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"
#include "SimState.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 nZconstraints; // the number of zConstraints

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

  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
  double resetTime;              // Use to reset the integrator periodically

  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

  int seed;                    //seed for random number generator
  // 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]);
  double matTrace3(double m[3][3]);

  SimState* getConfiguration( void ) { return myConfiguration; }
  
  void addProperty(GenericData* prop); 
  GenericData* getProperty(const string& propName);
  vector<GenericData*> getProperties();       

  int getSeed(void) {  return seed; }
  void setSeed(int theSeed) {  seed = theSeed;}

private:

  SimState* myConfiguration;

  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:	763
Committed:	Mon Sep 15 16:52:02 2003 UTC (20 years, 9 months ago) by tim
File size:	6265 byte(s)
Log Message:	add conserved quantity to statWriter fix bug of vector wrapping at NPTi
#	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	mmeineke	670	#include "SimState.hpp"
13	mmeineke	377
14			#define __C
15			#include "fSimulation.h"
16			#include "fortranWrapDefines.hpp"
17	tim	658	#include "GenericData.hpp"
18	mmeineke	377
19
20
21			class SimInfo{
22
23			public:
24
25			SimInfo();
26	tim	660	~SimInfo();
27	mmeineke	377
28			int n_atoms; // the number of atoms
29			Atom **atoms; // the array of atom objects
30
31			double tau[9]; // the stress tensor
32
33			unsigned int n_bonds; // number of bends
34			unsigned int n_bends; // number of bends
35			unsigned int n_torsions; // number of torsions
36			unsigned int n_oriented; // number of of atoms with orientation
37	gezelter	458	unsigned int ndf; // number of actual degrees of freedom
38			unsigned int ndfRaw; // number of settable degrees of freedom
39	mmeineke	675	unsigned int nZconstraints; // the number of zConstraints
40	mmeineke	377
41			unsigned int setTemp; // boolean to set the temperature at each sampleTime
42	mmeineke	746	unsigned int resetIntegrator; // boolean to reset the integrator
43	mmeineke	377
44			unsigned int n_dipoles; // number of dipoles
45
46	mmeineke	626
47	mmeineke	377	int n_exclude; // the # of pairs excluded from long range forces
48	mmeineke	427	Exclude** excludes; // the pairs themselves
49	mmeineke	377
50			int nGlobalExcludes;
51			int* globalExcludes; // same as above, but these guys participate in
52			// no long range forces.
53
54			int* identArray; // array of unique identifiers for the atoms
55	gezelter	483	int* molMembershipArray; // map of atom numbers onto molecule numbers
56	mmeineke	377
57			int n_constraints; // the number of constraints on the system
58
59			unsigned int n_SRI; // the number of short range interactions
60
61			double lrPot; // the potential energy from the long range calculations.
62
63	gezelter	588	double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the
64			// column vectors of the x, y, and z box vectors.
65			// h1 h2 h3
66			// [ Xx Yx Zx ]
67			// [ Xy Yy Zy ]
68			// [ Xz Yz Zz ]
69			//
70			double HmatInv[3][3];
71	mmeineke	568
72	gezelter	621	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
73	mmeineke	572	double boxVol;
74			int orthoRhombic;
75	mmeineke	568
76
77	mmeineke	626	double dielectric; // the dielectric of the medium for reaction field
78	mmeineke	568
79	mmeineke	377
80			int usePBC; // whether we use periodic boundry conditions.
81			int useLJ;
82			int useSticky;
83			int useDipole;
84			int useReactionField;
85			int useGB;
86			int useEAM;
87
88
89			double dt, run_time; // the time step and total time
90			double sampleTime, statusTime; // the position and energy dump frequencies
91			double target_temp; // the target temperature of the system
92			double thermalTime; // the temp kick interval
93	gezelter	637	double currentTime; // Used primarily for correlation Functions
94	mmeineke	746	double resetTime; // Use to reset the integrator periodically
95	mmeineke	377
96			int n_mol; // n_molecules;
97			Molecule* molecules; // the array of molecules
98
99			int nComponents; // the number of componentsin the system
100			int* componentsNmol; // the number of molecules of each component
101			MoleculeStamp** compStamps;// the stamps matching the components
102			LinkedMolStamp* headStamp; // list of stamps used in the simulation
103
104
105			char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
106			char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
107	mmeineke	542	BaseIntegrator *the_integrator; // the integrator of the simulation
108	mmeineke	377
109			char finalName[300]; // the name of the eor file to be written
110			char sampleName[300]; // the name of the dump file to be written
111			char statusName[300]; // the name of the stat file to be written
112
113	tim	708	int seed; //seed for random number generator
114	mmeineke	377	// refreshes the sim if things get changed (load balanceing, volume
115			// adjustment, etc.)
116
117			void refreshSim( void );
118
119
120			// sets the internal function pointer to fortran.
121
122			void setInternal( void (*fSetup) setFortranSimList,
123	mmeineke	626	void (*fBox) setFortranBoxList,
124			void (*fCut) notifyFortranCutOffList ){
125	mmeineke	377	setFsimulation = fSetup;
126			setFortranBoxSize = fBox;
127	mmeineke	626	notifyFortranCutOffs = fCut;
128	mmeineke	377	}
129
130	gezelter	458	int getNDF();
131			int getNDFraw();
132
133	gezelter	457	void setBox( double newBox[3] );
134	gezelter	588	void setBoxM( double newBox[3][3] );
135			void getBoxM( double theBox[3][3] );
136	gezelter	574	void scaleBox( double scale );
137	mmeineke	626
138			void setRcut( double theRcut );
139			void setEcr( double theEcr );
140			void setEcr( double theEcr, double theEst );
141	gezelter	457
142	mmeineke	626	double getRcut( void ) { return rCut; }
143			double getRlist( void ) { return rList; }
144			double getEcr( void ) { return ecr; }
145			double getEst( void ) { return est; }
146
147	mmeineke	644	void setTime( double theTime ) { currentTime = theTime; }
148	mmeineke	643	void incrTime( double dt ) { currentTime += dt; }
149			void decrTime( double dt ) { currentTime -= dt; }
150	mmeineke	644	double getTime( void ) { return currentTime; }
151	mmeineke	626
152	mmeineke	568	void wrapVector( double thePos[3] );
153
154	gezelter	588	void matMul3(double a[3][3], double b[3][3], double out[3][3]);
155			void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
156			void invertMat3(double in[3][3], double out[3][3]);
157	mmeineke	597	void transposeMat3(double in[3][3], double out[3][3]);
158			void printMat3(double A[3][3]);
159			void printMat9(double A[9]);
160	gezelter	588	double matDet3(double m[3][3]);
161	tim	763	double matTrace3(double m[3][3]);
162	mmeineke	670
163			SimState* getConfiguration( void ) { return myConfiguration; }
164	gezelter	588
165	tim	658	void addProperty(GenericData* prop);
166			GenericData* getProperty(const string& propName);
167			vector<GenericData*> getProperties();
168	mmeineke	670
169	tim	708	int getSeed(void) { return seed; }
170			void setSeed(int theSeed) { seed = theSeed;}
171
172	mmeineke	377	private:
173	mmeineke	626
174	mmeineke	670	SimState* myConfiguration;
175
176	mmeineke	626	double origRcut, origEcr;
177			int boxIsInit, haveOrigRcut, haveOrigEcr;
178
179			double oldEcr;
180			double oldRcut;
181
182			double rList, rCut; // variables for the neighborlist
183			double ecr; // the electrostatic cutoff radius
184			double est; // the electrostatic skin thickness
185			double maxCutoff;
186	mmeineke	377
187	gezelter	588	void calcHmatInv( void );
188	mmeineke	568	void calcBoxL();
189	mmeineke	626	void checkCutOffs( void );
190	mmeineke	568
191	mmeineke	377	// private function to initialize the fortran side of the simulation
192			void (*setFsimulation) setFortranSimList;
193
194			void (*setFortranBoxSize) setFortranBoxList;
195	mmeineke	626
196			void (*notifyFortranCutOffs) notifyFortranCutOffList;
197	tim	658
198			//Addtional Properties of SimInfo
199			map<string, GenericData*> properties;
200	mmeineke	626
201	mmeineke	377	};
202
203
204
205			#endif