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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 569 by mmeineke, Tue Jul 1 21:33:45 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  
# Line 39 | Line 41 | class SimInfo{ (public)
41    double dielectric;      // the dielectric of the medium for reaction field
42  
43    int n_exclude;  // the # of pairs excluded from long range forces
44 <  Exclude* excludes;       // the pairs themselves
44 >  Exclude** excludes;       // the pairs themselves
45  
46    int nGlobalExcludes;
47    int* globalExcludes; // same as above, but these guys participate in
48                         // no long range forces.
49  
50    int* identArray;     // array of unique identifiers for the atoms
51 +  int* molMembershipArray;  // map of atom numbers onto molecule numbers
52  
53    int n_constraints; // the number of constraints on the system
54  
55    unsigned int n_SRI;   // the number of short range interactions
53 –  SRI **sr_interactions;// the array of short range force objects
56  
57    double lrPot; // the potential energy from the long range calculations.
58  
59 <  double box_x, box_y, box_z; // the periodic boundry conditions
59 >  double Hmat[9]; // the periodic boundry conditions. The Hmat is the
60 >                  // column vectors of the x, y, and z box vectors.
61 >                  //
62 >                  //   h1  h2  h3
63 >                  // [ Xx  Yx  Zx ]
64 >                  // [ Xy  Yy  Zy ]
65 >                  // [ Xz  Yz  Zz ]
66 >                  //  
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 ]
73 >
74 >  double HmatI[9]; // the inverted Hmat;
75 >  double boxLx, boxLy, boxLz; // the box Lengths
76 >  double boxVol, orthoRhombic;
77 >  
78 >
79 >
80    double rList, rCut; // variables for the neighborlist
81    
82    int usePBC; // whether we use periodic boundry conditions.
# Line 82 | Line 104 | class SimInfo{ (public)
104    
105    char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
106    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
107 <  Integrator *the_integrator; // the integrator of the simulation
107 >  BaseIntegrator *the_integrator; // the integrator of the simulation
108  
109    char finalName[300];  // the name of the eor file to be written
110    char sampleName[300]; // the name of the dump file to be written
# Line 103 | Line 125 | class SimInfo{ (public)
125      setFortranBoxSize = fBox;
126    }
127  
128 +  int getNDF();
129 +  int getNDFraw();
130 +
131 +  void setBox( double newBox[3] );
132 +  void setBoxM( double newBox[9] );
133 +  void getBoxM( double theBox[9] );
134 +
135 +  void wrapVector( double thePos[3] );
136 +
137   private:
138    
139 +  void calcHmatI( void );
140 +  void calcBoxL();
141 +
142    // private function to initialize the fortran side of the simulation
143    void (*setFsimulation) setFortranSimList;
144  

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