OOPSE/libmdtools/SimInfo.hpp

#ifndef __SIMINFO_H__
#define __SIMINFO_H__

#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

  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 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 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

  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 setRcut( double theRcut );
  void setDefaultRcut( double theRcut );
  void setEcr( double theEcr );
  void setDefaultEcr( double theEcr );
  void setEcr( double theEcr, double theEst );
  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; }
  
  GenericData* getProperty(char* propName);
  GenericData* getProperties() {return properties; }

  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;

  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
  GenericData* properties;

};


#endif
Revision:	851
Committed:	Wed Nov 5 19:18:17 2003 UTC (21 years, 9 months ago) by mmeineke
File size:	6521 byte(s)
Log Message:	some work on trying to find the compression bug
#	User	Rev	Content
1	mmeineke	377	#ifndef __SIMINFO_H__
2			#define __SIMINFO_H__
3
4			#include "Atom.hpp"
5			#include "Molecule.hpp"
6			#include "AbstractClasses.hpp"
7			#include "MakeStamps.hpp"
8	mmeineke	670	#include "SimState.hpp"
9	mmeineke	377
10			#define __C
11			#include "fSimulation.h"
12			#include "fortranWrapDefines.hpp"
13	tim	658	#include "GenericData.hpp"
14	mmeineke	377
15
16
17			class SimInfo{
18
19			public:
20
21			SimInfo();
22	tim	660	~SimInfo();
23	mmeineke	377
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	mmeineke	787	int n_bonds; // number of bends
30			int n_bends; // number of bends
31			int n_torsions; // number of torsions
32			int n_oriented; // number of of atoms with orientation
33			int ndf; // number of actual degrees of freedom
34			int ndfRaw; // number of settable degrees of freedom
35			int ndfTrans; // number of translational degrees of freedom
36			int nZconstraints; // the number of zConstraints
37	mmeineke	377
38	mmeineke	787	int setTemp; // boolean to set the temperature at each sampleTime
39			int resetIntegrator; // boolean to reset the integrator
40	mmeineke	377
41	mmeineke	787	int n_dipoles; // number of dipoles
42	mmeineke	377
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	mmeineke	787	int n_SRI; // the number of short range interactions
57	mmeineke	377
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	746	double resetTime; // Use to reset the integrator periodically
92	mmeineke	377
93			int n_mol; // n_molecules;
94			Molecule* molecules; // the array of molecules
95
96	mmeineke	823	int nComponents; // the number of components in the system
97	mmeineke	377	int* componentsNmol; // the number of molecules of each component
98			MoleculeStamp** compStamps;// the stamps matching the components
99			LinkedMolStamp* headStamp; // list of stamps used in the simulation
100
101
102			char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
103			char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
104	mmeineke	542	BaseIntegrator *the_integrator; // the integrator of the simulation
105	mmeineke	377
106			char finalName[300]; // the name of the eor file to be written
107			char sampleName[300]; // the name of the dump file to be written
108			char statusName[300]; // the name of the stat file to be written
109
110	tim	708	int seed; //seed for random number generator
111	mmeineke	377	// refreshes the sim if things get changed (load balanceing, volume
112			// adjustment, etc.)
113
114			void refreshSim( void );
115
116
117			// sets the internal function pointer to fortran.
118
119	mmeineke	836	void setInternal( setFortranSim_TD fSetup,
120			setFortranBox_TD fBox,
121			notifyFortranCutOff_TD fCut){
122	mmeineke	377	setFsimulation = fSetup;
123			setFortranBoxSize = fBox;
124	mmeineke	626	notifyFortranCutOffs = fCut;
125	mmeineke	377	}
126
127	gezelter	458	int getNDF();
128			int getNDFraw();
129	tim	767	int getNDFtranslational();
130	gezelter	458
131	gezelter	457	void setBox( double newBox[3] );
132	gezelter	588	void setBoxM( double newBox[3][3] );
133			void getBoxM( double theBox[3][3] );
134	gezelter	574	void scaleBox( double scale );
135	mmeineke	626
136			void setRcut( double theRcut );
137	mmeineke	841	void setDefaultRcut( double theRcut );
138	mmeineke	626	void setEcr( double theEcr );
139	mmeineke	841	void setDefaultEcr( double theEcr );
140	mmeineke	626	void setEcr( double theEcr, double theEst );
141	mmeineke	841	void setDefaultEcr( double theEcr, double theEst );
142	gezelter	845	void checkCutOffs( void );
143	gezelter	457
144	mmeineke	626	double getRcut( void ) { return rCut; }
145			double getRlist( void ) { return rList; }
146			double getEcr( void ) { return ecr; }
147			double getEst( void ) { return est; }
148	mmeineke	797	double getMaxCutoff( void ) { return maxCutoff; }
149	mmeineke	626
150	mmeineke	644	void setTime( double theTime ) { currentTime = theTime; }
151	mmeineke	790	void incrTime( double the_dt ) { currentTime += the_dt; }
152			void decrTime( double the_dt ) { currentTime -= the_dt; }
153	mmeineke	644	double getTime( void ) { return currentTime; }
154	mmeineke	626
155	mmeineke	568	void wrapVector( double thePos[3] );
156
157	gezelter	588	void matMul3(double a[3][3], double b[3][3], double out[3][3]);
158			void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
159			void invertMat3(double in[3][3], double out[3][3]);
160	mmeineke	597	void transposeMat3(double in[3][3], double out[3][3]);
161			void printMat3(double A[3][3]);
162			void printMat9(double A[9]);
163	gezelter	588	double matDet3(double m[3][3]);
164	tim	763	double matTrace3(double m[3][3]);
165	mmeineke	670
166	tim	781	void crossProduct3(double a[3],double b[3], double out[3]);
167			double dotProduct3(double a[3], double b[3]);
168			double length3(double a[3]);
169
170	mmeineke	670	SimState* getConfiguration( void ) { return myConfiguration; }
171	gezelter	588
172	mmeineke	850	GenericData* getProperty(char* propName);
173			GenericData* getProperties() {return properties; }
174	mmeineke	670
175	tim	708	int getSeed(void) { return seed; }
176			void setSeed(int theSeed) { seed = theSeed;}
177
178	mmeineke	377	private:
179	mmeineke	626
180	mmeineke	670	SimState* myConfiguration;
181
182	mmeineke	626	double origRcut, origEcr;
183			int boxIsInit, haveOrigRcut, haveOrigEcr;
184
185			double oldEcr;
186			double oldRcut;
187
188			double rList, rCut; // variables for the neighborlist
189			double ecr; // the electrostatic cutoff radius
190			double est; // the electrostatic skin thickness
191			double maxCutoff;
192	tim	781
193			double distXY;
194			double distYZ;
195			double distZX;
196	mmeineke	377
197	gezelter	588	void calcHmatInv( void );
198	mmeineke	568	void calcBoxL();
199	tim	781	double calcMaxCutOff();
200	mmeineke	568
201	gezelter	845
202	mmeineke	377	// private function to initialize the fortran side of the simulation
203	mmeineke	836	setFortranSim_TD setFsimulation;
204	mmeineke	377
205	mmeineke	836	setFortranBox_TD setFortranBoxSize;
206	mmeineke	626
207	mmeineke	836	notifyFortranCutOff_TD notifyFortranCutOffs;
208	tim	658
209			//Addtional Properties of SimInfo
210	mmeineke	850	GenericData* properties;
211	mmeineke	626
212	mmeineke	377	};
213
214
215
216			#endif