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#ifndef _CUTOFFGROUP_H_ |
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#define _CUTOFFGROUP_H_ |
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#include "primitives/Atom.hpp" |
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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, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#ifndef PRIMITIVES_CUTOFFGROUP_HPP |
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class CutoffGroup{ |
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public: |
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|
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CutoffGroup() { |
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haveTotalMass = false; |
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totalMass = 0.0; |
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} |
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|
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void addAtom(Atom* atom) {cutoffAtomList.push_back(atom);} |
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|
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Atom* beginAtom(vector<Atom*>::iterator& i){ |
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i = cutoffAtomList.begin(); |
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return i != cutoffAtomList.end()? *i : NULL; |
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} |
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|
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Atom* nextAtom(vector<Atom*>::iterator& i){ |
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i++; |
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return i != cutoffAtomList.end()? *i : NULL; |
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} |
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|
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double getMass(){ |
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vector<Atom*>::iterator i; |
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Atom* atom; |
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double mass; |
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|
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if (!haveTotalMass) { |
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#define PRIMITIVES_CUTOFFGROUP_HPP |
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|
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totalMass = 0; |
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|
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for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){ |
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mass = atom->getMass(); |
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totalMass += mass; |
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} |
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#include "primitives/Atom.hpp" |
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#include "math/Vector3.hpp" |
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haveTotalMass = true; |
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namespace OpenMD { |
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class CutoffGroup { |
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public: |
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|
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CutoffGroup() { |
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haveTotalMass = false; |
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totalMass = 0.0; |
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} |
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return totalMass; |
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} |
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|
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void getCOM(double com[3]){ |
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|
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vector<Atom*>::iterator i; |
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Atom* atom; |
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double pos[3]; |
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double mass; |
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void addAtom(Atom *atom) { |
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cutoffAtomList.push_back(atom); |
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} |
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com[0] = 0; |
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com[1] = 0; |
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com[2] = 0; |
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totalMass = getMass(); |
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Atom *beginAtom(std::vector<Atom *>::iterator & i) { |
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i = cutoffAtomList.begin(); |
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return i != cutoffAtomList.end() ? *i : NULL; |
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} |
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if (cutoffAtomList.size() == 1) { |
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Atom *nextAtom(std::vector<Atom *>::iterator & i) { |
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i++; |
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return i != cutoffAtomList.end() ? *i : NULL; |
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} |
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|
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std::vector<Atom*> getAtoms() { return cutoffAtomList; } |
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RealType getMass() { |
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std::vector<Atom *>::iterator i; |
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Atom * atom; |
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RealType mass; |
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beginAtom(i)->getPos(com); |
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if (!haveTotalMass) { |
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totalMass = 0; |
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|
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for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
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mass = atom->getMass(); |
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totalMass += mass; |
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} |
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haveTotalMass = true; |
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} |
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} else { |
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return totalMass; |
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} |
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|
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void getCOM(Vector3d & com) { |
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std::vector<Atom *>::iterator i; |
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Atom * atom; |
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Vector3d pos; |
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RealType mass; |
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for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){ |
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mass = atom->getMass(); |
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atom->getPos(pos); |
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com[0] += pos[0] * mass; |
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com[1] += pos[1] * mass; |
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com[2] += pos[2] * mass; |
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} |
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com[0] = 0; |
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com[1] = 0; |
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com[2] = 0; |
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totalMass = getMass(); |
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com[0] /= totalMass; |
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com[1] /= totalMass; |
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com[2] /= totalMass; |
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if (cutoffAtomList.size() == 1) { |
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com = beginAtom(i)->getPos(); |
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} else { |
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for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
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mass = atom->getMass(); |
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pos = atom->getPos(); |
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com += pos * mass; |
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} |
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|
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com /= totalMass; |
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} |
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} |
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} |
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int getNumAtom() {return cutoffAtomList.size();} |
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int getGlobalIndex() {return globalIndex;} |
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void setGlobalIndex(int id) {this->globalIndex = id;} |
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private: |
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vector<Atom*> cutoffAtomList; |
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bool haveTotalMass; |
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double totalMass; |
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int globalIndex; |
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|
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}; |
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#endif |
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int getNumAtom() { |
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return cutoffAtomList.size(); |
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} |
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|
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int getGlobalIndex() { |
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return globalIndex; |
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} |
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|
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void setGlobalIndex(int id) { |
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this->globalIndex = id; |
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} |
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|
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private: |
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|
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std::vector<Atom *>cutoffAtomList; |
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bool haveTotalMass; |
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RealType totalMass; |
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int globalIndex; |
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}; |
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} //end namespace OpenMD |
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#endif //PRIMITIVES_CUTOFFGROUP_HPP |
