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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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* [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012). |
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*/ |
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|
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#include "applications/staticProps/TetrahedralityParamXYZ.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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#include <vector> |
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#include <algorithm> |
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#include <fstream> |
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|
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using namespace std; |
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namespace OpenMD { |
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TetrahedralityParamXYZ::TetrahedralityParamXYZ(SimInfo* info, |
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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 rCut, |
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RealType voxelSize, |
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RealType gaussWidth) |
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: StaticAnalyser(info, filename), |
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selectionScript1_(sele1), selectionScript2_(sele2), |
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seleMan1_(info), seleMan2_(info), evaluator1_(info), evaluator2_(info), |
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rCut_(rCut), voxelSize_(voxelSize), gaussWidth_(gaussWidth) { |
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|
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evaluator1_.loadScriptString(sele1); |
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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evaluator2_.loadScriptString(sele2); |
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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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} |
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|
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Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
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|
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nBins_(0) = int(hmat(0,0) / voxelSize); |
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nBins_(1) = int(hmat(1,1) / voxelSize); |
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nBins_(2) = int(hmat(2,2) / voxelSize); |
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|
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hist_.resize(nBins_(0)); |
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count_.resize(nBins_(0)); |
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for (int i = 0 ; i < nBins_(0); ++i) { |
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hist_[i].resize(nBins_(1)); |
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count_[i].resize(nBins_(1)); |
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for(int j = 0; j < nBins_(1); ++j) { |
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hist_[i][j].resize(nBins_(2)); |
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count_[i][j].resize(nBins_(2)); |
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std::fill(hist_[i][j].begin(), hist_[i][j].end(), 0.0); |
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std::fill(count_[i][j].begin(), count_[i][j].end(), 0.0); |
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|
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} |
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} |
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|
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setOutputName(getPrefix(filename) + ".Qxyz"); |
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} |
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|
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TetrahedralityParamXYZ::~TetrahedralityParamXYZ() { |
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} |
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|
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void TetrahedralityParamXYZ::process() { |
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Molecule* mol; |
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StuntDouble* sd; |
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StuntDouble* sd2; |
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StuntDouble* sdi; |
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StuntDouble* sdj; |
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RigidBody* rb; |
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int myIndex; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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Vector3d vec; |
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Vector3d ri, rj, rk, rik, rkj; |
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RealType r; |
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RealType cospsi; |
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RealType Qk; |
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std::vector<std::pair<RealType,StuntDouble*> > myNeighbors; |
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//std::vector<std::pair<Vector3d, RealType> > qvals; |
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//std::vector<std::pair<Vector3d, RealType> >::iterator qiter; |
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int isd1; |
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int isd2; |
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|
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|
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int kMax = int(5.0 * gaussWidth_ / voxelSize_); |
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int kSqLim = kMax*kMax; |
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cerr << "gw = " << gaussWidth_ << " vS = " << voxelSize_ << " kMax = " |
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<< kMax << " kSqLim = " << kSqLim << "\n"; |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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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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|
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Mat3x3d hmat = currentSnapshot_->getHmat(); |
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Vector3d halfBox = Vector3d(hmat(0,0), hmat(1,1), hmat(2,2)) / 2.0; |
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|
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if (evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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|
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if (evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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} |
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|
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// update the positions of atoms which belong to the rigidbodies |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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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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//qvals.clear(); |
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|
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// outer loop is over the selected StuntDoubles: |
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for (sd = seleMan1_.beginSelected(isd1); sd != NULL; |
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sd = seleMan1_.nextSelected(isd1)) { |
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|
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myIndex = sd->getGlobalIndex(); |
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|
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Qk = 1.0; |
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myNeighbors.clear(); |
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|
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for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL; |
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sd2 = seleMan2_.nextSelected(isd2)) { |
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|
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if (sd2->getGlobalIndex() != myIndex) { |
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|
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vec = sd->getPos() - sd2->getPos(); |
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|
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(vec); |
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|
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r = vec.length(); |
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|
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// Check to see if neighbor is in bond cutoff |
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|
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if (r < rCut_) { |
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myNeighbors.push_back(std::make_pair(r,sd2)); |
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} |
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} |
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} |
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|
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// Sort the vector using predicate and std::sort |
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std::sort(myNeighbors.begin(), myNeighbors.end()); |
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|
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// Use only the 4 closest neighbors to do the rest of the work: |
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|
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int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size(); |
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int nang = int (0.5 * (nbors * (nbors - 1))); |
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|
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rk = sd->getPos(); |
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|
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for (int i = 0; i < nbors-1; i++) { |
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|
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sdi = myNeighbors[i].second; |
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ri = sdi->getPos(); |
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rik = rk - ri; |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(rik); |
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|
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rik.normalize(); |
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|
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for (int j = i+1; j < nbors; j++) { |
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|
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sdj = myNeighbors[j].second; |
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rj = sdj->getPos(); |
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rkj = rk - rj; |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(rkj); |
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rkj.normalize(); |
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|
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cospsi = dot(rik,rkj); |
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|
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// Calculates scaled Qk for each molecule using calculated |
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// angles from 4 or fewer nearest neighbors. |
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Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang); |
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} |
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} |
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|
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if (nang > 0) { |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(rk); |
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//qvals.push_back(std::make_pair(rk, Qk)); |
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|
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Vector3d pos = rk + halfBox; |
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|
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|
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Vector3i whichVoxel(int(pos[0] / voxelSize_), |
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int(pos[1] / voxelSize_), |
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int(pos[2] / voxelSize_)); |
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|
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for (int l = -kMax; l <= kMax; l++) { |
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for (int m = -kMax; m <= kMax; m++) { |
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for (int n = -kMax; n <= kMax; n++) { |
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int kk = l*l + m*m + n*n; |
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if(kk <= kSqLim) { |
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|
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int ll = (whichVoxel[0] + l) % nBins_(0); |
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ll = ll < 0 ? nBins_(0) + ll : ll; |
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int mm = (whichVoxel[1] + m) % nBins_(1); |
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mm = mm < 0 ? nBins_(1) + mm : mm; |
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int nn = (whichVoxel[2] + n) % nBins_(2); |
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nn = nn < 0 ? nBins_(2) + nn : nn; |
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|
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Vector3d bPos = Vector3d(ll,mm,nn) * voxelSize_ - halfBox; |
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Vector3d d = bPos - rk; |
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currentSnapshot_->wrapVector(d); |
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RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3); |
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RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2); |
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RealType weight = exp(exponent) / denom; |
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count_[ll][mm][nn] += weight; |
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hist_[ll][mm][nn] += weight * Qk; |
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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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// for (int i = 0; i < nBins_(0); ++i) { |
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// for(int j = 0; j < nBins_(1); ++j) { |
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// for(int k = 0; k < nBins_(2); ++k) { |
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// Vector3d pos = Vector3d(i, j, k) * voxelSize_ - halfBox; |
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// for(qiter = qvals.begin(); qiter != qvals.end(); ++qiter) { |
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// Vector3d d = pos - (*qiter).first; |
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// currentSnapshot_->wrapVector(d); |
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// RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3); |
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// RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2); |
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// RealType weight = exp(exponent) / denom; |
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// count_[i][j][k] += weight; |
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// hist_[i][j][k] += weight * (*qiter).second; |
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// } |
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// } |
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// } |
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// } |
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} |
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writeQxyz(); |
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} |
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|
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void TetrahedralityParamXYZ::writeQxyz() { |
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|
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Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
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|
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// normalize by total weight in voxel: |
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for (unsigned int i = 0; i < hist_.size(); ++i) { |
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for(unsigned int j = 0; j < hist_[i].size(); ++j) { |
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for(unsigned int k = 0;k < hist_[i][j].size(); ++k) { |
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hist_[i][j][k] = hist_[i][j][k] / count_[i][j][k]; |
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} |
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} |
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} |
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|
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std::ofstream qXYZstream(outputFilename_.c_str()); |
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if (qXYZstream.is_open()) { |
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qXYZstream << "# AmiraMesh ASCII 1.0\n\n"; |
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qXYZstream << "# Dimensions in x-, y-, and z-direction\n"; |
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qXYZstream << " define Lattice " << hist_.size() << " " |
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<< hist_[0].size() << " " << hist_[0][0].size() << "\n"; |
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|
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qXYZstream << "Parameters {\n"; |
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qXYZstream << " CoordType \"uniform\",\n"; |
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qXYZstream << " # BoundingBox is xmin xmax ymin ymax zmin zmax\n"; |
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qXYZstream << " BoundingBox 0.0 " << hmat(0,0) << |
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" 0.0 " << hmat(1,1) << |
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" 0.0 " << hmat(2,2) << "\n"; |
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qXYZstream << "}\n"; |
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|
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qXYZstream << "Lattice { double ScalarField } = @1\n"; |
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|
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qXYZstream << "@1\n"; |
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|
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for (std::size_t k = 0; k < hist_[0][0].size(); ++k) { |
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for(std::size_t j = 0; j < hist_[0].size(); ++j) { |
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for(std::size_t i = 0; i < hist_.size(); ++i) { |
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qXYZstream << hist_[i][j][k] << " "; |
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|
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//qXYZstream.write(reinterpret_cast<char *>( &hist_[i][j][k] ), |
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// sizeof( hist_[i][j][k] )); |
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} |
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} |
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} |
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|
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} else { |
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sprintf(painCave.errMsg, "TetrahedralityParamXYZ: 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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qXYZstream.close(); |
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} |
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} |
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|
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|
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|
