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::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
107 |
|
#endif |
108 |
|
SimplePreprocessor preprocessor; |
109 |
|
preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream); |
111 |
|
#ifdef IS_MPI |
112 |
|
//brocasting the stream size |
113 |
|
streamSize = ppStream.str().size() +1; |
114 |
< |
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
115 |
< |
|
116 |
< |
commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
116 |
< |
|
117 |
< |
|
114 |
> |
MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); |
115 |
> |
MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode); |
116 |
> |
|
117 |
|
} else { |
118 |
< |
|
120 |
< |
commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
118 |
> |
MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
119 |
|
|
120 |
|
//get stream size |
121 |
< |
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
121 |
> |
MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); |
122 |
|
|
123 |
|
char* buf = new char[streamSize]; |
124 |
|
assert(buf); |
125 |
|
|
126 |
|
//receive file content |
127 |
< |
commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
127 |
> |
MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode); |
128 |
|
|
129 |
|
ppStream.str(buf); |
130 |
|
delete [] buf; |
133 |
– |
|
131 |
|
} |
132 |
|
#endif |
133 |
|
// Create a scanner that reads from the input stream |
252 |
|
std::string mdRawData; |
253 |
|
int metaDataBlockStart = -1; |
254 |
|
int metaDataBlockEnd = -1; |
255 |
< |
int i; |
256 |
< |
streamoff mdOffset(0); |
255 |
> |
int i, j; |
256 |
> |
streamoff mdOffset; |
257 |
|
int mdFileVersion; |
258 |
|
|
259 |
+ |
// Create a string for embedding the version information in the MetaData |
260 |
+ |
std::string version; |
261 |
+ |
version.assign("## Last run using OpenMD Version: "); |
262 |
+ |
version.append(OPENMD_VERSION_MAJOR); |
263 |
+ |
version.append("."); |
264 |
+ |
version.append(OPENMD_VERSION_MINOR); |
265 |
|
|
266 |
+ |
std::string svnrev; |
267 |
+ |
//convert a macro from compiler to a string in c++ |
268 |
+ |
STR_DEFINE(svnrev, SVN_REV ); |
269 |
+ |
version.append(" Revision: "); |
270 |
+ |
// If there's no SVN revision, just call this the RELEASE revision. |
271 |
+ |
if (!svnrev.empty()) { |
272 |
+ |
version.append(svnrev); |
273 |
+ |
} else { |
274 |
+ |
version.append("RELEASE"); |
275 |
+ |
} |
276 |
+ |
|
277 |
|
#ifdef IS_MPI |
278 |
|
const int masterNode = 0; |
279 |
|
if (worldRank == masterNode) { |
368 |
|
|
369 |
|
mdRawData.clear(); |
370 |
|
|
371 |
+ |
bool foundVersion = false; |
372 |
+ |
|
373 |
|
for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) { |
374 |
|
mdFile_.getline(buffer, bufferSize); |
375 |
< |
mdRawData += buffer; |
375 |
> |
std::string line = trimLeftCopy(buffer); |
376 |
> |
j = CaseInsensitiveFind(line, "## Last run using OpenMD Version"); |
377 |
> |
if (static_cast<size_t>(j) != string::npos) { |
378 |
> |
foundVersion = true; |
379 |
> |
mdRawData += version; |
380 |
> |
} else { |
381 |
> |
mdRawData += buffer; |
382 |
> |
} |
383 |
|
mdRawData += "\n"; |
384 |
|
} |
385 |
< |
|
385 |
> |
|
386 |
> |
if (!foundVersion) mdRawData += version + "\n"; |
387 |
> |
|
388 |
|
mdFile_.close(); |
389 |
|
|
390 |
|
#ifdef IS_MPI |
512 |
|
|
513 |
|
#ifdef IS_MPI |
514 |
|
void SimCreator::divideMolecules(SimInfo *info) { |
490 |
– |
RealType numerator; |
491 |
– |
RealType denominator; |
492 |
– |
RealType precast; |
493 |
– |
RealType x; |
494 |
– |
RealType y; |
515 |
|
RealType a; |
496 |
– |
int old_atoms; |
497 |
– |
int add_atoms; |
498 |
– |
int new_atoms; |
499 |
– |
int nTarget; |
500 |
– |
int done; |
501 |
– |
int i; |
502 |
– |
int j; |
503 |
– |
int loops; |
504 |
– |
int which_proc; |
516 |
|
int nProcessors; |
517 |
|
std::vector<int> atomsPerProc; |
518 |
|
int nGlobalMols = info->getNGlobalMolecules(); |
519 |
< |
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
519 |
> |
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an |
520 |
> |
// error |
521 |
> |
// condition: |
522 |
|
|
523 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
523 |
> |
nProcessors = MPI::COMM_WORLD.Get_size(); |
524 |
|
|
525 |
|
if (nProcessors > nGlobalMols) { |
526 |
|
sprintf(painCave.errMsg, |
529 |
|
"\tthe number of molecules. This will not result in a \n" |
530 |
|
"\tusable division of atoms for force decomposition.\n" |
531 |
|
"\tEither try a smaller number of processors, or run the\n" |
532 |
< |
"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols); |
532 |
> |
"\tsingle-processor version of OpenMD.\n", nProcessors, |
533 |
> |
nGlobalMols); |
534 |
|
|
535 |
|
painCave.isFatal = 1; |
536 |
|
simError(); |
537 |
|
} |
538 |
|
|
525 |
– |
int seedValue; |
539 |
|
Globals * simParams = info->getSimParams(); |
540 |
< |
SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
540 |
> |
SeqRandNumGen* myRandom; //divide labor does not need Parallel |
541 |
> |
//random number generator |
542 |
|
if (simParams->haveSeed()) { |
543 |
< |
seedValue = simParams->getSeed(); |
543 |
> |
int seedValue = simParams->getSeed(); |
544 |
|
myRandom = new SeqRandNumGen(seedValue); |
545 |
|
}else { |
546 |
|
myRandom = new SeqRandNumGen(); |
553 |
|
atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
554 |
|
|
555 |
|
if (worldRank == 0) { |
556 |
< |
numerator = info->getNGlobalAtoms(); |
557 |
< |
denominator = nProcessors; |
558 |
< |
precast = numerator / denominator; |
559 |
< |
nTarget = (int)(precast + 0.5); |
556 |
> |
RealType numerator = info->getNGlobalAtoms(); |
557 |
> |
RealType denominator = nProcessors; |
558 |
> |
RealType precast = numerator / denominator; |
559 |
> |
int nTarget = (int)(precast + 0.5); |
560 |
|
|
561 |
< |
for(i = 0; i < nGlobalMols; i++) { |
562 |
< |
done = 0; |
563 |
< |
loops = 0; |
561 |
> |
for(int i = 0; i < nGlobalMols; i++) { |
562 |
> |
|
563 |
> |
int done = 0; |
564 |
> |
int loops = 0; |
565 |
|
|
566 |
|
while (!done) { |
567 |
|
loops++; |
568 |
|
|
569 |
|
// Pick a processor at random |
570 |
|
|
571 |
< |
which_proc = (int) (myRandom->rand() * nProcessors); |
571 |
> |
int which_proc = (int) (myRandom->rand() * nProcessors); |
572 |
|
|
573 |
|
//get the molecule stamp first |
574 |
|
int stampId = info->getMoleculeStampId(i); |
575 |
|
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
576 |
|
|
577 |
|
// How many atoms does this processor have so far? |
578 |
< |
old_atoms = atomsPerProc[which_proc]; |
579 |
< |
add_atoms = moleculeStamp->getNAtoms(); |
580 |
< |
new_atoms = old_atoms + add_atoms; |
578 |
> |
int old_atoms = atomsPerProc[which_proc]; |
579 |
> |
int add_atoms = moleculeStamp->getNAtoms(); |
580 |
> |
int new_atoms = old_atoms + add_atoms; |
581 |
|
|
582 |
|
// If we've been through this loop too many times, we need |
583 |
|
// to just give up and assign the molecule to this processor |
584 |
|
// and be done with it. |
585 |
|
|
586 |
|
if (loops > 100) { |
587 |
+ |
|
588 |
|
sprintf(painCave.errMsg, |
589 |
< |
"I've tried 100 times to assign molecule %d to a " |
590 |
< |
" processor, but can't find a good spot.\n" |
591 |
< |
"I'm assigning it at random to processor %d.\n", |
589 |
> |
"There have been 100 attempts to assign molecule %d to an\n" |
590 |
> |
"\tunderworked processor, but there's no good place to\n" |
591 |
> |
"\tleave it. OpenMD is assigning it at random to processor %d.\n", |
592 |
|
i, which_proc); |
593 |
< |
|
593 |
> |
|
594 |
|
painCave.isFatal = 0; |
595 |
+ |
painCave.severity = OPENMD_INFO; |
596 |
|
simError(); |
597 |
|
|
598 |
|
molToProcMap[i] = which_proc; |
621 |
|
// Pacc(x) = exp(- a * x) |
622 |
|
// where a = penalty / (average atoms per molecule) |
623 |
|
|
624 |
< |
x = (RealType)(new_atoms - nTarget); |
625 |
< |
y = myRandom->rand(); |
624 |
> |
RealType x = (RealType)(new_atoms - nTarget); |
625 |
> |
RealType y = myRandom->rand(); |
626 |
|
|
627 |
|
if (y < exp(- a * x)) { |
628 |
|
molToProcMap[i] = which_proc; |
637 |
|
} |
638 |
|
|
639 |
|
delete myRandom; |
640 |
< |
|
640 |
> |
|
641 |
|
// Spray out this nonsense to all other processors: |
642 |
< |
|
626 |
< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
642 |
> |
MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
643 |
|
} else { |
644 |
|
|
645 |
|
// Listen to your marching orders from processor 0: |
646 |
< |
|
647 |
< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
646 |
> |
MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
647 |
> |
|
648 |
|
} |
649 |
|
|
650 |
|
info->setMolToProcMap(molToProcMap); |
691 |
|
set<AtomType*>::iterator i; |
692 |
|
bool hasDirectionalAtoms = false; |
693 |
|
bool hasFixedCharge = false; |
694 |
< |
bool hasMultipoles = false; |
694 |
> |
bool hasDipoles = false; |
695 |
> |
bool hasQuadrupoles = false; |
696 |
|
bool hasPolarizable = false; |
697 |
|
bool hasFluctuatingCharge = false; |
698 |
|
bool hasMetallic = false; |
714 |
|
if (da.isDirectional()){ |
715 |
|
hasDirectionalAtoms = true; |
716 |
|
} |
717 |
< |
if (ma.isMultipole()){ |
718 |
< |
hasMultipoles = true; |
717 |
> |
if (ma.isDipole()){ |
718 |
> |
hasDipoles = true; |
719 |
|
} |
720 |
+ |
if (ma.isQuadrupole()){ |
721 |
+ |
hasQuadrupoles = true; |
722 |
+ |
} |
723 |
|
if (ea.isEAM() || sca.isSuttonChen()){ |
724 |
|
hasMetallic = true; |
725 |
|
} |
743 |
|
storageLayout |= DataStorage::dslTorque; |
744 |
|
} |
745 |
|
} |
746 |
< |
if (hasMultipoles) { |
747 |
< |
storageLayout |= DataStorage::dslElectroFrame; |
746 |
> |
if (hasDipoles) { |
747 |
> |
storageLayout |= DataStorage::dslDipole; |
748 |
> |
} |
749 |
> |
if (hasQuadrupoles) { |
750 |
> |
storageLayout |= DataStorage::dslQuadrupole; |
751 |
|
} |
752 |
|
if (hasFixedCharge || hasFluctuatingCharge) { |
753 |
|
storageLayout |= DataStorage::dslSkippedCharge; |
783 |
|
} |
784 |
|
} |
785 |
|
|
786 |
< |
if (simParams->getOutputElectricField()) { |
786 |
> |
if (simParams->getOutputElectricField() | simParams->haveElectricField()) { |
787 |
|
storageLayout |= DataStorage::dslElectricField; |
788 |
|
} |
789 |
+ |
|
790 |
|
if (simParams->getOutputFluctuatingCharges()) { |
791 |
|
storageLayout |= DataStorage::dslFlucQPosition; |
792 |
|
storageLayout |= DataStorage::dslFlucQVelocity; |
793 |
|
storageLayout |= DataStorage::dslFlucQForce; |
794 |
|
} |
795 |
|
|
796 |
+ |
info->setStorageLayout(storageLayout); |
797 |
+ |
|
798 |
|
return storageLayout; |
799 |
|
} |
800 |
|
|
812 |
|
int beginRigidBodyIndex; |
813 |
|
int beginCutoffGroupIndex; |
814 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
815 |
+ |
int nGlobalRigidBodies = info->getNGlobalRigidBodies(); |
816 |
|
|
817 |
|
beginAtomIndex = 0; |
818 |
|
//rigidbody's index begins right after atom's |
879 |
|
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
880 |
|
// docs said we could. |
881 |
|
std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
882 |
< |
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
883 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
882 |
> |
MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0], |
883 |
> |
&tmpGroupMembership[0], nGlobalAtoms, |
884 |
> |
MPI::INT, MPI::SUM); |
885 |
|
info->setGlobalGroupMembership(tmpGroupMembership); |
886 |
|
#else |
887 |
|
info->setGlobalGroupMembership(globalGroupMembership); |
888 |
|
#endif |
889 |
|
|
890 |
|
//fill molMembership |
891 |
< |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
891 |
> |
std::vector<int> globalMolMembership(info->getNGlobalAtoms() + |
892 |
> |
info->getNGlobalRigidBodies(), 0); |
893 |
|
|
894 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
894 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; |
895 |
> |
mol = info->nextMolecule(mi)) { |
896 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
897 |
|
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
898 |
|
} |
899 |
+ |
for (rb = mol->beginRigidBody(ri); rb != NULL; |
900 |
+ |
rb = mol->nextRigidBody(ri)) { |
901 |
+ |
globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex(); |
902 |
+ |
} |
903 |
|
} |
904 |
|
|
905 |
|
#ifdef IS_MPI |
906 |
< |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0); |
906 |
> |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms() + |
907 |
> |
info->getNGlobalRigidBodies(), 0); |
908 |
> |
MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], |
909 |
> |
nGlobalAtoms + nGlobalRigidBodies, |
910 |
> |
MPI::INT, MPI::SUM); |
911 |
|
|
874 |
– |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
875 |
– |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
876 |
– |
|
912 |
|
info->setGlobalMolMembership(tmpMolMembership); |
913 |
|
#else |
914 |
|
info->setGlobalMolMembership(globalMolMembership); |
918 |
|
// here the molecules are listed by their global indices. |
919 |
|
|
920 |
|
std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0); |
921 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
921 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
922 |
> |
mol = info->nextMolecule(mi)) { |
923 |
|
nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects(); |
924 |
|
} |
925 |
|
|
926 |
|
#ifdef IS_MPI |
927 |
|
std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0); |
928 |
< |
MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
929 |
< |
info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
928 |
> |
MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
929 |
> |
info->getNGlobalMolecules(), MPI::INT, MPI::SUM); |
930 |
|
#else |
931 |
|
std::vector<int> numIntegrableObjectsPerMol = nIOPerMol; |
932 |
|
#endif |
940 |
|
} |
941 |
|
|
942 |
|
std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); |
943 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
943 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
944 |
> |
mol = info->nextMolecule(mi)) { |
945 |
|
int myGlobalIndex = mol->getGlobalIndex(); |
946 |
|
int globalIO = startingIOIndexForMol[myGlobalIndex]; |
947 |
|
for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL; |
957 |
|
} |
958 |
|
|
959 |
|
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
923 |
– |
Globals* simParams; |
924 |
– |
|
925 |
– |
simParams = info->getSimParams(); |
960 |
|
|
961 |
|
DumpReader reader(info, mdFileName); |
962 |
|
int nframes = reader.getNFrames(); |
963 |
< |
|
963 |
> |
|
964 |
|
if (nframes > 0) { |
965 |
|
reader.readFrame(nframes - 1); |
966 |
|
} else { |