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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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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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* |
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* RhoZ.cpp |
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* OOPSE-2.0 |
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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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* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
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* Created by Charles F. Vardeman II on 11/26/05. |
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* @author Charles F. Vardeman II |
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* @version $Id: RhoZ.cpp,v 1.7 2008-06-30 17:53:42 gpuliti Exp $ |
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* @version $Id$ |
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* |
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*/ |
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|
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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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namespace oopse { |
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namespace OpenMD { |
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|
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RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int nzbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nZBins_(nzbins){ |
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//loop over the slices to calculate the densities |
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for (i = 0; i < nZBins_; i++) { |
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RealType totalMass = 0; |
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for (int k = 0; k < sliceSDLists_[i].size(); ++k) { |
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for (unsigned int k = 0; k < sliceSDLists_[i].size(); ++k) { |
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totalMass += sliceSDLists_[i][k]->getMass(); |
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} |
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density_[i] += totalMass/sliceVolume; |
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rdfStream << "#nFrames:\t" << nProcessed_ << "\n"; |
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rdfStream << "#selection: (" << selectionScript_ << ")\n"; |
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rdfStream << "#z\tdensity\n"; |
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for (int i = 0; i < density_.size(); ++i) { |
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for (unsigned int i = 0; i < density_.size(); ++i) { |
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RealType z = zAve * (i+0.5)/density_.size(); |
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rdfStream << z << "\t" << 1.660535*density_[i]/nProcessed_ << "\n"; |
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} |
