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root/group/branches/no-template-branch/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 574 by gezelter, Tue Jul 8 20:56:10 2003 UTC vs.
Revision 660 by tim, Thu Jul 31 19:59:34 2003 UTC

# Line 1 | Line 1
1   #ifndef __SIMINFO_H__
2   #define __SIMINFO_H__
3  
4 + #include <map>
5 + #include <string>
6 + #include <vector>
7  
5 –
8   #include "Atom.hpp"
9   #include "Molecule.hpp"
10   #include "AbstractClasses.hpp"
# Line 11 | Line 13
13   #define __C
14   #include "fSimulation.h"
15   #include "fortranWrapDefines.hpp"
16 + #include "GenericData.hpp"
17  
18  
19  
# Line 19 | Line 22 | class SimInfo{ (public)
22   public:
23  
24    SimInfo();
25 <  ~SimInfo(){}
25 >  ~SimInfo();
26  
27    int n_atoms; // the number of atoms
28    Atom **atoms; // the array of atom objects
# Line 36 | Line 39 | class SimInfo{ (public)
39    unsigned int setTemp;   // boolean to set the temperature at each sampleTime
40  
41    unsigned int n_dipoles; // number of dipoles
39 –  double ecr;             // the electrostatic cutoff radius
40 –  double est;             // the electrostatic skin thickness
41 –  double dielectric;      // the dielectric of the medium for reaction field
42  
43 +
44    int n_exclude;  // the # of pairs excluded from long range forces
45    Exclude** excludes;       // the pairs themselves
46  
# Line 56 | Line 57 | class SimInfo{ (public)
57  
58    double lrPot; // the potential energy from the long range calculations.
59  
60 <  double Hmat[9]; // the periodic boundry conditions. The Hmat is the
61 <                  // column vectors of the x, y, and z box vectors.
62 <                  //
63 <                  //   h1  h2  h3
64 <                  // [ Xx  Yx  Zx ]
65 <                  // [ Xy  Yy  Zy ]
66 <                  // [ Xz  Yz  Zz ]
67 <                  //  
67 <                  // to preserve compatibility with Fortran the
68 <                  // ordering in the array is as follows:
69 <                  //
70 <                  // [ 0 3 6 ]
71 <                  // [ 1 4 7 ]
72 <                  // [ 2 5 8 ]
60 >  double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
61 >                      // column vectors of the x, y, and z box vectors.
62 >                      //   h1  h2  h3
63 >                      // [ Xx  Yx  Zx ]
64 >                      // [ Xy  Yy  Zy ]
65 >                      // [ Xz  Yz  Zz ]
66 >                      //  
67 >  double HmatInv[3][3];
68  
69 <  double HmatI[9]; // the inverted Hmat;
75 <  double boxLx, boxLy, boxLz; // the box Lengths
69 >  double boxL[3]; // The Lengths of the 3 column vectors of Hmat
70    double boxVol;
71    int orthoRhombic;
72    
73  
74 +  double dielectric;      // the dielectric of the medium for reaction field
75  
81 –  double rList, rCut; // variables for the neighborlist
76    
77    int usePBC; // whether we use periodic boundry conditions.
78    int useLJ;
# Line 93 | Line 87 | class SimInfo{ (public)
87    double sampleTime, statusTime; // the position and energy dump frequencies
88    double target_temp;            // the target temperature of the system
89    double thermalTime;            // the temp kick interval
90 +  double currentTime;            // Used primarily for correlation Functions
91  
92    int n_mol;           // n_molecules;
93    Molecule* molecules; // the array of molecules
# Line 121 | Line 116 | class SimInfo{ (public)
116    // sets the internal function pointer to fortran.
117  
118    void setInternal( void (*fSetup) setFortranSimList,
119 <                    void (*fBox) setFortranBoxList ){
119 >                    void (*fBox) setFortranBoxList,
120 >                    void (*fCut) notifyFortranCutOffList ){
121      setFsimulation = fSetup;
122      setFortranBoxSize = fBox;
123 +    notifyFortranCutOffs = fCut;
124    }
125  
126    int getNDF();
127    int getNDFraw();
128  
129    void setBox( double newBox[3] );
130 <  void setBoxM( double newBox[9] );
131 <  void getBoxM( double theBox[9] );
130 >  void setBoxM( double newBox[3][3] );
131 >  void getBoxM( double theBox[3][3] );
132    void scaleBox( double scale );
133 +  
134 +  void setRcut( double theRcut );
135 +  void setEcr( double theEcr );
136 +  void setEcr( double theEcr, double theEst );
137  
138 +  double getRcut( void )  { return rCut; }
139 +  double getRlist( void ) { return rList; }
140 +  double getEcr( void )   { return ecr; }
141 +  double getEst( void )   { return est; }
142 +
143 +  void setTime( double theTime ) { currentTime = theTime; }
144 +  void incrTime( double dt ) { currentTime += dt; }
145 +  void decrTime( double dt ) { currentTime -= dt; }
146 +  double getTime( void ) { return currentTime; }
147 +
148    void wrapVector( double thePos[3] );
149  
150 +  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
151 +  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
152 +  void invertMat3(double in[3][3], double out[3][3]);
153 +  void transposeMat3(double in[3][3], double out[3][3]);
154 +  void printMat3(double A[3][3]);
155 +  void printMat9(double A[9]);
156 +  double matDet3(double m[3][3]);
157 +  
158 +  
159 +  void addProperty(GenericData* prop);
160 +  GenericData* getProperty(const string& propName);
161 +  vector<GenericData*> getProperties();      
162 +  
163   private:
164 +
165 +  double origRcut, origEcr;
166 +  int boxIsInit, haveOrigRcut, haveOrigEcr;
167 +
168 +  double oldEcr;
169 +  double oldRcut;
170 +
171 +  double rList, rCut; // variables for the neighborlist
172 +  double ecr;             // the electrostatic cutoff radius
173 +  double est;             // the electrostatic skin thickness
174 +  double maxCutoff;
175    
176 <  void calcHmatI( void );
176 >  void calcHmatInv( void );
177    void calcBoxL();
178 +  void checkCutOffs( void );
179  
180    // private function to initialize the fortran side of the simulation
181    void (*setFsimulation) setFortranSimList;
182  
183    void (*setFortranBoxSize) setFortranBoxList;
184 +  
185 +  void (*notifyFortranCutOffs) notifyFortranCutOffList;
186 +  
187 +  //Addtional Properties of SimInfo
188 +  map<string, GenericData*> properties;
189 +
190   };
191  
192  

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