--- trunk/OOPSE-2.0/src/brains/Snapshot.hpp 2004/10/26 22:19:22 1648 +++ trunk/OOPSE-2.0/src/brains/Snapshot.hpp 2005/01/12 22:41:40 1930 @@ -1,28 +1,44 @@ -/* - * 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 @@ -37,32 +53,26 @@ #include #include "brains/DataStorage.hpp" +#include "brains/Stats.hpp" +#include "UseTheForce/DarkSide/simulation_interface.h" -using namespace std; - namespace oopse{ - class StuntDouble; - /** * @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) { - atomData.resize(nAtoms); - rigidbodyData.resize(nRigidbodies); + Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies), + currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) { + } - Snapshot(const Snapshot& s); - - Snapshot& operator =(const Snapshot& s); /** Returns the id of this Snapshot */ int getID() { @@ -74,11 +84,6 @@ namespace oopse{ id_ = id; } - //template - //static typename T::ElemPointerType getArrayPointer(vector& v) { - // return v[0]->getArrayPointer(); - //} - int getSize() { return atomData.getSize() + rigidbodyData.getSize(); } @@ -99,34 +104,74 @@ namespace oopse{ } /** Sets the H-Matrix */ - void setHamt(const Mat3x3d& m) { - hmat_ = m; - invHmat_ = hmat_.inverse(); + void setHmat(const Mat3x3d& m); + + double getVolume() { + return hmat_.determinant(); } /** Returns the inverse H-Matrix */ Mat3x3d getInvHmat() { - return invHmat_ + return invHmat_; } - double getTimeStamp() { - return timeStamp_; + /** Wrapping the vector according to periodic boundary condition*/ + void wrapVector(Vector3d& v); + + + double getTime() { + return currentTime_; } - void setTimeStamp(double timeStamp) { - timeStamp_ =timeStamp; + void increaseTime(double dt) { + setTime(getTime() + dt); } + void setTime(double time) { + currentTime_ =time; + //time at statData is redundant + statData[Stats::TIME] = currentTime_; + } + double getChi() { + return chi_; + } + + void setChi(double chi) { + chi_ = chi; + } + + double getIntegralOfChiDt() { + return integralOfChiDt_; + } + + void setIntegralOfChiDt(double integralOfChiDt) { + integralOfChiDt_ = integralOfChiDt; + } + + Mat3x3d getEta() { + return eta_; + } + + void setEta(const Mat3x3d& eta) { + eta_ = eta; + } + DataStorage atomData; DataStorage rigidbodyData; + Stats statData; - friend class StuntDouble; - private: - double timeStamp_; + double currentTime_; + Mat3x3d hmat_; Mat3x3d invHmat_; + int orthoRhombic_; + + double chi_; + double integralOfChiDt_; + Mat3x3d eta_; + int id_; /**< identification number of the snapshot */ };