--- branches/development/src/nonbonded/InteractionManager.cpp 2010/10/02 19:53:32 1502 +++ branches/development/src/nonbonded/InteractionManager.cpp 2010/12/28 21:47:55 1530 @@ -44,10 +44,21 @@ namespace OpenMD { namespace OpenMD { bool InteractionManager::initialized_ = false; + RealType InteractionManager::rCut_ = -1.0; + RealType InteractionManager::rSwitch_ = -1.0; ForceField* InteractionManager::forceField_ = NULL; InteractionManager* InteractionManager::_instance = NULL; map InteractionManager::typeMap_; map, set > InteractionManager::interactions_; + + LJ* InteractionManager::lj_ = new LJ(); + GB* InteractionManager::gb_ = new GB(); + Sticky* InteractionManager::sticky_ = new Sticky(); + Morse* InteractionManager::morse_ = new Morse(); + EAM* InteractionManager::eam_ = new EAM(); + SC* InteractionManager::sc_ = new SC(); + Electrostatic* InteractionManager::electrostatic_ = new Electrostatic(); + SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction(); InteractionManager* InteractionManager::Instance() { if (!_instance) { @@ -58,14 +69,6 @@ namespace OpenMD { void InteractionManager::initialize() { - lj_ = new LJ(); - gb_ = new GB(); - sticky_ = new Sticky(); - eam_ = new EAM(); - sc_ = new SC(); - morse_ = new Morse(); - electrostatic_ = new Electrostatic(); - lj_->setForceField(forceField_); gb_->setForceField(forceField_); sticky_->setForceField(forceField_); @@ -74,6 +77,25 @@ namespace OpenMD { morse_->setForceField(forceField_); electrostatic_->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: + // 0 = the atom itself + // 1 = bonded together + // 2 = connected via a bend + // 3 = connected via a torsion + + vdwScale_[0] = 0.0; + vdwScale_[1] = fopts.getvdw12scale(); + vdwScale_[2] = fopts.getvdw13scale(); + vdwScale_[3] = fopts.getvdw14scale(); + + electrostaticScale_[0] = 0.0; + electrostaticScale_[1] = fopts.getelectrostatic12scale(); + electrostaticScale_[2] = fopts.getelectrostatic13scale(); + electrostaticScale_[3] = fopts.getelectrostatic14scale(); + ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); ForceField::AtomTypeContainer::MapTypeIterator i1, i2; AtomType* atype1; @@ -231,73 +253,60 @@ namespace OpenMD { } } } - - - void InteractionManager::doPrePair(AtomType* atype1, - AtomType* atype2, - RealType rij, - RealType &rho_i_at_j, - RealType &rho_j_at_i) { - - } - void InteractionManager::doPreForce(AtomType* atype, - RealType rho, - RealType &frho, - RealType &dfrhodrho) { - } + void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){ + + if (!initialized_) initialize(); + + DensityData ddat; - void InteractionManager::doSkipCorrection(AtomType* atype1, - AtomType* atype2, - Vector3d d, - RealType rij, - RealType &skippedCharge1, - RealType &skippedCharge2, - RealType sw, - RealType electroMult, - RealType &pot, - RealType &vpair, - Vector3d &f1, - Mat3x3d eFrame1, - Mat3x3d eFrame2, - Vector3d &t1, - Vector3d &t2) { - } - - void InteractionManager::doSelfCorrection(AtomType* atype, - Mat3x3d eFrame, - RealType skippedCharge, - RealType &pot, - Vector3d &t) { - } + ddat.atype1 = typeMap_[*atid1]; + ddat.atype2 = typeMap_[*atid2]; + ddat.rij = *rij; + ddat.rho_i_at_j = *rho_i_at_j; + ddat.rho_j_at_i = *rho_j_at_i; - void InteractionManager::do_prepair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){ - - if (!initialized_) initialize(); - AtomType* atype1 = typeMap_[*atid1]; - AtomType* atype2 = typeMap_[*atid2]; - - doPrePair(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i); - - return; - } + pair key = make_pair(ddat.atype1, ddat.atype2); + set::iterator it; - void InteractionManager::do_preforce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){ - - if (!initialized_) initialize(); - AtomType* atype = typeMap_[*atid]; - - doPreForce(atype, *rho, *frho, *dfrhodrho); + for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ + if ((*it)->getFamily() == METALLIC_FAMILY) { + dynamic_cast(*it)->calcDensity(ddat); + } + } return; } + + void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){ - void InteractionManager::do_pair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *rcut, RealType *sw, RealType *vdwMult,RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *A1, RealType *A2, RealType *t1, RealType *t2, RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, RealType *fshift1, RealType *fshift2){ - if (!initialized_) initialize(); - InteractionData idat; + FunctionalData fdat; + fdat.atype = typeMap_[*atid]; + fdat.rho = *rho; + fdat.frho = *frho; + fdat.dfrhodrho = *dfrhodrho; + + pair key = make_pair(fdat.atype, fdat.atype); + set::iterator it; + + for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ + if ((*it)->getFamily() == METALLIC_FAMILY) { + dynamic_cast(*it)->calcFunctional(fdat); + } + } + + return; + } + + void InteractionManager::doPair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *rcut, RealType *sw, int *topoDist, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *A1, RealType *A2, RealType *t1, RealType *t2, RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, RealType *fshift1, RealType *fshift2){ + + if (!initialized_) initialize(); + + InteractionData idat; + idat.atype1 = typeMap_[*atid1]; idat.atype2 = typeMap_[*atid2]; idat.d = Vector3d(d); @@ -305,8 +314,8 @@ namespace OpenMD { idat.r2 = *r2; idat.rcut = *rcut; idat.sw = *sw; - idat.vdwMult = *vdwMult; - idat.electroMult = *electroMult; + idat.vdwMult = vdwScale_[*topoDist]; + idat.electroMult = electrostaticScale_[*topoDist]; idat.pot = *pot; idat.vpair = *vpair; idat.f1 = Vector3d(f1); @@ -344,54 +353,118 @@ namespace OpenMD { return; } - void InteractionManager::do_skip_correction(int *atid1, int *atid2, RealType *d, RealType *r, RealType *skippedCharge1, RealType *skippedCharge2, RealType *sw, RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *t1, RealType *t2){ + void InteractionManager::doSkipCorrection(int *atid1, int *atid2, RealType *d, RealType *r, RealType *skippedCharge1, RealType *skippedCharge2, RealType *sw, RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *t1, RealType *t2){ if (!initialized_) initialize(); - - AtomType* atype1 = typeMap_[*atid1]; - AtomType* atype2 = typeMap_[*atid2]; - Vector3d disp(d); - Vector3d frc(f1); - Vector3d trq1(t1); - Vector3d trq2(t2); - Mat3x3d eFi(eFrame1); - Mat3x3d eFj(eFrame2); - - doSkipCorrection(atype1, atype2, disp, *r, *skippedCharge1, *skippedCharge2, *sw, - *electroMult, *pot, *vpair, frc, eFi, eFj, trq1, trq2); - - f1[0] = frc.x(); - f1[1] = frc.y(); - f1[2] = frc.z(); - t1[0] = trq1.x(); - t1[1] = trq1.y(); - t1[2] = trq1.z(); + SkipCorrectionData skdat; - t2[0] = trq2.x(); - t2[1] = trq2.y(); - t2[2] = trq2.z(); + skdat.atype1 = typeMap_[*atid1]; + skdat.atype2 = typeMap_[*atid2]; + skdat.d = Vector3d(d); + skdat.rij = *r; + skdat.skippedCharge1 = *skippedCharge1; + skdat.skippedCharge2 = *skippedCharge2; + skdat.sw = *sw; + skdat.electroMult = *electroMult; + skdat.pot = *pot; + skdat.vpair = *vpair; + skdat.f1 = Vector3d(f1); + skdat.eFrame1 = Mat3x3d(eFrame1); + skdat.eFrame2 = Mat3x3d(eFrame2); + skdat.t1 = Vector3d(t1); + skdat.t2 = Vector3d(t2); - return; - } + pair key = make_pair(skdat.atype1, skdat.atype2); + set::iterator it; - void InteractionManager::do_self_correction(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){ + for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ + if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) { + dynamic_cast(*it)->calcSkipCorrection(skdat); + } + } + + f1[0] = skdat.f1.x(); + f1[1] = skdat.f1.y(); + f1[2] = skdat.f1.z(); + + t1[0] = skdat.t1.x(); + t1[1] = skdat.t1.y(); + t1[2] = skdat.t1.z(); + + t2[0] = skdat.t2.x(); + t2[1] = skdat.t2.y(); + t2[2] = skdat.t2.z(); + return; + } + + void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){ + if (!initialized_) initialize(); - + + SelfCorrectionData scdat; + + scdat.atype = typeMap_[*atid]; + scdat.eFrame = Mat3x3d(eFrame); + scdat.skippedCharge = *skippedCharge; + scdat.pot = *pot; + scdat.t = Vector3d(t); + + pair key = make_pair(scdat.atype, scdat.atype); + set::iterator it; + + for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ + if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) { + dynamic_cast(*it)->calcSelfCorrection(scdat); + } + } + + t[0] = scdat.t.x(); + t[1] = scdat.t.y(); + t[2] = scdat.t.z(); + + return; + } + + + RealType InteractionManager::getSuggestedCutoffRadius(int *atid) { + if (!initialized_) initialize(); + AtomType* atype = typeMap_[*atid]; - Mat3x3d eFi(eFrame); - Vector3d trq1(t); - - doSelfCorrection(atype, eFi, *skippedCharge, *pot, trq1); - t[0] = trq1.x(); - t[1] = trq1.y(); - t[2] = trq1.z(); + pair key = make_pair(atype, atype); + set::iterator it; + RealType cutoff = 0.0; + + for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) + cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype)); + return cutoff; + } - return; + RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) { + if (!initialized_) initialize(); + + pair key = make_pair(atype, atype); + set::iterator it; + RealType cutoff = 0.0; + + for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) + cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype)); + return cutoff; } + + void InteractionManager::setSwitch(RealType *rIn, RealType *rOut) { + switcher_->setSwitch(*rIn, *rOut); + } + + void InteractionManager::getSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r, + int *in_switching_region) { + bool isr = switcher_->getSwitch(*r2, *sw, *dswdr, *r); + *in_switching_region = (int)isr; + } + } //end namespace OpenMD extern "C" { @@ -402,59 +475,79 @@ extern "C" { #define fortranDoSkipCorrection FC_FUNC(do_skip_correction, DO_SKIP_CORRECTION) #define fortranDoSelfCorrection FC_FUNC(do_self_correction, DO_SELF_CORRECTION) #define fortranGetCutoff FC_FUNC(get_cutoff, GET_CUTOFF) +#define fortranSetSwitch FC_FUNC(set_switch, SET_SWITCH) +#define fortranGetSwitch FC_FUNC(get_switch, GET_SWITCH) void fortranDoPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i) { - return OpenMD::InteractionManager::Instance()->do_prepair(atid1, atid2, rij, - rho_i_at_j, - rho_j_at_i); + return OpenMD::InteractionManager::Instance()->doPrePair(atid1, atid2, rij, + rho_i_at_j, + rho_j_at_i); } - void fortranDoPreforce(int *atid, RealType *rho, RealType *frho, + void fortranDoPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho) { - return OpenMD::InteractionManager::Instance()->do_preforce(atid, rho, frho, - dfrhodrho); + return OpenMD::InteractionManager::Instance()->doPreForce(atid, rho, frho, + dfrhodrho); } void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r, - RealType *r2, RealType *rcut, RealType *sw, RealType *vdwMult, - RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, - RealType *eFrame1, RealType *eFrame2, RealType *A1, RealType *A2, - RealType *t1, RealType *t2, - RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, - RealType *fshift1, RealType *fshift2){ + RealType *r2, RealType *rcut, RealType *sw, int *topoDist, + RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, + RealType *eFrame2, RealType *A1, RealType *A2, + RealType *t1, RealType *t2, RealType *rho1, RealType *rho2, + RealType *dfrho1, RealType *dfrho2, RealType *fshift1, + RealType *fshift2){ - return OpenMD::InteractionManager::Instance()->do_pair(atid1, atid2, d, r, r2, rcut, - sw, vdwMult, electroMult, pot, - vpair, f1, eFrame1, eFrame2, - A1, A2, t1, t2, rho1, rho2, - dfrho1, dfrho2, fshift1, fshift2); + return OpenMD::InteractionManager::Instance()->doPair(atid1, atid2, d, r, + r2, rcut, sw, topoDist, + pot, vpair, f1, + eFrame1, eFrame2, + A1, A2, t1, t2, rho1, + rho2, dfrho1, dfrho2, + fshift1, fshift2); } - - void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d, RealType *r, - RealType *skippedCharge1, RealType *skippedCharge2, - RealType *sw, RealType *electroMult, RealType *pot, + + void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d, + RealType *r, RealType *skippedCharge1, + RealType *skippedCharge2, RealType *sw, + RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *t1, RealType *t2){ - return OpenMD::InteractionManager::Instance()->do_skip_correction(atid1, atid2, d, r, - skippedCharge1, - skippedCharge2, - sw, electroMult, pot, - vpair, f1, eFrame1, - eFrame2, t1, t2); + return OpenMD::InteractionManager::Instance()->doSkipCorrection(atid1, + atid2, d, + r, + skippedCharge1, + skippedCharge2, + sw, electroMult, pot, + vpair, f1, eFrame1, + eFrame2, t1, t2); } - + void fortranDoSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t) { - return OpenMD::InteractionManager::Instance()->do_self_correction(atid, eFrame, - skippedCharge, - pot, t); + return OpenMD::InteractionManager::Instance()->doSelfCorrection(atid, + eFrame, + skippedCharge, + pot, t); } - RealType fortranGetCutoff() { - return OpenMD::InteractionManager::Instance()->getCutoff(); + RealType fortranGetCutoff(int *atid) { + return OpenMD::InteractionManager::Instance()->getSuggestedCutoffRadius(atid); } + + void fortranGetSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r, + int *in_switching_region) { + + return OpenMD::InteractionManager::Instance()->getSwitch(r2, sw, dswdr, r, + in_switching_region); + } + + void fortranSetSwitch(RealType *rIn, RealType *rOut) { + return OpenMD::InteractionManager::Instance()->setSwitch(rIn, rOut); + } + }