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 |
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); |
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 |