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 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:	859
Committed:	Mon Nov 10 21:50:36 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	6493 byte(s)
Log Message:	reordered the rcut/ecr/boxSize initialization removed the rcut/ecr shrink and grow algorithm. the simulation will now exit when it runs into rcut or ecr.
#	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	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
42	int setTemp; // boolean to set the temperature at each sampleTime
43	int resetIntegrator; // boolean to reset the integrator
44
45	int n_dipoles; // number of dipoles
46
47
48	int n_exclude; // the # of pairs excluded from long range forces
49	Exclude** excludes; // the pairs themselves
50
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	int* molMembershipArray; // map of atom numbers onto molecule numbers
57
58	int n_constraints; // the number of constraints on the system
59
60	int n_SRI; // the number of short range interactions
61
62	double lrPot; // the potential energy from the long range calculations.
63
64	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
73	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
74	double boxVol;
75	int orthoRhombic;
76
77
78	double dielectric; // the dielectric of the medium for reaction field
79
80
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	bool useInitXSstate;
90	double orthoTolerance;
91
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	double currentTime; // Used primarily for correlation Functions
97	double resetTime; // Use to reset the integrator periodically
98
99	int n_mol; // n_molecules;
100	Molecule* molecules; // the array of molecules
101
102	int nComponents; // the number of components in the system
103	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	BaseIntegrator *the_integrator; // the integrator of the simulation
111
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	int seed; //seed for random number generator
117	// 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	void setInternal( setFortranSim_TD fSetup,
126	setFortranBox_TD fBox,
127	notifyFortranCutOff_TD fCut){
128	setFsimulation = fSetup;
129	setFortranBoxSize = fBox;
130	notifyFortranCutOffs = fCut;
131	}
132
133	int getNDF();
134	int getNDFraw();
135	int getNDFtranslational();
136
137	void setBox( double newBox[3] );
138	void setBoxM( double newBox[3][3] );
139	void getBoxM( double theBox[3][3] );
140	void scaleBox( double scale );
141
142	void setDefaultRcut( double theRcut );
143	void setDefaultEcr( double theEcr );
144	void setDefaultEcr( double theEcr, double theEst );
145	void checkCutOffs( void );
146
147	double getRcut( void ) { return rCut; }
148	double getRlist( void ) { return rList; }
149	double getEcr( void ) { return ecr; }
150	double getEst( void ) { return est; }
151	double getMaxCutoff( void ) { return maxCutoff; }
152
153	void setTime( double theTime ) { currentTime = theTime; }
154	void incrTime( double the_dt ) { currentTime += the_dt; }
155	void decrTime( double the_dt ) { currentTime -= the_dt; }
156	double getTime( void ) { return currentTime; }
157
158	void wrapVector( double thePos[3] );
159
160	void matMul3(double a[3][3], double b[3][3], double out[3][3]);
161	void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
162	void invertMat3(double in[3][3], double out[3][3]);
163	void transposeMat3(double in[3][3], double out[3][3]);
164	void printMat3(double A[3][3]);
165	void printMat9(double A[9]);
166	double matDet3(double m[3][3]);
167	double matTrace3(double m[3][3]);
168
169	void crossProduct3(double a[3],double b[3], double out[3]);
170	double dotProduct3(double a[3], double b[3]);
171	double length3(double a[3]);
172
173	SimState* getConfiguration( void ) { return myConfiguration; }
174
175	void addProperty(GenericData* prop);
176	GenericData* getProperty(const string& propName);
177	vector<GenericData*> getProperties();
178
179	int getSeed(void) { return seed; }
180	void setSeed(int theSeed) { seed = theSeed;}
181
182	private:
183
184	SimState* myConfiguration;
185
186	int boxIsInit, haveRcut, haveEcr;
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
193	double distXY;
194	double distYZ;
195	double distZX;
196
197
198
199	void calcHmatInv( void );
200	void calcBoxL();
201	double calcMaxCutOff();
202
203
204	// private function to initialize the fortran side of the simulation
205	setFortranSim_TD setFsimulation;
206
207	setFortranBox_TD setFortranBoxSize;
208
209	notifyFortranCutOff_TD notifyFortranCutOffs;
210
211	//Addtional Properties of SimInfo
212	map<string, GenericData*> properties;
213
214	};
215
216
217
218	#endif