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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 <functional> |
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#include "applications/sequentialProps/ContactAngle2.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 "utils/PhysicalConstants.hpp" |
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#include "math/Polynomial.hpp" |
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|
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namespace OpenMD { |
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|
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ContactAngle2::ContactAngle2(SimInfo* info, const std::string& filename, |
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const std::string& sele, RealType solidZ, |
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RealType threshDens, int nrbins, int nzbins) |
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: SequentialAnalyzer(info, filename), selectionScript_(sele), |
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evaluator_(info), seleMan_(info), solidZ_(solidZ), |
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threshDens_(threshDens), nRBins_(nrbins), nZBins_(nzbins) { |
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|
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setOutputName(getPrefix(filename) + ".ca2"); |
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|
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evaluator_.loadScriptString(sele); |
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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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|
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void ContactAngle2::doFrame() { |
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StuntDouble* sd; |
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int i; |
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|
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// set up the bins for density analysis |
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|
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Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
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RealType len = std::min(hmat(0, 0), hmat(1, 1)); |
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RealType zLen = hmat(2,2); |
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RealType dr = len / (RealType) nRBins_; |
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RealType dz = zLen / (RealType) nZBins_; |
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|
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std::vector<std::vector<RealType> > histo; |
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histo.resize(nRBins_); |
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for (int i = 0 ; i < nRBins_; ++i) { |
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histo[i].resize(nZBins_); |
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} |
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for (unsigned int i = 0; i < histo.size(); ++i){ |
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std::fill(histo[i].begin(), histo[i].end(), 0.0); |
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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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|
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RealType mtot = 0.0; |
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Vector3d com(V3Zero); |
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RealType mass; |
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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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mass = sd->getMass(); |
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mtot += mass; |
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com += sd->getPos() * mass; |
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} |
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|
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com /= mtot; |
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|
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// now that we have the centroid, we can make cylindrical density maps |
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Vector3d pos; |
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RealType r; |
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RealType z; |
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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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pos = sd->getPos() - com; |
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|
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r = sqrt(pow(pos.x(), 2) + pow(pos.y(), 2)); |
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z = pos.z() - solidZ_; |
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|
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int whichRBin = int(r / dr); |
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int whichZBin = int(z/ dz); |
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|
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if ((r <= len) && (z <= zLen)) |
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histo[whichRBin][whichZBin] += sd->getMass(); |
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|
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} |
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|
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for(unsigned int i = 0 ; i < histo.size(); ++i){ |
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|
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RealType rL = i * dr; |
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RealType rU = rL + dr; |
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RealType volSlice = NumericConstant::PI * dz * (( rU*rU ) - ( rL*rL )); |
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|
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for (unsigned int j = 0; j < histo[i].size(); ++j){ |
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histo[i][j] *= PhysicalConstants::densityConvert / volSlice; |
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} |
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} |
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|
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for (unsigned int i = 0; i < histo.size(); ++i) { |
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RealType ther = dr * (i + 0.5); |
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for(unsigned int j = 0; j < histo[i].size(); ++j) { |
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if (histo[i][j] <= threshDens_) { |
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RealType thez = dz * (j + 0.5); |
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cerr << ther << "\t" << thez << "\n"; |
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break; |
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} |
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} |
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} |
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|
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// values_.push_back( acos(maxct)*(180.0/M_PI) ); |
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|
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} |
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} |
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|
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|
