| 256 |
|
int metaDataBlockStart = -1; |
| 257 |
|
int metaDataBlockEnd = -1; |
| 258 |
|
int i; |
| 259 |
< |
int mdOffset; |
| 259 |
> |
streamoff mdOffset; |
| 260 |
|
int mdFileVersion; |
| 261 |
+ |
|
| 262 |
|
|
| 263 |
|
#ifdef IS_MPI |
| 264 |
|
const int masterNode = 0; |
| 265 |
|
if (worldRank == masterNode) { |
| 266 |
|
#endif |
| 267 |
|
|
| 268 |
< |
std::ifstream mdFile_(mdFileName.c_str()); |
| 268 |
> |
std::ifstream mdFile_; |
| 269 |
> |
mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary); |
| 270 |
|
|
| 271 |
|
if (mdFile_.fail()) { |
| 272 |
|
sprintf(painCave.errMsg, |
| 507 |
|
int nGlobalMols = info->getNGlobalMolecules(); |
| 508 |
|
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
| 509 |
|
|
| 510 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
| 510 |
> |
nProcessors = MPI::COMM_WORLD.Get_size(); |
| 511 |
|
|
| 512 |
|
if (nProcessors > nGlobalMols) { |
| 513 |
|
sprintf(painCave.errMsg, |
| 545 |
|
nTarget = (int)(precast + 0.5); |
| 546 |
|
|
| 547 |
|
for(i = 0; i < nGlobalMols; i++) { |
| 548 |
+ |
|
| 549 |
|
done = 0; |
| 550 |
|
loops = 0; |
| 551 |
|
|
| 570 |
|
// and be done with it. |
| 571 |
|
|
| 572 |
|
if (loops > 100) { |
| 573 |
+ |
|
| 574 |
|
sprintf(painCave.errMsg, |
| 575 |
< |
"I've tried 100 times to assign molecule %d to a " |
| 576 |
< |
" processor, but can't find a good spot.\n" |
| 577 |
< |
"I'm assigning it at random to processor %d.\n", |
| 575 |
> |
"There have been 100 attempts to assign molecule %d to an\n" |
| 576 |
> |
"\tunderworked processor, but there's no good place to\n" |
| 577 |
> |
"\tleave it. OpenMD is assigning it at random to processor %d.\n", |
| 578 |
|
i, which_proc); |
| 579 |
< |
|
| 579 |
> |
|
| 580 |
|
painCave.isFatal = 0; |
| 581 |
+ |
painCave.severity = OPENMD_INFO; |
| 582 |
|
simError(); |
| 583 |
|
|
| 584 |
|
molToProcMap[i] = which_proc; |
| 623 |
|
} |
| 624 |
|
|
| 625 |
|
delete myRandom; |
| 626 |
< |
|
| 626 |
> |
|
| 627 |
|
// Spray out this nonsense to all other processors: |
| 628 |
< |
|
| 624 |
< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 628 |
> |
MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
| 629 |
|
} else { |
| 630 |
|
|
| 631 |
|
// Listen to your marching orders from processor 0: |
| 632 |
< |
|
| 633 |
< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 632 |
> |
MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
| 633 |
> |
|
| 634 |
|
} |
| 635 |
|
|
| 636 |
|
info->setMolToProcMap(molToProcMap); |
| 677 |
|
set<AtomType*>::iterator i; |
| 678 |
|
bool hasDirectionalAtoms = false; |
| 679 |
|
bool hasFixedCharge = false; |
| 680 |
< |
bool hasMultipoles = false; |
| 680 |
> |
bool hasDipoles = false; |
| 681 |
> |
bool hasQuadrupoles = false; |
| 682 |
|
bool hasPolarizable = false; |
| 683 |
|
bool hasFluctuatingCharge = false; |
| 684 |
|
bool hasMetallic = false; |
| 700 |
|
if (da.isDirectional()){ |
| 701 |
|
hasDirectionalAtoms = true; |
| 702 |
|
} |
| 703 |
< |
if (ma.isMultipole()){ |
| 704 |
< |
hasMultipoles = true; |
| 703 |
> |
if (ma.isDipole()){ |
| 704 |
> |
hasDipoles = true; |
| 705 |
|
} |
| 706 |
+ |
if (ma.isQuadrupole()){ |
| 707 |
+ |
hasQuadrupoles = true; |
| 708 |
+ |
} |
| 709 |
|
if (ea.isEAM() || sca.isSuttonChen()){ |
| 710 |
|
hasMetallic = true; |
| 711 |
|
} |
| 729 |
|
storageLayout |= DataStorage::dslTorque; |
| 730 |
|
} |
| 731 |
|
} |
| 732 |
< |
if (hasMultipoles) { |
| 733 |
< |
storageLayout |= DataStorage::dslElectroFrame; |
| 732 |
> |
if (hasDipoles) { |
| 733 |
> |
storageLayout |= DataStorage::dslDipole; |
| 734 |
|
} |
| 735 |
+ |
if (hasQuadrupoles) { |
| 736 |
+ |
storageLayout |= DataStorage::dslQuadrupole; |
| 737 |
+ |
} |
| 738 |
|
if (hasFixedCharge || hasFluctuatingCharge) { |
| 739 |
|
storageLayout |= DataStorage::dslSkippedCharge; |
| 740 |
|
} |
| 772 |
|
if (simParams->getOutputElectricField()) { |
| 773 |
|
storageLayout |= DataStorage::dslElectricField; |
| 774 |
|
} |
| 775 |
+ |
|
| 776 |
|
if (simParams->getOutputFluctuatingCharges()) { |
| 777 |
|
storageLayout |= DataStorage::dslFlucQPosition; |
| 778 |
|
storageLayout |= DataStorage::dslFlucQVelocity; |
| 796 |
|
int beginRigidBodyIndex; |
| 797 |
|
int beginCutoffGroupIndex; |
| 798 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 799 |
+ |
int nGlobalRigidBodies = info->getNGlobalRigidBodies(); |
| 800 |
|
|
| 801 |
|
beginAtomIndex = 0; |
| 802 |
|
//rigidbody's index begins right after atom's |
| 863 |
|
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
| 864 |
|
// docs said we could. |
| 865 |
|
std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
| 866 |
< |
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
| 867 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 866 |
> |
MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0], |
| 867 |
> |
&tmpGroupMembership[0], nGlobalAtoms, |
| 868 |
> |
MPI::INT, MPI::SUM); |
| 869 |
|
info->setGlobalGroupMembership(tmpGroupMembership); |
| 870 |
|
#else |
| 871 |
|
info->setGlobalGroupMembership(globalGroupMembership); |
| 872 |
|
#endif |
| 873 |
|
|
| 874 |
|
//fill molMembership |
| 875 |
< |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
| 875 |
> |
std::vector<int> globalMolMembership(info->getNGlobalAtoms() + |
| 876 |
> |
info->getNGlobalRigidBodies(), 0); |
| 877 |
|
|
| 878 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 878 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 879 |
> |
mol = info->nextMolecule(mi)) { |
| 880 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 881 |
|
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 882 |
|
} |
| 883 |
+ |
for (rb = mol->beginRigidBody(ri); rb != NULL; |
| 884 |
+ |
rb = mol->nextRigidBody(ri)) { |
| 885 |
+ |
globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex(); |
| 886 |
+ |
} |
| 887 |
|
} |
| 888 |
|
|
| 889 |
|
#ifdef IS_MPI |
| 890 |
< |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0); |
| 890 |
> |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms() + |
| 891 |
> |
info->getNGlobalRigidBodies(), 0); |
| 892 |
> |
MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], |
| 893 |
> |
nGlobalAtoms + nGlobalRigidBodies, |
| 894 |
> |
MPI::INT, MPI::SUM); |
| 895 |
|
|
| 872 |
– |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
| 873 |
– |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 874 |
– |
|
| 896 |
|
info->setGlobalMolMembership(tmpMolMembership); |
| 897 |
|
#else |
| 898 |
|
info->setGlobalMolMembership(globalMolMembership); |
| 902 |
|
// here the molecules are listed by their global indices. |
| 903 |
|
|
| 904 |
|
std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0); |
| 905 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 905 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 906 |
> |
mol = info->nextMolecule(mi)) { |
| 907 |
|
nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects(); |
| 908 |
|
} |
| 909 |
|
|
| 910 |
|
#ifdef IS_MPI |
| 911 |
|
std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0); |
| 912 |
< |
MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 913 |
< |
info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 912 |
> |
MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 913 |
> |
info->getNGlobalMolecules(), MPI::INT, MPI::SUM); |
| 914 |
|
#else |
| 915 |
|
std::vector<int> numIntegrableObjectsPerMol = nIOPerMol; |
| 916 |
|
#endif |
| 924 |
|
} |
| 925 |
|
|
| 926 |
|
std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); |
| 927 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 927 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 928 |
> |
mol = info->nextMolecule(mi)) { |
| 929 |
|
int myGlobalIndex = mol->getGlobalIndex(); |
| 930 |
|
int globalIO = startingIOIndexForMol[myGlobalIndex]; |
| 931 |
< |
for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL; |
| 932 |
< |
integrableObject = mol->nextIntegrableObject(ioi)) { |
| 933 |
< |
integrableObject->setGlobalIntegrableObjectIndex(globalIO); |
| 934 |
< |
IOIndexToIntegrableObject[globalIO] = integrableObject; |
| 931 |
> |
for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL; |
| 932 |
> |
sd = mol->nextIntegrableObject(ioi)) { |
| 933 |
> |
sd->setGlobalIntegrableObjectIndex(globalIO); |
| 934 |
> |
IOIndexToIntegrableObject[globalIO] = sd; |
| 935 |
|
globalIO++; |
| 936 |
|
} |
| 937 |
|
} |
