OOPSE/libmdtools/SimInfo.hpp

#ifndef __SIMINFO_H__
#define __SIMINFO_H__


#include "Atom.hpp"
#include "Molecule.hpp"
#include "AbstractClasses.hpp"
#include "MakeStamps.hpp"

#define __C
#include "fSimulation.h"
#include "fortranWrapDefines.hpp"


class SimInfo{

public:

  SimInfo();
  ~SimInfo(){}

  int n_atoms; // the number of atoms
  Atom **atoms; // the array of atom objects
  
  double tau[9]; // the stress tensor

  unsigned int n_bonds;    // number of bends
  unsigned int n_bends;    // number of bends
  unsigned int n_torsions; // number of torsions
  unsigned int n_oriented; // number of of atoms with orientation
  unsigned int ndf;        // number of actual degrees of freedom
  unsigned int ndfRaw;     // number of settable degrees of freedom

  unsigned int setTemp;   // boolean to set the temperature at each sampleTime

  unsigned int n_dipoles; // number of dipoles
  double ecr;             // the electrostatic cutoff radius
  double est;             // the electrostatic skin thickness
  double dielectric;      // the dielectric of the medium for reaction field

  int n_exclude;  // the # of pairs excluded from long range forces
  Exclude** excludes;       // the pairs themselves

  int nGlobalExcludes;
  int* globalExcludes; // same as above, but these guys participate in
                       // no long range forces.

  int* identArray;     // array of unique identifiers for the atoms
  int* molMembershipArray;  // map of atom numbers onto molecule numbers

  int n_constraints; // the number of constraints on the system

  unsigned int n_SRI;   // the number of short range interactions

  double lrPot; // the potential energy from the long range calculations.

  double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
                      // column vectors of the x, y, and z box vectors.
                      //   h1  h2  h3
                      // [ Xx  Yx  Zx ]
                      // [ Xy  Yy  Zy ]
                      // [ Xz  Yz  Zz ]
                      //   
  double HmatInv[3][3];

  double boxLx, boxLy, boxLz; // the box Lengths
  double boxVol;
  int orthoRhombic;
  

  double rList, rCut; // variables for the neighborlist
  
  int usePBC; // whether we use periodic boundry conditions.
  int useLJ; 
  int useSticky;
  int useDipole;
  int useReactionField;
  int useGB;
  int useEAM;
  

  double dt, run_time;           // the time step and total time
  double sampleTime, statusTime; // the position and energy dump frequencies
  double target_temp;            // the target temperature of the system
  double thermalTime;            // the temp kick interval

  int n_mol;           // n_molecules;
  Molecule* molecules; // the array of molecules
  
  int nComponents;           // the number of componentsin the system
  int* componentsNmol;       // the number of molecules of each component
  MoleculeStamp** compStamps;// the stamps matching the components
  LinkedMolStamp* headStamp; // list of stamps used in the simulation
  
  
  char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
  char mixingRule[100]; // the mixing rules for Lennard jones/van der walls 
  BaseIntegrator *the_integrator; // the integrator of the simulation

  char finalName[300];  // the name of the eor file to be written
  char sampleName[300]; // the name of the dump file to be written
  char statusName[300]; // the name of the stat file to be written


  // refreshes the sim if things get changed (load balanceing, volume
  // adjustment, etc.)

  void refreshSim( void );
  

  // sets the internal function pointer to fortran.

  void setInternal( void (*fSetup) setFortranSimList, 
                    void (*fBox) setFortranBoxList ){
    setFsimulation = fSetup;
    setFortranBoxSize = fBox;
  }

  int getNDF();
  int getNDFraw();

  void setBox( double newBox[3] );
  void setBoxM( double newBox[3][3] );
  void getBoxM( double theBox[3][3] );
  void scaleBox( double scale );

  void wrapVector( double thePos[3] );

  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
  void invertMat3(double in[3][3], double out[3][3]);
  double matDet3(double m[3][3]);
  
private:
  
  void calcHmatInv( void );
  void calcBoxL();

  // private function to initialize the fortran side of the simulation
  void (*setFsimulation) setFortranSimList;

  void (*setFortranBoxSize) setFortranBoxList;
};


#endif
Revision:	588
Committed:	Thu Jul 10 17:10:56 2003 UTC (21 years ago) by gezelter
File size:	4443 byte(s)
Log Message:	Bunch of 1-d array -> 2-d array stuff
#	Content
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[3][3]; // the periodic boundry conditions. The Hmat is the
60	// column vectors of the x, y, and z box vectors.
61	// h1 h2 h3
62	// [ Xx Yx Zx ]
63	// [ Xy Yy Zy ]
64	// [ Xz Yz Zz ]
65	//
66	double HmatInv[3][3];
67
68	double boxLx, boxLy, boxLz; // the box Lengths
69	double boxVol;
70	int orthoRhombic;
71
72
73
74	double rList, rCut; // variables for the neighborlist
75
76	int usePBC; // whether we use periodic boundry conditions.
77	int useLJ;
78	int useSticky;
79	int useDipole;
80	int useReactionField;
81	int useGB;
82	int useEAM;
83
84
85	double dt, run_time; // the time step and total time
86	double sampleTime, statusTime; // the position and energy dump frequencies
87	double target_temp; // the target temperature of the system
88	double thermalTime; // the temp kick interval
89
90	int n_mol; // n_molecules;
91	Molecule* molecules; // the array of molecules
92
93	int nComponents; // the number of componentsin the system
94	int* componentsNmol; // the number of molecules of each component
95	MoleculeStamp** compStamps;// the stamps matching the components
96	LinkedMolStamp* headStamp; // list of stamps used in the simulation
97
98
99	char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
100	char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
101	BaseIntegrator *the_integrator; // the integrator of the simulation
102
103	char finalName[300]; // the name of the eor file to be written
104	char sampleName[300]; // the name of the dump file to be written
105	char statusName[300]; // the name of the stat file to be written
106
107
108	// refreshes the sim if things get changed (load balanceing, volume
109	// adjustment, etc.)
110
111	void refreshSim( void );
112
113
114	// sets the internal function pointer to fortran.
115
116	void setInternal( void (*fSetup) setFortranSimList,
117	void (*fBox) setFortranBoxList ){
118	setFsimulation = fSetup;
119	setFortranBoxSize = fBox;
120	}
121
122	int getNDF();
123	int getNDFraw();
124
125	void setBox( double newBox[3] );
126	void setBoxM( double newBox[3][3] );
127	void getBoxM( double theBox[3][3] );
128	void scaleBox( double scale );
129
130	void wrapVector( double thePos[3] );
131
132	void matMul3(double a[3][3], double b[3][3], double out[3][3]);
133	void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
134	void invertMat3(double in[3][3], double out[3][3]);
135	double matDet3(double m[3][3]);
136
137	private:
138
139	void calcHmatInv( void );
140	void calcBoxL();
141
142	// private function to initialize the fortran side of the simulation
143	void (*setFsimulation) setFortranSimList;
144
145	void (*setFortranBoxSize) setFortranBoxList;
146	};
147
148
149
150	#endif