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
#	Content
1	#ifndef __SIMINFO_H__
2	#define __SIMINFO_H__
3
4	#include <map>
5	#include <string>
6	#include <vector>
7
8	#include "Atom.hpp"
9	#include "Molecule.hpp"
10	#include "AbstractClasses.hpp"
11	#include "MakeStamps.hpp"
12	#include "SimState.hpp"
13
14	#define __C
15	#include "fSimulation.h"
16	#include "fortranWrapDefines.hpp"
17	#include "GenericData.hpp"
18	//#include "Minimizer.hpp"
19	//#include "OOPSEMinimizer.hpp"
20
21	class OOPSEMinimizer;
22	class SimInfo{
23
24	public:
25
26	SimInfo();
27	~SimInfo();
28
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	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
43	int setTemp; // boolean to set the temperature at each sampleTime
44	int resetIntegrator; // boolean to reset the integrator
45
46	int n_dipoles; // number of dipoles
47
48
49	int n_exclude; // the # of pairs excluded from long range forces
50	Exclude** excludes; // the pairs themselves
51
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	int* molMembershipArray; // map of atom numbers onto molecule numbers
58
59	int n_constraints; // the number of constraints on the system
60
61	int n_SRI; // the number of short range interactions
62
63	double lrPot; // the potential energy from the long range calculations.
64
65	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
74	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
75	double boxVol;
76	int orthoRhombic;
77
78
79	double dielectric; // the dielectric of the medium for reaction field
80
81
82	int usePBC; // whether we use periodic boundry conditions.
83	int useLJ;
84	int useSticky;
85	int useCharges;
86	int useDipoles;
87	int useReactionField;
88	int useGB;
89	int useEAM;
90
91	bool useInitXSstate;
92	double orthoTolerance;
93
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	double currentTime; // Used primarily for correlation Functions
99	double resetTime; // Use to reset the integrator periodically
100
101	int n_mol; // n_molecules;
102	Molecule* molecules; // the array of molecules
103
104	int nComponents; // the number of components in the system
105	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	BaseIntegrator *the_integrator; // the integrator of the simulation
113
114	OOPSEMinimizer* the_minimizer; // the energy minimizer
115	bool has_minimizer;
116
117	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	int seed; //seed for random number generator
122	// 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	void setInternal( setFortranSim_TD fSetup,
131	setFortranBox_TD fBox,
132	notifyFortranCutOff_TD fCut){
133	setFsimulation = fSetup;
134	setFortranBoxSize = fBox;
135	notifyFortranCutOffs = fCut;
136	}
137
138	int getNDF();
139	int getNDFraw();
140	int getNDFtranslational();
141
142	void setBox( double newBox[3] );
143	void setBoxM( double newBox[3][3] );
144	void getBoxM( double theBox[3][3] );
145	void scaleBox( double scale );
146
147	void setDefaultRcut( double theRcut );
148	void setDefaultEcr( double theEcr );
149	void setDefaultEcr( double theEcr, double theEst );
150	void checkCutOffs( void );
151
152	double getRcut( void ) { return rCut; }
153	double getRlist( void ) { return rList; }
154	double getEcr( void ) { return ecr; }
155	double getEst( void ) { return est; }
156	double getMaxCutoff( void ) { return maxCutoff; }
157
158	void setTime( double theTime ) { currentTime = theTime; }
159	void incrTime( double the_dt ) { currentTime += the_dt; }
160	void decrTime( double the_dt ) { currentTime -= the_dt; }
161	double getTime( void ) { return currentTime; }
162
163	void wrapVector( double thePos[3] );
164
165	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	void transposeMat3(double in[3][3], double out[3][3]);
169	void printMat3(double A[3][3]);
170	void printMat9(double A[9]);
171	double matDet3(double m[3][3]);
172	double matTrace3(double m[3][3]);
173
174	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	SimState* getConfiguration( void ) { return myConfiguration; }
179
180	void addProperty(GenericData* prop);
181	GenericData* getProperty(const string& propName);
182	vector<GenericData*> getProperties();
183
184	int getSeed(void) { return seed; }
185	void setSeed(int theSeed) { seed = theSeed;}
186
187	private:
188
189	SimState* myConfiguration;
190
191	int boxIsInit, haveRcut, haveEcr;
192
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
198	double distXY;
199	double distYZ;
200	double distZX;
201
202
203
204	void calcHmatInv( void );
205	void calcBoxL();
206	double calcMaxCutOff();
207
208
209	// private function to initialize the fortran side of the simulation
210	setFortranSim_TD setFsimulation;
211
212	setFortranBox_TD setFortranBoxSize;
213
214	notifyFortranCutOff_TD notifyFortranCutOffs;
215
216	//Addtional Properties of SimInfo
217	map<string, GenericData*> properties;
218
219	};
220
221
222
223	#endif