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
  // 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;

};

#endif
Revision:	1139
Committed:	Wed Apr 28 22:06:29 2004 UTC (20 years, 2 months ago) by gezelter
File size:	6392 byte(s)
Log Message:	Adding molecular cutoffs
#	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 "RigidBody.hpp"
10	#include "Molecule.hpp"
11	#include "Exclude.hpp"
12	#include "SkipList.hpp"
13	#include "AbstractClasses.hpp"
14	#include "MakeStamps.hpp"
15	#include "SimState.hpp"
16
17	#define __C
18	#include "fSimulation.h"
19	#include "fortranWrapDefines.hpp"
20	#include "GenericData.hpp"
21	//#include "Minimizer.hpp"
22	//#include "OOPSEMinimizer.hpp"
23	double roundMe( double x );
24	class OOPSEMinimizer;
25	class SimInfo{
26
27	public:
28
29	SimInfo();
30	~SimInfo();
31
32	int n_atoms; // the number of atoms
33	Atom **atoms; // the array of atom objects
34
35	vector<RigidBody*> rigidBodies; // A vector of rigid bodies
36	vector<StuntDouble*> integrableObjects;
37
38	double tau[9]; // the stress tensor
39
40	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
49	int setTemp; // boolean to set the temperature at each sampleTime
50	int resetIntegrator; // boolean to reset the integrator
51
52	int n_dipoles; // number of dipoles
53
54	int n_exclude;
55	Exclude* excludes; // the exclude list for ignoring pairs in fortran
56	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	int* molMembershipArray; // map of atom numbers onto molecule numbers
62
63	int n_constraints; // the number of constraints on the system
64
65	int n_SRI; // the number of short range interactions
66
67	double lrPot; // the potential energy from the long range calculations.
68
69	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
78	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
79	double boxVol;
80	int orthoRhombic;
81
82
83	double dielectric; // the dielectric of the medium for reaction field
84
85
86	int usePBC; // whether we use periodic boundry conditions.
87	int useLJ;
88	int useSticky;
89	int useCharges;
90	int useDipoles;
91	int useReactionField;
92	int useGB;
93	int useEAM;
94	int useMolecularCutoffs;
95
96	bool useInitXSstate;
97	double orthoTolerance;
98
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	double currentTime; // Used primarily for correlation Functions
104	double resetTime; // Use to reset the integrator periodically
105
106	int n_mol; // n_molecules;
107	Molecule* molecules; // the array of molecules
108
109	int nComponents; // the number of components in the system
110	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	BaseIntegrator *the_integrator; // the integrator of the simulation
118
119	OOPSEMinimizer* the_minimizer; // the energy minimizer
120	bool has_minimizer;
121
122	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	int seed; //seed for random number generator
127	// refreshes the sim if things get changed (load balanceing, volume
128	// adjustment, etc.)
129
130	void refreshSim( void );
131
132
133	// sets the internal function pointer to fortran.
134
135	void setInternal( setFortranSim_TD fSetup,
136	setFortranBox_TD fBox,
137	notifyFortranCutOff_TD fCut){
138	setFsimulation = fSetup;
139	setFortranBoxSize = fBox;
140	notifyFortranCutOffs = fCut;
141	}
142
143	int getNDF();
144	int getNDFraw();
145	int getNDFtranslational();
146	int getTotIntegrableObjects();
147	void setBox( double newBox[3] );
148	void setBoxM( double newBox[3][3] );
149	void getBoxM( double theBox[3][3] );
150	void scaleBox( double scale );
151
152	void setDefaultRcut( double theRcut );
153	void setDefaultEcr( double theEcr );
154	void setDefaultEcr( double theEcr, double theEst );
155	void checkCutOffs( void );
156
157	double getRcut( void ) { return rCut; }
158	double getRlist( void ) { return rList; }
159	double getEcr( void ) { return ecr; }
160	double getEst( void ) { return est; }
161	double getMaxCutoff( void ) { return maxCutoff; }
162
163	void setTime( double theTime ) { currentTime = theTime; }
164	void incrTime( double the_dt ) { currentTime += the_dt; }
165	void decrTime( double the_dt ) { currentTime -= the_dt; }
166	double getTime( void ) { return currentTime; }
167
168	void wrapVector( double thePos[3] );
169
170	SimState* getConfiguration( void ) { return myConfiguration; }
171
172	void addProperty(GenericData* prop);
173	GenericData* getProperty(const string& propName);
174	//vector<GenericData*>& getProperties() {return properties;}
175
176	int getSeed(void) { return seed; }
177	void setSeed(int theSeed) { seed = theSeed;}
178
179	private:
180
181	SimState* myConfiguration;
182
183	int boxIsInit, haveRcut, haveEcr;
184
185	double rList, rCut; // variables for the neighborlist
186	double ecr; // the electrostatic cutoff radius
187	double est; // the electrostatic skin thickness
188	double maxCutoff;
189
190	double distXY;
191	double distYZ;
192	double distZX;
193
194	void calcHmatInv( void );
195	void calcBoxL();
196	double calcMaxCutOff();
197
198	// private function to initialize the fortran side of the simulation
199	setFortranSim_TD setFsimulation;
200
201	setFortranBox_TD setFortranBoxSize;
202
203	notifyFortranCutOff_TD notifyFortranCutOffs;
204
205	//Addtional Properties of SimInfo
206	map<string, GenericData*> properties;
207
208	};
209
210	#endif