src/brains/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
  short int have_target_temp;

  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;

  string finalName;  // the name of the eor file to be written
  string sampleName; // the name of the dump file to be written
  string statusName; // the name of the stat 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;

  // 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:	2
Committed:	Fri Sep 24 04:16:43 2004 UTC (20 years, 7 months ago) by gezelter
Original Path:	*trunk/src/brains/SimInfo.hpp*
File size:	6984 byte(s)
Log Message:	Import of OOPSE v. 2.0
#	User	Rev	Content
1	gezelter	2	#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			#include "Restraints.hpp"
17
18			#define __C
19			#include "fSimulation.h"
20			#include "fortranWrapDefines.hpp"
21			#include "GenericData.hpp"
22
23
24			//#include "Minimizer.hpp"
25			//#include "OOPSEMinimizer.hpp"
26
27
28			double roundMe( double x );
29			class OOPSEMinimizer;
30			class SimInfo{
31
32			public:
33
34			SimInfo();
35			~SimInfo();
36
37			int n_atoms; // the number of atoms
38			Atom **atoms; // the array of atom objects
39
40			vector<RigidBody*> rigidBodies; // A vector of rigid bodies
41			vector<StuntDouble*> integrableObjects;
42
43			double tau[9]; // the stress tensor
44
45			int n_bonds; // number of bends
46			int n_bends; // number of bends
47			int n_torsions; // number of torsions
48			int n_oriented; // number of of atoms with orientation
49			int ndf; // number of actual degrees of freedom
50			int ndfRaw; // number of settable degrees of freedom
51			int ndfTrans; // number of translational degrees of freedom
52			int nZconstraints; // the number of zConstraints
53
54			int setTemp; // boolean to set the temperature at each sampleTime
55			int resetIntegrator; // boolean to reset the integrator
56
57			int n_dipoles; // number of dipoles
58
59			int n_exclude;
60			Exclude* excludes; // the exclude list for ignoring pairs in fortran
61			int nGlobalExcludes;
62			int* globalExcludes; // same as above, but these guys participate in
63			// no long range forces.
64
65			int* identArray; // array of unique identifiers for the atoms
66			int* molMembershipArray; // map of atom numbers onto molecule numbers
67
68			int n_constraints; // the number of constraints on the system
69
70			int n_SRI; // the number of short range interactions
71
72			double lrPot; // the potential energy from the long range calculations.
73
74			double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the
75			// column vectors of the x, y, and z box vectors.
76			// h1 h2 h3
77			// [ Xx Yx Zx ]
78			// [ Xy Yy Zy ]
79			// [ Xz Yz Zz ]
80			//
81			double HmatInv[3][3];
82
83			double boxL[3]; // The Lengths of the 3 column vectors of Hmat
84			double boxVol;
85			int orthoRhombic;
86
87
88			double dielectric; // the dielectric of the medium for reaction field
89
90
91			int usePBC; // whether we use periodic boundry conditions.
92			int useLJ;
93			int useSticky;
94			int useCharges;
95			int useDipoles;
96			int useReactionField;
97			int useGB;
98			int useEAM;
99			bool haveCutoffGroups;
100			bool useInitXSstate;
101			double orthoTolerance;
102
103			double dt, run_time; // the time step and total time
104			double sampleTime, statusTime; // the position and energy dump frequencies
105			double target_temp; // the target temperature of the system
106			double thermalTime; // the temp kick interval
107			double currentTime; // Used primarily for correlation Functions
108			double resetTime; // Use to reset the integrator periodically
109			short int have_target_temp;
110
111			int n_mol; // n_molecules;
112			Molecule* molecules; // the array of molecules
113
114			int nComponents; // the number of components in the system
115			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			BaseIntegrator *the_integrator; // the integrator of the simulation
123
124			OOPSEMinimizer* the_minimizer; // the energy minimizer
125			Restraints* restraint;
126			bool has_minimizer;
127
128			string finalName; // the name of the eor file to be written
129			string sampleName; // the name of the dump file to be written
130			string statusName; // the name of the stat file to be written
131
132			int seed; //seed for random number generator
133
134			int useSolidThermInt; // is solid-state thermodynamic integration being used
135			int useLiquidThermInt; // is liquid thermodynamic integration being used
136			double thermIntLambda; // lambda for TI
137			double thermIntK; // power of lambda for TI
138			double vRaw; // unperturbed potential for TI
139			double vHarm; // harmonic potential for TI
140			int i; // just an int
141
142			vector<double> mfact;
143			vector<int> FglobalGroupMembership;
144			int ngroup;
145			int* globalGroupMembership;
146
147			// refreshes the sim if things get changed (load balanceing, volume
148			// adjustment, etc.)
149
150			void refreshSim( void );
151
152
153			// sets the internal function pointer to fortran.
154
155			void setInternal( setFortranSim_TD fSetup,
156			setFortranBox_TD fBox,
157			notifyFortranCutOff_TD fCut){
158			setFsimulation = fSetup;
159			setFortranBoxSize = fBox;
160			notifyFortranCutOffs = fCut;
161			}
162
163			int getNDF();
164			int getNDFraw();
165			int getNDFtranslational();
166			int getTotIntegrableObjects();
167			void setBox( double newBox[3] );
168			void setBoxM( double newBox[3][3] );
169			void getBoxM( double theBox[3][3] );
170			void scaleBox( double scale );
171
172			void setDefaultRcut( double theRcut );
173			void setDefaultRcut( double theRcut, double theRsw );
174			void checkCutOffs( void );
175
176			double getRcut( void ) { return rCut; }
177			double getRlist( void ) { return rList; }
178			double getRsw( void ) { return rSw; }
179			double getMaxCutoff( void ) { return maxCutoff; }
180
181			void setTime( double theTime ) { currentTime = theTime; }
182			void incrTime( double the_dt ) { currentTime += the_dt; }
183			void decrTime( double the_dt ) { currentTime -= the_dt; }
184			double getTime( void ) { return currentTime; }
185
186			void wrapVector( double thePos[3] );
187
188			SimState* getConfiguration( void ) { return myConfiguration; }
189
190			void addProperty(GenericData* prop);
191			GenericData* getProperty(const string& propName);
192			//vector<GenericData*>& getProperties() {return properties;}
193
194			int getSeed(void) { return seed; }
195			void setSeed(int theSeed) { seed = theSeed;}
196
197			private:
198
199			SimState* myConfiguration;
200
201			int boxIsInit, haveRcut, haveRsw;
202
203			double rList, rCut; // variables for the neighborlist
204			double rSw; // the switching radius
205
206			double maxCutoff;
207
208			double distXY;
209			double distYZ;
210			double distZX;
211
212			void calcHmatInv( void );
213			void calcBoxL();
214			double calcMaxCutOff();
215
216			// private function to initialize the fortran side of the simulation
217			setFortranSim_TD setFsimulation;
218
219			setFortranBox_TD setFortranBoxSize;
220
221			notifyFortranCutOff_TD notifyFortranCutOffs;
222
223			//Addtional Properties of SimInfo
224			map<string, GenericData*> properties;
225			void getFortranGroupArrays(SimInfo* info,
226			vector<int>& FglobalGroupMembership,
227			vector<double>& mfact);
228
229
230			};
231
232
233			#endif