OOPSE/libmdtools/SimInfo.hpp

#ifndef __SIMINFO_H__
#define __SIMINFO_H__

#include <map>
#include <string>
#include <vector>

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

#define __C
#include "fSimulation.h"
#include "fortranWrapDefines.hpp"
#include "GenericData.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]);
  
  
  void addProperty(GenericData* prop); 
  GenericData* getProperty(const string& propName);
  vector<GenericData*> getProperties();       
  
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;
  
  //Addtional Properties of SimInfo
  map<string, GenericData*> properties;

};


#endif
Revision:	658
Committed:	Thu Jul 31 15:35:07 2003 UTC (20 years, 11 months ago) by tim
File size:	5759 byte(s)
Log Message:	Added Z constraint.
#	User	Rev	Content
1	mmeineke	377	#ifndef __SIMINFO_H__
2			#define __SIMINFO_H__
3
4	tim	658	#include <map>
5			#include <string>
6			#include <vector>
7	mmeineke	377
8			#include "Atom.hpp"
9			#include "Molecule.hpp"
10			#include "AbstractClasses.hpp"
11			#include "MakeStamps.hpp"
12
13			#define __C
14			#include "fSimulation.h"
15			#include "fortranWrapDefines.hpp"
16	tim	658	#include "GenericData.hpp"
17	mmeineke	377
18
19
20			class SimInfo{
21
22			public:
23
24			SimInfo();
25			~SimInfo(){}
26
27			int n_atoms; // the number of atoms
28			Atom **atoms; // the array of atom objects
29
30			double tau[9]; // the stress tensor
31
32			unsigned int n_bonds; // number of bends
33			unsigned int n_bends; // number of bends
34			unsigned int n_torsions; // number of torsions
35			unsigned int n_oriented; // number of of atoms with orientation
36	gezelter	458	unsigned int ndf; // number of actual degrees of freedom
37			unsigned int ndfRaw; // number of settable degrees of freedom
38	mmeineke	377
39			unsigned int setTemp; // boolean to set the temperature at each sampleTime
40
41			unsigned int n_dipoles; // number of dipoles
42
43	mmeineke	626
44	mmeineke	377	int n_exclude; // the # of pairs excluded from long range forces
45	mmeineke	427	Exclude** excludes; // the pairs themselves
46	mmeineke	377
47			int nGlobalExcludes;
48			int* globalExcludes; // same as above, but these guys participate in
49			// no long range forces.
50
51			int* identArray; // array of unique identifiers for the atoms
52	gezelter	483	int* molMembershipArray; // map of atom numbers onto molecule numbers
53	mmeineke	377
54			int n_constraints; // the number of constraints on the system
55
56			unsigned int n_SRI; // the number of short range interactions
57
58			double lrPot; // the potential energy from the long range calculations.
59
60	gezelter	588	double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the
61			// column vectors of the x, y, and z box vectors.
62			// h1 h2 h3
63			// [ Xx Yx Zx ]
64			// [ Xy Yy Zy ]
65			// [ Xz Yz Zz ]
66			//
67			double HmatInv[3][3];
68	mmeineke	568
69	gezelter	621	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
70	mmeineke	572	double boxVol;
71			int orthoRhombic;
72	mmeineke	568
73
74	mmeineke	626	double dielectric; // the dielectric of the medium for reaction field
75	mmeineke	568
76	mmeineke	377
77			int usePBC; // whether we use periodic boundry conditions.
78			int useLJ;
79			int useSticky;
80			int useDipole;
81			int useReactionField;
82			int useGB;
83			int useEAM;
84
85
86			double dt, run_time; // the time step and total time
87			double sampleTime, statusTime; // the position and energy dump frequencies
88			double target_temp; // the target temperature of the system
89			double thermalTime; // the temp kick interval
90	gezelter	637	double currentTime; // Used primarily for correlation Functions
91	mmeineke	377
92			int n_mol; // n_molecules;
93			Molecule* molecules; // the array of molecules
94
95			int nComponents; // the number of componentsin the system
96			int* componentsNmol; // the number of molecules of each component
97			MoleculeStamp** compStamps;// the stamps matching the components
98			LinkedMolStamp* headStamp; // list of stamps used in the simulation
99
100
101			char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
102			char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
103	mmeineke	542	BaseIntegrator *the_integrator; // the integrator of the simulation
104	mmeineke	377
105			char finalName[300]; // the name of the eor file to be written
106			char sampleName[300]; // the name of the dump file to be written
107			char statusName[300]; // the name of the stat file to be written
108
109
110			// refreshes the sim if things get changed (load balanceing, volume
111			// adjustment, etc.)
112
113			void refreshSim( void );
114
115
116			// sets the internal function pointer to fortran.
117
118			void setInternal( void (*fSetup) setFortranSimList,
119	mmeineke	626	void (*fBox) setFortranBoxList,
120			void (*fCut) notifyFortranCutOffList ){
121	mmeineke	377	setFsimulation = fSetup;
122			setFortranBoxSize = fBox;
123	mmeineke	626	notifyFortranCutOffs = fCut;
124	mmeineke	377	}
125
126	gezelter	458	int getNDF();
127			int getNDFraw();
128
129	gezelter	457	void setBox( double newBox[3] );
130	gezelter	588	void setBoxM( double newBox[3][3] );
131			void getBoxM( double theBox[3][3] );
132	gezelter	574	void scaleBox( double scale );
133	mmeineke	626
134			void setRcut( double theRcut );
135			void setEcr( double theEcr );
136			void setEcr( double theEcr, double theEst );
137	gezelter	457
138	mmeineke	626	double getRcut( void ) { return rCut; }
139			double getRlist( void ) { return rList; }
140			double getEcr( void ) { return ecr; }
141			double getEst( void ) { return est; }
142
143	mmeineke	644	void setTime( double theTime ) { currentTime = theTime; }
144	mmeineke	643	void incrTime( double dt ) { currentTime += dt; }
145			void decrTime( double dt ) { currentTime -= dt; }
146	mmeineke	644	double getTime( void ) { return currentTime; }
147	mmeineke	626
148	mmeineke	568	void wrapVector( double thePos[3] );
149
150	gezelter	588	void matMul3(double a[3][3], double b[3][3], double out[3][3]);
151			void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
152			void invertMat3(double in[3][3], double out[3][3]);
153	mmeineke	597	void transposeMat3(double in[3][3], double out[3][3]);
154			void printMat3(double A[3][3]);
155			void printMat9(double A[9]);
156	gezelter	588	double matDet3(double m[3][3]);
157
158	tim	658
159			void addProperty(GenericData* prop);
160			GenericData* getProperty(const string& propName);
161			vector<GenericData*> getProperties();
162
163	mmeineke	377	private:
164	mmeineke	626
165			double origRcut, origEcr;
166			int boxIsInit, haveOrigRcut, haveOrigEcr;
167
168			double oldEcr;
169			double oldRcut;
170
171			double rList, rCut; // variables for the neighborlist
172			double ecr; // the electrostatic cutoff radius
173			double est; // the electrostatic skin thickness
174			double maxCutoff;
175	mmeineke	377
176	gezelter	588	void calcHmatInv( void );
177	mmeineke	568	void calcBoxL();
178	mmeineke	626	void checkCutOffs( void );
179	mmeineke	568
180	mmeineke	377	// private function to initialize the fortran side of the simulation
181			void (*setFsimulation) setFortranSimList;
182
183			void (*setFortranBoxSize) setFortranBoxList;
184	mmeineke	626
185			void (*notifyFortranCutOffs) notifyFortranCutOffList;
186	tim	658
187			//Addtional Properties of SimInfo
188			map<string, GenericData*> properties;
189	mmeineke	626
190	mmeineke	377	};
191
192
193
194			#endif