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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 1180 by chrisfen, Thu May 20 20:24:07 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"
20   #include "fortranWrapDefines.hpp"
21   #include "GenericData.hpp"
22 + //#include "Minimizer.hpp"
23 + //#include "OOPSEMinimizer.hpp"
24  
25  
26 <
26 > double roundMe( double x );
27 > class OOPSEMinimizer;
28   class SimInfo{
29  
30   public:
# Line 27 | Line 34 | class SimInfo{ (public)
34  
35    int n_atoms; // the number of atoms
36    Atom **atoms; // the array of atom objects
37 +
38 +  vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
39 +  vector<StuntDouble*> integrableObjects;
40    
41    double tau[9]; // the stress tensor
42  
# Line 44 | Line 54 | class SimInfo{ (public)
54  
55    int n_dipoles; // number of dipoles
56  
57 <
58 <  int n_exclude;  // the # of pairs excluded from long range forces
49 <  Exclude** excludes;       // the pairs themselves
50 <
57 >  int n_exclude;
58 >  Exclude* excludes;  // the exclude list for ignoring pairs in fortran
59    int nGlobalExcludes;
60    int* globalExcludes; // same as above, but these guys participate in
61                         // no long range forces.
# Line 81 | Line 89 | class SimInfo{ (public)
89    int usePBC; // whether we use periodic boundry conditions.
90    int useLJ;
91    int useSticky;
92 <  int useDipole;
92 >  int useCharges;
93 >  int useDipoles;
94    int useReactionField;
95    int useGB;
96    int useEAM;
97 <  
97 >  bool haveCutoffGroups;
98 >  bool useInitXSstate;
99 >  double orthoTolerance;
100  
101    double dt, run_time;           // the time step and total time
102    double sampleTime, statusTime; // the position and energy dump frequencies
# Line 97 | Line 108 | class SimInfo{ (public)
108    int n_mol;           // n_molecules;
109    Molecule* molecules; // the array of molecules
110    
111 <  int nComponents;           // the number of componentsin the system
111 >  int nComponents;           // the number of components in the system
112    int* componentsNmol;       // the number of molecules of each component
113    MoleculeStamp** compStamps;// the stamps matching the components
114    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 107 | Line 118 | class SimInfo{ (public)
118    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
119    BaseIntegrator *the_integrator; // the integrator of the simulation
120  
121 +  OOPSEMinimizer* the_minimizer; // the energy minimizer
122 +  Restraints* restraint;
123 +  bool has_minimizer;
124 +
125    char finalName[300];  // the name of the eor file to be written
126    char sampleName[300]; // the name of the dump file to be written
127    char statusName[300]; // the name of the stat file to be written
128 +  char rawPotName[300];  // the name of the raw file to be written
129  
130    int seed;                    //seed for random number generator
131 +
132 +  bool useThermInt;
133 +  double thermIntLambda;
134 +  double thermIntK;
135 +
136 +  double vRaw;
137 +  double vHarm;
138 +
139 +
140 +  vector<double> mfact;
141 +  int ngroup;
142 +  vector<int> groupList;
143 +  vector<int> groupStart;
144 +  
145    // refreshes the sim if things get changed (load balanceing, volume
146    // adjustment, etc.)
147  
# Line 120 | Line 150 | class SimInfo{ (public)
150  
151    // sets the internal function pointer to fortran.
152  
153 <  void setInternal( void (*fSetup) setFortranSimList,
154 <                    void (*fBox) setFortranBoxList,
155 <                    void (*fCut) notifyFortranCutOffList ){
153 >  void setInternal( setFortranSim_TD fSetup,
154 >                    setFortranBox_TD fBox,
155 >                    notifyFortranCutOff_TD fCut){
156      setFsimulation = fSetup;
157      setFortranBoxSize = fBox;
158      notifyFortranCutOffs = fCut;
# Line 131 | Line 161 | class SimInfo{ (public)
161    int getNDF();
162    int getNDFraw();
163    int getNDFtranslational();
164 <
164 >  int getTotIntegrableObjects();
165    void setBox( double newBox[3] );
166    void setBoxM( double newBox[3][3] );
167    void getBoxM( double theBox[3][3] );
168    void scaleBox( double scale );
169    
170 <  void setRcut( double theRcut );
171 <  void setEcr( double theEcr );
172 <  void setEcr( double theEcr, double theEst );
170 >  void setDefaultRcut( double theRcut );
171 >  void setDefaultRcut( double theRcut, double theRsw );
172 >  void checkCutOffs( void );
173  
174    double getRcut( void )  { return rCut; }
175    double getRlist( void ) { return rList; }
176 <  double getEcr( void )   { return ecr; }
177 <  double getEst( void )   { return est; }
178 <
176 >  double getRsw( void )   { return rSw; }
177 >  double getMaxCutoff( void ) { return maxCutoff; }
178 >  
179    void setTime( double theTime ) { currentTime = theTime; }
180 <  void incrTime( double dt ) { currentTime += dt; }
181 <  void decrTime( double dt ) { currentTime -= dt; }
180 >  void incrTime( double the_dt ) { currentTime += the_dt; }
181 >  void decrTime( double the_dt ) { currentTime -= the_dt; }
182    double getTime( void ) { return currentTime; }
183  
184    void wrapVector( double thePos[3] );
185  
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 –  
186    SimState* getConfiguration( void ) { return myConfiguration; }
187    
188    void addProperty(GenericData* prop);
189    GenericData* getProperty(const string& propName);
190 <  vector<GenericData*> getProperties();      
190 >  //vector<GenericData*>& getProperties()  {return properties;}    
191  
192    int getSeed(void) {  return seed; }
193    void setSeed(int theSeed) {  seed = theSeed;}
# Line 179 | Line 196 | class SimInfo{ (public)
196  
197    SimState* myConfiguration;
198  
199 <  double origRcut, origEcr;
183 <  int boxIsInit, haveOrigRcut, haveOrigEcr;
199 >  int boxIsInit, haveRcut, haveRsw;
200  
185 –  double oldEcr;
186 –  double oldRcut;
187 –
201    double rList, rCut; // variables for the neighborlist
202 <  double ecr;             // the electrostatic cutoff radius
203 <  double est;             // the electrostatic skin thickness
202 >  double rSw;         // the switching radius
203 >
204    double maxCutoff;
205  
206    double distXY;
# Line 197 | Line 210 | class SimInfo{ (public)
210    void calcHmatInv( void );
211    void calcBoxL();
212    double calcMaxCutOff();
200 –  void checkCutOffs( void );
213  
214    // private function to initialize the fortran side of the simulation
215 <  void (*setFsimulation) setFortranSimList;
215 >  setFortranSim_TD setFsimulation;
216  
217 <  void (*setFortranBoxSize) setFortranBoxList;
217 >  setFortranBox_TD setFortranBoxSize;
218    
219 <  void (*notifyFortranCutOffs) notifyFortranCutOffList;
219 >  notifyFortranCutOff_TD notifyFortranCutOffs;
220    
221    //Addtional Properties of SimInfo
222    map<string, GenericData*> properties;
223  
224   };
225  
226 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
227 +                                                          vector<int>& groupList, vector<int>& groupStart);
228  
215 –
229   #endif

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