| 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 n_Zconstraints; // the number of zConstraints |
| 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 |
+ |
void crossProduct3(double a[3],double b[3], double out[3]); |
| 166 |
+ |
double dotProduct3(double a[3], double b[3]); |
| 167 |
+ |
double length3(double a[3]); |
| 168 |
+ |
|
| 169 |
|
SimState* getConfiguration( void ) { return myConfiguration; } |
| 170 |
|
|
| 171 |
|
void addProperty(GenericData* prop); |
| 172 |
|
GenericData* getProperty(const string& propName); |
| 173 |
|
vector<GenericData*> getProperties(); |
| 174 |
|
|
| 175 |
+ |
int getSeed(void) { return seed; } |
| 176 |
+ |
void setSeed(int theSeed) { seed = theSeed;} |
| 177 |
+ |
|
| 178 |
|
private: |
| 179 |
|
|
| 180 |
|
SimState* myConfiguration; |
| 189 |
|
double ecr; // the electrostatic cutoff radius |
| 190 |
|
double est; // the electrostatic skin thickness |
| 191 |
|
double maxCutoff; |
| 192 |
+ |
|
| 193 |
+ |
double distXY; |
| 194 |
+ |
double distYZ; |
| 195 |
+ |
double distZX; |
| 196 |
|
|
| 197 |
|
void calcHmatInv( void ); |
| 198 |
|
void calcBoxL(); |
| 199 |
+ |
double calcMaxCutOff(); |
| 200 |
|
void checkCutOffs( void ); |
| 201 |
|
|
| 202 |
|
// private function to initialize the fortran side of the simulation |
