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Revision 152 by tim, Tue Oct 26 17:28:53 2004 UTC vs.
Revision 1287 by gezelter, Wed Sep 10 18:11:32 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 +  /**
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) {
81  
82 <    //forward declaration
48 <    class Snapshot;
49 <    class SnapshotManager;
50 <    class StuntDouble;
51 <    
52 <    /**
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:
82 >    }
83  
84 <            enum{
85 <                slPosition = 1,
86 <                slVelocity = 2,
87 <                slAmat = 4,
88 <                slAngularMomentum = 8,
89 <                slUnitVector = 16,
90 <                slZAngle = 32,
67 <                slForce = 64,
68 <                slTorque = 128
69 <            };
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 <            DataStorage(int size);
92 >    /** Returns the id of this Snapshot */
93 >    int getID() {
94 >      return id_;
95 >    }
96  
97 <            /** return the size of this DataStorage */
98 <            int size();
99 <            void resize(int size);
100 <            void reserve(int size);
97 >    /** Sets the id of this Snapshot */
98 >    void setID(int id) {
99 >      id_ = id;
100 >    }
101  
102 <            void move(int source, int num, int target);
103 <            int getStorageLayout();
104 <            void setStorageLayout(int layout);
102 >    int getSize() {
103 >      return atomData.getSize() + rigidbodyData.getSize();
104 >    }
105  
106 <            double *getArrayPointer(int );
106 >    /** Returns the number of atoms */
107 >    int getNumberOfAtoms() {
108 >      return atomData.getSize();
109 >    }
110  
111 <            friend class StuntDouble;
111 >    /** Returns the number of rigid bodies */
112 >    int getNumberOfRigidBodies() {
113 >      return rigidbodyData.getSize();
114 >    }
115  
116 <        private:
117 <            int size_;
118 <            int storageLayout_;
119 <            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 <    };
116 >    /** Returns the H-Matrix */
117 >    Mat3x3d getHmat() {
118 >      return hmat_;
119 >    }
120  
121 <    /**
122 <     * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
101 <     * @brief Snapshot class is a repository class for storing dynamic data during
102 <     *  Simulation
103 <     * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
104 <     *  for rigid bodies.
105 <     * @see SimData
106 <     */
107 <    class Snapshot {
108 <        public:
121 >    /** Sets the H-Matrix */
122 >    void setHmat(const Mat3x3d& m);
123              
124 <            Snapshot(int nAtoms, int nRigidbodies) {
125 <                atomData.resize(nAtoms);
126 <                rigidbodyData.resize(nRigidbodies);
113 <            }
124 >    RealType getVolume() {
125 >      return hmat_.determinant();
126 >    }
127  
128 <            Snapshot(const Snapshot& s);
128 >    /** Returns the inverse H-Matrix */
129 >    Mat3x3d getInvHmat() {
130 >      return invHmat_;
131 >    }
132  
133 <            Snapshot& operator =(const Snapshot& s);
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 <            /** Returns the id of this Snapshot */
140 <            int getID() {
141 <                return id_;
122 <            }
139 >    RealType getTime() {
140 >      return currentTime_;
141 >    }
142  
143 <            /** Sets the id of this Snapshot */
144 <            void setID(int id) {
145 <                id_ = id;
127 <            }
143 >    void increaseTime(RealType dt) {
144 >      setTime(getTime() + dt);
145 >    }
146  
147 <            //template<typename T>
148 <            //static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
149 <            //    return v[0]->getArrayPointer();
150 <            //}
147 >    void setTime(RealType time) {
148 >      currentTime_ =time;
149 >      //time at statData is redundant
150 >      statData[Stats::TIME] = currentTime_;
151 >    }
152  
153 <            int getSize() {
154 <                return atomData.size() + rigidbodyData.size();
155 <            }
153 >    RealType getChi() {
154 >      return chi_;
155 >    }
156  
157 <            /** Returns the number of atoms */
158 <            int getNumberOfAtoms() {
159 <                return atomData.size();
141 <            }
157 >    void setChi(RealType chi) {
158 >      chi_ = chi;
159 >    }
160  
161 <            /** Returns the number of rigid bodies */
162 <            int getNumberOfRigidBodies() {
163 <                return rigidbodyData.size();
146 <            }
161 >    RealType getIntegralOfChiDt() {
162 >      return integralOfChiDt_;
163 >    }
164  
165 <            /** Returns the H-Matrix */
166 <            Mat3x3d getHmat() {
167 <                return hmat_;
168 <            }
165 >    void setIntegralOfChiDt(RealType integralOfChiDt) {
166 >      integralOfChiDt_ = integralOfChiDt;
167 >    }
168 >            
169  
170 <            /** Sets the H-Matrix */
171 <            void setHamt(const Mat3x3d& m) {
172 <                hmat_ = m;
156 <                invHmat_ = hmat_.inverse();
157 <            }
170 >    void setOrthoTolerance(RealType orthoTolerance) {
171 >      orthoTolerance_ = orthoTolerance;
172 >    }
173  
174 <            /** Returns the inverse H-Matrix */
175 <            Mat3x3d getInvHmat() {
176 <                return invHmat_
162 <            }
174 >    Mat3x3d getEta() {
175 >      return eta_;
176 >    }
177  
178 <            double getTimeStamp() {
179 <                return timeStamp_;
180 <            }
178 >    void setEta(const Mat3x3d& eta) {
179 >      eta_ = eta;
180 >    }
181  
182 <            void setTimeStamp(double timeStamp) {
183 <                timeStamp_ =timeStamp;
184 <            }
182 >    bool hasCOM() {
183 >      return hasCOM_;
184 >    }
185  
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 <            DataStorage atomData;
201 <            DataStorage rigidbodyData;
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 >    int id_; /**< identification number of the snapshot */
212 >    bool hasCOM_;
213              
214 <            friend class StuntDouble;
177 <            
178 <        private:
179 <            double timeStamp_;
180 <            Mat3x3d hmat_;
181 <            Mat3x3d invHmat_;
182 <            int id_; /**< identification number of the snapshot */
183 <    };
214 >  };
215  
216 <    typedef DataStorage (Snapshot::*DataStoragePointer);
216 >  typedef DataStorage (Snapshot::*DataStoragePointer);
217   }
218   #endif //BRAINS_SNAPSHOT_HPP

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