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[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. |
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 |
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 |
|
|