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

  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:	1636
Committed:	Fri Oct 22 22:54:01 2004 UTC (19 years, 8 months ago) by chrisfen
File size:	6756 byte(s)
Log Message:	fixey fixey the breakey breakey
#	Content
1	#ifndef __SIMINFO_H__
2	#define __SIMINFO_H__
3
4	#include <map>
5	#include <string>
6	#include <vector>
7
8	#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
18	#define __C
19	#include "brains/fSimulation.h"
20	#include "utils/GenericData.hpp"
21
22
23	//#include "Minimizer.hpp"
24	//#include "minimizers/OOPSEMinimizer.hpp"
25
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	int useDirectionalAtoms;
92	int useLennardJones;
93	int useElectrostatics;
94	int useCharges;
95	int useDipoles;
96	int useSticky;
97	int useGayBerne;
98	int useEAM;
99	int useShapes;
100	int useFLARB;
101	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
135	int seed; //seed for random number generator
136
137	int useSolidThermInt; // is solid-state thermodynamic integration being used
138	int useLiquidThermInt; // is liquid thermodynamic integration being used
139	double thermIntLambda; // lambda for TI
140	double thermIntK; // power of lambda for TI
141	double vRaw; // unperturbed potential for TI
142	double vHarm; // harmonic potential for TI
143	int i; // just an int
144
145	vector<double> mfact;
146	vector<int> FglobalGroupMembership;
147	int ngroup;
148	int* globalGroupMembership;
149
150	// 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
159	int getNDF();
160	int getNDFraw();
161	int getNDFtranslational();
162	int getTotIntegrableObjects();
163	void setBox( double newBox[3] );
164	void setBoxM( double newBox[3][3] );
165	void getBoxM( double theBox[3][3] );
166	void scaleBox( double scale );
167
168	void setDefaultRcut( double theRcut );
169	void setDefaultRcut( double theRcut, double theRsw );
170	void checkCutOffs( void );
171
172	double getRcut( void ) { return rCut; }
173	double getRlist( void ) { return rList; }
174	double getRsw( void ) { return rSw; }
175	double getMaxCutoff( void ) { return maxCutoff; }
176
177	void setTime( double theTime ) { currentTime = theTime; }
178	void incrTime( double the_dt ) { currentTime += the_dt; }
179	void decrTime( double the_dt ) { currentTime -= the_dt; }
180	double getTime( void ) { return currentTime; }
181
182	void wrapVector( double thePos[3] );
183
184	SimState* getConfiguration( void ) { return myConfiguration; }
185
186	void addProperty(GenericData* prop);
187	GenericData* getProperty(const string& propName);
188	//vector<GenericData*>& getProperties() {return properties;}
189
190	int getSeed(void) { return seed; }
191	void setSeed(int theSeed) { seed = theSeed;}
192
193	private:
194
195	SimState* myConfiguration;
196
197	int boxIsInit, haveRcut, haveRsw;
198
199	double rList, rCut; // variables for the neighborlist
200	double rSw; // the switching radius
201
202	double maxCutoff;
203
204	double distXY;
205	double distYZ;
206	double distZX;
207
208	void calcHmatInv( void );
209	void calcBoxL();
210	double calcMaxCutOff();
211
212
213	//Addtional Properties of SimInfo
214	map<string, GenericData*> properties;
215	void getFortranGroupArrays(SimInfo* info,
216	vector<int>& FglobalGroupMembership,
217	vector<double>& mfact);
218
219
220	};
221
222
223	#endif