--- trunk/OOPSE-3.0/src/brains/DataStorage.cpp 2004/10/26 22:19:22 1648 +++ trunk/OOPSE-3.0/src/brains/DataStorage.cpp 2005/01/12 22:41:40 1930 @@ -1,26 +1,42 @@ -/* - * 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. */ /** @@ -65,7 +81,7 @@ int DataStorage::getSize() { std::cerr << "size does not match"<< std::endl; } - if (storageLayout_ & dslUnitVector && unitVector.size() != size_) { + if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) { //error std::cerr << "size does not match"<< std::endl; } @@ -107,8 +123,8 @@ void DataStorage::resize(int newSize) { internalResize(angularMomentum, newSize); } - if (storageLayout_ & dslUnitVector) { - internalResize(unitVector, newSize); + if (storageLayout_ & dslElectroFrame) { + internalResize(electroFrame, newSize); } if (storageLayout_ & dslZAngle) { @@ -143,8 +159,8 @@ void DataStorage::reserve(int size) { angularMomentum.reserve(size); } - if (storageLayout_ & dslUnitVector) { - unitVector.reserve(size); + if (storageLayout_ & dslElectroFrame) { + electroFrame.reserve(size); } if (storageLayout_ & dslZAngle) { @@ -167,35 +183,35 @@ void DataStorage::copy(int source, int num, int target } if (storageLayout_ & dslPosition) { - interalCopy(position, source, num, target); + internalCopy(position, source, num, target); } if (storageLayout_ & dslVelocity) { - interalCopy(velocity, source, num, target); + internalCopy(velocity, source, num, target); } if (storageLayout_ & dslAmat) { - interalCopy(aMat, source, num, target); + internalCopy(aMat, source, num, target); } if (storageLayout_ & dslAngularMomentum) { - interalCopy(angularMomentum, source, num, target); + internalCopy(angularMomentum, source, num, target); } - if (storageLayout_ & dslUnitVector) { - interalCopy(unitVector, source, num, target); + if (storageLayout_ & dslElectroFrame) { + internalCopy(electroFrame, source, num, target); } if (storageLayout_ & dslZAngle) { - interalCopy(zAngle, source, num, target); + internalCopy(zAngle, source, num, target); } if (storageLayout_ & dslForce) { - interalCopy(force, source, num, target); + internalCopy(force, source, num, target); } if (storageLayout_ & dslTorque) { - interalCopy(torque, source, num, target); + internalCopy(torque, source, num, target); } @@ -214,7 +230,7 @@ double* DataStorage::getArrayPointer(int whichArray) { switch (whichArray) { case dslPosition: - return internalGetArrayPointer(torque); + return internalGetArrayPointer(position); break; case dslVelocity: @@ -229,8 +245,8 @@ double* DataStorage::getArrayPointer(int whichArray) { return internalGetArrayPointer(angularMomentum); break; - case dslUnitVector: - return internalGetArrayPointer(unitVector); + case dslElectroFrame: + return internalGetArrayPointer(electroFrame); break; case dslZAngle: @@ -295,7 +311,7 @@ void DataStorage::interalCopy(std::vector& v, int s } template -void DataStorage::interalCopy(std::vector& v, int source, int num, int target) { +void DataStorage::internalCopy(std::vector& v, int source, int num, int target) { typename std::vector::iterator first; typename std::vector::iterator last; typename std::vector::iterator result;