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Comparing trunk/OOPSE-2.0/src/brains/Snapshot.hpp (file contents):
Revision 1642 by tim, Mon Oct 25 04:08:14 2004 UTC vs.
Revision 2000 by tim, Fri Feb 11 22:41:02 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 –    enum DataStorageLayout {
47 –        dslPosition = 1,
48 –        dslVelocity = 2,
49 –        dslAMat = 4,
50 –        dslAngularMomentum = 8,
51 –        dslUnitVector = 16,
52 –        dslZAngle = 32,
53 –        dslForce = 64,
54 –        dslTorque = 128
55 –    };
56 –    //forward declaration
57 –    class Snapshot;
58 –    class SnapshotManager;
59 –    class StuntDouble;
60 –    
61      /**
62 –     * @class DataStorage
63 –     * @brief
64 –     * @warning do not try to insert element into (or ease element from) private member data
65 –     * of DataStorage directly.
66 –     */
67 –    class DataStorage {
68 –        public:
69 –            DataStorage() {};
70 –            DataStorage(size_t size);
71 –
72 –            int size();
73 –            void resize(size_t size);
74 –            void reserve(size_t size);
75 –            
76 –            friend class Snapshot;
77 –            friend class StuntDouble;
78 –        private:
79 –            vector<Vector3d> position;               /** position array */
80 –            vector<Vector3d> velocity;               /** velocity array */
81 –            vector<RotMat3x3d> aMat;            /** rotation matrix array */
82 –            vector<Vector3d> angularMomentum;/** velocity array */
83 –            vector<Vector3d> unitVector;                /** the lab frame unit vector array*/
84 –            vector<double> zAngle;              /** z -angle array */        
85 –            vector<Vector3d> force;               /** force array */
86 –            vector<Vector3d> torque;               /** torque array */
87 –
88 –    };
89 –
90 –    /**
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.
96 –     * @see SimData
67       */
68      class Snapshot {
69          public:
70              
71 <            Snapshot(int nAtoms, int nRigidbodies) {
72 <                atomData.resize(nAtoms);
73 <                rigidbodyData.resize(nRigidbodies);
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  
76 <            Snapshot(const Snapshot& s);
76 >            Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
77 >                : atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
78 >                currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
79  
80 <            Snapshot& operator =(const Snapshot& s);
80 >            }
81              
82              /** Returns the id of this Snapshot */
83              int getID() {
# Line 117 | Line 89 | namespace oopse{
89                  id_ = id;
90              }
91  
92 <            //template<typename T>
93 <            //static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
94 <            //    return v[0]->getArrayPointer();
123 <            //}
92 >            int getSize() {
93 >                return atomData.getSize() + rigidbodyData.getSize();
94 >            }
95  
96 <            static double* getArrayPointer(vector<Vector3d>& v) {
97 <                assert(v.size() > 0);
98 <                return v[0].getArrayPointer();
96 >            /** Returns the number of atoms */
97 >            int getNumberOfAtoms() {
98 >                return atomData.getSize();
99              }
100 <            
101 <            static double* getArrayPointer(vector<RotMat3x3d>& v) {
102 <                assert(v.size() > 0);
103 <                return v[0].getArrayPointer();
100 >
101 >            /** Returns the number of rigid bodies */
102 >            int getNumberOfRigidBodies() {
103 >                return rigidbodyData.getSize();
104              }
105 +
106 +            /** Returns the H-Matrix */
107 +            Mat3x3d getHmat() {
108 +                return hmat_;
109 +            }
110 +
111 +            /** Sets the H-Matrix */
112 +            void setHmat(const Mat3x3d& m);
113              
114 <            static double* getArrayPointer(vector<double>& v) {
115 <                assert(v.size() > 0);
137 <                return &(v[0]);
114 >            double getVolume() {
115 >                return hmat_.determinant();
116              }
117  
118 <            int getSize() {
119 <                return atomData.size() + rigidbodyData.size();
118 >            /** Returns the inverse H-Matrix */
119 >            Mat3x3d getInvHmat() {
120 >                return invHmat_;
121              }
122 +
123 +            /** Wrapping the vector according to periodic boundary condition*/
124 +            void wrapVector(Vector3d& v);
125 +
126              
127 <            int getSizeOfAtoms() {
128 <                return atomData.size();
127 >            double getTime() {
128 >                return currentTime_;
129              }
130 +
131 +            void increaseTime(double dt) {
132 +                setTime(getTime() + dt);
133 +            }
134 +
135 +            void setTime(double time) {
136 +                currentTime_ =time;
137 +                //time at statData is redundant
138 +                statData[Stats::TIME] = currentTime_;
139 +            }
140 +
141 +            double getChi() {
142 +                return chi_;
143 +            }
144 +
145 +            void setChi(double chi) {
146 +                chi_ = chi;
147 +            }
148 +
149 +            double getIntegralOfChiDt() {
150 +                return integralOfChiDt_;
151 +            }
152 +
153 +            void setIntegralOfChiDt(double integralOfChiDt) {
154 +                integralOfChiDt_ = integralOfChiDt;
155 +            }
156              
157 <            int getSizeOfRigidBodies() {
158 <                return rigidbodyData.size();
157 >            Mat3x3d getEta() {
158 >                return eta_;
159              }
160 +
161 +            void setEta(const Mat3x3d& eta) {
162 +                eta_ = eta;
163 +            }
164              
165              DataStorage atomData;
166              DataStorage rigidbodyData;
167 <
168 <            friend class StuntDouble;
167 >            Stats statData;
168 >            
169          private:
170 +            double currentTime_;
171  
172 +            Mat3x3d hmat_;
173 +            Mat3x3d invHmat_;
174 +            int orthoRhombic_;
175 +
176 +            double chi_;
177 +            double integralOfChiDt_;
178 +            Mat3x3d eta_;
179 +            
180              int id_; /**< identification number of the snapshot */
181      };
182  

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