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root/OpenMD/trunk/src/brains/Snapshot.hpp
Revision: 1925
Committed: Wed Aug 7 15:24:16 2013 UTC (11 years, 9 months ago) by gezelter
File size: 11708 byte(s)
Log Message:
More ewald fixes, reporting reciprocal potential in stats.

File Contents

# 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 gezelter 1879 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39 gezelter 1782 * [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 tim 122 #ifndef BRAINS_SNAPSHOT_HPP
44     #define BRAINS_SNAPSHOT_HPP
45 tim 137
46     #include <vector>
47    
48 tim 155 #include "brains/DataStorage.hpp"
49 gezelter 1782 #include "nonbonded/NonBondedInteraction.hpp"
50 gezelter 246 #include "brains/Stats.hpp"
51 tim 137
52 gezelter 1782 using namespace std;
53 gezelter 1390 namespace OpenMD{
54 tim 122
55 gezelter 507 /**
56 gezelter 1782 * FrameData is a structure for holding system-wide dynamic data
57     * about the simulation.
58 gezelter 507 */
59 gezelter 1782
60     struct FrameData {
61     int id; /**< identification number of the snapshot */
62     RealType currentTime; /**< current time */
63     Mat3x3d hmat; /**< axes of the periodic box in matrix form */
64     Mat3x3d invHmat; /**< the inverse of the Hmat matrix */
65 gezelter 1879 Mat3x3d bBox; /**< axes of a bounding box in matrix form */
66     Mat3x3d invBbox; /**< the inverse of the bounding box */
67 gezelter 1782 bool orthoRhombic; /**< is this an orthorhombic periodic box? */
68     RealType totalEnergy; /**< total energy of this frame */
69     RealType translationalKinetic; /**< translational kinetic energy of this frame */
70     RealType rotationalKinetic; /**< rotational kinetic 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 gezelter 1925 RealType reciprocalPotential; /**< reciprocal-space contributions to the potential */
76 gezelter 1782 RealType bondPotential; /**< bonded contribution to the potential */
77     RealType bendPotential; /**< angle-bending contribution to the potential */
78     RealType torsionPotential; /**< dihedral (torsion angle) contribution to the potential */
79     RealType inversionPotential; /**< inversion (planarity) contribution to the potential */
80     potVec lrPotentials; /**< breakdown of long-range potentials by family */
81     potVec excludedPotentials; /**< breakdown of excluded potentials by family */
82     RealType restraintPotential; /**< potential energy of restraints */
83     RealType rawPotential; /**< unrestrained potential energy (when restraints are applied) */
84     RealType xyArea; /**< XY area of this frame */
85     RealType volume; /**< total volume of this frame */
86     RealType pressure; /**< pressure of this frame */
87     RealType temperature; /**< temperature of this frame */
88     pair<RealType, RealType> thermostat; /**< thermostat variables */
89     RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
90     pair<RealType, RealType> electronicThermostat; /**< thermostat variables for electronic degrees of freedom */
91     Mat3x3d barostat; /**< barostat matrix */
92     Vector3d COM; /**< location of system center of mass */
93     Vector3d COMvel; /**< system center of mass velocity */
94     Vector3d COMw; /**< system center of mass angular velocity */
95     Mat3x3d inertiaTensor; /**< inertia tensor for entire system */
96     RealType gyrationalVolume; /**< gyrational volume for entire system */
97     RealType hullVolume; /**< hull volume for entire system */
98     Mat3x3d stressTensor; /**< stress tensor */
99     Mat3x3d pressureTensor; /**< pressure tensor */
100     Vector3d systemDipole; /**< total system dipole moment */
101     Vector3d conductiveHeatFlux; /**< heat flux vector (conductive only) */
102     Vector3d convectiveHeatFlux; /**< heat flux vector (convective only) */
103     RealType conservedQuantity; /**< anything conserved by the integrator */
104     };
105 gezelter 246
106 tim 137
107 gezelter 1782 /**
108     * @class Snapshot
109     * @brief The Snapshot class is a repository storing dynamic data during a
110     * Simulation. Every Snapshot contains FrameData (for global information)
111     * as well as DataStorage (one for Atoms, one for RigidBodies, and one for
112     * CutoffGroups).
113     */
114     class Snapshot {
115 tim 316
116 gezelter 1782 public:
117     Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
118     Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);
119 gezelter 507 /** Returns the id of this Snapshot */
120 gezelter 1782 int getID();
121 gezelter 507 /** Sets the id of this Snapshot */
122 gezelter 1782 void setID(int id);
123 tim 137
124 gezelter 1782 /** sets the state of the computed properties to false */
125     void clearDerivedProperties();
126 tim 152
127 gezelter 1782 int getSize();
128 gezelter 507 /** Returns the number of atoms */
129 gezelter 1782 int getNumberOfAtoms();
130 gezelter 507 /** Returns the number of rigid bodies */
131 gezelter 1782 int getNumberOfRigidBodies();
132     /** Returns the number of rigid bodies */
133     int getNumberOfCutoffGroups();
134 tim 152
135 gezelter 507 /** Returns the H-Matrix */
136 gezelter 1782 Mat3x3d getHmat();
137 gezelter 507 /** Sets the H-Matrix */
138 gezelter 1782 void setHmat(const Mat3x3d& m);
139     /** Returns the inverse H-Matrix */
140     Mat3x3d getInvHmat();
141 gezelter 1879
142     /** Returns the Bounding Box */
143     Mat3x3d getBoundingBox();
144     /** Sets the Bounding Box */
145     void setBoundingBox(const Mat3x3d& m);
146     /** Returns the inverse Bounding Box*/
147     Mat3x3d getInvBoundingBox();
148 gezelter 246
149 gezelter 1782 RealType getVolume();
150     RealType getXYarea();
151     void setVolume(const RealType vol);
152 tim 152
153 gezelter 1782 /** Wrapping the vector according to periodic boundary condition*/
154     void wrapVector(Vector3d& v);
155 chuckv 1302
156 gezelter 1782 /** Scaling a vector to multiples of the periodic box */
157     Vector3d scaleVector(Vector3d &v);
158 tim 152
159 gezelter 1782 void setCOM(const Vector3d &com);
160     void setCOMvel(const Vector3d &comVel);
161     void setCOMw(const Vector3d &comw);
162    
163 gezelter 1104 Vector3d getCOM();
164     Vector3d getCOMvel();
165     Vector3d getCOMw();
166 gezelter 246
167 gezelter 1782 RealType getTime();
168     void increaseTime(const RealType dt);
169     void setTime(const RealType time);
170 tim 152
171 gezelter 1782 void setBondPotential(const RealType bp);
172     void setBendPotential(const RealType bp);
173     void setTorsionPotential(const RealType tp);
174     void setInversionPotential(const RealType ip);
175     RealType getBondPotential();
176     RealType getBendPotential();
177     RealType getTorsionPotential();
178     RealType getInversionPotential();
179 tim 152
180 gezelter 1782 RealType getShortRangePotential();
181 tim 152
182 gezelter 1782 void setLongRangePotential(const potVec lrPot);
183     RealType getLongRangePotential();
184     potVec getLongRangePotentials();
185 gezelter 246
186 gezelter 1925 void setReciprocalPotential(const RealType rp);
187     RealType getReciprocalPotential();
188    
189 gezelter 1782 void setExcludedPotentials(const potVec exPot);
190     potVec getExcludedPotentials();
191    
192     void setRestraintPotential(const RealType rp);
193     RealType getRestraintPotential();
194 gezelter 246
195 gezelter 1782 void setRawPotential(const RealType rp);
196     RealType getRawPotential();
197 gezelter 246
198 gezelter 1782 RealType getPotentialEnergy();
199     RealType getKineticEnergy();
200     RealType getTranslationalKineticEnergy();
201     RealType getRotationalKineticEnergy();
202     void setKineticEnergy(const RealType ke);
203     void setTranslationalKineticEnergy(const RealType tke);
204     void setRotationalKineticEnergy(const RealType rke);
205     RealType getTotalEnergy();
206     void setTotalEnergy(const RealType te);
207     RealType getConservedQuantity();
208     void setConservedQuantity(const RealType cq);
209     RealType getTemperature();
210     void setTemperature(const RealType temp);
211     RealType getElectronicTemperature();
212     void setElectronicTemperature(const RealType eTemp);
213     RealType getPressure();
214     void setPressure(const RealType pressure);
215    
216     Mat3x3d getPressureTensor();
217     void setPressureTensor(const Mat3x3d& pressureTensor);
218    
219     Mat3x3d getStressTensor();
220     void setStressTensor(const Mat3x3d& stressTensor);
221    
222     Vector3d getConductiveHeatFlux();
223     void setConductiveHeatFlux(const Vector3d& chf);
224    
225     Vector3d getConvectiveHeatFlux();
226     void setConvectiveHeatFlux(const Vector3d& chf);
227    
228     Vector3d getHeatFlux();
229    
230     Vector3d getSystemDipole();
231     void setSystemDipole(const Vector3d& bd);
232    
233     pair<RealType, RealType> getThermostat();
234     void setThermostat(const pair<RealType, RealType>& thermostat);
235    
236     pair<RealType, RealType> getElectronicThermostat();
237     void setElectronicThermostat(const pair<RealType, RealType>& eThermostat);
238 gezelter 246
239 gezelter 1782 Mat3x3d getBarostat();
240     void setBarostat(const Mat3x3d& barostat);
241 gezelter 1021
242 gezelter 1782 Mat3x3d getInertiaTensor();
243     void setInertiaTensor(const Mat3x3d& inertiaTensor);
244 gezelter 1021
245 gezelter 1782 RealType getGyrationalVolume();
246     void setGyrationalVolume(const RealType gv);
247 gezelter 246
248 gezelter 1782 RealType getHullVolume();
249     void setHullVolume(const RealType hv);
250    
251     void setOrthoTolerance(RealType orthoTolerance);
252 gezelter 1104
253 gezelter 507 DataStorage atomData;
254     DataStorage rigidbodyData;
255 gezelter 1782 DataStorage cgData;
256     FrameData frameData;
257    
258     bool hasTotalEnergy;
259     bool hasTranslationalKineticEnergy;
260     bool hasRotationalKineticEnergy;
261     bool hasKineticEnergy;
262     bool hasShortRangePotential;
263     bool hasLongRangePotential;
264     bool hasPotentialEnergy;
265     bool hasXYarea;
266     bool hasVolume;
267     bool hasPressure;
268     bool hasTemperature;
269     bool hasElectronicTemperature;
270     bool hasCOM;
271     bool hasCOMvel;
272     bool hasCOMw;
273     bool hasPressureTensor;
274     bool hasSystemDipole;
275     bool hasConvectiveHeatFlux;
276     bool hasInertiaTensor;
277     bool hasGyrationalVolume;
278     bool hasHullVolume;
279     bool hasConservedQuantity;
280 gezelter 1879 bool hasBoundingBox;
281 gezelter 1782
282 gezelter 507 private:
283 gezelter 1021 RealType orthoTolerance_;
284 gezelter 1782
285 gezelter 507 };
286 tim 122
287 gezelter 507 typedef DataStorage (Snapshot::*DataStoragePointer);
288 tim 122 }
289     #endif //BRAINS_SNAPSHOT_HPP

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