97 |
|
int n_mol; // n_molecules; |
98 |
|
Molecule* molecules; // the array of molecules |
99 |
|
|
100 |
< |
int nComponents; // the number of componentsin the system |
100 |
> |
int nComponents; // the number of components in the system |
101 |
|
int* componentsNmol; // the number of molecules of each component |
102 |
|
MoleculeStamp** compStamps;// the stamps matching the components |
103 |
|
LinkedMolStamp* headStamp; // list of stamps used in the simulation |
120 |
|
|
121 |
|
// sets the internal function pointer to fortran. |
122 |
|
|
123 |
< |
void setInternal( void (*fSetup) setFortranSimList, |
124 |
< |
void (*fBox) setFortranBoxList, |
125 |
< |
void (*fCut) notifyFortranCutOffList ){ |
123 |
> |
void setInternal( setFortranSim_TD fSetup, |
124 |
> |
setFortranBox_TD fBox, |
125 |
> |
notifyFortranCutOff_TD fCut){ |
126 |
|
setFsimulation = fSetup; |
127 |
|
setFortranBoxSize = fBox; |
128 |
|
notifyFortranCutOffs = fCut; |
138 |
|
void scaleBox( double scale ); |
139 |
|
|
140 |
|
void setRcut( double theRcut ); |
141 |
+ |
void setDefaultRcut( double theRcut ); |
142 |
|
void setEcr( double theEcr ); |
143 |
+ |
void setDefaultEcr( double theEcr ); |
144 |
|
void setEcr( double theEcr, double theEst ); |
145 |
+ |
void setDefaultEcr( double theEcr, double theEst ); |
146 |
+ |
void checkCutOffs( void ); |
147 |
|
|
148 |
|
double getRcut( void ) { return rCut; } |
149 |
|
double getRlist( void ) { return rList; } |
150 |
|
double getEcr( void ) { return ecr; } |
151 |
|
double getEst( void ) { return est; } |
152 |
+ |
double getMaxCutoff( void ) { return maxCutoff; } |
153 |
|
|
154 |
|
void setTime( double theTime ) { currentTime = theTime; } |
155 |
|
void incrTime( double the_dt ) { currentTime += the_dt; } |
202 |
|
void calcHmatInv( void ); |
203 |
|
void calcBoxL(); |
204 |
|
double calcMaxCutOff(); |
200 |
– |
void checkCutOffs( void ); |
205 |
|
|
206 |
+ |
|
207 |
|
// private function to initialize the fortran side of the simulation |
208 |
< |
void (*setFsimulation) setFortranSimList; |
208 |
> |
setFortranSim_TD setFsimulation; |
209 |
|
|
210 |
< |
void (*setFortranBoxSize) setFortranBoxList; |
210 |
> |
setFortranBox_TD setFortranBoxSize; |
211 |
|
|
212 |
< |
void (*notifyFortranCutOffs) notifyFortranCutOffList; |
212 |
> |
notifyFortranCutOff_TD notifyFortranCutOffs; |
213 |
|
|
214 |
|
//Addtional Properties of SimInfo |
215 |
|
map<string, GenericData*> properties; |