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Revision 146 by tim, Fri Oct 22 23:09:57 2004 UTC vs.
Revision 1302 by chuckv, Tue Oct 7 17:12:48 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;
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 >    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), hasVolume_(false), volume_(0.0) {
81  
82 <    /**
83 <     * @struct DataStorage
84 <     * @brief
85 <     */
86 <    class DataStorage {
87 <        public:
88 <            DataStorage() {};
89 <            DataStorage(size_t size);
90 <            void resize(size_t size);
59 <            void reserve(size_t size);
82 >    }
83 >
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), hasVolume_(false),volume_(0.0)  {
89 >
90 >      }
91              
92 <        //friend Snapshot;
93 <        //friend SnapshotManager;
94 <        //private:
95 <            vector<Vector3d> position;               /** position array */
65 <            vector<Vector3d> velocity;               /** velocity array */
66 <            vector<RotMat3x3d> Amat;            /** rotation matrix array */
67 <            vector<Vector3d> angularMomentum;/** velocity array */
68 <            vector<Vector3d> ul;                /** the lab frame unit vector array*/
69 <            vector<double> zAngle;              /** z -angle array */        
70 <            vector<Vector3d> force;               /** force array */
71 <            vector<Vector3d> torque;               /** torque array */
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 <    /**
103 <     * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
104 <     * @brief Snapshot class is a repository class for storing dynamic data during
105 <     *  Simulation
106 <     * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
107 <     *  for rigid bodies.
108 <     * @see SimData
109 <     */
110 <    class Snapshot {
111 <        public:
102 >    int getSize() {
103 >      return atomData.getSize() + rigidbodyData.getSize();
104 >    }
105 >
106 >    /** Returns the number of atoms */
107 >    int getNumberOfAtoms() {
108 >      return atomData.getSize();
109 >    }
110 >
111 >    /** Returns the number of rigid bodies */
112 >    int getNumberOfRigidBodies() {
113 >      return rigidbodyData.getSize();
114 >    }
115 >
116 >    /** Returns the H-Matrix */
117 >    Mat3x3d getHmat() {
118 >      return hmat_;
119 >    }
120 >
121 >    /** Sets the H-Matrix */
122 >    void setHmat(const Mat3x3d& m);
123              
124 <            Snapshot() {}
125 <            Snapshot(int i) {
124 >    RealType getVolume() {
125 >      if (hasVolume_){
126 >        return volume_;
127 >      }else{
128 >        return hmat_.determinant();
129 >      }
130 >    }
131  
132 <            }
132 >    void setVolume(RealType volume){
133 >      hasVolume_=true;
134 >      volume_ = volume;
135 >    }
136  
137 <            Snapshot(const Snapshot& s);
137 >    /** Returns the inverse H-Matrix */
138 >    Mat3x3d getInvHmat() {
139 >      return invHmat_;
140 >    }
141  
142 <            Snapshot& operator =(const Snapshot& s);
142 >    /** Wrapping the vector according to periodic boundary condition*/
143 >    void wrapVector(Vector3d& v);
144 >    Vector3d getCOM();
145 >    Vector3d getCOMvel();
146 >    Vector3d getCOMw();
147              
148 <            /** Returns the id of this Snapshot */
149 <            int getID() {
150 <                return id_;
98 <            }
148 >    RealType getTime() {
149 >      return currentTime_;
150 >    }
151  
152 <            /** Sets the id of this Snapshot */
153 <            void setID(int id) {
154 <                id_ = id;
103 <            }
152 >    void increaseTime(RealType dt) {
153 >      setTime(getTime() + dt);
154 >    }
155  
156 <            //template<typename T>
157 <            //static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
158 <            //    return v[0]->getArrayPointer();
159 <            //}
156 >    void setTime(RealType time) {
157 >      currentTime_ =time;
158 >      //time at statData is redundant
159 >      statData[Stats::TIME] = currentTime_;
160 >    }
161  
162 <            static double* getArrayPointer(vector<Vector3d>& v) {
163 <                assert(v.size() > 0);
164 <                return v[0].getArrayPointer();
165 <            }
162 >    RealType getChi() {
163 >      return chi_;
164 >    }
165 >
166 >    void setChi(RealType chi) {
167 >      chi_ = chi;
168 >    }
169 >
170 >    RealType getIntegralOfChiDt() {
171 >      return integralOfChiDt_;
172 >    }
173 >
174 >    void setIntegralOfChiDt(RealType integralOfChiDt) {
175 >      integralOfChiDt_ = integralOfChiDt;
176 >    }
177              
115 –            static double* getArrayPointer(vector<RotMat3x3d>& v) {
116 –                assert(v.size() > 0);
117 –                return v[0].getArrayPointer();
118 –            }
119 –            
120 –            static double* getArrayPointer(vector<double>& v) {
121 –                assert(v.size() > 0);
122 –                return &(v[0]);
123 –            }
124 –            
125 –            /** */
126 –            void resize(size_t size);
178  
179 +    void setOrthoTolerance(RealType orthoTolerance) {
180 +      orthoTolerance_ = orthoTolerance;
181 +    }
182  
183 <            /** */
184 <            void reserve(size_t size);
183 >    Mat3x3d getEta() {
184 >      return eta_;
185 >    }
186  
187 <            DataStorage atomData;
188 <            DataStorage rigidbodyData;
187 >    void setEta(const Mat3x3d& eta) {
188 >      eta_ = eta;
189 >    }
190  
191 <            friend class SnapshotManager;
192 <        private:
191 >    bool hasCOM() {
192 >      return hasCOM_;
193 >    }
194  
195 <            int id_; /**< identification number of the snapshot */
196 <    };
195 >    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
196 >      COM_ = COM;
197 >      COMvel_ = COMvel;
198 >      COMw_ = COMw;
199 >      hasCOM_ = true;
200 >    }
201 >                  
202 >    DataStorage atomData;
203 >    DataStorage rigidbodyData;
204 >    Stats statData;
205 >            
206 >  private:
207 >    RealType currentTime_;
208  
209 <    typedef DataStorage* (Snapshot::*DataStoragePointer);
209 >    Mat3x3d hmat_;
210 >    Mat3x3d invHmat_;
211 >    RealType orthoTolerance_;
212 >    int orthoRhombic_;
213 >    RealType volume_;
214 >
215 >    RealType chi_;
216 >    RealType integralOfChiDt_;
217 >    Mat3x3d eta_;
218 >    Vector3d COM_;
219 >    Vector3d COMvel_;
220 >    Vector3d COMw_;
221 >    int id_; /**< identification number of the snapshot */
222 >    bool hasCOM_;
223 >    bool hasVolume_;
224 >            
225 >  };
226 >
227 >  typedef DataStorage (Snapshot::*DataStoragePointer);
228   }
229   #endif //BRAINS_SNAPSHOT_HPP

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