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(); |
184 |
|
SimState* getConfiguration( void ) { return myConfiguration; } |
185 |
|
|
186 |
|
void addProperty(GenericData* prop); |
187 |
< |
GenericData* getProperty(const string& propName); |
187 |
> |
GenericData* getPropertyByName(const string& propName); |
188 |
|
//vector<GenericData*>& getProperties() {return properties;} |
189 |
|
|
190 |
|
int getSeed(void) { return seed; } |
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, |