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"
#include "Restraints.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 ConstraintManager;
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;
  bool haveCutoffGroups;
  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
  Restraints* restraint;
  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
  char rawPotName[300];  // the name of the raw file to be written

  int seed;                    //seed for random number generator

  int useSolidThermInt;  // is solid-state thermodynamic integration being used
  int useLiquidThermInt; // is liquid thermodynamic integration being used
  double thermIntLambda; // lambda for TI
  double thermIntK;      // power of lambda for TI
  double vRaw;           // unperturbed potential for TI
  double vHarm;          // harmonic potential for TI
  int i;                 // just an int

  vector<double> mfact;
  vector<int> FglobalGroupMembership;
  int ngroup;
  int* globalGroupMembership;

  ConstraintManager* consMan; //constraint manager  holding the constraint pairs
  
  // 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 setDefaultRcut( double theRcut, double theRsw );
  void checkCutOffs( void );

  double getRcut( void )  { return rCut; }
  double getRlist( void ) { return rList; }
  double getRsw( void )   { return rSw; }
  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, haveRsw;

  double rList, rCut; // variables for the neighborlist
  double rSw;         // the switching radius

  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 getFortranGroupArrays(SimInfo* info, 
                             vector<int>& FglobalGroupMembership,
                             vector<double>& mfact);


};


#endif
Revision:	1234
Committed:	Fri Jun 4 03:15:31 2004 UTC (20 years, 1 month ago) by tim
File size:	7139 byte(s)
Log Message:	new rattle algorithm is working
#	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	chrisfen	1180	#include "Restraints.hpp"
17	mmeineke	377
18			#define __C
19			#include "fSimulation.h"
20			#include "fortranWrapDefines.hpp"
21	tim	658	#include "GenericData.hpp"
22	tim	1234
23
24	tim	1064	//#include "Minimizer.hpp"
25			//#include "OOPSEMinimizer.hpp"
26	chrisfen	1180
27
28	tim	1131	double roundMe( double x );
29	tim	1064	class OOPSEMinimizer;
30	tim	1234	class ConstraintManager;
31	mmeineke	377	class SimInfo{
32
33			public:
34
35			SimInfo();
36	tim	660	~SimInfo();
37	mmeineke	377
38			int n_atoms; // the number of atoms
39			Atom **atoms; // the array of atom objects
40	gezelter	1097
41			vector<RigidBody*> rigidBodies; // A vector of rigid bodies
42			vector<StuntDouble*> integrableObjects;
43	mmeineke	377
44			double tau[9]; // the stress tensor
45
46	mmeineke	787	int n_bonds; // number of bends
47			int n_bends; // number of bends
48			int n_torsions; // number of torsions
49			int n_oriented; // number of of atoms with orientation
50			int ndf; // number of actual degrees of freedom
51			int ndfRaw; // number of settable degrees of freedom
52			int ndfTrans; // number of translational degrees of freedom
53			int nZconstraints; // the number of zConstraints
54	mmeineke	377
55	mmeineke	787	int setTemp; // boolean to set the temperature at each sampleTime
56			int resetIntegrator; // boolean to reset the integrator
57	mmeineke	377
58	mmeineke	787	int n_dipoles; // number of dipoles
59	mmeineke	377
60	gezelter	1097	int n_exclude;
61			Exclude* excludes; // the exclude list for ignoring pairs in fortran
62	mmeineke	377	int nGlobalExcludes;
63			int* globalExcludes; // same as above, but these guys participate in
64			// no long range forces.
65
66			int* identArray; // array of unique identifiers for the atoms
67	gezelter	483	int* molMembershipArray; // map of atom numbers onto molecule numbers
68	mmeineke	377
69			int n_constraints; // the number of constraints on the system
70
71	mmeineke	787	int n_SRI; // the number of short range interactions
72	mmeineke	377
73			double lrPot; // the potential energy from the long range calculations.
74
75	gezelter	588	double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the
76			// column vectors of the x, y, and z box vectors.
77			// h1 h2 h3
78			// [ Xx Yx Zx ]
79			// [ Xy Yy Zy ]
80			// [ Xz Yz Zz ]
81			//
82			double HmatInv[3][3];
83	mmeineke	568
84	gezelter	621	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
85	mmeineke	572	double boxVol;
86			int orthoRhombic;
87	mmeineke	568
88
89	mmeineke	626	double dielectric; // the dielectric of the medium for reaction field
90	mmeineke	568
91	mmeineke	377
92			int usePBC; // whether we use periodic boundry conditions.
93			int useLJ;
94			int useSticky;
95	gezelter	941	int useCharges;
96			int useDipoles;
97	mmeineke	377	int useReactionField;
98			int useGB;
99			int useEAM;
100	tim	1157	bool haveCutoffGroups;
101	mmeineke	855	bool useInitXSstate;
102			double orthoTolerance;
103	mmeineke	377
104			double dt, run_time; // the time step and total time
105			double sampleTime, statusTime; // the position and energy dump frequencies
106			double target_temp; // the target temperature of the system
107			double thermalTime; // the temp kick interval
108	gezelter	637	double currentTime; // Used primarily for correlation Functions
109	mmeineke	746	double resetTime; // Use to reset the integrator periodically
110	mmeineke	377
111			int n_mol; // n_molecules;
112			Molecule* molecules; // the array of molecules
113
114	mmeineke	823	int nComponents; // the number of components in the system
115	mmeineke	377	int* componentsNmol; // the number of molecules of each component
116			MoleculeStamp** compStamps;// the stamps matching the components
117			LinkedMolStamp* headStamp; // list of stamps used in the simulation
118
119
120			char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
121			char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
122	mmeineke	542	BaseIntegrator *the_integrator; // the integrator of the simulation
123	mmeineke	377
124	tim	1064	OOPSEMinimizer* the_minimizer; // the energy minimizer
125	chrisfen	1180	Restraints* restraint;
126	tim	1031	bool has_minimizer;
127
128	mmeineke	377	char finalName[300]; // the name of the eor file to be written
129			char sampleName[300]; // the name of the dump file to be written
130			char statusName[300]; // the name of the stat file to be written
131	chrisfen	1180	char rawPotName[300]; // the name of the raw file to be written
132	mmeineke	377
133	tim	708	int seed; //seed for random number generator
134	tim	1144
135	chrisfen	1212	int useSolidThermInt; // is solid-state thermodynamic integration being used
136			int useLiquidThermInt; // is liquid thermodynamic integration being used
137	chrisfen	1187	double thermIntLambda; // lambda for TI
138			double thermIntK; // power of lambda for TI
139			double vRaw; // unperturbed potential for TI
140			double vHarm; // harmonic potential for TI
141			int i; // just an int
142	tim	1144
143			vector<double> mfact;
144	gezelter	1214	vector<int> FglobalGroupMembership;
145	tim	1144	int ngroup;
146	gezelter	1214	int* globalGroupMembership;
147	tim	1234
148			ConstraintManager* consMan; //constraint manager holding the constraint pairs
149	tim	1144
150	mmeineke	377	// refreshes the sim if things get changed (load balanceing, volume
151			// adjustment, etc.)
152
153			void refreshSim( void );
154
155
156			// sets the internal function pointer to fortran.
157
158	mmeineke	836	void setInternal( setFortranSim_TD fSetup,
159			setFortranBox_TD fBox,
160			notifyFortranCutOff_TD fCut){
161	mmeineke	377	setFsimulation = fSetup;
162			setFortranBoxSize = fBox;
163	mmeineke	626	notifyFortranCutOffs = fCut;
164	mmeineke	377	}
165
166	gezelter	458	int getNDF();
167			int getNDFraw();
168	tim	767	int getNDFtranslational();
169	tim	1108	int getTotIntegrableObjects();
170	gezelter	457	void setBox( double newBox[3] );
171	gezelter	588	void setBoxM( double newBox[3][3] );
172			void getBoxM( double theBox[3][3] );
173	gezelter	574	void scaleBox( double scale );
174	mmeineke	626
175	mmeineke	841	void setDefaultRcut( double theRcut );
176	gezelter	1154	void setDefaultRcut( double theRcut, double theRsw );
177	gezelter	845	void checkCutOffs( void );
178	gezelter	457
179	mmeineke	626	double getRcut( void ) { return rCut; }
180			double getRlist( void ) { return rList; }
181	gezelter	1154	double getRsw( void ) { return rSw; }
182	mmeineke	797	double getMaxCutoff( void ) { return maxCutoff; }
183	gezelter	1154
184	mmeineke	644	void setTime( double theTime ) { currentTime = theTime; }
185	mmeineke	790	void incrTime( double the_dt ) { currentTime += the_dt; }
186			void decrTime( double the_dt ) { currentTime -= the_dt; }
187	mmeineke	644	double getTime( void ) { return currentTime; }
188	mmeineke	626
189	mmeineke	568	void wrapVector( double thePos[3] );
190
191	mmeineke	670	SimState* getConfiguration( void ) { return myConfiguration; }
192	gezelter	588
193	tim	658	void addProperty(GenericData* prop);
194			GenericData* getProperty(const string& propName);
195	tim	1118	//vector<GenericData*>& getProperties() {return properties;}
196	mmeineke	670
197	tim	708	int getSeed(void) { return seed; }
198			void setSeed(int theSeed) { seed = theSeed;}
199
200	mmeineke	377	private:
201	mmeineke	626
202	mmeineke	670	SimState* myConfiguration;
203
204	gezelter	1154	int boxIsInit, haveRcut, haveRsw;
205	mmeineke	626
206			double rList, rCut; // variables for the neighborlist
207	gezelter	1154	double rSw; // the switching radius
208
209	mmeineke	626	double maxCutoff;
210	tim	781
211			double distXY;
212			double distYZ;
213			double distZX;
214	mmeineke	377
215	gezelter	588	void calcHmatInv( void );
216	mmeineke	568	void calcBoxL();
217	tim	781	double calcMaxCutOff();
218	mmeineke	568
219	mmeineke	377	// private function to initialize the fortran side of the simulation
220	mmeineke	836	setFortranSim_TD setFsimulation;
221	mmeineke	377
222	mmeineke	836	setFortranBox_TD setFortranBoxSize;
223	mmeineke	626
224	mmeineke	836	notifyFortranCutOff_TD notifyFortranCutOffs;
225	tim	658
226			//Addtional Properties of SimInfo
227			map<string, GenericData*> properties;
228	gezelter	1214	void getFortranGroupArrays(SimInfo* info,
229			vector<int>& FglobalGroupMembership,
230			vector<double>& mfact);
231	mmeineke	626
232	gezelter	1214
233	mmeineke	377	};
234
235	tim	1144
236	mmeineke	377	#endif