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Revision 1709 by gezelter, Tue May 15 13:04:08 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 <   * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
57 <   * @brief Snapshot class is a repository class for storing dynamic data during
64 <   *  Simulation
65 <   * Every snapshot class will contain one DataStorage for atoms and one DataStorage
66 <   *  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 <                                  volume_(0.0), hasVolume_(false) {
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 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 >    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  
83 –    }
102  
103 <    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
104 <             int storageLayout) : atomData(nAtoms, storageLayout),
105 <                                  rigidbodyData(nRigidbodies, storageLayout),
106 <                                  cgData(nCutoffGroups, DataStorage::dslPosition),
107 <                                  currentTime_(0), orthoTolerance_(1e-6),
108 <                                  orthoRhombic_(0), chi_(0.0),
109 <                                  integralOfChiDt_(0.0), eta_(0.0), id_(-1),
110 <                                  hasCOM_(false), volume_(0.0),
93 <                                  hasVolume_(false) {
94 <    }
95 <    
96 <    /** Returns the id of this Snapshot */
97 <    int getID() {
98 <      return id_;
99 <    }
103 >  /**
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 {
111  
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();
117      /** Sets the id of this Snapshot */
118 <    void setID(int id) {
103 <      id_ = id;
104 <    }
118 >    void     setID(int id);
119  
120 <    int getSize() {
121 <      return atomData.getSize() + rigidbodyData.getSize();
108 <    }
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() {
112 <      return atomData.getSize();
113 <    }
114 <
125 >    int      getNumberOfAtoms();
126      /** Returns the number of rigid bodies */
127 <    int getNumberOfRigidBodies() {
117 <      return rigidbodyData.getSize();
118 <    }
119 <
127 >    int      getNumberOfRigidBodies();
128      /** Returns the number of rigid bodies */
129 <    int getNumberOfCutoffGroups() {
122 <      return cgData.getSize();
123 <    }
129 >    int      getNumberOfCutoffGroups();
130  
131      /** Returns the H-Matrix */
132 <    Mat3x3d getHmat() {
127 <      return hmat_;
128 <    }
129 <
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_){
135 <        return volume_;
136 <      }else{
137 <        return hmat_.determinant();
138 <      }
139 <    }
138 >    RealType getVolume();
139 >    void     setVolume(const RealType vol);
140  
141 –    void setVolume(RealType volume){
142 –      hasVolume_=true;
143 –      volume_ = volume;
144 –    }
145 –
146 –    /** Returns the inverse H-Matrix */
147 –    Mat3x3d getInvHmat() {
148 –      return invHmat_;
149 –    }
150 –
141      /** Wrapping the vector according to periodic boundary condition*/
142 <    void wrapVector(Vector3d& v);
142 >    void     wrapVector(Vector3d& v);
143 >
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 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) {
170 <      currentTime_ =time;
171 <      //time at statData is redundant
172 <      statData[Stats::TIME] = currentTime_;
173 <    }
168 >    RealType getShortRangePotential();
169  
170 <    RealType getChi() {
171 <      return chi_;
172 <    }
170 >    void     setLongRangePotential(const potVec lrPot);
171 >    RealType getLongRangePotential();
172 >    potVec   getLongRangePotentials();
173  
174 <    void setChi(RealType chi) {
175 <      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 integralOfChiDt_;
185 <    }
180 >    void     setRawPotential(const RealType rp);
181 >    RealType getRawPotential();
182  
183 <    void setIntegralOfChiDt(RealType integralOfChiDt) {
184 <      integralOfChiDt_ = integralOfChiDt;
185 <    }
186 <            
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 setOrthoTolerance(RealType orthoTolerance) {
202 <      orthoTolerance_ = orthoTolerance;
194 <    }
201 >    Mat3x3d  getPressureTensor();
202 >    void     setPressureTensor(const Mat3x3d& pressureTensor);
203  
204 <    Mat3x3d getEta() {
205 <      return eta_;
198 <    }
204 >    Mat3x3d  getStressTensor();
205 >    void     setStressTensor(const Mat3x3d& stressTensor);
206  
207 <    void setEta(const Mat3x3d& eta) {
208 <      eta_ = eta;
202 <    }
207 >    Vector3d getConductiveHeatFlux();
208 >    void     setConductiveHeatFlux(const Vector3d& chf);
209  
210 <    Mat3x3d getTau() {
211 <      return tau_;
206 <    }
207 <        
208 <    void setTau(const Mat3x3d& tau) {
209 <      tau_ = tau;
210 <    }
210 >    Vector3d getConvectiveHeatFlux();
211 >    void     setConvectiveHeatFlux(const Vector3d& chf);
212  
213 <    bool hasCOM() {
214 <      return hasCOM_;
215 <    }
213 >    Vector3d getHeatFlux();
214 >    
215 >    Vector3d getSystemDipole();
216 >    void     setSystemDipole(const Vector3d& bd);
217  
218 <    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
219 <      COM_ = COM;
218 <      COMvel_ = COMvel;
219 <      COMw_ = COMw;
220 <      hasCOM_ = true;
221 <    }
218 >    pair<RealType, RealType> getThermostat();
219 >    void setThermostat(const pair<RealType, RealType>& thermostat);
220  
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 +    Mat3x3d  getInertiaTensor();
228 +    void     setInertiaTensor(const Mat3x3d& inertiaTensor);
229 +
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 <    Stats statData;
241 >    FrameData   frameData;
242  
243 <  private:
244 <    RealType currentTime_;
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 <    Mat3x3d hmat_;
232 <    Mat3x3d invHmat_;
265 >  private:
266      RealType orthoTolerance_;
267 <    int orthoRhombic_;
235 <    RealType volume_;
236 <
237 <    RealType chi_;
238 <    RealType integralOfChiDt_;
239 <    Mat3x3d eta_;
240 <    Vector3d COM_;
241 <    Vector3d COMvel_;
242 <    Vector3d COMw_;
243 <    int id_; /**< identification number of the snapshot */
244 <    bool hasCOM_;
245 <    bool hasVolume_;
246 <    Mat3x3d tau_;
267 >    
268    };
269  
270    typedef DataStorage (Snapshot::*DataStoragePointer);

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