src/brains/Snapshot.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
  
/**
 * @file Snapshot.hpp
 * @author tlin
 * @date 10/20/2004
 * @time 23:56am
 * @version 1.0
 */
  
#ifndef BRAINS_SNAPSHOT_HPP
#define BRAINS_SNAPSHOT_HPP

#include <vector>

#include "brains/DataStorage.hpp"
#include "nonbonded/NonBondedInteraction.hpp"
#include "brains/Stats.hpp"

namespace OpenMD{

  struct FrameData {
    int id;                   /**< identification number of the snapshot */
    RealType currentTime;     /**< current time */
    Mat3x3d hmat;             /**< axes of the periodic box in matrix form */
    Mat3x3d invHmat;          /**< the inverse of the Hmat matrix */
    bool orthoRhombic;        /**< is this an orthorhombic periodic box? */
    RealType volume;          /**< total volume of this frame */
    RealType pressure;        /**< pressure of this frame */
    RealType totalEnergy;     /**< total energy of this frame */
    RealType kineticEnergy;   /**< kinetic energy of this frame */
    RealType potentialEnergy; /**< potential energy of this frame */
    RealType shortRangePotential; /**< short-range contributions to the potential*/
    RealType longRangePotential; /**< long-range contributions to the potential */
    RealType bondPotential;   /**< bonded contribution to the potential */
    RealType bendPotential;   /**< angle-bending contribution to the potential */
    RealType torsionPotential; /**< dihedral (torsion angle) contribution to the potential */
    RealType inversionPotential; /**< inversion (planarity) contribution to the potential */
    potVec   lrPotentials;    /**< breakdown of long-range potentials by family */
    RealType temperature;     /**< temperature of this frame */
    RealType chi;             /**< thermostat velocity */
    RealType integralOfChiDt; /**< the actual thermostat */
    RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
    RealType chiQ;            /**< fluctuating charge thermostat velocity */
    RealType integralOfChiQDt; /**< the actual fluctuating charge thermostat */
    Mat3x3d eta;              /**< barostat matrix */
    Vector3d COM;             /**< location of center of mass */
    Vector3d COMvel;          /**< system center of mass velocity */
    Vector3d COMw;            /**< system center of mass angular velocity */
    Mat3x3d stressTensor;     /**< stress tensor */
    Mat3x3d pressureTensor;   /**< pressure tensor */
    Vector3d systemDipole;    /**< total system dipole moment */
    Vector3d conductiveHeatFlux; /**< heat flux vector (conductive only) */
  };


  /**
   * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
   * @brief Snapshot class is a repository class for storing dynamic data during 
   *  Simulation
   * Every snapshot class will contain one DataStorage for atoms and one DataStorage
   *  for rigid bodies.
   */
  class Snapshot {
  public:
            
    Snapshot(int nAtoms, int nRigidbodies, 
             int nCutoffGroups) : atomData(nAtoms), 
                                  rigidbodyData(nRigidbodies),
                                  cgData(nCutoffGroups, DataStorage::dslPosition), 
                                  orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false){
      
      frameData.id = -1;                   
      frameData.currentTime = 0;     
      frameData.hmat = Mat3x3d(0.0);             
      frameData.invHmat = Mat3x3d(0.0);          
      frameData.orthoRhombic = false;        
      frameData.volume = 0.0;          
      frameData.pressure = 0.0;        
      frameData.totalEnergy = 0.0;     
      frameData.kineticEnergy = 0.0;   
      frameData.potentialEnergy = 0.0; 
      frameData.temperature = 0.0;     
      frameData.chi = 0.0;             
      frameData.integralOfChiDt = 0.0; 
      frameData.electronicTemperature = 0.0;
      frameData.chiQ = 0.0;            
      frameData.integralOfChiQDt = 0.0; 
      frameData.eta = Mat3x3d(0.0);              
      frameData.COM = V3Zero;             
      frameData.COMvel = V3Zero;          
      frameData.COMw = V3Zero;            
      frameData.stressTensor = Mat3x3d(0.0);              
      frameData.pressureTensor = Mat3x3d(0.0);   
      frameData.systemDipole = Vector3d(0.0);            
      frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
    }

    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, 
             int storageLayout) : atomData(nAtoms, storageLayout), 
                                  rigidbodyData(nRigidbodies, storageLayout),
                                  cgData(nCutoffGroups, DataStorage::dslPosition),
                                  orthoTolerance_(1e-6),
                                  hasCOM_(false),
                                  hasVolume_(false) {
      frameData.id = -1;                   
      frameData.currentTime = 0;     
      frameData.hmat = Mat3x3d(0.0);             
      frameData.invHmat = Mat3x3d(0.0);          
      frameData.orthoRhombic = false;        
      frameData.volume = 0.0;          
      frameData.pressure = 0.0;        
      frameData.totalEnergy = 0.0;     
      frameData.kineticEnergy = 0.0;   
      frameData.potentialEnergy = 0.0; 
      frameData.temperature = 0.0;     
      frameData.chi = 0.0;             
      frameData.integralOfChiDt = 0.0; 
      frameData.electronicTemperature = 0.0;
      frameData.chiQ = 0.0;            
      frameData.integralOfChiQDt = 0.0; 
      frameData.eta = Mat3x3d(0.0);              
      frameData.COM = V3Zero;             
      frameData.COMvel = V3Zero;          
      frameData.COMw = V3Zero;            
      frameData.stressTensor = Mat3x3d(0.0);              
      frameData.pressureTensor = Mat3x3d(0.0);   
      frameData.systemDipole = V3Zero;            
      frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);            
    }
    
    /** Returns the id of this Snapshot */
    int getID() {
      return frameData.id;
    }

    /** Sets the id of this Snapshot */
    void setID(int id) {
      frameData.id = id;
    }

    int getSize() {
      return atomData.getSize() + rigidbodyData.getSize();
    }

    /** Returns the number of atoms */
    int getNumberOfAtoms() {
      return atomData.getSize();
    }

    /** Returns the number of rigid bodies */
    int getNumberOfRigidBodies() {
      return rigidbodyData.getSize();
    }

    /** Returns the number of rigid bodies */
    int getNumberOfCutoffGroups() {
      return cgData.getSize();
    }

    /** Returns the H-Matrix */
    Mat3x3d getHmat() {
      return frameData.hmat;
    }

    /** Sets the H-Matrix */
    void setHmat(const Mat3x3d& m);
            
    RealType getVolume() {
      if (hasVolume_){
        return frameData.volume;
      }else{
        return frameData.hmat.determinant();
      }
    }

    void setVolume(RealType volume){
      hasVolume_=true;
      frameData.volume = volume;
    }

    /** Returns the inverse H-Matrix */
    Mat3x3d getInvHmat() {
      return frameData.invHmat;
    }

    /** Wrapping the vector according to periodic boundary condition*/
    void wrapVector(Vector3d& v);
    /** Scaling a vector to multiples of the periodic box */
    Vector3d scaleVector(Vector3d &v);


    Vector3d getCOM();
    Vector3d getCOMvel();
    Vector3d getCOMw();
            
    RealType getTime() {
      return frameData.currentTime;
    }

    void increaseTime(RealType dt) {
      setTime(getTime() + dt);
    }

    void setTime(RealType time) {
      frameData.currentTime =time;
      //time at statData is redundant
      statData[Stats::TIME] = frameData.currentTime;
    }

    RealType getChi() {
      return frameData.chi;
    }

    void setChi(RealType chi) {
      frameData.chi = chi;
    }

    RealType getIntegralOfChiDt() {
      return frameData.integralOfChiDt;
    }

    void setIntegralOfChiDt(RealType integralOfChiDt) {
      frameData.integralOfChiDt = integralOfChiDt;
    }
            
    RealType getChiElectronic() {
      return frameData.chiQ;
    }

    void setChiElectronic(RealType chiQ) {
      frameData.chiQ = chiQ;
    }

    RealType getIntegralOfChiElectronicDt() {
      return frameData.integralOfChiQDt;
    }

    void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) {
      frameData.integralOfChiQDt = integralOfChiQDt;
    }
            

    void setOrthoTolerance(RealType orthoTolerance) {
      orthoTolerance_ = orthoTolerance;
    }

    Mat3x3d getEta() {
      return frameData.eta;
    }

    void setEta(const Mat3x3d& eta) {
      frameData.eta = eta;
    }

    Mat3x3d getStressTensor() {
      return frameData.stressTensor;
    }
        
    void setStressTensor(const Mat3x3d& stressTensor) {
      frameData.stressTensor = stressTensor;
    }

    Vector3d getConductiveHeatFlux() {
      return frameData.conductiveHeatFlux;
    }
        
    void setConductiveHeatFlux(const Vector3d& heatFlux) {
      frameData.conductiveHeatFlux = heatFlux;
    }

    bool hasCOM() {
      return hasCOM_;
    }

    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
      frameData.COM = COM;
      frameData.COMvel = COMvel;
      frameData.COMw = COMw;
      hasCOM_ = true;
    }

    DataStorage atomData;
    DataStorage rigidbodyData;
    DataStorage cgData;
    FrameData frameData;
    Stats statData;

  private:
    RealType orthoTolerance_;
    bool hasCOM_;
    bool hasVolume_;    
  };

  typedef DataStorage (Snapshot::*DataStoragePointer); 
}
#endif //BRAINS_SNAPSHOT_HPP
Revision:	1757
Committed:	Tue Jun 19 02:11:07 2012 UTC (12 years, 10 months ago) by gezelter
File size:	11712 byte(s)
Log Message:	Possibly fixed the rigid body global indexing issue. Reformatted comments. Started work on the FrameData section of Snapshot.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	122	*
4	gezelter	246	* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	122	*/
42	gezelter	246
43	gezelter	507	/**
44			* @file Snapshot.hpp
45			* @author tlin
46			* @date 10/20/2004
47			* @time 23:56am
48			* @version 1.0
49			*/
50	tim	146
51	tim	122	#ifndef BRAINS_SNAPSHOT_HPP
52			#define BRAINS_SNAPSHOT_HPP
53	tim	137
54			#include <vector>
55
56	tim	155	#include "brains/DataStorage.hpp"
57	gezelter	1757	#include "nonbonded/NonBondedInteraction.hpp"
58	gezelter	246	#include "brains/Stats.hpp"
59	tim	137
60	gezelter	1390	namespace OpenMD{
61	tim	122
62	gezelter	1715	struct FrameData {
63			int id; /*< identification number of the snapshot /
64			RealType currentTime; /*< current time /
65			Mat3x3d hmat; /*< axes of the periodic box in matrix form /
66			Mat3x3d invHmat; /*< the inverse of the Hmat matrix /
67			bool orthoRhombic; /*< is this an orthorhombic periodic box? /
68			RealType volume; /*< total volume of this frame /
69			RealType pressure; /*< pressure of this frame /
70			RealType totalEnergy; /*< total energy of this frame /
71			RealType kineticEnergy; /*< kinetic energy of this frame /
72			RealType potentialEnergy; /*< potential energy of this frame /
73	gezelter	1757	RealType shortRangePotential; /*< short-range contributions to the potential/
74			RealType longRangePotential; /*< long-range contributions to the potential /
75			RealType bondPotential; /*< bonded contribution to the potential /
76			RealType bendPotential; /*< angle-bending contribution to the potential /
77			RealType torsionPotential; /*< dihedral (torsion angle) contribution to the potential /
78			RealType inversionPotential; /*< inversion (planarity) contribution to the potential /
79			potVec lrPotentials; /*< breakdown of long-range potentials by family /
80	gezelter	1715	RealType temperature; /*< temperature of this frame /
81			RealType chi; /*< thermostat velocity /
82			RealType integralOfChiDt; /*< the actual thermostat /
83			RealType electronicTemperature; /*< temperature of the electronic degrees of freedom /
84			RealType chiQ; /*< fluctuating charge thermostat velocity /
85			RealType integralOfChiQDt; /*< the actual fluctuating charge thermostat /
86			Mat3x3d eta; /*< barostat matrix /
87			Vector3d COM; /*< location of center of mass /
88			Vector3d COMvel; /*< system center of mass velocity /
89			Vector3d COMw; /*< system center of mass angular velocity /
90	gezelter	1723	Mat3x3d stressTensor; /*< stress tensor /
91	gezelter	1715	Mat3x3d pressureTensor; /*< pressure tensor /
92			Vector3d systemDipole; /*< total system dipole moment /
93	gezelter	1723	Vector3d conductiveHeatFlux; /*< heat flux vector (conductive only) /
94	gezelter	1715	};
95
96
97	gezelter	507	/**
98			* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
99			* @brief Snapshot class is a repository class for storing dynamic data during
100			* Simulation
101	gezelter	1540	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
102	gezelter	507	* for rigid bodies.
103			*/
104			class Snapshot {
105			public:
106	tim	146
107	gezelter	1540	Snapshot(int nAtoms, int nRigidbodies,
108			int nCutoffGroups) : atomData(nAtoms),
109			rigidbodyData(nRigidbodies),
110	gezelter	1715	cgData(nCutoffGroups, DataStorage::dslPosition),
111			orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false){
112
113			frameData.id = -1;
114			frameData.currentTime = 0;
115			frameData.hmat = Mat3x3d(0.0);
116			frameData.invHmat = Mat3x3d(0.0);
117			frameData.orthoRhombic = false;
118			frameData.volume = 0.0;
119			frameData.pressure = 0.0;
120			frameData.totalEnergy = 0.0;
121			frameData.kineticEnergy = 0.0;
122			frameData.potentialEnergy = 0.0;
123			frameData.temperature = 0.0;
124			frameData.chi = 0.0;
125			frameData.integralOfChiDt = 0.0;
126			frameData.electronicTemperature = 0.0;
127			frameData.chiQ = 0.0;
128			frameData.integralOfChiQDt = 0.0;
129			frameData.eta = Mat3x3d(0.0);
130			frameData.COM = V3Zero;
131			frameData.COMvel = V3Zero;
132			frameData.COMw = V3Zero;
133	gezelter	1723	frameData.stressTensor = Mat3x3d(0.0);
134	gezelter	1715	frameData.pressureTensor = Mat3x3d(0.0);
135	gezelter	1744	frameData.systemDipole = Vector3d(0.0);
136			frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
137	gezelter	507	}
138	tim	137
139	gezelter	1540	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
140			int storageLayout) : atomData(nAtoms, storageLayout),
141			rigidbodyData(nRigidbodies, storageLayout),
142			cgData(nCutoffGroups, DataStorage::dslPosition),
143	gezelter	1715	orthoTolerance_(1e-6),
144			hasCOM_(false),
145	gezelter	1708	hasVolume_(false) {
146	gezelter	1715	frameData.id = -1;
147			frameData.currentTime = 0;
148			frameData.hmat = Mat3x3d(0.0);
149			frameData.invHmat = Mat3x3d(0.0);
150			frameData.orthoRhombic = false;
151			frameData.volume = 0.0;
152			frameData.pressure = 0.0;
153			frameData.totalEnergy = 0.0;
154			frameData.kineticEnergy = 0.0;
155			frameData.potentialEnergy = 0.0;
156			frameData.temperature = 0.0;
157			frameData.chi = 0.0;
158			frameData.integralOfChiDt = 0.0;
159			frameData.electronicTemperature = 0.0;
160			frameData.chiQ = 0.0;
161			frameData.integralOfChiQDt = 0.0;
162			frameData.eta = Mat3x3d(0.0);
163			frameData.COM = V3Zero;
164			frameData.COMvel = V3Zero;
165			frameData.COMw = V3Zero;
166	gezelter	1723	frameData.stressTensor = Mat3x3d(0.0);
167	gezelter	1715	frameData.pressureTensor = Mat3x3d(0.0);
168			frameData.systemDipole = V3Zero;
169	gezelter	1744	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
170	gezelter	1540	}
171
172	gezelter	507	/** Returns the id of this Snapshot */
173			int getID() {
174	gezelter	1715	return frameData.id;
175	gezelter	507	}
176	tim	137
177	gezelter	507	/** Sets the id of this Snapshot */
178			void setID(int id) {
179	gezelter	1715	frameData.id = id;
180	gezelter	507	}
181	tim	137
182	gezelter	507	int getSize() {
183			return atomData.getSize() + rigidbodyData.getSize();
184			}
185	tim	152
186	gezelter	507	/** Returns the number of atoms */
187			int getNumberOfAtoms() {
188			return atomData.getSize();
189			}
190	tim	152
191	gezelter	507	/** Returns the number of rigid bodies */
192			int getNumberOfRigidBodies() {
193			return rigidbodyData.getSize();
194			}
195	tim	152
196	gezelter	1544	/** Returns the number of rigid bodies */
197			int getNumberOfCutoffGroups() {
198			return cgData.getSize();
199			}
200
201	gezelter	507	/** Returns the H-Matrix */
202			Mat3x3d getHmat() {
203	gezelter	1715	return frameData.hmat;
204	gezelter	507	}
205	tim	152
206	gezelter	507	/** Sets the H-Matrix */
207			void setHmat(const Mat3x3d& m);
208	gezelter	246
209	tim	963	RealType getVolume() {
210	chuckv	1302	if (hasVolume_){
211	gezelter	1715	return frameData.volume;
212	chuckv	1302	}else{
213	gezelter	1715	return frameData.hmat.determinant();
214	chuckv	1302	}
215	gezelter	507	}
216	tim	152
217	chuckv	1302	void setVolume(RealType volume){
218			hasVolume_=true;
219	gezelter	1715	frameData.volume = volume;
220	chuckv	1302	}
221
222	gezelter	507	/** Returns the inverse H-Matrix */
223			Mat3x3d getInvHmat() {
224	gezelter	1715	return frameData.invHmat;
225	gezelter	507	}
226	tim	152
227	gezelter	507	/** Wrapping the vector according to periodic boundary condition*/
228			void wrapVector(Vector3d& v);
229	gezelter	1562	/** Scaling a vector to multiples of the periodic box */
230			Vector3d scaleVector(Vector3d &v);
231
232
233	gezelter	1104	Vector3d getCOM();
234			Vector3d getCOMvel();
235			Vector3d getCOMw();
236	gezelter	246
237	tim	963	RealType getTime() {
238	gezelter	1715	return frameData.currentTime;
239	gezelter	507	}
240	tim	152
241	tim	963	void increaseTime(RealType dt) {
242	gezelter	507	setTime(getTime() + dt);
243			}
244	tim	152
245	tim	963	void setTime(RealType time) {
246	gezelter	1715	frameData.currentTime =time;
247	gezelter	507	//time at statData is redundant
248	gezelter	1715	statData[Stats::TIME] = frameData.currentTime;
249	gezelter	507	}
250	tim	152
251	tim	963	RealType getChi() {
252	gezelter	1715	return frameData.chi;
253	gezelter	507	}
254	gezelter	246
255	tim	963	void setChi(RealType chi) {
256	gezelter	1715	frameData.chi = chi;
257	gezelter	507	}
258	gezelter	246
259	tim	963	RealType getIntegralOfChiDt() {
260	gezelter	1715	return frameData.integralOfChiDt;
261	gezelter	507	}
262	gezelter	246
263	tim	963	void setIntegralOfChiDt(RealType integralOfChiDt) {
264	gezelter	1715	frameData.integralOfChiDt = integralOfChiDt;
265	gezelter	507	}
266	gezelter	246
267	gezelter	1715	RealType getChiElectronic() {
268			return frameData.chiQ;
269			}
270	gezelter	1021
271	gezelter	1715	void setChiElectronic(RealType chiQ) {
272			frameData.chiQ = chiQ;
273			}
274
275			RealType getIntegralOfChiElectronicDt() {
276			return frameData.integralOfChiQDt;
277			}
278
279			void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) {
280			frameData.integralOfChiQDt = integralOfChiQDt;
281			}
282
283
284	gezelter	1021	void setOrthoTolerance(RealType orthoTolerance) {
285			orthoTolerance_ = orthoTolerance;
286			}
287
288	gezelter	507	Mat3x3d getEta() {
289	gezelter	1715	return frameData.eta;
290	gezelter	507	}
291	gezelter	246
292	gezelter	507	void setEta(const Mat3x3d& eta) {
293	gezelter	1715	frameData.eta = eta;
294	gezelter	507	}
295	gezelter	1104
296	gezelter	1723	Mat3x3d getStressTensor() {
297			return frameData.stressTensor;
298	gezelter	1709	}
299
300	gezelter	1723	void setStressTensor(const Mat3x3d& stressTensor) {
301			frameData.stressTensor = stressTensor;
302	gezelter	1709	}
303
304	gezelter	1723	Vector3d getConductiveHeatFlux() {
305			return frameData.conductiveHeatFlux;
306			}
307
308			void setConductiveHeatFlux(const Vector3d& heatFlux) {
309			frameData.conductiveHeatFlux = heatFlux;
310			}
311
312	gezelter	1104	bool hasCOM() {
313			return hasCOM_;
314			}
315
316			void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
317	gezelter	1715	frameData.COM = COM;
318			frameData.COMvel = COMvel;
319			frameData.COMw = COMw;
320	gezelter	1104	hasCOM_ = true;
321			}
322	gezelter	1540
323	gezelter	507	DataStorage atomData;
324			DataStorage rigidbodyData;
325	gezelter	1540	DataStorage cgData;
326	gezelter	1715	FrameData frameData;
327	gezelter	1541	Stats statData;
328	gezelter	1540
329	gezelter	507	private:
330	gezelter	1021	RealType orthoTolerance_;
331	gezelter	1104	bool hasCOM_;
332	gezelter	1715	bool hasVolume_;
333	gezelter	507	};
334	tim	122
335	gezelter	507	typedef DataStorage (Snapshot::*DataStoragePointer);
336	tim	122	}
337			#endif //BRAINS_SNAPSHOT_HPP