--- trunk/src/brains/SimInfo.cpp 2005/05/31 22:31:54 557 +++ branches/development/src/brains/SimInfo.cpp 2010/12/17 20:11:05 1528 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,15 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). */ /** @@ -48,148 +48,147 @@ #include #include +#include #include "brains/SimInfo.hpp" #include "math/Vector3.hpp" #include "primitives/Molecule.hpp" +#include "primitives/StuntDouble.hpp" +#include "UseTheForce/fCutoffPolicy.h" +#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" #include "UseTheForce/doForces_interface.h" -#include "UseTheForce/notifyCutoffs_interface.h" +#include "UseTheForce/DarkSide/neighborLists_interface.h" +#include "UseTheForce/DarkSide/switcheroo_interface.h" #include "utils/MemoryUtils.hpp" #include "utils/simError.h" #include "selection/SelectionManager.hpp" +#include "io/ForceFieldOptions.hpp" +#include "UseTheForce/ForceField.hpp" +#include "nonbonded/InteractionManager.hpp" + #ifdef IS_MPI #include "UseTheForce/mpiComponentPlan.h" #include "UseTheForce/DarkSide/simParallel_interface.h" #endif -namespace oopse { - - SimInfo::SimInfo(MakeStamps* stamps, std::vector >& molStampPairs, - ForceField* ff, Globals* simParams) : - stamps_(stamps), forceField_(ff), simParams_(simParams), - ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), +using namespace std; +namespace OpenMD { + + SimInfo::SimInfo(ForceField* ff, Globals* simParams) : + forceField_(ff), simParams_(simParams), + ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), - nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), - nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), - sman_(NULL), fortranInitialized_(false) { - - - std::vector >::iterator i; - MoleculeStamp* molStamp; - int nMolWithSameStamp; - int nCutoffAtoms = 0; // number of atoms belong to cutoff groups - int nGroups = 0; //total cutoff groups defined in meta-data file - CutoffGroupStamp* cgStamp; - RigidBodyStamp* rbStamp; - int nRigidAtoms = 0; + nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), + nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), + nConstraints_(0), sman_(NULL), fortranInitialized_(false), + calcBoxDipole_(false), useAtomicVirial_(true) { - for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { - molStamp = i->first; - nMolWithSameStamp = i->second; - - addMoleculeStamp(molStamp, nMolWithSameStamp); - - //calculate atoms in molecules - nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; - - - //calculate atoms in cutoff groups - int nAtomsInGroups = 0; - int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); - - for (int j=0; j < nCutoffGroupsInStamp; j++) { - cgStamp = molStamp->getCutoffGroup(j); - nAtomsInGroups += cgStamp->getNMembers(); - } - - nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; - nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; - - //calculate atoms in rigid bodies - int nAtomsInRigidBodies = 0; - int nRigidBodiesInStamp = molStamp->getNRigidBodies(); - - for (int j=0; j < nRigidBodiesInStamp; j++) { - rbStamp = molStamp->getRigidBody(j); - nAtomsInRigidBodies += rbStamp->getNMembers(); - } - - nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; - nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; - + MoleculeStamp* molStamp; + int nMolWithSameStamp; + int nCutoffAtoms = 0; // number of atoms belong to cutoff groups + int nGroups = 0; //total cutoff groups defined in meta-data file + CutoffGroupStamp* cgStamp; + RigidBodyStamp* rbStamp; + int nRigidAtoms = 0; + + vector components = simParams->getComponents(); + + for (vector::iterator i = components.begin(); i !=components.end(); ++i) { + molStamp = (*i)->getMoleculeStamp(); + nMolWithSameStamp = (*i)->getNMol(); + + addMoleculeStamp(molStamp, nMolWithSameStamp); + + //calculate atoms in molecules + nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; + + //calculate atoms in cutoff groups + int nAtomsInGroups = 0; + int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); + + for (int j=0; j < nCutoffGroupsInStamp; j++) { + cgStamp = molStamp->getCutoffGroupStamp(j); + nAtomsInGroups += cgStamp->getNMembers(); } - - //every free atom (atom does not belong to cutoff groups) is a cutoff group - //therefore the total number of cutoff groups in the system is equal to - //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data - //file plus the number of cutoff groups defined in meta-data file - nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; - - //every free atom (atom does not belong to rigid bodies) is an integrable object - //therefore the total number of integrable objects in the system is equal to - //the total number of atoms minus number of atoms belong to rigid body defined in meta-data - //file plus the number of rigid bodies defined in meta-data file - nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; - - nGlobalMols_ = molStampIds_.size(); - -#ifdef IS_MPI - molToProcMap_.resize(nGlobalMols_); -#endif - - } - + + nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; + + nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; + + //calculate atoms in rigid bodies + int nAtomsInRigidBodies = 0; + int nRigidBodiesInStamp = molStamp->getNRigidBodies(); + + for (int j=0; j < nRigidBodiesInStamp; j++) { + rbStamp = molStamp->getRigidBodyStamp(j); + nAtomsInRigidBodies += rbStamp->getNMembers(); + } + + nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; + nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; + + } + + //every free atom (atom does not belong to cutoff groups) is a cutoff + //group therefore the total number of cutoff groups in the system is + //equal to the total number of atoms minus number of atoms belong to + //cutoff group defined in meta-data file plus the number of cutoff + //groups defined in meta-data file + nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; + + //every free atom (atom does not belong to rigid bodies) is an + //integrable object therefore the total number of integrable objects + //in the system is equal to the total number of atoms minus number of + //atoms belong to rigid body defined in meta-data file plus the number + //of rigid bodies defined in meta-data file + nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + + nGlobalRigidBodies_; + + nGlobalMols_ = molStampIds_.size(); + molToProcMap_.resize(nGlobalMols_); + } + SimInfo::~SimInfo() { - std::map::iterator i; + map::iterator i; for (i = molecules_.begin(); i != molecules_.end(); ++i) { delete i->second; } molecules_.clear(); - delete stamps_; delete sman_; delete simParams_; delete forceField_; } - int SimInfo::getNGlobalConstraints() { - int nGlobalConstraints; -#ifdef IS_MPI - MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM, - MPI_COMM_WORLD); -#else - nGlobalConstraints = nConstraints_; -#endif - return nGlobalConstraints; - } bool SimInfo::addMolecule(Molecule* mol) { MoleculeIterator i; - + i = molecules_.find(mol->getGlobalIndex()); if (i == molecules_.end() ) { - - molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); - + + molecules_.insert(make_pair(mol->getGlobalIndex(), mol)); + nAtoms_ += mol->getNAtoms(); nBonds_ += mol->getNBonds(); nBends_ += mol->getNBends(); nTorsions_ += mol->getNTorsions(); + nInversions_ += mol->getNInversions(); nRigidBodies_ += mol->getNRigidBodies(); nIntegrableObjects_ += mol->getNIntegrableObjects(); nCutoffGroups_ += mol->getNCutoffGroups(); nConstraints_ += mol->getNConstraintPairs(); - - addExcludePairs(mol); - + + addInteractionPairs(mol); + return true; } else { return false; } } - + bool SimInfo::removeMolecule(Molecule* mol) { MoleculeIterator i; i = molecules_.find(mol->getGlobalIndex()); @@ -202,12 +201,13 @@ namespace oopse { nBonds_ -= mol->getNBonds(); nBends_ -= mol->getNBends(); nTorsions_ -= mol->getNTorsions(); + nInversions_ -= mol->getNInversions(); nRigidBodies_ -= mol->getNRigidBodies(); nIntegrableObjects_ -= mol->getNIntegrableObjects(); nCutoffGroups_ -= mol->getNCutoffGroups(); nConstraints_ -= mol->getNConstraintPairs(); - removeExcludePairs(mol); + removeInteractionPairs(mol); molecules_.erase(mol->getGlobalIndex()); delete mol; @@ -216,8 +216,6 @@ namespace oopse { } else { return false; } - - } @@ -235,7 +233,7 @@ namespace oopse { void SimInfo::calcNdf() { int ndf_local; MoleculeIterator i; - std::vector::iterator j; + vector::iterator j; Molecule* mol; StuntDouble* integrableObject; @@ -255,8 +253,8 @@ namespace oopse { } } - }//end for (integrableObject) - }// end for (mol) + } + } // n_constraints is local, so subtract them on each processor ndf_local -= nConstraints_; @@ -273,11 +271,20 @@ namespace oopse { } + int SimInfo::getFdf() { +#ifdef IS_MPI + MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); +#else + fdf_ = fdf_local; +#endif + return fdf_; + } + void SimInfo::calcNdfRaw() { int ndfRaw_local; MoleculeIterator i; - std::vector::iterator j; + vector::iterator j; Molecule* mol; StuntDouble* integrableObject; @@ -324,124 +331,324 @@ namespace oopse { } - void SimInfo::addExcludePairs(Molecule* mol) { - std::vector::iterator bondIter; - std::vector::iterator bendIter; - std::vector::iterator torsionIter; + void SimInfo::addInteractionPairs(Molecule* mol) { + ForceFieldOptions& options_ = forceField_->getForceFieldOptions(); + vector::iterator bondIter; + vector::iterator bendIter; + vector::iterator torsionIter; + vector::iterator inversionIter; Bond* bond; Bend* bend; Torsion* torsion; + Inversion* inversion; int a; int b; int c; int d; + + // atomGroups can be used to add special interaction maps between + // groups of atoms that are in two separate rigid bodies. + // However, most site-site interactions between two rigid bodies + // are probably not special, just the ones between the physically + // bonded atoms. Interactions *within* a single rigid body should + // always be excluded. These are done at the bottom of this + // function. + + map > atomGroups; + Molecule::RigidBodyIterator rbIter; + RigidBody* rb; + Molecule::IntegrableObjectIterator ii; + StuntDouble* integrableObject; - for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { + for (integrableObject = mol->beginIntegrableObject(ii); + integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { + + if (integrableObject->isRigidBody()) { + rb = static_cast(integrableObject); + vector atoms = rb->getAtoms(); + set rigidAtoms; + for (int i = 0; i < static_cast(atoms.size()); ++i) { + rigidAtoms.insert(atoms[i]->getGlobalIndex()); + } + for (int i = 0; i < static_cast(atoms.size()); ++i) { + atomGroups.insert(map >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); + } + } else { + set oneAtomSet; + oneAtomSet.insert(integrableObject->getGlobalIndex()); + atomGroups.insert(map >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); + } + } + + for (bond= mol->beginBond(bondIter); bond != NULL; + bond = mol->nextBond(bondIter)) { + a = bond->getAtomA()->getGlobalIndex(); - b = bond->getAtomB()->getGlobalIndex(); - exclude_.addPair(a, b); + b = bond->getAtomB()->getGlobalIndex(); + + if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { + oneTwoInteractions_.addPair(a, b); + } else { + excludedInteractions_.addPair(a, b); + } } - for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { + for (bend= mol->beginBend(bendIter); bend != NULL; + bend = mol->nextBend(bendIter)) { + a = bend->getAtomA()->getGlobalIndex(); b = bend->getAtomB()->getGlobalIndex(); c = bend->getAtomC()->getGlobalIndex(); + + if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { + oneTwoInteractions_.addPair(a, b); + oneTwoInteractions_.addPair(b, c); + } else { + excludedInteractions_.addPair(a, b); + excludedInteractions_.addPair(b, c); + } - exclude_.addPair(a, b); - exclude_.addPair(a, c); - exclude_.addPair(b, c); + if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) { + oneThreeInteractions_.addPair(a, c); + } else { + excludedInteractions_.addPair(a, c); + } } - for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { + for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; + torsion = mol->nextTorsion(torsionIter)) { + a = torsion->getAtomA()->getGlobalIndex(); b = torsion->getAtomB()->getGlobalIndex(); c = torsion->getAtomC()->getGlobalIndex(); - d = torsion->getAtomD()->getGlobalIndex(); + d = torsion->getAtomD()->getGlobalIndex(); - exclude_.addPair(a, b); - exclude_.addPair(a, c); - exclude_.addPair(a, d); - exclude_.addPair(b, c); - exclude_.addPair(b, d); - exclude_.addPair(c, d); + if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { + oneTwoInteractions_.addPair(a, b); + oneTwoInteractions_.addPair(b, c); + oneTwoInteractions_.addPair(c, d); + } else { + excludedInteractions_.addPair(a, b); + excludedInteractions_.addPair(b, c); + excludedInteractions_.addPair(c, d); + } + + if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) { + oneThreeInteractions_.addPair(a, c); + oneThreeInteractions_.addPair(b, d); + } else { + excludedInteractions_.addPair(a, c); + excludedInteractions_.addPair(b, d); + } + + if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) { + oneFourInteractions_.addPair(a, d); + } else { + excludedInteractions_.addPair(a, d); + } } - Molecule::RigidBodyIterator rbIter; - RigidBody* rb; - for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { - std::vector atoms = rb->getAtoms(); - for (int i = 0; i < atoms.size() -1 ; ++i) { - for (int j = i + 1; j < atoms.size(); ++j) { + for (inversion= mol->beginInversion(inversionIter); inversion != NULL; + inversion = mol->nextInversion(inversionIter)) { + + a = inversion->getAtomA()->getGlobalIndex(); + b = inversion->getAtomB()->getGlobalIndex(); + c = inversion->getAtomC()->getGlobalIndex(); + d = inversion->getAtomD()->getGlobalIndex(); + + if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { + oneTwoInteractions_.addPair(a, b); + oneTwoInteractions_.addPair(a, c); + oneTwoInteractions_.addPair(a, d); + } else { + excludedInteractions_.addPair(a, b); + excludedInteractions_.addPair(a, c); + excludedInteractions_.addPair(a, d); + } + + if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) { + oneThreeInteractions_.addPair(b, c); + oneThreeInteractions_.addPair(b, d); + oneThreeInteractions_.addPair(c, d); + } else { + excludedInteractions_.addPair(b, c); + excludedInteractions_.addPair(b, d); + excludedInteractions_.addPair(c, d); + } + } + + for (rb = mol->beginRigidBody(rbIter); rb != NULL; + rb = mol->nextRigidBody(rbIter)) { + vector atoms = rb->getAtoms(); + for (int i = 0; i < static_cast(atoms.size()) -1 ; ++i) { + for (int j = i + 1; j < static_cast(atoms.size()); ++j) { a = atoms[i]->getGlobalIndex(); b = atoms[j]->getGlobalIndex(); - exclude_.addPair(a, b); + excludedInteractions_.addPair(a, b); } } } } - void SimInfo::removeExcludePairs(Molecule* mol) { - std::vector::iterator bondIter; - std::vector::iterator bendIter; - std::vector::iterator torsionIter; + void SimInfo::removeInteractionPairs(Molecule* mol) { + ForceFieldOptions& options_ = forceField_->getForceFieldOptions(); + vector::iterator bondIter; + vector::iterator bendIter; + vector::iterator torsionIter; + vector::iterator inversionIter; Bond* bond; Bend* bend; Torsion* torsion; + Inversion* inversion; int a; int b; int c; int d; + + map > atomGroups; + Molecule::RigidBodyIterator rbIter; + RigidBody* rb; + Molecule::IntegrableObjectIterator ii; + StuntDouble* integrableObject; - for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { + for (integrableObject = mol->beginIntegrableObject(ii); + integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { + + if (integrableObject->isRigidBody()) { + rb = static_cast(integrableObject); + vector atoms = rb->getAtoms(); + set rigidAtoms; + for (int i = 0; i < static_cast(atoms.size()); ++i) { + rigidAtoms.insert(atoms[i]->getGlobalIndex()); + } + for (int i = 0; i < static_cast(atoms.size()); ++i) { + atomGroups.insert(map >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); + } + } else { + set oneAtomSet; + oneAtomSet.insert(integrableObject->getGlobalIndex()); + atomGroups.insert(map >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); + } + } + + for (bond= mol->beginBond(bondIter); bond != NULL; + bond = mol->nextBond(bondIter)) { + a = bond->getAtomA()->getGlobalIndex(); - b = bond->getAtomB()->getGlobalIndex(); - exclude_.removePair(a, b); + b = bond->getAtomB()->getGlobalIndex(); + + if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { + oneTwoInteractions_.removePair(a, b); + } else { + excludedInteractions_.removePair(a, b); + } } - for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { + for (bend= mol->beginBend(bendIter); bend != NULL; + bend = mol->nextBend(bendIter)) { + a = bend->getAtomA()->getGlobalIndex(); b = bend->getAtomB()->getGlobalIndex(); c = bend->getAtomC()->getGlobalIndex(); + + if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { + oneTwoInteractions_.removePair(a, b); + oneTwoInteractions_.removePair(b, c); + } else { + excludedInteractions_.removePair(a, b); + excludedInteractions_.removePair(b, c); + } - exclude_.removePair(a, b); - exclude_.removePair(a, c); - exclude_.removePair(b, c); + if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) { + oneThreeInteractions_.removePair(a, c); + } else { + excludedInteractions_.removePair(a, c); + } } - for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { + for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; + torsion = mol->nextTorsion(torsionIter)) { + a = torsion->getAtomA()->getGlobalIndex(); b = torsion->getAtomB()->getGlobalIndex(); c = torsion->getAtomC()->getGlobalIndex(); - d = torsion->getAtomD()->getGlobalIndex(); + d = torsion->getAtomD()->getGlobalIndex(); + + if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { + oneTwoInteractions_.removePair(a, b); + oneTwoInteractions_.removePair(b, c); + oneTwoInteractions_.removePair(c, d); + } else { + excludedInteractions_.removePair(a, b); + excludedInteractions_.removePair(b, c); + excludedInteractions_.removePair(c, d); + } - exclude_.removePair(a, b); - exclude_.removePair(a, c); - exclude_.removePair(a, d); - exclude_.removePair(b, c); - exclude_.removePair(b, d); - exclude_.removePair(c, d); + if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) { + oneThreeInteractions_.removePair(a, c); + oneThreeInteractions_.removePair(b, d); + } else { + excludedInteractions_.removePair(a, c); + excludedInteractions_.removePair(b, d); + } + + if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) { + oneFourInteractions_.removePair(a, d); + } else { + excludedInteractions_.removePair(a, d); + } } - Molecule::RigidBodyIterator rbIter; - RigidBody* rb; - for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { - std::vector atoms = rb->getAtoms(); - for (int i = 0; i < atoms.size() -1 ; ++i) { - for (int j = i + 1; j < atoms.size(); ++j) { + for (inversion= mol->beginInversion(inversionIter); inversion != NULL; + inversion = mol->nextInversion(inversionIter)) { + + a = inversion->getAtomA()->getGlobalIndex(); + b = inversion->getAtomB()->getGlobalIndex(); + c = inversion->getAtomC()->getGlobalIndex(); + d = inversion->getAtomD()->getGlobalIndex(); + + if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { + oneTwoInteractions_.removePair(a, b); + oneTwoInteractions_.removePair(a, c); + oneTwoInteractions_.removePair(a, d); + } else { + excludedInteractions_.removePair(a, b); + excludedInteractions_.removePair(a, c); + excludedInteractions_.removePair(a, d); + } + + if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) { + oneThreeInteractions_.removePair(b, c); + oneThreeInteractions_.removePair(b, d); + oneThreeInteractions_.removePair(c, d); + } else { + excludedInteractions_.removePair(b, c); + excludedInteractions_.removePair(b, d); + excludedInteractions_.removePair(c, d); + } + } + + for (rb = mol->beginRigidBody(rbIter); rb != NULL; + rb = mol->nextRigidBody(rbIter)) { + vector atoms = rb->getAtoms(); + for (int i = 0; i < static_cast(atoms.size()) -1 ; ++i) { + for (int j = i + 1; j < static_cast(atoms.size()); ++j) { a = atoms[i]->getGlobalIndex(); b = atoms[j]->getGlobalIndex(); - exclude_.removePair(a, b); + excludedInteractions_.removePair(a, b); } } } - + } - - + + void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { int curStampId; - + //index from 0 curStampId = moleculeStamps_.size(); @@ -452,179 +659,183 @@ namespace oopse { void SimInfo::update() { setupSimType(); + setupCutoffRadius(); + setupSwitchingRadius(); + setupCutoffMethod(); + setupSkinThickness(); + setupSwitchingFunction(); + setupAccumulateBoxDipole(); #ifdef IS_MPI setupFortranParallel(); #endif - setupFortranSim(); + fortranInitialized_ = true; - //setup fortran force field - /** @deprecate */ - int isError = 0; - initFortranFF( &fInfo_.SIM_uses_RF , &isError ); - if(isError){ - sprintf( painCave.errMsg, - "ForceField error: There was an error initializing the forceField in fortran.\n" ); - painCave.isFatal = 1; - simError(); - } - - - setupCutoff(); - calcNdf(); calcNdfRaw(); calcNdfTrans(); - - fortranInitialized_ = true; } - - std::set SimInfo::getUniqueAtomTypes() { + + set SimInfo::getSimulatedAtomTypes() { SimInfo::MoleculeIterator mi; Molecule* mol; Molecule::AtomIterator ai; Atom* atom; - std::set atomTypes; - + set atomTypes; + for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { - + for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { atomTypes.insert(atom->getAtomType()); } - + } - + return atomTypes; } - void SimInfo::setupSimType() { - std::set::iterator i; - std::set atomTypes; - atomTypes = getUniqueAtomTypes(); + /** + * setupCutoffRadius + * + * If the cutoffRadius was explicitly set, use that value. + * If the cutoffRadius was not explicitly set: + * Are there electrostatic atoms? Use 12.0 Angstroms. + * No electrostatic atoms? Poll the atom types present in the + * simulation for suggested cutoff values (e.g. 2.5 * sigma). + * Use the maximum suggested value that was found. + */ + void SimInfo::setupCutoffRadius() { - int useLennardJones = 0; - int useElectrostatic = 0; - int useEAM = 0; - int useCharge = 0; - int useDirectional = 0; - int useDipole = 0; - int useGayBerne = 0; - int useSticky = 0; - int useStickyPower = 0; - int useShape = 0; - int useFLARB = 0; //it is not in AtomType yet - int useDirectionalAtom = 0; - int useElectrostatics = 0; - //usePBC and useRF are from simParams - int usePBC = simParams_->getPBC(); - int useRF = simParams_->getUseRF(); - - //loop over all of the atom types - for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { - useLennardJones |= (*i)->isLennardJones(); - useElectrostatic |= (*i)->isElectrostatic(); - useEAM |= (*i)->isEAM(); - useCharge |= (*i)->isCharge(); - useDirectional |= (*i)->isDirectional(); - useDipole |= (*i)->isDipole(); - useGayBerne |= (*i)->isGayBerne(); - useSticky |= (*i)->isSticky(); - useStickyPower |= (*i)->isStickyPower(); - useShape |= (*i)->isShape(); + if (simParams_->haveCutoffRadius()) { + cutoffRadius_ = simParams_->getCutoffRadius(); + } else { + if (usesElectrostaticAtoms_) { + sprintf(painCave.errMsg, + "SimInfo Warning: No value was set for the cutoffRadius.\n" + "\tOpenMD will use a default value of 12.0 angstroms" + "\tfor the cutoffRadius.\n"); + painCave.isFatal = 0; + simError(); + cutoffRadius_ = 12.0; + } else { + RealType thisCut; + set::iterator i; + set atomTypes; + atomTypes = getSimulatedAtomTypes(); + for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { + thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i)); + cutoffRadius_ = max(thisCut, cutoffRadius_); + } + sprintf(painCave.errMsg, + "SimInfo Warning: No value was set for the cutoffRadius.\n" + "\tOpenMD will use %lf angstroms.\n", + cutoffRadius_); + painCave.isFatal = 0; + simError(); + } } - if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { - useDirectionalAtom = 1; - } - - if (useCharge || useDipole) { - useElectrostatics = 1; - } - -#ifdef IS_MPI - int temp; - - temp = usePBC; - MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - - temp = useDirectionalAtom; - MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - - temp = useLennardJones; - MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - - temp = useElectrostatics; - MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - - temp = useCharge; - MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - - temp = useDipole; - MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - - temp = useSticky; - MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - - temp = useStickyPower; - MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + InteractionManager::Instance()->setCutoffRadius(cutoffRadius_); + } + + /** + * setupSwitchingRadius + * + * If the switchingRadius was explicitly set, use that value (but check it) + * If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ + */ + void SimInfo::setupSwitchingRadius() { - temp = useGayBerne; - MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + if (simParams_->haveSwitchingRadius()) { + switchingRadius_ = simParams_->getSwitchingRadius(); + if (switchingRadius_ > cutoffRadius_) { + sprintf(painCave.errMsg, + "SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n", + switchingRadius_, cutoffRadius_); + painCave.isFatal = 1; + simError(); - temp = useEAM; - MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + } + } else { + switchingRadius_ = 0.85 * cutoffRadius_; + sprintf(painCave.errMsg, + "SimInfo Warning: No value was set for the switchingRadius.\n" + "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" + "\tswitchingRadius = %f. for this simulation\n", switchingRadius_); + painCave.isFatal = 0; + simError(); + } + InteractionManager::Instance()->setSwitchingRadius(switchingRadius_); + } - temp = useShape; - MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + /** + * setupSkinThickness + * + * If the skinThickness was explicitly set, use that value (but check it) + * If the skinThickness was not explicitly set: use 1.0 angstroms + */ + void SimInfo::setupSkinThickness() { + if (simParams_->haveSkinThickness()) { + skinThickness_ = simParams_->getSkinThickness(); + } else { + skinThickness_ = 1.0; + sprintf(painCave.errMsg, + "SimInfo Warning: No value was set for the skinThickness.\n" + "\tOpenMD will use a default value of %f Angstroms\n" + "\tfor this simulation\n", skinThickness_); + painCave.isFatal = 0; + simError(); + } + } - temp = useFLARB; - MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + void SimInfo::setupSimType() { + set::iterator i; + set atomTypes; + atomTypes = getSimulatedAtomTypes(); - temp = useRF; - MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - -#endif + useAtomicVirial_ = simParams_->getUseAtomicVirial(); - fInfo_.SIM_uses_PBC = usePBC; - fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; - fInfo_.SIM_uses_LennardJones = useLennardJones; - fInfo_.SIM_uses_Electrostatics = useElectrostatics; - fInfo_.SIM_uses_Charges = useCharge; - fInfo_.SIM_uses_Dipoles = useDipole; - fInfo_.SIM_uses_Sticky = useSticky; - fInfo_.SIM_uses_StickyPower = useStickyPower; - fInfo_.SIM_uses_GayBerne = useGayBerne; - fInfo_.SIM_uses_EAM = useEAM; - fInfo_.SIM_uses_Shapes = useShape; - fInfo_.SIM_uses_FLARB = useFLARB; - fInfo_.SIM_uses_RF = useRF; + int usesElectrostatic = 0; + int usesMetallic = 0; + int usesDirectional = 0; + //loop over all of the atom types + for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { + usesElectrostatic |= (*i)->isElectrostatic(); + usesMetallic |= (*i)->isMetal(); + usesDirectional |= (*i)->isDirectional(); + } - if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { +#ifdef IS_MPI + int temp; + temp = usesDirectional; + MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - if (simParams_->haveDielectric()) { - fInfo_.dielect = simParams_->getDielectric(); - } else { - sprintf(painCave.errMsg, - "SimSetup Error: No Dielectric constant was set.\n" - "\tYou are trying to use Reaction Field without" - "\tsetting a dielectric constant!\n"); - painCave.isFatal = 1; - simError(); - } - - } else { - fInfo_.dielect = 0.0; - } + temp = usesMetallic; + MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + temp = usesElectrostatic; + MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); +#endif + fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_; + fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_; + fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_; + fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_; + fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_; + fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_; } void SimInfo::setupFortranSim() { int isError; - int nExclude; - std::vector fortranGlobalGroupMembership; + int nExclude, nOneTwo, nOneThree, nOneFour; + vector fortranGlobalGroupMembership; - nExclude = exclude_.getSize(); + notifyFortranSkinThickness(&skinThickness_); + + int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0; + int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0; + notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf); + isError = 0; //globalGroupMembership_ is filled by SimCreator @@ -633,14 +844,14 @@ namespace oopse { } //calculate mass ratio of cutoff group - std::vector mfact; + vector mfact; SimInfo::MoleculeIterator mi; Molecule* mol; Molecule::CutoffGroupIterator ci; CutoffGroup* cg; Molecule::AtomIterator ai; Atom* atom; - double totalMass; + RealType totalMass; //to avoid memory reallocation, reserve enough space for mfact mfact.reserve(getNCutoffGroups()); @@ -650,14 +861,17 @@ namespace oopse { totalMass = cg->getMass(); for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { - mfact.push_back(atom->getMass()/totalMass); + // Check for massless groups - set mfact to 1 if true + if (totalMass != 0) + mfact.push_back(atom->getMass()/totalMass); + else + mfact.push_back( 1.0 ); } - } } //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) - std::vector identArray; + vector identArray; //to avoid memory reallocation, reserve enough space identArray identArray.reserve(getNAtoms()); @@ -670,42 +884,61 @@ namespace oopse { //fill molMembershipArray //molMembershipArray is filled by SimCreator - std::vector molMembershipArray(nGlobalAtoms_); + vector molMembershipArray(nGlobalAtoms_); for (int i = 0; i < nGlobalAtoms_; i++) { molMembershipArray[i] = globalMolMembership_[i] + 1; } //setup fortran simulation - int nGlobalExcludes = 0; - int* globalExcludes = NULL; - int* excludeList = exclude_.getExcludeList(); - setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , - &nGlobalExcludes, globalExcludes, &molMembershipArray[0], - &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); - if( isError ){ + nExclude = excludedInteractions_.getSize(); + nOneTwo = oneTwoInteractions_.getSize(); + nOneThree = oneThreeInteractions_.getSize(); + nOneFour = oneFourInteractions_.getSize(); + int* excludeList = excludedInteractions_.getPairList(); + int* oneTwoList = oneTwoInteractions_.getPairList(); + int* oneThreeList = oneThreeInteractions_.getPairList(); + int* oneFourList = oneFourInteractions_.getPairList(); + + setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], + &nExclude, excludeList, + &nOneTwo, oneTwoList, + &nOneThree, oneThreeList, + &nOneFour, oneFourList, + &molMembershipArray[0], &mfact[0], &nCutoffGroups_, + &fortranGlobalGroupMembership[0], &isError); + + if( isError ){ + sprintf( painCave.errMsg, "There was an error setting the simulation information in fortran.\n" ); painCave.isFatal = 1; - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; simError(); } - -#ifdef IS_MPI + + sprintf( checkPointMsg, "succesfully sent the simulation information to fortran.\n"); - MPIcheckPoint(); -#endif // is_mpi + + errorCheckPoint(); + + // Setup number of neighbors in neighbor list if present + if (simParams_->haveNeighborListNeighbors()) { + int nlistNeighbors = simParams_->getNeighborListNeighbors(); + setNeighbors(&nlistNeighbors); + } + + } -#ifdef IS_MPI void SimInfo::setupFortranParallel() { - +#ifdef IS_MPI //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex - std::vector localToGlobalAtomIndex(getNAtoms(), 0); - std::vector localToGlobalCutoffGroupIndex; + vector localToGlobalAtomIndex(getNAtoms(), 0); + vector localToGlobalCutoffGroupIndex; SimInfo::MoleculeIterator mi; Molecule::AtomIterator ai; Molecule::CutoffGroupIterator ci; @@ -752,97 +985,53 @@ namespace oopse { } sprintf(checkPointMsg, " mpiRefresh successful.\n"); - MPIcheckPoint(); + errorCheckPoint(); - +#endif } -#endif - double SimInfo::calcMaxCutoffRadius() { - - - std::set atomTypes; - std::set::iterator i; - std::vector cutoffRadius; - - //get the unique atom types - atomTypes = getUniqueAtomTypes(); - - //query the max cutoff radius among these atom types - for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { - cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); + void SimInfo::setupSwitchingFunction() { + int ft = CUBIC; + + if (simParams_->haveSwitchingFunctionType()) { + string funcType = simParams_->getSwitchingFunctionType(); + toUpper(funcType); + if (funcType == "CUBIC") { + ft = CUBIC; + } else { + if (funcType == "FIFTH_ORDER_POLYNOMIAL") { + ft = FIFTH_ORDER_POLY; + } else { + // throw error + sprintf( painCave.errMsg, + "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() ); + painCave.isFatal = 1; + simError(); + } + } } - double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); -#ifdef IS_MPI - //pick the max cutoff radius among the processors -#endif + // send switching function notification to switcheroo + setFunctionType(&ft); - return maxCutoffRadius; } - void SimInfo::getCutoff(double& rcut, double& rsw) { - - if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { - - if (!simParams_->haveRcut()){ - sprintf(painCave.errMsg, - "SimCreator Warning: No value was set for the cutoffRadius.\n" - "\tOOPSE will use a default value of 15.0 angstroms" - "\tfor the cutoffRadius.\n"); - painCave.isFatal = 0; - simError(); - rcut = 15.0; - } else{ - rcut = simParams_->getRcut(); - } + void SimInfo::setupAccumulateBoxDipole() { - if (!simParams_->haveRsw()){ - sprintf(painCave.errMsg, - "SimCreator Warning: No value was set for switchingRadius.\n" - "\tOOPSE will use a default value of\n" - "\t0.95 * cutoffRadius for the switchingRadius\n"); - painCave.isFatal = 0; - simError(); - rsw = 0.95 * rcut; - } else{ - rsw = simParams_->getRsw(); + // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true + if ( simParams_->haveAccumulateBoxDipole() ) + if ( simParams_->getAccumulateBoxDipole() ) { + calcBoxDipole_ = true; } - } else { - // if charge, dipole or reaction field is not used and the cutofff radius is not specified in - //meta-data file, the maximum cutoff radius calculated from forcefiled will be used - - if (simParams_->haveRcut()) { - rcut = simParams_->getRcut(); - } else { - //set cutoff radius to the maximum cutoff radius based on atom types in the whole system - rcut = calcMaxCutoffRadius(); - } - - if (simParams_->haveRsw()) { - rsw = simParams_->getRsw(); - } else { - rsw = rcut; - } - - } } - void SimInfo::setupCutoff() { - getCutoff(rcut_, rsw_); - double rnblist = rcut_ + 1; // skin of neighbor list - - //Pass these cutoff radius etc. to fortran. This function should be called once and only once - notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); - } - void SimInfo::addProperty(GenericData* genData) { properties_.addProperty(genData); } - void SimInfo::removeProperty(const std::string& propName) { + void SimInfo::removeProperty(const string& propName) { properties_.removeProperty(propName); } @@ -850,15 +1039,15 @@ namespace oopse { properties_.clearProperties(); } - std::vector SimInfo::getPropertyNames() { + vector SimInfo::getPropertyNames() { return properties_.getPropertyNames(); } - std::vector SimInfo::getProperties() { + vector SimInfo::getProperties() { return properties_.getProperties(); } - GenericData* SimInfo::getPropertyByName(const std::string& propName) { + GenericData* SimInfo::getPropertyByName(const string& propName) { return properties_.getPropertyByName(propName); } @@ -894,20 +1083,20 @@ namespace oopse { Molecule* mol; Vector3d comVel(0.0); - double totalMass = 0.0; + RealType totalMass = 0.0; for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { - double mass = mol->getMass(); + RealType mass = mol->getMass(); totalMass += mass; comVel += mass * mol->getComVel(); } #ifdef IS_MPI - double tmpMass = totalMass; + RealType tmpMass = totalMass; Vector3d tmpComVel(comVel); - MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); - MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); #endif comVel /= totalMass; @@ -920,19 +1109,19 @@ namespace oopse { Molecule* mol; Vector3d com(0.0); - double totalMass = 0.0; + RealType totalMass = 0.0; for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { - double mass = mol->getMass(); + RealType mass = mol->getMass(); totalMass += mass; com += mass * mol->getCom(); } #ifdef IS_MPI - double tmpMass = totalMass; + RealType tmpMass = totalMass; Vector3d tmpCom(com); - MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); - MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); #endif com /= totalMass; @@ -941,7 +1130,7 @@ namespace oopse { } - std::ostream& operator <<(std::ostream& o, SimInfo& info) { + ostream& operator <<(ostream& o, SimInfo& info) { return o; } @@ -956,23 +1145,23 @@ namespace oopse { Molecule* mol; - double totalMass = 0.0; + RealType totalMass = 0.0; for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { - double mass = mol->getMass(); + RealType mass = mol->getMass(); totalMass += mass; com += mass * mol->getCom(); comVel += mass * mol->getComVel(); } #ifdef IS_MPI - double tmpMass = totalMass; + RealType tmpMass = totalMass; Vector3d tmpCom(com); Vector3d tmpComVel(comVel); - MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); - MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); - MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); #endif com /= totalMass; @@ -984,19 +1173,19 @@ namespace oopse { [ Ixx -Ixy -Ixz ] - J =| -Iyx Iyy -Iyz | + J =| -Iyx Iyy -Iyz | [ -Izx -Iyz Izz ] */ void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ - double xx = 0.0; - double yy = 0.0; - double zz = 0.0; - double xy = 0.0; - double xz = 0.0; - double yz = 0.0; + RealType xx = 0.0; + RealType yy = 0.0; + RealType zz = 0.0; + RealType xy = 0.0; + RealType xz = 0.0; + RealType yz = 0.0; Vector3d com(0.0); Vector3d comVel(0.0); @@ -1008,7 +1197,7 @@ namespace oopse { Vector3d thisq(0.0); Vector3d thisv(0.0); - double thisMass = 0.0; + RealType thisMass = 0.0; @@ -1046,8 +1235,8 @@ namespace oopse { #ifdef IS_MPI Mat3x3d tmpI(inertiaTensor); Vector3d tmpAngMom; - MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); - MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); #endif return; @@ -1068,7 +1257,7 @@ namespace oopse { Vector3d thisr(0.0); Vector3d thisp(0.0); - double thisMass; + RealType thisMass; for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { thisMass = mol->getMass(); @@ -1081,12 +1270,78 @@ namespace oopse { #ifdef IS_MPI Vector3d tmpAngMom; - MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); #endif return angularMomentum; } - -}//end namespace oopse + StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) { + return IOIndexToIntegrableObject.at(index); + } + + void SimInfo::setIOIndexToIntegrableObject(const vector& v) { + IOIndexToIntegrableObject= v; + } + /* Returns the Volume of the simulation based on a ellipsoid with semi-axes + based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3 + where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to + V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536. + */ + void SimInfo::getGyrationalVolume(RealType &volume){ + Mat3x3d intTensor; + RealType det; + Vector3d dummyAngMom; + RealType sysconstants; + RealType geomCnst; + + geomCnst = 3.0/2.0; + /* Get the inertial tensor and angular momentum for free*/ + getInertiaTensor(intTensor,dummyAngMom); + + det = intTensor.determinant(); + sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; + volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); + return; + } + + void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){ + Mat3x3d intTensor; + Vector3d dummyAngMom; + RealType sysconstants; + RealType geomCnst; + + geomCnst = 3.0/2.0; + /* Get the inertial tensor and angular momentum for free*/ + getInertiaTensor(intTensor,dummyAngMom); + + detI = intTensor.determinant(); + sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; + volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); + return; + } +/* + void SimInfo::setStuntDoubleFromGlobalIndex(vector v) { + assert( v.size() == nAtoms_ + nRigidBodies_); + sdByGlobalIndex_ = v; + } + + StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) { + //assert(index < nAtoms_ + nRigidBodies_); + return sdByGlobalIndex_.at(index); + } +*/ + int SimInfo::getNGlobalConstraints() { + int nGlobalConstraints; +#ifdef IS_MPI + MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM, + MPI_COMM_WORLD); +#else + nGlobalConstraints = nConstraints_; +#endif + return nGlobalConstraints; + } + +}//end namespace OpenMD +