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


  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 boxL[3]; // The Lengths of the 3 column vectors of Hmat
  double boxVol;
  int orthoRhombic;
  

  double dielectric;      // the dielectric of the medium for reaction field

  
  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
  double currentTime;            // Used primarily for correlation Functions

  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, 
                    void (*fCut) notifyFortranCutOffList ){
    setFsimulation = fSetup;
    setFortranBoxSize = fBox;
    notifyFortranCutOffs = fCut;
  }

  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 setRcut( double theRcut );
  void setEcr( double theEcr );
  void setEcr( double theEcr, double theEst );

  double getRcut( void )  { return rCut; }
  double getRlist( void ) { return rList; }
  double getEcr( void )   { return ecr; }
  double getEst( void )   { return est; }

  void setTime( double theTime ) { currentTime = theTime; }
  void incrTime( double dt ) { currentTime += dt; }
  void decrTime( double dt ) { currentTime -= dt; }
  double getTime( void ) { return currentTime; }

  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]);
  void transposeMat3(double in[3][3], double out[3][3]);
  void printMat3(double A[3][3]);
  void printMat9(double A[9]);
  double matDet3(double m[3][3]);
  
private:

  double origRcut, origEcr;
  int boxIsInit, haveOrigRcut, haveOrigEcr;

  double oldEcr;
  double oldRcut;

  double rList, rCut; // variables for the neighborlist
  double ecr;             // the electrostatic cutoff radius
  double est;             // the electrostatic skin thickness
  double maxCutoff;
  
  void calcHmatInv( void );
  void calcBoxL();
  void checkCutOffs( void );

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

  void (*setFortranBoxSize) setFortranBoxList;
  
  void (*notifyFortranCutOffs) notifyFortranCutOffList;

};


#endif
Revision:	644
Committed:	Tue Jul 22 16:41:08 2003 UTC (22 years, 3 months ago) by mmeineke
Original Path:	*trunk/OOPSE/libmdtools/SimInfo.hpp*
File size:	5458 byte(s)
Log Message:	Fixed a current time initialization bug in InitFromFile.
#	User	Rev	Content
1	mmeineke	377	#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	gezelter	458	unsigned int ndf; // number of actual degrees of freedom
34			unsigned int ndfRaw; // number of settable degrees of freedom
35	mmeineke	377
36			unsigned int setTemp; // boolean to set the temperature at each sampleTime
37
38			unsigned int n_dipoles; // number of dipoles
39
40	mmeineke	626
41	mmeineke	377	int n_exclude; // the # of pairs excluded from long range forces
42	mmeineke	427	Exclude** excludes; // the pairs themselves
43	mmeineke	377
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	gezelter	483	int* molMembershipArray; // map of atom numbers onto molecule numbers
50	mmeineke	377
51			int n_constraints; // the number of constraints on the system
52
53			unsigned int n_SRI; // the number of short range interactions
54
55			double lrPot; // the potential energy from the long range calculations.
56
57	gezelter	588	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	mmeineke	568
66	gezelter	621	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
67	mmeineke	572	double boxVol;
68			int orthoRhombic;
69	mmeineke	568
70
71	mmeineke	626	double dielectric; // the dielectric of the medium for reaction field
72	mmeineke	568
73	mmeineke	377
74			int usePBC; // whether we use periodic boundry conditions.
75			int useLJ;
76			int useSticky;
77			int useDipole;
78			int useReactionField;
79			int useGB;
80			int useEAM;
81
82
83			double dt, run_time; // the time step and total time
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	gezelter	637	double currentTime; // Used primarily for correlation Functions
88	mmeineke	377
89			int n_mol; // n_molecules;
90			Molecule* molecules; // the array of molecules
91
92			int nComponents; // the number of componentsin the system
93			int* componentsNmol; // the number of molecules of each component
94			MoleculeStamp** compStamps;// the stamps matching the components
95			LinkedMolStamp* headStamp; // list of stamps used in the simulation
96
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	mmeineke	542	BaseIntegrator *the_integrator; // the integrator of the simulation
101	mmeineke	377
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
104			char statusName[300]; // the name of the stat file to be written
105
106
107			// refreshes the sim if things get changed (load balanceing, volume
108			// adjustment, etc.)
109
110			void refreshSim( void );
111
112
113			// sets the internal function pointer to fortran.
114
115			void setInternal( void (*fSetup) setFortranSimList,
116	mmeineke	626	void (*fBox) setFortranBoxList,
117			void (*fCut) notifyFortranCutOffList ){
118	mmeineke	377	setFsimulation = fSetup;
119			setFortranBoxSize = fBox;
120	mmeineke	626	notifyFortranCutOffs = fCut;
121	mmeineke	377	}
122
123	gezelter	458	int getNDF();
124			int getNDFraw();
125
126	gezelter	457	void setBox( double newBox[3] );
127	gezelter	588	void setBoxM( double newBox[3][3] );
128			void getBoxM( double theBox[3][3] );
129	gezelter	574	void scaleBox( double scale );
130	mmeineke	626
131			void setRcut( double theRcut );
132			void setEcr( double theEcr );
133			void setEcr( double theEcr, double theEst );
134	gezelter	457
135	mmeineke	626	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	mmeineke	644	void setTime( double theTime ) { currentTime = theTime; }
141	mmeineke	643	void incrTime( double dt ) { currentTime += dt; }
142			void decrTime( double dt ) { currentTime -= dt; }
143	mmeineke	644	double getTime( void ) { return currentTime; }
144	mmeineke	626
145	mmeineke	568	void wrapVector( double thePos[3] );
146
147	gezelter	588	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	mmeineke	597	void transposeMat3(double in[3][3], double out[3][3]);
151			void printMat3(double A[3][3]);
152			void printMat9(double A[9]);
153	gezelter	588	double matDet3(double m[3][3]);
154
155	mmeineke	377	private:
156	mmeineke	626
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	mmeineke	377
168	gezelter	588	void calcHmatInv( void );
169	mmeineke	568	void calcBoxL();
170	mmeineke	626	void checkCutOffs( void );
171	mmeineke	568
172	mmeineke	377	// private function to initialize the fortran side of the simulation
173			void (*setFsimulation) setFortranSimList;
174
175			void (*setFortranBoxSize) setFortranBoxList;
176	mmeineke	626
177			void (*notifyFortranCutOffs) notifyFortranCutOffList;
178
179	mmeineke	377	};
180
181
182
183			#endif