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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, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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#include <algorithm> |
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#include <functional> |
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#include "applications/staticProps/ObjectCount.hpp" |
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#include "utils/simError.h" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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namespace OpenMD { |
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ObjectCount::ObjectCount(SimInfo* info, const std::string& filename, |
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const std::string& sele) |
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: StaticAnalyser(info, filename), selectionScript_(sele), |
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evaluator_(info), seleMan_(info) { |
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setOutputName(getPrefix(filename) + ".counts"); |
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evaluator_.loadScriptString(sele); |
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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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void ObjectCount::process() { |
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Molecule* mol; |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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counts_.clear(); |
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counts_.resize(10, 0); |
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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unsigned long int nsum = 0; |
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unsigned long int n2sum = 0; |
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for (int i = 0; i < nFrames; i += step_) { |
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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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//change the positions of atoms which belong to the rigidbodies |
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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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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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int count = seleMan_.getSelectionCount(); |
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if (counts_.size() <= count) { |
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counts_.resize(count, 0); |
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} |
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counts_[count]++; |
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nsum += count; |
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n2sum += count * count; |
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} |
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int nProcessed = nFrames /step_; |
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nAvg = nsum / nProcessed; |
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n2Avg = n2sum / nProcessed; |
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sDev = sqrt(n2Avg - nAvg*nAvg); |
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writeCounts(); |
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} |
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void ObjectCount::writeCounts() { |
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std::ofstream ofs(outputFilename_.c_str(), std::ios::binary); |
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if (ofs.is_open()) { |
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ofs << "#counts\n"; |
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ofs << "#selection: (" << selectionScript_ << ")\n"; |
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ofs << "# <N> = "<< nAvg << "\n"; |
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ofs << "# <N^2> = " << n2Avg << "\n"; |
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ofs << "# sqrt(<N^2> - <N>^2) = " << sDev << "\n"; |
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ofs << "# N\tcounts[N]\n"; |
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for (int i = 0; i < counts_.size(); ++i) { |
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ofs << i << "\t" << counts_[i] << "\n"; |
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} |
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} else { |
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sprintf(painCave.errMsg, "ObjectCount: unable to open %s\n", outputFilename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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ofs.close(); |
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} |
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} |
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