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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 588 by gezelter, Thu Jul 10 17:10:56 2003 UTC vs.
Revision 670 by mmeineke, Thu Aug 7 21:47:18 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
# Line 36 | Line 40 | class SimInfo{ (public)
40    unsigned int setTemp;   // boolean to set the temperature at each sampleTime
41  
42    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
43  
44 +
45    int n_exclude;  // the # of pairs excluded from long range forces
46    Exclude** excludes;       // the pairs themselves
47  
# Line 65 | Line 67 | class SimInfo{ (public)
67                        //  
68    double HmatInv[3][3];
69  
70 <  double boxLx, boxLy, boxLz; // the box Lengths
70 >  double boxL[3]; // The Lengths of the 3 column vectors of Hmat
71    double boxVol;
72    int orthoRhombic;
73    
74  
75 +  double dielectric;      // the dielectric of the medium for reaction field
76  
74 –  double rList, rCut; // variables for the neighborlist
77    
78    int usePBC; // whether we use periodic boundry conditions.
79    int useLJ;
# Line 86 | Line 88 | class SimInfo{ (public)
88    double sampleTime, statusTime; // the position and energy dump frequencies
89    double target_temp;            // the target temperature of the system
90    double thermalTime;            // the temp kick interval
91 +  double currentTime;            // Used primarily for correlation Functions
92  
93    int n_mol;           // n_molecules;
94    Molecule* molecules; // the array of molecules
# Line 114 | Line 117 | class SimInfo{ (public)
117    // sets the internal function pointer to fortran.
118  
119    void setInternal( void (*fSetup) setFortranSimList,
120 <                    void (*fBox) setFortranBoxList ){
120 >                    void (*fBox) setFortranBoxList,
121 >                    void (*fCut) notifyFortranCutOffList ){
122      setFsimulation = fSetup;
123      setFortranBoxSize = fBox;
124 +    notifyFortranCutOffs = fCut;
125    }
126  
127    int getNDF();
# Line 126 | Line 131 | class SimInfo{ (public)
131    void setBoxM( double newBox[3][3] );
132    void getBoxM( double theBox[3][3] );
133    void scaleBox( double scale );
134 +  
135 +  void setRcut( double theRcut );
136 +  void setEcr( double theEcr );
137 +  void setEcr( double theEcr, double theEst );
138  
139 +  double getRcut( void )  { return rCut; }
140 +  double getRlist( void ) { return rList; }
141 +  double getEcr( void )   { return ecr; }
142 +  double getEst( void )   { return est; }
143 +
144 +  void setTime( double theTime ) { currentTime = theTime; }
145 +  void incrTime( double dt ) { currentTime += dt; }
146 +  void decrTime( double dt ) { currentTime -= dt; }
147 +  double getTime( void ) { return currentTime; }
148 +
149    void wrapVector( double thePos[3] );
150  
151    void matMul3(double a[3][3], double b[3][3], double out[3][3]);
152    void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
153    void invertMat3(double in[3][3], double out[3][3]);
154 +  void transposeMat3(double in[3][3], double out[3][3]);
155 +  void printMat3(double A[3][3]);
156 +  void printMat9(double A[9]);
157    double matDet3(double m[3][3]);
158 +
159 +  SimState* getConfiguration( void ) { return myConfiguration; }
160    
161 +  void addProperty(GenericData* prop);
162 +  GenericData* getProperty(const string& propName);
163 +  vector<GenericData*> getProperties();      
164 +
165   private:
166 +
167 +  SimState* myConfiguration;
168 +
169 +  double origRcut, origEcr;
170 +  int boxIsInit, haveOrigRcut, haveOrigEcr;
171 +
172 +  double oldEcr;
173 +  double oldRcut;
174 +
175 +  double rList, rCut; // variables for the neighborlist
176 +  double ecr;             // the electrostatic cutoff radius
177 +  double est;             // the electrostatic skin thickness
178 +  double maxCutoff;
179    
180    void calcHmatInv( void );
181    void calcBoxL();
182 +  void checkCutOffs( void );
183  
184    // private function to initialize the fortran side of the simulation
185    void (*setFsimulation) setFortranSimList;
186  
187    void (*setFortranBoxSize) setFortranBoxList;
188 +  
189 +  void (*notifyFortranCutOffs) notifyFortranCutOffList;
190 +  
191 +  //Addtional Properties of SimInfo
192 +  map<string, GenericData*> properties;
193 +
194   };
195  
196  

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