0 ){ |
| 615 |
|
| 616 |
// Node 0 needs a list of the magic potatoes for each processor; |
| 617 |
|
| 618 |
nProc = mpiSim->getNumberProcessors(); |
| 619 |
potatoes = new int[nProc]; |
| 620 |
|
| 621 |
for (i = 0; i < nProc; i++) |
| 622 |
potatoes[i] = 0; |
| 623 |
|
| 624 |
finalOut << mpiSim->getTotAtoms() << "\n"; |
| 625 |
|
| 626 |
finalOut << finalTime << ";\t" |
| 627 |
<< entry_plug->Hmat[0][0] << "\t" |
| 628 |
<< entry_plug->Hmat[1][0] << "\t" |
| 629 |
<< entry_plug->Hmat[2][0] << ";\t" |
| 630 |
|
| 631 |
<< entry_plug->Hmat[0][1] << "\t" |
| 632 |
<< entry_plug->Hmat[1][1] << "\t" |
| 633 |
<< entry_plug->Hmat[2][1] << ";\t" |
| 634 |
|
| 635 |
<< entry_plug->Hmat[0][2] << "\t" |
| 636 |
<< entry_plug->Hmat[1][2] << "\t" |
| 637 |
<< entry_plug->Hmat[2][2] << ";"; |
| 638 |
|
| 639 |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
| 640 |
finalOut << endl; |
| 641 |
finalOut.flush(); |
| 642 |
|
| 643 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
| 644 |
|
| 645 |
// Get the Node number which has this atom; |
| 646 |
|
| 647 |
which_node = AtomToProcMap[i]; |
| 648 |
|
| 649 |
if (which_node != 0) { |
| 650 |
|
| 651 |
if (potatoes[which_node] + 3 >= MAXTAG) { |
| 652 |
// The potato was going to exceed the maximum value, |
| 653 |
// so wrap this processor potato back to 0: |
| 654 |
|
| 655 |
potatoes[which_node] = 0; |
| 656 |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
| 657 |
|
| 658 |
} |
| 659 |
|
| 660 |
myPotato = potatoes[which_node]; |
| 661 |
|
| 662 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
| 663 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 664 |
|
| 665 |
atomTypeString = MPIatomTypeString; |
| 666 |
|
| 667 |
myPotato++; |
| 668 |
|
| 669 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
| 670 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 671 |
|
| 672 |
myPotato++; |
| 673 |
|
| 674 |
if (isDirectional) { |
| 675 |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
| 676 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 677 |
} else { |
| 678 |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
| 679 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 680 |
} |
| 681 |
|
| 682 |
myPotato++; |
| 683 |
potatoes[which_node] = myPotato; |
| 684 |
|
| 685 |
} else { |
| 686 |
|
| 687 |
haveError = 0; |
| 688 |
which_atom = i; |
| 689 |
local_index=-1; |
| 690 |
|
| 691 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
| 692 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
| 693 |
} |
| 694 |
|
| 695 |
if (local_index != -1) { |
| 696 |
|
| 697 |
atomTypeString = atoms[local_index]->getType(); |
| 698 |
|
| 699 |
atoms[local_index]->getPos(pos); |
| 700 |
atoms[local_index]->getVel(vel); |
| 701 |
|
| 702 |
atomData6[0] = pos[0]; |
| 703 |
atomData6[1] = pos[1]; |
| 704 |
atomData6[2] = pos[2]; |
| 705 |
|
| 706 |
atomData6[3] = vel[0]; |
| 707 |
atomData6[4] = vel[1]; |
| 708 |
atomData6[5] = vel[2]; |
| 709 |
|
| 710 |
isDirectional = 0; |
| 711 |
|
| 712 |
if( atoms[local_index]->isDirectional() ){ |
| 713 |
|
| 714 |
isDirectional = 1; |
| 715 |
|
| 716 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
| 717 |
dAtom->getQ( q ); |
| 718 |
|
| 719 |
for (int j = 0; j < 6 ; j++) |
| 720 |
atomData13[j] = atomData6[j]; |
| 721 |
|
| 722 |
atomData13[6] = q[0]; |
| 723 |
atomData13[7] = q[1]; |
| 724 |
atomData13[8] = q[2]; |
| 725 |
atomData13[9] = q[3]; |
| 726 |
|
| 727 |
atomData13[10] = dAtom->getJx(); |
| 728 |
atomData13[11] = dAtom->getJy(); |
| 729 |
atomData13[12] = dAtom->getJz(); |
| 730 |
} |
| 731 |
|
| 732 |
} else { |
| 733 |
sprintf(painCave.errMsg, |
| 734 |
"Atom %d not found on processor %d\n", |
| 735 |
i, worldRank ); |
| 736 |
haveError= 1; |
| 737 |
simError(); |
| 738 |
} |
| 739 |
|
| 740 |
if(haveError) DieDieDie(); |
| 741 |
|
| 742 |
} |
| 743 |
|
| 744 |
|
| 745 |
// If we've survived to here, format the line: |
| 746 |
|
| 747 |
if (!isDirectional) { |
| 748 |
|
| 749 |
sprintf( tempBuffer, |
| 750 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 751 |
atomTypeString, |
| 752 |
atomData6[0], |
| 753 |
atomData6[1], |
| 754 |
atomData6[2], |
| 755 |
atomData6[3], |
| 756 |
atomData6[4], |
| 757 |
atomData6[5]); |
| 758 |
|
| 759 |
strcpy( writeLine, tempBuffer ); |
| 760 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 761 |
|
| 762 |
} else { |
| 763 |
|
| 764 |
sprintf( tempBuffer, |
| 765 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 766 |
atomTypeString, |
| 767 |
atomData13[0], |
| 768 |
atomData13[1], |
| 769 |
atomData13[2], |
| 770 |
atomData13[3], |
| 771 |
atomData13[4], |
| 772 |
atomData13[5], |
| 773 |
atomData13[6], |
| 774 |
atomData13[7], |
| 775 |
atomData13[8], |
| 776 |
atomData13[9], |
| 777 |
atomData13[10], |
| 778 |
atomData13[11], |
| 779 |
atomData13[12]); |
| 780 |
|
| 781 |
strcpy( writeLine, tempBuffer ); |
| 782 |
|
| 783 |
} |
| 784 |
|
| 785 |
finalOut << writeLine; |
| 786 |
finalOut.flush(); |
| 787 |
} |
| 788 |
|
| 789 |
finalOut.flush(); |
| 790 |
sprintf( checkPointMsg, |
| 791 |
"Sucessfully took a dump.\n"); |
| 792 |
delete[] potatoes; |
| 793 |
|
| 794 |
MPIcheckPoint(); |
| 795 |
|
| 796 |
} else { |
| 797 |
|
| 798 |
// worldRank != 0, so I'm a remote node. |
| 799 |
|
| 800 |
// Set my magic potato to 0: |
| 801 |
|
| 802 |
myPotato = 0; |
| 803 |
|
| 804 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
| 805 |
|
| 806 |
// Am I the node which has this atom? |
| 807 |
|
| 808 |
if (AtomToProcMap[i] == worldRank) { |
| 809 |
|
| 810 |
if (myPotato + 3 >= MAXTAG) { |
| 811 |
|
| 812 |
// The potato was going to exceed the maximum value, |
| 813 |
// so wrap this processor potato back to 0 (and block until |
| 814 |
// node 0 says we can go: |
| 815 |
|
| 816 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
| 817 |
|
| 818 |
} |
| 819 |
which_atom = i; |
| 820 |
local_index=-1; |
| 821 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
| 822 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
| 823 |
} |
| 824 |
if (local_index != -1) { |
| 825 |
|
| 826 |
atomTypeString = atoms[local_index]->getType(); |
| 827 |
|
| 828 |
atoms[local_index]->getPos(pos); |
| 829 |
atoms[local_index]->getVel(vel); |
| 830 |
|
| 831 |
atomData6[0] = pos[0]; |
| 832 |
atomData6[1] = pos[1]; |
| 833 |
atomData6[2] = pos[2]; |
| 834 |
|
| 835 |
atomData6[3] = vel[0]; |
| 836 |
atomData6[4] = vel[1]; |
| 837 |
atomData6[5] = vel[2]; |
| 838 |
|
| 839 |
isDirectional = 0; |
| 840 |
|
| 841 |
if( atoms[local_index]->isDirectional() ){ |
| 842 |
|
| 843 |
isDirectional = 1; |
| 844 |
|
| 845 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
| 846 |
dAtom->getQ( q ); |
| 847 |
|
| 848 |
for (int j = 0; j < 6 ; j++) |
| 849 |
atomData13[j] = atomData6[j]; |
| 850 |
|
| 851 |
atomData13[6] = q[0]; |
| 852 |
atomData13[7] = q[1]; |
| 853 |
atomData13[8] = q[2]; |
| 854 |
atomData13[9] = q[3]; |
| 855 |
|
| 856 |
atomData13[10] = dAtom->getJx(); |
| 857 |
atomData13[11] = dAtom->getJy(); |
| 858 |
atomData13[12] = dAtom->getJz(); |
| 859 |
} |
| 860 |
|
| 861 |
} else { |
| 862 |
sprintf(painCave.errMsg, |
| 863 |
"Atom %d not found on processor %d\n", |
| 864 |
i, worldRank ); |
| 865 |
haveError= 1; |
| 866 |
simError(); |
| 867 |
} |
| 868 |
|
| 869 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
| 870 |
|
| 871 |
// null terminate the string before sending (just in case): |
| 872 |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
| 873 |
|
| 874 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
| 875 |
myPotato, MPI_COMM_WORLD); |
| 876 |
|
| 877 |
myPotato++; |
| 878 |
|
| 879 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
| 880 |
myPotato, MPI_COMM_WORLD); |
| 881 |
|
| 882 |
myPotato++; |
| 883 |
|
| 884 |
if (isDirectional) { |
| 885 |
|
| 886 |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
| 887 |
myPotato, MPI_COMM_WORLD); |
| 888 |
|
| 889 |
} else { |
| 890 |
|
| 891 |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
| 892 |
myPotato, MPI_COMM_WORLD); |
| 893 |
} |
| 894 |
|
| 895 |
myPotato++; |
| 896 |
} |
| 897 |
} |
| 898 |
|
| 899 |
sprintf( checkPointMsg, |
| 900 |
"Sucessfully took a dump.\n"); |
| 901 |
MPIcheckPoint(); |
| 902 |
|
| 903 |
} |
| 904 |
|
| 905 |
if( worldRank == 0 ) finalOut.close(); |
| 906 |
#endif // is_mpi |
| 907 |
} |
| 908 |
|
| 909 |
|
| 910 |
|
| 911 |
#ifdef IS_MPI |
| 912 |
|
| 913 |
// a couple of functions to let us escape the write loop |
| 914 |
|
| 915 |
void dWrite::DieDieDie( void ){ |
| 916 |
|
| 917 |
MPI_Finalize(); |
| 918 |
exit (0); |
| 919 |
} |
| 920 |
|
| 921 |
#endif //is_mpi |
