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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 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 <
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
52 >  int n_dipoles; // number of dipoles
53  
54 <
55 <  int n_exclude;  // the # of pairs excluded from long range forces
42 <  Exclude** 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.
# Line 50 | 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  
# Line 74 | Line 86 | class SimInfo{ (public)
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 <  
94 >  bool haveCutoffGroups;
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 98 | Line 115 | class SimInfo{ (public)
115    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
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 +  int seed;                    //seed for random number generator
126  
127 +
128 +  vector<double> mfact;
129 +  int ngroup;
130 +  vector<int> groupList;
131 +  vector<int> groupStart;
132 +  
133    // refreshes the sim if things get changed (load balanceing, volume
134    // adjustment, etc.)
135  
# Line 111 | Line 138 | class SimInfo{ (public)
138  
139    // sets the internal function pointer to fortran.
140  
141 <  void setInternal( void (*fSetup) setFortranSimList,
142 <                    void (*fBox) setFortranBoxList,
143 <                    void (*fCut) notifyFortranCutOffList ){
141 >  void setInternal( setFortranSim_TD fSetup,
142 >                    setFortranBox_TD fBox,
143 >                    notifyFortranCutOff_TD fCut){
144      setFsimulation = fSetup;
145      setFortranBoxSize = fBox;
146      notifyFortranCutOffs = fCut;
# Line 121 | Line 148 | class SimInfo{ (public)
148  
149    int getNDF();
150    int getNDFraw();
151 <
151 >  int getNDFtranslational();
152 >  int getTotIntegrableObjects();
153    void setBox( double newBox[3] );
154    void setBoxM( double newBox[3][3] );
155    void getBoxM( double theBox[3][3] );
156    void scaleBox( double scale );
157    
158 <  void setRcut( double theRcut );
159 <  void setEcr( double theEcr );
160 <  void setEcr( double theEcr, double theEst );
158 >  void setDefaultRcut( double theRcut );
159 >  void setDefaultRcut( double theRcut, double theRsw );
160 >  void checkCutOffs( void );
161  
162    double getRcut( void )  { return rCut; }
163    double getRlist( void ) { return rList; }
164 <  double getEcr( void )   { return ecr; }
165 <  double getEst( void )   { return est; }
164 >  double getRsw( void )   { return rSw; }
165 >  double getMaxCutoff( void ) { return maxCutoff; }
166 >  
167 >  void setTime( double theTime ) { currentTime = theTime; }
168 >  void incrTime( double the_dt ) { currentTime += the_dt; }
169 >  void decrTime( double the_dt ) { currentTime -= the_dt; }
170 >  double getTime( void ) { return currentTime; }
171  
139 –
172    void wrapVector( double thePos[3] );
173  
174 <  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
143 <  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
144 <  void invertMat3(double in[3][3], double out[3][3]);
145 <  void transposeMat3(double in[3][3], double out[3][3]);
146 <  void printMat3(double A[3][3]);
147 <  void printMat9(double A[9]);
148 <  double matDet3(double m[3][3]);
174 >  SimState* getConfiguration( void ) { return myConfiguration; }
175    
176 +  void addProperty(GenericData* prop);
177 +  GenericData* getProperty(const string& propName);
178 +  //vector<GenericData*>& getProperties()  {return properties;}    
179 +
180 +  int getSeed(void) {  return seed; }
181 +  void setSeed(int theSeed) {  seed = theSeed;}
182 +
183   private:
184  
185 <  double origRcut, origEcr;
153 <  int boxIsInit, haveOrigRcut, haveOrigEcr;
185 >  SimState* myConfiguration;
186  
187 <  double oldEcr;
156 <  double oldRcut;
187 >  int boxIsInit, haveRcut, haveRsw;
188  
189    double rList, rCut; // variables for the neighborlist
190 <  double ecr;             // the electrostatic cutoff radius
191 <  double est;             // the electrostatic skin thickness
190 >  double rSw;         // the switching radius
191 >
192    double maxCutoff;
193 +
194 +  double distXY;
195 +  double distYZ;
196 +  double distZX;
197    
198    void calcHmatInv( void );
199    void calcBoxL();
200 <  void checkCutOffs( void );
200 >  double calcMaxCutOff();
201  
202    // private function to initialize the fortran side of the simulation
203 <  void (*setFsimulation) setFortranSimList;
203 >  setFortranSim_TD setFsimulation;
204  
205 <  void (*setFortranBoxSize) setFortranBoxList;
205 >  setFortranBox_TD setFortranBoxSize;
206    
207 <  void (*notifyFortranCutOffs) notifyFortranCutOffList;
207 >  notifyFortranCutOff_TD notifyFortranCutOffs;
208 >  
209 >  //Addtional Properties of SimInfo
210 >  map<string, GenericData*> properties;
211  
212   };
213  
214 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
215 +                                                          vector<int>& groupList, vector<int>& groupStart);
216  
177 –
217   #endif

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