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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC

# Line 1 | Line 1
1   #ifndef __SIMINFO_H__
2   #define __SIMINFO_H__
3  
4 + #include <map>
5 + #include <string>
6 + #include <vector>
7  
5 –
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 ConstraintManager;
31   class SimInfo{
32  
33   public:
34  
35    SimInfo();
36 <  ~SimInfo(){}
36 >  ~SimInfo();
37  
38    int n_atoms; // the number of atoms
39    Atom **atoms; // the array of atom objects
40 +
41 +  vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
42 +  vector<StuntDouble*> integrableObjects;
43    
44    double tau[9]; // the stress tensor
45  
46 <  unsigned int n_bonds;    // number of bends
47 <  unsigned int n_bends;    // number of bends
48 <  unsigned int n_torsions; // number of torsions
49 <  unsigned int n_oriented; // number of of atoms with orientation
46 >  int n_bonds;    // number of bends
47 >  int n_bends;    // number of bends
48 >  int n_torsions; // number of torsions
49 >  int n_oriented; // number of of atoms with orientation
50 >  int ndf;        // number of actual degrees of freedom
51 >  int ndfRaw;     // number of settable degrees of freedom
52 >  int ndfTrans;   // number of translational degrees of freedom
53 >  int nZconstraints; // the number of zConstraints
54  
55 <  unsigned int setTemp;   // boolean to set the temperature at each sampleTime
55 >  int setTemp;   // boolean to set the temperature at each sampleTime
56 >  int resetIntegrator; // boolean to reset the integrator
57  
58 <  unsigned int n_dipoles; // number of dipoles
37 <  double ecr;             // the electrostatic cutoff radius
38 <  double est;             // the electrostatic skin thickness
39 <  double dielectric;      // the dielectric of the medium for reaction field
58 >  int n_dipoles; // number of dipoles
59  
60 <  int n_exclude;  // the # of pairs excluded from long range forces
61 <  int *excludes;       // the pairs themselves
43 <
60 >  int n_exclude;
61 >  Exclude* excludes;  // the exclude list for ignoring pairs in fortran
62    int nGlobalExcludes;
63    int* globalExcludes; // same as above, but these guys participate in
64                         // no long range forces.
65  
66    int* identArray;     // array of unique identifiers for the atoms
67 +  int* molMembershipArray;  // map of atom numbers onto molecule numbers
68  
69    int n_constraints; // the number of constraints on the system
70  
71 <  unsigned int n_SRI;   // the number of short range interactions
53 <  SRI **sr_interactions;// the array of short range force objects
71 >  int n_SRI;   // the number of short range interactions
72  
73    double lrPot; // the potential energy from the long range calculations.
74  
75 <  double box_x, box_y, box_z; // the periodic boundry conditions
76 <  double rList, rCut; // variables for the neighborlist
75 >  double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
76 >                      // column vectors of the x, y, and z box vectors.
77 >                      //   h1  h2  h3
78 >                      // [ Xx  Yx  Zx ]
79 >                      // [ Xy  Yy  Zy ]
80 >                      // [ Xz  Yz  Zz ]
81 >                      //  
82 >  double HmatInv[3][3];
83 >
84 >  double boxL[3]; // The Lengths of the 3 column vectors of Hmat
85 >  double boxVol;
86 >  int orthoRhombic;
87    
88 +
89 +  double dielectric;      // the dielectric of the medium for reaction field
90 +
91 +  
92    int usePBC; // whether we use periodic boundry conditions.
93    int useLJ;
94    int useSticky;
95 <  int useDipole;
95 >  int useCharges;
96 >  int useDipoles;
97    int useReactionField;
98    int useGB;
99    int useEAM;
100 <  
100 >  bool haveCutoffGroups;
101 >  bool useInitXSstate;
102 >  double orthoTolerance;
103  
104    double dt, run_time;           // the time step and total time
105    double sampleTime, statusTime; // the position and energy dump frequencies
106    double target_temp;            // the target temperature of the system
107    double thermalTime;            // the temp kick interval
108 +  double currentTime;            // Used primarily for correlation Functions
109 +  double resetTime;              // Use to reset the integrator periodically
110  
111    int n_mol;           // n_molecules;
112    Molecule* molecules; // the array of molecules
113    
114 <  int nComponents;           // the number of componentsin the system
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
# Line 82 | Line 119 | class SimInfo{ (public)
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 <  Integrator *the_integrator; // the integrator of the simulation
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    char finalName[300];  // the name of the eor file to be written
129    char sampleName[300]; // the name of the dump file to be written
130    char statusName[300]; // the name of the stat file to be written
131 +  char rawPotName[300];  // the name of the raw file to be written
132  
133 +  int seed;                    //seed for random number generator
134  
135 +  int useSolidThermInt;  // is solid-state thermodynamic integration being used
136 +  int useLiquidThermInt; // is liquid thermodynamic integration being used
137 +  double thermIntLambda; // lambda for TI
138 +  double thermIntK;      // power of lambda for TI
139 +  double vRaw;           // unperturbed potential for TI
140 +  double vHarm;          // harmonic potential for TI
141 +  int i;                 // just an int
142 +
143 +  vector<double> mfact;
144 +  vector<int> FglobalGroupMembership;
145 +  int ngroup;
146 +  int* globalGroupMembership;
147 +
148 +  ConstraintManager* consMan; //constraint manager  holding the constraint pairs
149 +  
150    // refreshes the sim if things get changed (load balanceing, volume
151    // adjustment, etc.)
152  
# Line 97 | Line 155 | class SimInfo{ (public)
155  
156    // sets the internal function pointer to fortran.
157  
158 <  void setInternal( void (*fSetup) setFortranSimList,
159 <                    void (*fBox) setFortranBoxList ){
158 >  void setInternal( setFortranSim_TD fSetup,
159 >                    setFortranBox_TD fBox,
160 >                    notifyFortranCutOff_TD fCut){
161      setFsimulation = fSetup;
162      setFortranBoxSize = fBox;
163 +    notifyFortranCutOffs = fCut;
164    }
165  
166 +  int getNDF();
167 +  int getNDFraw();
168 +  int getNDFtranslational();
169 +  int getTotIntegrableObjects();
170 +  void setBox( double newBox[3] );
171 +  void setBoxM( double newBox[3][3] );
172 +  void getBoxM( double theBox[3][3] );
173 +  void scaleBox( double scale );
174 +  
175 +  void setDefaultRcut( double theRcut );
176 +  void setDefaultRcut( double theRcut, double theRsw );
177 +  void checkCutOffs( void );
178 +
179 +  double getRcut( void )  { return rCut; }
180 +  double getRlist( void ) { return rList; }
181 +  double getRsw( void )   { return rSw; }
182 +  double getMaxCutoff( void ) { return maxCutoff; }
183 +  
184 +  void setTime( double theTime ) { currentTime = theTime; }
185 +  void incrTime( double the_dt ) { currentTime += the_dt; }
186 +  void decrTime( double the_dt ) { currentTime -= the_dt; }
187 +  double getTime( void ) { return currentTime; }
188 +
189 +  void wrapVector( double thePos[3] );
190 +
191 +  SimState* getConfiguration( void ) { return myConfiguration; }
192 +  
193 +  void addProperty(GenericData* prop);
194 +  GenericData* getProperty(const string& propName);
195 +  //vector<GenericData*>& getProperties()  {return properties;}    
196 +
197 +  int getSeed(void) {  return seed; }
198 +  void setSeed(int theSeed) {  seed = theSeed;}
199 +
200   private:
201 +
202 +  SimState* myConfiguration;
203 +
204 +  int boxIsInit, haveRcut, haveRsw;
205 +
206 +  double rList, rCut; // variables for the neighborlist
207 +  double rSw;         // the switching radius
208 +
209 +  double maxCutoff;
210 +
211 +  double distXY;
212 +  double distYZ;
213 +  double distZX;
214    
215 +  void calcHmatInv( void );
216 +  void calcBoxL();
217 +  double calcMaxCutOff();
218 +
219    // private function to initialize the fortran side of the simulation
220 <  void (*setFsimulation) setFortranSimList;
220 >  setFortranSim_TD setFsimulation;
221  
222 <  void (*setFortranBoxSize) setFortranBoxList;
223 < };
222 >  setFortranBox_TD setFortranBoxSize;
223 >  
224 >  notifyFortranCutOff_TD notifyFortranCutOffs;
225 >  
226 >  //Addtional Properties of SimInfo
227 >  map<string, GenericData*> properties;
228 >  void getFortranGroupArrays(SimInfo* info,
229 >                             vector<int>& FglobalGroupMembership,
230 >                             vector<double>& mfact);
231  
232  
233 + };
234  
235 +
236   #endif

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