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 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 useThermInt;        // whether or not we use thermodynamic integration
  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;
  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 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 getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
                                                          vector<int>& groupList, vector<int>& groupStart);

#endif
Revision:	1187
Committed:	Sat May 22 18:16:18 2004 UTC (20 years, 1 month ago) by chrisfen
File size:	6955 byte(s)
Log Message:	Fixed Thermodynamic integration code.
#	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	1064	//#include "Minimizer.hpp"
23			//#include "OOPSEMinimizer.hpp"
24	chrisfen	1180
25
26	tim	1131	double roundMe( double x );
27	tim	1064	class OOPSEMinimizer;
28	mmeineke	377	class SimInfo{
29
30			public:
31
32			SimInfo();
33	tim	660	~SimInfo();
34	mmeineke	377
35			int n_atoms; // the number of atoms
36			Atom **atoms; // the array of atom objects
37	gezelter	1097
38			vector<RigidBody*> rigidBodies; // A vector of rigid bodies
39			vector<StuntDouble*> integrableObjects;
40	mmeineke	377
41			double tau[9]; // the stress tensor
42
43	mmeineke	787	int n_bonds; // number of bends
44			int n_bends; // number of bends
45			int n_torsions; // number of torsions
46			int n_oriented; // number of of atoms with orientation
47			int ndf; // number of actual degrees of freedom
48			int ndfRaw; // number of settable degrees of freedom
49			int ndfTrans; // number of translational degrees of freedom
50			int nZconstraints; // the number of zConstraints
51	mmeineke	377
52	mmeineke	787	int setTemp; // boolean to set the temperature at each sampleTime
53			int resetIntegrator; // boolean to reset the integrator
54	mmeineke	377
55	mmeineke	787	int n_dipoles; // number of dipoles
56	mmeineke	377
57	gezelter	1097	int n_exclude;
58			Exclude* excludes; // the exclude list for ignoring pairs in fortran
59	mmeineke	377	int nGlobalExcludes;
60			int* globalExcludes; // same as above, but these guys participate in
61			// no long range forces.
62
63			int* identArray; // array of unique identifiers for the atoms
64	gezelter	483	int* molMembershipArray; // map of atom numbers onto molecule numbers
65	mmeineke	377
66			int n_constraints; // the number of constraints on the system
67
68	mmeineke	787	int n_SRI; // the number of short range interactions
69	mmeineke	377
70			double lrPot; // the potential energy from the long range calculations.
71
72	gezelter	588	double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the
73			// column vectors of the x, y, and z box vectors.
74			// h1 h2 h3
75			// [ Xx Yx Zx ]
76			// [ Xy Yy Zy ]
77			// [ Xz Yz Zz ]
78			//
79			double HmatInv[3][3];
80	mmeineke	568
81	gezelter	621	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
82	mmeineke	572	double boxVol;
83			int orthoRhombic;
84	mmeineke	568
85
86	mmeineke	626	double dielectric; // the dielectric of the medium for reaction field
87	mmeineke	568
88	mmeineke	377
89			int usePBC; // whether we use periodic boundry conditions.
90			int useLJ;
91			int useSticky;
92	gezelter	941	int useCharges;
93			int useDipoles;
94	mmeineke	377	int useReactionField;
95			int useGB;
96			int useEAM;
97	tim	1157	bool haveCutoffGroups;
98	mmeineke	855	bool useInitXSstate;
99			double orthoTolerance;
100	mmeineke	377
101			double dt, run_time; // the time step and total time
102			double sampleTime, statusTime; // the position and energy dump frequencies
103			double target_temp; // the target temperature of the system
104			double thermalTime; // the temp kick interval
105	gezelter	637	double currentTime; // Used primarily for correlation Functions
106	mmeineke	746	double resetTime; // Use to reset the integrator periodically
107	mmeineke	377
108			int n_mol; // n_molecules;
109			Molecule* molecules; // the array of molecules
110
111	mmeineke	823	int nComponents; // the number of components in the system
112	mmeineke	377	int* componentsNmol; // the number of molecules of each component
113			MoleculeStamp** compStamps;// the stamps matching the components
114			LinkedMolStamp* headStamp; // list of stamps used in the simulation
115
116
117			char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
118			char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
119	mmeineke	542	BaseIntegrator *the_integrator; // the integrator of the simulation
120	mmeineke	377
121	tim	1064	OOPSEMinimizer* the_minimizer; // the energy minimizer
122	chrisfen	1180	Restraints* restraint;
123	tim	1031	bool has_minimizer;
124
125	mmeineke	377	char finalName[300]; // the name of the eor file to be written
126			char sampleName[300]; // the name of the dump file to be written
127			char statusName[300]; // the name of the stat file to be written
128	chrisfen	1180	char rawPotName[300]; // the name of the raw file to be written
129	mmeineke	377
130	tim	708	int seed; //seed for random number generator
131	tim	1144
132	chrisfen	1187	int useThermInt; // whether or not we use thermodynamic integration
133			double thermIntLambda; // lambda for TI
134			double thermIntK; // power of lambda for TI
135			double vRaw; // unperturbed potential for TI
136			double vHarm; // harmonic potential for TI
137			int i; // just an int
138	tim	1144
139			vector<double> mfact;
140			int ngroup;
141			vector<int> groupList;
142			vector<int> groupStart;
143
144	mmeineke	377	// refreshes the sim if things get changed (load balanceing, volume
145			// adjustment, etc.)
146
147			void refreshSim( void );
148
149
150			// sets the internal function pointer to fortran.
151
152	mmeineke	836	void setInternal( setFortranSim_TD fSetup,
153			setFortranBox_TD fBox,
154			notifyFortranCutOff_TD fCut){
155	mmeineke	377	setFsimulation = fSetup;
156			setFortranBoxSize = fBox;
157	mmeineke	626	notifyFortranCutOffs = fCut;
158	mmeineke	377	}
159
160	gezelter	458	int getNDF();
161			int getNDFraw();
162	tim	767	int getNDFtranslational();
163	tim	1108	int getTotIntegrableObjects();
164	gezelter	457	void setBox( double newBox[3] );
165	gezelter	588	void setBoxM( double newBox[3][3] );
166			void getBoxM( double theBox[3][3] );
167	gezelter	574	void scaleBox( double scale );
168	mmeineke	626
169	mmeineke	841	void setDefaultRcut( double theRcut );
170	gezelter	1154	void setDefaultRcut( double theRcut, double theRsw );
171	gezelter	845	void checkCutOffs( void );
172	gezelter	457
173	mmeineke	626	double getRcut( void ) { return rCut; }
174			double getRlist( void ) { return rList; }
175	gezelter	1154	double getRsw( void ) { return rSw; }
176	mmeineke	797	double getMaxCutoff( void ) { return maxCutoff; }
177	gezelter	1154
178	mmeineke	644	void setTime( double theTime ) { currentTime = theTime; }
179	mmeineke	790	void incrTime( double the_dt ) { currentTime += the_dt; }
180			void decrTime( double the_dt ) { currentTime -= the_dt; }
181	mmeineke	644	double getTime( void ) { return currentTime; }
182	mmeineke	626
183	mmeineke	568	void wrapVector( double thePos[3] );
184
185	mmeineke	670	SimState* getConfiguration( void ) { return myConfiguration; }
186	gezelter	588
187	tim	658	void addProperty(GenericData* prop);
188			GenericData* getProperty(const string& propName);
189	tim	1118	//vector<GenericData*>& getProperties() {return properties;}
190	mmeineke	670
191	tim	708	int getSeed(void) { return seed; }
192			void setSeed(int theSeed) { seed = theSeed;}
193
194	mmeineke	377	private:
195	mmeineke	626
196	mmeineke	670	SimState* myConfiguration;
197
198	gezelter	1154	int boxIsInit, haveRcut, haveRsw;
199	mmeineke	626
200			double rList, rCut; // variables for the neighborlist
201	gezelter	1154	double rSw; // the switching radius
202
203	mmeineke	626	double maxCutoff;
204	tim	781
205			double distXY;
206			double distYZ;
207			double distZX;
208	mmeineke	377
209	gezelter	588	void calcHmatInv( void );
210	mmeineke	568	void calcBoxL();
211	tim	781	double calcMaxCutOff();
212	mmeineke	568
213	mmeineke	377	// private function to initialize the fortran side of the simulation
214	mmeineke	836	setFortranSim_TD setFsimulation;
215	mmeineke	377
216	mmeineke	836	setFortranBox_TD setFortranBoxSize;
217	mmeineke	626
218	mmeineke	836	notifyFortranCutOff_TD notifyFortranCutOffs;
219	tim	658
220			//Addtional Properties of SimInfo
221			map<string, GenericData*> properties;
222	mmeineke	626
223	mmeineke	377	};
224
225	tim	1144	void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
226			vector<int>& groupList, vector<int>& groupStart);
227
228	mmeineke	377	#endif