6 |
|
#include "AbstractClasses.hpp" |
7 |
|
#include "SimInfo.hpp" |
8 |
|
#include "ForceFields.hpp" |
9 |
+ |
#include "Thermo.hpp" |
10 |
+ |
#include "ReadWrite.hpp" |
11 |
|
|
12 |
< |
class Verlet : public Integrator { |
12 |
> |
class Integrator : public BaseIntegrator { |
13 |
|
|
14 |
|
public: |
15 |
< |
Verlet( SimInfo &info, ForceFields* the_ff ); |
16 |
< |
~Verlet(); |
15 |
> |
Integrator( SimInfo &theInfo, ForceFields* the_ff ); |
16 |
> |
virtual ~Integrator(); |
17 |
|
void integrate( void ); |
18 |
|
|
19 |
< |
private: |
19 |
> |
|
20 |
> |
protected: |
21 |
> |
|
22 |
|
|
23 |
< |
void move_a( double dt ); |
24 |
< |
void move_b( double dt ); |
23 |
> |
virtual void integrateStep( int calcPot, int calcStress ); |
24 |
> |
virtual void preMove( void ); |
25 |
> |
virtual void moveA( void ); |
26 |
> |
virtual void moveB( void ); |
27 |
> |
virtual void constrainA( void ); |
28 |
> |
virtual void constrainB( void ); |
29 |
> |
|
30 |
> |
|
31 |
> |
void checkConstraints( void ); |
32 |
> |
void rotate( int axes1, int axes2, double angle, double j[3], |
33 |
> |
double A[3][3] ); |
34 |
|
|
35 |
+ |
|
36 |
|
ForceFields* myFF; |
37 |
|
|
38 |
< |
SimInfo *entry_plug; // all the info we'll ever need |
39 |
< |
int c_natoms; /* the number of atoms */ |
40 |
< |
Atom **c_atoms; /* array of atom pointers */ |
41 |
< |
SRI **c_sr_interactions; /* array of SRI pointers */ |
42 |
< |
int c_n_SRI; /* the number of short range interactions */ |
38 |
> |
SimInfo *info; // all the info we'll ever need |
39 |
> |
int nAtoms; /* the number of atoms */ |
40 |
> |
int oldAtoms; |
41 |
> |
Atom **atoms; /* array of atom pointers */ |
42 |
> |
Molecule* molecules; |
43 |
> |
int nMols; |
44 |
|
|
45 |
< |
int c_is_constrained; /*boolean to know whether the systems contains |
46 |
< |
constraints. */ |
47 |
< |
int c_n_constrained; /*counter for number of constraints */ |
48 |
< |
int *c_constrained_i; /* the i of a constraint pair */ |
49 |
< |
int *c_constrained_j; /* the j of a constraint pair */ |
50 |
< |
double *c_constrained_dsqr; /* the square of the constraint distance */ |
51 |
< |
double *c_mass; /* the array of masses */ |
52 |
< |
short is_first; /*boolean for the first time integrate is called */ |
53 |
< |
double c_box_x; |
54 |
< |
double c_box_y; |
40 |
< |
double c_box_z; |
41 |
< |
}; |
45 |
> |
int isConstrained; // boolean to know whether the systems contains |
46 |
> |
// constraints. |
47 |
> |
int nConstrained; // counter for number of constraints |
48 |
> |
int *constrainedA; // the i of a constraint pair |
49 |
> |
int *constrainedB; // the j of a constraint pair |
50 |
> |
double *constrainedDsqr; // the square of the constraint distance |
51 |
> |
|
52 |
> |
int* moving; // tells whether we are moving atom i |
53 |
> |
int* moved; // tells whether we have moved atom i |
54 |
> |
double* prePos; // pre constrained positions |
55 |
|
|
56 |
< |
class Symplectic : public Integrator { |
56 |
> |
short isFirst; /*boolean for the first time integrate is called */ |
57 |
|
|
58 |
< |
public: |
59 |
< |
Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff ); |
60 |
< |
~Symplectic(); |
48 |
< |
|
49 |
< |
void integrate( void ); |
58 |
> |
double dt; |
59 |
> |
double dt2; |
60 |
> |
const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
61 |
|
|
62 |
< |
private: |
62 |
> |
const int maxIteration = 300; |
63 |
> |
const double tol = 1.0e-6; |
64 |
|
|
65 |
< |
void rotate( int axes1, int axes2, double angle, double j[3], |
66 |
< |
double A[3][3] ); |
65 |
> |
|
66 |
> |
double* pos; |
67 |
> |
double* vel; |
68 |
> |
double* frc; |
69 |
> |
double* trq; |
70 |
> |
double* Amat; |
71 |
> |
|
72 |
|
|
56 |
– |
SimInfo* entry_plug; |
57 |
– |
ForceFields* myFF; |
73 |
|
|
74 |
< |
int is_constrained; /*boolean to know whether the systems contains |
75 |
< |
constraints. */ |
76 |
< |
int n_constrained; /*counter for number of constraints */ |
77 |
< |
int *constrained_i; /* the i of a constraint pair */ |
78 |
< |
int *constrained_j; /* the j of a constraint pair */ |
64 |
< |
double *constrained_dsqr; /* the square of the constraint distance */ |
65 |
< |
double *mass; /* the array of masses */ |
74 |
> |
Thermo *tStats; |
75 |
> |
StatWriter* statOut; |
76 |
> |
DumpWriter* dumpOut; |
77 |
> |
|
78 |
> |
}; |
79 |
|
|
80 |
< |
short int isFirst; |
80 |
> |
class NVE : public Integrator{ |
81 |
|
|
82 |
< |
SRI **srInteractions; /* array of SRI pointers */ |
83 |
< |
int nSRI; /* the number of short range interactions */ |
82 |
> |
NVE ( void ): |
83 |
> |
Integrator( theInfo, the_ff ){} |
84 |
> |
virtual ~NVE(){} |
85 |
> |
|
86 |
|
|
87 |
+ |
|
88 |
|
}; |
89 |
|
|
90 |
+ |
class NVT : public Integrator{ |
91 |
+ |
|
92 |
+ |
NVT ( SimInfo &theInfo, ForceFields* the_ff ) : |
93 |
+ |
Integrator( theInfo, the_ff ); |
94 |
+ |
virtual ~NVT(); |
95 |
+ |
|
96 |
+ |
protected: |
97 |
+ |
virtual moveA( void ); |
98 |
+ |
virtual moveB( void ); |
99 |
+ |
|
100 |
+ |
}; |
101 |
+ |
|
102 |
+ |
|
103 |
+ |
|
104 |
+ |
|
105 |
|
#endif |