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.
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* 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	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	/**
44	* @file Snapshot.hpp
45	* @author tlin
46	* @date 10/20/2004
47	* @time 23:56am
48	* @version 1.0
49	*/
50
51	#ifndef BRAINS_SNAPSHOT_HPP
52	#define BRAINS_SNAPSHOT_HPP
53
54	#include <vector>
55
56	#include "brains/DataStorage.hpp"
57	#include "brains/Stats.hpp"
58
59	namespace OpenMD{
60
61	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	/**
89	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
90	* @brief Snapshot class is a repository class for storing dynamic data during
91	* Simulation
92	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
93	* for rigid bodies.
94	*/
95	class Snapshot {
96	public:
97
98	Snapshot(int nAtoms, int nRigidbodies,
99	int nCutoffGroups) : atomData(nAtoms),
100	rigidbodyData(nRigidbodies),
101	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	}
128
129	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
130	int storageLayout) : atomData(nAtoms, storageLayout),
131	rigidbodyData(nRigidbodies, storageLayout),
132	cgData(nCutoffGroups, DataStorage::dslPosition),
133	orthoTolerance_(1e-6),
134	hasCOM_(false),
135	hasVolume_(false) {
136	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	}
160
161	/** Returns the id of this Snapshot */
162	int getID() {
163	return frameData.id;
164	}
165
166	/** Sets the id of this Snapshot */
167	void setID(int id) {
168	frameData.id = id;
169	}
170
171	int getSize() {
172	return atomData.getSize() + rigidbodyData.getSize();
173	}
174
175	/** Returns the number of atoms */
176	int getNumberOfAtoms() {
177	return atomData.getSize();
178	}
179
180	/** Returns the number of rigid bodies */
181	int getNumberOfRigidBodies() {
182	return rigidbodyData.getSize();
183	}
184
185	/** Returns the number of rigid bodies */
186	int getNumberOfCutoffGroups() {
187	return cgData.getSize();
188	}
189
190	/** Returns the H-Matrix */
191	Mat3x3d getHmat() {
192	return frameData.hmat;
193	}
194
195	/** Sets the H-Matrix */
196	void setHmat(const Mat3x3d& m);
197
198	RealType getVolume() {
199	if (hasVolume_){
200	return frameData.volume;
201	}else{
202	return frameData.hmat.determinant();
203	}
204	}
205
206	void setVolume(RealType volume){
207	hasVolume_=true;
208	frameData.volume = volume;
209	}
210
211	/** Returns the inverse H-Matrix */
212	Mat3x3d getInvHmat() {
213	return frameData.invHmat;
214	}
215
216	/** Wrapping the vector according to periodic boundary condition*/
217	void wrapVector(Vector3d& v);
218	/** Scaling a vector to multiples of the periodic box */
219	Vector3d scaleVector(Vector3d &v);
220
221
222	Vector3d getCOM();
223	Vector3d getCOMvel();
224	Vector3d getCOMw();
225
226	RealType getTime() {
227	return frameData.currentTime;
228	}
229
230	void increaseTime(RealType dt) {
231	setTime(getTime() + dt);
232	}
233
234	void setTime(RealType time) {
235	frameData.currentTime =time;
236	//time at statData is redundant
237	statData[Stats::TIME] = frameData.currentTime;
238	}
239
240	RealType getChi() {
241	return frameData.chi;
242	}
243
244	void setChi(RealType chi) {
245	frameData.chi = chi;
246	}
247
248	RealType getIntegralOfChiDt() {
249	return frameData.integralOfChiDt;
250	}
251
252	void setIntegralOfChiDt(RealType integralOfChiDt) {
253	frameData.integralOfChiDt = integralOfChiDt;
254	}
255
256	RealType getChiElectronic() {
257	return frameData.chiQ;
258	}
259
260	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	void setOrthoTolerance(RealType orthoTolerance) {
274	orthoTolerance_ = orthoTolerance;
275	}
276
277	Mat3x3d getEta() {
278	return frameData.eta;
279	}
280
281	void setEta(const Mat3x3d& eta) {
282	frameData.eta = eta;
283	}
284
285	Mat3x3d getTau() {
286	return frameData.tau;
287	}
288
289	void setTau(const Mat3x3d& tau) {
290	frameData.tau = tau;
291	}
292
293	bool hasCOM() {
294	return hasCOM_;
295	}
296
297	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
298	frameData.COM = COM;
299	frameData.COMvel = COMvel;
300	frameData.COMw = COMw;
301	hasCOM_ = true;
302	}
303
304	DataStorage atomData;
305	DataStorage rigidbodyData;
306	DataStorage cgData;
307	FrameData frameData;
308	Stats statData;
309
310	private:
311	RealType orthoTolerance_;
312	bool hasCOM_;
313	bool hasVolume_;
314	};
315
316	typedef DataStorage (Snapshot::*DataStoragePointer);
317	}
318	#endif //BRAINS_SNAPSHOT_HPP