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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 836 by mmeineke, Tue Oct 28 22:25:46 2003 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 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 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 +  int useThermInt;        // whether or not we use thermodynamic integration
133 +  double thermIntLambda; // lambda for TI
134 +  double thermIntK;      // power of lambda for TI
135 +  double vRaw;           // unperturbed potential for TI
136 +  double vHarm;          // harmonic potential for TI
137 +  int i;                 // just an int
138 +
139 +  vector<double> mfact;
140 +  int ngroup;
141 +  vector<int> groupList;
142 +  vector<int> groupStart;
143 +  
144    // refreshes the sim if things get changed (load balanceing, volume
145    // adjustment, etc.)
146  
# Line 131 | Line 160 | class SimInfo{ (public)
160    int getNDF();
161    int getNDFraw();
162    int getNDFtranslational();
163 <
163 >  int getTotIntegrableObjects();
164    void setBox( double newBox[3] );
165    void setBoxM( double newBox[3][3] );
166    void getBoxM( double theBox[3][3] );
167    void scaleBox( double scale );
168    
169 <  void setRcut( double theRcut );
170 <  void setEcr( double theEcr );
171 <  void setEcr( double theEcr, double theEst );
169 >  void setDefaultRcut( double theRcut );
170 >  void setDefaultRcut( double theRcut, double theRsw );
171 >  void checkCutOffs( void );
172  
173    double getRcut( void )  { return rCut; }
174    double getRlist( void ) { return rList; }
175 <  double getEcr( void )   { return ecr; }
147 <  double getEst( void )   { return est; }
175 >  double getRsw( void )   { return rSw; }
176    double getMaxCutoff( void ) { return maxCutoff; }
177 <
177 >  
178    void setTime( double theTime ) { currentTime = theTime; }
179    void incrTime( double the_dt ) { currentTime += the_dt; }
180    void decrTime( double the_dt ) { currentTime -= the_dt; }
# Line 154 | Line 182 | class SimInfo{ (public)
182  
183    void wrapVector( double thePos[3] );
184  
157 –  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
158 –  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
159 –  void invertMat3(double in[3][3], double out[3][3]);
160 –  void transposeMat3(double in[3][3], double out[3][3]);
161 –  void printMat3(double A[3][3]);
162 –  void printMat9(double A[9]);
163 –  double matDet3(double m[3][3]);
164 –  double matTrace3(double m[3][3]);
165 –
166 –  void crossProduct3(double a[3],double b[3], double out[3]);
167 –  double dotProduct3(double a[3], double b[3]);
168 –  double length3(double a[3]);
169 –  
185    SimState* getConfiguration( void ) { return myConfiguration; }
186    
187    void addProperty(GenericData* prop);
188    GenericData* getProperty(const string& propName);
189 <  vector<GenericData*> getProperties();      
189 >  //vector<GenericData*>& getProperties()  {return properties;}    
190  
191    int getSeed(void) {  return seed; }
192    void setSeed(int theSeed) {  seed = theSeed;}
# Line 180 | Line 195 | class SimInfo{ (public)
195  
196    SimState* myConfiguration;
197  
198 <  double origRcut, origEcr;
184 <  int boxIsInit, haveOrigRcut, haveOrigEcr;
198 >  int boxIsInit, haveRcut, haveRsw;
199  
186 –  double oldEcr;
187 –  double oldRcut;
188 –
200    double rList, rCut; // variables for the neighborlist
201 <  double ecr;             // the electrostatic cutoff radius
202 <  double est;             // the electrostatic skin thickness
201 >  double rSw;         // the switching radius
202 >
203    double maxCutoff;
204  
205    double distXY;
# Line 198 | Line 209 | class SimInfo{ (public)
209    void calcHmatInv( void );
210    void calcBoxL();
211    double calcMaxCutOff();
201 –  void checkCutOffs( void );
212  
213    // private function to initialize the fortran side of the simulation
214    setFortranSim_TD setFsimulation;
# Line 212 | Line 222 | class SimInfo{ (public)
222  
223   };
224  
225 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
226 +                                                          vector<int>& groupList, vector<int>& groupStart);
227  
216 –
228   #endif

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