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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 941 by gezelter, Tue Jan 13 23:01:43 2004 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
30    
31    double tau[9]; // the stress tensor
32  
33 <  unsigned int n_bonds;    // number of bends
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
33 >  int n_bonds;    // number of bends
34 >  int n_bends;    // number of bends
35 >  int n_torsions; // number of torsions
36 >  int n_oriented; // number of of atoms with orientation
37 >  int ndf;        // number of actual degrees of freedom
38 >  int ndfRaw;     // number of settable degrees of freedom
39 >  int ndfTrans;   // number of translational degrees of freedom
40 >  int nZconstraints; // the number of zConstraints
41  
42 <  unsigned int setTemp;   // boolean to set the temperature at each sampleTime
42 >  int setTemp;   // boolean to set the temperature at each sampleTime
43 >  int resetIntegrator; // boolean to reset the integrator
44  
45 <  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
45 >  int n_dipoles; // number of dipoles
46  
47 +
48    int n_exclude;  // the # of pairs excluded from long range forces
49    Exclude** excludes;       // the pairs themselves
50  
# Line 46 | 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  
60 <  unsigned int n_SRI;   // the number of short range interactions
60 >  int n_SRI;   // the number of short range interactions
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;
84 <  int useDipole;
84 >  int useCharges;
85 >  int useDipoles;
86    int useReactionField;
87    int useGB;
88    int useEAM;
89    
90 +  bool useInitXSstate;
91 +  double orthoTolerance;
92  
93    double dt, run_time;           // the time step and total time
94    double sampleTime, statusTime; // the position and energy dump frequencies
95    double target_temp;            // the target temperature of the system
96    double thermalTime;            // the temp kick interval
97 +  double currentTime;            // Used primarily for correlation Functions
98 +  double resetTime;              // Use to reset the integrator periodically
99  
100    int n_mol;           // n_molecules;
101    Molecule* molecules; // the array of molecules
102    
103 <  int nComponents;           // the number of componentsin the system
103 >  int nComponents;           // the number of components in the system
104    int* componentsNmol;       // the number of molecules of each component
105    MoleculeStamp** compStamps;// the stamps matching the components
106    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 81 | Line 108 | class SimInfo{ (public)
108    
109    char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
110    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
111 <  Integrator *the_integrator; // the integrator of the simulation
111 >  BaseIntegrator *the_integrator; // the integrator of the simulation
112  
113    char finalName[300];  // the name of the eor file to be written
114    char sampleName[300]; // the name of the dump file to be written
115    char statusName[300]; // the name of the stat file to be written
116  
117 <
117 >  int seed;                    //seed for random number generator
118    // refreshes the sim if things get changed (load balanceing, volume
119    // adjustment, etc.)
120  
# Line 96 | Line 123 | class SimInfo{ (public)
123  
124    // sets the internal function pointer to fortran.
125  
126 <  void setInternal( void (*fSetup) setFortranSimList,
127 <                    void (*fBox) setFortranBoxList ){
126 >  void setInternal( setFortranSim_TD fSetup,
127 >                    setFortranBox_TD fBox,
128 >                    notifyFortranCutOff_TD fCut){
129      setFsimulation = fSetup;
130      setFortranBoxSize = fBox;
131 +    notifyFortranCutOffs = fCut;
132    }
133  
134 +  int getNDF();
135 +  int getNDFraw();
136 +  int getNDFtranslational();
137 +
138    void setBox( double newBox[3] );
139 <  void getBox( double theBox[3] );
139 >  void setBoxM( double newBox[3][3] );
140 >  void getBoxM( double theBox[3][3] );
141 >  void scaleBox( double scale );
142 >  
143 >  void setDefaultRcut( double theRcut );
144 >  void setDefaultEcr( double theEcr );
145 >  void setDefaultEcr( double theEcr, double theEst );
146 >  void checkCutOffs( void );
147  
148 +  double getRcut( void )  { return rCut; }
149 +  double getRlist( void ) { return rList; }
150 +  double getEcr( void )   { return ecr; }
151 +  double getEst( void )   { return est; }
152 +  double getMaxCutoff( void ) { return maxCutoff; }
153 +
154 +  void setTime( double theTime ) { currentTime = theTime; }
155 +  void incrTime( double the_dt ) { currentTime += the_dt; }
156 +  void decrTime( double the_dt ) { currentTime -= the_dt; }
157 +  double getTime( void ) { return currentTime; }
158 +
159 +  void wrapVector( double thePos[3] );
160 +
161 +  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
162 +  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
163 +  void invertMat3(double in[3][3], double out[3][3]);
164 +  void transposeMat3(double in[3][3], double out[3][3]);
165 +  void printMat3(double A[3][3]);
166 +  void printMat9(double A[9]);
167 +  double matDet3(double m[3][3]);
168 +  double matTrace3(double m[3][3]);
169 +
170 +  void crossProduct3(double a[3],double b[3], double out[3]);
171 +  double dotProduct3(double a[3], double b[3]);
172 +  double length3(double a[3]);
173 +  
174 +  SimState* getConfiguration( void ) { return myConfiguration; }
175 +  
176 +  void addProperty(GenericData* prop);
177 +  GenericData* getProperty(const string& propName);
178 +  vector<GenericData*> getProperties();      
179 +
180 +  int getSeed(void) {  return seed; }
181 +  void setSeed(int theSeed) {  seed = theSeed;}
182 +
183   private:
184 +
185 +  SimState* myConfiguration;
186 +
187 +  int boxIsInit, haveRcut, haveEcr;
188 +
189 +  double rList, rCut; // variables for the neighborlist
190 +  double ecr;             // the electrostatic cutoff radius
191 +  double est;             // the electrostatic skin thickness
192 +  double maxCutoff;
193 +
194 +  double distXY;
195 +  double distYZ;
196 +  double distZX;
197 +
198 +
199    
200 +  void calcHmatInv( void );
201 +  void calcBoxL();
202 +  double calcMaxCutOff();
203 +
204 +
205    // private function to initialize the fortran side of the simulation
206 <  void (*setFsimulation) setFortranSimList;
206 >  setFortranSim_TD setFsimulation;
207  
208 <  void (*setFortranBoxSize) setFortranBoxList;
208 >  setFortranBox_TD setFortranBoxSize;
209 >  
210 >  notifyFortranCutOff_TD notifyFortranCutOffs;
211 >  
212 >  //Addtional Properties of SimInfo
213 >  map<string, GenericData*> properties;
214 >
215   };
216  
217  

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