49 |
|
* Simulation |
50 |
|
* Every snapshot class will contain one DataStorage for atoms and one DataStorage |
51 |
|
* for rigid bodies. |
52 |
– |
* @see SimData |
52 |
|
*/ |
53 |
|
class Snapshot { |
54 |
|
public: |
55 |
|
|
56 |
< |
Snapshot(int nAtoms, int nRigidbodies) { |
56 |
> |
Snapshot(int nAtoms, int nRigidbodies) : currentTime_(0), chi_(0), integralOfChiDt_(0), eta_(0) { |
57 |
|
atomData.resize(nAtoms); |
58 |
|
rigidbodyData.resize(nRigidbodies); |
59 |
|
} |
60 |
|
|
62 |
– |
Snapshot(const Snapshot& s); |
63 |
– |
|
64 |
– |
Snapshot& operator =(const Snapshot& s); |
61 |
|
|
62 |
|
/** Returns the id of this Snapshot */ |
63 |
|
int getID() { |
89 |
|
} |
90 |
|
|
91 |
|
/** Sets the H-Matrix */ |
92 |
< |
void setHamt(const Mat3x3d& m) { |
92 |
> |
void setHmat(const Mat3x3d& m) { |
93 |
|
hmat_ = m; |
94 |
|
invHmat_ = hmat_.inverse(); |
95 |
+ |
|
96 |
+ |
//notify fortran Hmat is changed |
97 |
+ |
double fortranHmat[9]; |
98 |
+ |
double fortranInvHmat[9]; |
99 |
+ |
hmat_.getArray(fortranHmat); |
100 |
+ |
invHmat_.getArray(fortranInvHmat); |
101 |
+ |
setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_); |
102 |
|
} |
103 |
|
|
104 |
+ |
void getVolume() { |
105 |
+ |
return hmat_.determinant(); |
106 |
+ |
} |
107 |
+ |
|
108 |
|
/** Returns the inverse H-Matrix */ |
109 |
|
Mat3x3d getInvHmat() { |
110 |
|
return invHmat_; |
111 |
|
} |
112 |
|
|
113 |
< |
double getTimeStamp() { |
114 |
< |
return timeStamp_; |
113 |
> |
/** Wrapping the vector according to periodic boundary condition*/ |
114 |
> |
void wrapVector(Vector3d& v); |
115 |
> |
|
116 |
> |
|
117 |
> |
double getTime() { |
118 |
> |
return currentTime_; |
119 |
|
} |
120 |
|
|
121 |
< |
void setTimeStamp(double timeStamp) { |
122 |
< |
timeStamp_ =timeStamp; |
121 |
> |
void setTime(double time) { |
122 |
> |
currentTime_ =time; |
123 |
> |
//time at statData is redundant |
124 |
> |
statData[Stats::TIME] = currentTime_; |
125 |
|
} |
126 |
|
|
127 |
+ |
double getChi() { |
128 |
+ |
return chi_; |
129 |
+ |
} |
130 |
+ |
|
131 |
+ |
void setChi(double chi) { |
132 |
+ |
chi_ = chi; |
133 |
+ |
} |
134 |
+ |
|
135 |
+ |
double getIntegralOfChiDt() { |
136 |
+ |
return integralOfChiDt_; |
137 |
+ |
} |
138 |
+ |
|
139 |
+ |
void setIntegralOfChiDt(double integralOfChiDt) { |
140 |
+ |
integralOfChiDt_ = integralOfChiDt; |
141 |
+ |
} |
142 |
+ |
|
143 |
+ |
Mat3x3d getEta() { |
144 |
+ |
return eta_; |
145 |
+ |
} |
146 |
+ |
|
147 |
+ |
void setEta(const Mat3x3d& eta) { |
148 |
+ |
eta_ = eta; |
149 |
+ |
} |
150 |
+ |
|
151 |
|
DataStorage atomData; |
152 |
|
DataStorage rigidbodyData; |
153 |
|
Stats statData; |
154 |
|
|
155 |
|
private: |
156 |
< |
double timeStamp_; |
156 |
> |
double currentTime_; |
157 |
> |
|
158 |
|
Mat3x3d hmat_; |
159 |
|
Mat3x3d invHmat_; |
160 |
+ |
int orthoRhombic_; |
161 |
+ |
|
162 |
+ |
double chi_; |
163 |
+ |
double integralOfChiDt_; |
164 |
+ |
Mat3x3d eta_; |
165 |
+ |
|
166 |
|
int id_; /**< identification number of the snapshot */ |
167 |
|
}; |
168 |
|
|