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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 1108 by tim, Wed Apr 14 15:37:41 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 + #include "GenericData.hpp"
21 + //#include "Minimizer.hpp"
22 + //#include "OOPSEMinimizer.hpp"
23  
24 <
16 <
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
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
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
52 >  int n_dipoles; // number of dipoles
53  
54 <  int n_exclude;  // the # of pairs excluded from long range forces
55 <  int *excludes;       // the pairs themselves
43 <
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.
59  
60    int* identArray;     // array of unique identifiers for the atoms
61 +  int* molMembershipArray;  // map of atom numbers onto molecule numbers
62  
63    int n_constraints; // the number of constraints on the system
64  
65 <  unsigned int n_SRI;   // the number of short range interactions
53 <  SRI **sr_interactions;// the array of short range force objects
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 box_x, box_y, box_z; // the periodic boundry conditions
70 <  double rList, rCut; // variables for the neighborlist
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 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 +
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    
95 +  bool useInitXSstate;
96 +  double orthoTolerance;
97  
98    double dt, run_time;           // the time step and total time
99    double sampleTime, statusTime; // the position and energy dump frequencies
100    double target_temp;            // the target temperature of the system
101    double thermalTime;            // the temp kick interval
102 +  double currentTime;            // Used primarily for correlation Functions
103 +  double resetTime;              // Use to reset the integrator periodically
104  
105    int n_mol;           // n_molecules;
106    Molecule* molecules; // the array of molecules
107    
108 <  int nComponents;           // the number of componentsin the system
108 >  int nComponents;           // the number of components in the system
109    int* componentsNmol;       // the number of molecules of each component
110    MoleculeStamp** compStamps;// the stamps matching the components
111    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 82 | Line 113 | class SimInfo{ (public)
113    
114    char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
115    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
116 <  Integrator *the_integrator; // the integrator of the simulation
116 >  BaseIntegrator *the_integrator; // the integrator of the simulation
117  
118 +  OOPSEMinimizer* the_minimizer; // the energy minimizer
119 +  bool has_minimizer;
120 +
121    char finalName[300];  // the name of the eor file to be written
122    char sampleName[300]; // the name of the dump file to be written
123    char statusName[300]; // the name of the stat file to be written
124  
125 <
125 >  int seed;                    //seed for random number generator
126    // refreshes the sim if things get changed (load balanceing, volume
127    // adjustment, etc.)
128  
# Line 97 | Line 131 | class SimInfo{ (public)
131  
132    // sets the internal function pointer to fortran.
133  
134 <  void setInternal( void (*fSetup) setFortranSimList,
135 <                    void (*fBox) setFortranBoxList ){
134 >  void setInternal( setFortranSim_TD fSetup,
135 >                    setFortranBox_TD fBox,
136 >                    notifyFortranCutOff_TD fCut){
137      setFsimulation = fSetup;
138      setFortranBoxSize = fBox;
139 +    notifyFortranCutOffs = fCut;
140    }
141  
142 +  int getNDF();
143 +  int getNDFraw();
144 +  int getNDFtranslational();
145 +  int getTotIntegrableObjects();
146 +  void setBox( double newBox[3] );
147 +  void setBoxM( double newBox[3][3] );
148 +  void getBoxM( double theBox[3][3] );
149 +  void scaleBox( double scale );
150 +  
151 +  void setDefaultRcut( double theRcut );
152 +  void setDefaultEcr( double theEcr );
153 +  void setDefaultEcr( double theEcr, double theEst );
154 +  void checkCutOffs( void );
155 +
156 +  double getRcut( void )  { return rCut; }
157 +  double getRlist( void ) { return rList; }
158 +  double getEcr( void )   { return ecr; }
159 +  double getEst( void )   { return est; }
160 +  double getMaxCutoff( void ) { return maxCutoff; }
161 +
162 +  void setTime( double theTime ) { currentTime = theTime; }
163 +  void incrTime( double the_dt ) { currentTime += the_dt; }
164 +  void decrTime( double the_dt ) { currentTime -= the_dt; }
165 +  double getTime( void ) { return currentTime; }
166 +
167 +  void wrapVector( double thePos[3] );
168 +
169 +  SimState* getConfiguration( void ) { return myConfiguration; }
170 +  
171 +  void addProperty(GenericData* prop);
172 +  GenericData* getProperty(const string& propName);
173 +  vector<GenericData*> getProperties();      
174 +
175 +  int getSeed(void) {  return seed; }
176 +  void setSeed(int theSeed) {  seed = theSeed;}
177 +
178   private:
179 +
180 +  SimState* myConfiguration;
181 +
182 +  int boxIsInit, haveRcut, haveEcr;
183 +
184 +  double rList, rCut; // variables for the neighborlist
185 +  double ecr;             // the electrostatic cutoff radius
186 +  double est;             // the electrostatic skin thickness
187 +  double maxCutoff;
188 +
189 +  double distXY;
190 +  double distYZ;
191 +  double distZX;
192    
193 +  void calcHmatInv( void );
194 +  void calcBoxL();
195 +  double calcMaxCutOff();
196 +
197    // private function to initialize the fortran side of the simulation
198 <  void (*setFsimulation) setFortranSimList;
198 >  setFortranSim_TD setFsimulation;
199  
200 <  void (*setFortranBoxSize) setFortranBoxList;
200 >  setFortranBox_TD setFortranBoxSize;
201 >  
202 >  notifyFortranCutOff_TD notifyFortranCutOffs;
203 >  
204 >  //Addtional Properties of SimInfo
205 >  map<string, GenericData*> properties;
206 >
207   };
208  
114 –
115 –
209   #endif

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