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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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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 1234 by tim, Fri Jun 4 03:15:31 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"
16 + #include "Restraints.hpp"
17  
18   #define __C
19   #include "fSimulation.h"
# Line 17 | Line 21
21   #include "GenericData.hpp"
22  
23  
24 + //#include "Minimizer.hpp"
25 + //#include "OOPSEMinimizer.hpp"
26  
27 +
28 + double roundMe( double x );
29 + class OOPSEMinimizer;
30 + class ConstraintManager;
31   class SimInfo{
32  
33   public:
# Line 27 | Line 37 | class SimInfo{ (public)
37  
38    int n_atoms; // the number of atoms
39    Atom **atoms; // the array of atom objects
40 +
41 +  vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
42 +  vector<StuntDouble*> integrableObjects;
43    
44    double tau[9]; // the stress tensor
45  
# Line 44 | Line 57 | class SimInfo{ (public)
57  
58    int n_dipoles; // number of dipoles
59  
60 <
61 <  int n_exclude;  // the # of pairs excluded from long range forces
49 <  Exclude** excludes;       // the pairs themselves
50 <
60 >  int n_exclude;
61 >  Exclude* excludes;  // the exclude list for ignoring pairs in fortran
62    int nGlobalExcludes;
63    int* globalExcludes; // same as above, but these guys participate in
64                         // no long range forces.
# Line 81 | Line 92 | class SimInfo{ (public)
92    int usePBC; // whether we use periodic boundry conditions.
93    int useLJ;
94    int useSticky;
95 <  int useDipole;
95 >  int useCharges;
96 >  int useDipoles;
97    int useReactionField;
98    int useGB;
99    int useEAM;
100 <  
100 >  bool haveCutoffGroups;
101 >  bool useInitXSstate;
102 >  double orthoTolerance;
103  
104    double dt, run_time;           // the time step and total time
105    double sampleTime, statusTime; // the position and energy dump frequencies
# Line 97 | Line 111 | class SimInfo{ (public)
111    int n_mol;           // n_molecules;
112    Molecule* molecules; // the array of molecules
113    
114 <  int nComponents;           // the number of componentsin the system
114 >  int nComponents;           // the number of components in the system
115    int* componentsNmol;       // the number of molecules of each component
116    MoleculeStamp** compStamps;// the stamps matching the components
117    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 107 | Line 121 | class SimInfo{ (public)
121    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
122    BaseIntegrator *the_integrator; // the integrator of the simulation
123  
124 +  OOPSEMinimizer* the_minimizer; // the energy minimizer
125 +  Restraints* restraint;
126 +  bool has_minimizer;
127 +
128    char finalName[300];  // the name of the eor file to be written
129    char sampleName[300]; // the name of the dump file to be written
130    char statusName[300]; // the name of the stat file to be written
131 +  char rawPotName[300];  // the name of the raw file to be written
132  
133    int seed;                    //seed for random number generator
134 +
135 +  int useSolidThermInt;  // is solid-state thermodynamic integration being used
136 +  int useLiquidThermInt; // is liquid thermodynamic integration being used
137 +  double thermIntLambda; // lambda for TI
138 +  double thermIntK;      // power of lambda for TI
139 +  double vRaw;           // unperturbed potential for TI
140 +  double vHarm;          // harmonic potential for TI
141 +  int i;                 // just an int
142 +
143 +  vector<double> mfact;
144 +  vector<int> FglobalGroupMembership;
145 +  int ngroup;
146 +  int* globalGroupMembership;
147 +
148 +  ConstraintManager* consMan; //constraint manager  holding the constraint pairs
149 +  
150    // refreshes the sim if things get changed (load balanceing, volume
151    // adjustment, etc.)
152  
# Line 120 | Line 155 | class SimInfo{ (public)
155  
156    // sets the internal function pointer to fortran.
157  
158 <  void setInternal( void (*fSetup) setFortranSimList,
159 <                    void (*fBox) setFortranBoxList,
160 <                    void (*fCut) notifyFortranCutOffList ){
158 >  void setInternal( setFortranSim_TD fSetup,
159 >                    setFortranBox_TD fBox,
160 >                    notifyFortranCutOff_TD fCut){
161      setFsimulation = fSetup;
162      setFortranBoxSize = fBox;
163      notifyFortranCutOffs = fCut;
# Line 131 | Line 166 | class SimInfo{ (public)
166    int getNDF();
167    int getNDFraw();
168    int getNDFtranslational();
169 <
169 >  int getTotIntegrableObjects();
170    void setBox( double newBox[3] );
171    void setBoxM( double newBox[3][3] );
172    void getBoxM( double theBox[3][3] );
173    void scaleBox( double scale );
174    
175 <  void setRcut( double theRcut );
176 <  void setEcr( double theEcr );
177 <  void setEcr( double theEcr, double theEst );
175 >  void setDefaultRcut( double theRcut );
176 >  void setDefaultRcut( double theRcut, double theRsw );
177 >  void checkCutOffs( void );
178  
179    double getRcut( void )  { return rCut; }
180    double getRlist( void ) { return rList; }
181 <  double getEcr( void )   { return ecr; }
182 <  double getEst( void )   { return est; }
183 <
181 >  double getRsw( void )   { return rSw; }
182 >  double getMaxCutoff( void ) { return maxCutoff; }
183 >  
184    void setTime( double theTime ) { currentTime = theTime; }
185 <  void incrTime( double dt ) { currentTime += dt; }
186 <  void decrTime( double dt ) { currentTime -= dt; }
185 >  void incrTime( double the_dt ) { currentTime += the_dt; }
186 >  void decrTime( double the_dt ) { currentTime -= the_dt; }
187    double getTime( void ) { return currentTime; }
188  
189    void wrapVector( double thePos[3] );
190  
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 –  
191    SimState* getConfiguration( void ) { return myConfiguration; }
192    
193    void addProperty(GenericData* prop);
194    GenericData* getProperty(const string& propName);
195 <  vector<GenericData*> getProperties();      
195 >  //vector<GenericData*>& getProperties()  {return properties;}    
196  
197    int getSeed(void) {  return seed; }
198    void setSeed(int theSeed) {  seed = theSeed;}
# Line 179 | Line 201 | class SimInfo{ (public)
201  
202    SimState* myConfiguration;
203  
204 <  double origRcut, origEcr;
183 <  int boxIsInit, haveOrigRcut, haveOrigEcr;
204 >  int boxIsInit, haveRcut, haveRsw;
205  
185 –  double oldEcr;
186 –  double oldRcut;
187 –
206    double rList, rCut; // variables for the neighborlist
207 <  double ecr;             // the electrostatic cutoff radius
208 <  double est;             // the electrostatic skin thickness
207 >  double rSw;         // the switching radius
208 >
209    double maxCutoff;
210  
211    double distXY;
# Line 197 | Line 215 | class SimInfo{ (public)
215    void calcHmatInv( void );
216    void calcBoxL();
217    double calcMaxCutOff();
200 –  void checkCutOffs( void );
218  
219    // private function to initialize the fortran side of the simulation
220 <  void (*setFsimulation) setFortranSimList;
220 >  setFortranSim_TD setFsimulation;
221  
222 <  void (*setFortranBoxSize) setFortranBoxList;
222 >  setFortranBox_TD setFortranBoxSize;
223    
224 <  void (*notifyFortranCutOffs) notifyFortranCutOffList;
224 >  notifyFortranCutOff_TD notifyFortranCutOffs;
225    
226    //Addtional Properties of SimInfo
227    map<string, GenericData*> properties;
228 +  void getFortranGroupArrays(SimInfo* info,
229 +                             vector<int>& FglobalGroupMembership,
230 +                             vector<double>& mfact);
231  
232 +
233   };
234  
235  
215 –
236   #endif

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