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#ifndef _OTHERVISITOR_H_ |
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#define _OTHERVISITOR_H_ |
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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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#ifndef VISITORS_OTHERVISITOR_HPP |
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#define VISITORS_OTHERVISITOR_HPP |
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#include <set> |
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#include <string> |
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#include <vector> |
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|
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#include "BaseVisitor.hpp" |
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#include "StuntDouble.hpp" |
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using namespace std; |
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#include "visitors/BaseVisitor.hpp" |
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#include "primitives/StuntDouble.hpp" |
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#include "visitors/AtomData.hpp" |
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#include "selection/SelectionManager.hpp" |
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#include "selection/SelectionEvaluator.hpp" |
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|
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//IgnoreVisitor will turn on the ignoring flag of the stuntdouble |
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class IgnoreVisitor : public BaseVisitor{ |
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public: |
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IgnoreVisitor() : BaseVisitor() {visitorName = "IgnoreVisitor";} |
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namespace OpenMD { |
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|
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virtual void visit(Atom* atom); |
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virtual void visit(DirectionalAtom* datom); |
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virtual void visit(RigidBody* rb); |
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|
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virtual const string toString(); |
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class SimInfo; |
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|
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void addIgnoreType(const string& type) {itList.insert(type);} |
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|
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protected: |
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bool isIgnoreType(const string& name); |
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void internalVisit(StuntDouble* sd); |
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set<string> itList; //ignore type list; |
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}; |
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class WrappingVisitor : public BaseVisitor{ |
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class WrappingVisitor : public BaseVisitor{ |
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public: |
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WrappingVisitor(SimInfo* info) : BaseVisitor() { |
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WrappingVisitor(SimInfo* info, bool useCom = true) : BaseVisitor(), useCom_(useCom) { |
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this->info = info; |
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visitorName = "WrappingVisitor"; |
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} |
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virtual void visit(DirectionalAtom* datom); |
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virtual void visit(RigidBody* rb); |
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virtual const string toString(); |
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virtual const std::string toString(); |
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|
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protected: |
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virtual void update(); |
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|
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private: |
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void internalVisit(StuntDouble* sd); |
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SimInfo* info; |
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}; |
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SimInfo* info; |
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Vector3d origin_; |
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bool useCom_; |
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}; |
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class IntVec3 { |
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class ReplicateVisitor : public BaseVisitor{ |
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public: |
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IntVec3(){} |
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IntVec3(int i, int j, int k){ |
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vec[0] = i; |
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vec[1] = j; |
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vec[2] = k; |
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} |
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|
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int vec[3]; |
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int& operator[](int index) {return vec[index];} |
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}; |
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|
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class ReplicateVisitor : public BaseVisitor{ |
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public: |
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ReplicateVisitor(SimInfo* info, IntVec3 opt); |
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ReplicateVisitor(SimInfo* info, Vector3i opt); |
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virtual void visit(Atom* atom); |
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virtual void visit(DirectionalAtom* datom); |
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virtual void visit(RigidBody* rb); |
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|
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virtual const string toString(); |
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virtual const std::string toString(); |
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protected: |
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void internalVisit(StuntDouble* sd); |
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void replicate(vector<AtomInfo*>& infoList, AtomData* data, double boxM[3][3]); |
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void replicate(std::vector<AtomInfo*>& infoList, AtomData* data, const Mat3x3d& box); |
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|
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private: |
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vector<IntVec3> dir; |
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std::vector<Vector3i> dir; |
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SimInfo* info; |
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IntVec3 replicateOpt; |
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}; |
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Vector3i replicateOpt; |
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}; |
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class XYZVisitor : public BaseVisitor{ |
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class XYZVisitor : public BaseVisitor{ |
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public: |
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XYZVisitor(SimInfo* info, bool printDipole = true); |
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XYZVisitor(SimInfo* info); |
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XYZVisitor(SimInfo* info, const std::string& script); |
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|
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virtual void visit(Atom* atom); |
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virtual void visit(DirectionalAtom* datom); |
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virtual void visit(RigidBody* rb); |
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|
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virtual const string toString(); |
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virtual void update(); |
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|
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virtual const std::string toString(); |
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void writeFrame(ostream& outStream); |
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void writeFrame(std::ostream& outStream); |
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void clear() {frame.clear();} |
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|
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void doPositions(bool pos) {doPositions_ = pos;} |
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void doVelocities(bool vel) {doVelocities_ = vel;} |
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void doForces(bool frc) {doForces_ = frc;} |
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void doVectors(bool vec) {doVectors_ = vec;} |
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void doCharges(bool chg) {doCharges_ = chg;} |
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void doElectricFields(bool efl) {doElectricFields_ = efl;} |
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|
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protected: |
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void internalVisit(StuntDouble* sd); |
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bool isIgnore(StuntDouble* sd); |
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bool isSelected(StuntDouble* sd); |
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private: |
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std::string trimmedName(const std::string& atomType); |
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|
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SimInfo* info; |
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vector<string> frame; |
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bool printDipole; |
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}; |
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SelectionManager seleMan; |
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SelectionEvaluator evaluator; |
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std::vector<std::string> frame; |
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bool doPositions_; |
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bool doVelocities_; |
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bool doForces_; |
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bool doVectors_; |
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bool doCharges_; |
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bool doElectricFields_; |
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}; |
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class PrepareVisitor : public BaseVisitor{ |
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class PrepareVisitor : public BaseVisitor{ |
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public: |
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PrepareVisitor() : BaseVisitor() {visitorName = "prepareVisitor";} |
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|
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virtual void visit(Atom* atom) {internalVisit(atom);} |
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virtual void visit(DirectionalAtom* datom) {internalVisit((Atom*)datom);} |
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virtual void visit(DirectionalAtom* datom) {internalVisit(reinterpret_cast<Atom*>(datom));} |
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virtual void visit(RigidBody* rb) {internalVisit(rb);} |
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virtual const string toString(); |
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virtual const std::string toString(); |
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|
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protected: |
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void internalVisit(Atom* atom); |
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void internalVisit(RigidBody* rb); |
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}; |
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}; |
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class WaterTypeVisitor : public BaseVisitor{ |
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class WaterTypeVisitor : public BaseVisitor{ |
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public: |
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WaterTypeVisitor() ; |
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virtual void visit(Atom* atom) {} |
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virtual void visit(DirectionalAtom* datom) {} |
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virtual void visit(RigidBody* rb); |
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virtual const string toString(); |
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virtual const std::string toString(); |
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|
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private: |
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void replaceType(string& atomType); |
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set<string> waterTypeList; |
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}; |
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std::string trimmedName(const std::string& atomType); |
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|
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std::set<std::string> waterTypeList; |
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}; |
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|
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|
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}//namespace OpenMD |
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#endif //_OTHERVISITOR_H_ |
