ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 427 by mmeineke, Thu Mar 27 20:48:37 2003 UTC vs.
Revision 626 by mmeineke, Wed Jul 16 21:30:56 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 81 | Line 96 | class SimInfo{ (public)
96    
97    char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
98    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
99 <  Integrator *the_integrator; // the integrator of the simulation
99 >  BaseIntegrator *the_integrator; // the integrator of the simulation
100  
101    char finalName[300];  // the name of the eor file to be written
102    char sampleName[300]; // the name of the dump file to be written
# Line 97 | Line 112 | class SimInfo{ (public)
112    // sets the internal function pointer to fortran.
113  
114    void setInternal( void (*fSetup) setFortranSimList,
115 <                    void (*fBox) setFortranBoxList ){
115 >                    void (*fBox) setFortranBoxList,
116 >                    void (*fCut) notifyFortranCutOffList ){
117      setFsimulation = fSetup;
118      setFortranBoxSize = fBox;
119 +    notifyFortranCutOffs = fCut;
120    }
121  
122 +  int getNDF();
123 +  int getNDFraw();
124 +
125 +  void setBox( double newBox[3] );
126 +  void setBoxM( double newBox[3][3] );
127 +  void getBoxM( double theBox[3][3] );
128 +  void scaleBox( double scale );
129 +  
130 +  void setRcut( double theRcut );
131 +  void setEcr( double theEcr );
132 +  void setEcr( double theEcr, double theEst );
133 +
134 +  double getRcut( void )  { return rCut; }
135 +  double getRlist( void ) { return rList; }
136 +  double getEcr( void )   { return ecr; }
137 +  double getEst( void )   { return est; }
138 +
139 +
140 +  void wrapVector( double thePos[3] );
141 +
142 +  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
143 +  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
144 +  void invertMat3(double in[3][3], double out[3][3]);
145 +  void transposeMat3(double in[3][3], double out[3][3]);
146 +  void printMat3(double A[3][3]);
147 +  void printMat9(double A[9]);
148 +  double matDet3(double m[3][3]);
149 +  
150   private:
151 +
152 +  double origRcut, origEcr;
153 +  int boxIsInit, haveOrigRcut, haveOrigEcr;
154 +
155 +  double oldEcr;
156 +  double oldRcut;
157 +
158 +  double rList, rCut; // variables for the neighborlist
159 +  double ecr;             // the electrostatic cutoff radius
160 +  double est;             // the electrostatic skin thickness
161 +  double maxCutoff;
162    
163 +  void calcHmatInv( void );
164 +  void calcBoxL();
165 +  void checkCutOffs( void );
166 +
167    // private function to initialize the fortran side of the simulation
168    void (*setFsimulation) setFortranSimList;
169  
170    void (*setFortranBoxSize) setFortranBoxList;
171 +  
172 +  void (*notifyFortranCutOffs) notifyFortranCutOffList;
173 +
174   };
175  
176  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines