--- branches/development/src/nonbonded/InteractionManager.cpp 2010/12/28 21:47:55 1530 +++ branches/development/src/nonbonded/InteractionManager.cpp 2010/12/31 18:31:56 1535 @@ -40,14 +40,23 @@ */ #include "nonbonded/InteractionManager.hpp" +#include "UseTheForce/doForces_interface.h" namespace OpenMD { - + + InteractionManager* InteractionManager::_instance = NULL; + SimInfo* InteractionManager::info_ = NULL; bool InteractionManager::initialized_ = false; - RealType InteractionManager::rCut_ = -1.0; - RealType InteractionManager::rSwitch_ = -1.0; - ForceField* InteractionManager::forceField_ = NULL; - InteractionManager* InteractionManager::_instance = NULL; + + RealType InteractionManager::rCut_ = 0.0; + RealType InteractionManager::rSwitch_ = 0.0; + RealType InteractionManager::skinThickness_ = 0.0; + RealType InteractionManager::listRadius_ = 0.0; + CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE; + SwitchingFunctionType InteractionManager::sft_ = cubic; + RealType InteractionManager::vdwScale_[4] = {0.0, 0.0, 0.0, 0.0}; + RealType InteractionManager::electrostaticScale_[4] = {0.0, 0.0, 0.0, 0.0}; + map InteractionManager::typeMap_; map, set > InteractionManager::interactions_; @@ -58,6 +67,7 @@ namespace OpenMD { EAM* InteractionManager::eam_ = new EAM(); SC* InteractionManager::sc_ = new SC(); Electrostatic* InteractionManager::electrostatic_ = new Electrostatic(); + MAW* InteractionManager::maw_ = new MAW(); SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction(); InteractionManager* InteractionManager::Instance() { @@ -69,6 +79,8 @@ namespace OpenMD { void InteractionManager::initialize() { + ForceField* forceField_ = info_->getForceField(); + lj_->setForceField(forceField_); gb_->setForceField(forceField_); sticky_->setForceField(forceField_); @@ -76,8 +88,10 @@ namespace OpenMD { sc_->setForceField(forceField_); morse_->setForceField(forceField_); electrostatic_->setForceField(forceField_); + maw_->setForceField(forceField_); ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); + // Force fields can set options on how to scale van der Waals and electrostatic // interactions for atoms connected via bonds, bends and torsions // in this case the topological distance between atoms is: @@ -94,7 +108,7 @@ namespace OpenMD { electrostaticScale_[0] = 0.0; electrostaticScale_[1] = fopts.getelectrostatic12scale(); electrostaticScale_[2] = fopts.getelectrostatic13scale(); - electrostaticScale_[3] = fopts.getelectrostatic14scale(); + electrostaticScale_[3] = fopts.getelectrostatic14scale(); ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); ForceField::AtomTypeContainer::MapTypeIterator i1, i2; @@ -165,80 +179,117 @@ namespace OpenMD { // look for an explicitly-set non-bonded interaction type using the // two atom types. NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName()); + + if (nbiType != NULL) { - if (nbiType->isLennardJones()) { - // We found an explicit Lennard-Jones interaction. - // override all other vdw entries for this pair of atom types: - set::iterator it; - for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) { - InteractionFamily ifam = (*it)->getFamily(); - if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); + if (nbiType->isLennardJones()) { + // We found an explicit Lennard-Jones interaction. + // override all other vdw entries for this pair of atom types: + set::iterator it; + for (it = interactions_[key].begin(); + it != interactions_[key].end(); ++it) { + InteractionFamily ifam = (*it)->getFamily(); + if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); + } + interactions_[key].insert(lj_); + vdwExplicit = true; } - interactions_[key].insert(lj_); - vdwExplicit = true; - } - - if (nbiType->isMorse()) { - if (vdwExplicit) { - sprintf( painCave.errMsg, - "InteractionManager::initialize found more than one explicit\n" - "\tvan der Waals interaction for atom types %s - %s\n", - atype1->getName().c_str(), atype2->getName().c_str()); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); + + if (nbiType->isMorse()) { + if (vdwExplicit) { + sprintf( painCave.errMsg, + "InteractionManager::initialize found more than one " + "explicit \n" + "\tvan der Waals interaction for atom types %s - %s\n", + atype1->getName().c_str(), atype2->getName().c_str()); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + // We found an explicit Morse interaction. + // override all other vdw entries for this pair of atom types: + set::iterator it; + for (it = interactions_[key].begin(); + it != interactions_[key].end(); ++it) { + InteractionFamily ifam = (*it)->getFamily(); + if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); + } + interactions_[key].insert(morse_); + vdwExplicit = true; } - // We found an explicit Morse interaction. - // override all other vdw entries for this pair of atom types: - set::iterator it; - for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) { - InteractionFamily ifam = (*it)->getFamily(); - if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); + + if (nbiType->isEAM()) { + // We found an explicit EAM interaction. + // override all other metallic entries for this pair of atom types: + set::iterator it; + for (it = interactions_[key].begin(); + it != interactions_[key].end(); ++it) { + InteractionFamily ifam = (*it)->getFamily(); + if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it); + } + interactions_[key].insert(eam_); + metExplicit = true; } - interactions_[key].insert(morse_); - vdwExplicit = true; - } - - if (nbiType->isEAM()) { - // We found an explicit EAM interaction. - // override all other metallic entries for this pair of atom types: - set::iterator it; - for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) { - InteractionFamily ifam = (*it)->getFamily(); - if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it); + + if (nbiType->isSC()) { + if (metExplicit) { + sprintf( painCave.errMsg, + "InteractionManager::initialize found more than one " + "explicit\n" + "\tmetallic interaction for atom types %s - %s\n", + atype1->getName().c_str(), atype2->getName().c_str()); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + // We found an explicit Sutton-Chen interaction. + // override all other metallic entries for this pair of atom types: + set::iterator it; + for (it = interactions_[key].begin(); + it != interactions_[key].end(); ++it) { + InteractionFamily ifam = (*it)->getFamily(); + if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it); + } + interactions_[key].insert(sc_); + metExplicit = true; } - interactions_[key].insert(eam_); - metExplicit = true; + + if (nbiType->isMAW()) { + if (vdwExplicit) { + sprintf( painCave.errMsg, + "InteractionManager::initialize found more than one " + "explicit\n" + "\tvan der Waals interaction for atom types %s - %s\n", + atype1->getName().c_str(), atype2->getName().c_str()); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + // We found an explicit MAW interaction. + // override all other vdw entries for this pair of atom types: + set::iterator it; + for (it = interactions_[key].begin(); + it != interactions_[key].end(); ++it) { + InteractionFamily ifam = (*it)->getFamily(); + if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); + } + interactions_[key].insert(maw_); + vdwExplicit = true; + } } - - if (nbiType->isSC()) { - if (metExplicit) { - sprintf( painCave.errMsg, - "InteractionManager::initialize found more than one explicit\n" - "\tmetallic interaction for atom types %s - %s\n", - atype1->getName().c_str(), atype2->getName().c_str()); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - // We found an explicit Sutton-Chen interaction. - // override all other metallic entries for this pair of atom types: - set::iterator it; - for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) { - InteractionFamily ifam = (*it)->getFamily(); - if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it); - } - interactions_[key].insert(sc_); - metExplicit = true; - } } } - // make sure every pair of atom types has a non-bonded interaction: - for (atype1 = atomTypes->beginType(i1); atype1 != NULL; - atype1 = atomTypes->nextType(i1)) { - for (atype2 = atomTypes->beginType(i2); atype2 != NULL; - atype2 = atomTypes->nextType(i2)) { + + // make sure every pair of atom types in this simulation has a + // non-bonded interaction: + + set simTypes = info_->getSimulatedAtomTypes(); + set::iterator it, jt; + for (it = simTypes.begin(); it != simTypes.end(); ++it) { + atype1 = (*it); + for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) { + atype2 = (*jt); key = make_pair(atype1, atype2); if (interactions_[key].size() == 0) { @@ -252,8 +303,190 @@ namespace OpenMD { } } } - } + + setupCutoffs(); + setupSwitching(); + setupNeighborlists(); + notifyFortranSkinThickness(&skinThickness_); + + int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0; + int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0; + notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf); + + int isError; + initFortranFF(&isError); + + initialized_ = true; + } + /** + * setupCutoffs + * + * Sets the values of cutoffRadius and cutoffMethod + * + * cutoffRadius : realType + * 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. + * + * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL) + * If cutoffMethod was explicitly set, use that choice. + * If cutoffMethod was not explicitly set, use SHIFTED_FORCE + */ + void InteractionManager::setupCutoffs() { + + Globals* simParams_ = info_->getSimParams(); + + if (simParams_->haveCutoffRadius()) { + rCut_ = simParams_->getCutoffRadius(); + } else { + if (info_->usesElectrostaticAtoms()) { + sprintf(painCave.errMsg, + "InteractionManager::setupCutoffs: 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; + painCave.severity = OPENMD_INFO; + simError(); + rCut_ = 12.0; + } else { + RealType thisCut; + set::iterator i; + set atomTypes; + atomTypes = info_->getSimulatedAtomTypes(); + for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { + thisCut = getSuggestedCutoffRadius((*i)); + rCut_ = max(thisCut, rCut_); + } + sprintf(painCave.errMsg, + "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n" + "\tOpenMD will use %lf angstroms.\n", + rCut_); + painCave.isFatal = 0; + painCave.severity = OPENMD_INFO; + simError(); + } + } + + map stringToCutoffMethod; + stringToCutoffMethod["HARD"] = HARD; + stringToCutoffMethod["SWITCHED"] = SWITCHED; + stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL; + stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE; + + if (simParams_->haveCutoffMethod()) { + string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); + map::iterator i; + i = stringToCutoffMethod.find(cutMeth); + if (i == stringToCutoffMethod.end()) { + sprintf(painCave.errMsg, + "InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n" + "\tShould be one of: " + "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", + cutMeth.c_str()); + painCave.isFatal = 1; + painCave.severity = OPENMD_ERROR; + simError(); + } else { + cutoffMethod_ = i->second; + } + } else { + sprintf(painCave.errMsg, + "InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n" + "\tOpenMD will use SHIFTED_FORCE.\n"); + painCave.isFatal = 0; + painCave.severity = OPENMD_INFO; + simError(); + cutoffMethod_ = SHIFTED_FORCE; + } + } + + + /** + * setupSwitching + * + * Sets the values of switchingRadius and + * If the switchingRadius was explicitly set, use that value (but check it) + * If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ + */ + void InteractionManager::setupSwitching() { + Globals* simParams_ = info_->getSimParams(); + + if (simParams_->haveSwitchingRadius()) { + rSwitch_ = simParams_->getSwitchingRadius(); + if (rSwitch_ > rCut_) { + sprintf(painCave.errMsg, + "InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n", + rSwitch_, rCut_); + painCave.isFatal = 1; + painCave.severity = OPENMD_ERROR; + simError(); + } + } else { + rSwitch_ = 0.85 * rCut_; + sprintf(painCave.errMsg, + "InteractionManager::setupSwitching: 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", rSwitch_); + painCave.isFatal = 0; + painCave.severity = OPENMD_WARNING; + simError(); + } + + if (simParams_->haveSwitchingFunctionType()) { + string funcType = simParams_->getSwitchingFunctionType(); + toUpper(funcType); + if (funcType == "CUBIC") { + sft_ = cubic; + } else { + if (funcType == "FIFTH_ORDER_POLYNOMIAL") { + sft_ = fifth_order_poly; + } else { + // throw error + sprintf( painCave.errMsg, + "InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n" + "\tswitchingFunctionType must be one of: " + "\"cubic\" or \"fifth_order_polynomial\".", + funcType.c_str() ); + painCave.isFatal = 1; + painCave.severity = OPENMD_ERROR; + simError(); + } + } + } + } + + /** + * setupNeighborlists + * + * If the skinThickness was explicitly set, use that value (but check it) + * If the skinThickness was not explicitly set: use 1.0 angstroms + */ + void InteractionManager::setupNeighborlists() { + + Globals* simParams_ = info_->getSimParams(); + + if (simParams_->haveSkinThickness()) { + skinThickness_ = simParams_->getSkinThickness(); + } else { + skinThickness_ = 1.0; + sprintf(painCave.errMsg, + "InteractionManager::setupNeighborlists: No value was set for the skinThickness.\n" + "\tOpenMD will use a default value of %f Angstroms\n" + "\tfor this simulation\n", skinThickness_); + painCave.severity = OPENMD_INFO; + painCave.isFatal = 0; + simError(); + } + + listRadius_ = rCut_ + skinThickness_; + + } + + void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){ if (!initialized_) initialize();