--- trunk/src/brains/SimInfo.cpp 2005/12/12 19:32:50 809 +++ trunk/src/brains/SimInfo.cpp 2008/09/10 19:51:45 1290 @@ -53,17 +53,22 @@ #include "brains/SimInfo.hpp" #include "math/Vector3.hpp" #include "primitives/Molecule.hpp" +#include "primitives/StuntDouble.hpp" #include "UseTheForce/fCutoffPolicy.h" #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" #include "UseTheForce/DarkSide/fSwitchingFunctionType.h" #include "UseTheForce/doForces_interface.h" +#include "UseTheForce/DarkSide/neighborLists_interface.h" #include "UseTheForce/DarkSide/electrostatic_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" + #ifdef IS_MPI #include "UseTheForce/mpiComponentPlan.h" #include "UseTheForce/DarkSide/simParallel_interface.h" @@ -82,13 +87,15 @@ namespace oopse { SimInfo::SimInfo(ForceField* ff, Globals* simParams) : forceField_(ff), simParams_(simParams), - ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), + 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) { + 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) { + MoleculeStamp* molStamp; int nMolWithSameStamp; int nCutoffAtoms = 0; // number of atoms belong to cutoff groups @@ -96,6 +103,7 @@ namespace oopse { CutoffGroupStamp* cgStamp; RigidBodyStamp* rbStamp; int nRigidAtoms = 0; + std::vector components = simParams->getComponents(); for (std::vector::iterator i = components.begin(); i !=components.end(); ++i) { @@ -150,11 +158,7 @@ namespace oopse { + nGlobalRigidBodies_; nGlobalMols_ = molStampIds_.size(); - -#ifdef IS_MPI molToProcMap_.resize(nGlobalMols_); -#endif - } SimInfo::~SimInfo() { @@ -192,13 +196,14 @@ 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(); - addExcludePairs(mol); - + addInteractionPairs(mol); + return true; } else { return false; @@ -217,12 +222,13 @@ 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; @@ -288,6 +294,15 @@ 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; @@ -339,150 +354,202 @@ namespace oopse { } - void SimInfo::addExcludePairs(Molecule* mol) { + void SimInfo::addInteractionPairs(Molecule* mol) { + ForceFieldOptions& options_ = forceField_->getForceFieldOptions(); std::vector::iterator bondIter; std::vector::iterator bendIter; std::vector::iterator torsionIter; + std::vector::iterator inversionIter; Bond* bond; Bend* bend; Torsion* torsion; + Inversion* inversion; int a; int b; int c; int d; - std::map > atomGroups; + // 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. + std::map > atomGroups; Molecule::RigidBodyIterator rbIter; RigidBody* rb; Molecule::IntegrableObjectIterator ii; StuntDouble* integrableObject; - for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(ii)) { - + for (integrableObject = mol->beginIntegrableObject(ii); + integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { + if (integrableObject->isRigidBody()) { - rb = static_cast(integrableObject); - std::vector atoms = rb->getAtoms(); - std::set rigidAtoms; - for (int i = 0; i < atoms.size(); ++i) { - rigidAtoms.insert(atoms[i]->getGlobalIndex()); - } - for (int i = 0; i < atoms.size(); ++i) { - atomGroups.insert(std::map >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); - } + rb = static_cast(integrableObject); + std::vector atoms = rb->getAtoms(); + std::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(std::map >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); + } } else { std::set oneAtomSet; oneAtomSet.insert(integrableObject->getGlobalIndex()); atomGroups.insert(std::map >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); } } + + for (bond= mol->beginBond(bondIter); bond != NULL; + bond = mol->nextBond(bondIter)) { - - - 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(); - std::set rigidSetA = getRigidSet(a, atomGroups); - std::set rigidSetB = getRigidSet(b, atomGroups); - std::set rigidSetC = getRigidSet(c, atomGroups); - - exclude_.addPairs(rigidSetA, rigidSetB); - exclude_.addPairs(rigidSetA, rigidSetC); - exclude_.addPairs(rigidSetB, rigidSetC); - //exclude_.addPair(a, b); - //exclude_.addPair(a, c); - //exclude_.addPair(b, c); + if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { + oneTwoInteractions_.addPair(a, b); + oneTwoInteractions_.addPair(b, c); + } else { + excludedInteractions_.addPair(a, b); + excludedInteractions_.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(); - std::set rigidSetA = getRigidSet(a, atomGroups); - std::set rigidSetB = getRigidSet(b, atomGroups); - std::set rigidSetC = getRigidSet(c, atomGroups); - std::set rigidSetD = getRigidSet(d, atomGroups); + d = torsion->getAtomD()->getGlobalIndex(); - exclude_.addPairs(rigidSetA, rigidSetB); - exclude_.addPairs(rigidSetA, rigidSetC); - exclude_.addPairs(rigidSetA, rigidSetD); - exclude_.addPairs(rigidSetB, rigidSetC); - exclude_.addPairs(rigidSetB, rigidSetD); - exclude_.addPairs(rigidSetC, rigidSetD); + 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); + } - /* - exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); - exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); - exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); - exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); - exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); - exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); - - - 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_.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); + } } - for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { + 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)) { std::vector atoms = rb->getAtoms(); - for (int i = 0; i < atoms.size() -1 ; ++i) { - for (int j = i + 1; j < atoms.size(); ++j) { + 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) { + void SimInfo::removeInteractionPairs(Molecule* mol) { + ForceFieldOptions& options_ = forceField_->getForceFieldOptions(); std::vector::iterator bondIter; std::vector::iterator bendIter; std::vector::iterator torsionIter; + std::vector::iterator inversionIter; Bond* bond; Bend* bend; Torsion* torsion; + Inversion* inversion; int a; int b; int c; int d; std::map > atomGroups; - Molecule::RigidBodyIterator rbIter; RigidBody* rb; Molecule::IntegrableObjectIterator ii; StuntDouble* integrableObject; - for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(ii)) { - + for (integrableObject = mol->beginIntegrableObject(ii); + integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { + if (integrableObject->isRigidBody()) { - rb = static_cast(integrableObject); - std::vector atoms = rb->getAtoms(); - std::set rigidAtoms; - for (int i = 0; i < atoms.size(); ++i) { - rigidAtoms.insert(atoms[i]->getGlobalIndex()); - } - for (int i = 0; i < atoms.size(); ++i) { - atomGroups.insert(std::map >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); - } + rb = static_cast(integrableObject); + std::vector atoms = rb->getAtoms(); + std::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(std::map >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); + } } else { std::set oneAtomSet; oneAtomSet.insert(integrableObject->getGlobalIndex()); @@ -490,84 +557,121 @@ namespace oopse { } } - - for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { + 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(); - - std::set rigidSetA = getRigidSet(a, atomGroups); - std::set rigidSetB = getRigidSet(b, atomGroups); - std::set rigidSetC = getRigidSet(c, atomGroups); - - exclude_.removePairs(rigidSetA, rigidSetB); - exclude_.removePairs(rigidSetA, rigidSetC); - exclude_.removePairs(rigidSetB, rigidSetC); - //exclude_.removePair(a, b); - //exclude_.removePair(a, c); - //exclude_.removePair(b, c); + if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { + oneTwoInteractions_.removePair(a, b); + oneTwoInteractions_.removePair(b, c); + } else { + excludedInteractions_.removePair(a, b); + excludedInteractions_.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); + } - std::set rigidSetA = getRigidSet(a, atomGroups); - std::set rigidSetB = getRigidSet(b, atomGroups); - std::set rigidSetC = getRigidSet(c, atomGroups); - std::set rigidSetD = getRigidSet(d, atomGroups); + if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) { + oneThreeInteractions_.removePair(a, c); + oneThreeInteractions_.removePair(b, d); + } else { + excludedInteractions_.removePair(a, c); + excludedInteractions_.removePair(b, d); + } - exclude_.removePairs(rigidSetA, rigidSetB); - exclude_.removePairs(rigidSetA, rigidSetC); - exclude_.removePairs(rigidSetA, rigidSetD); - exclude_.removePairs(rigidSetB, rigidSetC); - exclude_.removePairs(rigidSetB, rigidSetD); - exclude_.removePairs(rigidSetC, rigidSetD); + if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) { + oneFourInteractions_.removePair(a, d); + } else { + excludedInteractions_.removePair(a, d); + } + } - /* - exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); - exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); - exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); - exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); - exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); - exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); + for (inversion= mol->beginInversion(inversionIter); inversion != NULL; + inversion = mol->nextInversion(inversionIter)) { - - exclude_.removePair(a, b); - exclude_.removePair(a, c); - exclude_.removePair(a, d); - exclude_.removePair(b, c); - exclude_.removePair(b, d); - exclude_.removePair(c, d); - */ + 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)) { + 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 (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(); @@ -589,8 +693,11 @@ namespace oopse { /** @deprecate */ int isError = 0; + setupCutoff(); + setupElectrostaticSummationMethod( isError ); setupSwitchingFunction(); + setupAccumulateBoxDipole(); if(isError){ sprintf( painCave.errMsg, @@ -598,9 +705,6 @@ namespace oopse { painCave.isFatal = 1; simError(); } - - - setupCutoff(); calcNdf(); calcNdfRaw(); @@ -650,25 +754,35 @@ namespace oopse { int usePBC = simParams_->getUsePeriodicBoundaryConditions(); int useRF; int useSF; + int useSP; + int useBoxDipole; + std::string myMethod; // set the useRF logical useRF = 0; useSF = 0; + useSP = 0; if (simParams_->haveElectrostaticSummationMethod()) { std::string myMethod = simParams_->getElectrostaticSummationMethod(); toUpper(myMethod); - if (myMethod == "REACTION_FIELD") { - useRF=1; - } else { - if (myMethod == "SHIFTED_FORCE") { - useSF = 1; - } + if (myMethod == "REACTION_FIELD"){ + useRF = 1; + } else if (myMethod == "SHIFTED_FORCE"){ + useSF = 1; + } else if (myMethod == "SHIFTED_POTENTIAL"){ + useSP = 1; } } + + if (simParams_->haveAccumulateBoxDipole()) + if (simParams_->getAccumulateBoxDipole()) + useBoxDipole = 1; + useAtomicVirial_ = simParams_->getUseAtomicVirial(); + //loop over all of the atom types for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { useLennardJones |= (*i)->isLennardJones(); @@ -738,8 +852,17 @@ namespace oopse { MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); temp = useSF; - MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + temp = useSP; + MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + + temp = useBoxDipole; + MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + + temp = useAtomicVirial_; + MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + #endif fInfo_.SIM_uses_PBC = usePBC; @@ -757,29 +880,16 @@ namespace oopse { fInfo_.SIM_uses_FLARB = useFLARB; fInfo_.SIM_uses_RF = useRF; fInfo_.SIM_uses_SF = useSF; - - if( myMethod == "REACTION_FIELD") { - - 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(); - } - } - + fInfo_.SIM_uses_SP = useSP; + fInfo_.SIM_uses_BoxDipole = useBoxDipole; + fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_; } void SimInfo::setupFortranSim() { int isError; - int nExclude; + int nExclude, nOneTwo, nOneThree, nOneFour; std::vector fortranGlobalGroupMembership; - nExclude = exclude_.getSize(); isError = 0; //globalGroupMembership_ is filled by SimCreator @@ -788,14 +898,14 @@ namespace oopse { } //calculate mass ratio of cutoff group - std::vector mfact; + std::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()); @@ -811,7 +921,6 @@ namespace oopse { else mfact.push_back( 1.0 ); } - } } @@ -835,33 +944,57 @@ namespace oopse { } //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(); + std::cerr << "excludedInteractions contains: " << excludedInteractions_.getSize() << " pairs \n"; + std::cerr << "oneTwoInteractions contains: " << oneTwoInteractions_.getSize() << " pairs \n"; + std::cerr << "oneThreeInteractions contains: " << oneThreeInteractions_.getSize() << " pairs \n"; + std::cerr << "oneFourInteractions contains: " << oneFourInteractions_.getSize() << " pairs \n"; + + 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; 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; @@ -911,19 +1044,30 @@ namespace oopse { } sprintf(checkPointMsg, " mpiRefresh successful.\n"); - MPIcheckPoint(); + errorCheckPoint(); - +#endif } -#endif - void SimInfo::setupCutoff() { + ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); + // Check the cutoff policy - int cp = TRADITIONAL_CUTOFF_POLICY; - if (simParams_->haveCutoffPolicy()) { - std::string myPolicy = simParams_->getCutoffPolicy(); + int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default + + // Set LJ shifting bools to false + ljsp_ = false; + ljsf_ = false; + + std::string myPolicy; + if (forceFieldOptions_.haveCutoffPolicy()){ + myPolicy = forceFieldOptions_.getCutoffPolicy(); + }else if (simParams_->haveCutoffPolicy()) { + myPolicy = simParams_->getCutoffPolicy(); + } + + if (!myPolicy.empty()){ toUpper(myPolicy); if (myPolicy == "MIX") { cp = MIX_CUTOFF_POLICY; @@ -946,7 +1090,7 @@ namespace oopse { notifyFortranCutoffPolicy(&cp); // Check the Skin Thickness for neighborlists - double skin; + RealType skin; if (simParams_->haveSkinThickness()) { skin = simParams_->getSkinThickness(); notifyFortranSkinThickness(&skin); @@ -958,9 +1102,39 @@ namespace oopse { if (simParams_->haveSwitchingRadius()) { rsw_ = simParams_->getSwitchingRadius(); } else { - rsw_ = rcut_; + if (fInfo_.SIM_uses_Charges | + fInfo_.SIM_uses_Dipoles | + fInfo_.SIM_uses_RF) { + + rsw_ = 0.85 * rcut_; + sprintf(painCave.errMsg, + "SimCreator Warning: No value was set for the switchingRadius.\n" + "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n" + "\tswitchingRadius = %f. for this simulation\n", rsw_); + painCave.isFatal = 0; + simError(); + } else { + rsw_ = rcut_; + sprintf(painCave.errMsg, + "SimCreator Warning: No value was set for the switchingRadius.\n" + "\tOOPSE will use the same value as the cutoffRadius.\n" + "\tswitchingRadius = %f. for this simulation\n", rsw_); + painCave.isFatal = 0; + simError(); + } } - notifyFortranCutoffs(&rcut_, &rsw_); + + if (simParams_->haveElectrostaticSummationMethod()) { + std::string myMethod = simParams_->getElectrostaticSummationMethod(); + toUpper(myMethod); + + if (myMethod == "SHIFTED_POTENTIAL") { + ljsp_ = true; + } else if (myMethod == "SHIFTED_FORCE") { + ljsf_ = true; + } + } + notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_); } else { @@ -977,7 +1151,15 @@ namespace oopse { if (simParams_->haveElectrostaticSummationMethod()) { std::string myMethod = simParams_->getElectrostaticSummationMethod(); toUpper(myMethod); - if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { + + // For the time being, we're tethering the LJ shifted behavior to the + // electrostaticSummationMethod keyword options + if (myMethod == "SHIFTED_POTENTIAL") { + ljsp_ = true; + } else if (myMethod == "SHIFTED_FORCE") { + ljsf_ = true; + } + if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { if (simParams_->haveSwitchingRadius()){ sprintf(painCave.errMsg, "SimInfo Warning: A value was set for the switchingRadius\n" @@ -1000,7 +1182,9 @@ namespace oopse { simError(); rsw_ = 0.85 * rcut_; } - notifyFortranCutoffs(&rcut_, &rsw_); + + notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_); + } else { // We didn't set rcut explicitly, and we don't have electrostatic atoms, so // We'll punt and let fortran figure out the cutoffs later. @@ -1016,12 +1200,10 @@ namespace oopse { int errorOut; int esm = NONE; int sm = UNDAMPED; - double alphaVal; - double dielectric; - + RealType alphaVal; + RealType dielectric; + errorOut = isError; - alphaVal = simParams_->getDampingAlpha(); - dielectric = simParams_->getDielectric(); if (simParams_->haveElectrostaticSummationMethod()) { std::string myMethod = simParams_->getElectrostaticSummationMethod(); @@ -1038,8 +1220,17 @@ namespace oopse { if (myMethod == "SHIFTED_FORCE") { esm = SHIFTED_FORCE; } else { - if (myMethod == "REACTION_FIELD") { + if (myMethod == "REACTION_FIELD") { esm = REACTION_FIELD; + dielectric = simParams_->getDielectric(); + if (!simParams_->haveDielectric()) { + // throw warning + sprintf( painCave.errMsg, + "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n" + "\tA default value of %f will be used for the dielectric.\n", dielectric); + painCave.isFatal = 0; + simError(); + } } else { // throw error sprintf( painCave.errMsg, @@ -1066,13 +1257,22 @@ namespace oopse { if (myScreen == "DAMPED") { sm = DAMPED; if (!simParams_->haveDampingAlpha()) { - //throw error + // first set a cutoff dependent alpha value + // we assume alpha depends linearly with rcut from 0 to 20.5 ang + alphaVal = 0.5125 - rcut_* 0.025; + // for values rcut > 20.5, alpha is zero + if (alphaVal < 0) alphaVal = 0; + + // throw warning sprintf( painCave.errMsg, "SimInfo warning: dampingAlpha was not specified in the input file.\n" - "\tA default value of %f (1/ang) will be used.\n", alphaVal); + "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_); painCave.isFatal = 0; simError(); + } else { + alphaVal = simParams_->getDampingAlpha(); } + } else { // throw error sprintf( painCave.errMsg, @@ -1087,7 +1287,7 @@ namespace oopse { } // let's pass some summation method variables to fortran - setElectrostaticSumMethod( &esm ); + setElectrostaticSummationMethod( &esm ); setFortranElectrostaticMethod( &esm ); setScreeningMethod( &sm ); setDampingAlpha( &alphaVal ); @@ -1121,6 +1321,17 @@ namespace oopse { } + void SimInfo::setupAccumulateBoxDipole() { + + // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true + if ( simParams_->haveAccumulateBoxDipole() ) + if ( simParams_->getAccumulateBoxDipole() ) { + setAccumulateBoxDipole(); + calcBoxDipole_ = true; + } + + } + void SimInfo::addProperty(GenericData* genData) { properties_.addProperty(genData); } @@ -1177,20 +1388,20 @@ 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; @@ -1203,19 +1414,19 @@ 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; @@ -1239,23 +1450,23 @@ 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; @@ -1274,12 +1485,12 @@ namespace oopse { 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); @@ -1291,7 +1502,7 @@ namespace oopse { Vector3d thisq(0.0); Vector3d thisv(0.0); - double thisMass = 0.0; + RealType thisMass = 0.0; @@ -1329,8 +1540,8 @@ 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; @@ -1351,7 +1562,7 @@ 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(); @@ -1364,12 +1575,67 @@ 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; } - + StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) { + return IOIndexToIntegrableObject.at(index); + } + + void SimInfo::setIOIndexToIntegrableObject(const std::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(std::vector v) { + assert( v.size() == nAtoms_ + nRigidBodies_); + sdByGlobalIndex_ = v; + } + + StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) { + //assert(index < nAtoms_ + nRigidBodies_); + return sdByGlobalIndex_.at(index); + } +*/ }//end namespace oopse