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using namespace std; |
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namespace OpenMD { |
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< |
RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), |
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< |
evaluatorA_(info), seleManA_(info), |
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< |
commonA_(info), evaluatorB_(info), |
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< |
seleManB_(info), commonB_(info), |
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hasData_(false), hasDividingArea_(false), |
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< |
usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) { |
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> |
RNEMD::RNEMD(SimInfo* info) : info_(info), |
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> |
evaluator_(info_), seleMan_(info_), |
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> |
evaluatorA_(info_), seleManA_(info_), |
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> |
evaluatorB_(info_), seleManB_(info_), |
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> |
commonA_(info_), commonB_(info_), |
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> |
usePeriodicBoundaryConditions_(info_->getSimParams()->getUsePeriodicBoundaryConditions()), |
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> |
hasDividingArea_(false), |
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> |
hasData_(false) { |
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trialCount_ = 0; |
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failTrialCount_ = 0; |
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RealType mass = sd->getMass(); |
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Vector3d vel = sd->getVel(); |
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RealType value; |
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> |
RealType value(0.0); |
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switch(rnemdFluxType_) { |
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case rnemdKE : |
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RealType mass = sd->getMass(); |
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Vector3d vel = sd->getVel(); |
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RealType value; |
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> |
RealType value(0.0); |
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|
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switch(rnemdFluxType_) { |
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case rnemdKE : |
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RealType px = Pcx / Phx; |
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RealType py = Pcy / Phy; |
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RealType pz = Pcz / Phz; |
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< |
RealType c, x, y, z; |
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> |
RealType c(0.0), x(0.0), y(0.0), z(0.0); |
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bool successfulScale = false; |
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if ((rnemdFluxType_ == rnemdFullKE) || |
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(rnemdFluxType_ == rnemdRotKE)) { |
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} |
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} |
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} else { |
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< |
RealType a000, a110, c0, a001, a111, b01, b11, c1; |
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> |
RealType a000(0.0), a110(0.0), c0(0.0); |
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> |
RealType a001(0.0), a111(0.0), b01(0.0), b11(0.0), c1(0.0); |
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switch(rnemdFluxType_) { |
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case rnemdKE : |
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/* used hotBin coeff's & only scale x & y dimensions |
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vector<pair<RealType,RealType> > rps; |
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for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) { |
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r2 = *ri; |
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//check if FindRealRoots() give the right answer |
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> |
// Check to see if FindRealRoots() gave the right answer: |
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if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) { |
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sprintf(painCave.errMsg, |
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"RNEMD Warning: polynomial solve seems to have an error!"); |
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simError(); |
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failRootCount_++; |
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} |
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< |
//might not be useful w/o rescaling coefficients |
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// Might not be useful w/o rescaling coefficients |
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alpha0 = -c0 - a110 * r2 * r2; |
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if (alpha0 >= 0.0) { |
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r1 = sqrt(alpha0 / a000); |
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} |
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} |
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} |
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< |
// Consider combining together the solving pair part w/ the searching |
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// best solution part so that we don't need the pairs vector |
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// Consider combining together the part for solving for the pair |
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// w/ the searching for the best solution part so that we don't |
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// need the pairs vector: |
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if (!rps.empty()) { |
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RealType smallestDiff = HONKING_LARGE_VALUE; |
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RealType diff; |
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pair<RealType,RealType> bestPair = make_pair(1.0, 1.0); |
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vector<pair<RealType,RealType> >::iterator rpi; |
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RealType diff(0.0); |
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> |
std::pair<RealType,RealType> bestPair = std::make_pair(1.0, 1.0); |
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> |
std::vector<std::pair<RealType,RealType> >::iterator rpi; |
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for (rpi = rps.begin(); rpi != rps.end(); ++rpi) { |
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r1 = (*rpi).first; |
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r2 = (*rpi).second; |
