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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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/** |
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* @file DataStorage.cpp |
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* @author tlin |
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* @date 10/26/2004 |
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* @time 11:56am |
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* @version 1.0 |
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*/ |
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/** |
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* @file DataStorage.cpp |
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* @author tlin |
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* @date 10/26/2004 |
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* @time 11:56am |
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* @version 1.0 |
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*/ |
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|
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#include "brains/DataStorage.hpp" |
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|
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namespace oopse { |
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|
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DataStorage::DataStorage() : size_(0), storageLayout_(0){ |
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DataStorage::DataStorage() : size_(0), storageLayout_(0){ |
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|
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} |
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} |
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|
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DataStorage::DataStorage(int size, int storageLayout) : size_(size){ |
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DataStorage::DataStorage(int size, int storageLayout) : size_(size){ |
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setStorageLayout(storageLayout); |
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resize(size); |
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} |
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} |
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|
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int DataStorage::getSize() { |
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int DataStorage::getSize() { |
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|
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if (storageLayout_ & dslPosition && position.size() != size_) { |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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} |
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|
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if (storageLayout_ & dslVelocity && velocity.size() != size_) { |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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} |
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|
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if (storageLayout_ & dslAmat && aMat.size() != size_) { |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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} |
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|
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if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) { |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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} |
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|
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if (storageLayout_ & dslUnitVector && unitVector.size() != size_) { |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) { |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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} |
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|
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if (storageLayout_ & dslZAngle && zAngle.size() != size_) { |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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} |
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|
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if (storageLayout_ & dslForce && force.size() != size_) { |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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} |
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|
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if (storageLayout_ & dslTorque && torque.size() != size_) { |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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//error |
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std::cerr << "size does not match"<< std::endl; |
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} |
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return size_; |
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} |
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} |
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void DataStorage::resize(int newSize) { |
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void DataStorage::resize(int newSize) { |
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|
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if (storageLayout_ & dslPosition) { |
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internalResize(position, newSize); |
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internalResize(position, newSize); |
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} |
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|
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if (storageLayout_ & dslVelocity) { |
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internalResize(velocity, newSize); |
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internalResize(velocity, newSize); |
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} |
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|
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if (storageLayout_ & dslAmat) { |
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internalResize(aMat, newSize); |
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internalResize(aMat, newSize); |
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} |
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if (storageLayout_ & dslAngularMomentum) { |
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internalResize(angularMomentum, newSize); |
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internalResize(angularMomentum, newSize); |
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} |
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|
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if (storageLayout_ & dslUnitVector) { |
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internalResize(unitVector, newSize); |
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if (storageLayout_ & dslElectroFrame) { |
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internalResize(electroFrame, newSize); |
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} |
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|
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if (storageLayout_ & dslZAngle) { |
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internalResize(zAngle, newSize); |
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internalResize(zAngle, newSize); |
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} |
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|
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if (storageLayout_ & dslForce) { |
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internalResize(force, newSize); |
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internalResize(force, newSize); |
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} |
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|
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if (storageLayout_ & dslTorque) { |
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internalResize(torque, newSize); |
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internalResize(torque, newSize); |
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} |
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size_ = newSize; |
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} |
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} |
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|
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void DataStorage::reserve(int size) { |
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void DataStorage::reserve(int size) { |
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if (storageLayout_ & dslPosition) { |
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position.reserve(size); |
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position.reserve(size); |
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} |
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|
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if (storageLayout_ & dslVelocity) { |
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velocity.reserve(size); |
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velocity.reserve(size); |
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} |
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|
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if (storageLayout_ & dslAmat) { |
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aMat.reserve(size); |
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aMat.reserve(size); |
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} |
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if (storageLayout_ & dslAngularMomentum) { |
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angularMomentum.reserve(size); |
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angularMomentum.reserve(size); |
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} |
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if (storageLayout_ & dslUnitVector) { |
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unitVector.reserve(size); |
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if (storageLayout_ & dslElectroFrame) { |
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electroFrame.reserve(size); |
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} |
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|
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if (storageLayout_ & dslZAngle) { |
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zAngle.reserve(size); |
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zAngle.reserve(size); |
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} |
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|
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if (storageLayout_ & dslForce) { |
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force.reserve(size); |
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force.reserve(size); |
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} |
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if (storageLayout_ & dslTorque) { |
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torque.reserve(size); |
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torque.reserve(size); |
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} |
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|
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} |
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} |
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void DataStorage::copy(int source, int num, int target) { |
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void DataStorage::copy(int source, int num, int target) { |
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if (num + target > size_ ) { |
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//error |
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//error |
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} |
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|
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if (storageLayout_ & dslPosition) { |
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interalCopy(position, source, num, target); |
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internalCopy(position, source, num, target); |
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} |
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|
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if (storageLayout_ & dslVelocity) { |
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interalCopy(velocity, source, num, target); |
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} |
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internalCopy(velocity, source, num, target); |
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} |
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|
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if (storageLayout_ & dslAmat) { |
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interalCopy(aMat, source, num, target); |
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} |
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internalCopy(aMat, source, num, target); |
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} |
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|
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if (storageLayout_ & dslAngularMomentum) { |
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interalCopy(angularMomentum, source, num, target); |
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internalCopy(angularMomentum, source, num, target); |
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} |
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|
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if (storageLayout_ & dslUnitVector) { |
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interalCopy(unitVector, source, num, target); |
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if (storageLayout_ & dslElectroFrame) { |
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internalCopy(electroFrame, source, num, target); |
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} |
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|
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if (storageLayout_ & dslZAngle) { |
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interalCopy(zAngle, source, num, target); |
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internalCopy(zAngle, source, num, target); |
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} |
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|
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if (storageLayout_ & dslForce) { |
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interalCopy(force, source, num, target); |
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internalCopy(force, source, num, target); |
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} |
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if (storageLayout_ & dslTorque) { |
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interalCopy(torque, source, num, target); |
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internalCopy(torque, source, num, target); |
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} |
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|
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|
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} |
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} |
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|
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int DataStorage::getStorageLayout() { |
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int DataStorage::getStorageLayout() { |
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return storageLayout_; |
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} |
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} |
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|
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void DataStorage::setStorageLayout(int layout) { |
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void DataStorage::setStorageLayout(int layout) { |
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storageLayout_ = layout; |
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resize(size_); |
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} |
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} |
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|
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double* DataStorage::getArrayPointer(int whichArray) { |
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double* DataStorage::getArrayPointer(int whichArray) { |
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|
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switch (whichArray) { |
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case dslPosition: |
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return internalGetArrayPointer(torque); |
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break; |
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case dslPosition: |
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return internalGetArrayPointer(position); |
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break; |
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|
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case dslVelocity: |
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return internalGetArrayPointer(velocity); |
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break; |
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case dslVelocity: |
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return internalGetArrayPointer(velocity); |
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break; |
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|
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case dslAmat: |
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return internalGetArrayPointer(aMat); |
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break; |
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case dslAmat: |
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return internalGetArrayPointer(aMat); |
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break; |
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|
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case dslAngularMomentum: |
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return internalGetArrayPointer(angularMomentum); |
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break; |
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case dslAngularMomentum: |
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return internalGetArrayPointer(angularMomentum); |
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break; |
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|
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< |
case dslUnitVector: |
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< |
return internalGetArrayPointer(unitVector); |
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break; |
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case dslElectroFrame: |
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> |
return internalGetArrayPointer(electroFrame); |
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> |
break; |
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|
|
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< |
case dslZAngle: |
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< |
return internalGetArrayPointer(zAngle); |
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< |
break; |
253 |
> |
case dslZAngle: |
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> |
return internalGetArrayPointer(zAngle); |
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> |
break; |
256 |
|
|
257 |
< |
case dslForce: |
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< |
return internalGetArrayPointer(force); |
259 |
< |
break; |
257 |
> |
case dslForce: |
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> |
return internalGetArrayPointer(force); |
259 |
> |
break; |
260 |
|
|
261 |
< |
case dslTorque: |
262 |
< |
return internalGetArrayPointer(torque); |
263 |
< |
break; |
261 |
> |
case dslTorque: |
262 |
> |
return internalGetArrayPointer(torque); |
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> |
break; |
264 |
|
|
265 |
< |
default: |
266 |
< |
//error message |
267 |
< |
return NULL; |
265 |
> |
default: |
266 |
> |
//error message |
267 |
> |
return NULL; |
268 |
|
|
269 |
|
} |
270 |
< |
} |
270 |
> |
} |
271 |
|
|
272 |
< |
double* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) { |
272 |
> |
double* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) { |
273 |
|
if (v.size() == 0) { |
274 |
< |
return NULL; |
274 |
> |
return NULL; |
275 |
|
} else { |
276 |
< |
return v[0].getArrayPointer(); |
276 |
> |
return v[0].getArrayPointer(); |
277 |
|
} |
278 |
< |
} |
278 |
> |
} |
279 |
|
|
280 |
< |
double* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) { |
280 |
> |
double* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) { |
281 |
|
if (v.size() == 0) { |
282 |
< |
return NULL; |
282 |
> |
return NULL; |
283 |
|
} else { |
284 |
< |
return v[0].getArrayPointer(); |
284 |
> |
return v[0].getArrayPointer(); |
285 |
|
} |
286 |
|
|
287 |
< |
} |
287 |
> |
} |
288 |
|
|
289 |
< |
double* DataStorage::internalGetArrayPointer(std::vector<double>& v) { |
289 |
> |
double* DataStorage::internalGetArrayPointer(std::vector<double>& v) { |
290 |
|
if (v.size() == 0) { |
291 |
< |
return NULL; |
291 |
> |
return NULL; |
292 |
|
} else { |
293 |
< |
return &(v[0]); |
293 |
> |
return &(v[0]); |
294 |
|
} |
295 |
|
|
296 |
< |
} |
296 |
> |
} |
297 |
|
|
298 |
< |
template<typename T> |
299 |
< |
void DataStorage::internalResize(std::vector<T>& v, int newSize){ |
298 |
> |
template<typename T> |
299 |
> |
void DataStorage::internalResize(std::vector<T>& v, int newSize){ |
300 |
|
int oldSize = v.size(); |
301 |
|
|
302 |
|
if (oldSize == newSize) { |
303 |
< |
return; |
303 |
> |
return; |
304 |
|
} else if (oldSize < newSize) { |
305 |
< |
v.insert(v.end(), newSize-oldSize, T()); |
305 |
> |
v.insert(v.end(), newSize-oldSize, T()); |
306 |
|
} else { |
307 |
< |
typename std::vector<T>::iterator i; |
308 |
< |
i = v.begin(); |
309 |
< |
std::advance(i, newSize); |
310 |
< |
v.erase(i, v.end()); |
307 |
> |
typename std::vector<T>::iterator i; |
308 |
> |
i = v.begin(); |
309 |
> |
std::advance(i, newSize); |
310 |
> |
v.erase(i, v.end()); |
311 |
|
} |
312 |
< |
} |
312 |
> |
} |
313 |
|
|
314 |
< |
template<typename T> |
315 |
< |
void DataStorage::interalCopy(std::vector<T>& v, int source, int num, int target) { |
314 |
> |
template<typename T> |
315 |
> |
void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) { |
316 |
|
typename std::vector<T>::iterator first; |
317 |
|
typename std::vector<T>::iterator last; |
318 |
|
typename std::vector<T>::iterator result; |
327 |
|
std::advance(result, target ); |
328 |
|
|
329 |
|
std::copy(first, last, result); |
330 |
+ |
} |
331 |
+ |
|
332 |
+ |
int DataStorage::getBytesPerStuntDouble(int layout) { |
333 |
+ |
int bytes = 0; |
334 |
+ |
if (layout & dslPosition) { |
335 |
+ |
bytes += sizeof(Vector3d); |
336 |
+ |
} |
337 |
+ |
if (layout & dslVelocity) { |
338 |
+ |
bytes += sizeof(Vector3d); |
339 |
+ |
} |
340 |
+ |
if (layout & dslAmat) { |
341 |
+ |
bytes += sizeof(Mat3x3d); |
342 |
+ |
} |
343 |
+ |
if (layout & dslAngularMomentum) { |
344 |
+ |
bytes += sizeof(Vector3d); |
345 |
+ |
} |
346 |
+ |
if (layout & dslElectroFrame) { |
347 |
+ |
bytes += sizeof(Mat3x3d); |
348 |
+ |
} |
349 |
+ |
if (layout & dslZAngle) { |
350 |
+ |
bytes += sizeof(Vector3d); |
351 |
+ |
} |
352 |
+ |
if (layout & dslForce) { |
353 |
+ |
bytes += sizeof(Vector3d); |
354 |
+ |
} |
355 |
+ |
if (layout & dslTorque) { |
356 |
+ |
bytes += sizeof(Vector3d); |
357 |
+ |
} |
358 |
+ |
return bytes; |
359 |
+ |
} |
360 |
+ |
|
361 |
|
} |