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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

# 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, 234107 (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 #ifndef BRAINS_SNAPSHOT_HPP
44 #define BRAINS_SNAPSHOT_HPP
45
46 #include <vector>
47
48 #include "brains/DataStorage.hpp"
49 #include "nonbonded/NonBondedInteraction.hpp"
50 #include "brains/Stats.hpp"
51
52 using namespace std;
53 namespace OpenMD{
54
55 /**
56 * FrameData is a structure for holding system-wide dynamic data
57 * about the simulation.
58 */
59
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 Mat3x3d bBox; /**< axes of a bounding box in matrix form */
66 Mat3x3d invBbox; /**< the inverse of the bounding box */
67 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 RealType reciprocalPotential; /**< reciprocal-space contributions to the potential */
76 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
106
107 /**
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
116 public:
117 Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
118 Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);
119 /** Returns the id of this Snapshot */
120 int getID();
121 /** Sets the id of this Snapshot */
122 void setID(int id);
123
124 /** sets the state of the computed properties to false */
125 void clearDerivedProperties();
126
127 int getSize();
128 /** Returns the number of atoms */
129 int getNumberOfAtoms();
130 /** Returns the number of rigid bodies */
131 int getNumberOfRigidBodies();
132 /** Returns the number of rigid bodies */
133 int getNumberOfCutoffGroups();
134
135 /** Returns the H-Matrix */
136 Mat3x3d getHmat();
137 /** Sets the H-Matrix */
138 void setHmat(const Mat3x3d& m);
139 /** Returns the inverse H-Matrix */
140 Mat3x3d getInvHmat();
141
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
149 RealType getVolume();
150 RealType getXYarea();
151 void setVolume(const RealType vol);
152
153 /** Wrapping the vector according to periodic boundary condition*/
154 void wrapVector(Vector3d& v);
155
156 /** Scaling a vector to multiples of the periodic box */
157 Vector3d scaleVector(Vector3d &v);
158
159 void setCOM(const Vector3d &com);
160 void setCOMvel(const Vector3d &comVel);
161 void setCOMw(const Vector3d &comw);
162
163 Vector3d getCOM();
164 Vector3d getCOMvel();
165 Vector3d getCOMw();
166
167 RealType getTime();
168 void increaseTime(const RealType dt);
169 void setTime(const RealType time);
170
171 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
180 RealType getShortRangePotential();
181
182 void setLongRangePotential(const potVec lrPot);
183 RealType getLongRangePotential();
184 potVec getLongRangePotentials();
185
186 void setReciprocalPotential(const RealType rp);
187 RealType getReciprocalPotential();
188
189 void setExcludedPotentials(const potVec exPot);
190 potVec getExcludedPotentials();
191
192 void setRestraintPotential(const RealType rp);
193 RealType getRestraintPotential();
194
195 void setRawPotential(const RealType rp);
196 RealType getRawPotential();
197
198 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
239 Mat3x3d getBarostat();
240 void setBarostat(const Mat3x3d& barostat);
241
242 Mat3x3d getInertiaTensor();
243 void setInertiaTensor(const Mat3x3d& inertiaTensor);
244
245 RealType getGyrationalVolume();
246 void setGyrationalVolume(const RealType gv);
247
248 RealType getHullVolume();
249 void setHullVolume(const RealType hv);
250
251 void setOrthoTolerance(RealType orthoTolerance);
252
253 DataStorage atomData;
254 DataStorage rigidbodyData;
255 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 bool hasBoundingBox;
281
282 private:
283 RealType orthoTolerance_;
284
285 };
286
287 typedef DataStorage (Snapshot::*DataStoragePointer);
288 }
289 #endif //BRAINS_SNAPSHOT_HPP

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