OOPSE/libmdtools/SimInfo.hpp

#ifndef __SIMINFO_H__
#define __SIMINFO_H__

#include <map>
#include <string>
#include <vector>

#include "Atom.hpp"
#include "RigidBody.hpp"
#include "Molecule.hpp"
#include "Exclude.hpp"
#include "SkipList.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"
double roundMe( double x );
class OOPSEMinimizer;
class SimInfo{

public:

  SimInfo();
  ~SimInfo();

  int n_atoms; // the number of atoms
  Atom **atoms; // the array of atom objects

  vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
  vector<StuntDouble*> integrableObjects;
  
  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;
  Exclude* excludes;  // the exclude list for ignoring pairs in fortran
  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;
  int useMolecularCutoffs;
  
  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


  vector<double> mfact;
  int ngroup;
  vector<int> groupList;
  vector<int> groupStart;
  
  // 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();
  int getTotIntegrableObjects();
  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] );

  SimState* getConfiguration( void ) { return myConfiguration; }
  
  void addProperty(GenericData* prop); 
  GenericData* getProperty(const string& propName);
  //vector<GenericData*>& getProperties()  {return properties;}     

  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;

};

void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
                                                          vector<int>& groupList, vector<int>& groupStart);

#endif
Revision:	1144
Committed:	Sat May 1 18:52:38 2004 UTC (20 years, 2 months ago) by tim
File size:	6672 byte(s)
Log Message:	C++ pass groupList to fortran
#	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	gezelter	1097	#include "RigidBody.hpp"
10	mmeineke	377	#include "Molecule.hpp"
11	gezelter	1097	#include "Exclude.hpp"
12			#include "SkipList.hpp"
13	mmeineke	377	#include "AbstractClasses.hpp"
14			#include "MakeStamps.hpp"
15	mmeineke	670	#include "SimState.hpp"
16	mmeineke	377
17			#define __C
18			#include "fSimulation.h"
19			#include "fortranWrapDefines.hpp"
20	tim	658	#include "GenericData.hpp"
21	tim	1064	//#include "Minimizer.hpp"
22			//#include "OOPSEMinimizer.hpp"
23	tim	1131	double roundMe( double x );
24	tim	1064	class OOPSEMinimizer;
25	mmeineke	377	class SimInfo{
26
27			public:
28
29			SimInfo();
30	tim	660	~SimInfo();
31	mmeineke	377
32			int n_atoms; // the number of atoms
33			Atom **atoms; // the array of atom objects
34	gezelter	1097
35			vector<RigidBody*> rigidBodies; // A vector of rigid bodies
36			vector<StuntDouble*> integrableObjects;
37	mmeineke	377
38			double tau[9]; // the stress tensor
39
40	mmeineke	787	int n_bonds; // number of bends
41			int n_bends; // number of bends
42			int n_torsions; // number of torsions
43			int n_oriented; // number of of atoms with orientation
44			int ndf; // number of actual degrees of freedom
45			int ndfRaw; // number of settable degrees of freedom
46			int ndfTrans; // number of translational degrees of freedom
47			int nZconstraints; // the number of zConstraints
48	mmeineke	377
49	mmeineke	787	int setTemp; // boolean to set the temperature at each sampleTime
50			int resetIntegrator; // boolean to reset the integrator
51	mmeineke	377
52	mmeineke	787	int n_dipoles; // number of dipoles
53	mmeineke	377
54	gezelter	1097	int n_exclude;
55			Exclude* excludes; // the exclude list for ignoring pairs in fortran
56	mmeineke	377	int nGlobalExcludes;
57			int* globalExcludes; // same as above, but these guys participate in
58			// no long range forces.
59
60			int* identArray; // array of unique identifiers for the atoms
61	gezelter	483	int* molMembershipArray; // map of atom numbers onto molecule numbers
62	mmeineke	377
63			int n_constraints; // the number of constraints on the system
64
65	mmeineke	787	int n_SRI; // the number of short range interactions
66	mmeineke	377
67			double lrPot; // the potential energy from the long range calculations.
68
69	gezelter	588	double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the
70			// column vectors of the x, y, and z box vectors.
71			// h1 h2 h3
72			// [ Xx Yx Zx ]
73			// [ Xy Yy Zy ]
74			// [ Xz Yz Zz ]
75			//
76			double HmatInv[3][3];
77	mmeineke	568
78	gezelter	621	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
79	mmeineke	572	double boxVol;
80			int orthoRhombic;
81	mmeineke	568
82
83	mmeineke	626	double dielectric; // the dielectric of the medium for reaction field
84	mmeineke	568
85	mmeineke	377
86			int usePBC; // whether we use periodic boundry conditions.
87			int useLJ;
88			int useSticky;
89	gezelter	941	int useCharges;
90			int useDipoles;
91	mmeineke	377	int useReactionField;
92			int useGB;
93			int useEAM;
94	gezelter	1139	int useMolecularCutoffs;
95	mmeineke	377
96	mmeineke	855	bool useInitXSstate;
97			double orthoTolerance;
98	mmeineke	377
99			double dt, run_time; // the time step and total time
100			double sampleTime, statusTime; // the position and energy dump frequencies
101			double target_temp; // the target temperature of the system
102			double thermalTime; // the temp kick interval
103	gezelter	637	double currentTime; // Used primarily for correlation Functions
104	mmeineke	746	double resetTime; // Use to reset the integrator periodically
105	mmeineke	377
106			int n_mol; // n_molecules;
107			Molecule* molecules; // the array of molecules
108
109	mmeineke	823	int nComponents; // the number of components in the system
110	mmeineke	377	int* componentsNmol; // the number of molecules of each component
111			MoleculeStamp** compStamps;// the stamps matching the components
112			LinkedMolStamp* headStamp; // list of stamps used in the simulation
113
114
115			char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
116			char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
117	mmeineke	542	BaseIntegrator *the_integrator; // the integrator of the simulation
118	mmeineke	377
119	tim	1064	OOPSEMinimizer* the_minimizer; // the energy minimizer
120	tim	1031	bool has_minimizer;
121
122	mmeineke	377	char finalName[300]; // the name of the eor file to be written
123			char sampleName[300]; // the name of the dump file to be written
124			char statusName[300]; // the name of the stat file to be written
125
126	tim	708	int seed; //seed for random number generator
127	tim	1144
128
129			vector<double> mfact;
130			int ngroup;
131			vector<int> groupList;
132			vector<int> groupStart;
133
134	mmeineke	377	// refreshes the sim if things get changed (load balanceing, volume
135			// adjustment, etc.)
136
137			void refreshSim( void );
138
139
140			// sets the internal function pointer to fortran.
141
142	mmeineke	836	void setInternal( setFortranSim_TD fSetup,
143			setFortranBox_TD fBox,
144			notifyFortranCutOff_TD fCut){
145	mmeineke	377	setFsimulation = fSetup;
146			setFortranBoxSize = fBox;
147	mmeineke	626	notifyFortranCutOffs = fCut;
148	mmeineke	377	}
149
150	gezelter	458	int getNDF();
151			int getNDFraw();
152	tim	767	int getNDFtranslational();
153	tim	1108	int getTotIntegrableObjects();
154	gezelter	457	void setBox( double newBox[3] );
155	gezelter	588	void setBoxM( double newBox[3][3] );
156			void getBoxM( double theBox[3][3] );
157	gezelter	574	void scaleBox( double scale );
158	mmeineke	626
159	mmeineke	841	void setDefaultRcut( double theRcut );
160			void setDefaultEcr( double theEcr );
161			void setDefaultEcr( double theEcr, double theEst );
162	gezelter	845	void checkCutOffs( void );
163	gezelter	457
164	mmeineke	626	double getRcut( void ) { return rCut; }
165			double getRlist( void ) { return rList; }
166			double getEcr( void ) { return ecr; }
167			double getEst( void ) { return est; }
168	mmeineke	797	double getMaxCutoff( void ) { return maxCutoff; }
169	mmeineke	626
170	mmeineke	644	void setTime( double theTime ) { currentTime = theTime; }
171	mmeineke	790	void incrTime( double the_dt ) { currentTime += the_dt; }
172			void decrTime( double the_dt ) { currentTime -= the_dt; }
173	mmeineke	644	double getTime( void ) { return currentTime; }
174	mmeineke	626
175	mmeineke	568	void wrapVector( double thePos[3] );
176
177	mmeineke	670	SimState* getConfiguration( void ) { return myConfiguration; }
178	gezelter	588
179	tim	658	void addProperty(GenericData* prop);
180			GenericData* getProperty(const string& propName);
181	tim	1118	//vector<GenericData*>& getProperties() {return properties;}
182	mmeineke	670
183	tim	708	int getSeed(void) { return seed; }
184			void setSeed(int theSeed) { seed = theSeed;}
185
186	mmeineke	377	private:
187	mmeineke	626
188	mmeineke	670	SimState* myConfiguration;
189
190	mmeineke	859	int boxIsInit, haveRcut, haveEcr;
191	mmeineke	626
192			double rList, rCut; // variables for the neighborlist
193			double ecr; // the electrostatic cutoff radius
194			double est; // the electrostatic skin thickness
195			double maxCutoff;
196	tim	781
197			double distXY;
198			double distYZ;
199			double distZX;
200	mmeineke	377
201	gezelter	588	void calcHmatInv( void );
202	mmeineke	568	void calcBoxL();
203	tim	781	double calcMaxCutOff();
204	mmeineke	568
205	mmeineke	377	// private function to initialize the fortran side of the simulation
206	mmeineke	836	setFortranSim_TD setFsimulation;
207	mmeineke	377
208	mmeineke	836	setFortranBox_TD setFortranBoxSize;
209	mmeineke	626
210	mmeineke	836	notifyFortranCutOff_TD notifyFortranCutOffs;
211	tim	658
212			//Addtional Properties of SimInfo
213			map<string, GenericData*> properties;
214	mmeineke	626
215	mmeineke	377	};
216
217	tim	1144	void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
218			vector<int>& groupList, vector<int>& groupStart);
219
220	mmeineke	377	#endif