#include <FreeEnergyRestrain.h>
Inheritance diagram for APosRestraint:
Public Member Functions | |
| APosRestraint () | |
| void | PrintInfo () |
| virtual AVector | GetPosTarget ()=0 |
| virtual double | GetDistance ()=0 |
Protected Member Functions | |
| double | GetE (AVector RefPos, double LambdaKf=1.0) |
| AVector | GetGrad (int WhichGroup, AVector RefPos, double LambdaKf=1.0) |
|
|
Definition at line 260 of file FreeEnergyRestrain.C. 00260 {
00261 //-----------------------------------------------------------------
00262 // each APosRestraint restrains 1 group of atoms to a location
00263 //-----------------------------------------------------------------
00264 m_NumGroups = 1;
00265 m_pGroups = new AGroup[m_NumGroups];
00266 m_pCOMs = new AVector[m_NumGroups];
00267 }
|
|
|
Implemented in AFixedPosRestraint, ABoundPosRestraint, and AForcingPosRestraint. Referenced by PrintInfo(). |
|
||||||||||||
|
Definition at line 299 of file FreeEnergyRestrain.C. References AVector::DistSqr(). Referenced by AForcingPosRestraint::GetEnergy(), and AFixedPosRestraint::GetEnergy(). 00299 {
00300 //--------------------------------------------------------------------
00301 // calculate and return the Energy for this position restraint.
00302 //
00303 // E = (Kf/2) * (|ri - rref|)**2
00304 //
00305 // where |ri - rref| is the distance between a) the center-of-mass
00306 // of the restrained atoms and b) the reference position.
00307 //
00308 // Note: COM is calculated before this routine is called.
00309 //--------------------------------------------------------------------
00310 return( ((m_Kf*LambdaKf)/2.0) * m_pCOMs[0].DistSqr(RefPos) );
00311 }
|
|
||||||||||||||||
|
Definition at line 314 of file FreeEnergyRestrain.C. Referenced by AForcingPosRestraint::GetGradient(), and AFixedPosRestraint::GetGradient(). 00315 {
00316 //-------------------------------------------------------------------------
00317 // calculate and return the gradient for this position restraint.
00318 //
00319 // E = (Kf/2) * (|ri - rref|)**2
00320 //
00321 // return: grad(E)
00322 //
00323 // Notes: COM is calculated before this routine is called.
00324 // m_pCOMs points to an array of vectors
00325 // m_pCOMS[0] references the only COM for a position restraint
00326 // m_pCOMS[0][0] returns the x value from the vector (x,y,z)
00327 // (operator[] is defined to return an item from the vector)
00328 //-------------------------------------------------------------------------
00329 // WhichGroup = 0; // don't care -- there's only 1 atom restrained
00330 AVector Vec(m_pCOMs[0][0] - RefPos[0],
00331 m_pCOMs[0][1] - RefPos[1],
00332 m_pCOMs[0][2] - RefPos[2]);
00333 return(Vec*m_Kf*LambdaKf);
00334 }
|
|
|
Implemented in AFixedPosRestraint, ABoundPosRestraint, and AForcingPosRestraint. Referenced by PrintInfo(). |
|
|
Implements ARestraint. Definition at line 270 of file FreeEnergyRestrain.C. References GetDistance(), GetPosTarget(), iout, and AVector::Out(). 00270 {
00271 //--------------------------------------------------------------------
00272 // print the position for this position restraint
00273 //--------------------------------------------------------------------
00274 double Distance;
00275 char Str[20];
00276
00277 Distance = GetDistance();
00278 sprintf(Str, "%7.3f", Distance);
00279
00280 #if defined(_VERBOSE_PMF)
00281 iout << "Position = ";
00282 m_pCOMs[0].Out();
00283 iout << " Target = ";
00284 GetPosTarget().Out();
00285 iout << " Distance = ";
00286 iout << Str;
00287 iout << std::endl << endi;
00288 #else
00289 m_pCOMs[0].Out();
00290 iout << " ";
00291 GetPosTarget().Out();
00292 iout << " ";
00293 iout << Str;
00294 iout << " | ";
00295 #endif
00296 }
|
1.3.9.1