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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 674 by mmeineke, Mon Aug 11 18:29:46 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 2003 UTC

# Line 30 | Line 30 | class SimInfo{ (public)
30    
31    double tau[9]; // the stress tensor
32  
33 <  unsigned int n_bonds;    // number of bends
34 <  unsigned int n_bends;    // number of bends
35 <  unsigned int n_torsions; // number of torsions
36 <  unsigned int n_oriented; // number of of atoms with orientation
37 <  unsigned int ndf;        // number of actual degrees of freedom
38 <  unsigned int ndfRaw;     // number of settable degrees of freedom
39 <  unsigned int n_Zconstraints; // the number of zConstraints
33 >  int n_bonds;    // number of bends
34 >  int n_bends;    // number of bends
35 >  int n_torsions; // number of torsions
36 >  int n_oriented; // number of of atoms with orientation
37 >  int ndf;        // number of actual degrees of freedom
38 >  int ndfRaw;     // number of settable degrees of freedom
39 >  int ndfTrans;   // number of translational degrees of freedom
40 >  int nZconstraints; // the number of zConstraints
41  
42 <  unsigned int setTemp;   // boolean to set the temperature at each sampleTime
42 >  int setTemp;   // boolean to set the temperature at each sampleTime
43 >  int resetIntegrator; // boolean to reset the integrator
44  
45 <  unsigned int n_dipoles; // number of dipoles
45 >  int n_dipoles; // number of dipoles
46  
47  
48    int n_exclude;  // the # of pairs excluded from long range forces
# Line 55 | Line 57 | class SimInfo{ (public)
57  
58    int n_constraints; // the number of constraints on the system
59  
60 <  unsigned int n_SRI;   // the number of short range interactions
60 >  int n_SRI;   // the number of short range interactions
61  
62    double lrPot; // the potential energy from the long range calculations.
63  
# Line 84 | Line 86 | class SimInfo{ (public)
86    int useGB;
87    int useEAM;
88    
89 +  bool useInitXSstate;
90 +  double orthoTolerance;
91  
92    double dt, run_time;           // the time step and total time
93    double sampleTime, statusTime; // the position and energy dump frequencies
94    double target_temp;            // the target temperature of the system
95    double thermalTime;            // the temp kick interval
96    double currentTime;            // Used primarily for correlation Functions
97 +  double resetTime;              // Use to reset the integrator periodically
98  
99    int n_mol;           // n_molecules;
100    Molecule* molecules; // the array of molecules
101    
102 <  int nComponents;           // the number of componentsin the system
102 >  int nComponents;           // the number of components in the system
103    int* componentsNmol;       // the number of molecules of each component
104    MoleculeStamp** compStamps;// the stamps matching the components
105    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 108 | Line 113 | class SimInfo{ (public)
113    char sampleName[300]; // the name of the dump file to be written
114    char statusName[300]; // the name of the stat file to be written
115  
116 <
116 >  int seed;                    //seed for random number generator
117    // refreshes the sim if things get changed (load balanceing, volume
118    // adjustment, etc.)
119  
# Line 117 | Line 122 | class SimInfo{ (public)
122  
123    // sets the internal function pointer to fortran.
124  
125 <  void setInternal( void (*fSetup) setFortranSimList,
126 <                    void (*fBox) setFortranBoxList,
127 <                    void (*fCut) notifyFortranCutOffList ){
125 >  void setInternal( setFortranSim_TD fSetup,
126 >                    setFortranBox_TD fBox,
127 >                    notifyFortranCutOff_TD fCut){
128      setFsimulation = fSetup;
129      setFortranBoxSize = fBox;
130      notifyFortranCutOffs = fCut;
# Line 127 | Line 132 | class SimInfo{ (public)
132  
133    int getNDF();
134    int getNDFraw();
135 +  int getNDFtranslational();
136  
137    void setBox( double newBox[3] );
138    void setBoxM( double newBox[3][3] );
# Line 134 | Line 140 | class SimInfo{ (public)
140    void scaleBox( double scale );
141    
142    void setRcut( double theRcut );
143 +  void setDefaultRcut( double theRcut );
144    void setEcr( double theEcr );
145 +  void setDefaultEcr( double theEcr );
146    void setEcr( double theEcr, double theEst );
147 +  void setDefaultEcr( double theEcr, double theEst );
148 +  void checkCutOffs( void );
149  
150    double getRcut( void )  { return rCut; }
151    double getRlist( void ) { return rList; }
152    double getEcr( void )   { return ecr; }
153    double getEst( void )   { return est; }
154 +  double getMaxCutoff( void ) { return maxCutoff; }
155  
156    void setTime( double theTime ) { currentTime = theTime; }
157 <  void incrTime( double dt ) { currentTime += dt; }
158 <  void decrTime( double dt ) { currentTime -= dt; }
157 >  void incrTime( double the_dt ) { currentTime += the_dt; }
158 >  void decrTime( double the_dt ) { currentTime -= the_dt; }
159    double getTime( void ) { return currentTime; }
160  
161    void wrapVector( double thePos[3] );
# Line 156 | Line 167 | class SimInfo{ (public)
167    void printMat3(double A[3][3]);
168    void printMat9(double A[9]);
169    double matDet3(double m[3][3]);
170 +  double matTrace3(double m[3][3]);
171  
172 +  void crossProduct3(double a[3],double b[3], double out[3]);
173 +  double dotProduct3(double a[3], double b[3]);
174 +  double length3(double a[3]);
175 +  
176    SimState* getConfiguration( void ) { return myConfiguration; }
177    
178    void addProperty(GenericData* prop);
179    GenericData* getProperty(const string& propName);
180    vector<GenericData*> getProperties();      
181  
182 +  int getSeed(void) {  return seed; }
183 +  void setSeed(int theSeed) {  seed = theSeed;}
184 +
185   private:
186  
187    SimState* myConfiguration;
# Line 177 | Line 196 | class SimInfo{ (public)
196    double ecr;             // the electrostatic cutoff radius
197    double est;             // the electrostatic skin thickness
198    double maxCutoff;
199 +
200 +  double distXY;
201 +  double distYZ;
202 +  double distZX;
203 +
204 +
205    
206    void calcHmatInv( void );
207    void calcBoxL();
208 <  void checkCutOffs( void );
208 >  double calcMaxCutOff();
209  
210 +
211    // private function to initialize the fortran side of the simulation
212 <  void (*setFsimulation) setFortranSimList;
212 >  setFortranSim_TD setFsimulation;
213  
214 <  void (*setFortranBoxSize) setFortranBoxList;
214 >  setFortranBox_TD setFortranBoxSize;
215    
216 <  void (*notifyFortranCutOffs) notifyFortranCutOffList;
216 >  notifyFortranCutOff_TD notifyFortranCutOffs;
217    
218    //Addtional Properties of SimInfo
219    map<string, GenericData*> properties;

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