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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 1031 by tim, Fri Feb 6 18:58:06 2004 UTC

# Line 15 | Line 15
15   #include "fSimulation.h"
16   #include "fortranWrapDefines.hpp"
17   #include "GenericData.hpp"
18 + #include "Minimizer.hpp"
19  
20  
20 –
21   class SimInfo{
22  
23   public:
# 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
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 54 | 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 78 | Line 81 | class SimInfo{ (public)
81    int usePBC; // whether we use periodic boundry conditions.
82    int useLJ;
83    int useSticky;
84 <  int useDipole;
84 >  int useCharges;
85 >  int useDipoles;
86    int useReactionField;
87    int useGB;
88    int useEAM;
89    
90 +  bool useInitXSstate;
91 +  double orthoTolerance;
92  
93    double dt, run_time;           // the time step and total time
94    double sampleTime, statusTime; // the position and energy dump frequencies
95    double target_temp;            // the target temperature of the system
96    double thermalTime;            // the temp kick interval
97    double currentTime;            // Used primarily for correlation Functions
98 +  double resetTime;              // Use to reset the integrator periodically
99  
100    int n_mol;           // n_molecules;
101    Molecule* molecules; // the array of molecules
102    
103 <  int nComponents;           // the number of componentsin the system
103 >  int nComponents;           // the number of components in the system
104    int* componentsNmol;       // the number of molecules of each component
105    MoleculeStamp** compStamps;// the stamps matching the components
106    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 103 | Line 110 | class SimInfo{ (public)
110    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
111    BaseIntegrator *the_integrator; // the integrator of the simulation
112  
113 +  Minimizer* the_minimizer; // the energy minimizer
114 +  bool has_minimizer;
115 +
116    char finalName[300];  // the name of the eor file to be written
117    char sampleName[300]; // the name of the dump file to be written
118    char statusName[300]; // the name of the stat file to be written
119  
120 <
120 >  int seed;                    //seed for random number generator
121    // refreshes the sim if things get changed (load balanceing, volume
122    // adjustment, etc.)
123  
# Line 116 | Line 126 | class SimInfo{ (public)
126  
127    // sets the internal function pointer to fortran.
128  
129 <  void setInternal( void (*fSetup) setFortranSimList,
130 <                    void (*fBox) setFortranBoxList,
131 <                    void (*fCut) notifyFortranCutOffList ){
129 >  void setInternal( setFortranSim_TD fSetup,
130 >                    setFortranBox_TD fBox,
131 >                    notifyFortranCutOff_TD fCut){
132      setFsimulation = fSetup;
133      setFortranBoxSize = fBox;
134      notifyFortranCutOffs = fCut;
# Line 126 | Line 136 | class SimInfo{ (public)
136  
137    int getNDF();
138    int getNDFraw();
139 +  int getNDFtranslational();
140  
141    void setBox( double newBox[3] );
142    void setBoxM( double newBox[3][3] );
143    void getBoxM( double theBox[3][3] );
144    void scaleBox( double scale );
145    
146 <  void setRcut( double theRcut );
147 <  void setEcr( double theEcr );
148 <  void setEcr( double theEcr, double theEst );
146 >  void setDefaultRcut( double theRcut );
147 >  void setDefaultEcr( double theEcr );
148 >  void setDefaultEcr( double theEcr, double theEst );
149 >  void checkCutOffs( void );
150  
151    double getRcut( void )  { return rCut; }
152    double getRlist( void ) { return rList; }
153    double getEcr( void )   { return ecr; }
154    double getEst( void )   { return est; }
155 +  double getMaxCutoff( void ) { return maxCutoff; }
156  
157    void setTime( double theTime ) { currentTime = theTime; }
158 <  void incrTime( double dt ) { currentTime += dt; }
159 <  void decrTime( double dt ) { currentTime -= dt; }
158 >  void incrTime( double the_dt ) { currentTime += the_dt; }
159 >  void decrTime( double the_dt ) { currentTime -= the_dt; }
160    double getTime( void ) { return currentTime; }
161  
162    void wrapVector( double thePos[3] );
# Line 155 | Line 168 | class SimInfo{ (public)
168    void printMat3(double A[3][3]);
169    void printMat9(double A[9]);
170    double matDet3(double m[3][3]);
171 +  double matTrace3(double m[3][3]);
172  
173 +  void crossProduct3(double a[3],double b[3], double out[3]);
174 +  double dotProduct3(double a[3], double b[3]);
175 +  double length3(double a[3]);
176 +  
177    SimState* getConfiguration( void ) { return myConfiguration; }
178    
179    void addProperty(GenericData* prop);
180    GenericData* getProperty(const string& propName);
181    vector<GenericData*> getProperties();      
182  
183 +  int getSeed(void) {  return seed; }
184 +  void setSeed(int theSeed) {  seed = theSeed;}
185 +
186   private:
187  
188    SimState* myConfiguration;
189  
190 <  double origRcut, origEcr;
170 <  int boxIsInit, haveOrigRcut, haveOrigEcr;
190 >  int boxIsInit, haveRcut, haveEcr;
191  
172 –  double oldEcr;
173 –  double oldRcut;
174 –
192    double rList, rCut; // variables for the neighborlist
193    double ecr;             // the electrostatic cutoff radius
194    double est;             // the electrostatic skin thickness
195    double maxCutoff;
196 +
197 +  double distXY;
198 +  double distYZ;
199 +  double distZX;
200 +
201 +
202    
203    void calcHmatInv( void );
204    void calcBoxL();
205 <  void checkCutOffs( void );
205 >  double calcMaxCutOff();
206  
207 +
208    // private function to initialize the fortran side of the simulation
209 <  void (*setFsimulation) setFortranSimList;
209 >  setFortranSim_TD setFsimulation;
210  
211 <  void (*setFortranBoxSize) setFortranBoxList;
211 >  setFortranBox_TD setFortranBoxSize;
212    
213 <  void (*notifyFortranCutOffs) notifyFortranCutOffList;
213 >  notifyFortranCutOff_TD notifyFortranCutOffs;
214    
215    //Addtional Properties of SimInfo
216    map<string, GenericData*> properties;

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