30 |
|
unsigned int n_bends; // number of bends |
31 |
|
unsigned int n_torsions; // number of torsions |
32 |
|
unsigned int n_oriented; // number of of atoms with orientation |
33 |
+ |
unsigned int ndf; // number of actual degrees of freedom |
34 |
+ |
unsigned int ndfRaw; // number of settable degrees of freedom |
35 |
|
|
36 |
|
unsigned int setTemp; // boolean to set the temperature at each sampleTime |
37 |
|
|
38 |
|
unsigned int n_dipoles; // number of dipoles |
37 |
– |
double ecr; // the electrostatic cutoff radius |
38 |
– |
double est; // the electrostatic skin thickness |
39 |
– |
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 |
42 |
> |
Exclude** excludes; // the pairs themselves |
43 |
|
|
44 |
|
int nGlobalExcludes; |
45 |
|
int* globalExcludes; // same as above, but these guys participate in |
46 |
|
// no long range forces. |
47 |
|
|
48 |
|
int* identArray; // array of unique identifiers for the atoms |
49 |
+ |
int* molMembershipArray; // map of atom numbers onto molecule numbers |
50 |
|
|
51 |
|
int n_constraints; // the number of constraints on the system |
52 |
|
|
54 |
|
|
55 |
|
double lrPot; // the potential energy from the long range calculations. |
56 |
|
|
57 |
< |
double box_x, box_y, box_z; // the periodic boundry conditions |
58 |
< |
double rList, rCut; // variables for the neighborlist |
57 |
> |
double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the |
58 |
> |
// column vectors of the x, y, and z box vectors. |
59 |
> |
// h1 h2 h3 |
60 |
> |
// [ Xx Yx Zx ] |
61 |
> |
// [ Xy Yy Zy ] |
62 |
> |
// [ Xz Yz Zz ] |
63 |
> |
// |
64 |
> |
double HmatInv[3][3]; |
65 |
> |
|
66 |
> |
double boxL[3]; // The Lengths of the 3 column vectors of Hmat |
67 |
> |
double boxVol; |
68 |
> |
int orthoRhombic; |
69 |
|
|
70 |
+ |
|
71 |
+ |
double dielectric; // the dielectric of the medium for reaction field |
72 |
+ |
|
73 |
+ |
|
74 |
|
int usePBC; // whether we use periodic boundry conditions. |
75 |
|
int useLJ; |
76 |
|
int useSticky; |
84 |
|
double sampleTime, statusTime; // the position and energy dump frequencies |
85 |
|
double target_temp; // the target temperature of the system |
86 |
|
double thermalTime; // the temp kick interval |
87 |
+ |
double currentTime; // Used primarily for correlation Functions |
88 |
|
|
89 |
|
int n_mol; // n_molecules; |
90 |
|
Molecule* molecules; // the array of molecules |
97 |
|
|
98 |
|
char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. ) |
99 |
|
char mixingRule[100]; // the mixing rules for Lennard jones/van der walls |
100 |
< |
Integrator *the_integrator; // the integrator of the simulation |
100 |
> |
BaseIntegrator *the_integrator; // the integrator of the simulation |
101 |
|
|
102 |
|
char finalName[300]; // the name of the eor file to be written |
103 |
|
char sampleName[300]; // the name of the dump file to be written |
113 |
|
// sets the internal function pointer to fortran. |
114 |
|
|
115 |
|
void setInternal( void (*fSetup) setFortranSimList, |
116 |
< |
void (*fBox) setFortranBoxList ){ |
116 |
> |
void (*fBox) setFortranBoxList, |
117 |
> |
void (*fCut) notifyFortranCutOffList ){ |
118 |
|
setFsimulation = fSetup; |
119 |
|
setFortranBoxSize = fBox; |
120 |
+ |
notifyFortranCutOffs = fCut; |
121 |
|
} |
122 |
|
|
123 |
+ |
int getNDF(); |
124 |
+ |
int getNDFraw(); |
125 |
+ |
|
126 |
+ |
void setBox( double newBox[3] ); |
127 |
+ |
void setBoxM( double newBox[3][3] ); |
128 |
+ |
void getBoxM( double theBox[3][3] ); |
129 |
+ |
void scaleBox( double scale ); |
130 |
+ |
|
131 |
+ |
void setRcut( double theRcut ); |
132 |
+ |
void setEcr( double theEcr ); |
133 |
+ |
void setEcr( double theEcr, double theEst ); |
134 |
+ |
|
135 |
+ |
double getRcut( void ) { return rCut; } |
136 |
+ |
double getRlist( void ) { return rList; } |
137 |
+ |
double getEcr( void ) { return ecr; } |
138 |
+ |
double getEst( void ) { return est; } |
139 |
+ |
|
140 |
+ |
void setTime( double theTime ) { currentTime = theTime; } |
141 |
+ |
void incrTime( double dt ) { currentTime += dt; } |
142 |
+ |
void decrTime( double dt ) { currentTime -= dt; } |
143 |
+ |
double getTime( void ) { return currentTime; } |
144 |
+ |
|
145 |
+ |
void wrapVector( double thePos[3] ); |
146 |
+ |
|
147 |
+ |
void matMul3(double a[3][3], double b[3][3], double out[3][3]); |
148 |
+ |
void matVecMul3(double m[3][3], double inVec[3], double outVec[3]); |
149 |
+ |
void invertMat3(double in[3][3], double out[3][3]); |
150 |
+ |
void transposeMat3(double in[3][3], double out[3][3]); |
151 |
+ |
void printMat3(double A[3][3]); |
152 |
+ |
void printMat9(double A[9]); |
153 |
+ |
double matDet3(double m[3][3]); |
154 |
+ |
|
155 |
|
private: |
156 |
+ |
|
157 |
+ |
double origRcut, origEcr; |
158 |
+ |
int boxIsInit, haveOrigRcut, haveOrigEcr; |
159 |
+ |
|
160 |
+ |
double oldEcr; |
161 |
+ |
double oldRcut; |
162 |
+ |
|
163 |
+ |
double rList, rCut; // variables for the neighborlist |
164 |
+ |
double ecr; // the electrostatic cutoff radius |
165 |
+ |
double est; // the electrostatic skin thickness |
166 |
+ |
double maxCutoff; |
167 |
|
|
168 |
+ |
void calcHmatInv( void ); |
169 |
+ |
void calcBoxL(); |
170 |
+ |
void checkCutOffs( void ); |
171 |
+ |
|
172 |
|
// private function to initialize the fortran side of the simulation |
173 |
|
void (*setFsimulation) setFortranSimList; |
174 |
|
|
175 |
|
void (*setFortranBoxSize) setFortranBoxList; |
176 |
+ |
|
177 |
+ |
void (*notifyFortranCutOffs) notifyFortranCutOffList; |
178 |
+ |
|
179 |
|
}; |
180 |
|
|
181 |
|
|