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"
//#include "Minimizer.hpp"
//#include "OOPSEMinimizer.hpp"

class OOPSEMinimizer;
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

  int n_bonds;    // number of bends
  int n_bends;    // number of bends
  int n_torsions; // number of torsions
  int n_oriented; // number of of atoms with orientation
  int ndf;        // number of actual degrees of freedom
  int ndfRaw;     // number of settable degrees of freedom
  int ndfTrans;   // number of translational degrees of freedom
  int nZconstraints; // the number of zConstraints

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

  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

  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 useCharges;
  int useDipoles;
  int useReactionField;
  int useGB;
  int useEAM;
  
  bool useInitXSstate;
  double orthoTolerance;

  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 components in 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

  OOPSEMinimizer* the_minimizer; // the energy minimizer
  bool has_minimizer;

  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( setFortranSim_TD fSetup,
                    setFortranBox_TD fBox,
                    notifyFortranCutOff_TD fCut){
    setFsimulation = fSetup;
    setFortranBoxSize = fBox;
    notifyFortranCutOffs = fCut;
  }

  int getNDF();
  int getNDFraw();
  int getNDFtranslational();

  void setBox( double newBox[3] );
  void setBoxM( double newBox[3][3] );
  void getBoxM( double theBox[3][3] );
  void scaleBox( double scale );
  
  void setDefaultRcut( double theRcut );
  void setDefaultEcr( double theEcr );
  void setDefaultEcr( double theEcr, double theEst );
  void checkCutOffs( void );

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

  void setTime( double theTime ) { currentTime = theTime; }
  void incrTime( double the_dt ) { currentTime += the_dt; }
  void decrTime( double the_dt ) { currentTime -= the_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]);

  void crossProduct3(double a[3],double b[3], double out[3]);
  double dotProduct3(double a[3], double b[3]);
  double length3(double a[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;

  int boxIsInit, haveRcut, haveEcr;

  double rList, rCut; // variables for the neighborlist
  double ecr;             // the electrostatic cutoff radius
  double est;             // the electrostatic skin thickness
  double maxCutoff;

  double distXY;
  double distYZ;
  double distZX;


  void calcHmatInv( void );
  void calcBoxL();
  double calcMaxCutOff();


  // private function to initialize the fortran side of the simulation
  setFortranSim_TD setFsimulation;

  setFortranBox_TD setFortranBoxSize;
  
  notifyFortranCutOff_TD notifyFortranCutOffs;
  
  //Addtional Properties of SimInfo
  map<string, GenericData*> properties;

};


#endif
Revision:	1064
Committed:	Tue Feb 24 15:44:45 2004 UTC (20 years, 4 months ago) by tim
File size:	6671 byte(s)
Log Message:	Using inherit instead of compose to implement Minimizer both versions are working
#	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	tim	1064	//#include "Minimizer.hpp"
19			//#include "OOPSEMinimizer.hpp"
20	mmeineke	377
21	tim	1064	class OOPSEMinimizer;
22	mmeineke	377	class SimInfo{
23
24			public:
25
26			SimInfo();
27	tim	660	~SimInfo();
28	mmeineke	377
29			int n_atoms; // the number of atoms
30			Atom **atoms; // the array of atom objects
31
32			double tau[9]; // the stress tensor
33
34	mmeineke	787	int n_bonds; // number of bends
35			int n_bends; // number of bends
36			int n_torsions; // number of torsions
37			int n_oriented; // number of of atoms with orientation
38			int ndf; // number of actual degrees of freedom
39			int ndfRaw; // number of settable degrees of freedom
40			int ndfTrans; // number of translational degrees of freedom
41			int nZconstraints; // the number of zConstraints
42	mmeineke	377
43	mmeineke	787	int setTemp; // boolean to set the temperature at each sampleTime
44			int resetIntegrator; // boolean to reset the integrator
45	mmeineke	377
46	mmeineke	787	int n_dipoles; // number of dipoles
47	mmeineke	377
48	mmeineke	626
49	mmeineke	377	int n_exclude; // the # of pairs excluded from long range forces
50	mmeineke	427	Exclude** excludes; // the pairs themselves
51	mmeineke	377
52			int nGlobalExcludes;
53			int* globalExcludes; // same as above, but these guys participate in
54			// no long range forces.
55
56			int* identArray; // array of unique identifiers for the atoms
57	gezelter	483	int* molMembershipArray; // map of atom numbers onto molecule numbers
58	mmeineke	377
59			int n_constraints; // the number of constraints on the system
60
61	mmeineke	787	int n_SRI; // the number of short range interactions
62	mmeineke	377
63			double lrPot; // the potential energy from the long range calculations.
64
65	gezelter	588	double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the
66			// column vectors of the x, y, and z box vectors.
67			// h1 h2 h3
68			// [ Xx Yx Zx ]
69			// [ Xy Yy Zy ]
70			// [ Xz Yz Zz ]
71			//
72			double HmatInv[3][3];
73	mmeineke	568
74	gezelter	621	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
75	mmeineke	572	double boxVol;
76			int orthoRhombic;
77	mmeineke	568
78
79	mmeineke	626	double dielectric; // the dielectric of the medium for reaction field
80	mmeineke	568
81	mmeineke	377
82			int usePBC; // whether we use periodic boundry conditions.
83			int useLJ;
84			int useSticky;
85	gezelter	941	int useCharges;
86			int useDipoles;
87	mmeineke	377	int useReactionField;
88			int useGB;
89			int useEAM;
90
91	mmeineke	855	bool useInitXSstate;
92			double orthoTolerance;
93	mmeineke	377
94			double dt, run_time; // the time step and total time
95			double sampleTime, statusTime; // the position and energy dump frequencies
96			double target_temp; // the target temperature of the system
97			double thermalTime; // the temp kick interval
98	gezelter	637	double currentTime; // Used primarily for correlation Functions
99	mmeineke	746	double resetTime; // Use to reset the integrator periodically
100	mmeineke	377
101			int n_mol; // n_molecules;
102			Molecule* molecules; // the array of molecules
103
104	mmeineke	823	int nComponents; // the number of components in the system
105	mmeineke	377	int* componentsNmol; // the number of molecules of each component
106			MoleculeStamp** compStamps;// the stamps matching the components
107			LinkedMolStamp* headStamp; // list of stamps used in the simulation
108
109
110			char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
111			char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
112	mmeineke	542	BaseIntegrator *the_integrator; // the integrator of the simulation
113	mmeineke	377
114	tim	1064	OOPSEMinimizer* the_minimizer; // the energy minimizer
115	tim	1031	bool has_minimizer;
116
117	mmeineke	377	char finalName[300]; // the name of the eor file to be written
118			char sampleName[300]; // the name of the dump file to be written
119			char statusName[300]; // the name of the stat file to be written
120
121	tim	708	int seed; //seed for random number generator
122	mmeineke	377	// refreshes the sim if things get changed (load balanceing, volume
123			// adjustment, etc.)
124
125			void refreshSim( void );
126
127
128			// sets the internal function pointer to fortran.
129
130	mmeineke	836	void setInternal( setFortranSim_TD fSetup,
131			setFortranBox_TD fBox,
132			notifyFortranCutOff_TD fCut){
133	mmeineke	377	setFsimulation = fSetup;
134			setFortranBoxSize = fBox;
135	mmeineke	626	notifyFortranCutOffs = fCut;
136	mmeineke	377	}
137
138	gezelter	458	int getNDF();
139			int getNDFraw();
140	tim	767	int getNDFtranslational();
141	gezelter	458
142	gezelter	457	void setBox( double newBox[3] );
143	gezelter	588	void setBoxM( double newBox[3][3] );
144			void getBoxM( double theBox[3][3] );
145	gezelter	574	void scaleBox( double scale );
146	mmeineke	626
147	mmeineke	841	void setDefaultRcut( double theRcut );
148			void setDefaultEcr( double theEcr );
149			void setDefaultEcr( double theEcr, double theEst );
150	gezelter	845	void checkCutOffs( void );
151	gezelter	457
152	mmeineke	626	double getRcut( void ) { return rCut; }
153			double getRlist( void ) { return rList; }
154			double getEcr( void ) { return ecr; }
155			double getEst( void ) { return est; }
156	mmeineke	797	double getMaxCutoff( void ) { return maxCutoff; }
157	mmeineke	626
158	mmeineke	644	void setTime( double theTime ) { currentTime = theTime; }
159	mmeineke	790	void incrTime( double the_dt ) { currentTime += the_dt; }
160			void decrTime( double the_dt ) { currentTime -= the_dt; }
161	mmeineke	644	double getTime( void ) { return currentTime; }
162	mmeineke	626
163	mmeineke	568	void wrapVector( double thePos[3] );
164
165	gezelter	588	void matMul3(double a[3][3], double b[3][3], double out[3][3]);
166			void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
167			void invertMat3(double in[3][3], double out[3][3]);
168	mmeineke	597	void transposeMat3(double in[3][3], double out[3][3]);
169			void printMat3(double A[3][3]);
170			void printMat9(double A[9]);
171	gezelter	588	double matDet3(double m[3][3]);
172	tim	763	double matTrace3(double m[3][3]);
173	mmeineke	670
174	tim	781	void crossProduct3(double a[3],double b[3], double out[3]);
175			double dotProduct3(double a[3], double b[3]);
176			double length3(double a[3]);
177
178	mmeineke	670	SimState* getConfiguration( void ) { return myConfiguration; }
179	gezelter	588
180	tim	658	void addProperty(GenericData* prop);
181			GenericData* getProperty(const string& propName);
182			vector<GenericData*> getProperties();
183	mmeineke	670
184	tim	708	int getSeed(void) { return seed; }
185			void setSeed(int theSeed) { seed = theSeed;}
186
187	mmeineke	377	private:
188	mmeineke	626
189	mmeineke	670	SimState* myConfiguration;
190
191	mmeineke	859	int boxIsInit, haveRcut, haveEcr;
192	mmeineke	626
193			double rList, rCut; // variables for the neighborlist
194			double ecr; // the electrostatic cutoff radius
195			double est; // the electrostatic skin thickness
196			double maxCutoff;
197	tim	781
198			double distXY;
199			double distYZ;
200			double distZX;
201	mmeineke	855
202
203	mmeineke	377
204	gezelter	588	void calcHmatInv( void );
205	mmeineke	568	void calcBoxL();
206	tim	781	double calcMaxCutOff();
207	mmeineke	568
208	gezelter	845
209	mmeineke	377	// private function to initialize the fortran side of the simulation
210	mmeineke	836	setFortranSim_TD setFsimulation;
211	mmeineke	377
212	mmeineke	836	setFortranBox_TD setFortranBoxSize;
213	mmeineke	626
214	mmeineke	836	notifyFortranCutOff_TD notifyFortranCutOffs;
215	tim	658
216			//Addtional Properties of SimInfo
217			map<string, GenericData*> properties;
218	mmeineke	626
219	mmeineke	377	};
220
221
222
223			#endif