--- trunk/src/brains/SimInfo.cpp 2006/09/22 22:19:59 1050 +++ trunk/src/brains/SimInfo.cpp 2008/10/22 20:01:49 1313 @@ -59,6 +59,7 @@ #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" @@ -67,6 +68,7 @@ #include "io/ForceFieldOptions.hpp" #include "UseTheForce/ForceField.hpp" + #ifdef IS_MPI #include "UseTheForce/mpiComponentPlan.h" #include "UseTheForce/DarkSide/simParallel_interface.h" @@ -88,10 +90,12 @@ namespace oopse { 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), calcBoxDipole_(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 @@ -99,6 +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) { @@ -153,11 +158,7 @@ namespace oopse { + nGlobalRigidBodies_; nGlobalMols_ = molStampIds_.size(); - -#ifdef IS_MPI molToProcMap_.resize(nGlobalMols_); -#endif - } SimInfo::~SimInfo() { @@ -195,13 +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; @@ -220,12 +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; @@ -351,150 +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()); @@ -502,84 +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(); @@ -664,18 +756,21 @@ namespace oopse { int useSF; int useSP; int useBoxDipole; + std::string myMethod; // set the useRF logical useRF = 0; useSF = 0; + useSP = 0; + useBoxDipole = 0; if (simParams_->haveElectrostaticSummationMethod()) { std::string myMethod = simParams_->getElectrostaticSummationMethod(); toUpper(myMethod); if (myMethod == "REACTION_FIELD"){ - useRF=1; + useRF = 1; } else if (myMethod == "SHIFTED_FORCE"){ useSF = 1; } else if (myMethod == "SHIFTED_POTENTIAL"){ @@ -687,6 +782,8 @@ namespace oopse { 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(); @@ -764,6 +861,9 @@ namespace oopse { 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; @@ -783,14 +883,14 @@ namespace oopse { fInfo_.SIM_uses_SF = useSF; 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 @@ -822,7 +922,6 @@ namespace oopse { else mfact.push_back( 1.0 ); } - } } @@ -846,33 +945,52 @@ 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(); + 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; @@ -922,13 +1040,11 @@ namespace oopse { } sprintf(checkPointMsg, " mpiRefresh successful.\n"); - MPIcheckPoint(); + errorCheckPoint(); - +#endif } -#endif - void SimInfo::setupCutoff() { ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); @@ -936,6 +1052,10 @@ namespace oopse { // Check the cutoff policy 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(); @@ -999,8 +1119,18 @@ namespace oopse { 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 { @@ -1017,7 +1147,15 @@ 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" @@ -1040,7 +1178,9 @@ 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. @@ -1125,7 +1265,10 @@ namespace oopse { "\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, @@ -1442,6 +1585,43 @@ namespace oopse { 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_);