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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 457 by gezelter, Fri Apr 4 19:16:11 2003 UTC vs.
Revision 708 by tim, Wed Aug 20 22:23:34 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"
11   #include "MakeStamps.hpp"
12 + #include "SimState.hpp"
13  
14   #define __C
15   #include "fSimulation.h"
16   #include "fortranWrapDefines.hpp"
17 + #include "GenericData.hpp"
18  
19  
20  
# Line 19 | Line 23 | class SimInfo{ (public)
23   public:
24  
25    SimInfo();
26 <  ~SimInfo(){}
26 >  ~SimInfo();
27  
28    int n_atoms; // the number of atoms
29    Atom **atoms; // the array of atom objects
# Line 30 | Line 34 | class SimInfo{ (public)
34    unsigned int n_bends;    // number of bends
35    unsigned int n_torsions; // number of torsions
36    unsigned int n_oriented; // number of of atoms with orientation
37 +  unsigned int ndf;        // number of actual degrees of freedom
38 +  unsigned int ndfRaw;     // number of settable degrees of freedom
39 +  unsigned int nZconstraints; // the number of zConstraints
40  
41    unsigned int setTemp;   // boolean to set the temperature at each sampleTime
42  
43    unsigned int n_dipoles; // number of dipoles
37 –  double ecr;             // the electrostatic cutoff radius
38 –  double est;             // the electrostatic skin thickness
39 –  double dielectric;      // the dielectric of the medium for reaction field
44  
45 +
46    int n_exclude;  // the # of pairs excluded from long range forces
47    Exclude** excludes;       // the pairs themselves
48  
# Line 46 | Line 51 | class SimInfo{ (public)
51                         // no long range forces.
52  
53    int* identArray;     // array of unique identifiers for the atoms
54 +  int* molMembershipArray;  // map of atom numbers onto molecule numbers
55  
56    int n_constraints; // the number of constraints on the system
57  
# Line 53 | Line 59 | class SimInfo{ (public)
59  
60    double lrPot; // the potential energy from the long range calculations.
61  
62 <  double box_x, box_y, box_z; // the periodic boundry conditions
63 <  double rList, rCut; // variables for the neighborlist
62 >  double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
63 >                      // column vectors of the x, y, and z box vectors.
64 >                      //   h1  h2  h3
65 >                      // [ Xx  Yx  Zx ]
66 >                      // [ Xy  Yy  Zy ]
67 >                      // [ Xz  Yz  Zz ]
68 >                      //  
69 >  double HmatInv[3][3];
70 >
71 >  double boxL[3]; // The Lengths of the 3 column vectors of Hmat
72 >  double boxVol;
73 >  int orthoRhombic;
74    
75 +
76 +  double dielectric;      // the dielectric of the medium for reaction field
77 +
78 +  
79    int usePBC; // whether we use periodic boundry conditions.
80    int useLJ;
81    int useSticky;
# Line 69 | Line 89 | class SimInfo{ (public)
89    double sampleTime, statusTime; // the position and energy dump frequencies
90    double target_temp;            // the target temperature of the system
91    double thermalTime;            // the temp kick interval
92 +  double currentTime;            // Used primarily for correlation Functions
93  
94    int n_mol;           // n_molecules;
95    Molecule* molecules; // the array of molecules
# Line 81 | Line 102 | class SimInfo{ (public)
102    
103    char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
104    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
105 <  Integrator *the_integrator; // the integrator of the simulation
105 >  BaseIntegrator *the_integrator; // the integrator of the simulation
106  
107    char finalName[300];  // the name of the eor file to be written
108    char sampleName[300]; // the name of the dump file to be written
109    char statusName[300]; // the name of the stat file to be written
110  
111 <
111 >  int seed;                    //seed for random number generator
112    // refreshes the sim if things get changed (load balanceing, volume
113    // adjustment, etc.)
114  
# Line 97 | Line 118 | class SimInfo{ (public)
118    // sets the internal function pointer to fortran.
119  
120    void setInternal( void (*fSetup) setFortranSimList,
121 <                    void (*fBox) setFortranBoxList ){
121 >                    void (*fBox) setFortranBoxList,
122 >                    void (*fCut) notifyFortranCutOffList ){
123      setFsimulation = fSetup;
124      setFortranBoxSize = fBox;
125 +    notifyFortranCutOffs = fCut;
126    }
127  
128 +  int getNDF();
129 +  int getNDFraw();
130 +
131    void setBox( double newBox[3] );
132 <  void getBox( double theBox[3] );
132 >  void setBoxM( double newBox[3][3] );
133 >  void getBoxM( double theBox[3][3] );
134 >  void scaleBox( double scale );
135 >  
136 >  void setRcut( double theRcut );
137 >  void setEcr( double theEcr );
138 >  void setEcr( double theEcr, double theEst );
139  
140 +  double getRcut( void )  { return rCut; }
141 +  double getRlist( void ) { return rList; }
142 +  double getEcr( void )   { return ecr; }
143 +  double getEst( void )   { return est; }
144 +
145 +  void setTime( double theTime ) { currentTime = theTime; }
146 +  void incrTime( double dt ) { currentTime += dt; }
147 +  void decrTime( double dt ) { currentTime -= dt; }
148 +  double getTime( void ) { return currentTime; }
149 +
150 +  void wrapVector( double thePos[3] );
151 +
152 +  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
153 +  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
154 +  void invertMat3(double in[3][3], double out[3][3]);
155 +  void transposeMat3(double in[3][3], double out[3][3]);
156 +  void printMat3(double A[3][3]);
157 +  void printMat9(double A[9]);
158 +  double matDet3(double m[3][3]);
159 +
160 +  SimState* getConfiguration( void ) { return myConfiguration; }
161 +  
162 +  void addProperty(GenericData* prop);
163 +  GenericData* getProperty(const string& propName);
164 +  vector<GenericData*> getProperties();      
165 +
166 +  int getSeed(void) {  return seed; }
167 +  void setSeed(int theSeed) {  seed = theSeed;}
168 +
169   private:
170 +
171 +  SimState* myConfiguration;
172 +
173 +  double origRcut, origEcr;
174 +  int boxIsInit, haveOrigRcut, haveOrigEcr;
175 +
176 +  double oldEcr;
177 +  double oldRcut;
178 +
179 +  double rList, rCut; // variables for the neighborlist
180 +  double ecr;             // the electrostatic cutoff radius
181 +  double est;             // the electrostatic skin thickness
182 +  double maxCutoff;
183    
184 +  void calcHmatInv( void );
185 +  void calcBoxL();
186 +  void checkCutOffs( void );
187 +
188    // private function to initialize the fortran side of the simulation
189    void (*setFsimulation) setFortranSimList;
190  
191    void (*setFortranBoxSize) setFortranBoxList;
192 +  
193 +  void (*notifyFortranCutOffs) notifyFortranCutOffList;
194 +  
195 +  //Addtional Properties of SimInfo
196 +  map<string, GenericData*> properties;
197 +
198   };
199  
200  

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