#include <FreeEnergyRestrain.h>
Inheritance diagram for ADistRestraint:
Public Member Functions | |
| ADistRestraint () | |
| void | PrintInfo () |
| virtual double | GetDistTarget ()=0 |
Protected Member Functions | |
| double | GetE (double RefDist, double LambdaKf=1.0) |
| AVector | GetGrad (int WhichGroup, double RefDist, double LambdaKf=1.0) |
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Definition at line 337 of file FreeEnergyRestrain.C. 00337 {
00338 //-----------------------------------------------------------------------
00339 // each ADistRestraint restrains the distance between 2 groups of atoms
00340 //-----------------------------------------------------------------------
00341 m_NumGroups = 2;
00342 m_pGroups = new AGroup[m_NumGroups];
00343 m_pCOMs = new AVector[m_NumGroups];
00344 }
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Implemented in AFixedDistRestraint, ABoundDistRestraint, and AForcingDistRestraint. Referenced by PrintInfo(). |
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Definition at line 374 of file FreeEnergyRestrain.C. References AVector::Dist(). Referenced by AForcingDistRestraint::GetEnergy(), ABoundDistRestraint::GetEnergy(), and AFixedDistRestraint::GetEnergy(). 00374 {
00375 //---------------------------------------------------------------------------
00376 // calculate and return the Energy for this distance restraint.
00377 //
00378 // E = (Kf/2) * (di-dref)**2
00379 //
00380 // where di is the distance between 2 centers-of-mass of restrained atoms,
00381 // and dref is the reference distance.
00382 //
00383 // Note: COM's are calculated before this routine is called.
00384 //---------------------------------------------------------------------------
00385 double Dist, Diff;
00386
00387 Dist = m_pCOMs[0].Dist(m_pCOMs[1]);
00388 Diff = Dist - RefDist;
00389 return( ((m_Kf*LambdaKf)/2.0) * (Diff*Diff) );
00390 }
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Definition at line 393 of file FreeEnergyRestrain.C. References ASSERT, AVector::Dist(), and AVector::Set(). Referenced by AForcingDistRestraint::GetGradient(), ABoundDistRestraint::GetGradient(), and AFixedDistRestraint::GetGradient(). 00394 {
00395 //---------------------------------------------------------------------------
00396 // calculate and return the gradient for this distance restraint.
00397 //
00398 // E = (Kf/2) * (di-dref)**2
00399 //
00400 // return: grad(E)
00401 //
00402 // Notes: COM is calculated before this routine is called.
00403 // m_pCOMS[0 & 1] reference the COM's of each group of atoms
00404 //---------------------------------------------------------------------------
00405 double Dist;
00406 AVector Vec, A, B;
00407
00408 ASSERT( (WhichGroup==0) || (WhichGroup==1) );
00409 if (WhichGroup == 0) {
00410 A = m_pCOMs[0];
00411 B = m_pCOMs[1];
00412 }
00413 else {
00414 A = m_pCOMs[1];
00415 B = m_pCOMs[0];
00416 }
00417
00418 Dist = A.Dist(B);
00419 Vec.Set(A[0]-B[0], A[1]-B[1], A[2]-B[2]);
00420 Vec *= m_Kf * LambdaKf * (Dist - RefDist) / Dist;
00421 return(Vec);
00422 }
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Implements ARestraint. Definition at line 347 of file FreeEnergyRestrain.C. References AVector::Dist(), GetDistTarget(), and iout. 00347 {
00348 //--------------------------------------------------------------------
00349 // print the distance for this distance restraint
00350 //--------------------------------------------------------------------
00351 double Distance;
00352 char Str1[20], Str2[20];
00353
00354 Distance = m_pCOMs[0].Dist(m_pCOMs[1]);
00355 sprintf(Str1, "%7.3f", Distance);
00356 Distance = GetDistTarget();
00357 sprintf(Str2, "%7.3f", Distance);
00358
00359 #if defined(_VERBOSE_PMF)
00360 iout << "Distance = ";
00361 iout << Str1;
00362 iout << " Target = ";
00363 iout << Str2;
00364 iout << std::endl << endi;
00365 #else
00366 iout << Str1;
00367 iout << " ";
00368 iout << Str2;
00369 iout << " | ";
00370 #endif
00371 }
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1.3.9.1