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 |
39 |
< |
double rRF; // the reaction field cut off radius |
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 |
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 |
52 |
– |
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 boxL[3]; // The Lengths of the 3 column vectors of Hmat |
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 |
+ |
void transposeMat3(double in[3][3], double out[3][3]); |
136 |
+ |
void printMat3(double A[3][3]); |
137 |
+ |
void printMat9(double A[9]); |
138 |
+ |
double matDet3(double m[3][3]); |
139 |
+ |
|
140 |
|
private: |
141 |
|
|
142 |
+ |
void calcHmatInv( void ); |
143 |
+ |
void calcBoxL(); |
144 |
+ |
|
145 |
|
// private function to initialize the fortran side of the simulation |
146 |
|
void (*setFsimulation) setFortranSimList; |
147 |
|
|