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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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*/ |
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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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* @date 10/20/2004 |
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* @time 23:56am |
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* @version 1.0 |
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*/ |
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|
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#ifndef BRAINS_SNAPSHOT_HPP |
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#define BRAINS_SNAPSHOT_HPP |
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|
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#include <vector> |
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|
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#include "brains/DataStorage.hpp" |
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#include "brains/Stats.hpp" |
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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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/** |
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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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*/ |
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class Snapshot { |
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public: |
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|
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Snapshot(int nAtoms, int nRigidbodies) : currentTime_(0), chi_(0), integralOfChiDt_(0), eta_(0) { |
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atomData.resize(nAtoms); |
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rigidbodyData.resize(nRigidbodies); |
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} |
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|
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|
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/** Returns the id of this Snapshot */ |
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int getID() { |
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return id_; |
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} |
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|
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/** Sets the id of this Snapshot */ |
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void setID(int id) { |
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id_ = id; |
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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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/** Returns the number of atoms */ |
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int getNumberOfAtoms() { |
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return atomData.getSize(); |
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} |
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|
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/** Returns the number of rigid bodies */ |
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int getNumberOfRigidBodies() { |
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return rigidbodyData.getSize(); |
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} |
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|
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/** Returns the H-Matrix */ |
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Mat3x3d getHmat() { |
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return hmat_; |
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} |
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|
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/** Sets the H-Matrix */ |
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void setHmat(const Mat3x3d& m) { |
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hmat_ = m; |
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invHmat_ = hmat_.inverse(); |
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|
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//notify fortran Hmat is changed |
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double fortranHmat[9]; |
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double fortranInvHmat[9]; |
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hmat_.getArray(fortranHmat); |
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invHmat_.getArray(fortranInvHmat); |
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setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_); |
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} |
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|
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void getVolume() { |
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return hmat_.determinant(); |
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} |
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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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} |
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|
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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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|
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double getTime() { |
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return currentTime_; |
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} |
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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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private: |
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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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|
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typedef DataStorage (Snapshot::*DataStoragePointer); |
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} |
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#endif //BRAINS_SNAPSHOT_HPP |
