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 |
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 |
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), 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), 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 |
> |
double 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 |
> |
double getTime() { |
128 |
> |
return currentTime_; |
129 |
> |
} |
130 |
|
|
131 |
< |
void increaseTime(double dt) { |
132 |
< |
setTime(getTime() + dt); |
133 |
< |
} |
131 |
> |
void increaseTime(double 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(double 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 |
> |
double getChi() { |
142 |
> |
return chi_; |
143 |
> |
} |
144 |
|
|
145 |
< |
void setChi(double chi) { |
146 |
< |
chi_ = chi; |
147 |
< |
} |
145 |
> |
void setChi(double chi) { |
146 |
> |
chi_ = chi; |
147 |
> |
} |
148 |
|
|
149 |
< |
double getIntegralOfChiDt() { |
150 |
< |
return integralOfChiDt_; |
151 |
< |
} |
149 |
> |
double getIntegralOfChiDt() { |
150 |
> |
return integralOfChiDt_; |
151 |
> |
} |
152 |
|
|
153 |
< |
void setIntegralOfChiDt(double integralOfChiDt) { |
154 |
< |
integralOfChiDt_ = integralOfChiDt; |
155 |
< |
} |
153 |
> |
void setIntegralOfChiDt(double integralOfChiDt) { |
154 |
> |
integralOfChiDt_ = integralOfChiDt; |
155 |
> |
} |
156 |
|
|
157 |
< |
Mat3x3d getEta() { |
158 |
< |
return eta_; |
159 |
< |
} |
157 |
> |
Mat3x3d getEta() { |
158 |
> |
return eta_; |
159 |
> |
} |
160 |
|
|
161 |
< |
void setEta(const Mat3x3d& eta) { |
162 |
< |
eta_ = eta; |
163 |
< |
} |
161 |
> |
void setEta(const Mat3x3d& eta) { |
162 |
> |
eta_ = eta; |
163 |
> |
} |
164 |
|
|
165 |
< |
DataStorage atomData; |
166 |
< |
DataStorage rigidbodyData; |
167 |
< |
Stats statData; |
165 |
> |
DataStorage atomData; |
166 |
> |
DataStorage rigidbodyData; |
167 |
> |
Stats statData; |
168 |
|
|
169 |
< |
private: |
170 |
< |
double currentTime_; |
169 |
> |
private: |
170 |
> |
double currentTime_; |
171 |
|
|
172 |
< |
Mat3x3d hmat_; |
173 |
< |
Mat3x3d invHmat_; |
174 |
< |
int orthoRhombic_; |
172 |
> |
Mat3x3d hmat_; |
173 |
> |
Mat3x3d invHmat_; |
174 |
> |
int orthoRhombic_; |
175 |
|
|
176 |
< |
double chi_; |
177 |
< |
double integralOfChiDt_; |
178 |
< |
Mat3x3d eta_; |
176 |
> |
double chi_; |
177 |
> |
double integralOfChiDt_; |
178 |
> |
Mat3x3d eta_; |
179 |
|
|
180 |
< |
int id_; /**< identification number of the snapshot */ |
181 |
< |
}; |
180 |
> |
int id_; /**< identification number of the snapshot */ |
181 |
> |
}; |
182 |
|
|
183 |
< |
typedef DataStorage (Snapshot::*DataStoragePointer); |
183 |
> |
typedef DataStorage (Snapshot::*DataStoragePointer); |
184 |
|
} |
185 |
|
#endif //BRAINS_SNAPSHOT_HPP |