| 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] Vardeman & Gezelter, in progress (2009). |
| 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 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 59 |
|
#include "utils/simError.h" |
| 60 |
|
#include "selection/SelectionManager.hpp" |
| 61 |
|
#include "io/ForceFieldOptions.hpp" |
| 62 |
< |
#include "UseTheForce/ForceField.hpp" |
| 62 |
> |
#include "brains/ForceField.hpp" |
| 63 |
|
#include "nonbonded/SwitchingFunction.hpp" |
| 64 |
+ |
#ifdef IS_MPI |
| 65 |
+ |
#include <mpi.h> |
| 66 |
+ |
#endif |
| 67 |
|
|
| 68 |
|
using namespace std; |
| 69 |
|
namespace OpenMD { |
| 72 |
|
forceField_(ff), simParams_(simParams), |
| 73 |
|
ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
| 74 |
|
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
| 75 |
< |
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
| 75 |
> |
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0), |
| 76 |
|
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), |
| 77 |
|
nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), |
| 78 |
< |
nConstraints_(0), sman_(NULL), topologyDone_(false), |
| 78 |
> |
nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false), |
| 79 |
|
calcBoxDipole_(false), useAtomicVirial_(true) { |
| 80 |
|
|
| 81 |
|
MoleculeStamp* molStamp; |
| 88 |
|
|
| 89 |
|
vector<Component*> components = simParams->getComponents(); |
| 90 |
|
|
| 91 |
< |
for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { |
| 91 |
> |
for (vector<Component*>::iterator i = components.begin(); |
| 92 |
> |
i !=components.end(); ++i) { |
| 93 |
|
molStamp = (*i)->getMoleculeStamp(); |
| 94 |
|
nMolWithSameStamp = (*i)->getNMol(); |
| 95 |
|
|
| 226 |
|
|
| 227 |
|
|
| 228 |
|
void SimInfo::calcNdf() { |
| 229 |
< |
int ndf_local; |
| 229 |
> |
int ndf_local, nfq_local; |
| 230 |
|
MoleculeIterator i; |
| 231 |
|
vector<StuntDouble*>::iterator j; |
| 232 |
+ |
vector<Atom*>::iterator k; |
| 233 |
+ |
|
| 234 |
|
Molecule* mol; |
| 235 |
< |
StuntDouble* integrableObject; |
| 235 |
> |
StuntDouble* sd; |
| 236 |
> |
Atom* atom; |
| 237 |
|
|
| 238 |
|
ndf_local = 0; |
| 239 |
+ |
nfq_local = 0; |
| 240 |
|
|
| 241 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 233 |
– |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 234 |
– |
integrableObject = mol->nextIntegrableObject(j)) { |
| 242 |
|
|
| 243 |
+ |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 244 |
+ |
sd = mol->nextIntegrableObject(j)) { |
| 245 |
+ |
|
| 246 |
|
ndf_local += 3; |
| 247 |
|
|
| 248 |
< |
if (integrableObject->isDirectional()) { |
| 249 |
< |
if (integrableObject->isLinear()) { |
| 248 |
> |
if (sd->isDirectional()) { |
| 249 |
> |
if (sd->isLinear()) { |
| 250 |
|
ndf_local += 2; |
| 251 |
|
} else { |
| 252 |
|
ndf_local += 3; |
| 253 |
|
} |
| 254 |
|
} |
| 245 |
– |
|
| 255 |
|
} |
| 256 |
+ |
|
| 257 |
+ |
for (atom = mol->beginFluctuatingCharge(k); atom != NULL; |
| 258 |
+ |
atom = mol->nextFluctuatingCharge(k)) { |
| 259 |
+ |
if (atom->isFluctuatingCharge()) { |
| 260 |
+ |
nfq_local++; |
| 261 |
+ |
} |
| 262 |
+ |
} |
| 263 |
|
} |
| 264 |
|
|
| 265 |
+ |
ndfLocal_ = ndf_local; |
| 266 |
+ |
|
| 267 |
|
// n_constraints is local, so subtract them on each processor |
| 268 |
|
ndf_local -= nConstraints_; |
| 269 |
|
|
| 270 |
|
#ifdef IS_MPI |
| 271 |
< |
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 271 |
> |
MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM); |
| 272 |
> |
MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1, |
| 273 |
> |
MPI::INT, MPI::SUM); |
| 274 |
|
#else |
| 275 |
|
ndf_ = ndf_local; |
| 276 |
+ |
nGlobalFluctuatingCharges_ = nfq_local; |
| 277 |
|
#endif |
| 278 |
|
|
| 279 |
|
// nZconstraints_ is global, as are the 3 COM translations for the |
| 284 |
|
|
| 285 |
|
int SimInfo::getFdf() { |
| 286 |
|
#ifdef IS_MPI |
| 287 |
< |
MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 287 |
> |
MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM); |
| 288 |
|
#else |
| 289 |
|
fdf_ = fdf_local; |
| 290 |
|
#endif |
| 316 |
|
MoleculeIterator i; |
| 317 |
|
vector<StuntDouble*>::iterator j; |
| 318 |
|
Molecule* mol; |
| 319 |
< |
StuntDouble* integrableObject; |
| 319 |
> |
StuntDouble* sd; |
| 320 |
|
|
| 321 |
|
// Raw degrees of freedom that we have to set |
| 322 |
|
ndfRaw_local = 0; |
| 323 |
|
|
| 324 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 304 |
– |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 305 |
– |
integrableObject = mol->nextIntegrableObject(j)) { |
| 325 |
|
|
| 326 |
+ |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 327 |
+ |
sd = mol->nextIntegrableObject(j)) { |
| 328 |
+ |
|
| 329 |
|
ndfRaw_local += 3; |
| 330 |
|
|
| 331 |
< |
if (integrableObject->isDirectional()) { |
| 332 |
< |
if (integrableObject->isLinear()) { |
| 331 |
> |
if (sd->isDirectional()) { |
| 332 |
> |
if (sd->isLinear()) { |
| 333 |
|
ndfRaw_local += 2; |
| 334 |
|
} else { |
| 335 |
|
ndfRaw_local += 3; |
| 340 |
|
} |
| 341 |
|
|
| 342 |
|
#ifdef IS_MPI |
| 343 |
< |
MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 343 |
> |
MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM); |
| 344 |
|
#else |
| 345 |
|
ndfRaw_ = ndfRaw_local; |
| 346 |
|
#endif |
| 353 |
|
|
| 354 |
|
|
| 355 |
|
#ifdef IS_MPI |
| 356 |
< |
MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 356 |
> |
MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1, |
| 357 |
> |
MPI::INT, MPI::SUM); |
| 358 |
|
#else |
| 359 |
|
ndfTrans_ = ndfTrans_local; |
| 360 |
|
#endif |
| 390 |
|
Molecule::RigidBodyIterator rbIter; |
| 391 |
|
RigidBody* rb; |
| 392 |
|
Molecule::IntegrableObjectIterator ii; |
| 393 |
< |
StuntDouble* integrableObject; |
| 393 |
> |
StuntDouble* sd; |
| 394 |
|
|
| 395 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); |
| 396 |
< |
integrableObject != NULL; |
| 374 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 395 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 396 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 397 |
|
|
| 398 |
< |
if (integrableObject->isRigidBody()) { |
| 399 |
< |
rb = static_cast<RigidBody*>(integrableObject); |
| 398 |
> |
if (sd->isRigidBody()) { |
| 399 |
> |
rb = static_cast<RigidBody*>(sd); |
| 400 |
|
vector<Atom*> atoms = rb->getAtoms(); |
| 401 |
|
set<int> rigidAtoms; |
| 402 |
|
for (int i = 0; i < static_cast<int>(atoms.size()); ++i) { |
| 407 |
|
} |
| 408 |
|
} else { |
| 409 |
|
set<int> oneAtomSet; |
| 410 |
< |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
| 411 |
< |
atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
| 410 |
> |
oneAtomSet.insert(sd->getGlobalIndex()); |
| 411 |
> |
atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet)); |
| 412 |
|
} |
| 413 |
|
} |
| 414 |
|
|
| 542 |
|
Molecule::RigidBodyIterator rbIter; |
| 543 |
|
RigidBody* rb; |
| 544 |
|
Molecule::IntegrableObjectIterator ii; |
| 545 |
< |
StuntDouble* integrableObject; |
| 545 |
> |
StuntDouble* sd; |
| 546 |
|
|
| 547 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); |
| 548 |
< |
integrableObject != NULL; |
| 527 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 547 |
> |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 548 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 549 |
|
|
| 550 |
< |
if (integrableObject->isRigidBody()) { |
| 551 |
< |
rb = static_cast<RigidBody*>(integrableObject); |
| 550 |
> |
if (sd->isRigidBody()) { |
| 551 |
> |
rb = static_cast<RigidBody*>(sd); |
| 552 |
|
vector<Atom*> atoms = rb->getAtoms(); |
| 553 |
|
set<int> rigidAtoms; |
| 554 |
|
for (int i = 0; i < static_cast<int>(atoms.size()); ++i) { |
| 559 |
|
} |
| 560 |
|
} else { |
| 561 |
|
set<int> oneAtomSet; |
| 562 |
< |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
| 563 |
< |
atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
| 562 |
> |
oneAtomSet.insert(sd->getGlobalIndex()); |
| 563 |
> |
atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet)); |
| 564 |
|
} |
| 565 |
|
} |
| 566 |
|
|
| 715 |
|
Atom* atom; |
| 716 |
|
set<AtomType*> atomTypes; |
| 717 |
|
|
| 718 |
< |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 719 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 718 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 719 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 720 |
> |
atom = mol->nextAtom(ai)) { |
| 721 |
|
atomTypes.insert(atom->getAtomType()); |
| 722 |
|
} |
| 723 |
|
} |
| 724 |
< |
|
| 724 |
> |
|
| 725 |
|
#ifdef IS_MPI |
| 726 |
|
|
| 727 |
|
// loop over the found atom types on this processor, and add their |
| 728 |
|
// numerical idents to a vector: |
| 729 |
< |
|
| 729 |
> |
|
| 730 |
|
vector<int> foundTypes; |
| 731 |
|
set<AtomType*>::iterator i; |
| 732 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) |
| 735 |
|
// count_local holds the number of found types on this processor |
| 736 |
|
int count_local = foundTypes.size(); |
| 737 |
|
|
| 738 |
< |
// count holds the total number of found types on all processors |
| 717 |
< |
// (some will be redundant with the ones found locally): |
| 718 |
< |
int count; |
| 719 |
< |
MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM); |
| 738 |
> |
int nproc = MPI::COMM_WORLD.Get_size(); |
| 739 |
|
|
| 740 |
< |
// create a vector to hold the globally found types, and resize it: |
| 741 |
< |
vector<int> ftGlobal; |
| 742 |
< |
ftGlobal.resize(count); |
| 743 |
< |
vector<int> counts; |
| 740 |
> |
// we need arrays to hold the counts and displacement vectors for |
| 741 |
> |
// all processors |
| 742 |
> |
vector<int> counts(nproc, 0); |
| 743 |
> |
vector<int> disps(nproc, 0); |
| 744 |
|
|
| 745 |
< |
int nproc = MPI::COMM_WORLD.Get_size(); |
| 746 |
< |
counts.resize(nproc); |
| 747 |
< |
vector<int> disps; |
| 748 |
< |
disps.resize(nproc); |
| 745 |
> |
// fill the counts array |
| 746 |
> |
MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0], |
| 747 |
> |
1, MPI::INT); |
| 748 |
> |
|
| 749 |
> |
// use the processor counts to compute the displacement array |
| 750 |
> |
disps[0] = 0; |
| 751 |
> |
int totalCount = counts[0]; |
| 752 |
> |
for (int iproc = 1; iproc < nproc; iproc++) { |
| 753 |
> |
disps[iproc] = disps[iproc-1] + counts[iproc-1]; |
| 754 |
> |
totalCount += counts[iproc]; |
| 755 |
> |
} |
| 756 |
|
|
| 757 |
< |
// now spray out the foundTypes to all the other processors: |
| 757 |
> |
// we need a (possibly redundant) set of all found types: |
| 758 |
> |
vector<int> ftGlobal(totalCount); |
| 759 |
|
|
| 760 |
+ |
// now spray out the foundTypes to all the other processors: |
| 761 |
|
MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT, |
| 762 |
< |
&ftGlobal[0], &counts[0], &disps[0], MPI::INT); |
| 762 |
> |
&ftGlobal[0], &counts[0], &disps[0], |
| 763 |
> |
MPI::INT); |
| 764 |
|
|
| 765 |
+ |
vector<int>::iterator j; |
| 766 |
+ |
|
| 767 |
|
// foundIdents is a stl set, so inserting an already found ident |
| 768 |
|
// will have no effect. |
| 769 |
|
set<int> foundIdents; |
| 770 |
< |
vector<int>::iterator j; |
| 770 |
> |
|
| 771 |
|
for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j) |
| 772 |
|
foundIdents.insert((*j)); |
| 773 |
|
|
| 774 |
|
// now iterate over the foundIdents and get the actual atom types |
| 775 |
|
// that correspond to these: |
| 776 |
|
set<int>::iterator it; |
| 777 |
< |
for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
| 777 |
> |
for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
| 778 |
|
atomTypes.insert( forceField_->getAtomType((*it)) ); |
| 779 |
|
|
| 780 |
|
#endif |
| 781 |
< |
|
| 781 |
> |
|
| 782 |
|
return atomTypes; |
| 783 |
|
} |
| 784 |
|
|
| 785 |
+ |
|
| 786 |
+ |
int getGlobalCountOfType(AtomType* atype) { |
| 787 |
+ |
/* |
| 788 |
+ |
set<AtomType*> atypes = getSimulatedAtomTypes(); |
| 789 |
+ |
map<AtomType*, int> counts_; |
| 790 |
+ |
|
| 791 |
+ |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 792 |
+ |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 793 |
+ |
atom = mol->nextAtom(ai)) { |
| 794 |
+ |
atom->getAtomType(); |
| 795 |
+ |
} |
| 796 |
+ |
} |
| 797 |
+ |
*/ |
| 798 |
+ |
return 0; |
| 799 |
+ |
} |
| 800 |
+ |
|
| 801 |
|
void SimInfo::setupSimVariables() { |
| 802 |
|
useAtomicVirial_ = simParams_->getUseAtomicVirial(); |
| 803 |
< |
// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true |
| 803 |
> |
// we only call setAccumulateBoxDipole if the accumulateBoxDipole |
| 804 |
> |
// parameter is true |
| 805 |
|
calcBoxDipole_ = false; |
| 806 |
|
if ( simParams_->haveAccumulateBoxDipole() ) |
| 807 |
|
if ( simParams_->getAccumulateBoxDipole() ) { |
| 808 |
|
calcBoxDipole_ = true; |
| 809 |
|
} |
| 810 |
< |
|
| 810 |
> |
|
| 811 |
|
set<AtomType*>::iterator i; |
| 812 |
|
set<AtomType*> atomTypes; |
| 813 |
|
atomTypes = getSimulatedAtomTypes(); |
| 814 |
< |
int usesElectrostatic = 0; |
| 815 |
< |
int usesMetallic = 0; |
| 816 |
< |
int usesDirectional = 0; |
| 814 |
> |
bool usesElectrostatic = false; |
| 815 |
> |
bool usesMetallic = false; |
| 816 |
> |
bool usesDirectional = false; |
| 817 |
> |
bool usesFluctuatingCharges = false; |
| 818 |
|
//loop over all of the atom types |
| 819 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 820 |
|
usesElectrostatic |= (*i)->isElectrostatic(); |
| 821 |
|
usesMetallic |= (*i)->isMetal(); |
| 822 |
|
usesDirectional |= (*i)->isDirectional(); |
| 823 |
+ |
usesFluctuatingCharges |= (*i)->isFluctuatingCharge(); |
| 824 |
|
} |
| 825 |
|
|
| 826 |
< |
#ifdef IS_MPI |
| 827 |
< |
int temp; |
| 826 |
> |
#ifdef IS_MPI |
| 827 |
> |
bool temp; |
| 828 |
|
temp = usesDirectional; |
| 829 |
< |
MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 830 |
< |
|
| 829 |
> |
MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL, |
| 830 |
> |
MPI::LOR); |
| 831 |
> |
|
| 832 |
|
temp = usesMetallic; |
| 833 |
< |
MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 834 |
< |
|
| 833 |
> |
MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL, |
| 834 |
> |
MPI::LOR); |
| 835 |
> |
|
| 836 |
|
temp = usesElectrostatic; |
| 837 |
< |
MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 837 |
> |
MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL, |
| 838 |
> |
MPI::LOR); |
| 839 |
> |
|
| 840 |
> |
temp = usesFluctuatingCharges; |
| 841 |
> |
MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL, |
| 842 |
> |
MPI::LOR); |
| 843 |
> |
#else |
| 844 |
> |
|
| 845 |
> |
usesDirectionalAtoms_ = usesDirectional; |
| 846 |
> |
usesMetallicAtoms_ = usesMetallic; |
| 847 |
> |
usesElectrostaticAtoms_ = usesElectrostatic; |
| 848 |
> |
usesFluctuatingCharges_ = usesFluctuatingCharges; |
| 849 |
> |
|
| 850 |
|
#endif |
| 851 |
+ |
|
| 852 |
+ |
requiresPrepair_ = usesMetallicAtoms_ ? true : false; |
| 853 |
+ |
requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false; |
| 854 |
+ |
requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false; |
| 855 |
|
} |
| 856 |
|
|
| 857 |
|
|
| 895 |
|
|
| 896 |
|
|
| 897 |
|
void SimInfo::prepareTopology() { |
| 830 |
– |
int nExclude, nOneTwo, nOneThree, nOneFour; |
| 898 |
|
|
| 899 |
|
//calculate mass ratio of cutoff group |
| 900 |
|
SimInfo::MoleculeIterator mi; |
| 905 |
|
Atom* atom; |
| 906 |
|
RealType totalMass; |
| 907 |
|
|
| 908 |
< |
//to avoid memory reallocation, reserve enough space for massFactors_ |
| 908 |
> |
/** |
| 909 |
> |
* The mass factor is the relative mass of an atom to the total |
| 910 |
> |
* mass of the cutoff group it belongs to. By default, all atoms |
| 911 |
> |
* are their own cutoff groups, and therefore have mass factors of |
| 912 |
> |
* 1. We need some special handling for massless atoms, which |
| 913 |
> |
* will be treated as carrying the entire mass of the cutoff |
| 914 |
> |
* group. |
| 915 |
> |
*/ |
| 916 |
|
massFactors_.clear(); |
| 917 |
< |
massFactors_.reserve(getNCutoffGroups()); |
| 917 |
> |
massFactors_.resize(getNAtoms(), 1.0); |
| 918 |
|
|
| 919 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 920 |
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 923 |
|
totalMass = cg->getMass(); |
| 924 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 925 |
|
// Check for massless groups - set mfact to 1 if true |
| 926 |
< |
if (totalMass != 0) |
| 927 |
< |
massFactors_.push_back(atom->getMass()/totalMass); |
| 926 |
> |
if (totalMass != 0) |
| 927 |
> |
massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass; |
| 928 |
|
else |
| 929 |
< |
massFactors_.push_back( 1.0 ); |
| 929 |
> |
massFactors_[atom->getLocalIndex()] = 1.0; |
| 930 |
|
} |
| 931 |
|
} |
| 932 |
|
} |
| 941 |
|
} |
| 942 |
|
} |
| 943 |
|
|
| 870 |
– |
//scan topology |
| 871 |
– |
|
| 872 |
– |
nExclude = excludedInteractions_.getSize(); |
| 873 |
– |
nOneTwo = oneTwoInteractions_.getSize(); |
| 874 |
– |
nOneThree = oneThreeInteractions_.getSize(); |
| 875 |
– |
nOneFour = oneFourInteractions_.getSize(); |
| 876 |
– |
|
| 877 |
– |
int* excludeList = excludedInteractions_.getPairList(); |
| 878 |
– |
int* oneTwoList = oneTwoInteractions_.getPairList(); |
| 879 |
– |
int* oneThreeList = oneThreeInteractions_.getPairList(); |
| 880 |
– |
int* oneFourList = oneFourInteractions_.getPairList(); |
| 881 |
– |
|
| 882 |
– |
//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], |
| 883 |
– |
// &nExclude, excludeList, |
| 884 |
– |
// &nOneTwo, oneTwoList, |
| 885 |
– |
// &nOneThree, oneThreeList, |
| 886 |
– |
// &nOneFour, oneFourList, |
| 887 |
– |
// &molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 888 |
– |
// &fortranGlobalGroupMembership[0], &isError); |
| 889 |
– |
|
| 944 |
|
topologyDone_ = true; |
| 945 |
|
} |
| 946 |
|
|
| 986 |
|
|
| 987 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 988 |
|
|
| 989 |
< |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
| 989 |
> |
for (atom = mol->beginAtom(atomIter); atom != NULL; |
| 990 |
> |
atom = mol->nextAtom(atomIter)) { |
| 991 |
|
atom->setSnapshotManager(sman_); |
| 992 |
|
} |
| 993 |
|
|
| 994 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 994 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 995 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 996 |
|
rb->setSnapshotManager(sman_); |
| 997 |
|
} |
| 998 |
|
|
| 999 |
< |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
| 999 |
> |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; |
| 1000 |
> |
cg = mol->nextCutoffGroup(cgIter)) { |
| 1001 |
|
cg->setSnapshotManager(sman_); |
| 1002 |
|
} |
| 1003 |
|
} |
| 1004 |
|
|
| 1005 |
|
} |
| 1006 |
|
|
| 950 |
– |
Vector3d SimInfo::getComVel(){ |
| 951 |
– |
SimInfo::MoleculeIterator i; |
| 952 |
– |
Molecule* mol; |
| 1007 |
|
|
| 954 |
– |
Vector3d comVel(0.0); |
| 955 |
– |
RealType totalMass = 0.0; |
| 956 |
– |
|
| 957 |
– |
|
| 958 |
– |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 959 |
– |
RealType mass = mol->getMass(); |
| 960 |
– |
totalMass += mass; |
| 961 |
– |
comVel += mass * mol->getComVel(); |
| 962 |
– |
} |
| 963 |
– |
|
| 964 |
– |
#ifdef IS_MPI |
| 965 |
– |
RealType tmpMass = totalMass; |
| 966 |
– |
Vector3d tmpComVel(comVel); |
| 967 |
– |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
| 968 |
– |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
| 969 |
– |
#endif |
| 970 |
– |
|
| 971 |
– |
comVel /= totalMass; |
| 972 |
– |
|
| 973 |
– |
return comVel; |
| 974 |
– |
} |
| 975 |
– |
|
| 976 |
– |
Vector3d SimInfo::getCom(){ |
| 977 |
– |
SimInfo::MoleculeIterator i; |
| 978 |
– |
Molecule* mol; |
| 979 |
– |
|
| 980 |
– |
Vector3d com(0.0); |
| 981 |
– |
RealType totalMass = 0.0; |
| 982 |
– |
|
| 983 |
– |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 984 |
– |
RealType mass = mol->getMass(); |
| 985 |
– |
totalMass += mass; |
| 986 |
– |
com += mass * mol->getCom(); |
| 987 |
– |
} |
| 988 |
– |
|
| 989 |
– |
#ifdef IS_MPI |
| 990 |
– |
RealType tmpMass = totalMass; |
| 991 |
– |
Vector3d tmpCom(com); |
| 992 |
– |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
| 993 |
– |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
| 994 |
– |
#endif |
| 995 |
– |
|
| 996 |
– |
com /= totalMass; |
| 997 |
– |
|
| 998 |
– |
return com; |
| 999 |
– |
|
| 1000 |
– |
} |
| 1001 |
– |
|
| 1008 |
|
ostream& operator <<(ostream& o, SimInfo& info) { |
| 1009 |
|
|
| 1010 |
|
return o; |
| 1011 |
|
} |
| 1012 |
|
|
| 1013 |
< |
|
| 1008 |
< |
/* |
| 1009 |
< |
Returns center of mass and center of mass velocity in one function call. |
| 1010 |
< |
*/ |
| 1011 |
< |
|
| 1012 |
< |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
| 1013 |
< |
SimInfo::MoleculeIterator i; |
| 1014 |
< |
Molecule* mol; |
| 1015 |
< |
|
| 1016 |
< |
|
| 1017 |
< |
RealType totalMass = 0.0; |
| 1018 |
< |
|
| 1019 |
< |
|
| 1020 |
< |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 1021 |
< |
RealType mass = mol->getMass(); |
| 1022 |
< |
totalMass += mass; |
| 1023 |
< |
com += mass * mol->getCom(); |
| 1024 |
< |
comVel += mass * mol->getComVel(); |
| 1025 |
< |
} |
| 1026 |
< |
|
| 1027 |
< |
#ifdef IS_MPI |
| 1028 |
< |
RealType tmpMass = totalMass; |
| 1029 |
< |
Vector3d tmpCom(com); |
| 1030 |
< |
Vector3d tmpComVel(comVel); |
| 1031 |
< |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
| 1032 |
< |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
| 1033 |
< |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
| 1034 |
< |
#endif |
| 1035 |
< |
|
| 1036 |
< |
com /= totalMass; |
| 1037 |
< |
comVel /= totalMass; |
| 1038 |
< |
} |
| 1039 |
< |
|
| 1040 |
< |
/* |
| 1041 |
< |
Return intertia tensor for entire system and angular momentum Vector. |
| 1042 |
< |
|
| 1043 |
< |
|
| 1044 |
< |
[ Ixx -Ixy -Ixz ] |
| 1045 |
< |
J =| -Iyx Iyy -Iyz | |
| 1046 |
< |
[ -Izx -Iyz Izz ] |
| 1047 |
< |
*/ |
| 1048 |
< |
|
| 1049 |
< |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
| 1050 |
< |
|
| 1051 |
< |
|
| 1052 |
< |
RealType xx = 0.0; |
| 1053 |
< |
RealType yy = 0.0; |
| 1054 |
< |
RealType zz = 0.0; |
| 1055 |
< |
RealType xy = 0.0; |
| 1056 |
< |
RealType xz = 0.0; |
| 1057 |
< |
RealType yz = 0.0; |
| 1058 |
< |
Vector3d com(0.0); |
| 1059 |
< |
Vector3d comVel(0.0); |
| 1060 |
< |
|
| 1061 |
< |
getComAll(com, comVel); |
| 1062 |
< |
|
| 1063 |
< |
SimInfo::MoleculeIterator i; |
| 1064 |
< |
Molecule* mol; |
| 1065 |
< |
|
| 1066 |
< |
Vector3d thisq(0.0); |
| 1067 |
< |
Vector3d thisv(0.0); |
| 1068 |
< |
|
| 1069 |
< |
RealType thisMass = 0.0; |
| 1070 |
< |
|
| 1071 |
< |
|
| 1072 |
< |
|
| 1073 |
< |
|
| 1074 |
< |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 1075 |
< |
|
| 1076 |
< |
thisq = mol->getCom()-com; |
| 1077 |
< |
thisv = mol->getComVel()-comVel; |
| 1078 |
< |
thisMass = mol->getMass(); |
| 1079 |
< |
// Compute moment of intertia coefficients. |
| 1080 |
< |
xx += thisq[0]*thisq[0]*thisMass; |
| 1081 |
< |
yy += thisq[1]*thisq[1]*thisMass; |
| 1082 |
< |
zz += thisq[2]*thisq[2]*thisMass; |
| 1083 |
< |
|
| 1084 |
< |
// compute products of intertia |
| 1085 |
< |
xy += thisq[0]*thisq[1]*thisMass; |
| 1086 |
< |
xz += thisq[0]*thisq[2]*thisMass; |
| 1087 |
< |
yz += thisq[1]*thisq[2]*thisMass; |
| 1088 |
< |
|
| 1089 |
< |
angularMomentum += cross( thisq, thisv ) * thisMass; |
| 1090 |
< |
|
| 1091 |
< |
} |
| 1092 |
< |
|
| 1093 |
< |
|
| 1094 |
< |
inertiaTensor(0,0) = yy + zz; |
| 1095 |
< |
inertiaTensor(0,1) = -xy; |
| 1096 |
< |
inertiaTensor(0,2) = -xz; |
| 1097 |
< |
inertiaTensor(1,0) = -xy; |
| 1098 |
< |
inertiaTensor(1,1) = xx + zz; |
| 1099 |
< |
inertiaTensor(1,2) = -yz; |
| 1100 |
< |
inertiaTensor(2,0) = -xz; |
| 1101 |
< |
inertiaTensor(2,1) = -yz; |
| 1102 |
< |
inertiaTensor(2,2) = xx + yy; |
| 1103 |
< |
|
| 1104 |
< |
#ifdef IS_MPI |
| 1105 |
< |
Mat3x3d tmpI(inertiaTensor); |
| 1106 |
< |
Vector3d tmpAngMom; |
| 1107 |
< |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
| 1108 |
< |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
| 1109 |
< |
#endif |
| 1110 |
< |
|
| 1111 |
< |
return; |
| 1112 |
< |
} |
| 1113 |
< |
|
| 1114 |
< |
//Returns the angular momentum of the system |
| 1115 |
< |
Vector3d SimInfo::getAngularMomentum(){ |
| 1116 |
< |
|
| 1117 |
< |
Vector3d com(0.0); |
| 1118 |
< |
Vector3d comVel(0.0); |
| 1119 |
< |
Vector3d angularMomentum(0.0); |
| 1120 |
< |
|
| 1121 |
< |
getComAll(com,comVel); |
| 1122 |
< |
|
| 1123 |
< |
SimInfo::MoleculeIterator i; |
| 1124 |
< |
Molecule* mol; |
| 1125 |
< |
|
| 1126 |
< |
Vector3d thisr(0.0); |
| 1127 |
< |
Vector3d thisp(0.0); |
| 1128 |
< |
|
| 1129 |
< |
RealType thisMass; |
| 1130 |
< |
|
| 1131 |
< |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 1132 |
< |
thisMass = mol->getMass(); |
| 1133 |
< |
thisr = mol->getCom()-com; |
| 1134 |
< |
thisp = (mol->getComVel()-comVel)*thisMass; |
| 1135 |
< |
|
| 1136 |
< |
angularMomentum += cross( thisr, thisp ); |
| 1137 |
< |
|
| 1138 |
< |
} |
| 1139 |
< |
|
| 1140 |
< |
#ifdef IS_MPI |
| 1141 |
< |
Vector3d tmpAngMom; |
| 1142 |
< |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
| 1143 |
< |
#endif |
| 1144 |
< |
|
| 1145 |
< |
return angularMomentum; |
| 1146 |
< |
} |
| 1147 |
< |
|
| 1013 |
> |
|
| 1014 |
|
StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) { |
| 1015 |
< |
return IOIndexToIntegrableObject.at(index); |
| 1015 |
> |
if (index >= int(IOIndexToIntegrableObject.size())) { |
| 1016 |
> |
sprintf(painCave.errMsg, |
| 1017 |
> |
"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n" |
| 1018 |
> |
"\tindex exceeds number of known objects!\n"); |
| 1019 |
> |
painCave.isFatal = 1; |
| 1020 |
> |
simError(); |
| 1021 |
> |
return NULL; |
| 1022 |
> |
} else |
| 1023 |
> |
return IOIndexToIntegrableObject.at(index); |
| 1024 |
|
} |
| 1025 |
|
|
| 1026 |
|
void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) { |
| 1027 |
|
IOIndexToIntegrableObject= v; |
| 1028 |
|
} |
| 1029 |
|
|
| 1156 |
– |
/* Returns the Volume of the simulation based on a ellipsoid with semi-axes |
| 1157 |
– |
based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3 |
| 1158 |
– |
where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to |
| 1159 |
– |
V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536. |
| 1160 |
– |
*/ |
| 1161 |
– |
void SimInfo::getGyrationalVolume(RealType &volume){ |
| 1162 |
– |
Mat3x3d intTensor; |
| 1163 |
– |
RealType det; |
| 1164 |
– |
Vector3d dummyAngMom; |
| 1165 |
– |
RealType sysconstants; |
| 1166 |
– |
RealType geomCnst; |
| 1167 |
– |
|
| 1168 |
– |
geomCnst = 3.0/2.0; |
| 1169 |
– |
/* Get the inertial tensor and angular momentum for free*/ |
| 1170 |
– |
getInertiaTensor(intTensor,dummyAngMom); |
| 1171 |
– |
|
| 1172 |
– |
det = intTensor.determinant(); |
| 1173 |
– |
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1174 |
– |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); |
| 1175 |
– |
return; |
| 1176 |
– |
} |
| 1177 |
– |
|
| 1178 |
– |
void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){ |
| 1179 |
– |
Mat3x3d intTensor; |
| 1180 |
– |
Vector3d dummyAngMom; |
| 1181 |
– |
RealType sysconstants; |
| 1182 |
– |
RealType geomCnst; |
| 1183 |
– |
|
| 1184 |
– |
geomCnst = 3.0/2.0; |
| 1185 |
– |
/* Get the inertial tensor and angular momentum for free*/ |
| 1186 |
– |
getInertiaTensor(intTensor,dummyAngMom); |
| 1187 |
– |
|
| 1188 |
– |
detI = intTensor.determinant(); |
| 1189 |
– |
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1190 |
– |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); |
| 1191 |
– |
return; |
| 1192 |
– |
} |
| 1193 |
– |
/* |
| 1194 |
– |
void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) { |
| 1195 |
– |
assert( v.size() == nAtoms_ + nRigidBodies_); |
| 1196 |
– |
sdByGlobalIndex_ = v; |
| 1197 |
– |
} |
| 1198 |
– |
|
| 1199 |
– |
StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) { |
| 1200 |
– |
//assert(index < nAtoms_ + nRigidBodies_); |
| 1201 |
– |
return sdByGlobalIndex_.at(index); |
| 1202 |
– |
} |
| 1203 |
– |
*/ |
| 1030 |
|
int SimInfo::getNGlobalConstraints() { |
| 1031 |
|
int nGlobalConstraints; |
| 1032 |
|
#ifdef IS_MPI |
| 1033 |
< |
MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM, |
| 1034 |
< |
MPI_COMM_WORLD); |
| 1033 |
> |
MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1, |
| 1034 |
> |
MPI::INT, MPI::SUM); |
| 1035 |
|
#else |
| 1036 |
|
nGlobalConstraints = nConstraints_; |
| 1037 |
|
#endif |
