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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 458 by gezelter, Fri Apr 4 19:47:19 2003 UTC vs.
Revision 767 by tim, Tue Sep 16 20:02:11 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 32 | Line 36 | class SimInfo{ (public)
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 ndfTrans;   // number of translational degrees of freedom
40 +  unsigned int nZconstraints; // the number of zConstraints
41  
42    unsigned int setTemp;   // boolean to set the temperature at each sampleTime
43 +  unsigned int resetIntegrator; // boolean to reset the integrator
44  
45    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
46  
47 +
48    int n_exclude;  // the # of pairs excluded from long range forces
49    Exclude** excludes;       // the pairs themselves
50  
# Line 48 | Line 53 | class SimInfo{ (public)
53                         // no long range forces.
54  
55    int* identArray;     // array of unique identifiers for the atoms
56 +  int* molMembershipArray;  // map of atom numbers onto molecule numbers
57  
58    int n_constraints; // the number of constraints on the system
59  
# Line 55 | Line 61 | class SimInfo{ (public)
61  
62    double lrPot; // the potential energy from the long range calculations.
63  
64 <  double box_x, box_y, box_z; // the periodic boundry conditions
65 <  double rList, rCut; // variables for the neighborlist
64 >  double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
65 >                      // column vectors of the x, y, and z box vectors.
66 >                      //   h1  h2  h3
67 >                      // [ Xx  Yx  Zx ]
68 >                      // [ Xy  Yy  Zy ]
69 >                      // [ Xz  Yz  Zz ]
70 >                      //  
71 >  double HmatInv[3][3];
72 >
73 >  double boxL[3]; // The Lengths of the 3 column vectors of Hmat
74 >  double boxVol;
75 >  int orthoRhombic;
76    
77 +
78 +  double dielectric;      // the dielectric of the medium for reaction field
79 +
80 +  
81    int usePBC; // whether we use periodic boundry conditions.
82    int useLJ;
83    int useSticky;
# Line 71 | Line 91 | class SimInfo{ (public)
91    double sampleTime, statusTime; // the position and energy dump frequencies
92    double target_temp;            // the target temperature of the system
93    double thermalTime;            // the temp kick interval
94 +  double currentTime;            // Used primarily for correlation Functions
95 +  double resetTime;              // Use to reset the integrator periodically
96  
97    int n_mol;           // n_molecules;
98    Molecule* molecules; // the array of molecules
# Line 83 | Line 105 | class SimInfo{ (public)
105    
106    char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
107    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
108 <  Integrator *the_integrator; // the integrator of the simulation
108 >  BaseIntegrator *the_integrator; // the integrator of the simulation
109  
110    char finalName[300];  // the name of the eor file to be written
111    char sampleName[300]; // the name of the dump file to be written
112    char statusName[300]; // the name of the stat file to be written
113  
114 <
114 >  int seed;                    //seed for random number generator
115    // refreshes the sim if things get changed (load balanceing, volume
116    // adjustment, etc.)
117  
# Line 99 | Line 121 | class SimInfo{ (public)
121    // sets the internal function pointer to fortran.
122  
123    void setInternal( void (*fSetup) setFortranSimList,
124 <                    void (*fBox) setFortranBoxList ){
124 >                    void (*fBox) setFortranBoxList,
125 >                    void (*fCut) notifyFortranCutOffList ){
126      setFsimulation = fSetup;
127      setFortranBoxSize = fBox;
128 +    notifyFortranCutOffs = fCut;
129    }
130  
131    int getNDF();
132    int getNDFraw();
133 +  int getNDFtranslational();
134  
135    void setBox( double newBox[3] );
136 <  void getBox( double theBox[3] );
136 >  void setBoxM( double newBox[3][3] );
137 >  void getBoxM( double theBox[3][3] );
138 >  void scaleBox( double scale );
139 >  
140 >  void setRcut( double theRcut );
141 >  void setEcr( double theEcr );
142 >  void setEcr( double theEcr, double theEst );
143  
144 +  double getRcut( void )  { return rCut; }
145 +  double getRlist( void ) { return rList; }
146 +  double getEcr( void )   { return ecr; }
147 +  double getEst( void )   { return est; }
148 +
149 +  void setTime( double theTime ) { currentTime = theTime; }
150 +  void incrTime( double dt ) { currentTime += dt; }
151 +  void decrTime( double dt ) { currentTime -= dt; }
152 +  double getTime( void ) { return currentTime; }
153 +
154 +  void wrapVector( double thePos[3] );
155 +
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 +  SimState* getConfiguration( void ) { return myConfiguration; }
166 +  
167 +  void addProperty(GenericData* prop);
168 +  GenericData* getProperty(const string& propName);
169 +  vector<GenericData*> getProperties();      
170 +
171 +  int getSeed(void) {  return seed; }
172 +  void setSeed(int theSeed) {  seed = theSeed;}
173 +
174   private:
175 +
176 +  SimState* myConfiguration;
177 +
178 +  double origRcut, origEcr;
179 +  int boxIsInit, haveOrigRcut, haveOrigEcr;
180 +
181 +  double oldEcr;
182 +  double oldRcut;
183 +
184 +  double rList, rCut; // variables for the neighborlist
185 +  double ecr;             // the electrostatic cutoff radius
186 +  double est;             // the electrostatic skin thickness
187 +  double maxCutoff;
188    
189 +  void calcHmatInv( void );
190 +  void calcBoxL();
191 +  void checkCutOffs( void );
192 +
193    // private function to initialize the fortran side of the simulation
194    void (*setFsimulation) setFortranSimList;
195  
196    void (*setFortranBoxSize) setFortranBoxList;
197 +  
198 +  void (*notifyFortranCutOffs) notifyFortranCutOffList;
199 +  
200 +  //Addtional Properties of SimInfo
201 +  map<string, GenericData*> properties;
202 +
203   };
204  
205  

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