# | Line 35 | Line 35 | |
---|---|---|
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 | /** | |
# | Line 58 | Line 59 | |
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 { | |
# | Line 68 | Line 72 | 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), fortranInitialized_(false), |
78 | > | nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false), |
79 | calcBoxDipole_(false), useAtomicVirial_(true) { | |
80 | ||
81 | MoleculeStamp* molStamp; | |
# | Line 84 | Line 88 | namespace OpenMD { | |
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 | ||
# | Line 125 | Line 130 | namespace OpenMD { | |
130 | //equal to the total number of atoms minus number of atoms belong to | |
131 | //cutoff group defined in meta-data file plus the number of cutoff | |
132 | //groups defined in meta-data file | |
128 | – | std::cerr << "nGA = " << nGlobalAtoms_ << "\n"; |
129 | – | std::cerr << "nCA = " << nCutoffAtoms << "\n"; |
130 | – | std::cerr << "nG = " << nGroups << "\n"; |
133 | ||
134 | nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; | |
133 | – | |
134 | – | std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n"; |
135 | ||
136 | //every free atom (atom does not belong to rigid bodies) is an | |
137 | //integrable object therefore the total number of integrable objects | |
# | Line 226 | Line 226 | namespace OpenMD { | |
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)) { | |
238 | – | for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
239 | – | 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 | } | |
255 | < | |
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 | |
# | Line 268 | Line 284 | namespace OpenMD { | |
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 | |
291 | return fdf_; | |
292 | } | |
293 | + | |
294 | + | unsigned int SimInfo::getNLocalCutoffGroups(){ |
295 | + | int nLocalCutoffAtoms = 0; |
296 | + | Molecule* mol; |
297 | + | MoleculeIterator mi; |
298 | + | CutoffGroup* cg; |
299 | + | Molecule::CutoffGroupIterator ci; |
300 | ||
301 | + | for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
302 | + | |
303 | + | for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
304 | + | cg = mol->nextCutoffGroup(ci)) { |
305 | + | nLocalCutoffAtoms += cg->getNumAtom(); |
306 | + | |
307 | + | } |
308 | + | } |
309 | + | |
310 | + | return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_; |
311 | + | } |
312 | + | |
313 | void SimInfo::calcNdfRaw() { | |
314 | int ndfRaw_local; | |
315 | ||
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)) { | |
290 | – | for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
291 | – | 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; | |
# | Line 304 | Line 340 | namespace OpenMD { | |
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 | |
# | Line 317 | Line 353 | namespace OpenMD { | |
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 | |
# | Line 353 | Line 390 | namespace OpenMD { | |
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; |
360 | < | 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) { | |
# | Line 371 | Line 407 | namespace OpenMD { | |
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 | ||
# | Line 506 | Line 542 | namespace OpenMD { | |
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; |
513 | < | 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) { | |
# | Line 524 | Line 559 | namespace OpenMD { | |
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 | ||
# | Line 680 | Line 715 | namespace OpenMD { | |
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) | |
# | Line 699 | Line 735 | namespace OpenMD { | |
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 |
703 | < | // (some will be redundant with the ones found locally): |
704 | < | int count; |
705 | < | 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 | ||
# | Line 812 | Line 894 | namespace OpenMD { | |
894 | } | |
895 | ||
896 | ||
897 | < | void SimInfo::setupFortran() { |
816 | < | int isError; |
817 | < | int nExclude, nOneTwo, nOneThree, nOneFour; |
818 | < | vector<int> fortranGlobalGroupMembership; |
819 | < | |
820 | < | isError = 0; |
897 | > | void SimInfo::prepareTopology() { |
898 | ||
822 | – | //globalGroupMembership_ is filled by SimCreator |
823 | – | for (int i = 0; i < nGlobalAtoms_; i++) { |
824 | – | fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
825 | – | } |
826 | – | |
899 | //calculate mass ratio of cutoff group | |
828 | – | vector<RealType> mfact; |
900 | SimInfo::MoleculeIterator mi; | |
901 | Molecule* mol; | |
902 | Molecule::CutoffGroupIterator ci; | |
# | Line 834 | Line 905 | namespace OpenMD { | |
905 | Atom* atom; | |
906 | RealType totalMass; | |
907 | ||
908 | < | //to avoid memory reallocation, reserve enough space for mfact |
909 | < | mfact.reserve(getNCutoffGroups()); |
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_.resize(getNAtoms(), 1.0); |
918 | ||
919 | for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { | |
920 | < | for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
920 | > | for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
921 | > | cg = mol->nextCutoffGroup(ci)) { |
922 | ||
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 | < | mfact.push_back(atom->getMass()/totalMass); |
926 | > | if (totalMass != 0) |
927 | > | massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass; |
928 | else | |
929 | < | mfact.push_back( 1.0 ); |
929 | > | massFactors_[atom->getLocalIndex()] = 1.0; |
930 | } | |
931 | } | |
932 | } | |
# | Line 860 | Line 940 | namespace OpenMD { | |
940 | identArray_.push_back(atom->getIdent()); | |
941 | } | |
942 | } | |
863 | – | |
864 | – | //fill molMembershipArray |
865 | – | //molMembershipArray is filled by SimCreator |
866 | – | vector<int> molMembershipArray(nGlobalAtoms_); |
867 | – | for (int i = 0; i < nGlobalAtoms_; i++) { |
868 | – | molMembershipArray[i] = globalMolMembership_[i] + 1; |
869 | – | } |
943 | ||
944 | < | //setup fortran simulation |
872 | < | |
873 | < | nExclude = excludedInteractions_.getSize(); |
874 | < | nOneTwo = oneTwoInteractions_.getSize(); |
875 | < | nOneThree = oneThreeInteractions_.getSize(); |
876 | < | nOneFour = oneFourInteractions_.getSize(); |
877 | < | |
878 | < | int* excludeList = excludedInteractions_.getPairList(); |
879 | < | int* oneTwoList = oneTwoInteractions_.getPairList(); |
880 | < | int* oneThreeList = oneThreeInteractions_.getPairList(); |
881 | < | int* oneFourList = oneFourInteractions_.getPairList(); |
882 | < | |
883 | < | //setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], |
884 | < | // &nExclude, excludeList, |
885 | < | // &nOneTwo, oneTwoList, |
886 | < | // &nOneThree, oneThreeList, |
887 | < | // &nOneFour, oneFourList, |
888 | < | // &molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
889 | < | // &fortranGlobalGroupMembership[0], &isError); |
890 | < | |
891 | < | // if( isError ){ |
892 | < | // |
893 | < | // sprintf( painCave.errMsg, |
894 | < | // "There was an error setting the simulation information in fortran.\n" ); |
895 | < | // painCave.isFatal = 1; |
896 | < | // painCave.severity = OPENMD_ERROR; |
897 | < | // simError(); |
898 | < | //} |
899 | < | |
900 | < | |
901 | < | // sprintf( checkPointMsg, |
902 | < | // "succesfully sent the simulation information to fortran.\n"); |
903 | < | |
904 | < | // errorCheckPoint(); |
905 | < | |
906 | < | // Setup number of neighbors in neighbor list if present |
907 | < | //if (simParams_->haveNeighborListNeighbors()) { |
908 | < | // int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
909 | < | // setNeighbors(&nlistNeighbors); |
910 | < | //} |
911 | < | |
912 | < | #ifdef IS_MPI |
913 | < | // mpiSimData parallelData; |
914 | < | |
915 | < | //fill up mpiSimData struct |
916 | < | // parallelData.nMolGlobal = getNGlobalMolecules(); |
917 | < | // parallelData.nMolLocal = getNMolecules(); |
918 | < | // parallelData.nAtomsGlobal = getNGlobalAtoms(); |
919 | < | // parallelData.nAtomsLocal = getNAtoms(); |
920 | < | // parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
921 | < | // parallelData.nGroupsLocal = getNCutoffGroups(); |
922 | < | // parallelData.myNode = worldRank; |
923 | < | // MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
924 | < | |
925 | < | //pass mpiSimData struct and index arrays to fortran |
926 | < | //setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
927 | < | // &localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
928 | < | // &localToGlobalCutoffGroupIndex[0], &isError); |
929 | < | |
930 | < | // if (isError) { |
931 | < | // sprintf(painCave.errMsg, |
932 | < | // "mpiRefresh errror: fortran didn't like something we gave it.\n"); |
933 | < | // painCave.isFatal = 1; |
934 | < | // simError(); |
935 | < | // } |
936 | < | |
937 | < | // sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
938 | < | // errorCheckPoint(); |
939 | < | #endif |
940 | < | |
941 | < | // initFortranFF(&isError); |
942 | < | // if (isError) { |
943 | < | // sprintf(painCave.errMsg, |
944 | < | // "initFortranFF errror: fortran didn't like something we gave it.\n"); |
945 | < | // painCave.isFatal = 1; |
946 | < | // simError(); |
947 | < | // } |
948 | < | // fortranInitialized_ = true; |
944 | > | topologyDone_ = true; |
945 | } | |
946 | ||
947 | void SimInfo::addProperty(GenericData* genData) { | |
# | Line 990 | Line 986 | namespace OpenMD { | |
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 | ||
1008 | – | Vector3d SimInfo::getComVel(){ |
1009 | – | SimInfo::MoleculeIterator i; |
1010 | – | Molecule* mol; |
1007 | ||
1012 | – | Vector3d comVel(0.0); |
1013 | – | RealType totalMass = 0.0; |
1014 | – | |
1015 | – | |
1016 | – | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1017 | – | RealType mass = mol->getMass(); |
1018 | – | totalMass += mass; |
1019 | – | comVel += mass * mol->getComVel(); |
1020 | – | } |
1021 | – | |
1022 | – | #ifdef IS_MPI |
1023 | – | RealType tmpMass = totalMass; |
1024 | – | Vector3d tmpComVel(comVel); |
1025 | – | MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1026 | – | MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1027 | – | #endif |
1028 | – | |
1029 | – | comVel /= totalMass; |
1030 | – | |
1031 | – | return comVel; |
1032 | – | } |
1033 | – | |
1034 | – | Vector3d SimInfo::getCom(){ |
1035 | – | SimInfo::MoleculeIterator i; |
1036 | – | Molecule* mol; |
1037 | – | |
1038 | – | Vector3d com(0.0); |
1039 | – | RealType totalMass = 0.0; |
1040 | – | |
1041 | – | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1042 | – | RealType mass = mol->getMass(); |
1043 | – | totalMass += mass; |
1044 | – | com += mass * mol->getCom(); |
1045 | – | } |
1046 | – | |
1047 | – | #ifdef IS_MPI |
1048 | – | RealType tmpMass = totalMass; |
1049 | – | Vector3d tmpCom(com); |
1050 | – | MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1051 | – | MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1052 | – | #endif |
1053 | – | |
1054 | – | com /= totalMass; |
1055 | – | |
1056 | – | return com; |
1057 | – | |
1058 | – | } |
1059 | – | |
1008 | ostream& operator <<(ostream& o, SimInfo& info) { | |
1009 | ||
1010 | return o; | |
1011 | } | |
1012 | ||
1013 | < | |
1066 | < | /* |
1067 | < | Returns center of mass and center of mass velocity in one function call. |
1068 | < | */ |
1069 | < | |
1070 | < | void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1071 | < | SimInfo::MoleculeIterator i; |
1072 | < | Molecule* mol; |
1073 | < | |
1074 | < | |
1075 | < | RealType totalMass = 0.0; |
1076 | < | |
1077 | < | |
1078 | < | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1079 | < | RealType mass = mol->getMass(); |
1080 | < | totalMass += mass; |
1081 | < | com += mass * mol->getCom(); |
1082 | < | comVel += mass * mol->getComVel(); |
1083 | < | } |
1084 | < | |
1085 | < | #ifdef IS_MPI |
1086 | < | RealType tmpMass = totalMass; |
1087 | < | Vector3d tmpCom(com); |
1088 | < | Vector3d tmpComVel(comVel); |
1089 | < | MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1090 | < | MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1091 | < | MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1092 | < | #endif |
1093 | < | |
1094 | < | com /= totalMass; |
1095 | < | comVel /= totalMass; |
1096 | < | } |
1097 | < | |
1098 | < | /* |
1099 | < | Return intertia tensor for entire system and angular momentum Vector. |
1100 | < | |
1101 | < | |
1102 | < | [ Ixx -Ixy -Ixz ] |
1103 | < | J =| -Iyx Iyy -Iyz | |
1104 | < | [ -Izx -Iyz Izz ] |
1105 | < | */ |
1106 | < | |
1107 | < | void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1108 | < | |
1109 | < | |
1110 | < | RealType xx = 0.0; |
1111 | < | RealType yy = 0.0; |
1112 | < | RealType zz = 0.0; |
1113 | < | RealType xy = 0.0; |
1114 | < | RealType xz = 0.0; |
1115 | < | RealType yz = 0.0; |
1116 | < | Vector3d com(0.0); |
1117 | < | Vector3d comVel(0.0); |
1118 | < | |
1119 | < | getComAll(com, comVel); |
1120 | < | |
1121 | < | SimInfo::MoleculeIterator i; |
1122 | < | Molecule* mol; |
1123 | < | |
1124 | < | Vector3d thisq(0.0); |
1125 | < | Vector3d thisv(0.0); |
1126 | < | |
1127 | < | RealType thisMass = 0.0; |
1128 | < | |
1129 | < | |
1130 | < | |
1131 | < | |
1132 | < | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1133 | < | |
1134 | < | thisq = mol->getCom()-com; |
1135 | < | thisv = mol->getComVel()-comVel; |
1136 | < | thisMass = mol->getMass(); |
1137 | < | // Compute moment of intertia coefficients. |
1138 | < | xx += thisq[0]*thisq[0]*thisMass; |
1139 | < | yy += thisq[1]*thisq[1]*thisMass; |
1140 | < | zz += thisq[2]*thisq[2]*thisMass; |
1141 | < | |
1142 | < | // compute products of intertia |
1143 | < | xy += thisq[0]*thisq[1]*thisMass; |
1144 | < | xz += thisq[0]*thisq[2]*thisMass; |
1145 | < | yz += thisq[1]*thisq[2]*thisMass; |
1146 | < | |
1147 | < | angularMomentum += cross( thisq, thisv ) * thisMass; |
1148 | < | |
1149 | < | } |
1150 | < | |
1151 | < | |
1152 | < | inertiaTensor(0,0) = yy + zz; |
1153 | < | inertiaTensor(0,1) = -xy; |
1154 | < | inertiaTensor(0,2) = -xz; |
1155 | < | inertiaTensor(1,0) = -xy; |
1156 | < | inertiaTensor(1,1) = xx + zz; |
1157 | < | inertiaTensor(1,2) = -yz; |
1158 | < | inertiaTensor(2,0) = -xz; |
1159 | < | inertiaTensor(2,1) = -yz; |
1160 | < | inertiaTensor(2,2) = xx + yy; |
1161 | < | |
1162 | < | #ifdef IS_MPI |
1163 | < | Mat3x3d tmpI(inertiaTensor); |
1164 | < | Vector3d tmpAngMom; |
1165 | < | MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1166 | < | MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1167 | < | #endif |
1168 | < | |
1169 | < | return; |
1170 | < | } |
1171 | < | |
1172 | < | //Returns the angular momentum of the system |
1173 | < | Vector3d SimInfo::getAngularMomentum(){ |
1174 | < | |
1175 | < | Vector3d com(0.0); |
1176 | < | Vector3d comVel(0.0); |
1177 | < | Vector3d angularMomentum(0.0); |
1178 | < | |
1179 | < | getComAll(com,comVel); |
1180 | < | |
1181 | < | SimInfo::MoleculeIterator i; |
1182 | < | Molecule* mol; |
1183 | < | |
1184 | < | Vector3d thisr(0.0); |
1185 | < | Vector3d thisp(0.0); |
1186 | < | |
1187 | < | RealType thisMass; |
1188 | < | |
1189 | < | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1190 | < | thisMass = mol->getMass(); |
1191 | < | thisr = mol->getCom()-com; |
1192 | < | thisp = (mol->getComVel()-comVel)*thisMass; |
1193 | < | |
1194 | < | angularMomentum += cross( thisr, thisp ); |
1195 | < | |
1196 | < | } |
1197 | < | |
1198 | < | #ifdef IS_MPI |
1199 | < | Vector3d tmpAngMom; |
1200 | < | MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1201 | < | #endif |
1202 | < | |
1203 | < | return angularMomentum; |
1204 | < | } |
1205 | < | |
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 | ||
1214 | – | /* Returns the Volume of the simulation based on a ellipsoid with semi-axes |
1215 | – | based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3 |
1216 | – | where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to |
1217 | – | V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536. |
1218 | – | */ |
1219 | – | void SimInfo::getGyrationalVolume(RealType &volume){ |
1220 | – | Mat3x3d intTensor; |
1221 | – | RealType det; |
1222 | – | Vector3d dummyAngMom; |
1223 | – | RealType sysconstants; |
1224 | – | RealType geomCnst; |
1225 | – | |
1226 | – | geomCnst = 3.0/2.0; |
1227 | – | /* Get the inertial tensor and angular momentum for free*/ |
1228 | – | getInertiaTensor(intTensor,dummyAngMom); |
1229 | – | |
1230 | – | det = intTensor.determinant(); |
1231 | – | sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
1232 | – | volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); |
1233 | – | return; |
1234 | – | } |
1235 | – | |
1236 | – | void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){ |
1237 | – | Mat3x3d intTensor; |
1238 | – | Vector3d dummyAngMom; |
1239 | – | RealType sysconstants; |
1240 | – | RealType geomCnst; |
1241 | – | |
1242 | – | geomCnst = 3.0/2.0; |
1243 | – | /* Get the inertial tensor and angular momentum for free*/ |
1244 | – | getInertiaTensor(intTensor,dummyAngMom); |
1245 | – | |
1246 | – | detI = intTensor.determinant(); |
1247 | – | sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
1248 | – | volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); |
1249 | – | return; |
1250 | – | } |
1251 | – | /* |
1252 | – | void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) { |
1253 | – | assert( v.size() == nAtoms_ + nRigidBodies_); |
1254 | – | sdByGlobalIndex_ = v; |
1255 | – | } |
1256 | – | |
1257 | – | StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) { |
1258 | – | //assert(index < nAtoms_ + nRigidBodies_); |
1259 | – | return sdByGlobalIndex_.at(index); |
1260 | – | } |
1261 | – | */ |
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 |
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