| 6 |
|
#include <vector> |
| 7 |
|
|
| 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" |
| 18 |
|
#include "fSimulation.h" |
| 19 |
|
#include "fortranWrapDefines.hpp" |
| 20 |
|
#include "GenericData.hpp" |
| 21 |
+ |
//#include "Minimizer.hpp" |
| 22 |
+ |
//#include "OOPSEMinimizer.hpp" |
| 23 |
|
|
| 24 |
< |
|
| 20 |
< |
|
| 24 |
> |
class OOPSEMinimizer; |
| 25 |
|
class SimInfo{ |
| 26 |
|
|
| 27 |
|
public: |
| 31 |
|
|
| 32 |
|
int n_atoms; // the number of atoms |
| 33 |
|
Atom **atoms; // the array of atom objects |
| 34 |
+ |
|
| 35 |
+ |
vector<RigidBody*> rigidBodies; // A vector of rigid bodies |
| 36 |
+ |
vector<StuntDouble*> integrableObjects; |
| 37 |
|
|
| 38 |
|
double tau[9]; // the stress tensor |
| 39 |
|
|
| 51 |
|
|
| 52 |
|
int n_dipoles; // number of dipoles |
| 53 |
|
|
| 54 |
< |
|
| 55 |
< |
int n_exclude; // the # of pairs excluded from long range forces |
| 49 |
< |
Exclude** excludes; // the pairs themselves |
| 50 |
< |
|
| 54 |
> |
int n_exclude; |
| 55 |
> |
Exclude* excludes; // the exclude list for ignoring pairs in fortran |
| 56 |
|
int nGlobalExcludes; |
| 57 |
|
int* globalExcludes; // same as above, but these guys participate in |
| 58 |
|
// no long range forces. |
| 86 |
|
int usePBC; // whether we use periodic boundry conditions. |
| 87 |
|
int useLJ; |
| 88 |
|
int useSticky; |
| 89 |
< |
int useDipole; |
| 89 |
> |
int useCharges; |
| 90 |
> |
int useDipoles; |
| 91 |
|
int useReactionField; |
| 92 |
|
int useGB; |
| 93 |
|
int useEAM; |
| 94 |
|
|
| 95 |
+ |
bool useInitXSstate; |
| 96 |
+ |
double orthoTolerance; |
| 97 |
|
|
| 98 |
|
double dt, run_time; // the time step and total time |
| 99 |
|
double sampleTime, statusTime; // the position and energy dump frequencies |
| 115 |
|
char mixingRule[100]; // the mixing rules for Lennard jones/van der walls |
| 116 |
|
BaseIntegrator *the_integrator; // the integrator of the simulation |
| 117 |
|
|
| 118 |
+ |
OOPSEMinimizer* the_minimizer; // the energy minimizer |
| 119 |
+ |
bool has_minimizer; |
| 120 |
+ |
|
| 121 |
|
char finalName[300]; // the name of the eor file to be written |
| 122 |
|
char sampleName[300]; // the name of the dump file to be written |
| 123 |
|
char statusName[300]; // the name of the stat file to be written |
| 142 |
|
int getNDF(); |
| 143 |
|
int getNDFraw(); |
| 144 |
|
int getNDFtranslational(); |
| 145 |
< |
|
| 145 |
> |
int getTotIntegrableObjects(); |
| 146 |
|
void setBox( double newBox[3] ); |
| 147 |
|
void setBoxM( double newBox[3][3] ); |
| 148 |
|
void getBoxM( double theBox[3][3] ); |
| 149 |
|
void scaleBox( double scale ); |
| 150 |
|
|
| 140 |
– |
void setRcut( double theRcut ); |
| 151 |
|
void setDefaultRcut( double theRcut ); |
| 142 |
– |
void setEcr( double theEcr ); |
| 152 |
|
void setDefaultEcr( double theEcr ); |
| 144 |
– |
void setEcr( double theEcr, double theEst ); |
| 153 |
|
void setDefaultEcr( double theEcr, double theEst ); |
| 154 |
|
void checkCutOffs( void ); |
| 155 |
|
|
| 166 |
|
|
| 167 |
|
void wrapVector( double thePos[3] ); |
| 168 |
|
|
| 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 |
– |
|
| 169 |
|
SimState* getConfiguration( void ) { return myConfiguration; } |
| 170 |
|
|
| 171 |
|
void addProperty(GenericData* prop); |
| 172 |
|
GenericData* getProperty(const string& propName); |
| 173 |
< |
vector<GenericData*> getProperties(); |
| 173 |
> |
//vector<GenericData*>& getProperties() {return properties;} |
| 174 |
|
|
| 175 |
|
int getSeed(void) { return seed; } |
| 176 |
|
void setSeed(int theSeed) { seed = theSeed;} |
| 179 |
|
|
| 180 |
|
SimState* myConfiguration; |
| 181 |
|
|
| 182 |
< |
double origRcut, origEcr; |
| 188 |
< |
int boxIsInit, haveOrigRcut, haveOrigEcr; |
| 182 |
> |
int boxIsInit, haveRcut, haveEcr; |
| 183 |
|
|
| 190 |
– |
double oldEcr; |
| 191 |
– |
double oldRcut; |
| 192 |
– |
|
| 184 |
|
double rList, rCut; // variables for the neighborlist |
| 185 |
|
double ecr; // the electrostatic cutoff radius |
| 186 |
|
double est; // the electrostatic skin thickness |
| 194 |
|
void calcBoxL(); |
| 195 |
|
double calcMaxCutOff(); |
| 196 |
|
|
| 206 |
– |
|
| 197 |
|
// private function to initialize the fortran side of the simulation |
| 198 |
|
setFortranSim_TD setFsimulation; |
| 199 |
|
|
| 206 |
|
|
| 207 |
|
}; |
| 208 |
|
|
| 219 |
– |
|
| 220 |
– |
|
| 209 |
|
#endif |
