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root/group/trunk/OOPSE/libmdtools/SimInfo.hpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.hpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 2003 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 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 "RigidBody.hpp"
10   #include "Molecule.hpp"
11 + #include "Exclude.hpp"
12 + #include "SkipList.hpp"
13   #include "AbstractClasses.hpp"
14   #include "MakeStamps.hpp"
15 + #include "SimState.hpp"
16 + #include "Restraints.hpp"
17  
18   #define __C
19   #include "fSimulation.h"
20   #include "fortranWrapDefines.hpp"
21 + #include "GenericData.hpp"
22 + //#include "Minimizer.hpp"
23 + //#include "OOPSEMinimizer.hpp"
24  
25  
26 <
26 > double roundMe( double x );
27 > class OOPSEMinimizer;
28   class SimInfo{
29  
30   public:
31  
32    SimInfo();
33 <  ~SimInfo(){}
33 >  ~SimInfo();
34  
35    int n_atoms; // the number of atoms
36    Atom **atoms; // the array of atom objects
37 +
38 +  vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
39 +  vector<StuntDouble*> integrableObjects;
40    
41    double tau[9]; // the stress tensor
42  
43 <  unsigned int n_bonds;    // number of bends
44 <  unsigned int n_bends;    // number of bends
45 <  unsigned int n_torsions; // number of torsions
46 <  unsigned int n_oriented; // number of of atoms with orientation
43 >  int n_bonds;    // number of bends
44 >  int n_bends;    // number of bends
45 >  int n_torsions; // number of torsions
46 >  int n_oriented; // number of of atoms with orientation
47 >  int ndf;        // number of actual degrees of freedom
48 >  int ndfRaw;     // number of settable degrees of freedom
49 >  int ndfTrans;   // number of translational degrees of freedom
50 >  int nZconstraints; // the number of zConstraints
51  
52 <  unsigned int setTemp;   // boolean to set the temperature at each sampleTime
52 >  int setTemp;   // boolean to set the temperature at each sampleTime
53 >  int resetIntegrator; // boolean to reset the integrator
54  
55 <  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
55 >  int n_dipoles; // number of dipoles
56  
57 <  int n_exclude;  // the # of pairs excluded from long range forces
58 <  int *excludes;       // the pairs themselves
43 <
57 >  int n_exclude;
58 >  Exclude* excludes;  // the exclude list for ignoring pairs in fortran
59    int nGlobalExcludes;
60    int* globalExcludes; // same as above, but these guys participate in
61                         // no long range forces.
62  
63    int* identArray;     // array of unique identifiers for the atoms
64 +  int* molMembershipArray;  // map of atom numbers onto molecule numbers
65  
66    int n_constraints; // the number of constraints on the system
67  
68 <  unsigned int n_SRI;   // the number of short range interactions
53 <  SRI **sr_interactions;// the array of short range force objects
68 >  int n_SRI;   // the number of short range interactions
69  
70    double lrPot; // the potential energy from the long range calculations.
71  
72 <  double box_x, box_y, box_z; // the periodic boundry conditions
73 <  double rList, rCut; // variables for the neighborlist
72 >  double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
73 >                      // column vectors of the x, y, and z box vectors.
74 >                      //   h1  h2  h3
75 >                      // [ Xx  Yx  Zx ]
76 >                      // [ Xy  Yy  Zy ]
77 >                      // [ Xz  Yz  Zz ]
78 >                      //  
79 >  double HmatInv[3][3];
80 >
81 >  double boxL[3]; // The Lengths of the 3 column vectors of Hmat
82 >  double boxVol;
83 >  int orthoRhombic;
84    
85 +
86 +  double dielectric;      // the dielectric of the medium for reaction field
87 +
88 +  
89    int usePBC; // whether we use periodic boundry conditions.
90    int useLJ;
91    int useSticky;
92 <  int useDipole;
92 >  int useCharges;
93 >  int useDipoles;
94    int useReactionField;
95    int useGB;
96    int useEAM;
97 <  
97 >  bool haveCutoffGroups;
98 >  bool useInitXSstate;
99 >  double orthoTolerance;
100  
101    double dt, run_time;           // the time step and total time
102    double sampleTime, statusTime; // the position and energy dump frequencies
103    double target_temp;            // the target temperature of the system
104    double thermalTime;            // the temp kick interval
105 +  double currentTime;            // Used primarily for correlation Functions
106 +  double resetTime;              // Use to reset the integrator periodically
107  
108    int n_mol;           // n_molecules;
109    Molecule* molecules; // the array of molecules
110    
111 <  int nComponents;           // the number of componentsin the system
111 >  int nComponents;           // the number of components in the system
112    int* componentsNmol;       // the number of molecules of each component
113    MoleculeStamp** compStamps;// the stamps matching the components
114    LinkedMolStamp* headStamp; // list of stamps used in the simulation
# Line 82 | Line 116 | class SimInfo{ (public)
116    
117    char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
118    char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
119 <  Integrator *the_integrator; // the integrator of the simulation
119 >  BaseIntegrator *the_integrator; // the integrator of the simulation
120  
121 +  OOPSEMinimizer* the_minimizer; // the energy minimizer
122 +  Restraints* restraint;
123 +  bool has_minimizer;
124 +
125    char finalName[300];  // the name of the eor file to be written
126    char sampleName[300]; // the name of the dump file to be written
127    char statusName[300]; // the name of the stat file to be written
128 +  char rawPotName[300];  // the name of the raw file to be written
129  
130 +  int seed;                    //seed for random number generator
131  
132 +  int useThermInt;        // whether or not we use thermodynamic integration
133 +  double thermIntLambda; // lambda for TI
134 +  double thermIntK;      // power of lambda for TI
135 +  double vRaw;           // unperturbed potential for TI
136 +  double vHarm;          // harmonic potential for TI
137 +  int i;                 // just an int
138 +
139 +  vector<double> mfact;
140 +  int ngroup;
141 +  vector<int> groupList;
142 +  vector<int> groupStart;
143 +  
144    // refreshes the sim if things get changed (load balanceing, volume
145    // adjustment, etc.)
146  
# Line 97 | Line 149 | class SimInfo{ (public)
149  
150    // sets the internal function pointer to fortran.
151  
152 <  void setInternal( void (*fSetup) setFortranSimList,
153 <                    void (*fBox) setFortranBoxList ){
152 >  void setInternal( setFortranSim_TD fSetup,
153 >                    setFortranBox_TD fBox,
154 >                    notifyFortranCutOff_TD fCut){
155      setFsimulation = fSetup;
156      setFortranBoxSize = fBox;
157 +    notifyFortranCutOffs = fCut;
158    }
159  
160 +  int getNDF();
161 +  int getNDFraw();
162 +  int getNDFtranslational();
163 +  int getTotIntegrableObjects();
164 +  void setBox( double newBox[3] );
165 +  void setBoxM( double newBox[3][3] );
166 +  void getBoxM( double theBox[3][3] );
167 +  void scaleBox( double scale );
168 +  
169 +  void setDefaultRcut( double theRcut );
170 +  void setDefaultRcut( double theRcut, double theRsw );
171 +  void checkCutOffs( void );
172 +
173 +  double getRcut( void )  { return rCut; }
174 +  double getRlist( void ) { return rList; }
175 +  double getRsw( void )   { return rSw; }
176 +  double getMaxCutoff( void ) { return maxCutoff; }
177 +  
178 +  void setTime( double theTime ) { currentTime = theTime; }
179 +  void incrTime( double the_dt ) { currentTime += the_dt; }
180 +  void decrTime( double the_dt ) { currentTime -= the_dt; }
181 +  double getTime( void ) { return currentTime; }
182 +
183 +  void wrapVector( double thePos[3] );
184 +
185 +  SimState* getConfiguration( void ) { return myConfiguration; }
186 +  
187 +  void addProperty(GenericData* prop);
188 +  GenericData* getProperty(const string& propName);
189 +  //vector<GenericData*>& getProperties()  {return properties;}    
190 +
191 +  int getSeed(void) {  return seed; }
192 +  void setSeed(int theSeed) {  seed = theSeed;}
193 +
194   private:
195 +
196 +  SimState* myConfiguration;
197 +
198 +  int boxIsInit, haveRcut, haveRsw;
199 +
200 +  double rList, rCut; // variables for the neighborlist
201 +  double rSw;         // the switching radius
202 +
203 +  double maxCutoff;
204 +
205 +  double distXY;
206 +  double distYZ;
207 +  double distZX;
208    
209 +  void calcHmatInv( void );
210 +  void calcBoxL();
211 +  double calcMaxCutOff();
212 +
213    // private function to initialize the fortran side of the simulation
214 <  void (*setFsimulation) setFortranSimList;
214 >  setFortranSim_TD setFsimulation;
215  
216 <  void (*setFortranBoxSize) setFortranBoxList;
216 >  setFortranBox_TD setFortranBoxSize;
217 >  
218 >  notifyFortranCutOff_TD notifyFortranCutOffs;
219 >  
220 >  //Addtional Properties of SimInfo
221 >  map<string, GenericData*> properties;
222 >
223   };
224  
225 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
226 +                                                          vector<int>& groupList, vector<int>& groupStart);
227  
115 –
228   #endif

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