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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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namespace OpenMD{ |
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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, |
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int nCutoffGroups) : atomData(nAtoms), |
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rigidbodyData(nRigidbodies), |
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cgData(nCutoffGroups, DataStorage::dslPosition), |
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currentTime_(0), |
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orthoTolerance_(1e-6), |
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orthoRhombic_(0), |
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chi_(0.0), |
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integralOfChiDt_(0.0), |
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eta_(0.0), id_(-1), hasCOM_(false), |
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volume_(0.0), hasVolume_(false) { |
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|
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} |
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|
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Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, |
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int storageLayout) : atomData(nAtoms, storageLayout), |
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rigidbodyData(nRigidbodies, storageLayout), |
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cgData(nCutoffGroups, DataStorage::dslPosition), |
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currentTime_(0), orthoTolerance_(1e-6), |
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orthoRhombic_(0), chi_(0.0), |
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integralOfChiDt_(0.0), eta_(0.0), id_(-1), |
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hasCOM_(false), volume_(0.0), |
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hasVolume_(false) { |
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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 number of rigid bodies */ |
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int getNumberOfCutoffGroups() { |
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return cgData.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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|
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RealType getVolume() { |
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if (hasVolume_){ |
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return volume_; |
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}else{ |
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return hmat_.determinant(); |
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} |
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} |
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|
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void setVolume(RealType volume){ |
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hasVolume_=true; |
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volume_ = volume; |
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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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/** Scaling a vector to multiples of the periodic box */ |
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Vector3d scaleVector(Vector3d &v); |
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|
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|
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Vector3d getCOM(); |
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Vector3d getCOMvel(); |
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Vector3d getCOMw(); |
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|
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RealType getTime() { |
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return currentTime_; |
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} |
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|
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void increaseTime(RealType dt) { |
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setTime(getTime() + dt); |
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} |
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|
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void setTime(RealType 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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RealType getChi() { |
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return chi_; |
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} |
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|
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void setChi(RealType chi) { |
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chi_ = chi; |
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} |
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|
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RealType getIntegralOfChiDt() { |
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return integralOfChiDt_; |
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} |
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|
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void setIntegralOfChiDt(RealType integralOfChiDt) { |
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integralOfChiDt_ = integralOfChiDt; |
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} |
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|
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|
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void setOrthoTolerance(RealType orthoTolerance) { |
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orthoTolerance_ = orthoTolerance; |
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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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bool hasCOM() { |
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return hasCOM_; |
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} |
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|
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void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) { |
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COM_ = COM; |
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COMvel_ = COMvel; |
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COMw_ = COMw; |
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hasCOM_ = true; |
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} |
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|
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DataStorage atomData; |
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DataStorage rigidbodyData; |
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DataStorage cgData; |
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Stats statData; |
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|
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private: |
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RealType currentTime_; |
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|
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Mat3x3d hmat_; |
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Mat3x3d invHmat_; |
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RealType orthoTolerance_; |
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int orthoRhombic_; |
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RealType volume_; |
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|
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RealType chi_; |
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RealType integralOfChiDt_; |
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Mat3x3d eta_; |
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Vector3d COM_; |
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Vector3d COMvel_; |
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Vector3d COMw_; |
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int id_; /**< identification number of the snapshot */ |
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bool hasCOM_; |
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bool hasVolume_; |
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|
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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 |
