| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 44 |
|
* @file SimCreator.cpp |
| 45 |
|
* @author tlin |
| 46 |
|
* @date 11/03/2004 |
| 47 |
– |
* @time 13:51am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
+ |
|
| 50 |
+ |
#ifdef IS_MPI |
| 51 |
+ |
#include "mpi.h" |
| 52 |
+ |
#include "math/ParallelRandNumGen.hpp" |
| 53 |
+ |
#endif |
| 54 |
+ |
|
| 55 |
|
#include <exception> |
| 56 |
|
#include <iostream> |
| 57 |
|
#include <sstream> |
| 89 |
|
#include "types/FixedChargeAdapter.hpp" |
| 90 |
|
#include "types/FluctuatingChargeAdapter.hpp" |
| 91 |
|
|
| 87 |
– |
#ifdef IS_MPI |
| 88 |
– |
#include "mpi.h" |
| 89 |
– |
#include "math/ParallelRandNumGen.hpp" |
| 90 |
– |
#endif |
| 92 |
|
|
| 93 |
|
namespace OpenMD { |
| 94 |
|
|
| 101 |
|
#ifdef IS_MPI |
| 102 |
|
int streamSize; |
| 103 |
|
const int masterNode = 0; |
| 104 |
< |
int commStatus; |
| 104 |
> |
|
| 105 |
|
if (worldRank == masterNode) { |
| 106 |
< |
commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 106 |
> |
MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 107 |
> |
// MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
| 108 |
|
#endif |
| 109 |
|
SimplePreprocessor preprocessor; |
| 110 |
< |
preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream); |
| 110 |
> |
preprocessor.preprocess(rawMetaDataStream, filename, |
| 111 |
> |
startOfMetaDataBlock, ppStream); |
| 112 |
|
|
| 113 |
|
#ifdef IS_MPI |
| 114 |
< |
//brocasting the stream size |
| 114 |
> |
//broadcasting the stream size |
| 115 |
|
streamSize = ppStream.str().size() +1; |
| 116 |
< |
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
| 116 |
> |
MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 117 |
> |
MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), |
| 118 |
> |
streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 119 |
|
|
| 120 |
< |
commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 121 |
< |
|
| 122 |
< |
|
| 120 |
> |
// MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); |
| 121 |
> |
// MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), |
| 122 |
> |
// streamSize, MPI::CHAR, masterNode); |
| 123 |
> |
|
| 124 |
|
} else { |
| 125 |
|
|
| 126 |
< |
commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 126 |
> |
MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 127 |
> |
// MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
| 128 |
|
|
| 129 |
|
//get stream size |
| 130 |
< |
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
| 131 |
< |
|
| 130 |
> |
MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 131 |
> |
// MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); |
| 132 |
|
char* buf = new char[streamSize]; |
| 133 |
|
assert(buf); |
| 134 |
|
|
| 135 |
|
//receive file content |
| 136 |
< |
commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 137 |
< |
|
| 136 |
> |
MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 137 |
> |
// MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode); |
| 138 |
> |
|
| 139 |
|
ppStream.str(buf); |
| 140 |
|
delete [] buf; |
| 133 |
– |
|
| 141 |
|
} |
| 142 |
|
#endif |
| 143 |
|
// Create a scanner that reads from the input stream |
| 159 |
|
parser.initializeASTFactory(factory); |
| 160 |
|
parser.setASTFactory(&factory); |
| 161 |
|
parser.mdfile(); |
| 155 |
– |
|
| 162 |
|
// Create a tree parser that reads information into Globals |
| 163 |
|
MDTreeParser treeParser; |
| 164 |
|
treeParser.initializeASTFactory(factory); |
| 261 |
|
std::string mdRawData; |
| 262 |
|
int metaDataBlockStart = -1; |
| 263 |
|
int metaDataBlockEnd = -1; |
| 264 |
< |
int i; |
| 264 |
> |
int i, j; |
| 265 |
|
streamoff mdOffset; |
| 266 |
|
int mdFileVersion; |
| 267 |
|
|
| 268 |
+ |
// Create a string for embedding the version information in the MetaData |
| 269 |
+ |
std::string version; |
| 270 |
+ |
version.assign("## Last run using OpenMD Version: "); |
| 271 |
+ |
version.append(OPENMD_VERSION_MAJOR); |
| 272 |
+ |
version.append("."); |
| 273 |
+ |
version.append(OPENMD_VERSION_MINOR); |
| 274 |
+ |
|
| 275 |
+ |
std::string svnrev; |
| 276 |
+ |
//convert a macro from compiler to a string in c++ |
| 277 |
+ |
STR_DEFINE(svnrev, SVN_REV ); |
| 278 |
+ |
version.append(" Revision: "); |
| 279 |
+ |
// If there's no SVN revision, just call this the RELEASE revision. |
| 280 |
+ |
if (!svnrev.empty()) { |
| 281 |
+ |
version.append(svnrev); |
| 282 |
+ |
} else { |
| 283 |
+ |
version.append("RELEASE"); |
| 284 |
+ |
} |
| 285 |
+ |
|
| 286 |
|
#ifdef IS_MPI |
| 287 |
|
const int masterNode = 0; |
| 288 |
|
if (worldRank == masterNode) { |
| 289 |
|
#endif |
| 290 |
|
|
| 291 |
< |
std::ifstream mdFile_(mdFileName.c_str()); |
| 291 |
> |
std::ifstream mdFile_; |
| 292 |
> |
mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary); |
| 293 |
|
|
| 294 |
|
if (mdFile_.fail()) { |
| 295 |
|
sprintf(painCave.errMsg, |
| 377 |
|
|
| 378 |
|
mdRawData.clear(); |
| 379 |
|
|
| 380 |
+ |
bool foundVersion = false; |
| 381 |
+ |
|
| 382 |
|
for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) { |
| 383 |
|
mdFile_.getline(buffer, bufferSize); |
| 384 |
< |
mdRawData += buffer; |
| 384 |
> |
std::string line = trimLeftCopy(buffer); |
| 385 |
> |
j = CaseInsensitiveFind(line, "## Last run using OpenMD Version"); |
| 386 |
> |
if (static_cast<size_t>(j) != string::npos) { |
| 387 |
> |
foundVersion = true; |
| 388 |
> |
mdRawData += version; |
| 389 |
> |
} else { |
| 390 |
> |
mdRawData += buffer; |
| 391 |
> |
} |
| 392 |
|
mdRawData += "\n"; |
| 393 |
|
} |
| 394 |
< |
|
| 394 |
> |
|
| 395 |
> |
if (!foundVersion) mdRawData += version + "\n"; |
| 396 |
> |
|
| 397 |
|
mdFile_.close(); |
| 398 |
|
|
| 399 |
|
#ifdef IS_MPI |
| 521 |
|
|
| 522 |
|
#ifdef IS_MPI |
| 523 |
|
void SimCreator::divideMolecules(SimInfo *info) { |
| 488 |
– |
RealType numerator; |
| 489 |
– |
RealType denominator; |
| 490 |
– |
RealType precast; |
| 491 |
– |
RealType x; |
| 492 |
– |
RealType y; |
| 524 |
|
RealType a; |
| 494 |
– |
int old_atoms; |
| 495 |
– |
int add_atoms; |
| 496 |
– |
int new_atoms; |
| 497 |
– |
int nTarget; |
| 498 |
– |
int done; |
| 499 |
– |
int i; |
| 500 |
– |
int j; |
| 501 |
– |
int loops; |
| 502 |
– |
int which_proc; |
| 525 |
|
int nProcessors; |
| 526 |
|
std::vector<int> atomsPerProc; |
| 527 |
|
int nGlobalMols = info->getNGlobalMolecules(); |
| 528 |
< |
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
| 528 |
> |
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an |
| 529 |
> |
// error |
| 530 |
> |
// condition: |
| 531 |
|
|
| 532 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
| 532 |
> |
MPI_Comm_size( MPI_COMM_WORLD, &nProcessors); |
| 533 |
> |
//nProcessors = MPI::COMM_WORLD.Get_size(); |
| 534 |
|
|
| 535 |
|
if (nProcessors > nGlobalMols) { |
| 536 |
|
sprintf(painCave.errMsg, |
| 539 |
|
"\tthe number of molecules. This will not result in a \n" |
| 540 |
|
"\tusable division of atoms for force decomposition.\n" |
| 541 |
|
"\tEither try a smaller number of processors, or run the\n" |
| 542 |
< |
"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols); |
| 542 |
> |
"\tsingle-processor version of OpenMD.\n", nProcessors, |
| 543 |
> |
nGlobalMols); |
| 544 |
|
|
| 545 |
|
painCave.isFatal = 1; |
| 546 |
|
simError(); |
| 547 |
|
} |
| 548 |
|
|
| 523 |
– |
int seedValue; |
| 549 |
|
Globals * simParams = info->getSimParams(); |
| 550 |
< |
SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
| 550 |
> |
SeqRandNumGen* myRandom; //divide labor does not need Parallel |
| 551 |
> |
//random number generator |
| 552 |
|
if (simParams->haveSeed()) { |
| 553 |
< |
seedValue = simParams->getSeed(); |
| 553 |
> |
int seedValue = simParams->getSeed(); |
| 554 |
|
myRandom = new SeqRandNumGen(seedValue); |
| 555 |
|
}else { |
| 556 |
|
myRandom = new SeqRandNumGen(); |
| 563 |
|
atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
| 564 |
|
|
| 565 |
|
if (worldRank == 0) { |
| 566 |
< |
numerator = info->getNGlobalAtoms(); |
| 567 |
< |
denominator = nProcessors; |
| 568 |
< |
precast = numerator / denominator; |
| 569 |
< |
nTarget = (int)(precast + 0.5); |
| 566 |
> |
RealType numerator = info->getNGlobalAtoms(); |
| 567 |
> |
RealType denominator = nProcessors; |
| 568 |
> |
RealType precast = numerator / denominator; |
| 569 |
> |
int nTarget = (int)(precast + 0.5); |
| 570 |
|
|
| 571 |
< |
for(i = 0; i < nGlobalMols; i++) { |
| 572 |
< |
done = 0; |
| 573 |
< |
loops = 0; |
| 571 |
> |
for(int i = 0; i < nGlobalMols; i++) { |
| 572 |
> |
|
| 573 |
> |
int done = 0; |
| 574 |
> |
int loops = 0; |
| 575 |
|
|
| 576 |
|
while (!done) { |
| 577 |
|
loops++; |
| 578 |
|
|
| 579 |
|
// Pick a processor at random |
| 580 |
|
|
| 581 |
< |
which_proc = (int) (myRandom->rand() * nProcessors); |
| 581 |
> |
int which_proc = (int) (myRandom->rand() * nProcessors); |
| 582 |
|
|
| 583 |
|
//get the molecule stamp first |
| 584 |
|
int stampId = info->getMoleculeStampId(i); |
| 585 |
|
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
| 586 |
|
|
| 587 |
|
// How many atoms does this processor have so far? |
| 588 |
< |
old_atoms = atomsPerProc[which_proc]; |
| 589 |
< |
add_atoms = moleculeStamp->getNAtoms(); |
| 590 |
< |
new_atoms = old_atoms + add_atoms; |
| 588 |
> |
int old_atoms = atomsPerProc[which_proc]; |
| 589 |
> |
int add_atoms = moleculeStamp->getNAtoms(); |
| 590 |
> |
int new_atoms = old_atoms + add_atoms; |
| 591 |
|
|
| 592 |
|
// If we've been through this loop too many times, we need |
| 593 |
|
// to just give up and assign the molecule to this processor |
| 594 |
|
// and be done with it. |
| 595 |
|
|
| 596 |
|
if (loops > 100) { |
| 597 |
+ |
|
| 598 |
|
sprintf(painCave.errMsg, |
| 599 |
< |
"I've tried 100 times to assign molecule %d to a " |
| 600 |
< |
" processor, but can't find a good spot.\n" |
| 601 |
< |
"I'm assigning it at random to processor %d.\n", |
| 599 |
> |
"There have been 100 attempts to assign molecule %d to an\n" |
| 600 |
> |
"\tunderworked processor, but there's no good place to\n" |
| 601 |
> |
"\tleave it. OpenMD is assigning it at random to processor %d.\n", |
| 602 |
|
i, which_proc); |
| 603 |
< |
|
| 603 |
> |
|
| 604 |
|
painCave.isFatal = 0; |
| 605 |
+ |
painCave.severity = OPENMD_INFO; |
| 606 |
|
simError(); |
| 607 |
|
|
| 608 |
|
molToProcMap[i] = which_proc; |
| 631 |
|
// Pacc(x) = exp(- a * x) |
| 632 |
|
// where a = penalty / (average atoms per molecule) |
| 633 |
|
|
| 634 |
< |
x = (RealType)(new_atoms - nTarget); |
| 635 |
< |
y = myRandom->rand(); |
| 634 |
> |
RealType x = (RealType)(new_atoms - nTarget); |
| 635 |
> |
RealType y = myRandom->rand(); |
| 636 |
|
|
| 637 |
|
if (y < exp(- a * x)) { |
| 638 |
|
molToProcMap[i] = which_proc; |
| 647 |
|
} |
| 648 |
|
|
| 649 |
|
delete myRandom; |
| 650 |
< |
|
| 650 |
> |
|
| 651 |
|
// Spray out this nonsense to all other processors: |
| 623 |
– |
|
| 652 |
|
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 653 |
+ |
// MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
| 654 |
|
} else { |
| 655 |
|
|
| 656 |
|
// Listen to your marching orders from processor 0: |
| 628 |
– |
|
| 657 |
|
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 658 |
+ |
// MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
| 659 |
+ |
|
| 660 |
|
} |
| 661 |
|
|
| 662 |
|
info->setMolToProcMap(molToProcMap); |
| 703 |
|
set<AtomType*>::iterator i; |
| 704 |
|
bool hasDirectionalAtoms = false; |
| 705 |
|
bool hasFixedCharge = false; |
| 706 |
< |
bool hasMultipoles = false; |
| 706 |
> |
bool hasDipoles = false; |
| 707 |
> |
bool hasQuadrupoles = false; |
| 708 |
|
bool hasPolarizable = false; |
| 709 |
|
bool hasFluctuatingCharge = false; |
| 710 |
|
bool hasMetallic = false; |
| 726 |
|
if (da.isDirectional()){ |
| 727 |
|
hasDirectionalAtoms = true; |
| 728 |
|
} |
| 729 |
< |
if (ma.isMultipole()){ |
| 730 |
< |
hasMultipoles = true; |
| 729 |
> |
if (ma.isDipole()){ |
| 730 |
> |
hasDipoles = true; |
| 731 |
|
} |
| 732 |
+ |
if (ma.isQuadrupole()){ |
| 733 |
+ |
hasQuadrupoles = true; |
| 734 |
+ |
} |
| 735 |
|
if (ea.isEAM() || sca.isSuttonChen()){ |
| 736 |
|
hasMetallic = true; |
| 737 |
|
} |
| 755 |
|
storageLayout |= DataStorage::dslTorque; |
| 756 |
|
} |
| 757 |
|
} |
| 758 |
< |
if (hasMultipoles) { |
| 759 |
< |
storageLayout |= DataStorage::dslElectroFrame; |
| 758 |
> |
if (hasDipoles) { |
| 759 |
> |
storageLayout |= DataStorage::dslDipole; |
| 760 |
|
} |
| 761 |
+ |
if (hasQuadrupoles) { |
| 762 |
+ |
storageLayout |= DataStorage::dslQuadrupole; |
| 763 |
+ |
} |
| 764 |
|
if (hasFixedCharge || hasFluctuatingCharge) { |
| 765 |
|
storageLayout |= DataStorage::dslSkippedCharge; |
| 766 |
|
} |
| 795 |
|
} |
| 796 |
|
} |
| 797 |
|
|
| 798 |
< |
if (simParams->getOutputElectricField()) { |
| 798 |
> |
if (simParams->getOutputElectricField() | simParams->haveElectricField()) { |
| 799 |
|
storageLayout |= DataStorage::dslElectricField; |
| 800 |
|
} |
| 801 |
+ |
|
| 802 |
|
if (simParams->getOutputFluctuatingCharges()) { |
| 803 |
|
storageLayout |= DataStorage::dslFlucQPosition; |
| 804 |
|
storageLayout |= DataStorage::dslFlucQVelocity; |
| 805 |
|
storageLayout |= DataStorage::dslFlucQForce; |
| 806 |
|
} |
| 807 |
|
|
| 808 |
+ |
info->setStorageLayout(storageLayout); |
| 809 |
+ |
|
| 810 |
|
return storageLayout; |
| 811 |
|
} |
| 812 |
|
|
| 815 |
|
Molecule::AtomIterator ai; |
| 816 |
|
Molecule::RigidBodyIterator ri; |
| 817 |
|
Molecule::CutoffGroupIterator ci; |
| 818 |
+ |
Molecule::BondIterator boi; |
| 819 |
+ |
Molecule::BendIterator bei; |
| 820 |
+ |
Molecule::TorsionIterator ti; |
| 821 |
+ |
Molecule::InversionIterator ii; |
| 822 |
|
Molecule::IntegrableObjectIterator ioi; |
| 823 |
< |
Molecule * mol; |
| 824 |
< |
Atom * atom; |
| 825 |
< |
RigidBody * rb; |
| 826 |
< |
CutoffGroup * cg; |
| 823 |
> |
Molecule* mol; |
| 824 |
> |
Atom* atom; |
| 825 |
> |
RigidBody* rb; |
| 826 |
> |
CutoffGroup* cg; |
| 827 |
> |
Bond* bond; |
| 828 |
> |
Bend* bend; |
| 829 |
> |
Torsion* torsion; |
| 830 |
> |
Inversion* inversion; |
| 831 |
|
int beginAtomIndex; |
| 832 |
|
int beginRigidBodyIndex; |
| 833 |
|
int beginCutoffGroupIndex; |
| 834 |
+ |
int beginBondIndex; |
| 835 |
+ |
int beginBendIndex; |
| 836 |
+ |
int beginTorsionIndex; |
| 837 |
+ |
int beginInversionIndex; |
| 838 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 839 |
+ |
int nGlobalRigidBodies = info->getNGlobalRigidBodies(); |
| 840 |
|
|
| 841 |
|
beginAtomIndex = 0; |
| 842 |
< |
//rigidbody's index begins right after atom's |
| 842 |
> |
// The rigid body indices begin immediately after the atom indices: |
| 843 |
|
beginRigidBodyIndex = info->getNGlobalAtoms(); |
| 844 |
|
beginCutoffGroupIndex = 0; |
| 845 |
< |
|
| 845 |
> |
beginBondIndex = 0; |
| 846 |
> |
beginBendIndex = 0; |
| 847 |
> |
beginTorsionIndex = 0; |
| 848 |
> |
beginInversionIndex = 0; |
| 849 |
> |
|
| 850 |
|
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 851 |
|
|
| 852 |
|
#ifdef IS_MPI |
| 855 |
|
// stuff to do if I own this molecule |
| 856 |
|
mol = info->getMoleculeByGlobalIndex(i); |
| 857 |
|
|
| 858 |
< |
//local index(index in DataStorge) of atom is important |
| 859 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 858 |
> |
// The local index(index in DataStorge) of the atom is important: |
| 859 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 860 |
> |
atom = mol->nextAtom(ai)) { |
| 861 |
|
atom->setGlobalIndex(beginAtomIndex++); |
| 862 |
|
} |
| 863 |
|
|
| 866 |
|
rb->setGlobalIndex(beginRigidBodyIndex++); |
| 867 |
|
} |
| 868 |
|
|
| 869 |
< |
//local index of cutoff group is trivial, it only depends on |
| 870 |
< |
//the order of travesing |
| 869 |
> |
// The local index of other objects only depends on the order |
| 870 |
> |
// of traversal: |
| 871 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 872 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 873 |
|
cg->setGlobalIndex(beginCutoffGroupIndex++); |
| 874 |
|
} |
| 875 |
+ |
for(bond = mol->beginBond(boi); bond != NULL; |
| 876 |
+ |
bond = mol->nextBond(boi)) { |
| 877 |
+ |
bond->setGlobalIndex(beginBondIndex++); |
| 878 |
+ |
} |
| 879 |
+ |
for(bend = mol->beginBend(bei); bend != NULL; |
| 880 |
+ |
bend = mol->nextBend(bei)) { |
| 881 |
+ |
bend->setGlobalIndex(beginBendIndex++); |
| 882 |
+ |
} |
| 883 |
+ |
for(torsion = mol->beginTorsion(ti); torsion != NULL; |
| 884 |
+ |
torsion = mol->nextTorsion(ti)) { |
| 885 |
+ |
torsion->setGlobalIndex(beginTorsionIndex++); |
| 886 |
+ |
} |
| 887 |
+ |
for(inversion = mol->beginInversion(ii); inversion != NULL; |
| 888 |
+ |
inversion = mol->nextInversion(ii)) { |
| 889 |
+ |
inversion->setGlobalIndex(beginInversionIndex++); |
| 890 |
+ |
} |
| 891 |
|
|
| 892 |
|
#ifdef IS_MPI |
| 893 |
|
} else { |
| 900 |
|
beginAtomIndex += stamp->getNAtoms(); |
| 901 |
|
beginRigidBodyIndex += stamp->getNRigidBodies(); |
| 902 |
|
beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms(); |
| 903 |
+ |
beginBondIndex += stamp->getNBonds(); |
| 904 |
+ |
beginBendIndex += stamp->getNBends(); |
| 905 |
+ |
beginTorsionIndex += stamp->getNTorsions(); |
| 906 |
+ |
beginInversionIndex += stamp->getNInversions(); |
| 907 |
|
} |
| 908 |
|
#endif |
| 909 |
|
|
| 911 |
|
|
| 912 |
|
//fill globalGroupMembership |
| 913 |
|
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
| 914 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 915 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 916 |
< |
|
| 914 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 915 |
> |
mol = info->nextMolecule(mi)) { |
| 916 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 917 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 918 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 919 |
|
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
| 920 |
|
} |
| 929 |
|
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
| 930 |
|
// docs said we could. |
| 931 |
|
std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
| 932 |
< |
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
| 932 |
> |
MPI_Allreduce(&globalGroupMembership[0], |
| 933 |
> |
&tmpGroupMembership[0], nGlobalAtoms, |
| 934 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 935 |
+ |
// MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0], |
| 936 |
+ |
// &tmpGroupMembership[0], nGlobalAtoms, |
| 937 |
+ |
// MPI::INT, MPI::SUM); |
| 938 |
|
info->setGlobalGroupMembership(tmpGroupMembership); |
| 939 |
|
#else |
| 940 |
|
info->setGlobalGroupMembership(globalGroupMembership); |
| 941 |
|
#endif |
| 942 |
|
|
| 943 |
|
//fill molMembership |
| 944 |
< |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
| 944 |
> |
std::vector<int> globalMolMembership(info->getNGlobalAtoms() + |
| 945 |
> |
info->getNGlobalRigidBodies(), 0); |
| 946 |
|
|
| 947 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 947 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 948 |
> |
mol = info->nextMolecule(mi)) { |
| 949 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 950 |
|
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 951 |
|
} |
| 952 |
+ |
for (rb = mol->beginRigidBody(ri); rb != NULL; |
| 953 |
+ |
rb = mol->nextRigidBody(ri)) { |
| 954 |
+ |
globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex(); |
| 955 |
+ |
} |
| 956 |
|
} |
| 957 |
|
|
| 958 |
|
#ifdef IS_MPI |
| 959 |
< |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0); |
| 960 |
< |
|
| 961 |
< |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
| 959 |
> |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms() + |
| 960 |
> |
info->getNGlobalRigidBodies(), 0); |
| 961 |
> |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], |
| 962 |
> |
nGlobalAtoms + nGlobalRigidBodies, |
| 963 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 964 |
+ |
// MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], |
| 965 |
+ |
// nGlobalAtoms + nGlobalRigidBodies, |
| 966 |
+ |
// MPI::INT, MPI::SUM); |
| 967 |
|
|
| 968 |
|
info->setGlobalMolMembership(tmpMolMembership); |
| 969 |
|
#else |
| 974 |
|
// here the molecules are listed by their global indices. |
| 975 |
|
|
| 976 |
|
std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0); |
| 977 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 977 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 978 |
> |
mol = info->nextMolecule(mi)) { |
| 979 |
|
nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects(); |
| 980 |
|
} |
| 981 |
|
|
| 982 |
|
#ifdef IS_MPI |
| 983 |
|
std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0); |
| 984 |
|
MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 985 |
< |
info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 985 |
> |
info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 986 |
> |
// MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 987 |
> |
// info->getNGlobalMolecules(), MPI::INT, MPI::SUM); |
| 988 |
|
#else |
| 989 |
|
std::vector<int> numIntegrableObjectsPerMol = nIOPerMol; |
| 990 |
|
#endif |
| 998 |
|
} |
| 999 |
|
|
| 1000 |
|
std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); |
| 1001 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 1001 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 1002 |
> |
mol = info->nextMolecule(mi)) { |
| 1003 |
|
int myGlobalIndex = mol->getGlobalIndex(); |
| 1004 |
|
int globalIO = startingIOIndexForMol[myGlobalIndex]; |
| 1005 |
|
for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL; |
| 1015 |
|
} |
| 1016 |
|
|
| 1017 |
|
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
| 921 |
– |
Globals* simParams; |
| 922 |
– |
|
| 923 |
– |
simParams = info->getSimParams(); |
| 1018 |
|
|
| 1019 |
|
DumpReader reader(info, mdFileName); |
| 1020 |
|
int nframes = reader.getNFrames(); |
| 1021 |
< |
|
| 1021 |
> |
|
| 1022 |
|
if (nframes > 0) { |
| 1023 |
|
reader.readFrame(nframes - 1); |
| 1024 |
|
} else { |
