ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC vs.
Revision 941 by gezelter, Tue Jan 13 23:01:43 2004 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 79 | 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 117 | Line 123 | class SimInfo{ (public)
123  
124    // sets the internal function pointer to fortran.
125  
126 <  void setInternal( void (*fSetup) setFortranSimList,
127 <                    void (*fBox) setFortranBoxList,
128 <                    void (*fCut) notifyFortranCutOffList ){
126 >  void setInternal( setFortranSim_TD fSetup,
127 >                    setFortranBox_TD fBox,
128 >                    notifyFortranCutOff_TD fCut){
129      setFsimulation = fSetup;
130      setFortranBoxSize = fBox;
131      notifyFortranCutOffs = fCut;
# Line 127 | Line 133 | class SimInfo{ (public)
133  
134    int getNDF();
135    int getNDFraw();
136 +  int getNDFtranslational();
137  
138    void setBox( double newBox[3] );
139    void setBoxM( double newBox[3][3] );
140    void getBoxM( double theBox[3][3] );
141    void scaleBox( double scale );
142    
143 <  void setRcut( double theRcut );
144 <  void setEcr( double theEcr );
145 <  void setEcr( double theEcr, double theEst );
143 >  void setDefaultRcut( double theRcut );
144 >  void setDefaultEcr( double theEcr );
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);
# Line 170 | Line 184 | class SimInfo{ (public)
184  
185    SimState* myConfiguration;
186  
187 <  double origRcut, origEcr;
174 <  int boxIsInit, haveOrigRcut, haveOrigEcr;
187 >  int boxIsInit, haveRcut, haveEcr;
188  
176 –  double oldEcr;
177 –  double oldRcut;
178 –
189    double rList, rCut; // variables for the neighborlist
190    double ecr;             // the electrostatic cutoff radius
191    double est;             // the electrostatic skin thickness
192    double maxCutoff;
193 +
194 +  double distXY;
195 +  double distYZ;
196 +  double distZX;
197 +
198 +
199    
200    void calcHmatInv( void );
201    void calcBoxL();
202 <  void checkCutOffs( void );
202 >  double calcMaxCutOff();
203  
204 +
205    // private function to initialize the fortran side of the simulation
206 <  void (*setFsimulation) setFortranSimList;
206 >  setFortranSim_TD setFsimulation;
207  
208 <  void (*setFortranBoxSize) setFortranBoxList;
208 >  setFortranBox_TD setFortranBoxSize;
209    
210 <  void (*notifyFortranCutOffs) notifyFortranCutOffList;
210 >  notifyFortranCutOff_TD notifyFortranCutOffs;
211    
212    //Addtional Properties of SimInfo
213    map<string, GenericData*> properties;

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines