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Comparing trunk/src/brains/Snapshot.hpp (file contents):
Revision 146 by tim, Fri Oct 22 23:09:57 2004 UTC vs.
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC

# Line 1 | Line 1
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
# Line 36 | Line 52
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 –    //forward declaration
47 –    class Snapshot;
48 –    class SnapshotManager;
49 –
61      /**
51 –     * @struct DataStorage
52 –     * @brief
53 –     */
54 –    class DataStorage {
55 –        public:
56 –            DataStorage() {};
57 –            DataStorage(size_t size);
58 –            void resize(size_t size);
59 –            void reserve(size_t size);
60 –            
61 –        //friend Snapshot;
62 –        //friend SnapshotManager;
63 –        //private:
64 –            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 */
72 –
73 –    };
74 –
75 –    /**
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.
81 –     * @see SimData
67       */
68      class Snapshot {
69          public:
70              
71 <            Snapshot() {}
72 <            Snapshot(int i) {
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  
91 –            Snapshot(const Snapshot& s);
92 –
93 –            Snapshot& operator =(const Snapshot& s);
76              
77              /** Returns the id of this Snapshot */
78              int getID() {
# Line 102 | Line 84 | namespace oopse{
84                  id_ = id;
85              }
86  
87 <            //template<typename T>
88 <            //static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
89 <            //    return v[0]->getArrayPointer();
108 <            //}
87 >            int getSize() {
88 >                return atomData.getSize() + rigidbodyData.getSize();
89 >            }
90  
91 <            static double* getArrayPointer(vector<Vector3d>& v) {
92 <                assert(v.size() > 0);
93 <                return v[0].getArrayPointer();
91 >            /** Returns the number of atoms */
92 >            int getNumberOfAtoms() {
93 >                return atomData.getSize();
94              }
95 <            
96 <            static double* getArrayPointer(vector<RotMat3x3d>& v) {
97 <                assert(v.size() > 0);
98 <                return v[0].getArrayPointer();
95 >
96 >            /** Returns the number of rigid bodies */
97 >            int getNumberOfRigidBodies() {
98 >                return rigidbodyData.getSize();
99              }
100 +
101 +            /** Returns the H-Matrix */
102 +            Mat3x3d getHmat() {
103 +                return hmat_;
104 +            }
105 +
106 +            /** Sets the H-Matrix */
107 +            void setHmat(const Mat3x3d& m);
108              
109 <            static double* getArrayPointer(vector<double>& v) {
110 <                assert(v.size() > 0);
122 <                return &(v[0]);
109 >            double getVolume() {
110 >                return hmat_.determinant();
111              }
112 +
113 +            /** Returns the inverse H-Matrix */
114 +            Mat3x3d getInvHmat() {
115 +                return invHmat_;
116 +            }
117 +
118 +            /** Wrapping the vector according to periodic boundary condition*/
119 +            void wrapVector(Vector3d& v);
120 +
121              
122 <            /** */
123 <            void resize(size_t size);
122 >            double getTime() {
123 >                return currentTime_;
124 >            }
125  
126 +            void increaseTime(double dt) {
127 +                setTime(getTime() + dt);
128 +            }
129  
130 <            /** */
131 <            void reserve(size_t size);
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 <
163 <            friend class SnapshotManager;
162 >            Stats statData;
163 >            
164          private:
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  
178 <    typedef DataStorage* (Snapshot::*DataStoragePointer);
178 >    typedef DataStorage (Snapshot::*DataStoragePointer);
179   }
180   #endif //BRAINS_SNAPSHOT_HPP

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