| 1 |
/* |
| 2 |
* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 35 |
* |
| 36 |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
#define _LARGEFILE_SOURCE64 |
| 44 |
#define _FILE_OFFSET_BITS 64 |
| 45 |
|
| 46 |
#include <sys/types.h> |
| 47 |
#include <sys/stat.h> |
| 48 |
|
| 49 |
#include <iostream> |
| 50 |
#include <math.h> |
| 51 |
|
| 52 |
#include <stdio.h> |
| 53 |
#include <stdlib.h> |
| 54 |
#include <string.h> |
| 55 |
|
| 56 |
#include "io/DumpReader.hpp" |
| 57 |
#include "primitives/Molecule.hpp" |
| 58 |
#include "utils/simError.h" |
| 59 |
#include "utils/MemoryUtils.hpp" |
| 60 |
#include "utils/StringTokenizer.hpp" |
| 61 |
#include "brains/Thermo.hpp" |
| 62 |
|
| 63 |
#ifdef IS_MPI |
| 64 |
#include <mpi.h> |
| 65 |
#endif |
| 66 |
|
| 67 |
|
| 68 |
namespace OpenMD { |
| 69 |
|
| 70 |
DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
| 71 |
: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) { |
| 72 |
|
| 73 |
#ifdef IS_MPI |
| 74 |
|
| 75 |
if (worldRank == 0) { |
| 76 |
#endif |
| 77 |
|
| 78 |
inFile_ = new std::ifstream(filename_.c_str()); |
| 79 |
|
| 80 |
if (inFile_->fail()) { |
| 81 |
sprintf(painCave.errMsg, |
| 82 |
"DumpReader: Cannot open file: %s\n", |
| 83 |
filename_.c_str()); |
| 84 |
painCave.isFatal = 1; |
| 85 |
simError(); |
| 86 |
} |
| 87 |
|
| 88 |
#ifdef IS_MPI |
| 89 |
|
| 90 |
} |
| 91 |
|
| 92 |
strcpy(checkPointMsg, "Dump file opened for reading successfully."); |
| 93 |
errorCheckPoint(); |
| 94 |
|
| 95 |
#endif |
| 96 |
|
| 97 |
return; |
| 98 |
} |
| 99 |
|
| 100 |
DumpReader::~DumpReader() { |
| 101 |
|
| 102 |
#ifdef IS_MPI |
| 103 |
|
| 104 |
if (worldRank == 0) { |
| 105 |
#endif |
| 106 |
|
| 107 |
delete inFile_; |
| 108 |
|
| 109 |
#ifdef IS_MPI |
| 110 |
|
| 111 |
} |
| 112 |
|
| 113 |
strcpy(checkPointMsg, "Dump file closed successfully."); |
| 114 |
errorCheckPoint(); |
| 115 |
|
| 116 |
#endif |
| 117 |
|
| 118 |
return; |
| 119 |
} |
| 120 |
|
| 121 |
int DumpReader::getNFrames(void) { |
| 122 |
|
| 123 |
if (!isScanned_) |
| 124 |
scanFile(); |
| 125 |
|
| 126 |
return nframes_; |
| 127 |
} |
| 128 |
|
| 129 |
void DumpReader::scanFile(void) { |
| 130 |
int lineNo = 0; |
| 131 |
std::streampos prevPos; |
| 132 |
std::streampos currPos; |
| 133 |
|
| 134 |
#ifdef IS_MPI |
| 135 |
|
| 136 |
if (worldRank == 0) { |
| 137 |
#endif // is_mpi |
| 138 |
|
| 139 |
currPos = inFile_->tellg(); |
| 140 |
prevPos = currPos; |
| 141 |
bool foundOpenSnapshotTag = false; |
| 142 |
bool foundClosedSnapshotTag = false; |
| 143 |
bool foundOpenSiteDataTag = false; |
| 144 |
while(inFile_->getline(buffer, bufferSize)) { |
| 145 |
++lineNo; |
| 146 |
|
| 147 |
std::string line = buffer; |
| 148 |
currPos = inFile_->tellg(); |
| 149 |
if (line.find("<Snapshot>")!= std::string::npos) { |
| 150 |
if (foundOpenSnapshotTag) { |
| 151 |
sprintf(painCave.errMsg, |
| 152 |
"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo, |
| 153 |
filename_.c_str()); |
| 154 |
painCave.isFatal = 1; |
| 155 |
simError(); |
| 156 |
} |
| 157 |
foundOpenSnapshotTag = true; |
| 158 |
foundClosedSnapshotTag = false; |
| 159 |
framePos_.push_back(prevPos); |
| 160 |
|
| 161 |
} else if (line.find("</Snapshot>") != std::string::npos){ |
| 162 |
if (!foundOpenSnapshotTag) { |
| 163 |
sprintf(painCave.errMsg, |
| 164 |
"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo, |
| 165 |
filename_.c_str()); |
| 166 |
painCave.isFatal = 1; |
| 167 |
simError(); |
| 168 |
} |
| 169 |
|
| 170 |
if (foundClosedSnapshotTag) { |
| 171 |
sprintf(painCave.errMsg, |
| 172 |
"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo, |
| 173 |
filename_.c_str()); |
| 174 |
painCave.isFatal = 1; |
| 175 |
simError(); |
| 176 |
} |
| 177 |
foundClosedSnapshotTag = true; |
| 178 |
foundOpenSnapshotTag = false; |
| 179 |
} |
| 180 |
prevPos = currPos; |
| 181 |
} |
| 182 |
|
| 183 |
// only found <Snapshot> for the last frame means the file is corrupted, we should discard |
| 184 |
// it and give a warning message |
| 185 |
if (foundOpenSnapshotTag) { |
| 186 |
sprintf(painCave.errMsg, |
| 187 |
"DumpReader: last frame in %s is invalid\n", filename_.c_str()); |
| 188 |
painCave.isFatal = 0; |
| 189 |
simError(); |
| 190 |
framePos_.pop_back(); |
| 191 |
} |
| 192 |
|
| 193 |
nframes_ = framePos_.size(); |
| 194 |
|
| 195 |
if (nframes_ == 0) { |
| 196 |
sprintf(painCave.errMsg, |
| 197 |
"DumpReader: %s does not contain a valid frame\n", filename_.c_str()); |
| 198 |
painCave.isFatal = 1; |
| 199 |
simError(); |
| 200 |
} |
| 201 |
#ifdef IS_MPI |
| 202 |
} |
| 203 |
|
| 204 |
MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
| 205 |
|
| 206 |
#endif // is_mpi |
| 207 |
|
| 208 |
isScanned_ = true; |
| 209 |
} |
| 210 |
|
| 211 |
void DumpReader::readFrame(int whichFrame) { |
| 212 |
if (!isScanned_) |
| 213 |
scanFile(); |
| 214 |
|
| 215 |
int storageLayout = info_->getSnapshotManager()->getStorageLayout(); |
| 216 |
|
| 217 |
if (storageLayout & DataStorage::dslPosition) { |
| 218 |
needPos_ = true; |
| 219 |
} else { |
| 220 |
needPos_ = false; |
| 221 |
} |
| 222 |
|
| 223 |
if (storageLayout & DataStorage::dslVelocity) { |
| 224 |
needVel_ = true; |
| 225 |
} else { |
| 226 |
needVel_ = false; |
| 227 |
} |
| 228 |
|
| 229 |
if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { |
| 230 |
needQuaternion_ = true; |
| 231 |
} else { |
| 232 |
needQuaternion_ = false; |
| 233 |
} |
| 234 |
|
| 235 |
if (storageLayout & DataStorage::dslAngularMomentum) { |
| 236 |
needAngMom_ = true; |
| 237 |
} else { |
| 238 |
needAngMom_ = false; |
| 239 |
} |
| 240 |
|
| 241 |
readSet(whichFrame); |
| 242 |
|
| 243 |
if (needCOMprops_) { |
| 244 |
Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 245 |
Thermo thermo(info_); |
| 246 |
Vector3d com; |
| 247 |
|
| 248 |
if (needPos_ && needVel_) { |
| 249 |
Vector3d comvel; |
| 250 |
Vector3d comw; |
| 251 |
thermo.getComAll(com, comvel); |
| 252 |
comw = thermo.getAngularMomentum(); |
| 253 |
} else { |
| 254 |
com = thermo.getCom(); |
| 255 |
} |
| 256 |
} |
| 257 |
} |
| 258 |
|
| 259 |
void DumpReader::readSet(int whichFrame) { |
| 260 |
std::string line; |
| 261 |
|
| 262 |
#ifndef IS_MPI |
| 263 |
inFile_->clear(); |
| 264 |
inFile_->seekg(framePos_[whichFrame]); |
| 265 |
|
| 266 |
std::istream& inputStream = *inFile_; |
| 267 |
|
| 268 |
#else |
| 269 |
int masterNode = 0; |
| 270 |
std::stringstream sstream; |
| 271 |
if (worldRank == masterNode) { |
| 272 |
std::string sendBuffer; |
| 273 |
|
| 274 |
inFile_->clear(); |
| 275 |
inFile_->seekg(framePos_[whichFrame]); |
| 276 |
|
| 277 |
while (inFile_->getline(buffer, bufferSize)) { |
| 278 |
|
| 279 |
line = buffer; |
| 280 |
sendBuffer += line; |
| 281 |
sendBuffer += '\n'; |
| 282 |
if (line.find("</Snapshot>") != std::string::npos) { |
| 283 |
break; |
| 284 |
} |
| 285 |
} |
| 286 |
|
| 287 |
int sendBufferSize = sendBuffer.size(); |
| 288 |
MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 289 |
MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 290 |
|
| 291 |
sstream.str(sendBuffer); |
| 292 |
} else { |
| 293 |
int sendBufferSize; |
| 294 |
MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 295 |
char * recvBuffer = new char[sendBufferSize+1]; |
| 296 |
assert(recvBuffer); |
| 297 |
recvBuffer[sendBufferSize] = '\0'; |
| 298 |
MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 299 |
sstream.str(recvBuffer); |
| 300 |
delete [] recvBuffer; |
| 301 |
} |
| 302 |
|
| 303 |
std::istream& inputStream = sstream; |
| 304 |
#endif |
| 305 |
|
| 306 |
inputStream.getline(buffer, bufferSize); |
| 307 |
|
| 308 |
line = buffer; |
| 309 |
if (line.find("<Snapshot>") == std::string::npos) { |
| 310 |
sprintf(painCave.errMsg, |
| 311 |
"DumpReader Error: can not find <Snapshot>\n"); |
| 312 |
painCave.isFatal = 1; |
| 313 |
simError(); |
| 314 |
} |
| 315 |
|
| 316 |
//read frameData |
| 317 |
readFrameProperties(inputStream); |
| 318 |
|
| 319 |
//read StuntDoubles |
| 320 |
readStuntDoubles(inputStream); |
| 321 |
|
| 322 |
inputStream.getline(buffer, bufferSize); |
| 323 |
line = buffer; |
| 324 |
|
| 325 |
if (line.find("<SiteData>") != std::string::npos) { |
| 326 |
//read SiteData |
| 327 |
readSiteData(inputStream); |
| 328 |
} else { |
| 329 |
if (line.find("</Snapshot>") == std::string::npos) { |
| 330 |
sprintf(painCave.errMsg, |
| 331 |
"DumpReader Error: can not find </Snapshot>\n"); |
| 332 |
painCave.isFatal = 1; |
| 333 |
simError(); |
| 334 |
} |
| 335 |
} |
| 336 |
} |
| 337 |
|
| 338 |
void DumpReader::parseDumpLine(const std::string& line) { |
| 339 |
|
| 340 |
|
| 341 |
StringTokenizer tokenizer(line); |
| 342 |
int nTokens; |
| 343 |
|
| 344 |
nTokens = tokenizer.countTokens(); |
| 345 |
|
| 346 |
if (nTokens < 2) { |
| 347 |
sprintf(painCave.errMsg, |
| 348 |
"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
| 349 |
painCave.isFatal = 1; |
| 350 |
simError(); |
| 351 |
} |
| 352 |
|
| 353 |
int index = tokenizer.nextTokenAsInt(); |
| 354 |
|
| 355 |
StuntDouble* sd = info_->getIOIndexToIntegrableObject(index); |
| 356 |
|
| 357 |
if (sd == NULL) { |
| 358 |
return; |
| 359 |
} |
| 360 |
std::string type = tokenizer.nextToken(); |
| 361 |
int size = type.size(); |
| 362 |
|
| 363 |
size_t found; |
| 364 |
|
| 365 |
if (needPos_) { |
| 366 |
found = type.find("p"); |
| 367 |
if (found == std::string::npos) { |
| 368 |
sprintf(painCave.errMsg, |
| 369 |
"DumpReader Error: StuntDouble %d has no Position\n" |
| 370 |
"\tField (\"p\") specified.\n%s\n", index, |
| 371 |
line.c_str()); |
| 372 |
painCave.isFatal = 1; |
| 373 |
simError(); |
| 374 |
} |
| 375 |
} |
| 376 |
|
| 377 |
if (sd->isDirectional()) { |
| 378 |
if (needQuaternion_) { |
| 379 |
found = type.find("q"); |
| 380 |
if (found == std::string::npos) { |
| 381 |
sprintf(painCave.errMsg, |
| 382 |
"DumpReader Error: Directional StuntDouble %d has no\n" |
| 383 |
"\tQuaternion Field (\"q\") specified.\n%s\n", index, |
| 384 |
line.c_str()); |
| 385 |
painCave.isFatal = 1; |
| 386 |
simError(); |
| 387 |
} |
| 388 |
} |
| 389 |
} |
| 390 |
|
| 391 |
for(int i = 0; i < size; ++i) { |
| 392 |
switch(type[i]) { |
| 393 |
|
| 394 |
case 'p': { |
| 395 |
Vector3d pos; |
| 396 |
pos[0] = tokenizer.nextTokenAsDouble(); |
| 397 |
pos[1] = tokenizer.nextTokenAsDouble(); |
| 398 |
pos[2] = tokenizer.nextTokenAsDouble(); |
| 399 |
if (needPos_) { |
| 400 |
sd->setPos(pos); |
| 401 |
} |
| 402 |
break; |
| 403 |
} |
| 404 |
case 'v' : { |
| 405 |
Vector3d vel; |
| 406 |
vel[0] = tokenizer.nextTokenAsDouble(); |
| 407 |
vel[1] = tokenizer.nextTokenAsDouble(); |
| 408 |
vel[2] = tokenizer.nextTokenAsDouble(); |
| 409 |
if (needVel_) { |
| 410 |
sd->setVel(vel); |
| 411 |
} |
| 412 |
break; |
| 413 |
} |
| 414 |
|
| 415 |
case 'q' : { |
| 416 |
Quat4d q; |
| 417 |
if (sd->isDirectional()) { |
| 418 |
|
| 419 |
q[0] = tokenizer.nextTokenAsDouble(); |
| 420 |
q[1] = tokenizer.nextTokenAsDouble(); |
| 421 |
q[2] = tokenizer.nextTokenAsDouble(); |
| 422 |
q[3] = tokenizer.nextTokenAsDouble(); |
| 423 |
|
| 424 |
RealType qlen = q.length(); |
| 425 |
if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0 |
| 426 |
|
| 427 |
sprintf(painCave.errMsg, |
| 428 |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); |
| 429 |
painCave.isFatal = 1; |
| 430 |
simError(); |
| 431 |
|
| 432 |
} |
| 433 |
|
| 434 |
q.normalize(); |
| 435 |
if (needQuaternion_) { |
| 436 |
sd->setQ(q); |
| 437 |
} |
| 438 |
} |
| 439 |
break; |
| 440 |
} |
| 441 |
case 'j' : { |
| 442 |
Vector3d ji; |
| 443 |
if (sd->isDirectional()) { |
| 444 |
ji[0] = tokenizer.nextTokenAsDouble(); |
| 445 |
ji[1] = tokenizer.nextTokenAsDouble(); |
| 446 |
ji[2] = tokenizer.nextTokenAsDouble(); |
| 447 |
if (needAngMom_) { |
| 448 |
sd->setJ(ji); |
| 449 |
} |
| 450 |
} |
| 451 |
break; |
| 452 |
} |
| 453 |
case 'f': { |
| 454 |
|
| 455 |
Vector3d force; |
| 456 |
force[0] = tokenizer.nextTokenAsDouble(); |
| 457 |
force[1] = tokenizer.nextTokenAsDouble(); |
| 458 |
force[2] = tokenizer.nextTokenAsDouble(); |
| 459 |
sd->setFrc(force); |
| 460 |
break; |
| 461 |
} |
| 462 |
case 't' : { |
| 463 |
|
| 464 |
Vector3d torque; |
| 465 |
torque[0] = tokenizer.nextTokenAsDouble(); |
| 466 |
torque[1] = tokenizer.nextTokenAsDouble(); |
| 467 |
torque[2] = tokenizer.nextTokenAsDouble(); |
| 468 |
sd->setTrq(torque); |
| 469 |
break; |
| 470 |
} |
| 471 |
case 'u' : { |
| 472 |
|
| 473 |
RealType particlePot; |
| 474 |
particlePot = tokenizer.nextTokenAsDouble(); |
| 475 |
sd->setParticlePot(particlePot); |
| 476 |
break; |
| 477 |
} |
| 478 |
case 'c' : { |
| 479 |
|
| 480 |
RealType flucQPos; |
| 481 |
flucQPos = tokenizer.nextTokenAsDouble(); |
| 482 |
sd->setFlucQPos(flucQPos); |
| 483 |
break; |
| 484 |
} |
| 485 |
case 'w' : { |
| 486 |
|
| 487 |
RealType flucQVel; |
| 488 |
flucQVel = tokenizer.nextTokenAsDouble(); |
| 489 |
sd->setFlucQVel(flucQVel); |
| 490 |
break; |
| 491 |
} |
| 492 |
case 'g' : { |
| 493 |
|
| 494 |
RealType flucQFrc; |
| 495 |
flucQFrc = tokenizer.nextTokenAsDouble(); |
| 496 |
sd->setFlucQFrc(flucQFrc); |
| 497 |
break; |
| 498 |
} |
| 499 |
case 'e' : { |
| 500 |
|
| 501 |
Vector3d eField; |
| 502 |
eField[0] = tokenizer.nextTokenAsDouble(); |
| 503 |
eField[1] = tokenizer.nextTokenAsDouble(); |
| 504 |
eField[2] = tokenizer.nextTokenAsDouble(); |
| 505 |
sd->setElectricField(eField); |
| 506 |
break; |
| 507 |
} |
| 508 |
default: { |
| 509 |
sprintf(painCave.errMsg, |
| 510 |
"DumpReader Error: %s is an unrecognized type\n", type.c_str()); |
| 511 |
painCave.isFatal = 1; |
| 512 |
simError(); |
| 513 |
break; |
| 514 |
} |
| 515 |
|
| 516 |
} |
| 517 |
} |
| 518 |
|
| 519 |
} |
| 520 |
|
| 521 |
|
| 522 |
void DumpReader::parseSiteLine(const std::string& line) { |
| 523 |
|
| 524 |
StringTokenizer tokenizer(line); |
| 525 |
int nTokens; |
| 526 |
|
| 527 |
nTokens = tokenizer.countTokens(); |
| 528 |
|
| 529 |
if (nTokens < 2) { |
| 530 |
sprintf(painCave.errMsg, |
| 531 |
"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
| 532 |
painCave.isFatal = 1; |
| 533 |
simError(); |
| 534 |
} |
| 535 |
|
| 536 |
/** |
| 537 |
* The first token is the global integrable object index. |
| 538 |
*/ |
| 539 |
|
| 540 |
int index = tokenizer.nextTokenAsInt(); |
| 541 |
StuntDouble* sd = info_->getIOIndexToIntegrableObject(index); |
| 542 |
if (sd == NULL) { |
| 543 |
return; |
| 544 |
} |
| 545 |
|
| 546 |
/** |
| 547 |
* Test to see if the next token is an integer or not. If not, |
| 548 |
* we've got data on the integrable object itself. If there is an |
| 549 |
* integer, we're parsing data for a site on a rigid body. |
| 550 |
*/ |
| 551 |
|
| 552 |
std::string indexTest = tokenizer.peekNextToken(); |
| 553 |
std::istringstream i(indexTest); |
| 554 |
int siteIndex; |
| 555 |
if (i >> siteIndex) { |
| 556 |
// chew up this token and parse as an int: |
| 557 |
siteIndex = tokenizer.nextTokenAsInt(); |
| 558 |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 559 |
sd = rb->getAtoms()[siteIndex]; |
| 560 |
} |
| 561 |
|
| 562 |
/** |
| 563 |
* The next token contains information on what follows. |
| 564 |
*/ |
| 565 |
std::string type = tokenizer.nextToken(); |
| 566 |
int size = type.size(); |
| 567 |
|
| 568 |
for(int i = 0; i < size; ++i) { |
| 569 |
switch(type[i]) { |
| 570 |
|
| 571 |
case 'u' : { |
| 572 |
|
| 573 |
RealType particlePot; |
| 574 |
particlePot = tokenizer.nextTokenAsDouble(); |
| 575 |
sd->setParticlePot(particlePot); |
| 576 |
break; |
| 577 |
} |
| 578 |
case 'c' : { |
| 579 |
|
| 580 |
RealType flucQPos; |
| 581 |
flucQPos = tokenizer.nextTokenAsDouble(); |
| 582 |
sd->setFlucQPos(flucQPos); |
| 583 |
break; |
| 584 |
} |
| 585 |
case 'w' : { |
| 586 |
|
| 587 |
RealType flucQVel; |
| 588 |
flucQVel = tokenizer.nextTokenAsDouble(); |
| 589 |
sd->setFlucQVel(flucQVel); |
| 590 |
break; |
| 591 |
} |
| 592 |
case 'g' : { |
| 593 |
|
| 594 |
RealType flucQFrc; |
| 595 |
flucQFrc = tokenizer.nextTokenAsDouble(); |
| 596 |
sd->setFlucQFrc(flucQFrc); |
| 597 |
break; |
| 598 |
} |
| 599 |
case 'e' : { |
| 600 |
|
| 601 |
Vector3d eField; |
| 602 |
eField[0] = tokenizer.nextTokenAsDouble(); |
| 603 |
eField[1] = tokenizer.nextTokenAsDouble(); |
| 604 |
eField[2] = tokenizer.nextTokenAsDouble(); |
| 605 |
sd->setElectricField(eField); |
| 606 |
break; |
| 607 |
} |
| 608 |
default: { |
| 609 |
sprintf(painCave.errMsg, |
| 610 |
"DumpReader Error: %s is an unrecognized type\n", type.c_str()); |
| 611 |
painCave.isFatal = 1; |
| 612 |
simError(); |
| 613 |
break; |
| 614 |
} |
| 615 |
} |
| 616 |
} |
| 617 |
} |
| 618 |
|
| 619 |
|
| 620 |
void DumpReader::readStuntDoubles(std::istream& inputStream) { |
| 621 |
|
| 622 |
inputStream.getline(buffer, bufferSize); |
| 623 |
std::string line(buffer); |
| 624 |
|
| 625 |
if (line.find("<StuntDoubles>") == std::string::npos) { |
| 626 |
sprintf(painCave.errMsg, |
| 627 |
"DumpReader Error: Missing <StuntDoubles>\n"); |
| 628 |
painCave.isFatal = 1; |
| 629 |
simError(); |
| 630 |
} |
| 631 |
|
| 632 |
while(inputStream.getline(buffer, bufferSize)) { |
| 633 |
line = buffer; |
| 634 |
|
| 635 |
if(line.find("</StuntDoubles>") != std::string::npos) { |
| 636 |
break; |
| 637 |
} |
| 638 |
|
| 639 |
parseDumpLine(line); |
| 640 |
} |
| 641 |
|
| 642 |
} |
| 643 |
|
| 644 |
void DumpReader::readSiteData(std::istream& inputStream) { |
| 645 |
|
| 646 |
inputStream.getline(buffer, bufferSize); |
| 647 |
std::string line(buffer); |
| 648 |
|
| 649 |
if (line.find("<SiteData>") == std::string::npos) { |
| 650 |
// site data isn't required for a simulation, so skip |
| 651 |
return; |
| 652 |
} |
| 653 |
|
| 654 |
while(inputStream.getline(buffer, bufferSize)) { |
| 655 |
line = buffer; |
| 656 |
|
| 657 |
if(line.find("</SiteData>") != std::string::npos) { |
| 658 |
break; |
| 659 |
} |
| 660 |
|
| 661 |
parseSiteLine(line); |
| 662 |
} |
| 663 |
|
| 664 |
} |
| 665 |
|
| 666 |
void DumpReader::readFrameProperties(std::istream& inputStream) { |
| 667 |
|
| 668 |
Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 669 |
inputStream.getline(buffer, bufferSize); |
| 670 |
std::string line(buffer); |
| 671 |
|
| 672 |
if (line.find("<FrameData>") == std::string::npos) { |
| 673 |
sprintf(painCave.errMsg, |
| 674 |
"DumpReader Error: Missing <FrameData>\n"); |
| 675 |
painCave.isFatal = 1; |
| 676 |
simError(); |
| 677 |
} |
| 678 |
|
| 679 |
while(inputStream.getline(buffer, bufferSize)) { |
| 680 |
line = buffer; |
| 681 |
|
| 682 |
if(line.find("</FrameData>") != std::string::npos) { |
| 683 |
break; |
| 684 |
} |
| 685 |
|
| 686 |
StringTokenizer tokenizer(line, " ;\t\n\r{}:,"); |
| 687 |
if (!tokenizer.hasMoreTokens()) { |
| 688 |
sprintf(painCave.errMsg, |
| 689 |
"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
| 690 |
painCave.isFatal = 1; |
| 691 |
simError(); |
| 692 |
} |
| 693 |
|
| 694 |
std::string propertyName = tokenizer.nextToken(); |
| 695 |
if (propertyName == "Time") { |
| 696 |
RealType currTime = tokenizer.nextTokenAsDouble(); |
| 697 |
s->setTime(currTime); |
| 698 |
} else if (propertyName == "Hmat"){ |
| 699 |
Mat3x3d hmat; |
| 700 |
hmat(0, 0) = tokenizer.nextTokenAsDouble(); |
| 701 |
hmat(0, 1) = tokenizer.nextTokenAsDouble(); |
| 702 |
hmat(0, 2) = tokenizer.nextTokenAsDouble(); |
| 703 |
hmat(1, 0) = tokenizer.nextTokenAsDouble(); |
| 704 |
hmat(1, 1) = tokenizer.nextTokenAsDouble(); |
| 705 |
hmat(1, 2) = tokenizer.nextTokenAsDouble(); |
| 706 |
hmat(2, 0) = tokenizer.nextTokenAsDouble(); |
| 707 |
hmat(2, 1) = tokenizer.nextTokenAsDouble(); |
| 708 |
hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
| 709 |
s->setHmat(hmat); |
| 710 |
} else if (propertyName == "Thermostat") { |
| 711 |
pair<RealType, RealType> thermostat; |
| 712 |
thermostat.first = tokenizer.nextTokenAsDouble(); |
| 713 |
thermostat.second = tokenizer.nextTokenAsDouble(); |
| 714 |
s->setThermostat(thermostat); |
| 715 |
} else if (propertyName == "Barostat") { |
| 716 |
Mat3x3d eta; |
| 717 |
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
| 718 |
eta(0, 1) = tokenizer.nextTokenAsDouble(); |
| 719 |
eta(0, 2) = tokenizer.nextTokenAsDouble(); |
| 720 |
eta(1, 0) = tokenizer.nextTokenAsDouble(); |
| 721 |
eta(1, 1) = tokenizer.nextTokenAsDouble(); |
| 722 |
eta(1, 2) = tokenizer.nextTokenAsDouble(); |
| 723 |
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
| 724 |
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
| 725 |
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
| 726 |
s->setBarostat(eta); |
| 727 |
} else { |
| 728 |
sprintf(painCave.errMsg, |
| 729 |
"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str()); |
| 730 |
painCave.isFatal = 0; |
| 731 |
simError(); |
| 732 |
} |
| 733 |
|
| 734 |
} |
| 735 |
|
| 736 |
} |
| 737 |
|
| 738 |
|
| 739 |
}//end namespace OpenMD |
