30 |
|
|
31 |
|
double tau[9]; // the stress tensor |
32 |
|
|
33 |
< |
unsigned int n_bonds; // number of bends |
34 |
< |
unsigned int n_bends; // number of bends |
35 |
< |
unsigned int n_torsions; // number of torsions |
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 nZconstraints; // the number of zConstraints |
33 |
> |
int n_bonds; // number of bends |
34 |
> |
int n_bends; // number of bends |
35 |
> |
int n_torsions; // number of torsions |
36 |
> |
int n_oriented; // number of of atoms with orientation |
37 |
> |
int ndf; // number of actual degrees of freedom |
38 |
> |
int ndfRaw; // number of settable degrees of freedom |
39 |
> |
int ndfTrans; // number of translational degrees of freedom |
40 |
> |
int nZconstraints; // the number of zConstraints |
41 |
|
|
42 |
< |
unsigned int setTemp; // boolean to set the temperature at each sampleTime |
42 |
> |
int setTemp; // boolean to set the temperature at each sampleTime |
43 |
> |
int resetIntegrator; // boolean to reset the integrator |
44 |
|
|
45 |
< |
unsigned int n_dipoles; // number of dipoles |
45 |
> |
int n_dipoles; // number of dipoles |
46 |
|
|
47 |
|
|
48 |
|
int n_exclude; // the # of pairs excluded from long range forces |
57 |
|
|
58 |
|
int n_constraints; // the number of constraints on the system |
59 |
|
|
60 |
< |
unsigned int n_SRI; // the number of short range interactions |
60 |
> |
int n_SRI; // the number of short range interactions |
61 |
|
|
62 |
|
double lrPot; // the potential energy from the long range calculations. |
63 |
|
|
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] ); |
147 |
|
double getEst( void ) { return est; } |
148 |
|
|
149 |
|
void setTime( double theTime ) { currentTime = theTime; } |
150 |
< |
void incrTime( double dt ) { currentTime += dt; } |
151 |
< |
void decrTime( double dt ) { currentTime -= dt; } |
150 |
> |
void incrTime( double the_dt ) { currentTime += the_dt; } |
151 |
> |
void decrTime( double the_dt ) { currentTime -= the_dt; } |
152 |
|
double getTime( void ) { return currentTime; } |
153 |
|
|
154 |
|
void wrapVector( double thePos[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 |