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#include <cmath> |
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#include "nonbonded/Sticky.hpp" |
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#include "nonbonded/LJ.hpp" |
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#include "types/StickyAdapter.hpp" |
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#include "utils/simError.h" |
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using namespace std; |
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namespace OpenMD { |
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Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {} |
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StickyParam Sticky::getStickyParam(AtomType* atomType) { |
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// Do sanity checking on the AtomType we were passed before |
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// building any data structures: |
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if (!atomType->isSticky() && !atomType->isStickyPower()) { |
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sprintf( painCave.errMsg, |
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"Sticky::getStickyParam was passed an atomType (%s) that does\n" |
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"\tnot appear to be a Sticky atom.\n", |
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atomType->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType); |
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GenericData* data = daType->getPropertyByName("Sticky"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "Sticky::getStickyParam could not find\n" |
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"\tSticky parameters for atomType %s.\n", |
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daType->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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StickyParamGenericData* stickyData = dynamic_cast<StickyParamGenericData*>(data); |
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if (stickyData == NULL) { |
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sprintf( painCave.errMsg, |
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"Sticky::getStickyParam could not convert GenericData to\n" |
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"\tStickyParamGenericData for atom type %s\n", |
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daType->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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return stickyData->getData(); |
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} |
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void Sticky::initialize() { |
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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for (at = atomTypes->beginType(i); at != NULL; |
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at = atomTypes->nextType(i)) { |
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if (at->isSticky() || at->isStickyPower()) |
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addType(at); |
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StickyAdapter sa = StickyAdapter(at); |
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if (sa.isSticky()) addType(at); |
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} |
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initialized_ = true; |
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void Sticky::addType(AtomType* atomType){ |
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// add it to the map: |
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AtomTypeProperties atp = atomType->getATP(); |
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pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = StickyMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
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ret = StickyMap.insert( pair<int, AtomType*>(atomType->getIdent(), |
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atomType) ); |
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if (ret.second == false) { |
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sprintf( painCave.errMsg, |
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"Sticky already had a previous entry with ident %d\n", |
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atp.ident); |
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atomType->getIdent() ); |
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painCave.severity = OPENMD_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} |
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RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi; |
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StickyParam sticky1 = getStickyParam(atomType); |
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StickyAdapter sticky1 = StickyAdapter(atomType); |
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// Now, iterate over all known types and add to the mixing map: |
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for( it = StickyMap.begin(); it != StickyMap.end(); ++it) { |
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AtomType* atype2 = (*it).second; |
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StickyParam sticky2 = getStickyParam(atype2); |
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StickyAdapter sticky2 = StickyAdapter(atype2); |
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StickyInteractionData mixer; |
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// Lorentz- Berthelot mixing rules (which happen to do the right thing |
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// when atomType and atype2 happen to be the same. |
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mixer.rl = 0.5 * ( sticky1.rl + sticky2.rl ); |
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mixer.ru = 0.5 * ( sticky1.ru + sticky2.ru ); |
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mixer.rlp = 0.5 * ( sticky1.rlp + sticky2.rlp ); |
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mixer.rup = 0.5 * ( sticky1.rup + sticky2.rup ); |
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mixer.rl = 0.5 * ( sticky1.getRl() + sticky2.getRl() ); |
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mixer.ru = 0.5 * ( sticky1.getRu() + sticky2.getRu() ); |
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mixer.rlp = 0.5 * ( sticky1.getRlp() + sticky2.getRlp() ); |
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mixer.rup = 0.5 * ( sticky1.getRup() + sticky2.getRup() ); |
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mixer.rbig = max(mixer.ru, mixer.rup); |
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mixer.w0 = sqrt( sticky1.w0 * sticky2.w0 ); |
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mixer.v0 = sqrt( sticky1.v0 * sticky2.v0 ); |
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mixer.v0p = sqrt( sticky1.v0p * sticky2.v0p ); |
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mixer.isPower = atomType->isStickyPower() && atype2->isStickyPower(); |
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mixer.w0 = sqrt( sticky1.getW0() * sticky2.getW0() ); |
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mixer.v0 = sqrt( sticky1.getV0() * sticky2.getV0() ); |
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mixer.v0p = sqrt( sticky1.getV0p() * sticky2.getV0p() ); |
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mixer.isPower = sticky1.isStickyPower() && sticky2.isStickyPower(); |
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CubicSpline* s = new CubicSpline(); |
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s->addPoint(mixer.rl, 1.0); |
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// sticky power has no w' function: |
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w = frac1 * wi * wi2 + frac2*wi + frac1*wj*wj2 + frac2*wj + v0p; |
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wp = 0.0; |
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dwi = frac1*3.0*wi2*dwi + frac2*dwi; |
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dwj = frac1*3.0*wj2*dwi + frac2*dwi; |
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dwi = frac1*RealType(3.0)*wi2*dwi + frac2*dwi; |
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dwj = frac1*RealType(3.0)*wj2*dwi + frac2*dwi; |
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dwip = V3Zero; |
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dwjp = V3Zero; |
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dwidu = frac1*3.0*wi2*dwidu + frac2*dwidu; |
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dwidu = frac1*3.0*wj2*dwjdu + frac2*dwjdu; |
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dwidu = frac1*RealType(3.0)*wi2*dwidu + frac2*dwidu; |
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dwidu = frac1*RealType(3.0)*wj2*dwjdu + frac2*dwjdu; |
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dwipdu = V3Zero; |
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dwjpdu = V3Zero; |
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sp = 0.0; |
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dspdr = 0.0; |
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} |
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*(idat.vpair) += 0.5*(v0*s*w + v0p*sp*wp); |
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(*(idat.pot))[HYDROGENBONDING_FAMILY] += 0.5*(v0*s*w + v0p*sp*wp)* *(idat.sw) ; |
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*(idat.vpair) += RealType(0.5)*(v0*s*w + v0p*sp*wp); |
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(*(idat.pot))[HYDROGENBONDING_FAMILY] += RealType(0.5)*(v0*s*w + v0p*sp*wp)* *(idat.sw) ; |
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// do the torques first since they are easy: |
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// remember that these are still in the body-fixed axes |
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Vector3d ti = 0.5* *(idat.sw) *(v0*s*dwidu + v0p*sp*dwipdu); |
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Vector3d tj = 0.5* *(idat.sw) *(v0*s*dwjdu + v0p*sp*dwjpdu); |
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Vector3d ti = RealType(0.5)* *(idat.sw) *(v0*s*dwidu + v0p*sp*dwipdu); |
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Vector3d tj = RealType(0.5)* *(idat.sw) *(v0*s*dwjdu + v0p*sp*dwjpdu); |
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// go back to lab frame using transpose of rotation matrix: |
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// now assemble these with the radial-only terms: |
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*(idat.f1) += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * *(idat.d) / |
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*(idat.rij) + fii - fjj); |
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*(idat.f1) += RealType(0.5) * ((v0*dsdr*w + v0p*dspdr*wp) * *(idat.d) / |
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*(idat.rij) + fii - fjj); |
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} |
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} |
