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 |
< |
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 |
|
|
84 |
|
|
85 |
|
char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. ) |
86 |
|
char mixingRule[100]; // the mixing rules for Lennard jones/van der walls |
87 |
< |
Integrator *the_integrator; // the integrator of the simulation |
87 |
> |
BaseIntegrator *the_integrator; // the integrator of the simulation |
88 |
|
|
89 |
|
char finalName[300]; // the name of the eor file to be written |
90 |
|
char sampleName[300]; // the name of the dump file to be written |
105 |
|
setFortranBoxSize = fBox; |
106 |
|
} |
107 |
|
|
108 |
+ |
int getNDF(); |
109 |
+ |
int getNDFraw(); |
110 |
+ |
|
111 |
+ |
void setBox( double newBox[3] ); |
112 |
+ |
void getBox( double theBox[3] ); |
113 |
+ |
|
114 |
|
private: |
115 |
|
|
116 |
|
// private function to initialize the fortran side of the simulation |