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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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/* |
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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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* @file Snapshot.hpp |
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* @author tlin |
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#include <vector> |
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#include "brains/DataStorage.hpp" |
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#include "brains/Stats.hpp" |
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#include "UseTheForce/DarkSide/simulation_interface.h" |
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|
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using namespace std; |
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|
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namespace oopse{ |
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|
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class StuntDouble; |
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|
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/** |
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* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp" |
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* @brief Snapshot class is a repository class for storing dynamic data during |
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* Simulation |
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* Every snapshot class will contain one DataStorage for atoms and one DataStorage |
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* for rigid bodies. |
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* @see SimData |
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*/ |
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class Snapshot { |
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public: |
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Snapshot(int nAtoms, int nRigidbodies) { |
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atomData.resize(nAtoms); |
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rigidbodyData.resize(nRigidbodies); |
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Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies), |
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currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) { |
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|
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} |
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Snapshot(const Snapshot& s); |
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Snapshot& operator =(const Snapshot& s); |
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/** Returns the id of this Snapshot */ |
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int getID() { |
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id_ = id; |
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} |
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//template<typename T> |
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//static typename T::ElemPointerType getArrayPointer(vector<T>& v) { |
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// return v[0]->getArrayPointer(); |
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//} |
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|
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int getSize() { |
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return atomData.getSize() + rigidbodyData.getSize(); |
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} |
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} |
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/** Sets the H-Matrix */ |
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void setHamt(const Mat3x3d& m) { |
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hmat_ = m; |
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invHmat_ = hmat_.inverse(); |
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void setHmat(const Mat3x3d& m); |
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|
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double getVolume() { |
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return hmat_.determinant(); |
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} |
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/** Returns the inverse H-Matrix */ |
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Mat3x3d getInvHmat() { |
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return invHmat_ |
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return invHmat_; |
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} |
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double getTimeStamp() { |
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return timeStamp_; |
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/** Wrapping the vector according to periodic boundary condition*/ |
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void wrapVector(Vector3d& v); |
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|
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double getTime() { |
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return currentTime_; |
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} |
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void setTimeStamp(double timeStamp) { |
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timeStamp_ =timeStamp; |
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void increaseTime(double dt) { |
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setTime(getTime() + dt); |
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} |
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void setTime(double time) { |
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currentTime_ =time; |
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//time at statData is redundant |
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statData[Stats::TIME] = currentTime_; |
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} |
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|
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double getChi() { |
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return chi_; |
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} |
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|
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void setChi(double chi) { |
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chi_ = chi; |
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} |
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|
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double getIntegralOfChiDt() { |
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return integralOfChiDt_; |
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} |
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|
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void setIntegralOfChiDt(double integralOfChiDt) { |
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integralOfChiDt_ = integralOfChiDt; |
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} |
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|
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Mat3x3d getEta() { |
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return eta_; |
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} |
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|
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void setEta(const Mat3x3d& eta) { |
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eta_ = eta; |
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} |
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|
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DataStorage atomData; |
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DataStorage rigidbodyData; |
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Stats statData; |
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|
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friend class StuntDouble; |
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private: |
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double timeStamp_; |
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double currentTime_; |
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|
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Mat3x3d hmat_; |
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Mat3x3d invHmat_; |
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int orthoRhombic_; |
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|
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double chi_; |
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double integralOfChiDt_; |
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Mat3x3d eta_; |
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|
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int id_; /**< identification number of the snapshot */ |
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}; |
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