| 1 |
#include <cstring> |
| 2 |
#include <iostream> |
| 3 |
#include <fstream> |
| 4 |
|
| 5 |
#ifdef IS_MPI |
| 6 |
#include <mpi.h> |
| 7 |
#include <mpi++.h> |
| 8 |
#include "mpiSimulation.hpp" |
| 9 |
#define TAKE_THIS_TAG_CHAR 1 |
| 10 |
#define TAKE_THIS_TAG_INT 2 |
| 11 |
#endif //is_mpi |
| 12 |
|
| 13 |
#include "ReadWrite.hpp" |
| 14 |
#include "simError.h" |
| 15 |
|
| 16 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
| 17 |
|
| 18 |
entry_plug = the_entry_plug; |
| 19 |
|
| 20 |
#ifdef IS_MPI |
| 21 |
if(worldRank == 0 ){ |
| 22 |
#endif // is_mpi |
| 23 |
|
| 24 |
|
| 25 |
|
| 26 |
strcpy( outName, entry_plug->sampleName ); |
| 27 |
|
| 28 |
outFile.open(outName, ios::out | ios::trunc ); |
| 29 |
|
| 30 |
if( !outFile ){ |
| 31 |
|
| 32 |
sprintf( painCave.errMsg, |
| 33 |
"Could not open \"%s\" for dump output.\n", |
| 34 |
outName); |
| 35 |
painCave.isFatal = 1; |
| 36 |
simError(); |
| 37 |
} |
| 38 |
|
| 39 |
//outFile.setf( ios::scientific ); |
| 40 |
|
| 41 |
#ifdef IS_MPI |
| 42 |
} |
| 43 |
|
| 44 |
sprintf( checkPointMsg, |
| 45 |
"Sucessfully opened output file for dumping.\n"); |
| 46 |
MPIcheckPoint(); |
| 47 |
#endif // is_mpi |
| 48 |
} |
| 49 |
|
| 50 |
DumpWriter::~DumpWriter( ){ |
| 51 |
|
| 52 |
#ifdef IS_MPI |
| 53 |
if(worldRank == 0 ){ |
| 54 |
#endif // is_mpi |
| 55 |
|
| 56 |
outFile.close(); |
| 57 |
|
| 58 |
#ifdef IS_MPI |
| 59 |
} |
| 60 |
#endif // is_mpi |
| 61 |
} |
| 62 |
|
| 63 |
void DumpWriter::writeDump( double currentTime ){ |
| 64 |
|
| 65 |
const int BUFFERSIZE = 2000; |
| 66 |
char tempBuffer[BUFFERSIZE]; |
| 67 |
char writeLine[BUFFERSIZE]; |
| 68 |
|
| 69 |
int i, j, which_node, done, game_over, which_atom, local_index; |
| 70 |
double q[4]; |
| 71 |
DirectionalAtom* dAtom; |
| 72 |
int nAtoms = entry_plug->n_atoms; |
| 73 |
Atom** atoms = entry_plug->atoms; |
| 74 |
|
| 75 |
|
| 76 |
#ifndef IS_MPI |
| 77 |
|
| 78 |
outFile << nAtoms << "\n"; |
| 79 |
|
| 80 |
outFile << currentTime << "\t" |
| 81 |
<< entry_plug->box_x << "\t" |
| 82 |
<< entry_plug->box_y << "\t" |
| 83 |
<< entry_plug->box_z << "\n"; |
| 84 |
|
| 85 |
for( i=0; i<nAtoms; i++ ){ |
| 86 |
|
| 87 |
|
| 88 |
sprintf( tempBuffer, |
| 89 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 90 |
atoms[i]->getType(), |
| 91 |
atoms[i]->getX(), |
| 92 |
atoms[i]->getY(), |
| 93 |
atoms[i]->getZ(), |
| 94 |
atoms[i]->get_vx(), |
| 95 |
atoms[i]->get_vy(), |
| 96 |
atoms[i]->get_vz()); |
| 97 |
strcpy( writeLine, tempBuffer ); |
| 98 |
|
| 99 |
if( atoms[i]->isDirectional() ){ |
| 100 |
|
| 101 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 102 |
dAtom->getQ( q ); |
| 103 |
|
| 104 |
sprintf( tempBuffer, |
| 105 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 106 |
q[0], |
| 107 |
q[1], |
| 108 |
q[2], |
| 109 |
q[3], |
| 110 |
dAtom->getJx(), |
| 111 |
dAtom->getJy(), |
| 112 |
dAtom->getJz()); |
| 113 |
strcat( writeLine, tempBuffer ); |
| 114 |
} |
| 115 |
else |
| 116 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 117 |
|
| 118 |
outFile << writeLine; |
| 119 |
} |
| 120 |
outFile.flush(); |
| 121 |
|
| 122 |
#else // is_mpi |
| 123 |
|
| 124 |
MPI::Status istatus; |
| 125 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
| 126 |
|
| 127 |
// write out header and node 0's coordinates |
| 128 |
|
| 129 |
if( worldRank == 0 ){ |
| 130 |
outFile << mpiSim->getTotAtoms() << "\n"; |
| 131 |
|
| 132 |
outFile << currentTime << "\t" |
| 133 |
<< entry_plug->box_x << "\t" |
| 134 |
<< entry_plug->box_y << "\t" |
| 135 |
<< entry_plug->box_z << "\n"; |
| 136 |
outFile.flush(); |
| 137 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
| 138 |
// Get the Node number which has this atom; |
| 139 |
|
| 140 |
which_node = AtomToProcMap[i]; |
| 141 |
|
| 142 |
if (which_node == 0 ) { |
| 143 |
|
| 144 |
which_atom = i; |
| 145 |
local_index=-1; |
| 146 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
| 147 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
| 148 |
} |
| 149 |
if (local_index != -1) { |
| 150 |
//format the line |
| 151 |
sprintf( tempBuffer, |
| 152 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 153 |
atoms[local_index]->getType(), |
| 154 |
atoms[local_index]->getX(), |
| 155 |
atoms[local_index]->getY(), |
| 156 |
atoms[local_index]->getZ(), |
| 157 |
atoms[local_index]->get_vx(), |
| 158 |
atoms[local_index]->get_vy(), |
| 159 |
atoms[local_index]->get_vz()); // check here. |
| 160 |
strcpy( writeLine, tempBuffer ); |
| 161 |
|
| 162 |
if( atoms[local_index]->isDirectional() ){ |
| 163 |
|
| 164 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
| 165 |
dAtom->getQ( q ); |
| 166 |
|
| 167 |
sprintf( tempBuffer, |
| 168 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 169 |
q[0], |
| 170 |
q[1], |
| 171 |
q[2], |
| 172 |
q[3], |
| 173 |
dAtom->getJx(), |
| 174 |
dAtom->getJy(), |
| 175 |
dAtom->getJz()); |
| 176 |
strcat( writeLine, tempBuffer ); |
| 177 |
|
| 178 |
} |
| 179 |
else |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 181 |
} |
| 182 |
else { |
| 183 |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
| 184 |
} |
| 185 |
} |
| 186 |
else { |
| 187 |
|
| 188 |
//std::cerr << "node 0: sending node " << which_node << " request for atom " << i << "\n"; |
| 189 |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
| 190 |
//std::cerr << "node 0: sent!\n"; |
| 191 |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
| 192 |
TAKE_THIS_TAG_CHAR, istatus); |
| 193 |
//std::cerr << "node 0: got this line: " << writeLine; |
| 194 |
} |
| 195 |
|
| 196 |
outFile << writeLine; |
| 197 |
outFile.flush(); |
| 198 |
} |
| 199 |
|
| 200 |
// kill everyone off: |
| 201 |
game_over = -1; |
| 202 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
| 203 |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT); |
| 204 |
} |
| 205 |
|
| 206 |
} else { |
| 207 |
|
| 208 |
done = 0; |
| 209 |
while (!done) { |
| 210 |
//std::cerr << "node: " << mpiSim->getMyNode() << " Waiting for receive \n"; |
| 211 |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
| 212 |
TAKE_THIS_TAG_INT, istatus); |
| 213 |
//std::cerr << "node: " << mpiSim->getMyNode() << " got request for atom " << which_atom << "\n"; |
| 214 |
if (which_atom == -1) { |
| 215 |
done=1; |
| 216 |
continue; |
| 217 |
} else { |
| 218 |
local_index=-1; |
| 219 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
| 220 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
| 221 |
} |
| 222 |
if (local_index != -1) { |
| 223 |
//format the line |
| 224 |
sprintf( tempBuffer, |
| 225 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 226 |
atoms[local_index]->getType(), |
| 227 |
atoms[local_index]->getX(), |
| 228 |
atoms[local_index]->getY(), |
| 229 |
atoms[local_index]->getZ(), |
| 230 |
atoms[local_index]->get_vx(), |
| 231 |
atoms[local_index]->get_vy(), |
| 232 |
atoms[local_index]->get_vz()); // check here. |
| 233 |
strcpy( writeLine, tempBuffer ); |
| 234 |
|
| 235 |
if( atoms[local_index]->isDirectional() ){ |
| 236 |
|
| 237 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
| 238 |
dAtom->getQ( q ); |
| 239 |
|
| 240 |
sprintf( tempBuffer, |
| 241 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 242 |
q[0], |
| 243 |
q[1], |
| 244 |
q[2], |
| 245 |
q[3], |
| 246 |
dAtom->getJx(), |
| 247 |
dAtom->getJy(), |
| 248 |
dAtom->getJz()); |
| 249 |
strcat( writeLine, tempBuffer ); |
| 250 |
} |
| 251 |
else |
| 252 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 253 |
// std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine; |
| 254 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
| 255 |
TAKE_THIS_TAG_CHAR); |
| 256 |
} else { |
| 257 |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
| 258 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
| 259 |
TAKE_THIS_TAG_CHAR); |
| 260 |
} |
| 261 |
} |
| 262 |
} |
| 263 |
} |
| 264 |
outFile.flush(); |
| 265 |
sprintf( checkPointMsg, |
| 266 |
"Sucessfully took a dump.\n"); |
| 267 |
MPIcheckPoint(); |
| 268 |
#endif // is_mpi |
| 269 |
} |
| 270 |
|
| 271 |
void DumpWriter::writeFinal(){ |
| 272 |
|
| 273 |
char finalName[500]; |
| 274 |
ofstream finalOut; |
| 275 |
|
| 276 |
const int BUFFERSIZE = 2000; |
| 277 |
char tempBuffer[BUFFERSIZE]; |
| 278 |
char writeLine[BUFFERSIZE]; |
| 279 |
|
| 280 |
double q[4]; |
| 281 |
DirectionalAtom* dAtom; |
| 282 |
int nAtoms = entry_plug->n_atoms; |
| 283 |
Atom** atoms = entry_plug->atoms; |
| 284 |
int i, j, which_node, done, game_over, which_atom, local_index; |
| 285 |
|
| 286 |
|
| 287 |
#ifdef IS_MPI |
| 288 |
if(worldRank == 0 ){ |
| 289 |
#endif // is_mpi |
| 290 |
|
| 291 |
strcpy( finalName, entry_plug->finalName ); |
| 292 |
|
| 293 |
finalOut.open( finalName, ios::out | ios::trunc ); |
| 294 |
if( !finalOut ){ |
| 295 |
sprintf( painCave.errMsg, |
| 296 |
"Could not open \"%s\" for final dump output.\n", |
| 297 |
finalName ); |
| 298 |
painCave.isFatal = 1; |
| 299 |
simError(); |
| 300 |
} |
| 301 |
|
| 302 |
// finalOut.setf( ios::scientific ); |
| 303 |
|
| 304 |
#ifdef IS_MPI |
| 305 |
} |
| 306 |
|
| 307 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
| 308 |
MPIcheckPoint(); |
| 309 |
|
| 310 |
#endif //is_mpi |
| 311 |
|
| 312 |
|
| 313 |
#ifndef IS_MPI |
| 314 |
|
| 315 |
finalOut << nAtoms << "\n"; |
| 316 |
|
| 317 |
finalOut << entry_plug->box_x << "\t" |
| 318 |
<< entry_plug->box_y << "\t" |
| 319 |
<< entry_plug->box_z << "\n"; |
| 320 |
|
| 321 |
for( i=0; i<nAtoms; i++ ){ |
| 322 |
|
| 323 |
sprintf( tempBuffer, |
| 324 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 325 |
atoms[i]->getType(), |
| 326 |
atoms[i]->getX(), |
| 327 |
atoms[i]->getY(), |
| 328 |
atoms[i]->getZ(), |
| 329 |
atoms[i]->get_vx(), |
| 330 |
atoms[i]->get_vy(), |
| 331 |
atoms[i]->get_vz()); |
| 332 |
strcpy( writeLine, tempBuffer ); |
| 333 |
|
| 334 |
if( atoms[i]->isDirectional() ){ |
| 335 |
|
| 336 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 337 |
dAtom->getQ( q ); |
| 338 |
|
| 339 |
sprintf( tempBuffer, |
| 340 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 341 |
q[0], |
| 342 |
q[1], |
| 343 |
q[2], |
| 344 |
q[3], |
| 345 |
dAtom->getJx(), |
| 346 |
dAtom->getJy(), |
| 347 |
dAtom->getJz()); |
| 348 |
strcat( writeLine, tempBuffer ); |
| 349 |
} |
| 350 |
else |
| 351 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 352 |
|
| 353 |
finalOut << writeLine; |
| 354 |
} |
| 355 |
finalOut.flush(); |
| 356 |
finalOut.close(); |
| 357 |
|
| 358 |
#else // is_mpi |
| 359 |
|
| 360 |
MPI::Status istatus; |
| 361 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
| 362 |
|
| 363 |
// write out header and node 0's coordinates |
| 364 |
|
| 365 |
if( worldRank == 0 ){ |
| 366 |
finalOut << mpiSim->getTotAtoms() << "\n"; |
| 367 |
|
| 368 |
finalOut << entry_plug->box_x << "\t" |
| 369 |
<< entry_plug->box_y << "\t" |
| 370 |
<< entry_plug->box_z << "\n"; |
| 371 |
|
| 372 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
| 373 |
// Get the Node number which has this molecule: |
| 374 |
|
| 375 |
which_node = AtomToProcMap[i]; |
| 376 |
|
| 377 |
if (which_node == mpiSim->getMyNode()) { |
| 378 |
|
| 379 |
which_atom = i; |
| 380 |
local_index=-1; |
| 381 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
| 382 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
| 383 |
} |
| 384 |
if (local_index != -1) { |
| 385 |
sprintf( tempBuffer, |
| 386 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 387 |
atoms[local_index]->getType(), |
| 388 |
atoms[local_index]->getX(), |
| 389 |
atoms[local_index]->getY(), |
| 390 |
atoms[local_index]->getZ(), |
| 391 |
atoms[local_index]->get_vx(), |
| 392 |
atoms[local_index]->get_vy(), |
| 393 |
atoms[local_index]->get_vz()); |
| 394 |
strcpy( writeLine, tempBuffer ); |
| 395 |
|
| 396 |
if( atoms[local_index]->isDirectional() ){ |
| 397 |
|
| 398 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
| 399 |
dAtom->getQ( q ); |
| 400 |
|
| 401 |
sprintf( tempBuffer, |
| 402 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 403 |
q[0], |
| 404 |
q[1], |
| 405 |
q[2], |
| 406 |
q[3], |
| 407 |
dAtom->getJx(), |
| 408 |
dAtom->getJy(), |
| 409 |
dAtom->getJz()); |
| 410 |
strcat( writeLine, tempBuffer ); |
| 411 |
} |
| 412 |
else |
| 413 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 414 |
} |
| 415 |
else { |
| 416 |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
| 417 |
} |
| 418 |
|
| 419 |
} else { |
| 420 |
|
| 421 |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
| 422 |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
| 423 |
TAKE_THIS_TAG_CHAR, istatus); |
| 424 |
} |
| 425 |
|
| 426 |
finalOut << writeLine; |
| 427 |
} |
| 428 |
|
| 429 |
// kill everyone off: |
| 430 |
game_over = -1; |
| 431 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
| 432 |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT); |
| 433 |
} |
| 434 |
|
| 435 |
} else { |
| 436 |
|
| 437 |
done = 0; |
| 438 |
while (!done) { |
| 439 |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
| 440 |
TAKE_THIS_TAG_INT, istatus); |
| 441 |
|
| 442 |
if (which_atom == -1) { |
| 443 |
done=1; |
| 444 |
continue; |
| 445 |
} else { |
| 446 |
|
| 447 |
local_index=-1; |
| 448 |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
| 449 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
| 450 |
} |
| 451 |
if (local_index != -1) { |
| 452 |
|
| 453 |
//format the line |
| 454 |
sprintf( tempBuffer, |
| 455 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 456 |
atoms[local_index]->getType(), |
| 457 |
atoms[local_index]->getX(), |
| 458 |
atoms[local_index]->getY(), |
| 459 |
atoms[local_index]->getZ(), |
| 460 |
atoms[local_index]->get_vx(), |
| 461 |
atoms[local_index]->get_vy(), |
| 462 |
atoms[local_index]->get_vz()); // check here. |
| 463 |
strcpy( writeLine, tempBuffer ); |
| 464 |
|
| 465 |
if( atoms[local_index]->isDirectional() ){ |
| 466 |
|
| 467 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
| 468 |
dAtom->getQ( q ); |
| 469 |
|
| 470 |
sprintf( tempBuffer, |
| 471 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 472 |
q[0], |
| 473 |
q[1], |
| 474 |
q[2], |
| 475 |
q[3], |
| 476 |
dAtom->getJx(), |
| 477 |
dAtom->getJy(), |
| 478 |
dAtom->getJz()); |
| 479 |
strcat( writeLine, tempBuffer ); |
| 480 |
} |
| 481 |
else |
| 482 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 483 |
|
| 484 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
| 485 |
TAKE_THIS_TAG_CHAR); |
| 486 |
} else { |
| 487 |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
| 488 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
| 489 |
TAKE_THIS_TAG_CHAR); |
| 490 |
} |
| 491 |
} |
| 492 |
} |
| 493 |
} |
| 494 |
finalOut.flush(); |
| 495 |
sprintf( checkPointMsg, |
| 496 |
"Sucessfully took a dump.\n"); |
| 497 |
MPIcheckPoint(); |
| 498 |
|
| 499 |
if( worldRank == 0 ) finalOut.close(); |
| 500 |
#endif // is_mpi |
| 501 |
} |
