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 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

  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]);

  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:	708
Committed:	Wed Aug 20 22:23:34 2003 UTC (20 years, 10 months ago) by tim
File size:	6085 byte(s)
Log Message:	user can setup seed in bass file now, if he does not specify any value for seed, oopse will take the value of seconds of system time as seed
#	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
19
20
21	class SimInfo{
22
23	public:
24
25	SimInfo();
26	~SimInfo();
27
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	unsigned int ndf; // number of actual degrees of freedom
38	unsigned int ndfRaw; // number of settable degrees of freedom
39	unsigned int nZconstraints; // the number of zConstraints
40
41	unsigned int setTemp; // boolean to set the temperature at each sampleTime
42
43	unsigned int n_dipoles; // number of dipoles
44
45
46	int n_exclude; // the # of pairs excluded from long range forces
47	Exclude** excludes; // the pairs themselves
48
49	int nGlobalExcludes;
50	int* globalExcludes; // same as above, but these guys participate in
51	// no long range forces.
52
53	int* identArray; // array of unique identifiers for the atoms
54	int* molMembershipArray; // map of atom numbers onto molecule numbers
55
56	int n_constraints; // the number of constraints on the system
57
58	unsigned int n_SRI; // the number of short range interactions
59
60	double lrPot; // the potential energy from the long range calculations.
61
62	double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the
63	// column vectors of the x, y, and z box vectors.
64	// h1 h2 h3
65	// [ Xx Yx Zx ]
66	// [ Xy Yy Zy ]
67	// [ Xz Yz Zz ]
68	//
69	double HmatInv[3][3];
70
71	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
72	double boxVol;
73	int orthoRhombic;
74
75
76	double dielectric; // the dielectric of the medium for reaction field
77
78
79	int usePBC; // whether we use periodic boundry conditions.
80	int useLJ;
81	int useSticky;
82	int useDipole;
83	int useReactionField;
84	int useGB;
85	int useEAM;
86
87
88	double dt, run_time; // the time step and total time
89	double sampleTime, statusTime; // the position and energy dump frequencies
90	double target_temp; // the target temperature of the system
91	double thermalTime; // the temp kick interval
92	double currentTime; // Used primarily for correlation Functions
93
94	int n_mol; // n_molecules;
95	Molecule* molecules; // the array of molecules
96
97	int nComponents; // the number of componentsin the system
98	int* componentsNmol; // the number of molecules of each component
99	MoleculeStamp** compStamps;// the stamps matching the components
100	LinkedMolStamp* headStamp; // list of stamps used in the simulation
101
102
103	char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
104	char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
105	BaseIntegrator *the_integrator; // the integrator of the simulation
106
107	char finalName[300]; // the name of the eor file to be written
108	char sampleName[300]; // the name of the dump file to be written
109	char statusName[300]; // the name of the stat file to be written
110
111	int seed; //seed for random number generator
112	// refreshes the sim if things get changed (load balanceing, volume
113	// adjustment, etc.)
114
115	void refreshSim( void );
116
117
118	// sets the internal function pointer to fortran.
119
120	void setInternal( void (*fSetup) setFortranSimList,
121	void (*fBox) setFortranBoxList,
122	void (*fCut) notifyFortranCutOffList ){
123	setFsimulation = fSetup;
124	setFortranBoxSize = fBox;
125	notifyFortranCutOffs = fCut;
126	}
127
128	int getNDF();
129	int getNDFraw();
130
131	void setBox( double newBox[3] );
132	void setBoxM( double newBox[3][3] );
133	void getBoxM( double theBox[3][3] );
134	void scaleBox( double scale );
135
136	void setRcut( double theRcut );
137	void setEcr( double theEcr );
138	void setEcr( double theEcr, double theEst );
139
140	double getRcut( void ) { return rCut; }
141	double getRlist( void ) { return rList; }
142	double getEcr( void ) { return ecr; }
143	double getEst( void ) { return est; }
144
145	void setTime( double theTime ) { currentTime = theTime; }
146	void incrTime( double dt ) { currentTime += dt; }
147	void decrTime( double dt ) { currentTime -= dt; }
148	double getTime( void ) { return currentTime; }
149
150	void wrapVector( double thePos[3] );
151
152	void matMul3(double a[3][3], double b[3][3], double out[3][3]);
153	void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
154	void invertMat3(double in[3][3], double out[3][3]);
155	void transposeMat3(double in[3][3], double out[3][3]);
156	void printMat3(double A[3][3]);
157	void printMat9(double A[9]);
158	double matDet3(double m[3][3]);
159
160	SimState* getConfiguration( void ) { return myConfiguration; }
161
162	void addProperty(GenericData* prop);
163	GenericData* getProperty(const string& propName);
164	vector<GenericData*> getProperties();
165
166	int getSeed(void) { return seed; }
167	void setSeed(int theSeed) { seed = theSeed;}
168
169	private:
170
171	SimState* myConfiguration;
172
173	double origRcut, origEcr;
174	int boxIsInit, haveOrigRcut, haveOrigEcr;
175
176	double oldEcr;
177	double oldRcut;
178
179	double rList, rCut; // variables for the neighborlist
180	double ecr; // the electrostatic cutoff radius
181	double est; // the electrostatic skin thickness
182	double maxCutoff;
183
184	void calcHmatInv( void );
185	void calcBoxL();
186	void checkCutOffs( void );
187
188	// private function to initialize the fortran side of the simulation
189	void (*setFsimulation) setFortranSimList;
190
191	void (*setFortranBoxSize) setFortranBoxList;
192
193	void (*notifyFortranCutOffs) notifyFortranCutOffList;
194
195	//Addtional Properties of SimInfo
196	map<string, GenericData*> properties;
197
198	};
199
200
201
202	#endif