ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-2.0/src/brains/Snapshot.hpp
(Generate patch)

Comparing trunk/OOPSE-2.0/src/brains/Snapshot.hpp (file contents):
Revision 1630 by tim, Thu Oct 21 21:31:39 2004 UTC vs.
Revision 1930 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 30 | Line 46
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  
41 – using namespace std;
42 –
59   namespace oopse{
60  
61      /**
62       * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
63       * @brief Snapshot class is a repository class for storing dynamic data during
64       *  Simulation
65 <     * @see SimData
65 >     * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
66 >     *  for rigid bodies.
67       */
68      class Snapshot {
69          public:
70 +            
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  
54 –            Snapshot(int i) {
55 –
74              }
75  
58 –            Snapshot(const Snapshot& s);
59 –
60 –            Snapshot& operator =(const Snapshot& s);
76              
77              /** Returns the id of this Snapshot */
78              int getID() {
# Line 69 | Line 84 | namespace oopse{
84                  id_ = id;
85              }
86  
87 <            /** */
88 <            Snapshot* clone() {
74 <                return new Snapshot(*this);
87 >            int getSize() {
88 >                return atomData.getSize() + rigidbodyData.getSize();
89              }
90  
91 +            /** Returns the number of atoms */
92 +            int getNumberOfAtoms() {
93 +                return atomData.getSize();
94 +            }
95  
96 <            //template<typename T>
97 <            //static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
98 <            //    return v[0]->getArrayPointer();
99 <            //}
96 >            /** Returns the number of rigid bodies */
97 >            int getNumberOfRigidBodies() {
98 >                return rigidbodyData.getSize();
99 >            }
100  
101 <            static double* getArrayPointer(vector<Vector3d>& v) {
102 <                return v[0].getArrayPointer();
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<RotMat3x3d>& v) {
110 <                return v[0].getArrayPointer();
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 <            static double* getArrayPointer(vector<double>& v) {
123 <                assert(v.size() > 0);
93 <                return &(v[0]);
122 >            double getTime() {
123 >                return currentTime_;
124              }
125 +
126 +            void increaseTime(double dt) {
127 +                setTime(getTime() + dt);
128 +            }
129 +
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 <            vector<Vector3d> pos;
153 <            vector<Vector3d> vel;
154 <            vector<Vector3d> frc;
155 <            vector<Vector3d> trq;
156 <            vector<RotMat3x3d> Amat;
157 <            vector<Vector3d> mu;
158 <            vector<Vector3d> ul;
103 <            vector<double> zAngle;
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 +            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);
179   }
180   #endif //BRAINS_SNAPSHOT_HPP

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines