src/brains/SimInfo.hpp

#ifndef __SIMINFO_H__
#define __SIMINFO_H__

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

#include "primitives/Atom.hpp"
#include "primitives/RigidBody.hpp"
#include "primitives/Molecule.hpp"
#include "brains/Exclude.hpp"
#include "brains/SkipList.hpp"
#include "primitives/AbstractClasses.hpp"
#include "types/MakeStamps.hpp"
#include "brains/SimState.hpp"
#include "restraints/Restraints.hpp"

#define __C
#include "brains/fSimulation.h"
#include "utils/GenericData.hpp"


//#include "Minimizer.hpp"
//#include "minimizers/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 useDirectionalAtoms;
  int useLennardJones; 
  int useElectrostatics;
  int useCharges;
  int useDipoles;
  int useSticky;
  int useGayBerne;
  int useEAM;
  int useShapes;
  int useFLARB;
  int useReactionField;
  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
  string zAngleName; // the name of the ang 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.


  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();

  
  //Addtional Properties of SimInfo
  map<string, GenericData*> properties;
  void getFortranGroupArrays(SimInfo* info, 
                             vector<int>& FglobalGroupMembership,
                             vector<double>& mfact);


};


#endif
Revision:	1772
Committed:	Tue Nov 23 22:48:31 2004 UTC (19 years, 7 months ago) by chrisfen
File size:	6819 byte(s)
Log Message:	Improvements to restraints
#	User	Rev	Content
1	gezelter	1490	#ifndef __SIMINFO_H__
2			#define __SIMINFO_H__
3
4			#include <map>
5			#include <string>
6			#include <vector>
7
8	tim	1492	#include "primitives/Atom.hpp"
9			#include "primitives/RigidBody.hpp"
10			#include "primitives/Molecule.hpp"
11			#include "brains/Exclude.hpp"
12			#include "brains/SkipList.hpp"
13			#include "primitives/AbstractClasses.hpp"
14			#include "types/MakeStamps.hpp"
15			#include "brains/SimState.hpp"
16			#include "restraints/Restraints.hpp"
17	gezelter	1490
18			#define __C
19	tim	1492	#include "brains/fSimulation.h"
20			#include "utils/GenericData.hpp"
21	gezelter	1490
22
23			//#include "Minimizer.hpp"
24	tim	1492	//#include "minimizers/OOPSEMinimizer.hpp"
25	gezelter	1490
26
27			double roundMe( double x );
28			class OOPSEMinimizer;
29			class SimInfo{
30
31			public:
32
33			SimInfo();
34			~SimInfo();
35
36			int n_atoms; // the number of atoms
37			Atom **atoms; // the array of atom objects
38
39			vector<RigidBody*> rigidBodies; // A vector of rigid bodies
40			vector<StuntDouble*> integrableObjects;
41
42			double tau[9]; // the stress tensor
43
44			int n_bonds; // number of bends
45			int n_bends; // number of bends
46			int n_torsions; // number of torsions
47			int n_oriented; // number of of atoms with orientation
48			int ndf; // number of actual degrees of freedom
49			int ndfRaw; // number of settable degrees of freedom
50			int ndfTrans; // number of translational degrees of freedom
51			int nZconstraints; // the number of zConstraints
52
53			int setTemp; // boolean to set the temperature at each sampleTime
54			int resetIntegrator; // boolean to reset the integrator
55
56			int n_dipoles; // number of dipoles
57
58			int n_exclude;
59			Exclude* excludes; // the exclude list for ignoring pairs in fortran
60			int nGlobalExcludes;
61			int* globalExcludes; // same as above, but these guys participate in
62			// no long range forces.
63
64			int* identArray; // array of unique identifiers for the atoms
65			int* molMembershipArray; // map of atom numbers onto molecule numbers
66
67			int n_constraints; // the number of constraints on the system
68
69			int n_SRI; // the number of short range interactions
70
71			double lrPot; // the potential energy from the long range calculations.
72
73			double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the
74			// column vectors of the x, y, and z box vectors.
75			// h1 h2 h3
76			// [ Xx Yx Zx ]
77			// [ Xy Yy Zy ]
78			// [ Xz Yz Zz ]
79			//
80			double HmatInv[3][3];
81
82			double boxL[3]; // The Lengths of the 3 column vectors of Hmat
83			double boxVol;
84			int orthoRhombic;
85
86
87			double dielectric; // the dielectric of the medium for reaction field
88
89
90			int usePBC; // whether we use periodic boundry conditions.
91	chrisfen	1636	int useDirectionalAtoms;
92			int useLennardJones;
93			int useElectrostatics;
94	gezelter	1490	int useCharges;
95			int useDipoles;
96	chrisfen	1636	int useSticky;
97			int useGayBerne;
98			int useEAM;
99			int useShapes;
100			int useFLARB;
101	gezelter	1490	int useReactionField;
102			bool haveCutoffGroups;
103			bool useInitXSstate;
104			double orthoTolerance;
105
106			double dt, run_time; // the time step and total time
107			double sampleTime, statusTime; // the position and energy dump frequencies
108			double target_temp; // the target temperature of the system
109			double thermalTime; // the temp kick interval
110			double currentTime; // Used primarily for correlation Functions
111			double resetTime; // Use to reset the integrator periodically
112			short int have_target_temp;
113
114			int n_mol; // n_molecules;
115			Molecule* molecules; // the array of molecules
116
117			int nComponents; // the number of components in the system
118			int* componentsNmol; // the number of molecules of each component
119			MoleculeStamp** compStamps;// the stamps matching the components
120			LinkedMolStamp* headStamp; // list of stamps used in the simulation
121
122
123			char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
124			char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
125			BaseIntegrator *the_integrator; // the integrator of the simulation
126
127			OOPSEMinimizer* the_minimizer; // the energy minimizer
128			Restraints* restraint;
129			bool has_minimizer;
130
131			string finalName; // the name of the eor file to be written
132			string sampleName; // the name of the dump file to be written
133			string statusName; // the name of the stat file to be written
134	chrisfen	1772	string zAngleName; // the name of the ang file to be written
135	gezelter	1490
136			int seed; //seed for random number generator
137
138			int useSolidThermInt; // is solid-state thermodynamic integration being used
139			int useLiquidThermInt; // is liquid thermodynamic integration being used
140			double thermIntLambda; // lambda for TI
141			double thermIntK; // power of lambda for TI
142			double vRaw; // unperturbed potential for TI
143			double vHarm; // harmonic potential for TI
144			int i; // just an int
145
146			vector<double> mfact;
147			vector<int> FglobalGroupMembership;
148			int ngroup;
149			int* globalGroupMembership;
150
151			// refreshes the sim if things get changed (load balanceing, volume
152			// adjustment, etc.)
153
154			void refreshSim( void );
155
156
157			// sets the internal function pointer to fortran.
158
159
160			int getNDF();
161			int getNDFraw();
162			int getNDFtranslational();
163			int getTotIntegrableObjects();
164			void setBox( double newBox[3] );
165			void setBoxM( double newBox[3][3] );
166			void getBoxM( double theBox[3][3] );
167			void scaleBox( double scale );
168
169			void setDefaultRcut( double theRcut );
170			void setDefaultRcut( double theRcut, double theRsw );
171			void checkCutOffs( void );
172
173			double getRcut( void ) { return rCut; }
174			double getRlist( void ) { return rList; }
175			double getRsw( void ) { return rSw; }
176			double getMaxCutoff( void ) { return maxCutoff; }
177
178			void setTime( double theTime ) { currentTime = theTime; }
179			void incrTime( double the_dt ) { currentTime += the_dt; }
180			void decrTime( double the_dt ) { currentTime -= the_dt; }
181			double getTime( void ) { return currentTime; }
182
183			void wrapVector( double thePos[3] );
184
185			SimState* getConfiguration( void ) { return myConfiguration; }
186
187			void addProperty(GenericData* prop);
188			GenericData* getProperty(const string& propName);
189			//vector<GenericData*>& getProperties() {return properties;}
190
191			int getSeed(void) { return seed; }
192			void setSeed(int theSeed) { seed = theSeed;}
193
194			private:
195
196			SimState* myConfiguration;
197
198			int boxIsInit, haveRcut, haveRsw;
199
200			double rList, rCut; // variables for the neighborlist
201			double rSw; // the switching radius
202
203			double maxCutoff;
204
205			double distXY;
206			double distYZ;
207			double distZX;
208
209			void calcHmatInv( void );
210			void calcBoxL();
211			double calcMaxCutOff();
212
213
214			//Addtional Properties of SimInfo
215			map<string, GenericData*> properties;
216			void getFortranGroupArrays(SimInfo* info,
217			vector<int>& FglobalGroupMembership,
218			vector<double>& mfact);
219
220
221			};
222
223
224			#endif