--- branches/development/src/nonbonded/Sticky.cpp 2010/10/02 19:53:32 1502 +++ trunk/src/nonbonded/Sticky.cpp 2015/03/07 21:41:51 2071 @@ -35,8 +35,9 @@ * * [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). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include @@ -45,99 +46,71 @@ #include #include "nonbonded/Sticky.hpp" #include "nonbonded/LJ.hpp" +#include "types/StickyAdapter.hpp" #include "utils/simError.h" using namespace std; namespace OpenMD { - Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {} - - StickyParam Sticky::getStickyParam(AtomType* atomType) { + Sticky::Sticky() : initialized_(false), forceField_(NULL), name_("Sticky") {} - // Do sanity checking on the AtomType we were passed before - // building any data structures: - if (!atomType->isSticky() && !atomType->isStickyPower()) { - sprintf( painCave.errMsg, - "Sticky::getStickyParam was passed an atomType (%s) that does\n" - "\tnot appear to be a Sticky atom.\n", - atomType->getName().c_str()); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - - DirectionalAtomType* daType = dynamic_cast(atomType); - GenericData* data = daType->getPropertyByName("Sticky"); - if (data == NULL) { - sprintf( painCave.errMsg, "Sticky::getStickyParam could not find\n" - "\tSticky parameters for atomType %s.\n", - daType->getName().c_str()); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - - StickyParamGenericData* stickyData = dynamic_cast(data); - if (stickyData == NULL) { - sprintf( painCave.errMsg, - "Sticky::getStickyParam could not convert GenericData to\n" - "\tStickyParamGenericData for atom type %s\n", - daType->getName().c_str()); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - - return stickyData->getData(); - } - void Sticky::initialize() { - - ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); - ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); - ForceField::AtomTypeContainer::MapTypeIterator i; - AtomType* at; + Stypes.clear(); + Stids.clear(); + MixingMap.clear(); + nSticky_=0; + Stids.resize( forceField_->getNAtomType(), -1); + // Sticky handles all of the Sticky-Sticky interactions - for (at = atomTypes->beginType(i); at != NULL; - at = atomTypes->nextType(i)) { - - if (at->isSticky() || at->isStickyPower()) - addType(at); + set::iterator at; + for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { + if ((*at)->isSticky()) nSticky_++; } + + MixingMap.resize(nSticky_); + + for (at = simTypes_.begin(); at != simTypes_.end(); ++at) { + if ((*at)->isSticky()) addType( *at ); + } initialized_ = true; } void Sticky::addType(AtomType* atomType){ + StickyAdapter sticky1 = StickyAdapter(atomType); + // add it to the map: - AtomTypeProperties atp = atomType->getATP(); - pair::iterator,bool> ret; - ret = StickyMap.insert( pair(atp.ident, atomType) ); + int atid = atomType->getIdent(); + int stid = Stypes.size(); + + pair::iterator,bool> ret; + ret = Stypes.insert( atid ); if (ret.second == false) { sprintf( painCave.errMsg, "Sticky already had a previous entry with ident %d\n", - atp.ident); + atid) ; painCave.severity = OPENMD_INFO; painCave.isFatal = 0; simError(); } - - RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi; - - StickyParam sticky1 = getStickyParam(atomType); + Stids[atid] = stid; + MixingMap[stid].resize( nSticky_ ); + + // Now, iterate over all known types and add to the mixing map: - map::iterator it; - for( it = StickyMap.begin(); it != StickyMap.end(); ++it) { + std::set::iterator it; + for( it = Stypes.begin(); it != Stypes.end(); ++it) { - AtomType* atype2 = (*it).second; - - StickyParam sticky2 = getStickyParam(atype2); + int stid2 = Stids[ (*it) ]; + AtomType* atype2 = forceField_->getAtomType( (*it) ); + StickyAdapter sticky2 = StickyAdapter(atype2); + StickyInteractionData mixer; // Mixing two different sticky types is silly, but if you want 2 @@ -145,15 +118,15 @@ namespace OpenMD { // Lorentz- Berthelot mixing rules (which happen to do the right thing // when atomType and atype2 happen to be the same. - mixer.rl = 0.5 * ( sticky1.rl + sticky2.rl ); - mixer.ru = 0.5 * ( sticky1.ru + sticky2.ru ); - mixer.rlp = 0.5 * ( sticky1.rlp + sticky2.rlp ); - mixer.rup = 0.5 * ( sticky1.rup + sticky2.rup ); + mixer.rl = 0.5 * ( sticky1.getRl() + sticky2.getRl() ); + mixer.ru = 0.5 * ( sticky1.getRu() + sticky2.getRu() ); + mixer.rlp = 0.5 * ( sticky1.getRlp() + sticky2.getRlp() ); + mixer.rup = 0.5 * ( sticky1.getRup() + sticky2.getRup() ); mixer.rbig = max(mixer.ru, mixer.rup); - mixer.w0 = sqrt( sticky1.w0 * sticky2.w0 ); - mixer.v0 = sqrt( sticky1.v0 * sticky2.v0 ); - mixer.v0p = sqrt( sticky1.v0p * sticky2.v0p ); - mixer.isPower = atomType->isStickyPower() && atype2->isStickyPower(); + mixer.w0 = sqrt( sticky1.getW0() * sticky2.getW0() ); + mixer.v0 = sqrt( sticky1.getV0() * sticky2.getV0() ); + mixer.v0p = sqrt( sticky1.getV0p() * sticky2.getV0p() ); + mixer.isPower = sticky1.isStickyPower() && sticky2.isStickyPower(); CubicSpline* s = new CubicSpline(); s->addPoint(mixer.rl, 1.0); @@ -165,14 +138,11 @@ namespace OpenMD { sp->addPoint(mixer.rup, 0.0); mixer.sp = sp; - - pair key1, key2; - key1 = make_pair(atomType, atype2); - key2 = make_pair(atype2, atomType); - - MixingMap[key1] = mixer; - if (key2 != key1) { - MixingMap[key2] = mixer; + MixingMap[stid2].resize( nSticky_ ); + + MixingMap[stid][stid2] = mixer; + if (stid2 != stid) { + MixingMap[stid2][stid] = mixer; } } } @@ -186,13 +156,12 @@ namespace OpenMD { * idat structure. */ - void Sticky::calcForce(InteractionData idat) { + void Sticky::calcForce(InteractionData &idat) { if (!initialized_) initialize(); - pair key = make_pair(idat.atype1, idat.atype2); - StickyInteractionData mixer = MixingMap[key]; - + StickyInteractionData &mixer = MixingMap[Stids[idat.atid1]][Stids[idat.atid2]]; + RealType w0 = mixer.w0; RealType v0 = mixer.v0; RealType v0p = mixer.v0p; @@ -202,88 +171,83 @@ namespace OpenMD { RealType rup = mixer.rup; RealType rbig = mixer.rbig; bool isPower = mixer.isPower; - - if (idat.rij <= rbig) { - - RealType r3 = idat.r2 * idat.rij; - RealType r5 = r3 * idat.r2; - - RotMat3x3d A1trans = idat.A1.transpose(); - RotMat3x3d A2trans = idat.A2.transpose(); - + + if ( *(idat.rij) <= rbig) { + + RealType r3 = *(idat.r2) * *(idat.rij); + RealType r5 = r3 * *(idat.r2); + + RotMat3x3d A1trans = idat.A1->transpose(); + RotMat3x3d A2trans = idat.A2->transpose(); + // rotate the inter-particle separation into the two different // body-fixed coordinate systems: - - Vector3d ri = idat.A1 * idat.d; - + + Vector3d ri = *(idat.A1) * *(idat.d); + // negative sign because this is the vector from j to i: - - Vector3d rj = - idat.A2 * idat.d; - + + Vector3d rj = - *(idat.A2) * *(idat.d); + RealType xi = ri.x(); RealType yi = ri.y(); RealType zi = ri.z(); - + RealType xj = rj.x(); RealType yj = rj.y(); RealType zj = rj.z(); - + RealType xi2 = xi * xi; RealType yi2 = yi * yi; RealType zi2 = zi * zi; - + RealType xj2 = xj * xj; RealType yj2 = yj * yj; RealType zj2 = zj * zj; - + // calculate the switching info. from the splines - + RealType s = 0.0; RealType dsdr = 0.0; RealType sp = 0.0; RealType dspdr = 0.0; - - if (idat.rij < ru) { - if (idat.rij < rl) { + + if ( *(idat.rij) < ru) { + if ( *(idat.rij) < rl) { s = 1.0; dsdr = 0.0; } else { - // we are in the switching region - - pair res = mixer.s->getValueAndDerivativeAt(idat.rij); - s = res.first; - dsdr = res.second; + // we are in the switching region + mixer.s->getValueAndDerivativeAt(*(idat.rij), s, dsdr); } } - - if (idat.rij < rup) { - if (idat.rij < rlp) { + + if (*(idat.rij) < rup) { + if ( *(idat.rij) < rlp) { sp = 1.0; dspdr = 0.0; } else { - // we are in the switching region - - pair res =mixer.sp->getValueAndDerivativeAt(idat.rij); - sp = res.first; - dspdr = res.second; + // we are in the switching region + mixer.sp->getValueAndDerivativeAt( *(idat.rij), sp, dspdr); } } - + + RealType wi = 2.0*(xi2-yi2)*zi / r3; RealType wj = 2.0*(xj2-yj2)*zj / r3; RealType w = wi+wj; - - - RealType zif = zi/idat.rij - 0.6; - RealType zis = zi/idat.rij + 0.8; - - RealType zjf = zj/idat.rij - 0.6; - RealType zjs = zj/idat.rij + 0.8; - + + + RealType zif = zi/ *(idat.rij) - 0.6; + RealType zis = zi/ *(idat.rij) + 0.8; + + RealType zjf = zj/ *(idat.rij) - 0.6; + RealType zjs = zj/ *(idat.rij) + 0.8; + RealType wip = zif*zif*zis*zis - w0; RealType wjp = zjf*zjf*zjs*zjs - w0; RealType wp = wip + wjp; - + Vector3d dwi(4.0*xi*zi/r3 - 6.0*xi*zi*(xi2-yi2)/r5, - 4.0*yi*zi/r3 - 6.0*yi*zi*(xi2-yi2)/r5, 2.0*(xi2-yi2)/r3 - 6.0*zi2*(xi2-yi2)/r5); @@ -291,35 +255,36 @@ namespace OpenMD { Vector3d dwj(4.0*xj*zj/r3 - 6.0*xj*zj*(xj2-yj2)/r5, - 4.0*yj*zj/r3 - 6.0*yj*zj*(xj2-yj2)/r5, 2.0*(xj2-yj2)/r3 - 6.0*zj2*(xj2-yj2)/r5); - + RealType uglyi = zif*zif*zis + zif*zis*zis; RealType uglyj = zjf*zjf*zjs + zjf*zjs*zjs; - + Vector3d dwip(-2.0*xi*zi*uglyi/r3, -2.0*yi*zi*uglyi/r3, - 2.0*(1.0/idat.rij - zi2/r3)*uglyi); - + 2.0*(1.0/ *(idat.rij) - zi2/r3)*uglyi); + Vector3d dwjp(-2.0*xj*zj*uglyj/r3, -2.0*yj*zj*uglyj/r3, - 2.0*(1.0/idat.rij - zj2/r3)*uglyj); - + 2.0*(1.0/ *(idat.rij) - zj2/r3)*uglyj); + Vector3d dwidu(4.0*(yi*zi2 + 0.5*yi*(xi2-yi2))/r3, 4.0*(xi*zi2 - 0.5*xi*(xi2-yi2))/r3, - 8.0*xi*yi*zi/r3); - + Vector3d dwjdu(4.0*(yj*zj2 + 0.5*yj*(xj2-yj2))/r3, 4.0*(xj*zj2 - 0.5*xj*(xj2-yj2))/r3, - 8.0*xj*yj*zj/r3); - Vector3d dwipdu(2.0*yi*uglyi/idat.rij, - -2.0*xi*uglyi/idat.rij, + Vector3d dwipdu(2.0*yi*uglyi/ *(idat.rij) , + -2.0*xi*uglyi/ *(idat.rij) , 0.0); - - Vector3d dwjpdu(2.0*yj*uglyj/idat.rij, - -2.0*xj*uglyj/idat.rij, + + Vector3d dwjpdu(2.0*yj*uglyj/ *(idat.rij) , + -2.0*xj*uglyj/ *(idat.rij) , 0.0); - + if (isPower) { + cerr << "This is probably an error!\n"; RealType frac1 = 0.25; RealType frac2 = 0.75; RealType wi2 = wi*wi; @@ -327,50 +292,64 @@ namespace OpenMD { // sticky power has no w' function: w = frac1 * wi * wi2 + frac2*wi + frac1*wj*wj2 + frac2*wj + v0p; wp = 0.0; - dwi = frac1*3.0*wi2*dwi + frac2*dwi; - dwj = frac1*3.0*wj2*dwi + frac2*dwi; + dwi = frac1*RealType(3.0)*wi2*dwi + frac2*dwi; + dwj = frac1*RealType(3.0)*wj2*dwi + frac2*dwi; dwip = V3Zero; dwjp = V3Zero; - dwidu = frac1*3.0*wi2*dwidu + frac2*dwidu; - dwidu = frac1*3.0*wj2*dwjdu + frac2*dwjdu; + dwidu = frac1*RealType(3.0)*wi2*dwidu + frac2*dwidu; + dwidu = frac1*RealType(3.0)*wj2*dwjdu + frac2*dwjdu; dwipdu = V3Zero; dwjpdu = V3Zero; sp = 0.0; dspdr = 0.0; } - - idat.vpair += 0.5*(v0*s*w + v0p*sp*wp); - idat.pot += 0.5*(v0*s*w + v0p*sp*wp)*idat.sw; - + + + + *(idat.vpair) += RealType(0.5)*(v0*s*w + v0p*sp*wp); + (*(idat.pot))[HYDROGENBONDING_FAMILY] += RealType(0.5)*(v0*s*w + v0p*sp*wp)* *(idat.sw) ; + // do the torques first since they are easy: // remember that these are still in the body-fixed axes - - Vector3d ti = 0.5*idat.sw*(v0*s*dwidu + v0p*sp*dwipdu); - Vector3d tj = 0.5*idat.sw*(v0*s*dwjdu + v0p*sp*dwjpdu); - + + Vector3d ti = RealType(0.5)* *(idat.sw) *(v0*s*dwidu + v0p*sp*dwipdu); + Vector3d tj = RealType(0.5)* *(idat.sw) *(v0*s*dwjdu + v0p*sp*dwjpdu); + // go back to lab frame using transpose of rotation matrix: - - idat.t1 += A1trans * ti; - idat.t2 += A2trans * tj; - + + *(idat.t1) += A1trans * ti; + *(idat.t2) += A2trans * tj; + // Now, on to the forces: - + // first rotate the i terms back into the lab frame: - - Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * idat.sw; - Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * idat.sw; - + + Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * *(idat.sw); + Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * *(idat.sw); + Vector3d fii = A1trans * radcomi; Vector3d fjj = A2trans * radcomj; // now assemble these with the radial-only terms: - idat.f1 += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * idat.d / - idat.rij + fii - fjj); - - } + *(idat.f1) += RealType(0.5) * ((v0*dsdr*w + v0p*dspdr*wp) * *(idat.d) / + *(idat.rij) + fii - fjj); - return; + } + return; } + + RealType Sticky::getSuggestedCutoffRadius(pair atypes) { + if (!initialized_) initialize(); + int atid1 = atypes.first->getIdent(); + int atid2 = atypes.second->getIdent(); + int stid1 = Stids[atid1]; + int stid2 = Stids[atid2]; + + if (stid1 == -1 || stid2 == -1) return 0.0; + else { + return MixingMap[stid1][stid2].rbig; + } + } }