86 |
|
int useGB; |
87 |
|
int useEAM; |
88 |
|
|
89 |
+ |
bool useInitXSstate; |
90 |
+ |
double orthoTolerance; |
91 |
|
|
92 |
|
double dt, run_time; // the time step and total time |
93 |
|
double sampleTime, statusTime; // the position and energy dump frequencies |
99 |
|
int n_mol; // n_molecules; |
100 |
|
Molecule* molecules; // the array of molecules |
101 |
|
|
102 |
< |
int nComponents; // the number of componentsin the system |
102 |
> |
int nComponents; // the number of components in the system |
103 |
|
int* componentsNmol; // the number of molecules of each component |
104 |
|
MoleculeStamp** compStamps;// the stamps matching the components |
105 |
|
LinkedMolStamp* headStamp; // list of stamps used in the simulation |
122 |
|
|
123 |
|
// sets the internal function pointer to fortran. |
124 |
|
|
125 |
< |
void setInternal( void (*fSetup) setFortranSimList, |
126 |
< |
void (*fBox) setFortranBoxList, |
127 |
< |
void (*fCut) notifyFortranCutOffList ){ |
125 |
> |
void setInternal( setFortranSim_TD fSetup, |
126 |
> |
setFortranBox_TD fBox, |
127 |
> |
notifyFortranCutOff_TD fCut){ |
128 |
|
setFsimulation = fSetup; |
129 |
|
setFortranBoxSize = fBox; |
130 |
|
notifyFortranCutOffs = fCut; |
140 |
|
void scaleBox( double scale ); |
141 |
|
|
142 |
|
void setRcut( double theRcut ); |
143 |
+ |
void setDefaultRcut( double theRcut ); |
144 |
|
void setEcr( double theEcr ); |
145 |
+ |
void setDefaultEcr( double theEcr ); |
146 |
|
void setEcr( double theEcr, double theEst ); |
147 |
+ |
void setDefaultEcr( double theEcr, double theEst ); |
148 |
+ |
void checkCutOffs( void ); |
149 |
|
|
150 |
|
double getRcut( void ) { return rCut; } |
151 |
|
double getRlist( void ) { return rList; } |
152 |
|
double getEcr( void ) { return ecr; } |
153 |
|
double getEst( void ) { return est; } |
154 |
+ |
double getMaxCutoff( void ) { return maxCutoff; } |
155 |
|
|
156 |
|
void setTime( double theTime ) { currentTime = theTime; } |
157 |
< |
void incrTime( double dt ) { currentTime += dt; } |
158 |
< |
void decrTime( double dt ) { currentTime -= dt; } |
157 |
> |
void incrTime( double the_dt ) { currentTime += the_dt; } |
158 |
> |
void decrTime( double the_dt ) { currentTime -= the_dt; } |
159 |
|
double getTime( void ) { return currentTime; } |
160 |
|
|
161 |
|
void wrapVector( double thePos[3] ); |
200 |
|
double distXY; |
201 |
|
double distYZ; |
202 |
|
double distZX; |
203 |
+ |
|
204 |
+ |
|
205 |
|
|
206 |
|
void calcHmatInv( void ); |
207 |
|
void calcBoxL(); |
208 |
|
double calcMaxCutOff(); |
200 |
– |
void checkCutOffs( void ); |
209 |
|
|
210 |
+ |
|
211 |
|
// private function to initialize the fortran side of the simulation |
212 |
< |
void (*setFsimulation) setFortranSimList; |
212 |
> |
setFortranSim_TD setFsimulation; |
213 |
|
|
214 |
< |
void (*setFortranBoxSize) setFortranBoxList; |
214 |
> |
setFortranBox_TD setFortranBoxSize; |
215 |
|
|
216 |
< |
void (*notifyFortranCutOffs) notifyFortranCutOffList; |
216 |
> |
notifyFortranCutOff_TD notifyFortranCutOffs; |
217 |
|
|
218 |
|
//Addtional Properties of SimInfo |
219 |
|
map<string, GenericData*> properties; |