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

  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;
  
  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

  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; }
  
  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;

  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:	855
Committed:	Thu Nov 6 22:01:37 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	6678 byte(s)
Log Message:	added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
#	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	mmeineke	787	int n_bonds; // number of bends
34			int n_bends; // number of bends
35			int n_torsions; // number of torsions
36			int n_oriented; // number of of atoms with orientation
37			int ndf; // number of actual degrees of freedom
38			int ndfRaw; // number of settable degrees of freedom
39			int ndfTrans; // number of translational degrees of freedom
40			int nZconstraints; // the number of zConstraints
41	mmeineke	377
42	mmeineke	787	int setTemp; // boolean to set the temperature at each sampleTime
43			int resetIntegrator; // boolean to reset the integrator
44	mmeineke	377
45	mmeineke	787	int n_dipoles; // number of dipoles
46	mmeineke	377
47	mmeineke	626
48	mmeineke	377	int n_exclude; // the # of pairs excluded from long range forces
49	mmeineke	427	Exclude** excludes; // the pairs themselves
50	mmeineke	377
51			int nGlobalExcludes;
52			int* globalExcludes; // same as above, but these guys participate in
53			// no long range forces.
54
55			int* identArray; // array of unique identifiers for the atoms
56	gezelter	483	int* molMembershipArray; // map of atom numbers onto molecule numbers
57	mmeineke	377
58			int n_constraints; // the number of constraints on the system
59
60	mmeineke	787	int n_SRI; // the number of short range interactions
61	mmeineke	377
62			double lrPot; // the potential energy from the long range calculations.
63
64	gezelter	588	double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the
65			// column vectors of the x, y, and z box vectors.
66			// h1 h2 h3
67			// [ Xx Yx Zx ]
68			// [ Xy Yy Zy ]
69			// [ Xz Yz Zz ]
70			//
71			double HmatInv[3][3];
72	mmeineke	568
73	gezelter	621	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
74	mmeineke	572	double boxVol;
75			int orthoRhombic;
76	mmeineke	568
77
78	mmeineke	626	double dielectric; // the dielectric of the medium for reaction field
79	mmeineke	568
80	mmeineke	377
81			int usePBC; // whether we use periodic boundry conditions.
82			int useLJ;
83			int useSticky;
84			int useDipole;
85			int useReactionField;
86			int useGB;
87			int useEAM;
88
89	mmeineke	855	bool useInitXSstate;
90			double orthoTolerance;
91	mmeineke	377
92			double dt, run_time; // the time step and total time
93			double sampleTime, statusTime; // the position and energy dump frequencies
94			double target_temp; // the target temperature of the system
95			double thermalTime; // the temp kick interval
96	gezelter	637	double currentTime; // Used primarily for correlation Functions
97	mmeineke	746	double resetTime; // Use to reset the integrator periodically
98	mmeineke	377
99			int n_mol; // n_molecules;
100			Molecule* molecules; // the array of molecules
101
102	mmeineke	823	int nComponents; // the number of components in the system
103	mmeineke	377	int* componentsNmol; // the number of molecules of each component
104			MoleculeStamp** compStamps;// the stamps matching the components
105			LinkedMolStamp* headStamp; // list of stamps used in the simulation
106
107
108			char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
109			char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
110	mmeineke	542	BaseIntegrator *the_integrator; // the integrator of the simulation
111	mmeineke	377
112			char finalName[300]; // the name of the eor file to be written
113			char sampleName[300]; // the name of the dump file to be written
114			char statusName[300]; // the name of the stat file to be written
115
116	tim	708	int seed; //seed for random number generator
117	mmeineke	377	// refreshes the sim if things get changed (load balanceing, volume
118			// adjustment, etc.)
119
120			void refreshSim( void );
121
122
123			// sets the internal function pointer to fortran.
124
125	mmeineke	836	void setInternal( setFortranSim_TD fSetup,
126			setFortranBox_TD fBox,
127			notifyFortranCutOff_TD fCut){
128	mmeineke	377	setFsimulation = fSetup;
129			setFortranBoxSize = fBox;
130	mmeineke	626	notifyFortranCutOffs = fCut;
131	mmeineke	377	}
132
133	gezelter	458	int getNDF();
134			int getNDFraw();
135	tim	767	int getNDFtranslational();
136	gezelter	458
137	gezelter	457	void setBox( double newBox[3] );
138	gezelter	588	void setBoxM( double newBox[3][3] );
139			void getBoxM( double theBox[3][3] );
140	gezelter	574	void scaleBox( double scale );
141	mmeineke	626
142			void setRcut( double theRcut );
143	mmeineke	841	void setDefaultRcut( double theRcut );
144	mmeineke	626	void setEcr( double theEcr );
145	mmeineke	841	void setDefaultEcr( double theEcr );
146	mmeineke	626	void setEcr( double theEcr, double theEst );
147	mmeineke	841	void setDefaultEcr( double theEcr, double theEst );
148	gezelter	845	void checkCutOffs( void );
149	gezelter	457
150	mmeineke	626	double getRcut( void ) { return rCut; }
151			double getRlist( void ) { return rList; }
152			double getEcr( void ) { return ecr; }
153			double getEst( void ) { return est; }
154	mmeineke	797	double getMaxCutoff( void ) { return maxCutoff; }
155	mmeineke	626
156	mmeineke	644	void setTime( double theTime ) { currentTime = theTime; }
157	mmeineke	790	void incrTime( double the_dt ) { currentTime += the_dt; }
158			void decrTime( double the_dt ) { currentTime -= the_dt; }
159	mmeineke	644	double getTime( void ) { return currentTime; }
160	mmeineke	626
161	mmeineke	568	void wrapVector( double thePos[3] );
162
163	gezelter	588	void matMul3(double a[3][3], double b[3][3], double out[3][3]);
164			void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
165			void invertMat3(double in[3][3], double out[3][3]);
166	mmeineke	597	void transposeMat3(double in[3][3], double out[3][3]);
167			void printMat3(double A[3][3]);
168			void printMat9(double A[9]);
169	gezelter	588	double matDet3(double m[3][3]);
170	tim	763	double matTrace3(double m[3][3]);
171	mmeineke	670
172	tim	781	void crossProduct3(double a[3],double b[3], double out[3]);
173			double dotProduct3(double a[3], double b[3]);
174			double length3(double a[3]);
175
176	mmeineke	670	SimState* getConfiguration( void ) { return myConfiguration; }
177	gezelter	588
178	tim	658	void addProperty(GenericData* prop);
179			GenericData* getProperty(const string& propName);
180			vector<GenericData*> getProperties();
181	mmeineke	670
182	tim	708	int getSeed(void) { return seed; }
183			void setSeed(int theSeed) { seed = theSeed;}
184
185	mmeineke	377	private:
186	mmeineke	626
187	mmeineke	670	SimState* myConfiguration;
188
189	mmeineke	626	double origRcut, origEcr;
190			int boxIsInit, haveOrigRcut, haveOrigEcr;
191
192			double oldEcr;
193			double oldRcut;
194
195			double rList, rCut; // variables for the neighborlist
196			double ecr; // the electrostatic cutoff radius
197			double est; // the electrostatic skin thickness
198			double maxCutoff;
199	tim	781
200			double distXY;
201			double distYZ;
202			double distZX;
203	mmeineke	855
204
205	mmeineke	377
206	gezelter	588	void calcHmatInv( void );
207	mmeineke	568	void calcBoxL();
208	tim	781	double calcMaxCutOff();
209	mmeineke	568
210	gezelter	845
211	mmeineke	377	// private function to initialize the fortran side of the simulation
212	mmeineke	836	setFortranSim_TD setFsimulation;
213	mmeineke	377
214	mmeineke	836	setFortranBox_TD setFortranBoxSize;
215	mmeineke	626
216	mmeineke	836	notifyFortranCutOff_TD notifyFortranCutOffs;
217	tim	658
218			//Addtional Properties of SimInfo
219			map<string, GenericData*> properties;
220	mmeineke	626
221	mmeineke	377	};
222
223
224
225			#endif