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.
#	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 "nonbonded/NonBondedInteraction.hpp"
58	#include "brains/Stats.hpp"
59
60	namespace OpenMD{
61
62	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	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	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	Mat3x3d stressTensor; /*< stress tensor /
91	Mat3x3d pressureTensor; /*< pressure tensor /
92	Vector3d systemDipole; /*< total system dipole moment /
93	Vector3d conductiveHeatFlux; /*< heat flux vector (conductive only) /
94	};
95
96
97	/**
98	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
99	* @brief Snapshot class is a repository class for storing dynamic data during
100	* Simulation
101	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
102	* for rigid bodies.
103	*/
104	class Snapshot {
105	public:
106
107	Snapshot(int nAtoms, int nRigidbodies,
108	int nCutoffGroups) : atomData(nAtoms),
109	rigidbodyData(nRigidbodies),
110	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	frameData.stressTensor = Mat3x3d(0.0);
134	frameData.pressureTensor = Mat3x3d(0.0);
135	frameData.systemDipole = Vector3d(0.0);
136	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
137	}
138
139	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
140	int storageLayout) : atomData(nAtoms, storageLayout),
141	rigidbodyData(nRigidbodies, storageLayout),
142	cgData(nCutoffGroups, DataStorage::dslPosition),
143	orthoTolerance_(1e-6),
144	hasCOM_(false),
145	hasVolume_(false) {
146	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	frameData.stressTensor = Mat3x3d(0.0);
167	frameData.pressureTensor = Mat3x3d(0.0);
168	frameData.systemDipole = V3Zero;
169	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
170	}
171
172	/** Returns the id of this Snapshot */
173	int getID() {
174	return frameData.id;
175	}
176
177	/** Sets the id of this Snapshot */
178	void setID(int id) {
179	frameData.id = id;
180	}
181
182	int getSize() {
183	return atomData.getSize() + rigidbodyData.getSize();
184	}
185
186	/** Returns the number of atoms */
187	int getNumberOfAtoms() {
188	return atomData.getSize();
189	}
190
191	/** Returns the number of rigid bodies */
192	int getNumberOfRigidBodies() {
193	return rigidbodyData.getSize();
194	}
195
196	/** Returns the number of rigid bodies */
197	int getNumberOfCutoffGroups() {
198	return cgData.getSize();
199	}
200
201	/** Returns the H-Matrix */
202	Mat3x3d getHmat() {
203	return frameData.hmat;
204	}
205
206	/** Sets the H-Matrix */
207	void setHmat(const Mat3x3d& m);
208
209	RealType getVolume() {
210	if (hasVolume_){
211	return frameData.volume;
212	}else{
213	return frameData.hmat.determinant();
214	}
215	}
216
217	void setVolume(RealType volume){
218	hasVolume_=true;
219	frameData.volume = volume;
220	}
221
222	/** Returns the inverse H-Matrix */
223	Mat3x3d getInvHmat() {
224	return frameData.invHmat;
225	}
226
227	/** Wrapping the vector according to periodic boundary condition*/
228	void wrapVector(Vector3d& v);
229	/** Scaling a vector to multiples of the periodic box */
230	Vector3d scaleVector(Vector3d &v);
231
232
233	Vector3d getCOM();
234	Vector3d getCOMvel();
235	Vector3d getCOMw();
236
237	RealType getTime() {
238	return frameData.currentTime;
239	}
240
241	void increaseTime(RealType dt) {
242	setTime(getTime() + dt);
243	}
244
245	void setTime(RealType time) {
246	frameData.currentTime =time;
247	//time at statData is redundant
248	statData[Stats::TIME] = frameData.currentTime;
249	}
250
251	RealType getChi() {
252	return frameData.chi;
253	}
254
255	void setChi(RealType chi) {
256	frameData.chi = chi;
257	}
258
259	RealType getIntegralOfChiDt() {
260	return frameData.integralOfChiDt;
261	}
262
263	void setIntegralOfChiDt(RealType integralOfChiDt) {
264	frameData.integralOfChiDt = integralOfChiDt;
265	}
266
267	RealType getChiElectronic() {
268	return frameData.chiQ;
269	}
270
271	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	void setOrthoTolerance(RealType orthoTolerance) {
285	orthoTolerance_ = orthoTolerance;
286	}
287
288	Mat3x3d getEta() {
289	return frameData.eta;
290	}
291
292	void setEta(const Mat3x3d& eta) {
293	frameData.eta = eta;
294	}
295
296	Mat3x3d getStressTensor() {
297	return frameData.stressTensor;
298	}
299
300	void setStressTensor(const Mat3x3d& stressTensor) {
301	frameData.stressTensor = stressTensor;
302	}
303
304	Vector3d getConductiveHeatFlux() {
305	return frameData.conductiveHeatFlux;
306	}
307
308	void setConductiveHeatFlux(const Vector3d& heatFlux) {
309	frameData.conductiveHeatFlux = heatFlux;
310	}
311
312	bool hasCOM() {
313	return hasCOM_;
314	}
315
316	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
317	frameData.COM = COM;
318	frameData.COMvel = COMvel;
319	frameData.COMw = COMw;
320	hasCOM_ = true;
321	}
322
323	DataStorage atomData;
324	DataStorage rigidbodyData;
325	DataStorage cgData;
326	FrameData frameData;
327	Stats statData;
328
329	private:
330	RealType orthoTolerance_;
331	bool hasCOM_;
332	bool hasVolume_;
333	};
334
335	typedef DataStorage (Snapshot::*DataStoragePointer);
336	}
337	#endif //BRAINS_SNAPSHOT_HPP