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/* |
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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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* 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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* 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, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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#ifndef VISITOR_ATOMDATA_HPP |
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#include "utils/GenericData.hpp" |
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#include "math/Vector3.hpp" |
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namespace oopse { |
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namespace OpenMD { |
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|
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struct AtomInfo { |
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struct AtomInfo { |
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AtomInfo() : hasCharge(false), hasVector(false) {} |
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|
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std::string atomTypeName; |
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Vector3d pos; |
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Vector3d dipole; |
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}; |
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RealType charge; |
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bool hasCharge; |
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bool hasVector; |
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}; |
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class AtomData : public GenericData{ |
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public: |
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class AtomData : public GenericData{ |
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public: |
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AtomData(const std::string& id = "ATOMDATA") : GenericData(id) {} |
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AtomData(const std::string& id = "ATOMDATA") : GenericData(id) {} |
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~AtomData() { |
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std::vector<AtomInfo*>::iterator i; |
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AtomInfo* atomInfo; |
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~AtomData() { |
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std::vector<AtomInfo*>::iterator i; |
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AtomInfo* atomInfo; |
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for(atomInfo = beginAtomInfo(i); atomInfo; atomInfo = nextAtomInfo(i)) { |
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delete atomInfo; |
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} |
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data.clear(); |
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} |
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for(atomInfo = beginAtomInfo(i); atomInfo; atomInfo = nextAtomInfo(i)) { |
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delete atomInfo; |
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} |
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data.clear(); |
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} |
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void addAtomInfo(AtomInfo* info) {data.push_back(info);} |
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void addAtomInfo(AtomInfo* info) {data.push_back(info);} |
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void clearAllAtomInfo(); |
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void clearAllAtomInfo(); |
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AtomInfo* beginAtomInfo(std::vector<AtomInfo*>::iterator& i){ |
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i = data.begin(); |
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return i != data.end()? *i : NULL; |
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} |
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AtomInfo* beginAtomInfo(std::vector<AtomInfo*>::iterator& i){ |
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i = data.begin(); |
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return i != data.end()? *i : NULL; |
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} |
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AtomInfo* nextAtomInfo(std::vector<AtomInfo*>::iterator& i){ |
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++i; |
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return i != data.end()? *i: NULL; |
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} |
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AtomInfo* nextAtomInfo(std::vector<AtomInfo*>::iterator& i){ |
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++i; |
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return i != data.end()? *i: NULL; |
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} |
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std::vector<AtomInfo*> getData() {return data;} |
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std::vector<AtomInfo*> getData() {return data;} |
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int getSize() {return data.size();} |
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int getSize() {return data.size();} |
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protected: |
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protected: |
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std::vector<AtomInfo*> data; |
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}; |
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std::vector<AtomInfo*> data; |
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}; |
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} |
