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Comparing trunk/src/brains/Snapshot.hpp (file contents):
Revision 122 by tim, Wed Oct 20 05:52:25 2004 UTC vs.
Revision 1112 by chuckv, Wed Jan 3 20:47:00 2007 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   */
41 <
42 < /**
43 <  * @file Snapshot.hpp
44 <  * @author tlin
45 <  * @date 10/20/2004
46 <  * @time 23:56am
47 <  * @version 1.0
48 <  */
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 "brains/DataStorage.hpp"
56 + #include "brains/Stats.hpp"
57 + #include "UseTheForce/DarkSide/simulation_interface.h"
58 +
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 <     * @see SimData
67 <     */
68 <    class Snapshot {
69 <        public:
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 <            PropertyMap properties_;
72 >    Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
73 >                                             currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false) {
74 >
75 >    }
76 >
77 >    Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
78 >      : atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
79 >        currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false)  {
80 >
81 >      }
82              
83 <        private:
83 >    /** Returns the id of this Snapshot */
84 >    int getID() {
85 >      return id_;
86 >    }
87 >
88 >    /** Sets the id of this Snapshot */
89 >    void setID(int id) {
90 >      id_ = id;
91 >    }
92 >
93 >    int getSize() {
94 >      return atomData.getSize() + rigidbodyData.getSize();
95 >    }
96 >
97 >    /** Returns the number of atoms */
98 >    int getNumberOfAtoms() {
99 >      return atomData.getSize();
100 >    }
101 >
102 >    /** Returns the number of rigid bodies */
103 >    int getNumberOfRigidBodies() {
104 >      return rigidbodyData.getSize();
105 >    }
106 >
107 >    /** Returns the H-Matrix */
108 >    Mat3x3d getHmat() {
109 >      return hmat_;
110 >    }
111 >
112 >    /** Sets the H-Matrix */
113 >    void setHmat(const Mat3x3d& m);
114              
115 <    };
115 >    RealType getVolume() {
116 >      return hmat_.determinant();
117 >    }
118  
119 +    /** Returns the inverse H-Matrix */
120 +    Mat3x3d getInvHmat() {
121 +      return invHmat_;
122 +    }
123 +
124 +    /** Wrapping the vector according to periodic boundary condition*/
125 +    void wrapVector(Vector3d& v);
126 +    Vector3d getCOM();
127 +    Vector3d getCOMvel();
128 +    Vector3d getCOMw();
129 +            
130 +    RealType getTime() {
131 +      return currentTime_;
132 +    }
133 +
134 +    void increaseTime(RealType dt) {
135 +      setTime(getTime() + dt);
136 +    }
137 +
138 +    void setTime(RealType time) {
139 +      currentTime_ =time;
140 +      //time at statData is redundant
141 +      statData[Stats::TIME] = currentTime_;
142 +    }
143 +
144 +    RealType getChi() {
145 +      return chi_;
146 +    }
147 +
148 +    void setChi(RealType chi) {
149 +      chi_ = chi;
150 +    }
151 +
152 +    RealType getIntegralOfChiDt() {
153 +      return integralOfChiDt_;
154 +    }
155 +
156 +    void setIntegralOfChiDt(RealType integralOfChiDt) {
157 +      integralOfChiDt_ = integralOfChiDt;
158 +    }
159 +            
160 +
161 +    void setOrthoTolerance(RealType orthoTolerance) {
162 +      orthoTolerance_ = orthoTolerance;
163 +    }
164 +
165 +    Mat3x3d getEta() {
166 +      return eta_;
167 +    }
168 +
169 +    void setEta(const Mat3x3d& eta) {
170 +      eta_ = eta;
171 +    }
172 +
173 +    bool hasCOM() {
174 +      return hasCOM_;
175 +    }
176 +
177 +    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
178 +      COM_ = COM;
179 +      COMvel_ = COMvel;
180 +      COMw_ = COMw;
181 +      hasCOM_ = true;
182 +    }
183 +                  
184 +    DataStorage atomData;
185 +    DataStorage rigidbodyData;
186 +    Stats statData;
187 +            
188 +  private:
189 +    RealType currentTime_;
190 +
191 +    Mat3x3d hmat_;
192 +    Mat3x3d invHmat_;
193 +    RealType orthoTolerance_;
194 +    int orthoRhombic_;
195 +
196 +    RealType chi_;
197 +    RealType integralOfChiDt_;
198 +    Mat3x3d eta_;
199 +    Vector3d COM_;
200 +    Vector3d COMvel_;
201 +    Vector3d COMw_;
202 +    bool hasCOM_;
203 +            
204 +    int id_; /**< identification number of the snapshot */
205 +  };
206 +
207 +  typedef DataStorage (Snapshot::*DataStoragePointer);
208   }
209   #endif //BRAINS_SNAPSHOT_HPP

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