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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 1064 by tim, Tue Feb 24 15:44:45 2004 UTC

# Line 15 | Line 15
15   #include "fSimulation.h"
16   #include "fortranWrapDefines.hpp"
17   #include "GenericData.hpp"
18 + //#include "Minimizer.hpp"
19 + //#include "OOPSEMinimizer.hpp"
20  
21 <
20 <
21 > class OOPSEMinimizer;
22   class SimInfo{
23  
24   public:
# Line 30 | Line 31 | class SimInfo{ (public)
31    
32    double tau[9]; // the stress tensor
33  
34 <  unsigned int n_bonds;    // number of bends
35 <  unsigned int n_bends;    // number of bends
36 <  unsigned int n_torsions; // number of torsions
37 <  unsigned int n_oriented; // number of of atoms with orientation
38 <  unsigned int ndf;        // number of actual degrees of freedom
39 <  unsigned int ndfRaw;     // number of settable degrees of freedom
34 >  int n_bonds;    // number of bends
35 >  int n_bends;    // number of bends
36 >  int n_torsions; // number of torsions
37 >  int n_oriented; // number of of atoms with orientation
38 >  int ndf;        // number of actual degrees of freedom
39 >  int ndfRaw;     // number of settable degrees of freedom
40 >  int ndfTrans;   // number of translational degrees of freedom
41 >  int nZconstraints; // the number of zConstraints
42  
43 <  unsigned int setTemp;   // boolean to set the temperature at each sampleTime
43 >  int setTemp;   // boolean to set the temperature at each sampleTime
44 >  int resetIntegrator; // boolean to reset the integrator
45  
46 <  unsigned int n_dipoles; // number of dipoles
46 >  int n_dipoles; // number of dipoles
47  
48  
49    int n_exclude;  // the # of pairs excluded from long range forces
# Line 54 | Line 58 | class SimInfo{ (public)
58  
59    int n_constraints; // the number of constraints on the system
60  
61 <  unsigned int n_SRI;   // the number of short range interactions
61 >  int n_SRI;   // the number of short range interactions
62  
63    double lrPot; // the potential energy from the long range calculations.
64  
# Line 78 | Line 82 | class SimInfo{ (public)
82    int usePBC; // whether we use periodic boundry conditions.
83    int useLJ;
84    int useSticky;
85 <  int useDipole;
85 >  int useCharges;
86 >  int useDipoles;
87    int useReactionField;
88    int useGB;
89    int useEAM;
90    
91 +  bool useInitXSstate;
92 +  double orthoTolerance;
93  
94    double dt, run_time;           // the time step and total time
95    double sampleTime, statusTime; // the position and energy dump frequencies
96    double target_temp;            // the target temperature of the system
97    double thermalTime;            // the temp kick interval
98    double currentTime;            // Used primarily for correlation Functions
99 +  double resetTime;              // Use to reset the integrator periodically
100  
101    int n_mol;           // n_molecules;
102    Molecule* molecules; // the array of molecules
103    
104 <  int nComponents;           // the number of componentsin the system
104 >  int nComponents;           // the number of components in the system
105    int* componentsNmol;       // the number of molecules of each component
106    MoleculeStamp** compStamps;// the stamps matching the components
107    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 103 | Line 111 | class SimInfo{ (public)
111    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
112    BaseIntegrator *the_integrator; // the integrator of the simulation
113  
114 +  OOPSEMinimizer* the_minimizer; // the energy minimizer
115 +  bool has_minimizer;
116 +
117    char finalName[300];  // the name of the eor file to be written
118    char sampleName[300]; // the name of the dump file to be written
119    char statusName[300]; // the name of the stat file to be written
120  
121 <
121 >  int seed;                    //seed for random number generator
122    // refreshes the sim if things get changed (load balanceing, volume
123    // adjustment, etc.)
124  
# Line 116 | Line 127 | class SimInfo{ (public)
127  
128    // sets the internal function pointer to fortran.
129  
130 <  void setInternal( void (*fSetup) setFortranSimList,
131 <                    void (*fBox) setFortranBoxList,
132 <                    void (*fCut) notifyFortranCutOffList ){
130 >  void setInternal( setFortranSim_TD fSetup,
131 >                    setFortranBox_TD fBox,
132 >                    notifyFortranCutOff_TD fCut){
133      setFsimulation = fSetup;
134      setFortranBoxSize = fBox;
135      notifyFortranCutOffs = fCut;
# Line 126 | Line 137 | class SimInfo{ (public)
137  
138    int getNDF();
139    int getNDFraw();
140 +  int getNDFtranslational();
141  
142    void setBox( double newBox[3] );
143    void setBoxM( double newBox[3][3] );
144    void getBoxM( double theBox[3][3] );
145    void scaleBox( double scale );
146    
147 <  void setRcut( double theRcut );
148 <  void setEcr( double theEcr );
149 <  void setEcr( double theEcr, double theEst );
147 >  void setDefaultRcut( double theRcut );
148 >  void setDefaultEcr( double theEcr );
149 >  void setDefaultEcr( double theEcr, double theEst );
150 >  void checkCutOffs( void );
151  
152    double getRcut( void )  { return rCut; }
153    double getRlist( void ) { return rList; }
154    double getEcr( void )   { return ecr; }
155    double getEst( void )   { return est; }
156 +  double getMaxCutoff( void ) { return maxCutoff; }
157  
158    void setTime( double theTime ) { currentTime = theTime; }
159 <  void incrTime( double dt ) { currentTime += dt; }
160 <  void decrTime( double dt ) { currentTime -= dt; }
159 >  void incrTime( double the_dt ) { currentTime += the_dt; }
160 >  void decrTime( double the_dt ) { currentTime -= the_dt; }
161    double getTime( void ) { return currentTime; }
162  
163    void wrapVector( double thePos[3] );
# Line 155 | Line 169 | class SimInfo{ (public)
169    void printMat3(double A[3][3]);
170    void printMat9(double A[9]);
171    double matDet3(double m[3][3]);
172 +  double matTrace3(double m[3][3]);
173  
174 +  void crossProduct3(double a[3],double b[3], double out[3]);
175 +  double dotProduct3(double a[3], double b[3]);
176 +  double length3(double a[3]);
177 +  
178    SimState* getConfiguration( void ) { return myConfiguration; }
179    
180    void addProperty(GenericData* prop);
181    GenericData* getProperty(const string& propName);
182    vector<GenericData*> getProperties();      
183  
184 +  int getSeed(void) {  return seed; }
185 +  void setSeed(int theSeed) {  seed = theSeed;}
186 +
187   private:
188  
189    SimState* myConfiguration;
190  
191 <  double origRcut, origEcr;
170 <  int boxIsInit, haveOrigRcut, haveOrigEcr;
191 >  int boxIsInit, haveRcut, haveEcr;
192  
172 –  double oldEcr;
173 –  double oldRcut;
174 –
193    double rList, rCut; // variables for the neighborlist
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 +
203    
204    void calcHmatInv( void );
205    void calcBoxL();
206 <  void checkCutOffs( void );
206 >  double calcMaxCutOff();
207  
208 +
209    // private function to initialize the fortran side of the simulation
210 <  void (*setFsimulation) setFortranSimList;
210 >  setFortranSim_TD setFsimulation;
211  
212 <  void (*setFortranBoxSize) setFortranBoxList;
212 >  setFortranBox_TD setFortranBoxSize;
213    
214 <  void (*notifyFortranCutOffs) notifyFortranCutOffList;
214 >  notifyFortranCutOff_TD notifyFortranCutOffs;
215    
216    //Addtional Properties of SimInfo
217    map<string, GenericData*> properties;

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