| 1 |
< |
#ifndef _OTHERVISITOR_H_ |
| 2 |
< |
#define _OTHERVISITOR_H_ |
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
> |
* notice, this list of conditions and the following disclaimer. |
| 11 |
> |
* |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
> |
* documentation and/or other materials provided with the |
| 15 |
> |
* distribution. |
| 16 |
> |
* |
| 17 |
> |
* This software is provided "AS IS," without a warranty of any |
| 18 |
> |
* kind. All express or implied conditions, representations and |
| 19 |
> |
* warranties, including any implied warranty of merchantability, |
| 20 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
> |
* be liable for any damages suffered by licensee as a result of |
| 23 |
> |
* using, modifying or distributing the software or its |
| 24 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
> |
* damages, however caused and regardless of the theory of liability, |
| 28 |
> |
* arising out of the use of or inability to use software, even if the |
| 29 |
> |
* University of Notre Dame has been advised of the possibility of |
| 30 |
> |
* such damages. |
| 31 |
> |
* |
| 32 |
> |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
> |
* research, please cite the appropriate papers when you publish your |
| 34 |
> |
* work. Good starting points are: |
| 35 |
> |
* |
| 36 |
> |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
> |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
> |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
> |
*/ |
| 41 |
> |
|
| 42 |
> |
#ifndef VISITORS_OTHERVISITOR_HPP |
| 43 |
> |
#define VISITORS_OTHERVISITOR_HPP |
| 44 |
|
#include <set> |
| 45 |
|
#include <string> |
| 46 |
|
#include <vector> |
| 47 |
|
|
| 48 |
|
#include "visitors/BaseVisitor.hpp" |
| 49 |
|
#include "primitives/StuntDouble.hpp" |
| 50 |
< |
using namespace std; |
| 50 |
> |
#include "visitors/AtomData.hpp" |
| 51 |
> |
#include "selection/SelectionManager.hpp" |
| 52 |
> |
#include "selection/SelectionEvaluator.hpp" |
| 53 |
|
|
| 54 |
< |
//IgnoreVisitor will turn on the ignoring flag of the stuntdouble |
| 12 |
< |
class IgnoreVisitor : public BaseVisitor{ |
| 13 |
< |
public: |
| 14 |
< |
IgnoreVisitor() : BaseVisitor() {visitorName = "IgnoreVisitor";} |
| 54 |
> |
namespace OpenMD { |
| 55 |
|
|
| 56 |
< |
virtual void visit(Atom* atom); |
| 17 |
< |
virtual void visit(DirectionalAtom* datom); |
| 18 |
< |
virtual void visit(RigidBody* rb); |
| 19 |
< |
|
| 20 |
< |
virtual const string toString(); |
| 56 |
> |
class SimInfo; |
| 57 |
|
|
| 22 |
– |
void addIgnoreType(const string& type) {itList.insert(type);} |
| 23 |
– |
|
| 24 |
– |
protected: |
| 25 |
– |
bool isIgnoreType(const string& name); |
| 26 |
– |
void internalVisit(StuntDouble* sd); |
| 27 |
– |
set<string> itList; //ignore type list; |
| 28 |
– |
}; |
| 58 |
|
|
| 59 |
< |
|
| 31 |
< |
class WrappingVisitor : public BaseVisitor{ |
| 59 |
> |
class WrappingVisitor : public BaseVisitor{ |
| 60 |
|
public: |
| 61 |
< |
WrappingVisitor(SimInfo* info) : BaseVisitor() { |
| 61 |
> |
WrappingVisitor(SimInfo* info, bool useCom = true) : BaseVisitor(), useCom_(useCom) { |
| 62 |
|
this->info = info; |
| 63 |
|
visitorName = "WrappingVisitor"; |
| 64 |
|
} |
| 66 |
|
virtual void visit(DirectionalAtom* datom); |
| 67 |
|
virtual void visit(RigidBody* rb); |
| 68 |
|
|
| 69 |
< |
virtual const string toString(); |
| 69 |
> |
virtual const std::string toString(); |
| 70 |
|
|
| 71 |
< |
protected: |
| 71 |
> |
virtual void update(); |
| 72 |
> |
|
| 73 |
> |
private: |
| 74 |
|
void internalVisit(StuntDouble* sd); |
| 75 |
< |
SimInfo* info; |
| 76 |
< |
}; |
| 75 |
> |
SimInfo* info; |
| 76 |
> |
Vector3d origin_; |
| 77 |
> |
bool useCom_; |
| 78 |
> |
}; |
| 79 |
|
|
| 80 |
|
|
| 81 |
< |
class IntVec3 { |
| 81 |
> |
class ReplicateVisitor : public BaseVisitor{ |
| 82 |
|
public: |
| 83 |
< |
IntVec3(){} |
| 52 |
< |
IntVec3(int i, int j, int k){ |
| 53 |
< |
vec[0] = i; |
| 54 |
< |
vec[1] = j; |
| 55 |
< |
vec[2] = k; |
| 56 |
< |
} |
| 57 |
< |
|
| 58 |
< |
int vec[3]; |
| 59 |
< |
int& operator[](int index) {return vec[index];} |
| 60 |
< |
}; |
| 61 |
< |
|
| 62 |
< |
class ReplicateVisitor : public BaseVisitor{ |
| 63 |
< |
public: |
| 64 |
< |
ReplicateVisitor(SimInfo* info, IntVec3 opt); |
| 83 |
> |
ReplicateVisitor(SimInfo* info, Vector3i opt); |
| 84 |
|
virtual void visit(Atom* atom); |
| 85 |
|
virtual void visit(DirectionalAtom* datom); |
| 86 |
|
virtual void visit(RigidBody* rb); |
| 87 |
|
|
| 88 |
< |
virtual const string toString(); |
| 88 |
> |
virtual const std::string toString(); |
| 89 |
|
protected: |
| 90 |
|
void internalVisit(StuntDouble* sd); |
| 91 |
< |
void replicate(vector<AtomInfo*>& infoList, AtomData* data, double boxM[3][3]); |
| 91 |
> |
void replicate(std::vector<AtomInfo*>& infoList, AtomData* data, const Mat3x3d& box); |
| 92 |
|
|
| 93 |
|
private: |
| 94 |
< |
vector<IntVec3> dir; |
| 94 |
> |
std::vector<Vector3i> dir; |
| 95 |
|
SimInfo* info; |
| 96 |
< |
IntVec3 replicateOpt; |
| 97 |
< |
}; |
| 96 |
> |
Vector3i replicateOpt; |
| 97 |
> |
}; |
| 98 |
|
|
| 99 |
< |
class XYZVisitor : public BaseVisitor{ |
| 99 |
> |
class XYZVisitor : public BaseVisitor{ |
| 100 |
|
public: |
| 82 |
– |
XYZVisitor(SimInfo* info, bool printDipole = true); |
| 101 |
|
|
| 102 |
+ |
XYZVisitor(SimInfo* info); |
| 103 |
+ |
|
| 104 |
+ |
XYZVisitor(SimInfo* info, const std::string& script); |
| 105 |
+ |
|
| 106 |
|
virtual void visit(Atom* atom); |
| 107 |
|
virtual void visit(DirectionalAtom* datom); |
| 108 |
|
virtual void visit(RigidBody* rb); |
| 109 |
|
|
| 110 |
< |
virtual const string toString(); |
| 110 |
> |
virtual void update(); |
| 111 |
> |
|
| 112 |
> |
virtual const std::string toString(); |
| 113 |
|
|
| 114 |
< |
void writeFrame(ostream& outStream); |
| 114 |
> |
void writeFrame(std::ostream& outStream); |
| 115 |
|
void clear() {frame.clear();} |
| 116 |
< |
|
| 116 |
> |
void doPositions(bool pos) {doPositions_ = pos;} |
| 117 |
> |
void doVelocities(bool vel){doVelocities_ = vel;} |
| 118 |
> |
void doForces(bool frc) {doForces_ = frc;} |
| 119 |
> |
void doVectors(bool vec) {doVectors_ = vec;} |
| 120 |
> |
void doCharges(bool chg) {doCharges_ = chg;} |
| 121 |
> |
|
| 122 |
|
protected: |
| 123 |
|
void internalVisit(StuntDouble* sd); |
| 124 |
< |
bool isIgnore(StuntDouble* sd); |
| 124 |
> |
bool isSelected(StuntDouble* sd); |
| 125 |
|
|
| 126 |
|
private: |
| 127 |
+ |
std::string trimmedName(const std::string& atomType); |
| 128 |
+ |
|
| 129 |
|
SimInfo* info; |
| 130 |
< |
vector<string> frame; |
| 131 |
< |
bool printDipole; |
| 132 |
< |
}; |
| 130 |
> |
SelectionManager seleMan; |
| 131 |
> |
SelectionEvaluator evaluator; |
| 132 |
> |
std::vector<std::string> frame; |
| 133 |
> |
bool doPositions_; |
| 134 |
> |
bool doVelocities_; |
| 135 |
> |
bool doForces_; |
| 136 |
> |
bool doVectors_; |
| 137 |
> |
bool doCharges_; |
| 138 |
> |
}; |
| 139 |
|
|
| 140 |
|
|
| 141 |
< |
class PrepareVisitor : public BaseVisitor{ |
| 141 |
> |
class PrepareVisitor : public BaseVisitor{ |
| 142 |
|
public: |
| 143 |
|
PrepareVisitor() : BaseVisitor() {visitorName = "prepareVisitor";} |
| 144 |
|
|
| 146 |
|
virtual void visit(DirectionalAtom* datom) {internalVisit((Atom*)datom);} |
| 147 |
|
virtual void visit(RigidBody* rb) {internalVisit(rb);} |
| 148 |
|
|
| 149 |
< |
virtual const string toString(); |
| 149 |
> |
virtual const std::string toString(); |
| 150 |
|
|
| 151 |
|
protected: |
| 152 |
|
void internalVisit(Atom* atom); |
| 153 |
|
void internalVisit(RigidBody* rb); |
| 154 |
< |
}; |
| 154 |
> |
}; |
| 155 |
|
|
| 156 |
< |
class WaterTypeVisitor : public BaseVisitor{ |
| 156 |
> |
class WaterTypeVisitor : public BaseVisitor{ |
| 157 |
|
public: |
| 158 |
|
WaterTypeVisitor() ; |
| 159 |
|
virtual void visit(Atom* atom) {} |
| 160 |
|
virtual void visit(DirectionalAtom* datom) {} |
| 161 |
|
virtual void visit(RigidBody* rb); |
| 125 |
– |
|
| 126 |
– |
virtual const string toString(); |
| 162 |
|
|
| 163 |
+ |
virtual const std::string toString(); |
| 164 |
+ |
|
| 165 |
|
private: |
| 166 |
< |
void replaceType(string& atomType); |
| 167 |
< |
|
| 168 |
< |
set<string> waterTypeList; |
| 169 |
< |
}; |
| 166 |
> |
std::string trimmedName(const std::string& atomType); |
| 167 |
> |
|
| 168 |
> |
std::set<std::string> waterTypeList; |
| 169 |
> |
}; |
| 170 |
> |
|
| 171 |
> |
|
| 172 |
> |
}//namespace OpenMD |
| 173 |
|
#endif //_OTHERVISITOR_H_ |
