1 |
#ifndef __SIMINFO_H__ |
2 |
#define __SIMINFO_H__ |
3 |
|
4 |
|
5 |
|
6 |
#include "Atom.hpp" |
7 |
#include "Molecule.hpp" |
8 |
#include "AbstractClasses.hpp" |
9 |
#include "MakeStamps.hpp" |
10 |
|
11 |
#define __C |
12 |
#include "fSimulation.h" |
13 |
#include "fortranWrapDefines.hpp" |
14 |
|
15 |
|
16 |
|
17 |
class SimInfo{ |
18 |
|
19 |
public: |
20 |
|
21 |
SimInfo(); |
22 |
~SimInfo(){} |
23 |
|
24 |
int n_atoms; // the number of atoms |
25 |
Atom **atoms; // the array of atom objects |
26 |
|
27 |
double tau[9]; // the stress tensor |
28 |
|
29 |
unsigned int n_bonds; // number of bends |
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 |
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 |
42 |
|
43 |
int n_exclude; // the # of pairs excluded from long range forces |
44 |
Exclude** excludes; // the pairs themselves |
45 |
|
46 |
int nGlobalExcludes; |
47 |
int* globalExcludes; // same as above, but these guys participate in |
48 |
// no long range forces. |
49 |
|
50 |
int* identArray; // array of unique identifiers for the atoms |
51 |
int* molMembershipArray; // map of atom numbers onto molecule numbers |
52 |
|
53 |
int n_constraints; // the number of constraints on the system |
54 |
|
55 |
unsigned int n_SRI; // the number of short range interactions |
56 |
|
57 |
double lrPot; // the potential energy from the long range calculations. |
58 |
|
59 |
double Hmat[9]; // the periodic boundry conditions. The Hmat is the |
60 |
// column vectors of the x, y, and z box vectors. |
61 |
// |
62 |
// h1 h2 h3 |
63 |
// [ Xx Yx Zx ] |
64 |
// [ Xy Yy Zy ] |
65 |
// [ Xz Yz Zz ] |
66 |
// |
67 |
// to preserve compatibility with Fortran the |
68 |
// ordering in the array is as follows: |
69 |
// |
70 |
// [ 0 3 6 ] |
71 |
// [ 1 4 7 ] |
72 |
// [ 2 5 8 ] |
73 |
|
74 |
double HmatI[9]; // the inverted Hmat; |
75 |
double boxLx, boxLy, boxLz; // the box Lengths |
76 |
double boxVol; |
77 |
int orthoRhombic; |
78 |
|
79 |
|
80 |
|
81 |
double rList, rCut; // variables for the neighborlist |
82 |
|
83 |
int usePBC; // whether we use periodic boundry conditions. |
84 |
int useLJ; |
85 |
int useSticky; |
86 |
int useDipole; |
87 |
int useReactionField; |
88 |
int useGB; |
89 |
int useEAM; |
90 |
|
91 |
|
92 |
double dt, run_time; // the time step and total time |
93 |
double sampleTime, statusTime; // the position and energy dump frequencies |
94 |
double target_temp; // the target temperature of the system |
95 |
double thermalTime; // the temp kick interval |
96 |
|
97 |
int n_mol; // n_molecules; |
98 |
Molecule* molecules; // the array of molecules |
99 |
|
100 |
int nComponents; // the number of componentsin the system |
101 |
int* componentsNmol; // the number of molecules of each component |
102 |
MoleculeStamp** compStamps;// the stamps matching the components |
103 |
LinkedMolStamp* headStamp; // list of stamps used in the simulation |
104 |
|
105 |
|
106 |
char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. ) |
107 |
char mixingRule[100]; // the mixing rules for Lennard jones/van der walls |
108 |
BaseIntegrator *the_integrator; // the integrator of the simulation |
109 |
|
110 |
char finalName[300]; // the name of the eor file to be written |
111 |
char sampleName[300]; // the name of the dump file to be written |
112 |
char statusName[300]; // the name of the stat file to be written |
113 |
|
114 |
|
115 |
// refreshes the sim if things get changed (load balanceing, volume |
116 |
// adjustment, etc.) |
117 |
|
118 |
void refreshSim( void ); |
119 |
|
120 |
|
121 |
// sets the internal function pointer to fortran. |
122 |
|
123 |
void setInternal( void (*fSetup) setFortranSimList, |
124 |
void (*fBox) setFortranBoxList ){ |
125 |
setFsimulation = fSetup; |
126 |
setFortranBoxSize = fBox; |
127 |
} |
128 |
|
129 |
int getNDF(); |
130 |
int getNDFraw(); |
131 |
|
132 |
void setBox( double newBox[3] ); |
133 |
void setBoxM( double newBox[9] ); |
134 |
void getBoxM( double theBox[9] ); |
135 |
|
136 |
void wrapVector( double thePos[3] ); |
137 |
|
138 |
private: |
139 |
|
140 |
void calcHmatI( void ); |
141 |
void calcBoxL(); |
142 |
|
143 |
// private function to initialize the fortran side of the simulation |
144 |
void (*setFsimulation) setFortranSimList; |
145 |
|
146 |
void (*setFortranBoxSize) setFortranBoxList; |
147 |
}; |
148 |
|
149 |
|
150 |
|
151 |
#endif |