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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 574 by gezelter, Tue Jul 8 20:56:10 2003 UTC vs.
Revision 1144 by tim, Sat May 1 18:52:38 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  
17   #define __C
18   #include "fSimulation.h"
19   #include "fortranWrapDefines.hpp"
20 <
21 <
22 <
20 > #include "GenericData.hpp"
21 > //#include "Minimizer.hpp"
22 > //#include "OOPSEMinimizer.hpp"
23 > double roundMe( double x );
24 > class OOPSEMinimizer;
25   class SimInfo{
26  
27   public:
28  
29    SimInfo();
30 <  ~SimInfo(){}
30 >  ~SimInfo();
31  
32    int n_atoms; // the number of atoms
33    Atom **atoms; // the array of atom objects
34 +
35 +  vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
36 +  vector<StuntDouble*> integrableObjects;
37    
38    double tau[9]; // the stress tensor
39  
40 <  unsigned int n_bonds;    // number of bends
41 <  unsigned int n_bends;    // number of bends
42 <  unsigned int n_torsions; // number of torsions
43 <  unsigned int n_oriented; // number of of atoms with orientation
44 <  unsigned int ndf;        // number of actual degrees of freedom
45 <  unsigned int ndfRaw;     // number of settable degrees of freedom
40 >  int n_bonds;    // number of bends
41 >  int n_bends;    // number of bends
42 >  int n_torsions; // number of torsions
43 >  int n_oriented; // number of of atoms with orientation
44 >  int ndf;        // number of actual degrees of freedom
45 >  int ndfRaw;     // number of settable degrees of freedom
46 >  int ndfTrans;   // number of translational degrees of freedom
47 >  int nZconstraints; // the number of zConstraints
48  
49 <  unsigned int setTemp;   // boolean to set the temperature at each sampleTime
49 >  int setTemp;   // boolean to set the temperature at each sampleTime
50 >  int resetIntegrator; // boolean to reset the integrator
51  
52 <  unsigned int n_dipoles; // number of dipoles
39 <  double ecr;             // the electrostatic cutoff radius
40 <  double est;             // the electrostatic skin thickness
41 <  double dielectric;      // the dielectric of the medium for reaction field
52 >  int n_dipoles; // number of dipoles
53  
54 <  int n_exclude;  // the # of pairs excluded from long range forces
55 <  Exclude** excludes;       // the pairs themselves
45 <
54 >  int n_exclude;
55 >  Exclude* excludes;  // the exclude list for ignoring pairs in fortran
56    int nGlobalExcludes;
57    int* globalExcludes; // same as above, but these guys participate in
58                         // no long range forces.
# Line 52 | Line 62 | class SimInfo{ (public)
62  
63    int n_constraints; // the number of constraints on the system
64  
65 <  unsigned int n_SRI;   // the number of short range interactions
65 >  int n_SRI;   // the number of short range interactions
66  
67    double lrPot; // the potential energy from the long range calculations.
68  
69 <  double Hmat[9]; // the periodic boundry conditions. The Hmat is the
70 <                  // column vectors of the x, y, and z box vectors.
71 <                  //
72 <                  //   h1  h2  h3
73 <                  // [ Xx  Yx  Zx ]
74 <                  // [ Xy  Yy  Zy ]
75 <                  // [ Xz  Yz  Zz ]
76 <                  //  
67 <                  // to preserve compatibility with Fortran the
68 <                  // ordering in the array is as follows:
69 <                  //
70 <                  // [ 0 3 6 ]
71 <                  // [ 1 4 7 ]
72 <                  // [ 2 5 8 ]
69 >  double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
70 >                      // column vectors of the x, y, and z box vectors.
71 >                      //   h1  h2  h3
72 >                      // [ Xx  Yx  Zx ]
73 >                      // [ Xy  Yy  Zy ]
74 >                      // [ Xz  Yz  Zz ]
75 >                      //  
76 >  double HmatInv[3][3];
77  
78 <  double HmatI[9]; // the inverted Hmat;
75 <  double boxLx, boxLy, boxLz; // the box Lengths
78 >  double boxL[3]; // The Lengths of the 3 column vectors of Hmat
79    double boxVol;
80    int orthoRhombic;
81    
82  
83 +  double dielectric;      // the dielectric of the medium for reaction field
84  
81 –  double rList, rCut; // variables for the neighborlist
85    
86    int usePBC; // whether we use periodic boundry conditions.
87    int useLJ;
88    int useSticky;
89 <  int useDipole;
89 >  int useCharges;
90 >  int useDipoles;
91    int useReactionField;
92    int useGB;
93    int useEAM;
94 +  int useMolecularCutoffs;
95    
96 +  bool useInitXSstate;
97 +  double orthoTolerance;
98  
99    double dt, run_time;           // the time step and total time
100    double sampleTime, statusTime; // the position and energy dump frequencies
101    double target_temp;            // the target temperature of the system
102    double thermalTime;            // the temp kick interval
103 +  double currentTime;            // Used primarily for correlation Functions
104 +  double resetTime;              // Use to reset the integrator periodically
105  
106    int n_mol;           // n_molecules;
107    Molecule* molecules; // the array of molecules
108    
109 <  int nComponents;           // the number of componentsin the system
109 >  int nComponents;           // the number of components in the system
110    int* componentsNmol;       // the number of molecules of each component
111    MoleculeStamp** compStamps;// the stamps matching the components
112    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 107 | Line 116 | class SimInfo{ (public)
116    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
117    BaseIntegrator *the_integrator; // the integrator of the simulation
118  
119 +  OOPSEMinimizer* the_minimizer; // the energy minimizer
120 +  bool has_minimizer;
121 +
122    char finalName[300];  // the name of the eor file to be written
123    char sampleName[300]; // the name of the dump file to be written
124    char statusName[300]; // the name of the stat file to be written
125  
126 +  int seed;                    //seed for random number generator
127  
128 +
129 +  vector<double> mfact;
130 +  int ngroup;
131 +  vector<int> groupList;
132 +  vector<int> groupStart;
133 +  
134    // refreshes the sim if things get changed (load balanceing, volume
135    // adjustment, etc.)
136  
# Line 120 | Line 139 | class SimInfo{ (public)
139  
140    // sets the internal function pointer to fortran.
141  
142 <  void setInternal( void (*fSetup) setFortranSimList,
143 <                    void (*fBox) setFortranBoxList ){
142 >  void setInternal( setFortranSim_TD fSetup,
143 >                    setFortranBox_TD fBox,
144 >                    notifyFortranCutOff_TD fCut){
145      setFsimulation = fSetup;
146      setFortranBoxSize = fBox;
147 +    notifyFortranCutOffs = fCut;
148    }
149  
150    int getNDF();
151    int getNDFraw();
152 <
152 >  int getNDFtranslational();
153 >  int getTotIntegrableObjects();
154    void setBox( double newBox[3] );
155 <  void setBoxM( double newBox[9] );
156 <  void getBoxM( double theBox[9] );
155 >  void setBoxM( double newBox[3][3] );
156 >  void getBoxM( double theBox[3][3] );
157    void scaleBox( double scale );
158 +  
159 +  void setDefaultRcut( double theRcut );
160 +  void setDefaultEcr( double theEcr );
161 +  void setDefaultEcr( double theEcr, double theEst );
162 +  void checkCutOffs( void );
163  
164 +  double getRcut( void )  { return rCut; }
165 +  double getRlist( void ) { return rList; }
166 +  double getEcr( void )   { return ecr; }
167 +  double getEst( void )   { return est; }
168 +  double getMaxCutoff( void ) { return maxCutoff; }
169 +
170 +  void setTime( double theTime ) { currentTime = theTime; }
171 +  void incrTime( double the_dt ) { currentTime += the_dt; }
172 +  void decrTime( double the_dt ) { currentTime -= the_dt; }
173 +  double getTime( void ) { return currentTime; }
174 +
175    void wrapVector( double thePos[3] );
176  
177 +  SimState* getConfiguration( void ) { return myConfiguration; }
178 +  
179 +  void addProperty(GenericData* prop);
180 +  GenericData* getProperty(const string& propName);
181 +  //vector<GenericData*>& getProperties()  {return properties;}    
182 +
183 +  int getSeed(void) {  return seed; }
184 +  void setSeed(int theSeed) {  seed = theSeed;}
185 +
186   private:
187 +
188 +  SimState* myConfiguration;
189 +
190 +  int boxIsInit, haveRcut, haveEcr;
191 +
192 +  double rList, rCut; // variables for the neighborlist
193 +  double ecr;             // the electrostatic cutoff radius
194 +  double est;             // the electrostatic skin thickness
195 +  double maxCutoff;
196 +
197 +  double distXY;
198 +  double distYZ;
199 +  double distZX;
200    
201 <  void calcHmatI( void );
201 >  void calcHmatInv( void );
202    void calcBoxL();
203 +  double calcMaxCutOff();
204  
205    // private function to initialize the fortran side of the simulation
206 <  void (*setFsimulation) setFortranSimList;
206 >  setFortranSim_TD setFsimulation;
207  
208 <  void (*setFortranBoxSize) setFortranBoxList;
208 >  setFortranBox_TD setFortranBoxSize;
209 >  
210 >  notifyFortranCutOff_TD notifyFortranCutOffs;
211 >  
212 >  //Addtional Properties of SimInfo
213 >  map<string, GenericData*> properties;
214 >
215   };
216  
217 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
218 +                                                          vector<int>& groupList, vector<int>& groupStart);
219  
151 –
220   #endif

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