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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 675 by mmeineke, Mon Aug 11 19:38:44 2003 UTC vs.
Revision 845 by gezelter, Thu Oct 30 18:59:20 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 nZconstraints; // 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 90 | Line 92 | class SimInfo{ (public)
92    double target_temp;            // the target temperature of the system
93    double thermalTime;            // the temp kick interval
94    double currentTime;            // Used primarily for correlation Functions
95 +  double resetTime;              // Use to reset the integrator periodically
96  
97    int n_mol;           // n_molecules;
98    Molecule* molecules; // the array of molecules
99    
100 <  int nComponents;           // the number of componentsin the system
100 >  int nComponents;           // the number of components in the system
101    int* componentsNmol;       // the number of molecules of each component
102    MoleculeStamp** compStamps;// the stamps matching the components
103    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 108 | Line 111 | class SimInfo{ (public)
111    char sampleName[300]; // the name of the dump file to be written
112    char statusName[300]; // the name of the stat file to be written
113  
114 <
114 >  int seed;                    //seed for random number generator
115    // refreshes the sim if things get changed (load balanceing, volume
116    // adjustment, etc.)
117  
# Line 117 | Line 120 | class SimInfo{ (public)
120  
121    // sets the internal function pointer to fortran.
122  
123 <  void setInternal( void (*fSetup) setFortranSimList,
124 <                    void (*fBox) setFortranBoxList,
125 <                    void (*fCut) notifyFortranCutOffList ){
123 >  void setInternal( setFortranSim_TD fSetup,
124 >                    setFortranBox_TD fBox,
125 >                    notifyFortranCutOff_TD fCut){
126      setFsimulation = fSetup;
127      setFortranBoxSize = fBox;
128      notifyFortranCutOffs = fCut;
# Line 127 | Line 130 | class SimInfo{ (public)
130  
131    int getNDF();
132    int getNDFraw();
133 +  int getNDFtranslational();
134  
135    void setBox( double newBox[3] );
136    void setBoxM( double newBox[3][3] );
# Line 134 | Line 138 | class SimInfo{ (public)
138    void scaleBox( double scale );
139    
140    void setRcut( double theRcut );
141 +  void setDefaultRcut( double theRcut );
142    void setEcr( double theEcr );
143 +  void setDefaultEcr( double theEcr );
144    void setEcr( double theEcr, double theEst );
145 +  void setDefaultEcr( double theEcr, double theEst );
146 +  void checkCutOffs( void );
147  
148    double getRcut( void )  { return rCut; }
149    double getRlist( void ) { return rList; }
150    double getEcr( void )   { return ecr; }
151    double getEst( void )   { return est; }
152 +  double getMaxCutoff( void ) { return maxCutoff; }
153  
154    void setTime( double theTime ) { currentTime = theTime; }
155 <  void incrTime( double dt ) { currentTime += dt; }
156 <  void decrTime( double dt ) { currentTime -= dt; }
155 >  void incrTime( double the_dt ) { currentTime += the_dt; }
156 >  void decrTime( double the_dt ) { currentTime -= the_dt; }
157    double getTime( void ) { return currentTime; }
158  
159    void wrapVector( double thePos[3] );
# Line 156 | Line 165 | class SimInfo{ (public)
165    void printMat3(double A[3][3]);
166    void printMat9(double A[9]);
167    double matDet3(double m[3][3]);
168 +  double matTrace3(double m[3][3]);
169  
170 +  void crossProduct3(double a[3],double b[3], double out[3]);
171 +  double dotProduct3(double a[3], double b[3]);
172 +  double length3(double a[3]);
173 +  
174    SimState* getConfiguration( void ) { return myConfiguration; }
175    
176    void addProperty(GenericData* prop);
177    GenericData* getProperty(const string& propName);
178    vector<GenericData*> getProperties();      
179  
180 +  int getSeed(void) {  return seed; }
181 +  void setSeed(int theSeed) {  seed = theSeed;}
182 +
183   private:
184  
185    SimState* myConfiguration;
# Line 177 | Line 194 | class SimInfo{ (public)
194    double ecr;             // the electrostatic cutoff radius
195    double est;             // the electrostatic skin thickness
196    double maxCutoff;
197 +
198 +  double distXY;
199 +  double distYZ;
200 +  double distZX;
201    
202    void calcHmatInv( void );
203    void calcBoxL();
204 <  void checkCutOffs( void );
204 >  double calcMaxCutOff();
205  
206 +
207    // private function to initialize the fortran side of the simulation
208 <  void (*setFsimulation) setFortranSimList;
208 >  setFortranSim_TD setFsimulation;
209  
210 <  void (*setFortranBoxSize) setFortranBoxList;
210 >  setFortranBox_TD setFortranBoxSize;
211    
212 <  void (*notifyFortranCutOffs) notifyFortranCutOffList;
212 >  notifyFortranCutOff_TD notifyFortranCutOffs;
213    
214    //Addtional Properties of SimInfo
215    map<string, GenericData*> properties;

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