36 |
|
unsigned int n_oriented; // number of of atoms with orientation |
37 |
|
unsigned int ndf; // number of actual degrees of freedom |
38 |
|
unsigned int ndfRaw; // number of settable degrees of freedom |
39 |
+ |
unsigned int ndfTrans; // number of translational degrees of freedom |
40 |
+ |
unsigned int nZconstraints; // the number of zConstraints |
41 |
|
|
42 |
|
unsigned int setTemp; // boolean to set the temperature at each sampleTime |
43 |
+ |
unsigned int resetIntegrator; // boolean to reset the integrator |
44 |
|
|
45 |
|
unsigned int n_dipoles; // number of dipoles |
46 |
|
|
92 |
|
double target_temp; // the target temperature of the system |
93 |
|
double thermalTime; // the temp kick interval |
94 |
|
double currentTime; // Used primarily for correlation Functions |
95 |
+ |
double resetTime; // Use to reset the integrator periodically |
96 |
|
|
97 |
|
int n_mol; // n_molecules; |
98 |
|
Molecule* molecules; // the array of molecules |
111 |
|
char sampleName[300]; // the name of the dump file to be written |
112 |
|
char statusName[300]; // the name of the stat file to be written |
113 |
|
|
114 |
< |
|
114 |
> |
int seed; //seed for random number generator |
115 |
|
// refreshes the sim if things get changed (load balanceing, volume |
116 |
|
// adjustment, etc.) |
117 |
|
|
130 |
|
|
131 |
|
int getNDF(); |
132 |
|
int getNDFraw(); |
133 |
+ |
int getNDFtranslational(); |
134 |
|
|
135 |
|
void setBox( double newBox[3] ); |
136 |
|
void setBoxM( double newBox[3][3] ); |
160 |
|
void printMat3(double A[3][3]); |
161 |
|
void printMat9(double A[9]); |
162 |
|
double matDet3(double m[3][3]); |
163 |
+ |
double matTrace3(double m[3][3]); |
164 |
|
|
165 |
|
SimState* getConfiguration( void ) { return myConfiguration; } |
166 |
|
|
168 |
|
GenericData* getProperty(const string& propName); |
169 |
|
vector<GenericData*> getProperties(); |
170 |
|
|
171 |
+ |
int getSeed(void) { return seed; } |
172 |
+ |
void setSeed(int theSeed) { seed = theSeed;} |
173 |
+ |
|
174 |
|
private: |
175 |
|
|
176 |
|
SimState* myConfiguration; |