| 88 | 
  | 
 | 
| 89 | 
  | 
   | 
| 90 | 
  | 
  int usePBC; // whether we use periodic boundry conditions. | 
| 91 | 
< | 
  int useLJ;  | 
| 92 | 
< | 
  int useSticky; | 
| 91 | 
> | 
  int useDirectionalAtoms; | 
| 92 | 
> | 
  int useLennardJones;  | 
| 93 | 
> | 
  int useElectrostatics; | 
| 94 | 
  | 
  int useCharges; | 
| 95 | 
  | 
  int useDipoles; | 
| 96 | 
< | 
  int useReactionField; | 
| 97 | 
< | 
  int useGB; | 
| 96 | 
> | 
  int useSticky; | 
| 97 | 
> | 
  int useGayBerne; | 
| 98 | 
  | 
  int useEAM; | 
| 99 | 
+ | 
  int useShapes; | 
| 100 | 
+ | 
  int useFLARB; | 
| 101 | 
+ | 
  int useReactionField; | 
| 102 | 
  | 
  bool haveCutoffGroups; | 
| 103 | 
  | 
  bool useInitXSstate; | 
| 104 | 
  | 
  double orthoTolerance; | 
| 131 | 
  | 
  string finalName;  // the name of the eor file to be written | 
| 132 | 
  | 
  string sampleName; // the name of the dump file to be written | 
| 133 | 
  | 
  string statusName; // the name of the stat file to be written | 
| 134 | 
+ | 
  string zAngleName; // the name of the ang file to be written | 
| 135 | 
  | 
 | 
| 136 | 
  | 
  int seed;                    //seed for random number generator | 
| 137 | 
  | 
 |