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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 <algorithm> |
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#include <fstream> |
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#include "applications/staticProps/GofRAngle.hpp" |
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#include "primitives/Atom.hpp" |
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#include "types/MultipoleAdapter.hpp" |
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#include "utils/simError.h" |
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|
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namespace OpenMD { |
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|
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GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, |
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const std::string& sele1, |
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const std::string& sele2, |
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RealType len, int nrbins, int nangleBins) |
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: RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins), |
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len_(len), nRBins_(nrbins), |
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doSele3_(false), seleMan3_(info), evaluator3_(info) { |
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|
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deltaR_ = len_ /(double) nRBins_; |
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deltaCosAngle_ = 2.0 / (double)nAngleBins_; |
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histogram_.resize(nRBins_); |
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avgGofr_.resize(nRBins_); |
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for (int i = 0 ; i < nRBins_; ++i) { |
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histogram_[i].resize(nAngleBins_); |
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avgGofr_[i].resize(nAngleBins_); |
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} |
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} |
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|
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GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, |
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const std::string& sele1, |
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const std::string& sele2, |
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const std::string& sele3, |
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RealType len, int nrbins, int nangleBins) |
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: RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins), |
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len_(len), nRBins_(nrbins), doSele3_(true), selectionScript3_(sele3), |
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seleMan3_(info), evaluator3_(info) { |
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|
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deltaR_ = len_ /(double) nRBins_; |
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deltaCosAngle_ = 2.0 / (double)nAngleBins_; |
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histogram_.resize(nRBins_); |
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avgGofr_.resize(nRBins_); |
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for (int i = 0 ; i < nRBins_; ++i) { |
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histogram_[i].resize(nAngleBins_); |
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avgGofr_[i].resize(nAngleBins_); |
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} |
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|
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evaluator3_.loadScriptString(sele3); |
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if (!evaluator3_.isDynamic()) { |
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seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
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} |
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|
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} |
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|
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void GofRAngle::processNonOverlapping( SelectionManager& sman1, |
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SelectionManager& sman2) { |
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StuntDouble* sd1; |
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StuntDouble* sd2; |
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StuntDouble* sd3; |
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int i; |
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int j; |
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int k; |
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|
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// This is the same as a non-overlapping pairwise loop structure: |
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// for (int i = 0; i < ni ; ++i ) { |
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// for (int j = 0; j < nj; ++j) {} |
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// } |
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|
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if (doSele3_) { |
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if (evaluator3_.isDynamic()) { |
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seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
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} |
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if (sman1.getSelectionCount() != seleMan3_.getSelectionCount() ) { |
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RadialDistrFunc::processNonOverlapping( sman1, sman2 ); |
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} |
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|
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for (sd1 = sman1.beginSelected(i), sd3 = seleMan3_.beginSelected(k); |
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sd1 != NULL && sd3 != NULL; |
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sd1 = sman1.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) { |
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for (sd2 = sman2.beginSelected(j); sd2 != NULL; |
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sd2 = sman2.nextSelected(j)) { |
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collectHistogram(sd1, sd2, sd3); |
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} |
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} |
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} else { |
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RadialDistrFunc::processNonOverlapping( sman1, sman2 ); |
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} |
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} |
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|
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void GofRAngle::processOverlapping( SelectionManager& sman) { |
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StuntDouble* sd1; |
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StuntDouble* sd2; |
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StuntDouble* sd3; |
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int i; |
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int j; |
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int k; |
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|
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// This is the same as a pairwise loop structure: |
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// for (int i = 0; i < n-1 ; ++i ) { |
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// for (int j = i + 1; j < n; ++j) {} |
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// } |
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|
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if (doSele3_) { |
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if (evaluator3_.isDynamic()) { |
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seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
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} |
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if (sman.getSelectionCount() != seleMan3_.getSelectionCount() ) { |
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RadialDistrFunc::processOverlapping( sman); |
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} |
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for (sd1 = sman.beginSelected(i), sd3 = seleMan3_.beginSelected(k); |
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sd1 != NULL && sd3 != NULL; |
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sd1 = sman.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) { |
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for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; |
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sd2 = sman.nextSelected(j)) { |
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collectHistogram(sd1, sd2, sd3); |
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} |
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} |
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} else { |
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RadialDistrFunc::processOverlapping( sman); |
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} |
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} |
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|
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|
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void GofRAngle::preProcess() { |
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for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
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std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
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} |
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} |
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|
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void GofRAngle::initializeHistogram() { |
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npairs_ = 0; |
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for (unsigned int i = 0; i < histogram_.size(); ++i){ |
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std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
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} |
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} |
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|
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void GofRAngle::processHistogram() { |
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int nPairs = getNPairs(); |
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RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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RealType pairDensity = nPairs /volume; |
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RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
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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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RealType rLower = i * deltaR_; |
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RealType rUpper = rLower + deltaR_; |
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RealType volSlice = ( rUpper * rUpper * rUpper ) - |
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( rLower * rLower * rLower ); |
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RealType nIdeal = volSlice * pairConstant; |
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|
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for (unsigned int j = 0; j < histogram_[i].size(); ++j){ |
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avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
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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 GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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|
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if (sd1 == sd2) { |
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return; |
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} |
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Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos2 - pos1; |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(r12); |
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|
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RealType distance = r12.length(); |
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int whichRBin = int(distance / deltaR_); |
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|
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if (distance <= len_) { |
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|
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RealType cosAngle = evaluateAngle(sd1, sd2); |
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RealType halfBin = (nAngleBins_ - 1) * 0.5; |
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int whichThetaBin = int(halfBin * (cosAngle + 1.0)); |
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++histogram_[whichRBin][whichThetaBin]; |
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|
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++npairs_; |
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} |
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} |
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|
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void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2, |
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StuntDouble* sd3) { |
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|
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if (sd1 == sd2) { |
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return; |
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} |
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|
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Vector3d p1 = sd1->getPos(); |
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Vector3d p3 = sd3->getPos(); |
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|
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Vector3d c = 0.5 * (p1 + p3); |
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Vector3d r13 = p3 - p1; |
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|
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Vector3d r12 = sd2->getPos() - c; |
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|
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if (usePeriodicBoundaryConditions_) { |
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currentSnapshot_->wrapVector(r12); |
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currentSnapshot_->wrapVector(r13); |
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} |
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|
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RealType distance = r12.length(); |
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int whichRBin = int(distance / deltaR_); |
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|
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if (distance <= len_) { |
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|
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RealType cosAngle = evaluateAngle(sd1, sd2, sd3); |
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RealType halfBin = (nAngleBins_ - 1) * 0.5; |
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int whichThetaBin = int(halfBin * (cosAngle + 1.0)); |
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++histogram_[whichRBin][whichThetaBin]; |
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|
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++npairs_; |
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} |
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} |
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|
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void GofRAngle::writeRdf() { |
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std::ofstream rdfStream(outputFilename_.c_str()); |
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if (rdfStream.is_open()) { |
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rdfStream << "#radial distribution function\n"; |
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rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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rdfStream << "selection2: (" << selectionScript2_ << ")"; |
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if (doSele3_) { |
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rdfStream << "\tselection3: (" << selectionScript3_ << ")\n"; |
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} else { |
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rdfStream << "\n"; |
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} |
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rdfStream << "#nRBins = " << nRBins_ << "\tmaxLen = " |
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<< len_ << "\tdeltaR = " << deltaR_ <<"\n"; |
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rdfStream << "#nAngleBins =" << nAngleBins_ << "\tdeltaCosAngle = " |
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<< deltaCosAngle_ << "\n"; |
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for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
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// RealType r = deltaR_ * (i + 0.5); |
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|
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for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { |
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// RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; |
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rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; |
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} |
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|
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rdfStream << "\n"; |
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} |
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|
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} else { |
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sprintf(painCave.errMsg, "GofRAngle: 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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rdfStream.close(); |
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} |
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|
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RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
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Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos2 - pos1; |
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|
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(r12); |
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|
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r12.normalize(); |
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|
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Vector3d vec; |
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|
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if (!sd1->isDirectional()) { |
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sprintf(painCave.errMsg, |
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"GofRTheta: attempted to use a non-directional object: %s\n", |
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sd1->getType().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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if (sd1->isAtom()) { |
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AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
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MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
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|
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if (ma1.isDipole() ) |
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vec = sd1->getDipole(); |
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else |
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vec = sd1->getA().transpose() * V3Z; |
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} else { |
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vec = sd1->getA().transpose() * V3Z; |
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} |
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|
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vec.normalize(); |
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|
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return dot(r12, vec); |
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} |
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|
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RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, |
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StuntDouble* sd3) { |
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Vector3d p1 = sd1->getPos(); |
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Vector3d p3 = sd3->getPos(); |
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|
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Vector3d c = 0.5 * (p1 + p3); |
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Vector3d r13 = p3 - p1; |
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|
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Vector3d r12 = sd2->getPos() - c; |
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|
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if (usePeriodicBoundaryConditions_) { |
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currentSnapshot_->wrapVector(r12); |
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currentSnapshot_->wrapVector(r13); |
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} |
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|
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r12.normalize(); |
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r13.normalize(); |
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|
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return dot(r12, r13); |
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} |
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|
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RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
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Vector3d v1, v2; |
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|
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if (!sd1->isDirectional()) { |
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sprintf(painCave.errMsg, |
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"GofROmega: attempted to use a non-directional object: %s\n", |
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sd1->getType().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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if (sd1->isAtom()){ |
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AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
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MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
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if (ma1.isDipole() ) |
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v1 = sd1->getDipole(); |
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else |
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v1 = sd1->getA().transpose() * V3Z; |
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} else { |
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v1 = sd1->getA().transpose() * V3Z; |
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} |
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|
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if (!sd2->isDirectional()) { |
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sprintf(painCave.errMsg, |
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"GofROmega attempted to use a non-directional object: %s\n", |
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sd2->getType().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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if (sd2->isAtom()) { |
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AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType(); |
| 383 |
MultipoleAdapter ma2 = MultipoleAdapter(atype2); |
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|
| 385 |
if (ma2.isDipole() ) |
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v2 = sd2->getDipole(); |
| 387 |
else |
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v2 = sd2->getA().transpose() * V3Z; |
| 389 |
} else { |
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v2 = sd2->getA().transpose() * V3Z; |
| 391 |
} |
| 392 |
|
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v1.normalize(); |
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v2.normalize(); |
| 395 |
return dot(v1, v2); |
| 396 |
} |
| 397 |
|
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RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, |
| 399 |
StuntDouble* sd3) { |
| 400 |
|
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Vector3d v1; |
| 402 |
Vector3d v2; |
| 403 |
|
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v1 = sd3->getPos() - sd1->getPos(); |
| 405 |
if (usePeriodicBoundaryConditions_) |
| 406 |
currentSnapshot_->wrapVector(v1); |
| 407 |
|
| 408 |
if (!sd2->isDirectional()) { |
| 409 |
sprintf(painCave.errMsg, |
| 410 |
"GofROmega: attempted to use a non-directional object: %s\n", |
| 411 |
sd2->getType().c_str()); |
| 412 |
painCave.isFatal = 1; |
| 413 |
simError(); |
| 414 |
} |
| 415 |
|
| 416 |
if (sd2->isAtom()) { |
| 417 |
AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType(); |
| 418 |
MultipoleAdapter ma2 = MultipoleAdapter(atype2); |
| 419 |
|
| 420 |
if (ma2.isDipole() ) |
| 421 |
v2 = sd2->getDipole(); |
| 422 |
else |
| 423 |
v2 = sd2->getA().transpose() * V3Z; |
| 424 |
} else { |
| 425 |
v2 = sd2->getA().transpose() * V3Z; |
| 426 |
} |
| 427 |
|
| 428 |
v1.normalize(); |
| 429 |
v2.normalize(); |
| 430 |
return dot(v1, v2); |
| 431 |
} |
| 432 |
} |
| 433 |
|
| 434 |
|
