--- trunk/src/brains/DataStorage.hpp 2004/10/28 22:34:01 189 +++ trunk/src/brains/DataStorage.hpp 2005/02/13 15:56:10 323 @@ -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 Vector.hpp * @author Teng Lin @@ -37,14 +53,7 @@ #include #include -using namespace oopse; - - - - //forward declaration - class Snapshot; - class StuntDouble; - class DataStorageTestCase; +namespace oopse { /** * @class DataStorage * @warning do not try to insert element into (or ease element from) private member data @@ -60,7 +69,7 @@ using namespace oopse; dslVelocity = 2, dslAmat = 4, dslAngularMomentum = 8, - dslUnitVector = 16, + dslElectroFrame = 16, dslZAngle = 32, dslForce = 64, dslTorque = 128 @@ -68,7 +77,7 @@ using namespace oopse; DataStorage(); - DataStorage(int size, int storageLayout = 0x11111111); + DataStorage(int size, int storageLayout = 255); /** return the size of this DataStorage. */ int getSize(); /** @@ -97,11 +106,20 @@ using namespace oopse; void setStorageLayout(int layout); /** Returns the pointer of internal array */ double *getArrayPointer(int whichArray); - friend class StuntDouble; - friend class DataStorageTestCase; - private: + std::vector position; /** position array */ + std::vector velocity; /** velocity array */ + std::vector aMat; /** rotation matrix array */ + std::vector angularMomentum;/** angular momentum array (body-fixed) */ + std::vector electroFrame; /** the lab frame unit std::vector array*/ + std::vector zAngle; /** z -angle array */ + std::vector force; /** force array */ + std::vector torque; /** torque array */ + static int getBytesPerStuntDouble(int layout); + + private: + double* internalGetArrayPointer(std::vector& v); double* internalGetArrayPointer(std::vector& v); @@ -111,19 +129,12 @@ using namespace oopse; void internalResize(std::vector& v, int newSize); template - void interalCopy(std::vector& v, int source, int num, int target); + void internalCopy(std::vector& v, int source, int num, int target); int size_; int storageLayout_; - std::vector position; /** position array */ - std::vector velocity; /** velocity array */ - std::vector aMat; /** rotation matrix array */ - std::vector angularMomentum;/** angular momentum array (body-fixed) */ - std::vector unitVector; /** the lab frame unit std::vector array*/ - std::vector zAngle; /** z -angle array */ - std::vector force; /** force array */ - std::vector torque; /** torque array */ + }; - +} #endif //BRAINS_DATASTORAGE_HPP