ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 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
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 <  int *excludes;       // the pairs themselves
49 >  Exclude** excludes;       // the pairs themselves
50  
51    int nGlobalExcludes;
52    int* globalExcludes; // same as above, but these guys participate in
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
53 <  SRI **sr_interactions;// the array of short range force objects
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;
# Line 65 | Line 86 | class SimInfo{ (public)
86    int useGB;
87    int useEAM;
88    
89 +  bool useInitXSstate;
90 +  double orthoTolerance;
91  
92    double dt, run_time;           // the time step and total time
93    double sampleTime, statusTime; // the position and energy dump frequencies
94    double target_temp;            // the target temperature of the system
95    double thermalTime;            // the temp kick interval
96 +  double currentTime;            // Used primarily for correlation Functions
97 +  double resetTime;              // Use to reset the integrator periodically
98  
99    int n_mol;           // n_molecules;
100    Molecule* molecules; // the array of molecules
101    
102 <  int nComponents;           // the number of componentsin the system
102 >  int nComponents;           // the number of components in the system
103    int* componentsNmol;       // the number of molecules of each component
104    MoleculeStamp** compStamps;// the stamps matching the components
105    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 82 | Line 107 | class SimInfo{ (public)
107    
108    char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
109    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
110 <  Integrator *the_integrator; // the integrator of the simulation
110 >  BaseIntegrator *the_integrator; // the integrator of the simulation
111  
112    char finalName[300];  // the name of the eor file to be written
113    char sampleName[300]; // the name of the dump file to be written
114    char statusName[300]; // the name of the stat file to be written
115  
116 <
116 >  int seed;                    //seed for random number generator
117    // refreshes the sim if things get changed (load balanceing, volume
118    // adjustment, etc.)
119  
# Line 97 | Line 122 | class SimInfo{ (public)
122  
123    // sets the internal function pointer to fortran.
124  
125 <  void setInternal( void (*fSetup) setFortranSimList,
126 <                    void (*fBox) setFortranBoxList ){
125 >  void setInternal( setFortranSim_TD fSetup,
126 >                    setFortranBox_TD fBox,
127 >                    notifyFortranCutOff_TD fCut){
128      setFsimulation = fSetup;
129      setFortranBoxSize = fBox;
130 +    notifyFortranCutOffs = fCut;
131    }
132  
133 +  int getNDF();
134 +  int getNDFraw();
135 +  int getNDFtranslational();
136 +
137 +  void setBox( double newBox[3] );
138 +  void setBoxM( double newBox[3][3] );
139 +  void getBoxM( double theBox[3][3] );
140 +  void scaleBox( double scale );
141 +  
142 +  void setRcut( double theRcut );
143 +  void setDefaultRcut( double theRcut );
144 +  void setEcr( double theEcr );
145 +  void setDefaultEcr( double theEcr );
146 +  void setEcr( double theEcr, double theEst );
147 +  void setDefaultEcr( double theEcr, double theEst );
148 +  void checkCutOffs( void );
149 +
150 +  double getRcut( void )  { return rCut; }
151 +  double getRlist( void ) { return rList; }
152 +  double getEcr( void )   { return ecr; }
153 +  double getEst( void )   { return est; }
154 +  double getMaxCutoff( void ) { return maxCutoff; }
155 +
156 +  void setTime( double theTime ) { currentTime = theTime; }
157 +  void incrTime( double the_dt ) { currentTime += the_dt; }
158 +  void decrTime( double the_dt ) { currentTime -= the_dt; }
159 +  double getTime( void ) { return currentTime; }
160 +
161 +  void wrapVector( double thePos[3] );
162 +
163 +  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
164 +  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
165 +  void invertMat3(double in[3][3], double out[3][3]);
166 +  void transposeMat3(double in[3][3], double out[3][3]);
167 +  void printMat3(double A[3][3]);
168 +  void printMat9(double A[9]);
169 +  double matDet3(double m[3][3]);
170 +  double matTrace3(double m[3][3]);
171 +
172 +  void crossProduct3(double a[3],double b[3], double out[3]);
173 +  double dotProduct3(double a[3], double b[3]);
174 +  double length3(double a[3]);
175 +  
176 +  SimState* getConfiguration( void ) { return myConfiguration; }
177 +  
178 +  void addProperty(GenericData* prop);
179 +  GenericData* getProperty(const string& propName);
180 +  vector<GenericData*> getProperties();      
181 +
182 +  int getSeed(void) {  return seed; }
183 +  void setSeed(int theSeed) {  seed = theSeed;}
184 +
185   private:
186 +
187 +  SimState* myConfiguration;
188 +
189 +  double origRcut, origEcr;
190 +  int boxIsInit, haveOrigRcut, haveOrigEcr;
191 +
192 +  double oldEcr;
193 +  double oldRcut;
194 +
195 +  double rList, rCut; // variables for the neighborlist
196 +  double ecr;             // the electrostatic cutoff radius
197 +  double est;             // the electrostatic skin thickness
198 +  double maxCutoff;
199 +
200 +  double distXY;
201 +  double distYZ;
202 +  double distZX;
203 +
204 +
205    
206 +  void calcHmatInv( void );
207 +  void calcBoxL();
208 +  double calcMaxCutOff();
209 +
210 +
211    // private function to initialize the fortran side of the simulation
212 <  void (*setFsimulation) setFortranSimList;
212 >  setFortranSim_TD setFsimulation;
213  
214 <  void (*setFortranBoxSize) setFortranBoxList;
214 >  setFortranBox_TD setFortranBoxSize;
215 >  
216 >  notifyFortranCutOff_TD notifyFortranCutOffs;
217 >  
218 >  //Addtional Properties of SimInfo
219 >  map<string, GenericData*> properties;
220 >
221   };
222  
223  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines