--- trunk/OOPSE-2.0/src/brains/Snapshot.hpp 2004/10/22 23:09:57 1639 +++ trunk/OOPSE-2.0/src/brains/Snapshot.hpp 2005/04/15 22:04:00 2204 @@ -1,143 +1,185 @@ /* - * Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project - * - * Contact: oopse@oopse.org - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * All we ask is that proper credit is given for our work, which includes - * - but is not limited to - adding the above copyright notice to the beginning - * of your source code files, and to any copyright notice that you may distribute - * with programs based on this work. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * + * The University of Notre Dame grants you ("Licensee") a + * non-exclusive, royalty free, license to use, modify and + * redistribute this software in source and binary code form, provided + * that the following conditions are met: + * + * 1. Acknowledgement of the program authors must be made in any + * publication of scientific results based in part on use of the + * program. An acceptable form of acknowledgement is citation of + * the article in which the program was described (Matthew + * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher + * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented + * Parallel Simulation Engine for Molecular Dynamics," + * J. Comput. Chem. 26, pp. 252-271 (2005)) + * + * 2. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * 3. Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the + * distribution. + * + * This software is provided "AS IS," without a warranty of any + * kind. All express or implied conditions, representations and + * warranties, including any implied warranty of merchantability, + * fitness for a particular purpose or non-infringement, are hereby + * excluded. The University of Notre Dame and its licensors shall not + * be liable for any damages suffered by licensee as a result of + * using, modifying or distributing the software or its + * derivatives. In no event will the University of Notre Dame or its + * licensors be liable for any lost revenue, profit or data, or for + * direct, indirect, special, consequential, incidental or punitive + * damages, however caused and regardless of the theory of liability, + * arising out of the use of or inability to use software, even if the + * University of Notre Dame has been advised of the possibility of + * such damages. */ - - /** - * @file Snapshot.hpp - * @author tlin - * @date 10/20/2004 - * @time 23:56am - * @version 1.0 - */ +/** + * @file Snapshot.hpp + * @author tlin + * @date 10/20/2004 + * @time 23:56am + * @version 1.0 + */ + #ifndef BRAINS_SNAPSHOT_HPP #define BRAINS_SNAPSHOT_HPP #include -#include "math/Vector3.hpp" -#include "math/SquareMatrix3.hpp" +#include "brains/DataStorage.hpp" +#include "brains/Stats.hpp" +#include "UseTheForce/DarkSide/simulation_interface.h" -using namespace std; - namespace oopse{ - //forward declaration - class Snapshot; - class SnapshotManager; - - /** - * @struct DataStorage - * @brief - */ - class DataStorage { - public: - DataStorage() {}; - DataStorage(size_t size); - void resize(size_t size); - void reserve(size_t size); + /** + * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp" + * @brief Snapshot class is a repository class for storing dynamic data during + * Simulation + * Every snapshot class will contain one DataStorage for atoms and one DataStorage + * for rigid bodies. + */ + class Snapshot { + public: - //friend Snapshot; - //friend SnapshotManager; - //private: - vector position; /** position array */ - vector velocity; /** velocity array */ - vector Amat; /** rotation matrix array */ - vector angularMomentum;/** velocity array */ - vector ul; /** the lab frame unit vector array*/ - vector zAngle; /** z -angle array */ - vector force; /** force array */ - vector torque; /** torque array */ + Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies), + currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) { - }; + } - /** - * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp" - * @brief Snapshot class is a repository class for storing dynamic data during - * Simulation - * Every snapshot class will contain one DataStorage for atoms and one DataStorage - * for rigid bodies. - * @see SimData - */ - class Snapshot { - public: + Snapshot(int nAtoms, int nRigidbodies, int storageLayout) + : atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout), + currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) { + + } - Snapshot() {} - Snapshot(int i) { + /** Returns the id of this Snapshot */ + int getID() { + return id_; + } - } + /** Sets the id of this Snapshot */ + void setID(int id) { + id_ = id; + } - Snapshot(const Snapshot& s); + int getSize() { + return atomData.getSize() + rigidbodyData.getSize(); + } - Snapshot& operator =(const Snapshot& s); + /** Returns the number of atoms */ + int getNumberOfAtoms() { + return atomData.getSize(); + } + + /** Returns the number of rigid bodies */ + int getNumberOfRigidBodies() { + return rigidbodyData.getSize(); + } + + /** Returns the H-Matrix */ + Mat3x3d getHmat() { + return hmat_; + } + + /** Sets the H-Matrix */ + void setHmat(const Mat3x3d& m); - /** Returns the id of this Snapshot */ - int getID() { - return id_; - } + double getVolume() { + return hmat_.determinant(); + } - /** Sets the id of this Snapshot */ - void setID(int id) { - id_ = id; - } + /** Returns the inverse H-Matrix */ + Mat3x3d getInvHmat() { + return invHmat_; + } - //template - //static typename T::ElemPointerType getArrayPointer(vector& v) { - // return v[0]->getArrayPointer(); - //} + /** Wrapping the vector according to periodic boundary condition*/ + void wrapVector(Vector3d& v); - static double* getArrayPointer(vector& v) { - assert(v.size() > 0); - return v[0].getArrayPointer(); - } - static double* getArrayPointer(vector& v) { - assert(v.size() > 0); - return v[0].getArrayPointer(); - } - - static double* getArrayPointer(vector& v) { - assert(v.size() > 0); - return &(v[0]); - } - - /** */ - void resize(size_t size); + double getTime() { + return currentTime_; + } + void increaseTime(double dt) { + setTime(getTime() + dt); + } - /** */ - void reserve(size_t size); + void setTime(double time) { + currentTime_ =time; + //time at statData is redundant + statData[Stats::TIME] = currentTime_; + } - DataStorage atomData; - DataStorage rigidbodyData; + double getChi() { + return chi_; + } - friend class SnapshotManager; - private: + void setChi(double chi) { + chi_ = chi; + } - int id_; /**< identification number of the snapshot */ - }; + double getIntegralOfChiDt() { + return integralOfChiDt_; + } - typedef DataStorage* (Snapshot::*DataStoragePointer); + void setIntegralOfChiDt(double integralOfChiDt) { + integralOfChiDt_ = integralOfChiDt; + } + + Mat3x3d getEta() { + return eta_; + } + + void setEta(const Mat3x3d& eta) { + eta_ = eta; + } + + DataStorage atomData; + DataStorage rigidbodyData; + Stats statData; + + private: + double currentTime_; + + Mat3x3d hmat_; + Mat3x3d invHmat_; + int orthoRhombic_; + + double chi_; + double integralOfChiDt_; + Mat3x3d eta_; + + int id_; /**< identification number of the snapshot */ + }; + + typedef DataStorage (Snapshot::*DataStoragePointer); } #endif //BRAINS_SNAPSHOT_HPP