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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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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "applications/staticProps/SpatialStatistics.hpp" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#ifdef _MSC_VER |
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#define isnan(x) _isnan((x)) |
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#define isinf(x) (!_finite(x) && !_isnan(x)) |
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#endif |
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|
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namespace OpenMD { |
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|
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SpatialStatistics::SpatialStatistics(SimInfo* info, const string& filename, |
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const string& sele, int nbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), |
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seleMan_(info), nBins_(nbins){ |
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|
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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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// Pre-load an OutputData for the count of objects: |
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counts_ = new OutputData; |
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counts_->units = "objects"; |
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counts_->title = "Objects"; |
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counts_->dataType = odtReal; |
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counts_->dataHandling = odhTotal; |
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counts_->accumulator.reserve(nBins_); |
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for (int i = 0; i < nBins_; i++) |
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counts_->accumulator.push_back( new Accumulator() ); |
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|
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setOutputName(getPrefix(filename) + ".spst"); |
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} |
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|
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SpatialStatistics::~SpatialStatistics() { |
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vector<OutputData*>::iterator i; |
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OutputData* outputData; |
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|
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for(outputData = beginOutputData(i); outputData; |
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outputData = nextOutputData(i)) { |
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delete outputData; |
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} |
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data_.clear(); |
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|
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delete counts_; |
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} |
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|
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|
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void SpatialStatistics::process() { |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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nProcessed_ = nFrames/step_; |
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|
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for (int istep = 0; istep < nFrames; istep += step_) { |
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reader.readFrame(istep); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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processFrame(istep); |
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} |
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writeOutput(); |
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} |
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|
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|
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void SpatialStatistics::processFrame(int istep) { |
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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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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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// 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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|
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Vector3d pos = sd->getPos(); |
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|
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int bin = getBin(pos); |
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|
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// forward the work of statistics on to the subclass: |
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|
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processStuntDouble( sd, bin ); |
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|
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dynamic_cast<Accumulator *>(counts_->accumulator[bin])->add(1); |
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} |
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} |
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|
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|
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void SpatialStatistics::writeOutput() { |
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|
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vector<OutputData*>::iterator i; |
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OutputData* outputData; |
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|
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ofstream outStream(outputFilename_.c_str()); |
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if (outStream.is_open()) { |
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|
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//write title |
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outStream << "# SPATIAL STATISTICS\n"; |
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outStream << "#"; |
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|
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for(outputData = beginOutputData(i); outputData; |
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outputData = nextOutputData(i)) { |
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outStream << "\t" << outputData->title << |
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"(" << outputData->units << ")"; |
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// add some extra tabs for column alignment |
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if (outputData->dataType == odtVector3) outStream << "\t\t"; |
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} |
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|
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outStream << std::endl; |
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|
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outStream.precision(8); |
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|
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for (int j = 0; j < nBins_; j++) { |
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|
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int counts = counts_->accumulator[j]->count(); |
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|
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if (counts > 0) { |
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for(outputData = beginOutputData(i); outputData; |
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outputData = nextOutputData(i)) { |
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|
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int n = outputData->accumulator[j]->count(); |
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if (n != 0) { |
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writeData( outStream, outputData, j ); |
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} |
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} |
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outStream << std::endl; |
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} |
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} |
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|
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outStream << "#######################################################\n"; |
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outStream << "# 95% confidence intervals in those quantities follow:\n"; |
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outStream << "#######################################################\n"; |
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|
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for (int j = 0; j < nBins_; j++) { |
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int counts = counts_->accumulator[j]->count(); |
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if (counts > 0) { |
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|
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outStream << "#"; |
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for(outputData = beginOutputData(i); outputData; |
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outputData = nextOutputData(i)) { |
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|
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int n = outputData->accumulator[j]->count(); |
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if (n != 0) { |
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writeErrorBars( outStream, outputData, j ); |
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} |
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} |
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outStream << std::endl; |
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} |
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} |
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|
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outStream.flush(); |
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outStream.close(); |
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|
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} else { |
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sprintf(painCave.errMsg, "SpatialStatistics: unable to open %s\n", |
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outputFilename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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|
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void SpatialStatistics::writeData(ostream& os, OutputData* dat, |
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unsigned int bin) { |
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assert(int(bin) < nBins_); |
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int n = dat->accumulator[bin]->count(); |
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if (n == 0) return; |
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|
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if( dat->dataType == odtReal ) { |
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RealType r; |
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dynamic_cast<Accumulator*>(dat->accumulator[bin])->getAverage(r); |
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if (isinf(r) || isnan(r) ) { |
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sprintf( painCave.errMsg, |
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"SpatialStatistics detected a numerical error writing:\n" |
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"\t%s for bin %u", |
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dat->title.c_str(), bin); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (dat->dataHandling == odhTotal) r *= dat->accumulator[bin]->count(); |
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os << "\t" << r; |
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|
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} else if ( dat->dataType == odtVector3 ) { |
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Vector3d v; |
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dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getAverage(v); |
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if (isinf(v[0]) || isnan(v[0]) || |
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isinf(v[1]) || isnan(v[1]) || |
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isinf(v[2]) || isnan(v[2]) ) { |
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sprintf( painCave.errMsg, |
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"SpatialStatistics detected a numerical error writing:\n" |
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"\t%s for bin %u", |
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dat->title.c_str(), bin); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (dat->dataHandling == odhTotal) v *= dat->accumulator[bin]->count(); |
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os << "\t" << v[0] << "\t" << v[1] << "\t" << v[2]; |
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} |
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} |
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|
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void SpatialStatistics::writeErrorBars(ostream& os, OutputData* dat, |
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unsigned int bin) { |
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assert(int(bin) < nBins_); |
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int n = dat->accumulator[bin]->count(); |
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if (n == 0) return; |
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|
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if( dat->dataType == odtReal ) { |
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RealType r; |
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dynamic_cast<Accumulator*>(dat->accumulator[bin])->get95percentConfidenceInterval(r); |
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if (isinf(r) || isnan(r) ) { |
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sprintf( painCave.errMsg, |
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"SpatialStatistics detected a numerical error writing:\n" |
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"\tstandard deviation of %s for bin %u", |
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dat->title.c_str(), bin); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (dat->dataHandling == odhTotal) r *= dat->accumulator[bin]->count(); |
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os << "\t" << r; |
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|
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} else if ( dat->dataType == odtVector3 ) { |
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Vector3d v; |
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dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->get95percentConfidenceInterval(v); |
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if (isinf(v[0]) || isnan(v[0]) || |
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isinf(v[1]) || isnan(v[1]) || |
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isinf(v[2]) || isnan(v[2]) ) { |
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sprintf( painCave.errMsg, |
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"SpatialStatistics detected a numerical error writing:\n" |
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"\tstandard deviation of %s for bin %u", |
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dat->title.c_str(), bin); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (dat->dataHandling == odhTotal) v *= dat->accumulator[bin]->count(); |
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os << "\t" << v[0] << "\t" << v[1] << "\t" << v[2]; |
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} |
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} |
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|
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|
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OutputData* SpatialStatistics::beginOutputData(vector<OutputData*>::iterator& i) { |
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i = data_.begin(); |
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return i != data_.end()? *i : NULL; |
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} |
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|
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OutputData* SpatialStatistics::nextOutputData(vector<OutputData*>::iterator& i){ |
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++i; |
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return i != data_.end()? *i: NULL; |
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} |
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|
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|
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SlabStatistics::SlabStatistics(SimInfo* info, const string& filename, |
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const string& sele, int nbins) : |
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SpatialStatistics(info, filename, sele, nbins) { |
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|
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z_ = new OutputData; |
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z_->units = "Angstroms"; |
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z_->title = "Z"; |
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z_->dataType = odtReal; |
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z_->dataHandling = odhAverage; |
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z_->accumulator.reserve(nbins); |
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for (int i = 0; i < nbins; i++) |
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z_->accumulator.push_back( new Accumulator() ); |
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data_.push_back(z_); |
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} |
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|
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SlabStatistics::~SlabStatistics() { |
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} |
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|
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|
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void SlabStatistics::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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SpatialStatistics::processFrame(istep); |
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} |
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|
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int SlabStatistics::getBin(Vector3d pos) { |
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currentSnapshot_->wrapVector(pos); |
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// which bin is this stuntdouble in? |
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// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] |
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// Shift molecules by half a box to have bins start at 0 |
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// The modulo operator is used to wrap the case when we are |
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// beyond the end of the bins back to the beginning. |
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return int(nBins_ * (pos.z() / hmat_(2,2) + 0.5)) % nBins_; |
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} |
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|
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ShellStatistics::ShellStatistics(SimInfo* info, const string& filename, |
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const string& sele, int nbins) : |
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SpatialStatistics(info, filename, sele, nbins), coordinateOrigin_(V3Zero) { |
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|
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binWidth_ = 1.0; |
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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 hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin(); |
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|
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if (hasCoordinateOrigin) { |
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std::vector<RealType> co = rnemdParams->getCoordinateOrigin(); |
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if (co.size() != 3) { |
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sprintf(painCave.errMsg, |
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"RNEMD: Incorrect number of parameters specified for coordinateOrigin.\n" |
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"\tthere should be 3 parameters, but %lu were specified.\n", |
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co.size()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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coordinateOrigin_.x() = co[0]; |
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coordinateOrigin_.y() = co[1]; |
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coordinateOrigin_.z() = co[2]; |
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} else { |
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coordinateOrigin_ = V3Zero; |
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} |
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|
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r_ = new OutputData; |
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r_->units = "Angstroms"; |
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r_->title = "R"; |
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r_->dataType = odtReal; |
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r_->dataHandling = odhAverage; |
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r_->accumulator.reserve(nbins); |
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for (int i = 0; i < nbins; i++) |
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r_->accumulator.push_back( new Accumulator() ); |
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data_.push_back(r_); |
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|
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for (int i = 0; i < nbins; i++) { |
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RealType r = (((RealType)i + 0.5) * binWidth_); |
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dynamic_cast<Accumulator*>(r_->accumulator[i])->add(r); |
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} |
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} |
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|
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ShellStatistics::~ShellStatistics() { |
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} |
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|
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int ShellStatistics::getBin(Vector3d pos) { |
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Vector3d rPos = pos - coordinateOrigin_; |
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return int(rPos.length() / binWidth_); |
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} |
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} |
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|
