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 "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 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 tau;              /**< stress tensor */
    Mat3x3d pressureTensor;   /**< pressure tensor */
    Vector3d systemDipole;    /**< total system dipole moment */
  };


  /**
   * @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.tau = Mat3x3d(0.0);              
      frameData.pressureTensor = Mat3x3d(0.0);   
      frameData.systemDipole = V3Zero;            
    }

    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.tau = Mat3x3d(0.0);              
      frameData.pressureTensor = Mat3x3d(0.0);   
      frameData.systemDipole = V3Zero;            
    }
    
    /** 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 getTau() {
      return frameData.tau;
    }
        
    void setTau(const Mat3x3d& tau) {
      frameData.tau = tau;
    }

    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:	1715
Committed:	Tue May 22 21:55:31 2012 UTC (12 years, 11 months ago) by gezelter
File size:	10571 byte(s)
Log Message:	Adding more support structure for Fluctuating Charges.
#	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	246	#include "brains/Stats.hpp"
58	tim	137
59	gezelter	1390	namespace OpenMD{
60	tim	122
61	gezelter	1715	struct FrameData {
62			int id; /*< identification number of the snapshot /
63			RealType currentTime; /*< current time /
64			Mat3x3d hmat; /*< axes of the periodic box in matrix form /
65			Mat3x3d invHmat; /*< the inverse of the Hmat matrix /
66			bool orthoRhombic; /*< is this an orthorhombic periodic box? /
67			RealType volume; /*< total volume of this frame /
68			RealType pressure; /*< pressure of this frame /
69			RealType totalEnergy; /*< total energy of this frame /
70			RealType kineticEnergy; /*< kinetic energy of this frame /
71			RealType potentialEnergy; /*< potential energy of this frame /
72			RealType temperature; /*< temperature of this frame /
73			RealType chi; /*< thermostat velocity /
74			RealType integralOfChiDt; /*< the actual thermostat /
75			RealType electronicTemperature; /*< temperature of the electronic degrees of freedom /
76			RealType chiQ; /*< fluctuating charge thermostat velocity /
77			RealType integralOfChiQDt; /*< the actual fluctuating charge thermostat /
78			Mat3x3d eta; /*< barostat matrix /
79			Vector3d COM; /*< location of center of mass /
80			Vector3d COMvel; /*< system center of mass velocity /
81			Vector3d COMw; /*< system center of mass angular velocity /
82			Mat3x3d tau; /*< stress tensor /
83			Mat3x3d pressureTensor; /*< pressure tensor /
84			Vector3d systemDipole; /*< total system dipole moment /
85			};
86
87
88	gezelter	507	/**
89			* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
90			* @brief Snapshot class is a repository class for storing dynamic data during
91			* Simulation
92	gezelter	1540	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
93	gezelter	507	* for rigid bodies.
94			*/
95			class Snapshot {
96			public:
97	tim	146
98	gezelter	1540	Snapshot(int nAtoms, int nRigidbodies,
99			int nCutoffGroups) : atomData(nAtoms),
100			rigidbodyData(nRigidbodies),
101	gezelter	1715	cgData(nCutoffGroups, DataStorage::dslPosition),
102			orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false){
103
104			frameData.id = -1;
105			frameData.currentTime = 0;
106			frameData.hmat = Mat3x3d(0.0);
107			frameData.invHmat = Mat3x3d(0.0);
108			frameData.orthoRhombic = false;
109			frameData.volume = 0.0;
110			frameData.pressure = 0.0;
111			frameData.totalEnergy = 0.0;
112			frameData.kineticEnergy = 0.0;
113			frameData.potentialEnergy = 0.0;
114			frameData.temperature = 0.0;
115			frameData.chi = 0.0;
116			frameData.integralOfChiDt = 0.0;
117			frameData.electronicTemperature = 0.0;
118			frameData.chiQ = 0.0;
119			frameData.integralOfChiQDt = 0.0;
120			frameData.eta = Mat3x3d(0.0);
121			frameData.COM = V3Zero;
122			frameData.COMvel = V3Zero;
123			frameData.COMw = V3Zero;
124			frameData.tau = Mat3x3d(0.0);
125			frameData.pressureTensor = Mat3x3d(0.0);
126			frameData.systemDipole = V3Zero;
127	gezelter	507	}
128	tim	137
129	gezelter	1540	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
130			int storageLayout) : atomData(nAtoms, storageLayout),
131			rigidbodyData(nRigidbodies, storageLayout),
132			cgData(nCutoffGroups, DataStorage::dslPosition),
133	gezelter	1715	orthoTolerance_(1e-6),
134			hasCOM_(false),
135	gezelter	1708	hasVolume_(false) {
136	gezelter	1715	frameData.id = -1;
137			frameData.currentTime = 0;
138			frameData.hmat = Mat3x3d(0.0);
139			frameData.invHmat = Mat3x3d(0.0);
140			frameData.orthoRhombic = false;
141			frameData.volume = 0.0;
142			frameData.pressure = 0.0;
143			frameData.totalEnergy = 0.0;
144			frameData.kineticEnergy = 0.0;
145			frameData.potentialEnergy = 0.0;
146			frameData.temperature = 0.0;
147			frameData.chi = 0.0;
148			frameData.integralOfChiDt = 0.0;
149			frameData.electronicTemperature = 0.0;
150			frameData.chiQ = 0.0;
151			frameData.integralOfChiQDt = 0.0;
152			frameData.eta = Mat3x3d(0.0);
153			frameData.COM = V3Zero;
154			frameData.COMvel = V3Zero;
155			frameData.COMw = V3Zero;
156			frameData.tau = Mat3x3d(0.0);
157			frameData.pressureTensor = Mat3x3d(0.0);
158			frameData.systemDipole = V3Zero;
159	gezelter	1540	}
160
161	gezelter	507	/** Returns the id of this Snapshot */
162			int getID() {
163	gezelter	1715	return frameData.id;
164	gezelter	507	}
165	tim	137
166	gezelter	507	/** Sets the id of this Snapshot */
167			void setID(int id) {
168	gezelter	1715	frameData.id = id;
169	gezelter	507	}
170	tim	137
171	gezelter	507	int getSize() {
172			return atomData.getSize() + rigidbodyData.getSize();
173			}
174	tim	152
175	gezelter	507	/** Returns the number of atoms */
176			int getNumberOfAtoms() {
177			return atomData.getSize();
178			}
179	tim	152
180	gezelter	507	/** Returns the number of rigid bodies */
181			int getNumberOfRigidBodies() {
182			return rigidbodyData.getSize();
183			}
184	tim	152
185	gezelter	1544	/** Returns the number of rigid bodies */
186			int getNumberOfCutoffGroups() {
187			return cgData.getSize();
188			}
189
190	gezelter	507	/** Returns the H-Matrix */
191			Mat3x3d getHmat() {
192	gezelter	1715	return frameData.hmat;
193	gezelter	507	}
194	tim	152
195	gezelter	507	/** Sets the H-Matrix */
196			void setHmat(const Mat3x3d& m);
197	gezelter	246
198	tim	963	RealType getVolume() {
199	chuckv	1302	if (hasVolume_){
200	gezelter	1715	return frameData.volume;
201	chuckv	1302	}else{
202	gezelter	1715	return frameData.hmat.determinant();
203	chuckv	1302	}
204	gezelter	507	}
205	tim	152
206	chuckv	1302	void setVolume(RealType volume){
207			hasVolume_=true;
208	gezelter	1715	frameData.volume = volume;
209	chuckv	1302	}
210
211	gezelter	507	/** Returns the inverse H-Matrix */
212			Mat3x3d getInvHmat() {
213	gezelter	1715	return frameData.invHmat;
214	gezelter	507	}
215	tim	152
216	gezelter	507	/** Wrapping the vector according to periodic boundary condition*/
217			void wrapVector(Vector3d& v);
218	gezelter	1562	/** Scaling a vector to multiples of the periodic box */
219			Vector3d scaleVector(Vector3d &v);
220
221
222	gezelter	1104	Vector3d getCOM();
223			Vector3d getCOMvel();
224			Vector3d getCOMw();
225	gezelter	246
226	tim	963	RealType getTime() {
227	gezelter	1715	return frameData.currentTime;
228	gezelter	507	}
229	tim	152
230	tim	963	void increaseTime(RealType dt) {
231	gezelter	507	setTime(getTime() + dt);
232			}
233	tim	152
234	tim	963	void setTime(RealType time) {
235	gezelter	1715	frameData.currentTime =time;
236	gezelter	507	//time at statData is redundant
237	gezelter	1715	statData[Stats::TIME] = frameData.currentTime;
238	gezelter	507	}
239	tim	152
240	tim	963	RealType getChi() {
241	gezelter	1715	return frameData.chi;
242	gezelter	507	}
243	gezelter	246
244	tim	963	void setChi(RealType chi) {
245	gezelter	1715	frameData.chi = chi;
246	gezelter	507	}
247	gezelter	246
248	tim	963	RealType getIntegralOfChiDt() {
249	gezelter	1715	return frameData.integralOfChiDt;
250	gezelter	507	}
251	gezelter	246
252	tim	963	void setIntegralOfChiDt(RealType integralOfChiDt) {
253	gezelter	1715	frameData.integralOfChiDt = integralOfChiDt;
254	gezelter	507	}
255	gezelter	246
256	gezelter	1715	RealType getChiElectronic() {
257			return frameData.chiQ;
258			}
259	gezelter	1021
260	gezelter	1715	void setChiElectronic(RealType chiQ) {
261			frameData.chiQ = chiQ;
262			}
263
264			RealType getIntegralOfChiElectronicDt() {
265			return frameData.integralOfChiQDt;
266			}
267
268			void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) {
269			frameData.integralOfChiQDt = integralOfChiQDt;
270			}
271
272
273	gezelter	1021	void setOrthoTolerance(RealType orthoTolerance) {
274			orthoTolerance_ = orthoTolerance;
275			}
276
277	gezelter	507	Mat3x3d getEta() {
278	gezelter	1715	return frameData.eta;
279	gezelter	507	}
280	gezelter	246
281	gezelter	507	void setEta(const Mat3x3d& eta) {
282	gezelter	1715	frameData.eta = eta;
283	gezelter	507	}
284	gezelter	1104
285	gezelter	1709	Mat3x3d getTau() {
286	gezelter	1715	return frameData.tau;
287	gezelter	1709	}
288
289			void setTau(const Mat3x3d& tau) {
290	gezelter	1715	frameData.tau = tau;
291	gezelter	1709	}
292
293	gezelter	1104	bool hasCOM() {
294			return hasCOM_;
295			}
296
297			void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
298	gezelter	1715	frameData.COM = COM;
299			frameData.COMvel = COMvel;
300			frameData.COMw = COMw;
301	gezelter	1104	hasCOM_ = true;
302			}
303	gezelter	1540
304	gezelter	507	DataStorage atomData;
305			DataStorage rigidbodyData;
306	gezelter	1540	DataStorage cgData;
307	gezelter	1715	FrameData frameData;
308	gezelter	1541	Stats statData;
309	gezelter	1540
310	gezelter	507	private:
311	gezelter	1021	RealType orthoTolerance_;
312	gezelter	1104	bool hasCOM_;
313	gezelter	1715	bool hasVolume_;
314	gezelter	507	};
315	tim	122
316	gezelter	507	typedef DataStorage (Snapshot::*DataStoragePointer);
317	tim	122	}
318			#endif //BRAINS_SNAPSHOT_HPP