36 |
|
unsigned int setTemp; // boolean to set the temperature at each sampleTime |
37 |
|
|
38 |
|
unsigned int n_dipoles; // number of dipoles |
39 |
– |
double ecr; // the electrostatic cutoff radius |
40 |
– |
double est; // the electrostatic skin thickness |
41 |
– |
double dielectric; // the dielectric of the medium for reaction field |
39 |
|
|
40 |
+ |
|
41 |
|
int n_exclude; // the # of pairs excluded from long range forces |
42 |
|
Exclude** excludes; // the pairs themselves |
43 |
|
|
68 |
|
int orthoRhombic; |
69 |
|
|
70 |
|
|
71 |
+ |
double dielectric; // the dielectric of the medium for reaction field |
72 |
|
|
74 |
– |
double rList, rCut; // variables for the neighborlist |
73 |
|
|
74 |
|
int usePBC; // whether we use periodic boundry conditions. |
75 |
|
int useLJ; |
112 |
|
// sets the internal function pointer to fortran. |
113 |
|
|
114 |
|
void setInternal( void (*fSetup) setFortranSimList, |
115 |
< |
void (*fBox) setFortranBoxList ){ |
115 |
> |
void (*fBox) setFortranBoxList, |
116 |
> |
void (*fCut) notifyFortranCutOffList ){ |
117 |
|
setFsimulation = fSetup; |
118 |
|
setFortranBoxSize = fBox; |
119 |
+ |
notifyFortranCutOffs = fCut; |
120 |
|
} |
121 |
|
|
122 |
|
int getNDF(); |
126 |
|
void setBoxM( double newBox[3][3] ); |
127 |
|
void getBoxM( double theBox[3][3] ); |
128 |
|
void scaleBox( double scale ); |
129 |
+ |
|
130 |
+ |
void setRcut( double theRcut ); |
131 |
+ |
void setEcr( double theEcr ); |
132 |
+ |
void setEcr( double theEcr, double theEst ); |
133 |
|
|
134 |
+ |
double getRcut( void ) { return rCut; } |
135 |
+ |
double getRlist( void ) { return rList; } |
136 |
+ |
double getEcr( void ) { return ecr; } |
137 |
+ |
double getEst( void ) { return est; } |
138 |
+ |
|
139 |
+ |
|
140 |
|
void wrapVector( double thePos[3] ); |
141 |
|
|
142 |
|
void matMul3(double a[3][3], double b[3][3], double out[3][3]); |
148 |
|
double matDet3(double m[3][3]); |
149 |
|
|
150 |
|
private: |
151 |
+ |
|
152 |
+ |
double origRcut, origEcr; |
153 |
+ |
int boxIsInit, haveOrigRcut, haveOrigEcr; |
154 |
+ |
|
155 |
+ |
double oldEcr; |
156 |
+ |
double oldRcut; |
157 |
+ |
|
158 |
+ |
double rList, rCut; // variables for the neighborlist |
159 |
+ |
double ecr; // the electrostatic cutoff radius |
160 |
+ |
double est; // the electrostatic skin thickness |
161 |
+ |
double maxCutoff; |
162 |
|
|
163 |
|
void calcHmatInv( void ); |
164 |
|
void calcBoxL(); |
165 |
+ |
void checkCutOffs( void ); |
166 |
|
|
167 |
|
// private function to initialize the fortran side of the simulation |
168 |
|
void (*setFsimulation) setFortranSimList; |
169 |
|
|
170 |
|
void (*setFortranBoxSize) setFortranBoxList; |
171 |
+ |
|
172 |
+ |
void (*notifyFortranCutOffs) notifyFortranCutOffList; |
173 |
+ |
|
174 |
|
}; |
175 |
|
|
176 |
|
|