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Comparing trunk/src/brains/Snapshot.hpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1021 by gezelter, Wed Aug 2 19:40:39 2006 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 39 | Line 39
39   * such damages.
40   */
41    
42 < /**
43 <  * @file Snapshot.hpp
44 <  * @author tlin
45 <  * @date 10/20/2004
46 <  * @time 23:56am
47 <  * @version 1.0
48 <  */
42 > /**
43 > * @file Snapshot.hpp
44 > * @author tlin
45 > * @date 10/20/2004
46 > * @time 23:56am
47 > * @version 1.0
48 > */
49    
50   #ifndef BRAINS_SNAPSHOT_HPP
51   #define BRAINS_SNAPSHOT_HPP
# Line 58 | Line 58 | namespace oopse{
58  
59   namespace oopse{
60  
61 <    /**
62 <     * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
63 <     * @brief Snapshot class is a repository class for storing dynamic data during
64 <     *  Simulation
65 <     * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
66 <     *  for rigid bodies.
67 <     */
68 <    class Snapshot {
69 <        public:
61 >  /**
62 >   * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
63 >   * @brief Snapshot class is a repository class for storing dynamic data during
64 >   *  Simulation
65 >   * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
66 >   *  for rigid bodies.
67 >   */
68 >  class Snapshot {
69 >  public:
70              
71 <            Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
72 <                currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
71 >    Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
72 >                                             currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
73  
74 <            }
74 >    }
75  
76 +    Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
77 +      : atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
78 +        currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
79 +
80 +      }
81              
82 <            /** Returns the id of this Snapshot */
83 <            int getID() {
84 <                return id_;
85 <            }
82 >    /** Returns the id of this Snapshot */
83 >    int getID() {
84 >      return id_;
85 >    }
86  
87 <            /** Sets the id of this Snapshot */
88 <            void setID(int id) {
89 <                id_ = id;
90 <            }
87 >    /** Sets the id of this Snapshot */
88 >    void setID(int id) {
89 >      id_ = id;
90 >    }
91  
92 <            int getSize() {
93 <                return atomData.getSize() + rigidbodyData.getSize();
94 <            }
92 >    int getSize() {
93 >      return atomData.getSize() + rigidbodyData.getSize();
94 >    }
95  
96 <            /** Returns the number of atoms */
97 <            int getNumberOfAtoms() {
98 <                return atomData.getSize();
99 <            }
96 >    /** Returns the number of atoms */
97 >    int getNumberOfAtoms() {
98 >      return atomData.getSize();
99 >    }
100  
101 <            /** Returns the number of rigid bodies */
102 <            int getNumberOfRigidBodies() {
103 <                return rigidbodyData.getSize();
104 <            }
101 >    /** Returns the number of rigid bodies */
102 >    int getNumberOfRigidBodies() {
103 >      return rigidbodyData.getSize();
104 >    }
105  
106 <            /** Returns the H-Matrix */
107 <            Mat3x3d getHmat() {
108 <                return hmat_;
109 <            }
106 >    /** Returns the H-Matrix */
107 >    Mat3x3d getHmat() {
108 >      return hmat_;
109 >    }
110  
111 <            /** Sets the H-Matrix */
112 <            void setHmat(const Mat3x3d& m);
111 >    /** Sets the H-Matrix */
112 >    void setHmat(const Mat3x3d& m);
113              
114 <            double getVolume() {
115 <                return hmat_.determinant();
116 <            }
114 >    RealType getVolume() {
115 >      return hmat_.determinant();
116 >    }
117  
118 <            /** Returns the inverse H-Matrix */
119 <            Mat3x3d getInvHmat() {
120 <                return invHmat_;
121 <            }
118 >    /** Returns the inverse H-Matrix */
119 >    Mat3x3d getInvHmat() {
120 >      return invHmat_;
121 >    }
122  
123 <            /** Wrapping the vector according to periodic boundary condition*/
124 <            void wrapVector(Vector3d& v);
123 >    /** Wrapping the vector according to periodic boundary condition*/
124 >    void wrapVector(Vector3d& v);
125  
126              
127 <            double getTime() {
128 <                return currentTime_;
129 <            }
127 >    RealType getTime() {
128 >      return currentTime_;
129 >    }
130  
131 <            void increaseTime(double dt) {
132 <                setTime(getTime() + dt);
133 <            }
131 >    void increaseTime(RealType dt) {
132 >      setTime(getTime() + dt);
133 >    }
134  
135 <            void setTime(double time) {
136 <                currentTime_ =time;
137 <                //time at statData is redundant
138 <                statData[Stats::TIME] = currentTime_;
139 <            }
135 >    void setTime(RealType time) {
136 >      currentTime_ =time;
137 >      //time at statData is redundant
138 >      statData[Stats::TIME] = currentTime_;
139 >    }
140  
141 <            double getChi() {
142 <                return chi_;
143 <            }
141 >    RealType getChi() {
142 >      return chi_;
143 >    }
144  
145 <            void setChi(double chi) {
146 <                chi_ = chi;
147 <            }
145 >    void setChi(RealType chi) {
146 >      chi_ = chi;
147 >    }
148  
149 <            double getIntegralOfChiDt() {
150 <                return integralOfChiDt_;
151 <            }
149 >    RealType getIntegralOfChiDt() {
150 >      return integralOfChiDt_;
151 >    }
152  
153 <            void setIntegralOfChiDt(double integralOfChiDt) {
154 <                integralOfChiDt_ = integralOfChiDt;
155 <            }
153 >    void setIntegralOfChiDt(RealType integralOfChiDt) {
154 >      integralOfChiDt_ = integralOfChiDt;
155 >    }
156              
152 –            Mat3x3d getEta() {
153 –                return eta_;
154 –            }
157  
158 <            void setEta(const Mat3x3d& eta) {
159 <                eta_ = eta;
160 <            }
158 >    void setOrthoTolerance(RealType orthoTolerance) {
159 >      orthoTolerance_ = orthoTolerance;
160 >    }
161 >
162 >    Mat3x3d getEta() {
163 >      return eta_;
164 >    }
165 >
166 >    void setEta(const Mat3x3d& eta) {
167 >      eta_ = eta;
168 >    }
169              
170 <            DataStorage atomData;
171 <            DataStorage rigidbodyData;
172 <            Stats statData;
170 >    DataStorage atomData;
171 >    DataStorage rigidbodyData;
172 >    Stats statData;
173              
174 <        private:
175 <            double currentTime_;
174 >  private:
175 >    RealType currentTime_;
176  
177 <            Mat3x3d hmat_;
178 <            Mat3x3d invHmat_;
179 <            int orthoRhombic_;
177 >    Mat3x3d hmat_;
178 >    Mat3x3d invHmat_;
179 >    RealType orthoTolerance_;
180 >    int orthoRhombic_;
181  
182 <            double chi_;
183 <            double integralOfChiDt_;
184 <            Mat3x3d eta_;
182 >    RealType chi_;
183 >    RealType integralOfChiDt_;
184 >    Mat3x3d eta_;
185              
186 <            int id_; /**< identification number of the snapshot */
187 <    };
186 >    int id_; /**< identification number of the snapshot */
187 >  };
188  
189 <    typedef DataStorage (Snapshot::*DataStoragePointer);
189 >  typedef DataStorage (Snapshot::*DataStoragePointer);
190   }
191   #endif //BRAINS_SNAPSHOT_HPP

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