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Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC vs.
Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

# Line 40 | Line 40
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 –  
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 <    bool orthoRhombic;        /**< is this an orthorhombic periodic box? */
66 <    RealType volume;          /**< total volume of this frame */
67 <    RealType pressure;        /**< pressure of this frame */
68 <    RealType totalEnergy;     /**< total energy of this frame */
69 <    RealType kineticEnergy;   /**< kinetic energy of this frame */
70 <    RealType potentialEnergy; /**< potential energy of this frame */
71 <    RealType temperature;     /**< temperature of this frame */
72 <    RealType chi;             /**< thermostat velocity */
73 <    RealType integralOfChiDt; /**< the actual thermostat */
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 >    bool     orthoRhombic;        /**< is this an orthorhombic periodic box? */
66 >    RealType totalEnergy;         /**< total energy of this frame */
67 >    RealType translationalKinetic; /**< translational kinetic energy of this frame */
68 >    RealType rotationalKinetic;   /**< rotational kinetic energy of this frame */
69 >    RealType kineticEnergy;       /**< kinetic energy of this frame */
70 >    RealType potentialEnergy;     /**< potential energy of this frame */
71 >    RealType shortRangePotential; /**< short-range contributions to the potential*/
72 >    RealType longRangePotential;  /**< long-range contributions to the potential */
73 >    RealType bondPotential;       /**< bonded contribution to the potential */
74 >    RealType bendPotential;       /**< angle-bending contribution to the potential */
75 >    RealType torsionPotential;    /**< dihedral (torsion angle) contribution to the potential */
76 >    RealType inversionPotential;  /**< inversion (planarity) contribution to the potential */
77 >    potVec   lrPotentials;        /**< breakdown of long-range potentials by family */
78 >    potVec   excludedPotentials;  /**< breakdown of excluded potentials by family */
79 >    RealType restraintPotential;  /**< potential energy of restraints */
80 >    RealType rawPotential;        /**< unrestrained potential energy (when restraints are applied) */
81 >    RealType volume;              /**< total volume of this frame */
82 >    RealType pressure;            /**< pressure of this frame */
83 >    RealType temperature;         /**< temperature of this frame */
84 >    pair<RealType, RealType> thermostat;    /**< thermostat variables */
85      RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
86 <    RealType chiQ;            /**< fluctuating charge thermostat velocity */
87 <    RealType integralOfChiQDt; /**< the actual fluctuating charge thermostat */
88 <    Mat3x3d eta;              /**< barostat matrix */
89 <    Vector3d COM;             /**< location of center of mass */
90 <    Vector3d COMvel;          /**< system center of mass velocity */
91 <    Vector3d COMw;            /**< system center of mass angular velocity */
92 <    Mat3x3d tau;              /**< stress tensor */
93 <    Mat3x3d pressureTensor;   /**< pressure tensor */
94 <    Vector3d systemDipole;    /**< total system dipole moment */
86 >    pair<RealType, RealType> electronicThermostat; /**< thermostat variables for electronic degrees of freedom */
87 >    Mat3x3d  barostat;            /**< barostat matrix */
88 >    Vector3d COM;                 /**< location of system center of mass */
89 >    Vector3d COMvel;              /**< system center of mass velocity */
90 >    Vector3d COMw;                /**< system center of mass angular velocity */
91 >    Mat3x3d  inertiaTensor;       /**< inertia tensor for entire system */
92 >    RealType gyrationalVolume;    /**< gyrational volume for entire system */
93 >    RealType hullVolume;          /**< hull volume for entire system */
94 >    Mat3x3d  stressTensor;        /**< stress tensor */
95 >    Mat3x3d  pressureTensor;      /**< pressure tensor */
96 >    Vector3d systemDipole;        /**< total system dipole moment */
97 >    Vector3d conductiveHeatFlux;  /**< heat flux vector (conductive only) */
98 >    Vector3d convectiveHeatFlux;  /**< heat flux vector (convective only) */
99 >    RealType conservedQuantity;   /**< anything conserved by the integrator */
100    };
101  
102  
103    /**
104 <   * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
105 <   * @brief Snapshot class is a repository class for storing dynamic data during
106 <   *  Simulation
107 <   * Every snapshot class will contain one DataStorage for atoms and one DataStorage
108 <   *  for rigid bodies.
104 >   * @class Snapshot
105 >   * @brief The Snapshot class is a repository storing dynamic data during a
106 >   * Simulation.  Every Snapshot contains FrameData (for global information)
107 >   * as well as DataStorage (one for Atoms, one for RigidBodies, and one for
108 >   * CutoffGroups).
109     */
110    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 –    }
111  
112 <    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
113 <             int storageLayout) : atomData(nAtoms, storageLayout),
114 <                                  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 <    
112 >  public:            
113 >    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
114 >    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);    
115      /** Returns the id of this Snapshot */
116 <    int getID() {
163 <      return frameData.id;
164 <    }
165 <
116 >    int      getID();
117      /** Sets the id of this Snapshot */
118 <    void setID(int id) {
168 <      frameData.id = id;
169 <    }
118 >    void     setID(int id);
119  
120 <    int getSize() {
121 <      return atomData.getSize() + rigidbodyData.getSize();
173 <    }
120 >    /** sets the state of the computed properties to false */
121 >    void     clearDerivedProperties();
122  
123 +    int      getSize();
124      /** Returns the number of atoms */
125 <    int getNumberOfAtoms() {
177 <      return atomData.getSize();
178 <    }
179 <
125 >    int      getNumberOfAtoms();
126      /** Returns the number of rigid bodies */
127 <    int getNumberOfRigidBodies() {
182 <      return rigidbodyData.getSize();
183 <    }
184 <
127 >    int      getNumberOfRigidBodies();
128      /** Returns the number of rigid bodies */
129 <    int getNumberOfCutoffGroups() {
187 <      return cgData.getSize();
188 <    }
129 >    int      getNumberOfCutoffGroups();
130  
131      /** Returns the H-Matrix */
132 <    Mat3x3d getHmat() {
192 <      return frameData.hmat;
193 <    }
194 <
132 >    Mat3x3d  getHmat();
133      /** Sets the H-Matrix */
134 <    void setHmat(const Mat3x3d& m);
134 >    void     setHmat(const Mat3x3d& m);
135 >    /** Returns the inverse H-Matrix */
136 >    Mat3x3d  getInvHmat();
137              
138 <    RealType getVolume() {
139 <      if (hasVolume_){
200 <        return frameData.volume;
201 <      }else{
202 <        return frameData.hmat.determinant();
203 <      }
204 <    }
138 >    RealType getVolume();
139 >    void     setVolume(const RealType vol);
140  
141 <    void setVolume(RealType volume){
142 <      hasVolume_=true;
208 <      frameData.volume = volume;
209 <    }
141 >    /** Wrapping the vector according to periodic boundary condition*/
142 >    void     wrapVector(Vector3d& v);
143  
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);
144      /** Scaling a vector to multiples of the periodic box */
145      Vector3d scaleVector(Vector3d &v);
146  
147 +    void     setCOM(const Vector3d &com);
148 +    void     setCOMvel(const Vector3d &comVel);
149 +    void     setCOMw(const Vector3d &comw);
150  
151      Vector3d getCOM();
152      Vector3d getCOMvel();
153      Vector3d getCOMw();
154              
155 <    RealType getTime() {
156 <      return frameData.currentTime;
157 <    }
155 >    RealType getTime();
156 >    void     increaseTime(const RealType dt);
157 >    void     setTime(const RealType time);
158  
159 <    void increaseTime(RealType dt) {
160 <      setTime(getTime() + dt);
161 <    }
159 >    void     setBondPotential(const RealType bp);
160 >    void     setBendPotential(const RealType bp);
161 >    void     setTorsionPotential(const RealType tp);
162 >    void     setInversionPotential(const RealType ip);
163 >    RealType getBondPotential();
164 >    RealType getBendPotential();
165 >    RealType getTorsionPotential();
166 >    RealType getInversionPotential();
167  
168 <    void setTime(RealType time) {
235 <      frameData.currentTime =time;
236 <      //time at statData is redundant
237 <      statData[Stats::TIME] = frameData.currentTime;
238 <    }
168 >    RealType getShortRangePotential();
169  
170 <    RealType getChi() {
171 <      return frameData.chi;
172 <    }
170 >    void     setLongRangePotential(const potVec lrPot);
171 >    RealType getLongRangePotential();
172 >    potVec   getLongRangePotentials();
173  
174 <    void setChi(RealType chi) {
175 <      frameData.chi = chi;
176 <    }
174 >    void     setExcludedPotentials(const potVec exPot);
175 >    potVec   getExcludedPotentials();
176 >  
177 >    void     setRestraintPotential(const RealType rp);
178 >    RealType getRestraintPotential();
179  
180 <    RealType getIntegralOfChiDt() {
181 <      return frameData.integralOfChiDt;
250 <    }
180 >    void     setRawPotential(const RealType rp);
181 >    RealType getRawPotential();
182  
183 <    void setIntegralOfChiDt(RealType integralOfChiDt) {
184 <      frameData.integralOfChiDt = integralOfChiDt;
185 <    }
186 <            
187 <    RealType getChiElectronic() {
188 <      return frameData.chiQ;
189 <    }
183 >    RealType getPotentialEnergy();
184 >    RealType getKineticEnergy();
185 >    RealType getTranslationalKineticEnergy();
186 >    RealType getRotationalKineticEnergy();
187 >    void     setKineticEnergy(const RealType ke);
188 >    void     setTranslationalKineticEnergy(const RealType tke);
189 >    void     setRotationalKineticEnergy(const RealType rke);
190 >    RealType getTotalEnergy();
191 >    void     setTotalEnergy(const RealType te);
192 >    RealType getConservedQuantity();
193 >    void     setConservedQuantity(const RealType cq);
194 >    RealType getTemperature();
195 >    void     setTemperature(const RealType temp);
196 >    RealType getElectronicTemperature();
197 >    void     setElectronicTemperature(const RealType eTemp);
198 >    RealType getPressure();
199 >    void     setPressure(const RealType pressure);
200  
201 <    void setChiElectronic(RealType chiQ) {
202 <      frameData.chiQ = chiQ;
262 <    }
201 >    Mat3x3d  getPressureTensor();
202 >    void     setPressureTensor(const Mat3x3d& pressureTensor);
203  
204 <    RealType getIntegralOfChiElectronicDt() {
205 <      return frameData.integralOfChiQDt;
266 <    }
204 >    Mat3x3d  getStressTensor();
205 >    void     setStressTensor(const Mat3x3d& stressTensor);
206  
207 <    void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) {
208 <      frameData.integralOfChiQDt = integralOfChiQDt;
270 <    }
271 <            
207 >    Vector3d getConductiveHeatFlux();
208 >    void     setConductiveHeatFlux(const Vector3d& chf);
209  
210 <    void setOrthoTolerance(RealType orthoTolerance) {
211 <      orthoTolerance_ = orthoTolerance;
275 <    }
210 >    Vector3d getConvectiveHeatFlux();
211 >    void     setConvectiveHeatFlux(const Vector3d& chf);
212  
213 <    Mat3x3d getEta() {
214 <      return frameData.eta;
215 <    }
213 >    Vector3d getHeatFlux();
214 >    
215 >    Vector3d getSystemDipole();
216 >    void     setSystemDipole(const Vector3d& bd);
217  
218 <    void setEta(const Mat3x3d& eta) {
219 <      frameData.eta = eta;
283 <    }
218 >    pair<RealType, RealType> getThermostat();
219 >    void setThermostat(const pair<RealType, RealType>& thermostat);
220  
221 <    Mat3x3d getTau() {
222 <      return frameData.tau;
223 <    }
224 <        
225 <    void setTau(const Mat3x3d& tau) {
290 <      frameData.tau = tau;
291 <    }
221 >    pair<RealType, RealType> getElectronicThermostat();
222 >    void setElectronicThermostat(const pair<RealType, RealType>& eThermostat);
223 >            
224 >    Mat3x3d  getBarostat();
225 >    void     setBarostat(const Mat3x3d& barostat);
226  
227 <    bool hasCOM() {
228 <      return hasCOM_;
295 <    }
227 >    Mat3x3d  getInertiaTensor();
228 >    void     setInertiaTensor(const Mat3x3d& inertiaTensor);
229  
230 <    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
231 <      frameData.COM = COM;
299 <      frameData.COMvel = COMvel;
300 <      frameData.COMw = COMw;
301 <      hasCOM_ = true;
302 <    }
230 >    RealType getGyrationalVolume();
231 >    void     setGyrationalVolume(const RealType gv);
232  
233 +    RealType getHullVolume();
234 +    void     setHullVolume(const RealType hv);
235 +    
236 +    void     setOrthoTolerance(RealType orthoTolerance);
237 +
238      DataStorage atomData;
239      DataStorage rigidbodyData;
240      DataStorage cgData;
241 <    FrameData frameData;
308 <    Stats statData;
241 >    FrameData   frameData;
242  
243 +    bool hasTotalEnergy;        
244 +    bool hasTranslationalKineticEnergy;    
245 +    bool hasRotationalKineticEnergy;    
246 +    bool hasKineticEnergy;    
247 +    bool hasShortRangePotential;
248 +    bool hasLongRangePotential;
249 +    bool hasPotentialEnergy;    
250 +    bool hasVolume;        
251 +    bool hasPressure;      
252 +    bool hasTemperature;    
253 +    bool hasElectronicTemperature;
254 +    bool hasCOM;            
255 +    bool hasCOMvel;
256 +    bool hasCOMw;
257 +    bool hasPressureTensor;    
258 +    bool hasSystemDipole;    
259 +    bool hasConvectiveHeatFlux;
260 +    bool hasInertiaTensor;
261 +    bool hasGyrationalVolume;
262 +    bool hasHullVolume;
263 +    bool hasConservedQuantity;
264 +
265    private:
266      RealType orthoTolerance_;
267 <    bool hasCOM_;
313 <    bool hasVolume_;    
267 >    
268    };
269  
270    typedef DataStorage (Snapshot::*DataStoragePointer);

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