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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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*/ |
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|
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|
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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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|
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RNEMDZ::RNEMDZ(SimInfo* info, const std::string& filename, |
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const std::string& sele, int nzbins) |
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: SlabStatistics(info, filename, sele, nzbins) { |
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|
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setOutputName(getPrefix(filename) + ".rnemdZ"); |
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|
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temperature = new OutputData; |
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temperature->units = "K"; |
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temperature->title = "Temperature"; |
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temperature->dataType = odtReal; |
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temperature->dataHandling = odhAverage; |
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temperature->accumulator.reserve(nBins_); |
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for (int i = 0; i < nBins_; i++) |
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temperature->accumulator.push_back( new Accumulator() ); |
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data_.push_back(temperature); |
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|
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velocity = new OutputData; |
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velocity->units = "angstroms/fs"; |
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velocity->title = "Velocity"; |
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velocity->dataType = odtVector3; |
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velocity->dataHandling = odhAverage; |
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velocity->accumulator.reserve(nBins_); |
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for (int i = 0; i < nBins_; i++) |
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velocity->accumulator.push_back( new VectorAccumulator() ); |
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data_.push_back(velocity); |
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|
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density = new OutputData; |
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density->units = "g cm^-3"; |
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density->title = "Density"; |
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density->dataType = odtReal; |
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density->dataHandling = odhAverage; |
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density->accumulator.reserve(nBins_); |
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for (int i = 0; i < nBins_; i++) |
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density->accumulator.push_back( new Accumulator() ); |
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data_.push_back(density); |
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} |
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|
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void RNEMDZ::processFrame(int istep) { |
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RealType z; |
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|
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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> binP(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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|
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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->updateAtomVel(); |
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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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// loop over the selected atoms: |
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|
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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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binMass[bin] += m; |
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binP[bin] += m * 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 (int i = 0; i < nBins_; i++) { |
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|
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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 = binP[i] / binMass[i]; |
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|
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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) |
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: ShellStatistics(info, filename, sele, nrbins) { |
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|
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|
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setOutputName(getPrefix(filename) + ".rnemdR"); |
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|
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temperature = new OutputData; |
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temperature->units = "K"; |
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temperature->title = "Temperature"; |
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temperature->dataType = odtReal; |
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temperature->dataHandling = odhAverage; |
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temperature->accumulator.reserve(nBins_); |
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for (int i = 0; i < nBins_; i++) |
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temperature->accumulator.push_back( new Accumulator() ); |
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data_.push_back(temperature); |
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|
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angularVelocity = new OutputData; |
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angularVelocity->units = "angstroms^2/fs"; |
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angularVelocity->title = "Angular Velocity"; |
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angularVelocity->dataType = odtVector3; |
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angularVelocity->dataHandling = odhAverage; |
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angularVelocity->accumulator.reserve(nBins_); |
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for (int i = 0; i < nBins_; i++) |
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angularVelocity->accumulator.push_back( new VectorAccumulator() ); |
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data_.push_back(angularVelocity); |
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|
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density = new OutputData; |
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density->units = "g cm^-3"; |
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density->title = "Density"; |
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density->dataType = odtReal; |
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density->dataHandling = odhAverage; |
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density->accumulator.reserve(nBins_); |
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for (int i = 0; i < nBins_; i++) |
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density->accumulator.push_back( new Accumulator() ); |
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data_.push_back(density); |
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} |
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|
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|
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void RNEMDR::processFrame(int istep) { |
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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<Mat3x3d> binI(nBins_); |
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vector<Vector3d> binL(nBins_, V3Zero); |
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vector<RealType> binKE(nBins_, 0.0); |
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vector<int> binDof(nBins_, 0); |
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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->updateAtomVel(); |
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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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// loop over the selected atoms: |
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|
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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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int bin = getBin( sd->getPos() ); |
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|
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if (bin >= 0 && bin < nBins_) { |
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|
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Vector3d rPos = sd->getPos() - coordinateOrigin_; |
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Vector3d vel = sd->getVel(); |
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RealType m = sd->getMass(); |
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Vector3d L = m * cross(rPos, vel); |
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Mat3x3d I(0.0); |
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I = outProduct(rPos, rPos) * m; |
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RealType r2 = rPos.lengthSquare(); |
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I(0, 0) += m * r2; |
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I(1, 1) += m * r2; |
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I(2, 2) += m * r2; |
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|
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binMass[bin] += m; |
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binI[bin] += I; |
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binL[bin] += L; |
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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 Ia = 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] / Ia(j, j) + |
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angMom[k] * angMom[k] / Ia(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] / Ia(0, 0) + |
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angMom[1] * angMom[1] / Ia(1, 1) + |
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angMom[2] * angMom[2] / Ia(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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|
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for (int i = 0; i < nBins_; i++) { |
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RealType rinner = (RealType)i * binWidth_; |
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RealType router = (RealType)(i+1) * binWidth_; |
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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] * 3.0 * PhysicalConstants::densityConvert |
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/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3))); |
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|
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Vector3d omega = binI[i].inverse() * binL[i]; |
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|
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dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp); |
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dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[i])->add(omega); |
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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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|
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void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) { |
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} |
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|
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RNEMDRTheta::RNEMDRTheta(SimInfo* info, const std::string& filename, |
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const std::string& sele, int nrbins, int nangleBins) |
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: ShellStatistics(info, filename, sele, nrbins), nAngleBins_(nangleBins) { |
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|
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Globals* simParams = info->getSimParams(); |
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RNEMDParameters* rnemdParams = simParams->getRNEMDParameters(); |
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bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector(); |
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|
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if (hasAngularMomentumFluxVector) { |
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std::vector<RealType> amf = rnemdParams->getAngularMomentumFluxVector(); |
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if (amf.size() != 3) { |
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sprintf(painCave.errMsg, |
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"RNEMDRTheta: Incorrect number of parameters specified for angularMomentumFluxVector.\n" |
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"\tthere should be 3 parameters, but %lu were specified.\n", |
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amf.size()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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fluxVector_.x() = amf[0]; |
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fluxVector_.y() = amf[1]; |
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fluxVector_.z() = amf[2]; |
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} else { |
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|
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std::string fluxStr = rnemdParams->getFluxType(); |
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if (fluxStr.find("Lx") != std::string::npos) { |
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fluxVector_ = V3X; |
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} else if (fluxStr.find("Ly") != std::string::npos) { |
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fluxVector_ = V3Y; |
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} else { |
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fluxVector_ = V3Z; |
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} |
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} |
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|
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fluxVector_.normalize(); |
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|
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setOutputName(getPrefix(filename) + ".rnemdRTheta"); |
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|
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angularVelocity = new OutputData; |
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angularVelocity->units = "angstroms^2/fs"; |
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angularVelocity->title = "Angular Velocity"; |
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angularVelocity->dataType = odtArray2d; |
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angularVelocity->dataHandling = odhAverage; |
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angularVelocity->accumulatorArray2d.reserve(nBins_); |
| 364 |
for (int i = 0; i < nBins_; i++) { |
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angularVelocity->accumulatorArray2d[i].reserve(nAngleBins_); |
| 366 |
for (int j = 0 ; j < nAngleBins_; j++) { |
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angularVelocity->accumulatorArray2d[i][j] = new Accumulator(); |
| 368 |
} |
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} |
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data_.push_back(angularVelocity); |
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|
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} |
| 373 |
|
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|
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std::pair<int,int> RNEMDRTheta::getBins(Vector3d pos) { |
| 376 |
std::pair<int,int> result; |
| 377 |
|
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Vector3d rPos = pos - coordinateOrigin_; |
| 379 |
RealType cosAngle= dot(rPos, fluxVector_) / rPos.length(); |
| 380 |
|
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result.first = int(rPos.length() / binWidth_); |
| 382 |
result.second = int( (nAngleBins_ - 1) * 0.5 * (cosAngle + 1.0) ); |
| 383 |
return result; |
| 384 |
} |
| 385 |
|
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void RNEMDRTheta::processStuntDouble(StuntDouble* sd, int bin) { |
| 387 |
} |
| 388 |
|
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void RNEMDRTheta::processFrame(int istep) { |
| 390 |
|
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Molecule* mol; |
| 392 |
RigidBody* rb; |
| 393 |
StuntDouble* sd; |
| 394 |
SimInfo::MoleculeIterator mi; |
| 395 |
Molecule::RigidBodyIterator rbIter; |
| 396 |
int i; |
| 397 |
|
| 398 |
vector<vector<Mat3x3d> > binI; |
| 399 |
vector<vector<Vector3d> > binL; |
| 400 |
vector<vector<int> > binCount; |
| 401 |
|
| 402 |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 403 |
mol = info_->nextMolecule(mi)) { |
| 404 |
|
| 405 |
// change the positions of atoms which belong to the rigidbodies |
| 406 |
|
| 407 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 408 |
rb = mol->nextRigidBody(rbIter)) { |
| 409 |
rb->updateAtomVel(); |
| 410 |
} |
| 411 |
} |
| 412 |
|
| 413 |
if (evaluator_.isDynamic()) { |
| 414 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 415 |
} |
| 416 |
|
| 417 |
// loop over the selected atoms: |
| 418 |
|
| 419 |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 420 |
sd = seleMan_.nextSelected(i)) { |
| 421 |
|
| 422 |
// figure out where that object is: |
| 423 |
std::pair<int,int> bins = getBins( sd->getPos() ); |
| 424 |
|
| 425 |
if (bins.first >= 0 && bins.first < nBins_) { |
| 426 |
if (bins.second >= 0 && bins.second < nAngleBins_) { |
| 427 |
|
| 428 |
Vector3d rPos = sd->getPos() - coordinateOrigin_; |
| 429 |
Vector3d vel = sd->getVel(); |
| 430 |
RealType m = sd->getMass(); |
| 431 |
Vector3d L = m * cross(rPos, vel); |
| 432 |
Mat3x3d I(0.0); |
| 433 |
I = outProduct(rPos, rPos) * m; |
| 434 |
RealType r2 = rPos.lengthSquare(); |
| 435 |
I(0, 0) += m * r2; |
| 436 |
I(1, 1) += m * r2; |
| 437 |
I(2, 2) += m * r2; |
| 438 |
|
| 439 |
binI[bins.first][bins.second] += I; |
| 440 |
binL[bins.first][bins.second] += L; |
| 441 |
binCount[bins.first][bins.second]++; |
| 442 |
} |
| 443 |
} |
| 444 |
} |
| 445 |
|
| 446 |
|
| 447 |
for (int i = 0; i < nBins_; i++) { |
| 448 |
for (int j = 0; j < nAngleBins_; j++) { |
| 449 |
|
| 450 |
if (binCount[i][j] > 0) { |
| 451 |
Vector3d omega = binI[i][j].inverse() * binL[i][j]; |
| 452 |
RealType omegaProj = dot(omega, fluxVector_); |
| 453 |
|
| 454 |
dynamic_cast<Accumulator *>(angularVelocity->accumulatorArray2d[i][j])->add(omegaProj); |
| 455 |
} |
| 456 |
} |
| 457 |
} |
| 458 |
} |
| 459 |
|
| 460 |
void RNEMDRTheta::writeOutput() { |
| 461 |
|
| 462 |
vector<OutputData*>::iterator i; |
| 463 |
OutputData* outputData; |
| 464 |
|
| 465 |
ofstream outStream(outputFilename_.c_str()); |
| 466 |
if (outStream.is_open()) { |
| 467 |
|
| 468 |
//write title |
| 469 |
outStream << "# SPATIAL STATISTICS\n"; |
| 470 |
outStream << "#"; |
| 471 |
|
| 472 |
for(outputData = beginOutputData(i); outputData; |
| 473 |
outputData = nextOutputData(i)) { |
| 474 |
outStream << "\t" << outputData->title << |
| 475 |
"(" << outputData->units << ")"; |
| 476 |
// add some extra tabs for column alignment |
| 477 |
if (outputData->dataType == odtVector3) outStream << "\t\t"; |
| 478 |
} |
| 479 |
|
| 480 |
outStream << std::endl; |
| 481 |
|
| 482 |
outStream.precision(8); |
| 483 |
|
| 484 |
for (int j = 0; j < nBins_; j++) { |
| 485 |
|
| 486 |
int counts = counts_->accumulator[j]->count(); |
| 487 |
|
| 488 |
if (counts > 0) { |
| 489 |
for(outputData = beginOutputData(i); outputData; |
| 490 |
outputData = nextOutputData(i)) { |
| 491 |
|
| 492 |
int n = outputData->accumulator[j]->count(); |
| 493 |
if (n != 0) { |
| 494 |
writeData( outStream, outputData, j ); |
| 495 |
} |
| 496 |
} |
| 497 |
outStream << std::endl; |
| 498 |
} |
| 499 |
} |
| 500 |
} |
| 501 |
} |
| 502 |
} |
| 503 |
|
