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Revision 146 by tim, Fri Oct 22 23:09:57 2004 UTC vs.
Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC

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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.
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   */
25 –
26 – /**
27 –  * @file Snapshot.hpp
28 –  * @author tlin
29 –  * @date 10/20/2004
30 –  * @time 23:56am
31 –  * @version 1.0
32 –  */
41    
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
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;
59  
60   namespace oopse{
61  
62 <    //forward declaration
63 <    class Snapshot;
64 <    class SnapshotManager;
65 <
66 <    /**
67 <     * @struct DataStorage
68 <     * @brief
69 <     */
70 <    class DataStorage {
55 <        public:
56 <            DataStorage() {};
57 <            DataStorage(size_t size);
58 <            void resize(size_t size);
59 <            void reserve(size_t size);
62 >  /**
63 >   * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
64 >   * @brief Snapshot class is a repository class for storing dynamic data during
65 >   *  Simulation
66 >   * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
67 >   *  for rigid bodies.
68 >   */
69 >  class Snapshot {
70 >  public:
71              
72 <        //friend Snapshot;
73 <        //friend SnapshotManager;
74 <        //private:
75 <            vector<Vector3d> position;               /** position array */
76 <            vector<Vector3d> velocity;               /** velocity array */
77 <            vector<RotMat3x3d> Amat;            /** rotation matrix array */
78 <            vector<Vector3d> angularMomentum;/** velocity array */
79 <            vector<Vector3d> ul;                /** the lab frame unit vector array*/
80 <            vector<double> zAngle;              /** z -angle array */        
70 <            vector<Vector3d> force;               /** force array */
71 <            vector<Vector3d> torque;               /** torque array */
72 >    Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms),
73 >                                             rigidbodyData(nRigidbodies),
74 >                                             currentTime_(0),
75 >                                             orthoTolerance_(1e-6),
76 >                                             orthoRhombic_(0),
77 >                                             chi_(0.0),
78 >                                             integralOfChiDt_(0.0),
79 >                                             eta_(0.0), id_(-1),
80 >                                             hasCOM_(false) {
81  
82 <    };
82 >    }
83  
84 <    /**
85 <     * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
86 <     * @brief Snapshot class is a repository class for storing dynamic data during
87 <     *  Simulation
88 <     * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
89 <     *  for rigid bodies.
90 <     * @see SimData
82 <     */
83 <    class Snapshot {
84 <        public:
84 >    Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
85 >      : atomData(nAtoms, storageLayout),
86 >        rigidbodyData(nRigidbodies, storageLayout),
87 >        currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0),
88 >        integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false)  {
89 >
90 >      }
91              
92 <            Snapshot() {}
93 <            Snapshot(int i) {
92 >    /** Returns the id of this Snapshot */
93 >    int getID() {
94 >      return id_;
95 >    }
96  
97 <            }
97 >    /** Sets the id of this Snapshot */
98 >    void setID(int id) {
99 >      id_ = id;
100 >    }
101  
102 <            Snapshot(const Snapshot& s);
102 >    int getSize() {
103 >      return atomData.getSize() + rigidbodyData.getSize();
104 >    }
105  
106 <            Snapshot& operator =(const Snapshot& s);
107 <            
108 <            /** Returns the id of this Snapshot */
109 <            int getID() {
97 <                return id_;
98 <            }
106 >    /** Returns the number of atoms */
107 >    int getNumberOfAtoms() {
108 >      return atomData.getSize();
109 >    }
110  
111 <            /** Sets the id of this Snapshot */
112 <            void setID(int id) {
113 <                id_ = id;
114 <            }
111 >    /** Returns the number of rigid bodies */
112 >    int getNumberOfRigidBodies() {
113 >      return rigidbodyData.getSize();
114 >    }
115  
116 <            //template<typename T>
117 <            //static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
118 <            //    return v[0]->getArrayPointer();
119 <            //}
116 >    /** Returns the H-Matrix */
117 >    Mat3x3d getHmat() {
118 >      return hmat_;
119 >    }
120  
121 <            static double* getArrayPointer(vector<Vector3d>& v) {
122 <                assert(v.size() > 0);
112 <                return v[0].getArrayPointer();
113 <            }
121 >    /** Sets the H-Matrix */
122 >    void setHmat(const Mat3x3d& m);
123              
124 <            static double* getArrayPointer(vector<RotMat3x3d>& v) {
125 <                assert(v.size() > 0);
126 <                return v[0].getArrayPointer();
127 <            }
124 >    RealType getVolume() {
125 >      return hmat_.determinant();
126 >    }
127 >
128 >    /** Returns the inverse H-Matrix */
129 >    Mat3x3d getInvHmat() {
130 >      return invHmat_;
131 >    }
132 >
133 >    /** Wrapping the vector according to periodic boundary condition*/
134 >    void wrapVector(Vector3d& v);
135 >    Vector3d getCOM();
136 >    Vector3d getCOMvel();
137 >    Vector3d getCOMw();
138              
139 <            static double* getArrayPointer(vector<double>& v) {
140 <                assert(v.size() > 0);
141 <                return &(v[0]);
142 <            }
139 >    RealType getTime() {
140 >      return currentTime_;
141 >    }
142 >
143 >    void increaseTime(RealType dt) {
144 >      setTime(getTime() + dt);
145 >    }
146 >
147 >    void setTime(RealType time) {
148 >      currentTime_ =time;
149 >      //time at statData is redundant
150 >      statData[Stats::TIME] = currentTime_;
151 >    }
152 >
153 >    RealType getChi() {
154 >      return chi_;
155 >    }
156 >
157 >    void setChi(RealType chi) {
158 >      chi_ = chi;
159 >    }
160 >
161 >    RealType getIntegralOfChiDt() {
162 >      return integralOfChiDt_;
163 >    }
164 >
165 >    void setIntegralOfChiDt(RealType integralOfChiDt) {
166 >      integralOfChiDt_ = integralOfChiDt;
167 >    }
168              
125 –            /** */
126 –            void resize(size_t size);
169  
170 +    void setOrthoTolerance(RealType orthoTolerance) {
171 +      orthoTolerance_ = orthoTolerance;
172 +    }
173  
174 <            /** */
175 <            void reserve(size_t size);
174 >    Mat3x3d getEta() {
175 >      return eta_;
176 >    }
177  
178 <            DataStorage atomData;
179 <            DataStorage rigidbodyData;
178 >    void setEta(const Mat3x3d& eta) {
179 >      eta_ = eta;
180 >    }
181  
182 <            friend class SnapshotManager;
183 <        private:
182 >    bool hasCOM() {
183 >      return hasCOM_;
184 >    }
185  
186 <            int id_; /**< identification number of the snapshot */
187 <    };
186 >    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
187 >      COM_ = COM;
188 >      COMvel_ = COMvel;
189 >      COMw_ = COMw;
190 >      hasCOM_ = true;
191 >    }
192 >                  
193 >    DataStorage atomData;
194 >    DataStorage rigidbodyData;
195 >    Stats statData;
196 >            
197 >  private:
198 >    RealType currentTime_;
199  
200 <    typedef DataStorage* (Snapshot::*DataStoragePointer);
200 >    Mat3x3d hmat_;
201 >    Mat3x3d invHmat_;
202 >    RealType orthoTolerance_;
203 >    int orthoRhombic_;
204 >
205 >    RealType chi_;
206 >    RealType integralOfChiDt_;
207 >    Mat3x3d eta_;
208 >    Vector3d COM_;
209 >    Vector3d COMvel_;
210 >    Vector3d COMw_;
211 >    bool hasCOM_;
212 >            
213 >    int id_; /**< identification number of the snapshot */
214 >  };
215 >
216 >  typedef DataStorage (Snapshot::*DataStoragePointer);
217   }
218   #endif //BRAINS_SNAPSHOT_HPP

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