1 |
< |
/* |
2 |
< |
* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
3 |
< |
* |
4 |
< |
* Contact: oopse@oopse.org |
5 |
< |
* |
6 |
< |
* This program is free software; you can redistribute it and/or |
7 |
< |
* modify it under the terms of the GNU Lesser General Public License |
8 |
< |
* as published by the Free Software Foundation; either version 2.1 |
9 |
< |
* of the License, or (at your option) any later version. |
10 |
< |
* All we ask is that proper credit is given for our work, which includes |
11 |
< |
* - but is not limited to - adding the above copyright notice to the beginning |
12 |
< |
* of your source code files, and to any copyright notice that you may distribute |
13 |
< |
* with programs based on this work. |
14 |
< |
* |
15 |
< |
* This program is distributed in the hope that it will be useful, |
16 |
< |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
17 |
< |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
18 |
< |
* GNU Lesser General Public License for more details. |
19 |
< |
* |
20 |
< |
* You should have received a copy of the GNU Lesser General Public License |
21 |
< |
* along with this program; if not, write to the Free Software |
22 |
< |
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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. Acknowledgement of the program authors must be made in any |
10 |
+ |
* publication of scientific results based in part on use of the |
11 |
+ |
* program. An acceptable form of acknowledgement is citation of |
12 |
+ |
* the article in which the program was described (Matthew |
13 |
+ |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
14 |
+ |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
15 |
+ |
* Parallel Simulation Engine for Molecular Dynamics," |
16 |
+ |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 |
+ |
* |
18 |
+ |
* 2. Redistributions of source code must retain the above copyright |
19 |
+ |
* notice, this list of conditions and the following disclaimer. |
20 |
+ |
* |
21 |
+ |
* 3. Redistributions in binary form must reproduce the above copyright |
22 |
+ |
* notice, this list of conditions and the following disclaimer in the |
23 |
+ |
* documentation and/or other materials provided with the |
24 |
+ |
* distribution. |
25 |
+ |
* |
26 |
+ |
* This software is provided "AS IS," without a warranty of any |
27 |
+ |
* kind. All express or implied conditions, representations and |
28 |
+ |
* warranties, including any implied warranty of merchantability, |
29 |
+ |
* fitness for a particular purpose or non-infringement, are hereby |
30 |
+ |
* excluded. The University of Notre Dame and its licensors shall not |
31 |
+ |
* be liable for any damages suffered by licensee as a result of |
32 |
+ |
* using, modifying or distributing the software or its |
33 |
+ |
* derivatives. In no event will the University of Notre Dame or its |
34 |
+ |
* licensors be liable for any lost revenue, profit or data, or for |
35 |
+ |
* direct, indirect, special, consequential, incidental or punitive |
36 |
+ |
* damages, however caused and regardless of the theory of liability, |
37 |
+ |
* arising out of the use of or inability to use software, even if the |
38 |
+ |
* University of Notre Dame has been advised of the possibility of |
39 |
+ |
* such damages. |
40 |
|
*/ |
41 |
< |
|
41 |
> |
|
42 |
|
/** |
43 |
|
* @file Snapshot.hpp |
44 |
|
* @author tlin |
52 |
|
|
53 |
|
#include <vector> |
54 |
|
|
55 |
< |
#include "math/Vector3.hpp" |
56 |
< |
#include "math/SquareMatrix3.hpp" |
55 |
> |
#include "brains/DataStorage.hpp" |
56 |
> |
#include "brains/Stats.hpp" |
57 |
> |
#include "UseTheForce/DarkSide/simulation_interface.h" |
58 |
|
|
42 |
– |
using namespace std; |
43 |
– |
|
59 |
|
namespace oopse{ |
60 |
|
|
46 |
– |
|
47 |
– |
//forward declaration |
48 |
– |
class Snapshot; |
49 |
– |
class SnapshotManager; |
50 |
– |
class StuntDouble; |
51 |
– |
|
61 |
|
/** |
53 |
– |
* @class DataStorage |
54 |
– |
* @warning do not try to insert element into (or ease element from) private member data |
55 |
– |
* of DataStorage directly. |
56 |
– |
*/ |
57 |
– |
class DataStorage { |
58 |
– |
public: |
59 |
– |
|
60 |
– |
enum{ |
61 |
– |
slPosition = 1, |
62 |
– |
slVelocity = 2, |
63 |
– |
slAmat = 4, |
64 |
– |
slAngularMomentum = 8, |
65 |
– |
slUnitVector = 16, |
66 |
– |
slZAngle = 32, |
67 |
– |
slForce = 64, |
68 |
– |
slTorque = 128 |
69 |
– |
}; |
70 |
– |
|
71 |
– |
DataStorage(int size); |
72 |
– |
|
73 |
– |
/** return the size of this DataStorage */ |
74 |
– |
int size(); |
75 |
– |
void resize(int size); |
76 |
– |
void reserve(int size); |
77 |
– |
|
78 |
– |
void move(int source, int num, int target); |
79 |
– |
int getStorageLayout(); |
80 |
– |
void setStorageLayout(int layout); |
81 |
– |
|
82 |
– |
double *getArrayPointer(int ); |
83 |
– |
|
84 |
– |
friend class StuntDouble; |
85 |
– |
|
86 |
– |
private: |
87 |
– |
int size_; |
88 |
– |
int storageLayout_; |
89 |
– |
vector<Vector3d> position; /** position array */ |
90 |
– |
vector<Vector3d> velocity; /** velocity array */ |
91 |
– |
vector<RotMat3x3d> aMat; /** rotation matrix array */ |
92 |
– |
vector<Vector3d> angularMomentum;/** velocity array */ |
93 |
– |
vector<Vector3d> unitVector; /** the lab frame unit vector array*/ |
94 |
– |
vector<double> zAngle; /** z -angle array */ |
95 |
– |
vector<Vector3d> force; /** force array */ |
96 |
– |
vector<Vector3d> torque; /** torque array */ |
97 |
– |
}; |
98 |
– |
|
99 |
– |
/** |
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. |
105 |
– |
* @see SimData |
67 |
|
*/ |
68 |
|
class Snapshot { |
69 |
|
public: |
70 |
|
|
71 |
< |
Snapshot(int nAtoms, int nRigidbodies) { |
72 |
< |
atomData.resize(nAtoms); |
73 |
< |
rigidbodyData.resize(nRigidbodies); |
71 |
> |
Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies), |
72 |
> |
currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) { |
73 |
> |
|
74 |
|
} |
75 |
|
|
115 |
– |
Snapshot(const Snapshot& s); |
116 |
– |
|
117 |
– |
Snapshot& operator =(const Snapshot& s); |
76 |
|
|
77 |
|
/** Returns the id of this Snapshot */ |
78 |
|
int getID() { |
84 |
|
id_ = id; |
85 |
|
} |
86 |
|
|
129 |
– |
//template<typename T> |
130 |
– |
//static typename T::ElemPointerType getArrayPointer(vector<T>& v) { |
131 |
– |
// return v[0]->getArrayPointer(); |
132 |
– |
//} |
133 |
– |
|
87 |
|
int getSize() { |
88 |
< |
return atomData.size() + rigidbodyData.size(); |
88 |
> |
return atomData.getSize() + rigidbodyData.getSize(); |
89 |
|
} |
90 |
|
|
91 |
|
/** Returns the number of atoms */ |
92 |
|
int getNumberOfAtoms() { |
93 |
< |
return atomData.size(); |
93 |
> |
return atomData.getSize(); |
94 |
|
} |
95 |
|
|
96 |
|
/** Returns the number of rigid bodies */ |
97 |
|
int getNumberOfRigidBodies() { |
98 |
< |
return rigidbodyData.size(); |
98 |
> |
return rigidbodyData.getSize(); |
99 |
|
} |
100 |
|
|
101 |
|
/** Returns the H-Matrix */ |
104 |
|
} |
105 |
|
|
106 |
|
/** Sets the H-Matrix */ |
107 |
< |
void setHamt(const Mat3x3d& m) { |
108 |
< |
hmat_ = m; |
109 |
< |
invHmat_ = hmat_.inverse(); |
107 |
> |
void setHmat(const Mat3x3d& m); |
108 |
> |
|
109 |
> |
double getVolume() { |
110 |
> |
return hmat_.determinant(); |
111 |
|
} |
112 |
|
|
113 |
|
/** Returns the inverse H-Matrix */ |
114 |
|
Mat3x3d getInvHmat() { |
115 |
< |
return invHmat_ |
115 |
> |
return invHmat_; |
116 |
|
} |
117 |
|
|
118 |
< |
double getTimeStamp() { |
119 |
< |
return timeStamp_; |
118 |
> |
/** Wrapping the vector according to periodic boundary condition*/ |
119 |
> |
void wrapVector(Vector3d& v); |
120 |
> |
|
121 |
> |
|
122 |
> |
double getTime() { |
123 |
> |
return currentTime_; |
124 |
|
} |
125 |
|
|
126 |
< |
void setTimeStamp(double timeStamp) { |
127 |
< |
timeStamp_ =timeStamp; |
126 |
> |
void increaseTime(double dt) { |
127 |
> |
setTime(getTime() + dt); |
128 |
|
} |
129 |
|
|
130 |
+ |
void setTime(double time) { |
131 |
+ |
currentTime_ =time; |
132 |
+ |
//time at statData is redundant |
133 |
+ |
statData[Stats::TIME] = currentTime_; |
134 |
+ |
} |
135 |
|
|
136 |
+ |
double getChi() { |
137 |
+ |
return chi_; |
138 |
+ |
} |
139 |
+ |
|
140 |
+ |
void setChi(double chi) { |
141 |
+ |
chi_ = chi; |
142 |
+ |
} |
143 |
+ |
|
144 |
+ |
double getIntegralOfChiDt() { |
145 |
+ |
return integralOfChiDt_; |
146 |
+ |
} |
147 |
+ |
|
148 |
+ |
void setIntegralOfChiDt(double integralOfChiDt) { |
149 |
+ |
integralOfChiDt_ = integralOfChiDt; |
150 |
+ |
} |
151 |
+ |
|
152 |
+ |
Mat3x3d getEta() { |
153 |
+ |
return eta_; |
154 |
+ |
} |
155 |
+ |
|
156 |
+ |
void setEta(const Mat3x3d& eta) { |
157 |
+ |
eta_ = eta; |
158 |
+ |
} |
159 |
+ |
|
160 |
|
DataStorage atomData; |
161 |
|
DataStorage rigidbodyData; |
162 |
+ |
Stats statData; |
163 |
|
|
176 |
– |
friend class StuntDouble; |
177 |
– |
|
164 |
|
private: |
165 |
< |
double timeStamp_; |
165 |
> |
double currentTime_; |
166 |
> |
|
167 |
|
Mat3x3d hmat_; |
168 |
|
Mat3x3d invHmat_; |
169 |
+ |
int orthoRhombic_; |
170 |
+ |
|
171 |
+ |
double chi_; |
172 |
+ |
double integralOfChiDt_; |
173 |
+ |
Mat3x3d eta_; |
174 |
+ |
|
175 |
|
int id_; /**< identification number of the snapshot */ |
176 |
|
}; |
177 |
|
|