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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] 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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/* Calculates Angle(R) for DirectionalAtoms*/ |
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#include <algorithm> |
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#include <fstream> |
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#include "applications/staticProps/AngleR.hpp" |
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#include "utils/simError.h" |
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#include "utils/NumericConstant.hpp" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "brains/Thermo.hpp" |
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#include <math.h> |
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|
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namespace OpenMD { |
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|
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|
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AngleR::AngleR(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){ |
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|
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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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|
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deltaR_ = len_ /nRBins_; |
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|
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histogram_.resize(nRBins_); |
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count_.resize(nRBins_); |
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avgAngleR_.resize(nRBins_); |
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setOutputName(getPrefix(filename) + ".AngleR"); |
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} |
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|
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|
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void AngleR::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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std::fill(avgAngleR_.begin(), avgAngleR_.end(), 0.0); |
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std::fill(histogram_.begin(), histogram_.end(), 0.0); |
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std::fill(count_.begin(), count_.end(), 0); |
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|
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for (int istep = 0; istep < nFrames; istep += step_) { |
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|
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int i; |
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StuntDouble* sd; |
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reader.readFrame(istep); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Thermo thermo(info_); |
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Vector3d CenterOfMass = thermo.getCom(); |
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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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//determine which atom belongs to which slice |
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for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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Vector3d pos = sd->getPos(); |
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Vector3d r1 = CenterOfMass - pos; |
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// only do this if the stunt double actually has a vector associated |
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// with it |
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if (sd->isDirectional()) { |
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Vector3d dipole = sd->getA().getColumn(2); |
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// std::cerr << "pos = " << pos << " dipole = " << dipole << "\n"; |
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RealType distance = r1.length(); |
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|
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dipole.normalize(); |
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r1.normalize(); |
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RealType cosangle = dot(r1, dipole); |
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|
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if (distance < len_) { |
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int whichBin = int(distance / deltaR_); |
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histogram_[whichBin] += cosangle; |
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count_[whichBin] += 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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} |
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|
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processHistogram(); |
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writeAngleR(); |
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} |
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|
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|
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|
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void AngleR::processHistogram() { |
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|
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for(unsigned int i = 0 ; i < histogram_.size(); ++i){ |
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|
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if (count_[i] > 0) |
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avgAngleR_[i] += histogram_[i] / count_[i]; |
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else |
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avgAngleR_[i] = 0.0; |
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|
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std::cerr << " count = " << count_[i] << " avgAngle = " << avgAngleR_[i] << "\n"; |
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} |
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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 AngleR::writeAngleR() { |
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std::ofstream rdfStream(outputFilename_.c_str()); |
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if (rdfStream.is_open()) { |
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rdfStream << "#radial density function Angle(r)\n"; |
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rdfStream << "#r\tcorrValue\n"; |
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for (unsigned int i = 0; i < avgAngleR_.size(); ++i) { |
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RealType r = deltaR_ * (i + 0.5); |
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rdfStream << r << "\t" << avgAngleR_[i] << "\n"; |
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} |
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|
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} else { |
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|
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sprintf(painCave.errMsg, "AngleR: 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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|
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rdfStream.close(); |
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} |
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|
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} |
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|
