| 5 |
|
#include <string> |
| 6 |
|
#include <vector> |
| 7 |
|
|
| 8 |
< |
#include "Atom.hpp" |
| 9 |
< |
#include "RigidBody.hpp" |
| 10 |
< |
#include "Molecule.hpp" |
| 11 |
< |
#include "Exclude.hpp" |
| 12 |
< |
#include "SkipList.hpp" |
| 13 |
< |
#include "AbstractClasses.hpp" |
| 14 |
< |
#include "MakeStamps.hpp" |
| 15 |
< |
#include "SimState.hpp" |
| 16 |
< |
#include "Restraints.hpp" |
| 8 |
> |
#include "primitives/Atom.hpp" |
| 9 |
> |
#include "primitives/RigidBody.hpp" |
| 10 |
> |
#include "primitives/Molecule.hpp" |
| 11 |
> |
#include "brains/Exclude.hpp" |
| 12 |
> |
#include "brains/SkipList.hpp" |
| 13 |
> |
#include "primitives/AbstractClasses.hpp" |
| 14 |
> |
#include "types/MakeStamps.hpp" |
| 15 |
> |
#include "brains/SimState.hpp" |
| 16 |
> |
#include "restraints/Restraints.hpp" |
| 17 |
|
|
| 18 |
|
#define __C |
| 19 |
< |
#include "fSimulation.h" |
| 20 |
< |
#include "fortranWrapDefines.hpp" |
| 21 |
< |
#include "GenericData.hpp" |
| 19 |
> |
#include "brains/fSimulation.h" |
| 20 |
> |
#include "utils/GenericData.hpp" |
| 21 |
|
|
| 22 |
|
|
| 23 |
|
//#include "Minimizer.hpp" |
| 24 |
< |
//#include "OOPSEMinimizer.hpp" |
| 24 |
> |
//#include "minimizers/OOPSEMinimizer.hpp" |
| 25 |
|
|
| 26 |
|
|
| 27 |
|
double roundMe( double x ); |
| 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; |
| 155 |
|
|
| 156 |
|
// sets the internal function pointer to fortran. |
| 157 |
|
|
| 155 |
– |
void setInternal( setFortranSim_TD fSetup, |
| 156 |
– |
setFortranBox_TD fBox, |
| 157 |
– |
notifyFortranCutOff_TD fCut){ |
| 158 |
– |
setFsimulation = fSetup; |
| 159 |
– |
setFortranBoxSize = fBox; |
| 160 |
– |
notifyFortranCutOffs = fCut; |
| 161 |
– |
} |
| 158 |
|
|
| 159 |
|
int getNDF(); |
| 160 |
|
int getNDFraw(); |
| 209 |
|
void calcBoxL(); |
| 210 |
|
double calcMaxCutOff(); |
| 211 |
|
|
| 216 |
– |
// private function to initialize the fortran side of the simulation |
| 217 |
– |
setFortranSim_TD setFsimulation; |
| 218 |
– |
|
| 219 |
– |
setFortranBox_TD setFortranBoxSize; |
| 212 |
|
|
| 221 |
– |
notifyFortranCutOff_TD notifyFortranCutOffs; |
| 222 |
– |
|
| 213 |
|
//Addtional Properties of SimInfo |
| 214 |
|
map<string, GenericData*> properties; |
| 215 |
|
void getFortranGroupArrays(SimInfo* info, |
