| 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 |
|
|
| 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 |
< |
int *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[3][3]; // the periodic boundry conditions. The Hmat is the |
| 60 |
> |
// column vectors of the x, y, and z box vectors. |
| 61 |
> |
// h1 h2 h3 |
| 62 |
> |
// [ Xx Yx Zx ] |
| 63 |
> |
// [ Xy Yy Zy ] |
| 64 |
> |
// [ Xz Yz Zz ] |
| 65 |
> |
// |
| 66 |
> |
double HmatInv[3][3]; |
| 67 |
> |
|
| 68 |
> |
double boxLx, boxLy, boxLz; // the box Lengths |
| 69 |
> |
double boxVol; |
| 70 |
> |
int orthoRhombic; |
| 71 |
> |
|
| 72 |
> |
|
| 73 |
> |
|
| 74 |
|
double rList, rCut; // variables for the neighborlist |
| 75 |
|
|
| 76 |
|
int usePBC; // whether we use periodic boundry conditions. |
| 98 |
|
|
| 99 |
|
char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. ) |
| 100 |
|
char mixingRule[100]; // the mixing rules for Lennard jones/van der walls |
| 101 |
< |
Integrator *the_integrator; // the integrator of the simulation |
| 101 |
> |
BaseIntegrator *the_integrator; // the integrator of the simulation |
| 102 |
|
|
| 103 |
|
char finalName[300]; // the name of the eor file to be written |
| 104 |
|
char sampleName[300]; // the name of the dump file to be written |
| 119 |
|
setFortranBoxSize = fBox; |
| 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 wrapVector( double thePos[3] ); |
| 131 |
+ |
|
| 132 |
+ |
void matMul3(double a[3][3], double b[3][3], double out[3][3]); |
| 133 |
+ |
void matVecMul3(double m[3][3], double inVec[3], double outVec[3]); |
| 134 |
+ |
void invertMat3(double in[3][3], double out[3][3]); |
| 135 |
+ |
double matDet3(double m[3][3]); |
| 136 |
+ |
|
| 137 |
|
private: |
| 138 |
|
|
| 139 |
+ |
void calcHmatInv( void ); |
| 140 |
+ |
void calcBoxL(); |
| 141 |
+ |
|
| 142 |
|
// private function to initialize the fortran side of the simulation |
| 143 |
|
void (*setFsimulation) setFortranSimList; |
| 144 |
|
|
