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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 457 by gezelter, Fri Apr 4 19:16:11 2003 UTC vs.
Revision 643 by mmeineke, Mon Jul 21 21:27:40 2003 UTC

# Line 30 | Line 30 | class SimInfo{ (public)
30    unsigned int n_bends;    // number of bends
31    unsigned int n_torsions; // number of torsions
32    unsigned int n_oriented; // number of of atoms with orientation
33 +  unsigned int ndf;        // number of actual degrees of freedom
34 +  unsigned int ndfRaw;     // number of settable degrees of freedom
35  
36    unsigned int setTemp;   // boolean to set the temperature at each sampleTime
37  
38    unsigned int n_dipoles; // number of dipoles
37 –  double ecr;             // the electrostatic cutoff radius
38 –  double est;             // the electrostatic skin thickness
39 –  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 46 | Line 46 | class SimInfo{ (public)
46                         // no long range forces.
47  
48    int* identArray;     // array of unique identifiers for the atoms
49 +  int* molMembershipArray;  // map of atom numbers onto molecule numbers
50  
51    int n_constraints; // the number of constraints on the system
52  
# Line 53 | Line 54 | class SimInfo{ (public)
54  
55    double lrPot; // the potential energy from the long range calculations.
56  
57 <  double box_x, box_y, box_z; // the periodic boundry conditions
58 <  double rList, rCut; // variables for the neighborlist
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 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 +
73 +  
74    int usePBC; // whether we use periodic boundry conditions.
75    int useLJ;
76    int useSticky;
# Line 69 | 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 81 | Line 97 | class SimInfo{ (public)
97    
98    char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
99    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
100 <  Integrator *the_integrator; // the integrator of the simulation
100 >  BaseIntegrator *the_integrator; // the integrator of the simulation
101  
102    char finalName[300];  // the name of the eor file to be written
103    char sampleName[300]; // the name of the dump file to be written
# Line 97 | 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 getBox( double theBox[3] );
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 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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