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#include <algorithm> |
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#include <fstream> |
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#include "applications/staticProps/RNEMDStats.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/PhysicalConstants.hpp" |
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|
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namespace OpenMD { |
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data_.push_back(density); |
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} |
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|
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void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) { |
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RealType mass = sd->getMass(); |
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Vector3d pos = sd->getPos(); |
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Vector3d vel = sd->getVel(); |
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RealType KE = 0.5 * (mass * vel.lengthSquare()); |
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int dof = 3; |
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void RNEMDZ::processFrame(int istep) { |
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RealType z; |
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|
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if (sd->isDirectional()) { |
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Vector3d angMom = sd->getJ(); |
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Mat3x3d I = sd->getI(); |
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if (sd->isLinear()) { |
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int i = sd->linearAxis(); |
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int j = (i + 1) % 3; |
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int k = (i + 2) % 3; |
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KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) + |
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angMom[k] * angMom[k] / I(k, k)); |
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dof += 2; |
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} else { |
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KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) + |
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angMom[1] * angMom[1] / I(1, 1) + |
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angMom[2] * angMom[2] / I(2, 2)); |
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dof += 3; |
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hmat_ = currentSnapshot_->getHmat(); |
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for (int i = 0; i < nBins_; i++) { |
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z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat_(2,2); |
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dynamic_cast<Accumulator*>(z_->accumulator[i])->add(z); |
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} |
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volume_ = currentSnapshot_->getVolume(); |
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|
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|
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Molecule* mol; |
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RigidBody* rb; |
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StuntDouble* sd; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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int i; |
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|
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vector<RealType> binMass(nBins_, 0.0); |
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vector<Vector3d> binVel(nBins_, V3Zero); |
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vector<RealType> binKE(nBins_, 0.0); |
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vector<unsigned int> binDof(nBins_, 0); |
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vector<unsigned int> binCount(nBins_, 0); |
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|
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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|
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// change the positions of atoms which belong to the rigidbodies |
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|
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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|
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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|
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RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb * |
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PhysicalConstants::energyConvert); |
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RealType den = mass * nBins_ * PhysicalConstants::densityConvert / volume_; |
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// loop over the selected atoms: |
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|
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dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp); |
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dynamic_cast<VectorAccumulator *>(velocity->accumulator[bin])->add(vel); |
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dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den); |
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for (sd = seleMan_.beginSelected(i); sd != NULL; |
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sd = seleMan_.nextSelected(i)) { |
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|
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// figure out where that object is: |
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Vector3d pos = sd->getPos(); |
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Vector3d vel = sd->getVel(); |
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RealType m = sd->getMass(); |
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|
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int bin = getBin(pos); |
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|
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binCount[bin] += 1; |
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|
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binMass[bin] += m; |
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binVel[bin] += vel; |
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binKE[bin] += 0.5 * (m * vel.lengthSquare()); |
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binDof[bin] += 3; |
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|
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if (sd->isDirectional()) { |
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Vector3d angMom = sd->getJ(); |
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Mat3x3d I = sd->getI(); |
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if (sd->isLinear()) { |
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int i = sd->linearAxis(); |
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int j = (i + 1) % 3; |
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int k = (i + 2) % 3; |
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binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) + |
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angMom[k] * angMom[k] / I(k, k)); |
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binDof[bin] += 2; |
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} else { |
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binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) + |
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angMom[1] * angMom[1] / I(1, 1) + |
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angMom[2] * angMom[2] / I(2, 2)); |
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binDof[bin] += 3; |
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} |
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} |
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} |
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|
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for (unsigned int i = 0; i < nBins_; i++) { |
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if (binDof[i] > 0) { |
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RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb * |
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PhysicalConstants::energyConvert); |
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RealType den = binMass[i] * nBins_ * PhysicalConstants::densityConvert |
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/ volume_; |
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Vector3d vel = binVel[i] / RealType(binCount[i]); |
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dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp); |
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dynamic_cast<VectorAccumulator *>(velocity->accumulator[i])->add(vel); |
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dynamic_cast<Accumulator *>(density->accumulator[i])->add(den); |
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dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1); |
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} |
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} |
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} |
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|
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void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) { |
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} |
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|
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RNEMDR::RNEMDR(SimInfo* info, const std::string& filename, |
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const std::string& sele, int nrbins) |
