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.
#	Content
1	#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	//#include "Minimizer.hpp"
23	//#include "OOPSEMinimizer.hpp"
24
25
26	double roundMe( double x );
27	class OOPSEMinimizer;
28	class SimInfo{
29
30	public:
31
32	SimInfo();
33	~SimInfo();
34
35	int n_atoms; // the number of atoms
36	Atom **atoms; // the array of atom objects
37
38	vector<RigidBody*> rigidBodies; // A vector of rigid bodies
39	vector<StuntDouble*> integrableObjects;
40
41	double tau[9]; // the stress tensor
42
43	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
52	int setTemp; // boolean to set the temperature at each sampleTime
53	int resetIntegrator; // boolean to reset the integrator
54
55	int n_dipoles; // number of dipoles
56
57	int n_exclude;
58	Exclude* excludes; // the exclude list for ignoring pairs in fortran
59	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	int* molMembershipArray; // map of atom numbers onto molecule numbers
65
66	int n_constraints; // the number of constraints on the system
67
68	int n_SRI; // the number of short range interactions
69
70	double lrPot; // the potential energy from the long range calculations.
71
72	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
81	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
82	double boxVol;
83	int orthoRhombic;
84
85
86	double dielectric; // the dielectric of the medium for reaction field
87
88
89	int usePBC; // whether we use periodic boundry conditions.
90	int useLJ;
91	int useSticky;
92	int useCharges;
93	int useDipoles;
94	int useReactionField;
95	int useGB;
96	int useEAM;
97	bool haveCutoffGroups;
98	bool useInitXSstate;
99	double orthoTolerance;
100
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	double currentTime; // Used primarily for correlation Functions
106	double resetTime; // Use to reset the integrator periodically
107
108	int n_mol; // n_molecules;
109	Molecule* molecules; // the array of molecules
110
111	int nComponents; // the number of components in the system
112	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	BaseIntegrator *the_integrator; // the integrator of the simulation
120
121	OOPSEMinimizer* the_minimizer; // the energy minimizer
122	Restraints* restraint;
123	bool has_minimizer;
124
125	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	char rawPotName[300]; // the name of the raw file to be written
129
130	int seed; //seed for random number generator
131
132	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
139	vector<double> mfact;
140	int ngroup;
141	vector<int> groupList;
142	vector<int> groupStart;
143
144	// 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	void setInternal( setFortranSim_TD fSetup,
153	setFortranBox_TD fBox,
154	notifyFortranCutOff_TD fCut){
155	setFsimulation = fSetup;
156	setFortranBoxSize = fBox;
157	notifyFortranCutOffs = fCut;
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	// private function to initialize the fortran side of the simulation
214	setFortranSim_TD setFsimulation;
215
216	setFortranBox_TD setFortranBoxSize;
217
218	notifyFortranCutOff_TD notifyFortranCutOffs;
219
220	//Addtional Properties of SimInfo
221	map<string, GenericData*> properties;
222
223	};
224
225	void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
226	vector<int>& groupList, vector<int>& groupStart);
227
228	#endif