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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 597 by mmeineke, Mon Jul 14 21:28:54 2003 UTC vs.
Revision 790 by mmeineke, Mon Sep 29 21:16:11 2003 UTC

# Line 1 | Line 1
1   #ifndef __SIMINFO_H__
2   #define __SIMINFO_H__
3  
4 + #include <map>
5 + #include <string>
6 + #include <vector>
7  
5 –
8   #include "Atom.hpp"
9   #include "Molecule.hpp"
10   #include "AbstractClasses.hpp"
11   #include "MakeStamps.hpp"
12 + #include "SimState.hpp"
13  
14   #define __C
15   #include "fSimulation.h"
16   #include "fortranWrapDefines.hpp"
17 + #include "GenericData.hpp"
18  
19  
20  
# Line 19 | Line 23 | class SimInfo{ (public)
23   public:
24  
25    SimInfo();
26 <  ~SimInfo(){}
26 >  ~SimInfo();
27  
28    int n_atoms; // the number of atoms
29    Atom **atoms; // the array of atom objects
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
39 <  double ecr;             // the electrostatic cutoff radius
40 <  double est;             // the electrostatic skin thickness
41 <  double dielectric;      // the dielectric of the medium for reaction field
45 >  int n_dipoles; // number of dipoles
46  
47 +
48    int n_exclude;  // the # of pairs excluded from long range forces
49    Exclude** excludes;       // the pairs themselves
50  
# Line 52 | 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 65 | Line 70 | class SimInfo{ (public)
70                        //  
71    double HmatInv[3][3];
72  
73 <  double boxLx, boxLy, boxLz; // the box Lengths
73 >  double boxL[3]; // The Lengths of the 3 column vectors of Hmat
74    double boxVol;
75    int orthoRhombic;
76    
77  
78 +  double dielectric;      // the dielectric of the medium for reaction field
79  
74 –  double rList, rCut; // variables for the neighborlist
80    
81    int usePBC; // whether we use periodic boundry conditions.
82    int useLJ;
# Line 86 | Line 91 | class SimInfo{ (public)
91    double sampleTime, statusTime; // the position and energy dump frequencies
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
# Line 104 | 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 114 | Line 121 | class SimInfo{ (public)
121    // sets the internal function pointer to fortran.
122  
123    void setInternal( void (*fSetup) setFortranSimList,
124 <                    void (*fBox) setFortranBoxList ){
124 >                    void (*fBox) setFortranBoxList,
125 >                    void (*fCut) notifyFortranCutOffList ){
126      setFsimulation = fSetup;
127      setFortranBoxSize = fBox;
128 +    notifyFortranCutOffs = fCut;
129    }
130  
131    int getNDF();
132    int getNDFraw();
133 +  int getNDFtranslational();
134  
135    void setBox( double newBox[3] );
136    void setBoxM( double newBox[3][3] );
137    void getBoxM( double theBox[3][3] );
138    void scaleBox( double scale );
139 +  
140 +  void setRcut( double theRcut );
141 +  void setEcr( double theEcr );
142 +  void setEcr( double theEcr, double theEst );
143  
144 +  double getRcut( void )  { return rCut; }
145 +  double getRlist( void ) { return rList; }
146 +  double getEcr( void )   { return ecr; }
147 +  double getEst( void )   { return est; }
148 +
149 +  void setTime( double theTime ) { currentTime = theTime; }
150 +  void incrTime( double the_dt ) { currentTime += the_dt; }
151 +  void decrTime( double the_dt ) { currentTime -= the_dt; }
152 +  double getTime( void ) { return currentTime; }
153 +
154    void wrapVector( double thePos[3] );
155  
156    void matMul3(double a[3][3], double b[3][3], double out[3][3]);
# Line 136 | Line 160 | class SimInfo{ (public)
160    void printMat3(double A[3][3]);
161    void printMat9(double A[9]);
162    double matDet3(double m[3][3]);
163 +  double matTrace3(double m[3][3]);
164 +
165 +  void crossProduct3(double a[3],double b[3], double out[3]);
166 +  double dotProduct3(double a[3], double b[3]);
167 +  double length3(double a[3]);
168    
169 +  SimState* getConfiguration( void ) { return myConfiguration; }
170 +  
171 +  void addProperty(GenericData* prop);
172 +  GenericData* getProperty(const string& propName);
173 +  vector<GenericData*> getProperties();      
174 +
175 +  int getSeed(void) {  return seed; }
176 +  void setSeed(int theSeed) {  seed = theSeed;}
177 +
178   private:
179 +
180 +  SimState* myConfiguration;
181 +
182 +  double origRcut, origEcr;
183 +  int boxIsInit, haveOrigRcut, haveOrigEcr;
184 +
185 +  double oldEcr;
186 +  double oldRcut;
187 +
188 +  double rList, rCut; // variables for the neighborlist
189 +  double ecr;             // the electrostatic cutoff radius
190 +  double est;             // the electrostatic skin thickness
191 +  double maxCutoff;
192 +
193 +  double distXY;
194 +  double distYZ;
195 +  double distZX;
196    
197    void calcHmatInv( void );
198    void calcBoxL();
199 +  double calcMaxCutOff();
200 +  void checkCutOffs( void );
201  
202    // private function to initialize the fortran side of the simulation
203    void (*setFsimulation) setFortranSimList;
204  
205    void (*setFortranBoxSize) setFortranBoxList;
206 +  
207 +  void (*notifyFortranCutOffs) notifyFortranCutOffList;
208 +  
209 +  //Addtional Properties of SimInfo
210 +  map<string, GenericData*> properties;
211 +
212   };
213  
214  

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