--- trunk/src/brains/DataStorage.hpp 2004/10/26 22:19:22 155 +++ trunk/src/brains/DataStorage.hpp 2014/04/29 17:32:31 1993 @@ -1,28 +1,45 @@ /* - * 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. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * 2. 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. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ - + /** * @file Vector.hpp * @author Teng Lin @@ -37,93 +54,113 @@ #include #include -using namespace oopse; +using namespace std; +namespace OpenMD { + /** + * @class DataStorage + * @warning do not try to insert element into (or ease element from) private member data + * of DataStorage directly. + * @todo DataStorage may need refactoring. Every vector can inherit from the same base class + * which will make it easy to maintain + */ + class DataStorage { + public: + enum{ + dslPosition = 1, + dslVelocity = 2, + dslForce = 4, + dslAmat = 8, + dslAngularMomentum = 16, + dslTorque = 32, + dslParticlePot = 64, + dslDensity = 128, + dslFunctional = 256, + dslFunctionalDerivative = 512, + dslDipole = 1024, + dslQuadrupole = 2048, + dslElectricField = 4096, + dslSkippedCharge = 8192, + dslFlucQPosition = 16384, + dslFlucQVelocity = 32768, + dslFlucQForce = 65536, + dslSitePotential = 131072 + }; - - //forward declaration - class Snapshot; - class StuntDouble; - class DataStorageTestCase; + DataStorage(); + DataStorage(int size, int storageLayout = 0); + /** return the size of this DataStorage. */ + int getSize(); /** - * @class DataStorage - * @warning do not try to insert element into (or ease element from) private member data - * of DataStorage directly. - * @todo DataStorage may need refactorying. Every std::vector can inherit from the same base class - * which will make it easy to maintain + * Changes the size of this DataStorage. + * @param newSize new size of this DataStorage */ - class DataStorage { - public: + void resize(int newSize); + /** + * Reallocates memory manually. + * + * The main reason for using reserve() is efficiency if you know + * the capacity to which your vector must eventually grow, + * then it is usually more efficient to allocate that memory all + * at once. + */ + void reserve(int size); + /** + * Copies data inside DataStorage class. + * + * Copy function actually calls copy for every vector in + * DataStorage class. One Precondition of copy is that + * target is not within the range [source, soruce + num] + * + * @param source + * @param num number of element to be moved + * @param target + */ + void copy(int source, int num, int target); + /** Returns the storage layout */ + int getStorageLayout(); + /** Sets the storage layout */ + void setStorageLayout(int layout); + /** Returns the pointer of internal array */ + RealType *getArrayPointer(int whichArray); - enum{ - dslPosition = 1, - dslVelocity = 2, - dslAmat = 4, - dslAngularMomentum = 8, - dslUnitVector = 16, - dslZAngle = 32, - dslForce = 64, - dslTorque = 128 - }; + vector position; /** position array */ + vector velocity; /** velocity array */ + vector force; /** force array */ + vector aMat; /** rotation matrix array */ + vector angularMomentum; /** angular momentum array (body-fixed) */ + vector torque; /** torque array */ + vector particlePot; /** particle potential arrray */ + vector density; /** electron density */ + vector functional; /** density functional */ + vector functionalDerivative; /** derivative of functional */ + vector dipole; /** space-frame dipole vector */ + vector quadrupole; /** space-frame quadrupole tensor */ + vector electricField; /** local electric field */ + vector skippedCharge; /** charge skipped during normal pairwise calculation */ + vector flucQPos; /** fluctuating charges */ + vector flucQVel; /** fluctuating charge velocities */ + vector flucQFrc; /** fluctuating charge forces */ + vector sitePotential; /** electrostatic site potentials */ + static int getBytesPerStuntDouble(int layout); - DataStorage(); - DataStorage(int size, int storageLayout = 0x11111111); - /** return the size of this DataStorage. */ - int getSize(); - /** - * Changes the size of this DataStorage. - * @param size new size of this DataStorage - */ - void resize(int newSize); - /** - * Reallocates memory manually. The main reason for using reserve() is efficiency - * if you know the capacity to which your std::vector must eventually grow, then it is usually more - * efficient to allocate that memory all at once. - */ - void reserve(int size); - /** - * Copies data inside DataStorage class. - * Copy function actually call std::copy for every std::vector in DataStorage class. - * One Precondition of std::copy is that target is not within the range [soruce, soruce + num] - * @param souce - * @param num number of element to be moved - * @param target - */ - void copy(int source, int num, int target); - /** Returns the storage layout */ - int getStorageLayout(); - /** Sets the storage layout */ - void setStorageLayout(int layout); - /** Returns the pointer of internal array */ - double *getArrayPointer(int whichArray); - friend class StuntDouble; - friend class DataStorageTestCase; - private: + private: - - double* internalGetArrayPointer(std::vector& v); + RealType* internalGetArrayPointer(vector& v); + RealType* internalGetArrayPointer(vector& v); + RealType* internalGetArrayPointer(vector& v); - double* internalGetArrayPointer(std::vector& v); - double* internalGetArrayPointer(std::vector& v); - - template - void internalResize(std::vector& v, int newSize); + template + void internalResize(std::vector& v, int newSize); - template - void interalCopy(std::vector& v, int source, int num, int target); + template + 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;/** velocity array */ - 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 */ - }; + int size_; + int storageLayout_; + }; +} #endif //BRAINS_DATASTORAGE_HPP