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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 2004 UTC

# Line 6 | Line 6
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"
# Line 15 | Line 18
18   #include "fSimulation.h"
19   #include "fortranWrapDefines.hpp"
20   #include "GenericData.hpp"
21 <
22 <
23 <
21 > //#include "Minimizer.hpp"
22 > //#include "OOPSEMinimizer.hpp"
23 > double roundMe( double x );
24 > class OOPSEMinimizer;
25   class SimInfo{
26  
27   public:
# Line 27 | Line 31 | class SimInfo{ (public)
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  
# Line 44 | Line 51 | class SimInfo{ (public)
51  
52    int n_dipoles; // number of dipoles
53  
54 <
55 <  int n_exclude;  // the # of pairs excluded from long range forces
49 <  Exclude** excludes;       // the pairs themselves
50 <
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 81 | 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
# Line 97 | Line 105 | class SimInfo{ (public)
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 107 | 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 120 | 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 131 | Line 149 | class SimInfo{ (public)
149    int getNDF();
150    int getNDFraw();
151    int getNDFtranslational();
152 <
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; }
166 <
164 >  double getRsw( void )   { return rSw; }
165 >  double getMaxCutoff( void ) { return maxCutoff; }
166 >  
167    void setTime( double theTime ) { currentTime = theTime; }
168 <  void incrTime( double dt ) { currentTime += dt; }
169 <  void decrTime( double dt ) { currentTime -= dt; }
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  
172    void wrapVector( double thePos[3] );
173  
156 –  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
157 –  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
158 –  void invertMat3(double in[3][3], double out[3][3]);
159 –  void transposeMat3(double in[3][3], double out[3][3]);
160 –  void printMat3(double A[3][3]);
161 –  void printMat9(double A[9]);
162 –  double matDet3(double m[3][3]);
163 –  double matTrace3(double m[3][3]);
164 –
165 –  void crossProduct3(double a[3],double b[3], double out[3]);
166 –  double dotProduct3(double a[3], double b[3]);
167 –  double length3(double a[3]);
168 –  
174    SimState* getConfiguration( void ) { return myConfiguration; }
175    
176    void addProperty(GenericData* prop);
177    GenericData* getProperty(const string& propName);
178 <  vector<GenericData*> getProperties();      
178 >  //vector<GenericData*>& getProperties()  {return properties;}    
179  
180    int getSeed(void) {  return seed; }
181    void setSeed(int theSeed) {  seed = theSeed;}
# Line 179 | Line 184 | class SimInfo{ (public)
184  
185    SimState* myConfiguration;
186  
187 <  double origRcut, origEcr;
183 <  int boxIsInit, haveOrigRcut, haveOrigEcr;
187 >  int boxIsInit, haveRcut, haveRsw;
188  
185 –  double oldEcr;
186 –  double oldRcut;
187 –
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;
# Line 197 | Line 198 | class SimInfo{ (public)
198    void calcHmatInv( void );
199    void calcBoxL();
200    double calcMaxCutOff();
200 –  void checkCutOffs( void );
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  
215 –
217   #endif

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