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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 790 by mmeineke, Mon Sep 29 21:16:11 2003 UTC vs.
Revision 1154 by gezelter, Tue May 11 16:00:22 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 +  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
# Line 97 | Line 106 | class SimInfo{ (public)
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,
144 <                    void (*fCut) notifyFortranCutOffList ){
142 >  void setInternal( setFortranSim_TD fSetup,
143 >                    setFortranBox_TD fBox,
144 >                    notifyFortranCutOff_TD fCut){
145      setFsimulation = fSetup;
146      setFortranBoxSize = fBox;
147      notifyFortranCutOffs = fCut;
# Line 131 | Line 150 | class SimInfo{ (public)
150    int getNDF();
151    int getNDFraw();
152    int getNDFtranslational();
153 <
153 >  int getTotIntegrableObjects();
154    void setBox( double newBox[3] );
155    void setBoxM( double newBox[3][3] );
156    void getBoxM( double theBox[3][3] );
157    void scaleBox( double scale );
158    
159 <  void setRcut( double theRcut );
160 <  void setEcr( double theEcr );
161 <  void setEcr( double theEcr, double theEst );
159 >  void setDefaultRcut( double theRcut );
160 >  void setDefaultRcut( double theRcut, double theRsw );
161 >  void checkCutOffs( void );
162  
163    double getRcut( void )  { return rCut; }
164    double getRlist( void ) { return rList; }
165 <  double getEcr( void )   { return ecr; }
166 <  double getEst( void )   { return est; }
167 <
165 >  double getRsw( void )   { return rSw; }
166 >  double getMaxCutoff( void ) { return maxCutoff; }
167 >  
168    void setTime( double theTime ) { currentTime = theTime; }
169    void incrTime( double the_dt ) { currentTime += the_dt; }
170    void decrTime( double the_dt ) { currentTime -= the_dt; }
# Line 153 | Line 172 | class SimInfo{ (public)
172  
173    void wrapVector( double thePos[3] );
174  
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 –  
175    SimState* getConfiguration( void ) { return myConfiguration; }
176    
177    void addProperty(GenericData* prop);
178    GenericData* getProperty(const string& propName);
179 <  vector<GenericData*> getProperties();      
179 >  //vector<GenericData*>& getProperties()  {return properties;}    
180  
181    int getSeed(void) {  return seed; }
182    void setSeed(int theSeed) {  seed = theSeed;}
# Line 179 | Line 185 | class SimInfo{ (public)
185  
186    SimState* myConfiguration;
187  
188 <  double origRcut, origEcr;
183 <  int boxIsInit, haveOrigRcut, haveOrigEcr;
188 >  int boxIsInit, haveRcut, haveRsw;
189  
185 –  double oldEcr;
186 –  double oldRcut;
187 –
190    double rList, rCut; // variables for the neighborlist
191 <  double ecr;             // the electrostatic cutoff radius
192 <  double est;             // the electrostatic skin thickness
191 >  double rSw;         // the switching radius
192 >
193    double maxCutoff;
194  
195    double distXY;
# Line 197 | Line 199 | class SimInfo{ (public)
199    void calcHmatInv( void );
200    void calcBoxL();
201    double calcMaxCutOff();
200 –  void checkCutOffs( void );
202  
203    // private function to initialize the fortran side of the simulation
204 <  void (*setFsimulation) setFortranSimList;
204 >  setFortranSim_TD setFsimulation;
205  
206 <  void (*setFortranBoxSize) setFortranBoxList;
206 >  setFortranBox_TD setFortranBoxSize;
207    
208 <  void (*notifyFortranCutOffs) notifyFortranCutOffList;
208 >  notifyFortranCutOff_TD notifyFortranCutOffs;
209    
210    //Addtional Properties of SimInfo
211    map<string, GenericData*> properties;
212  
213   };
214  
215 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
216 +                                                          vector<int>& groupList, vector<int>& groupStart);
217  
215 –
218   #endif

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