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Revision 1551 by gezelter, Thu Apr 28 18:38:21 2011 UTC vs.
Revision 1858 by gezelter, Wed Apr 3 21:32:13 2013 UTC

# Line 35 | Line 35
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]  Vardeman & Gezelter, in progress (2009).                        
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    
42 – /**
43 – * @file Snapshot.hpp
44 – * @author tlin
45 – * @date 10/20/2004
46 – * @time 23:56am
47 – * @version 1.0
48 – */
49 –  
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 <   * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
57 <   * @brief Snapshot class is a repository class for storing dynamic data during
63 <   *  Simulation
64 <   * Every snapshot class will contain one DataStorage for atoms and one DataStorage
65 <   *  for rigid bodies.
56 >   * FrameData is a structure for holding system-wide dynamic data
57 >   * about the simulation.
58     */
59 <  class Snapshot {
60 <  public:
61 <            
62 <    Snapshot(int nAtoms, int nRigidbodies,
63 <             int nCutoffGroups) : atomData(nAtoms),
64 <                                  rigidbodyData(nRigidbodies),
65 <                                  cgData(nCutoffGroups, DataStorage::dslPosition),
66 <                                  currentTime_(0),
67 <                                  orthoTolerance_(1e-6),
68 <                                  orthoRhombic_(0),
69 <                                  chi_(0.0),
70 <                                  integralOfChiDt_(0.0),
71 <                                  eta_(0.0), id_(-1), hasCOM_(false),
72 <                                  hasVolume_(false), volume_(0.0) {
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 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 >    potVec   excludedPotentials;  /**< breakdown of excluded potentials by family */
81 >    RealType restraintPotential;  /**< potential energy of restraints */
82 >    RealType rawPotential;        /**< unrestrained potential energy (when restraints are applied) */
83 >    RealType xyArea;              /**< XY area of this frame */
84 >    RealType volume;              /**< total volume of this frame */
85 >    RealType pressure;            /**< pressure of this frame */
86 >    RealType temperature;         /**< temperature of this frame */
87 >    pair<RealType, RealType> thermostat;    /**< thermostat variables */
88 >    RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
89 >    pair<RealType, RealType> electronicThermostat; /**< thermostat variables for electronic degrees of freedom */
90 >    Mat3x3d  barostat;            /**< barostat matrix */
91 >    Vector3d COM;                 /**< location of system center of mass */
92 >    Vector3d COMvel;              /**< system center of mass velocity */
93 >    Vector3d COMw;                /**< system center of mass angular velocity */
94 >    Mat3x3d  inertiaTensor;       /**< inertia tensor for entire system */
95 >    RealType gyrationalVolume;    /**< gyrational volume for entire system */
96 >    RealType hullVolume;          /**< hull volume for entire system */
97 >    Mat3x3d  stressTensor;        /**< stress tensor */
98 >    Mat3x3d  pressureTensor;      /**< pressure tensor */
99 >    Vector3d systemDipole;        /**< total system dipole moment */
100 >    Vector3d conductiveHeatFlux;  /**< heat flux vector (conductive only) */
101 >    Vector3d convectiveHeatFlux;  /**< heat flux vector (convective only) */
102 >    RealType conservedQuantity;   /**< anything conserved by the integrator */
103 >  };
104  
82 –    }
105  
106 <    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
107 <             int storageLayout) : atomData(nAtoms, storageLayout),
108 <                                  rigidbodyData(nRigidbodies, storageLayout),
109 <                                  cgData(nCutoffGroups, DataStorage::dslPosition),
110 <                                  currentTime_(0), orthoTolerance_(1e-6),
111 <                                  orthoRhombic_(0), chi_(0.0),
112 <                                  integralOfChiDt_(0.0), eta_(0.0), id_(-1),
113 <                                  hasCOM_(false), hasVolume_(false),
92 <                                  volume_(0.0)  {
93 <    }
94 <    
95 <    /** Returns the id of this Snapshot */
96 <    int getID() {
97 <      return id_;
98 <    }
106 >  /**
107 >   * @class Snapshot
108 >   * @brief The Snapshot class is a repository storing dynamic data during a
109 >   * Simulation.  Every Snapshot contains FrameData (for global information)
110 >   * as well as DataStorage (one for Atoms, one for RigidBodies, and one for
111 >   * CutoffGroups).
112 >   */
113 >  class Snapshot {
114  
115 +  public:            
116 +    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
117 +    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);    
118 +    /** Returns the id of this Snapshot */
119 +    int      getID();
120      /** Sets the id of this Snapshot */
121 <    void setID(int id) {
102 <      id_ = id;
103 <    }
121 >    void     setID(int id);
122  
123 <    int getSize() {
124 <      return atomData.getSize() + rigidbodyData.getSize();
107 <    }
123 >    /** sets the state of the computed properties to false */
124 >    void     clearDerivedProperties();
125  
126 +    int      getSize();
127      /** Returns the number of atoms */
128 <    int getNumberOfAtoms() {
111 <      return atomData.getSize();
112 <    }
113 <
128 >    int      getNumberOfAtoms();
129      /** Returns the number of rigid bodies */
130 <    int getNumberOfRigidBodies() {
116 <      return rigidbodyData.getSize();
117 <    }
118 <
130 >    int      getNumberOfRigidBodies();
131      /** Returns the number of rigid bodies */
132 <    int getNumberOfCutoffGroups() {
121 <      return cgData.getSize();
122 <    }
132 >    int      getNumberOfCutoffGroups();
133  
134      /** Returns the H-Matrix */
135 <    Mat3x3d getHmat() {
126 <      return hmat_;
127 <    }
128 <
135 >    Mat3x3d  getHmat();
136      /** Sets the H-Matrix */
137 <    void setHmat(const Mat3x3d& m);
137 >    void     setHmat(const Mat3x3d& m);
138 >    /** Returns the inverse H-Matrix */
139 >    Mat3x3d  getInvHmat();
140 >
141 >    /** Returns the Bounding Box */
142 >    Mat3x3d  getBoundingBox();
143 >    /** Sets the Bounding Box */
144 >    void     setBoundingBox(const Mat3x3d& m);
145 >    /** Returns the inverse Bounding Box*/
146 >    Mat3x3d  getInvBoundingBox();
147              
148 <    RealType getVolume() {
149 <      if (hasVolume_){
150 <        return volume_;
135 <      }else{
136 <        return hmat_.determinant();
137 <      }
138 <    }
148 >    RealType getVolume();
149 >    RealType getXYarea();
150 >    void     setVolume(const RealType vol);
151  
152 <    void setVolume(RealType volume){
153 <      hasVolume_=true;
142 <      volume_ = volume;
143 <    }
152 >    /** Wrapping the vector according to periodic boundary condition*/
153 >    void     wrapVector(Vector3d& v);
154  
155 <    /** Returns the inverse H-Matrix */
156 <    Mat3x3d getInvHmat() {
147 <      return invHmat_;
148 <    }
155 >    /** Scaling a vector to multiples of the periodic box */
156 >    Vector3d scaleVector(Vector3d &v);
157  
158 <    /** Wrapping the vector according to periodic boundary condition*/
159 <    void wrapVector(Vector3d& v);
158 >    void     setCOM(const Vector3d &com);
159 >    void     setCOMvel(const Vector3d &comVel);
160 >    void     setCOMw(const Vector3d &comw);
161 >
162      Vector3d getCOM();
163      Vector3d getCOMvel();
164      Vector3d getCOMw();
165              
166 <    RealType getTime() {
167 <      return currentTime_;
168 <    }
166 >    RealType getTime();
167 >    void     increaseTime(const RealType dt);
168 >    void     setTime(const RealType time);
169  
170 <    void increaseTime(RealType dt) {
171 <      setTime(getTime() + dt);
172 <    }
170 >    void     setBondPotential(const RealType bp);
171 >    void     setBendPotential(const RealType bp);
172 >    void     setTorsionPotential(const RealType tp);
173 >    void     setInversionPotential(const RealType ip);
174 >    RealType getBondPotential();
175 >    RealType getBendPotential();
176 >    RealType getTorsionPotential();
177 >    RealType getInversionPotential();
178  
179 <    void setTime(RealType time) {
165 <      currentTime_ =time;
166 <      //time at statData is redundant
167 <      statData[Stats::TIME] = currentTime_;
168 <    }
179 >    RealType getShortRangePotential();
180  
181 <    RealType getChi() {
182 <      return chi_;
183 <    }
181 >    void     setLongRangePotential(const potVec lrPot);
182 >    RealType getLongRangePotential();
183 >    potVec   getLongRangePotentials();
184  
185 <    void setChi(RealType chi) {
186 <      chi_ = chi;
187 <    }
185 >    void     setExcludedPotentials(const potVec exPot);
186 >    potVec   getExcludedPotentials();
187 >  
188 >    void     setRestraintPotential(const RealType rp);
189 >    RealType getRestraintPotential();
190  
191 <    RealType getIntegralOfChiDt() {
192 <      return integralOfChiDt_;
180 <    }
191 >    void     setRawPotential(const RealType rp);
192 >    RealType getRawPotential();
193  
194 <    void setIntegralOfChiDt(RealType integralOfChiDt) {
195 <      integralOfChiDt_ = integralOfChiDt;
196 <    }
197 <            
194 >    RealType getPotentialEnergy();
195 >    RealType getKineticEnergy();
196 >    RealType getTranslationalKineticEnergy();
197 >    RealType getRotationalKineticEnergy();
198 >    void     setKineticEnergy(const RealType ke);
199 >    void     setTranslationalKineticEnergy(const RealType tke);
200 >    void     setRotationalKineticEnergy(const RealType rke);
201 >    RealType getTotalEnergy();
202 >    void     setTotalEnergy(const RealType te);
203 >    RealType getConservedQuantity();
204 >    void     setConservedQuantity(const RealType cq);
205 >    RealType getTemperature();
206 >    void     setTemperature(const RealType temp);
207 >    RealType getElectronicTemperature();
208 >    void     setElectronicTemperature(const RealType eTemp);
209 >    RealType getPressure();
210 >    void     setPressure(const RealType pressure);
211  
212 <    void setOrthoTolerance(RealType orthoTolerance) {
213 <      orthoTolerance_ = orthoTolerance;
189 <    }
212 >    Mat3x3d  getPressureTensor();
213 >    void     setPressureTensor(const Mat3x3d& pressureTensor);
214  
215 <    Mat3x3d getEta() {
216 <      return eta_;
193 <    }
215 >    Mat3x3d  getStressTensor();
216 >    void     setStressTensor(const Mat3x3d& stressTensor);
217  
218 <    void setEta(const Mat3x3d& eta) {
219 <      eta_ = eta;
197 <    }
218 >    Vector3d getConductiveHeatFlux();
219 >    void     setConductiveHeatFlux(const Vector3d& chf);
220  
221 <    bool hasCOM() {
222 <      return hasCOM_;
201 <    }
221 >    Vector3d getConvectiveHeatFlux();
222 >    void     setConvectiveHeatFlux(const Vector3d& chf);
223  
224 <    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
225 <      COM_ = COM;
226 <      COMvel_ = COMvel;
227 <      COMw_ = COMw;
207 <      hasCOM_ = true;
208 <    }
224 >    Vector3d getHeatFlux();
225 >    
226 >    Vector3d getSystemDipole();
227 >    void     setSystemDipole(const Vector3d& bd);
228  
229 +    pair<RealType, RealType> getThermostat();
230 +    void setThermostat(const pair<RealType, RealType>& thermostat);
231 +
232 +    pair<RealType, RealType> getElectronicThermostat();
233 +    void setElectronicThermostat(const pair<RealType, RealType>& eThermostat);
234 +            
235 +    Mat3x3d  getBarostat();
236 +    void     setBarostat(const Mat3x3d& barostat);
237 +
238 +    Mat3x3d  getInertiaTensor();
239 +    void     setInertiaTensor(const Mat3x3d& inertiaTensor);
240 +
241 +    RealType getGyrationalVolume();
242 +    void     setGyrationalVolume(const RealType gv);
243 +
244 +    RealType getHullVolume();
245 +    void     setHullVolume(const RealType hv);
246 +    
247 +    void     setOrthoTolerance(RealType orthoTolerance);
248 +
249      DataStorage atomData;
250      DataStorage rigidbodyData;
251      DataStorage cgData;
252 <    Stats statData;
252 >    FrameData   frameData;
253  
254 <  private:
255 <    RealType currentTime_;
254 >    bool hasTotalEnergy;        
255 >    bool hasTranslationalKineticEnergy;    
256 >    bool hasRotationalKineticEnergy;    
257 >    bool hasKineticEnergy;    
258 >    bool hasShortRangePotential;
259 >    bool hasLongRangePotential;
260 >    bool hasPotentialEnergy;    
261 >    bool hasXYarea;
262 >    bool hasVolume;        
263 >    bool hasPressure;      
264 >    bool hasTemperature;    
265 >    bool hasElectronicTemperature;
266 >    bool hasCOM;            
267 >    bool hasCOMvel;
268 >    bool hasCOMw;
269 >    bool hasPressureTensor;    
270 >    bool hasSystemDipole;    
271 >    bool hasConvectiveHeatFlux;
272 >    bool hasInertiaTensor;
273 >    bool hasGyrationalVolume;
274 >    bool hasHullVolume;
275 >    bool hasConservedQuantity;
276 >    bool hasBoundingBox;
277  
278 <    Mat3x3d hmat_;
219 <    Mat3x3d invHmat_;
278 >  private:
279      RealType orthoTolerance_;
280 <    int orthoRhombic_;
222 <    RealType volume_;
223 <
224 <    RealType chi_;
225 <    RealType integralOfChiDt_;
226 <    Mat3x3d eta_;
227 <    Vector3d COM_;
228 <    Vector3d COMvel_;
229 <    Vector3d COMw_;
230 <    int id_; /**< identification number of the snapshot */
231 <    bool hasCOM_;
232 <    bool hasVolume_;
233 <            
280 >    
281    };
282  
283    typedef DataStorage (Snapshot::*DataStoragePointer);

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