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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 568 by mmeineke, Mon Jun 30 22:04:01 2003 UTC vs.
Revision 644 by mmeineke, Tue Jul 22 16:41:08 2003 UTC

# Line 36 | Line 36 | class SimInfo{ (public)
36    unsigned int setTemp;   // boolean to set the temperature at each sampleTime
37  
38    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
39  
40 +
41    int n_exclude;  // the # of pairs excluded from long range forces
42    Exclude** excludes;       // the pairs themselves
43  
# Line 56 | Line 54 | class SimInfo{ (public)
54  
55    double lrPot; // the potential energy from the long range calculations.
56  
57 <  double Hmat[9]; // the periodic boundry conditions. The Hmat is the
58 <                  // column vectors of the x, y, and z box vectors.
59 <                  //
60 <                  //   h1  h2  h3
61 <                  // [ Xx  Yx  Zx ]
62 <                  // [ Xy  Yy  Zy ]
63 <                  // [ Xz  Yz  Zz ]
64 <                  //  
67 <                  // to preserve compatibility with Fortran the
68 <                  // ordering in the array is as follows:
69 <                  //
70 <                  // [ 0 3 6 ]
71 <                  // [ 1 4 7 ]
72 <                  // [ 2 5 8 ]
57 >  double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
58 >                      // column vectors of the x, y, and z box vectors.
59 >                      //   h1  h2  h3
60 >                      // [ Xx  Yx  Zx ]
61 >                      // [ Xy  Yy  Zy ]
62 >                      // [ Xz  Yz  Zz ]
63 >                      //  
64 >  double HmatInv[3][3];
65  
66 <  double HmatI[9]; // the inverted Hmat;
75 <  double boxLx, boxLy, boxLz; // the box Lengths
66 >  double boxL[3]; // The Lengths of the 3 column vectors of Hmat
67    double boxVol;
68 +  int orthoRhombic;
69    
70  
71 +  double dielectric;      // the dielectric of the medium for reaction field
72  
80 –  double rList, rCut; // variables for the neighborlist
73    
74    int usePBC; // whether we use periodic boundry conditions.
75    int useLJ;
# Line 92 | Line 84 | class SimInfo{ (public)
84    double sampleTime, statusTime; // the position and energy dump frequencies
85    double target_temp;            // the target temperature of the system
86    double thermalTime;            // the temp kick interval
87 +  double currentTime;            // Used primarily for correlation Functions
88  
89    int n_mol;           // n_molecules;
90    Molecule* molecules; // the array of molecules
# Line 120 | Line 113 | class SimInfo{ (public)
113    // sets the internal function pointer to fortran.
114  
115    void setInternal( void (*fSetup) setFortranSimList,
116 <                    void (*fBox) setFortranBoxList ){
116 >                    void (*fBox) setFortranBoxList,
117 >                    void (*fCut) notifyFortranCutOffList ){
118      setFsimulation = fSetup;
119      setFortranBoxSize = fBox;
120 +    notifyFortranCutOffs = fCut;
121    }
122  
123    int getNDF();
124    int getNDFraw();
125  
126    void setBox( double newBox[3] );
127 <  void setBoxM( double newBox[9] );
128 <  void getBoxM( double theBox[9] );
127 >  void setBoxM( double newBox[3][3] );
128 >  void getBoxM( double theBox[3][3] );
129 >  void scaleBox( double scale );
130 >  
131 >  void setRcut( double theRcut );
132 >  void setEcr( double theEcr );
133 >  void setEcr( double theEcr, double theEst );
134  
135 +  double getRcut( void )  { return rCut; }
136 +  double getRlist( void ) { return rList; }
137 +  double getEcr( void )   { return ecr; }
138 +  double getEst( void )   { return est; }
139 +
140 +  void setTime( double theTime ) { currentTime = theTime; }
141 +  void incrTime( double dt ) { currentTime += dt; }
142 +  void decrTime( double dt ) { currentTime -= dt; }
143 +  double getTime( void ) { return currentTime; }
144 +
145    void wrapVector( double thePos[3] );
146  
147 +  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
148 +  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
149 +  void invertMat3(double in[3][3], double out[3][3]);
150 +  void transposeMat3(double in[3][3], double out[3][3]);
151 +  void printMat3(double A[3][3]);
152 +  void printMat9(double A[9]);
153 +  double matDet3(double m[3][3]);
154 +  
155   private:
156 +
157 +  double origRcut, origEcr;
158 +  int boxIsInit, haveOrigRcut, haveOrigEcr;
159 +
160 +  double oldEcr;
161 +  double oldRcut;
162 +
163 +  double rList, rCut; // variables for the neighborlist
164 +  double ecr;             // the electrostatic cutoff radius
165 +  double est;             // the electrostatic skin thickness
166 +  double maxCutoff;
167    
168 <  void calcHmatI( void );
168 >  void calcHmatInv( void );
169    void calcBoxL();
170 +  void checkCutOffs( void );
171  
172    // private function to initialize the fortran side of the simulation
173    void (*setFsimulation) setFortranSimList;
174  
175    void (*setFortranBoxSize) setFortranBoxList;
176 +  
177 +  void (*notifyFortranCutOffs) notifyFortranCutOffList;
178 +
179   };
180  
181  

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