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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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struct FrameData { |
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int id; /**< identification number of the snapshot */ |
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RealType currentTime; /**< current time */ |
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Mat3x3d hmat; /**< axes of the periodic box in matrix form */ |
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Mat3x3d invHmat; /**< the inverse of the Hmat matrix */ |
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bool orthoRhombic; /**< is this an orthorhombic periodic box? */ |
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RealType volume; /**< total volume of this frame */ |
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RealType pressure; /**< pressure of this frame */ |
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RealType totalEnergy; /**< total energy of this frame */ |
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RealType kineticEnergy; /**< kinetic energy of this frame */ |
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RealType potentialEnergy; /**< potential energy of this frame */ |
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RealType temperature; /**< temperature of this frame */ |
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RealType chi; /**< thermostat velocity */ |
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RealType integralOfChiDt; /**< the actual thermostat */ |
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RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */ |
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RealType chiQ; /**< fluctuating charge thermostat velocity */ |
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RealType integralOfChiQDt; /**< the actual fluctuating charge thermostat */ |
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Mat3x3d eta; /**< barostat matrix */ |
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Vector3d COM; /**< location of center of mass */ |
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Vector3d COMvel; /**< system center of mass velocity */ |
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Vector3d COMw; /**< system center of mass angular velocity */ |
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Mat3x3d stressTensor; /**< stress tensor */ |
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Mat3x3d pressureTensor; /**< pressure tensor */ |
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Vector3d systemDipole; /**< total system dipole moment */ |
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Vector3d conductiveHeatFlux; /**< heat flux vector (conductive only) */ |
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}; |
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|
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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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orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false){ |
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|
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frameData.id = -1; |
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frameData.currentTime = 0; |
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frameData.hmat = Mat3x3d(0.0); |
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frameData.invHmat = Mat3x3d(0.0); |
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frameData.orthoRhombic = false; |
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frameData.volume = 0.0; |
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frameData.pressure = 0.0; |
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frameData.totalEnergy = 0.0; |
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frameData.kineticEnergy = 0.0; |
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frameData.potentialEnergy = 0.0; |
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frameData.temperature = 0.0; |
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frameData.chi = 0.0; |
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frameData.integralOfChiDt = 0.0; |
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frameData.electronicTemperature = 0.0; |
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frameData.chiQ = 0.0; |
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frameData.integralOfChiQDt = 0.0; |
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frameData.eta = Mat3x3d(0.0); |
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frameData.COM = V3Zero; |
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frameData.COMvel = V3Zero; |
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frameData.COMw = V3Zero; |
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frameData.stressTensor = Mat3x3d(0.0); |
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frameData.pressureTensor = Mat3x3d(0.0); |
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frameData.systemDipole = Vector3d(0.0); |
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frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0); |
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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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orthoTolerance_(1e-6), |
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hasCOM_(false), |
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hasVolume_(false) { |
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frameData.id = -1; |
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frameData.currentTime = 0; |
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frameData.hmat = Mat3x3d(0.0); |
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frameData.invHmat = Mat3x3d(0.0); |
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frameData.orthoRhombic = false; |
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frameData.volume = 0.0; |
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frameData.pressure = 0.0; |
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frameData.totalEnergy = 0.0; |
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frameData.kineticEnergy = 0.0; |
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frameData.potentialEnergy = 0.0; |
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frameData.temperature = 0.0; |
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frameData.chi = 0.0; |
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frameData.integralOfChiDt = 0.0; |
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frameData.electronicTemperature = 0.0; |
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frameData.chiQ = 0.0; |
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frameData.integralOfChiQDt = 0.0; |
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frameData.eta = Mat3x3d(0.0); |
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frameData.COM = V3Zero; |
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frameData.COMvel = V3Zero; |
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frameData.COMw = V3Zero; |
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frameData.stressTensor = Mat3x3d(0.0); |
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frameData.pressureTensor = Mat3x3d(0.0); |
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frameData.systemDipole = V3Zero; |
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frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0); |
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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 frameData.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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frameData.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 frameData.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 frameData.volume; |
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}else{ |
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return frameData.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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frameData.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 frameData.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 frameData.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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frameData.currentTime =time; |
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//time at statData is redundant |
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statData[Stats::TIME] = frameData.currentTime; |
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} |
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|
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RealType getChi() { |
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return frameData.chi; |
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} |
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|
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void setChi(RealType chi) { |
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frameData.chi = chi; |
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} |
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|
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RealType getIntegralOfChiDt() { |
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return frameData.integralOfChiDt; |
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} |
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|
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void setIntegralOfChiDt(RealType integralOfChiDt) { |
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frameData.integralOfChiDt = integralOfChiDt; |
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} |
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|
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RealType getChiElectronic() { |
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return frameData.chiQ; |
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} |
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|
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void setChiElectronic(RealType chiQ) { |
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frameData.chiQ = chiQ; |
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} |
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|
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RealType getIntegralOfChiElectronicDt() { |
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return frameData.integralOfChiQDt; |
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} |
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|
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void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) { |
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frameData.integralOfChiQDt = integralOfChiQDt; |
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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 frameData.eta; |
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} |
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|
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void setEta(const Mat3x3d& eta) { |
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frameData.eta = eta; |
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} |
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|
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Mat3x3d getStressTensor() { |
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return frameData.stressTensor; |
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} |
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|
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void setStressTensor(const Mat3x3d& stressTensor) { |
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frameData.stressTensor = stressTensor; |
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} |
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|
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Vector3d getConductiveHeatFlux() { |
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return frameData.conductiveHeatFlux; |
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} |
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|
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void setConductiveHeatFlux(const Vector3d& heatFlux) { |
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frameData.conductiveHeatFlux = heatFlux; |
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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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frameData.COM = COM; |
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frameData.COMvel = COMvel; |
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frameData.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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FrameData frameData; |
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Stats statData; |
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|
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private: |
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RealType orthoTolerance_; |
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bool hasCOM_; |
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bool hasVolume_; |
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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 |
