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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 |
| 12 |
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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 |
| 15 |
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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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+ |
* 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 |
| 34 |
+ |
* 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] Vardeman & Gezelter, in progress (2009). |
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* |
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* RhoZ.hpp |
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* OOPSE-2.0 |
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* |
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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.hpp,v 1.1 2005-11-30 21:00:39 chuckv Exp $ |
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* @version $Id: RhoZ.hpp,v 1.6 2009-11-25 20:01:59 gezelter Exp $ |
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* |
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*/ |
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#ifndef APPLICATIONS_STATICPROPS_RHOZ_HPP |
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#define APPLICATIONS_STATICPROPS_RHOZ_HPP |
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|
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#include "applications/staticProps/RadialDistrFunc.hpp" |
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namespace oopse { |
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#include <string> |
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#include <vector> |
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#include "selection/SelectionEvaluator.hpp" |
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#include "selection/SelectionManager.hpp" |
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#include "utils/NumericConstant.hpp" |
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#include "applications/staticProps/StaticAnalyser.hpp" |
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|
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namespace OpenMD { |
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|
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class RhoZ : public RadialDistrFunc { |
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class RhoZ : public StaticAnalyser { |
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|
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public: |
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RhoZ(SimInfo* info, const std::string& filename, const std::string& sele1, |
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const std::string& sele2, double len, int nrbins); |
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public: |
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RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int nzbins); |
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|
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int getNRBins() { |
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return nRBins_; |
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int getNZBins() { |
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return nZBins_; |
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} |
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|
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double getLength() { |
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return len_; |
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} |
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virtual void process(); |
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|
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private: |
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|
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virtual void preProcess(); |
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virtual void initalizeHistogram(); |
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virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2); |
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virtual void processHistogram(); |
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private: |
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|
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virtual void writeRdf(); |
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virtual void writeDensity(); |
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|
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double len_; |
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int nRBins_; |
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double deltaR_; |
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|
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std::vector<int> histogram_; |
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std::vector<double> avgGofr_; |
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Snapshot* currentSnapshot_; |
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|
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> |
int nProcessed_; |
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> |
std::string selectionScript_; |
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> |
SelectionEvaluator evaluator_; |
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> |
SelectionManager seleMan_; |
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> |
|
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> |
int nZBins_; |
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|
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std::vector<std::vector<StuntDouble*> > sliceSDLists_; |
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std::vector<RealType> zBox_; |
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std::vector<RealType> density_; |
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}; |
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|
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} |
