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#include <cmath> |
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#include "nonbonded/GB.hpp" |
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#include "nonbonded/LJ.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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|
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< |
bool GB::initialized_ = false; |
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RealType GB::mu_ = 2.0; |
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RealType GB::nu_ = 1.0; |
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< |
ForceField* GB::forceField_ = NULL; |
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map<int, AtomType*> GB::GBMap; |
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map<pair<AtomType*, AtomType*>, GBInteractionData> GB::MixingMap; |
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GB::GB() : name_("GB"), initialized_(false), mu_(2.0), nu_(1.0), forceField_(NULL) {} |
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|
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GB* GB::_instance = NULL; |
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|
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GB* GB::Instance() { |
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if (!_instance) { |
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_instance = new GB(); |
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} |
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return _instance; |
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} |
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|
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GayBerneParam GB::getGayBerneParam(AtomType* atomType) { |
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// Do sanity checking on the AtomType we were passed before |
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return gbData->getData(); |
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} |
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LJParam GB::getLJParam(AtomType* atomType) { |
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|
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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->isLennardJones()) { |
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sprintf( painCave.errMsg, |
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"GB::getLJParam was passed an atomType (%s) that does not\n" |
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"\tappear to be a Lennard-Jones 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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|
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GenericData* data = atomType->getPropertyByName("LennardJones"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "GB::getLJParam could not find Lennard-Jones\n" |
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"\tparameters for atomType %s.\n", 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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|
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LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
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if (ljData == NULL) { |
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sprintf( painCave.errMsg, |
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"GB::getLJParam could not convert GenericData to LJParam for\n" |
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"\tatom type %s\n", 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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|
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return ljData->getData(); |
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} |
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|
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RealType GB::getLJEpsilon(AtomType* atomType) { |
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LJParam ljParam = getLJParam(atomType); |
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return ljParam.epsilon; |
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} |
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RealType GB::getLJSigma(AtomType* atomType) { |
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LJParam ljParam = getLJParam(atomType); |
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return ljParam.sigma; |
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} |
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|
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void GB::initialize() { |
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|
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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mu_ = fopts.getGayBerneMu(); |
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nu_ = fopts.getGayBerneNu(); |
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ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
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ForceField::AtomTypeContainer::MapTypeIterator i; |
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AtomType* at; |
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er1 = gb1.GB_eps_ratio; |
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dw1 = gb1.GB_dw; |
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} else if (atomType->isLennardJones()) { |
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d1 = LJ::Instance()->getSigma(atomType) / sqrt(2.0); |
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e1 = LJ::Instance()->getEpsilon(atomType); |
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d1 = getLJSigma(atomType) / sqrt(2.0); |
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e1 = getLJEpsilon(atomType); |
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l1 = d1; |
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er1 = 1.0; |
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dw1 = 1.0; |
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er2 = gb2.GB_eps_ratio; |
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dw2 = gb2.GB_dw; |
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} else if (atype2->isLennardJones()) { |
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d2 = LJ::Instance()->getSigma(atype2) / sqrt(2.0); |
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e2 = LJ::Instance()->getEpsilon(atype2); |
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d2 = getLJSigma(atype2) / sqrt(2.0); |
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e2 = getLJEpsilon(atype2); |
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l2 = d2; |
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er2 = 1.0; |
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dw2 = 1.0; |
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} |
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} |
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} |
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RealType GB::getGayBerneCut(int atid) { |
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if (!initialized_) initialize(); |
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std::map<int, AtomType*> :: const_iterator it; |
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it = GBMap.find(atid); |
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if (it == GBMap.end()) { |
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sprintf( painCave.errMsg, |
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"GB::getGayBerneCut could not find atid %d in GBMap\n", |
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(atid)); |
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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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AtomType* atype = it->second; |
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RealType gbCut; |
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if (atype->isGayBerne()) { |
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GayBerneParam gb = getGayBerneParam(atype); |
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// sigma is actually sqrt(2) * l for prolate ellipsoids |
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gbCut = 2.5 * sqrt(2.0) * max(gb.GB_l, gb.GB_d); |
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} else if (atype->isLennardJones()) { |
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gbCut = 2.5 * LJ::Instance()->getSigma(atype); |
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} |
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return gbCut; |
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} |
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void GB::calcForce(AtomType* at1, AtomType* at2, Vector3d d, |
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RealType r, RealType r2, RealType sw, |
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RealType vdwMult, RealType &vpair, RealType &pot, |
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RotMat3x3d A1, RotMat3x3d A2, Vector3d &f1, |
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Vector3d &t1, Vector3d &t2) { |
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void GB::calcForce(InteractionData idat) { |
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if (!initialized_) initialize(); |
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pair<AtomType*, AtomType*> key = make_pair(at1, at2); |
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pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
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GBInteractionData mixer = MixingMap[key]; |
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RealType sigma0 = mixer.sigma0; |
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RealType xpap2 = mixer.xpap2; |
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RealType xpapi2 = mixer.xpapi2; |
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Vector3d ul1 = A1.getColumn(2); |
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Vector3d ul2 = A2.getColumn(2); |
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Vector3d ul1 = idat.A1.getRow(2); |
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Vector3d ul2 = idat.A2.getRow(2); |
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RealType a, b, g; |
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bool i_is_LJ = at1->isLennardJones(); |
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bool j_is_LJ = at2->isLennardJones(); |
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bool i_is_LJ = idat.atype1->isLennardJones(); |
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bool j_is_LJ = idat.atype2->isLennardJones(); |
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if (i_is_LJ) { |
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a = 0.0; |
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ul1 = V3Zero; |
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} else { |
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a = dot(d, ul1); |
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a = dot(idat.d, ul1); |
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} |
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if (j_is_LJ) { |
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b = 0.0; |
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ul2 = V3Zero; |
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} else { |
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b = dot(d, ul2); |
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b = dot(idat.d, ul2); |
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} |
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if (i_is_LJ || j_is_LJ) |
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else |
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g = dot(ul1, ul2); |
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RealType au = a / r; |
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RealType bu = b / r; |
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RealType au = a / idat.rij; |
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RealType bu = b / idat.rij; |
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RealType au2 = au * au; |
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RealType bu2 = bu * bu; |
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RealType e1 = 1.0 / sqrt(1.0 - x2*g2); |
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RealType e2 = 1.0 - Hp; |
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RealType eps = eps0 * pow(e1,nu_) * pow(e2,mu_); |
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RealType BigR = dw*sigma0 / (r - sigma + dw*sigma0); |
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RealType BigR = dw*sigma0 / (idat.rij - sigma + dw*sigma0); |
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RealType R3 = BigR*BigR*BigR; |
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RealType R6 = R3*R3; |
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RealType R12 = R6*R6; |
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RealType R13 = R6*R7; |
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RealType U = vdwMult * 4.0 * eps * (R12 - R6); |
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RealType U = idat.vdwMult * 4.0 * eps * (R12 - R6); |
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RealType s3 = sigma*sigma*sigma; |
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RealType s03 = sigma0*sigma0*sigma0; |
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RealType pref1 = - vdwMult * 8.0 * eps * mu_ * (R12 - R6) / (e2 * r); |
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RealType pref1 = - idat.vdwMult * 8.0 * eps * mu_ * (R12 - R6) / (e2 * idat.rij); |
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RealType pref2 = vdwMult * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) /(dw*r*s03); |
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RealType pref2 = idat.vdwMult * 8.0 * eps * s3 * (6.0*R13 - 3.0*R7) /(dw*idat.rij*s03); |
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RealType dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*r/s3 + H)); |
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RealType dUdr = - (pref1 * Hp + pref2 * (sigma0*sigma0*idat.rij/s3 + H)); |
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RealType dUda = pref1 * (xpap2*au - xp2*bu*g) / (1.0 - xp2 * g2) |
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+ pref2 * (xa2 * au - x2 *bu*g) / (1.0 - x2 * g2); |
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(x2 * au * bu - H * x2 * g) / (1.0 - x2 * g2) / (dw * s03); |
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Vector3d rhat = d / r; |
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Vector3d rxu1 = cross(d, ul1); |
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Vector3d rxu2 = cross(d, ul2); |
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Vector3d rhat = idat.d / idat.rij; |
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> |
Vector3d rxu1 = cross(idat.d, ul1); |
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> |
Vector3d rxu2 = cross(idat.d, ul2); |
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Vector3d uxu = cross(ul1, ul2); |
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pot += U*sw; |
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f1 += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
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t1 += dUda * rxu1 - dUdg * uxu; |
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t2 += dUdb * rxu2 - dUdg * uxu; |
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vpair += U*sw; |
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idat.pot += U*idat.sw; |
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> |
idat.f1 += dUdr * rhat + dUda * ul1 + dUdb * ul2; |
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> |
idat.t1 += dUda * rxu1 - dUdg * uxu; |
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> |
idat.t2 += dUdb * rxu2 - dUdg * uxu; |
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> |
idat.vpair += U*idat.sw; |
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return; |
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} |
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|
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void GB::do_gb_pair(int *atid1, int *atid2, RealType *d, RealType *r, |
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RealType *r2, RealType *sw, RealType *vdwMult, |
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RealType *vpair, RealType *pot, RealType *A1, |
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RealType *A2, RealType *f1, RealType *t1, RealType *t2) { |
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|
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if (!initialized_) initialize(); |
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|
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AtomType* atype1 = GBMap[*atid1]; |
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AtomType* atype2 = GBMap[*atid2]; |
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|
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Vector3d disp(d); |
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Vector3d frc(f1); |
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Vector3d trq1(t1); |
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Vector3d trq2(t2); |
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RotMat3x3d Ai(A1); |
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RotMat3x3d Aj(A2); |
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|
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// Fortran has the opposite matrix ordering from c++, so we'll use |
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// transpose here. When we finish the conversion to C++, this wrapper |
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// will disappear, as will the transpose below: |
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|
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calcForce(atype1, atype2, disp, *r, *r2, *sw, *vdwMult, *vpair, *pot, |
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Ai.transpose(), Aj.transpose(), frc, trq1, trq1); |
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|
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f1[0] = frc.x(); |
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f1[1] = frc.y(); |
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f1[2] = frc.z(); |
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|
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t1[0] = trq1.x(); |
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t1[1] = trq1.y(); |
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t1[2] = trq1.z(); |
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|
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t2[0] = trq2.x(); |
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t2[1] = trq2.y(); |
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t2[2] = trq2.z(); |
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|
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return; |
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} |
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} |
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|
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extern "C" { |
| 413 |
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|
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#define fortranGetGayBerneCut FC_FUNC(getgaybernecut, GETGAYBERNECUT) |
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#define fortranDoGBPair FC_FUNC(do_gb_pair, DO_GB_PAIR) |
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|
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RealType fortranGetGayBerneCut(int* atid) { |
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return OpenMD::GB::Instance()->getGayBerneCut(*atid); |
| 419 |
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} |
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|
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void fortranDoGBPair(int *atid1, int *atid2, RealType *d, RealType *r, |
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RealType *r2, RealType *sw, RealType *vdwMult, |
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RealType *vpair, RealType *pot, RealType *A1, |
| 424 |
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RealType *A2, RealType *f1, RealType *t1, RealType *t2){ |
| 425 |
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|
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return OpenMD::GB::Instance()->do_gb_pair(atid1, atid2, d, r, r2, sw, |
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vdwMult, vpair, pot, A1, A2, f1, |
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t1, t2); |
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} |
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} |
