NAMD
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#include <FreeEnergyRestrain.h>
Public Member Functions | |
ARestraint () | |
virtual | ~ARestraint () |
int | GetNumGroups () |
void | SetKf (double Kf) |
double | GetKf () |
void | SetLambdaKf (double LambdaKf) |
void | SetLambdaRef (double LambdaRef) |
double | GetLambdaKf () |
double | GetLambdaRef () |
void | SetGroup (AGroup &Group, int GroupIndex) |
void | SetGroups (AGroup &Group1) |
void | SetGroups (AGroup &Group1, AGroup &Group2) |
void | SetGroups (AGroup &Group1, AGroup &Group2, AGroup &Group3) |
void | SetGroups (AGroup &Group1, AGroup &Group2, AGroup &Group3, AGroup &Group4) |
void | UpdateCOMs (GlobalMasterFreeEnergy &CFE) |
void | DistributeForce (int WhichGroup, AVector Force, GlobalMasterFreeEnergy &CFE) |
virtual AVector | GetGradient (int WhichGroup)=0 |
virtual double | GetEnergy ()=0 |
virtual void | GetStr (char *Str)=0 |
virtual void | PrintInfo ()=0 |
virtual Bool_t | IsForcing () |
virtual double | Get_dU_dLambda () |
virtual void | SetRefPos (AVector) |
virtual void | SetRefDist (double) |
virtual void | SetRefAngle (double) |
virtual void | SetBound (Bound_t) |
virtual void | SetLowerAngle (double) |
virtual void | SetUpperAngle (double) |
virtual void | SetIntervalAngle (double) |
virtual void | SetStartPos (AVector) |
virtual void | SetStopPos (AVector) |
virtual void | SetStartDist (double) |
virtual void | SetStopDist (double) |
virtual void | SetStartAngle (double) |
virtual void | SetStopAngle (double) |
Protected Member Functions | |
double | GetAngle (AVector &A, AVector &B, AVector &C) |
double | GetDihe (AVector &A, AVector &B, AVector &C, AVector &D) |
void | EarlyExit (const char *Str, int AtomID) |
Protected Attributes | |
double | m_Kf |
int | m_NumGroups |
AGroup * | m_pGroups |
AVector * | m_pCOMs |
Static Protected Attributes | |
static double | m_LambdaKf = 1.0 |
static double | m_LambdaRef = 0.0 |
Definition at line 17 of file FreeEnergyRestrain.h.
ARestraint::ARestraint | ( | ) |
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void ARestraint::DistributeForce | ( | int | WhichGroup, |
AVector | Force, | ||
GlobalMasterFreeEnergy & | CFE | ||
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Definition at line 179 of file FreeEnergyRestrain.C.
References GlobalMasterFreeEnergy::addForce(), ASSERT, EarlyExit(), GlobalMasterFreeEnergy::getMass(), AGroup::GetNumInGroup(), m_NumGroups, m_pGroups, and SetEqual().
Referenced by ARestraintManager::AddForces().
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Definition at line 64 of file FreeEnergyRestrain.C.
References endi(), iout, and NAMD_die().
Referenced by DistributeForce(), and UpdateCOMs().
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Reimplemented in AForcingDiheRestraint, AForcingAngleRestraint, AForcingDistRestraint, and AForcingPosRestraint.
Definition at line 77 of file FreeEnergyRestrain.h.
Referenced by ARestraintManager::Print_dU_dLambda_Info(), and ARestraintManager::Sum_dU_dLambdas().
Definition at line 127 of file FreeEnergyRestrain.C.
References AVector::Dist().
Referenced by AForcingAngleRestraint::Get_dU_dLambda(), AnAngleRestraint::GetE(), ABoundAngleRestraint::GetEnergy(), ABoundAngleRestraint::GetGradient(), and AnAngleRestraint::PrintInfo().
Definition at line 144 of file FreeEnergyRestrain.C.
References AVector::cross(), AVector::Dist(), AVector::dot(), and dot().
Referenced by AForcingDiheRestraint::Get_dU_dLambda(), ADiheRestraint::GetE(), ABoundDiheRestraint::GetEnergy(), ADiheRestraint::GetGrad(), ABoundDiheRestraint::GetGradient(), and ADiheRestraint::PrintInfo().
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pure virtual |
Implemented in AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, AForcingPosRestraint, ABoundPosRestraint, and AFixedPosRestraint.
Referenced by ARestraintManager::PrintEnergyInfo().
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pure virtual |
Implemented in AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, AForcingPosRestraint, ABoundPosRestraint, and AFixedPosRestraint.
Referenced by ARestraintManager::AddForces().
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Definition at line 49 of file FreeEnergyRestrain.h.
References m_NumGroups.
Referenced by ARestraintManager::AddForces().
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pure virtual |
Implemented in AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, AForcingPosRestraint, ABoundPosRestraint, and AFixedPosRestraint.
Referenced by ARestraintManager::PrintPreInfo().
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inlinevirtual |
Reimplemented in AForcingDiheRestraint, AForcingAngleRestraint, AForcingDistRestraint, and AForcingPosRestraint.
Definition at line 76 of file FreeEnergyRestrain.h.
References kFalse.
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pure virtual |
Implemented in ADiheRestraint, AnAngleRestraint, ADistRestraint, and APosRestraint.
Referenced by ARestraintManager::PrintRestraintInfo().
Reimplemented in ABoundAngleRestraint, ABoundDistRestraint, and ABoundPosRestraint.
Definition at line 82 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
Definition at line 85 of file FreeEnergyRestrain.C.
References ASSERT, m_NumGroups, and m_pGroups.
Referenced by GetRestraint().
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Reimplemented in ABoundDiheRestraint.
Definition at line 85 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
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Definition at line 52 of file FreeEnergyRestrain.h.
References m_LambdaKf.
Referenced by ARestraintManager::SetLambdaKf(), and ARestraintManager::SetLambdas().
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Definition at line 53 of file FreeEnergyRestrain.h.
References m_LambdaRef.
Referenced by ARestraintManager::SetLambdaRef(), and ARestraintManager::SetLambdas().
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inlinevirtual |
Reimplemented in ABoundDiheRestraint.
Definition at line 83 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
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Reimplemented in AFixedDiheRestraint, ABoundAngleRestraint, and AFixedAngleRestraint.
Definition at line 81 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
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Reimplemented in ABoundDistRestraint, AFixedDistRestraint, and ABoundPosRestraint.
Definition at line 80 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
Reimplemented in ABoundPosRestraint, and AFixedPosRestraint.
Definition at line 79 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
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inlinevirtual |
Reimplemented in AForcingDiheRestraint, and AForcingAngleRestraint.
Definition at line 90 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
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Reimplemented in AForcingDistRestraint.
Definition at line 88 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
Reimplemented in AForcingPosRestraint.
Definition at line 86 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
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Reimplemented in AForcingDiheRestraint, and AForcingAngleRestraint.
Definition at line 91 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
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Reimplemented in AForcingDistRestraint.
Definition at line 89 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
Reimplemented in AForcingPosRestraint.
Definition at line 87 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
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inlinevirtual |
Reimplemented in ABoundDiheRestraint.
Definition at line 84 of file FreeEnergyRestrain.h.
References ASSERT, and kFalse.
Referenced by GetRestraint().
void ARestraint::UpdateCOMs | ( | GlobalMasterFreeEnergy & | CFE | ) |
Definition at line 219 of file FreeEnergyRestrain.C.
References ASSERT, EarlyExit(), GlobalMasterFreeEnergy::getMass(), AGroup::GetNumInGroup(), GlobalMasterFreeEnergy::getPosition(), m_NumGroups, m_pCOMs, m_pGroups, AVector::Set(), and SetEqual().
Referenced by ARestraintManager::UpdateCOMs().
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Definition at line 37 of file FreeEnergyRestrain.h.
Referenced by AForcingPosRestraint::Get_dU_dLambda(), AForcingDistRestraint::Get_dU_dLambda(), AForcingAngleRestraint::Get_dU_dLambda(), AForcingDiheRestraint::Get_dU_dLambda(), APosRestraint::GetE(), ADistRestraint::GetE(), AnAngleRestraint::GetE(), ABoundPosRestraint::GetEnergy(), AFixedDiheRestraint::GetEnergy(), ABoundDiheRestraint::GetEnergy(), AForcingDiheRestraint::GetEnergy(), APosRestraint::GetGrad(), ADistRestraint::GetGrad(), AnAngleRestraint::GetGrad(), ABoundPosRestraint::GetGradient(), AFixedDiheRestraint::GetGradient(), ABoundDiheRestraint::GetGradient(), AForcingDiheRestraint::GetGradient(), GetKf(), and SetKf().
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staticprotected |
Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.
Definition at line 43 of file FreeEnergyRestrain.h.
Referenced by AForcingPosRestraint::Get_dU_dLambda(), AForcingDistRestraint::Get_dU_dLambda(), AForcingAngleRestraint::Get_dU_dLambda(), AForcingDiheRestraint::Get_dU_dLambda(), AForcingPosRestraint::GetEnergy(), AForcingDistRestraint::GetEnergy(), AForcingAngleRestraint::GetEnergy(), AForcingDiheRestraint::GetEnergy(), AForcingPosRestraint::GetGradient(), AForcingDistRestraint::GetGradient(), AForcingAngleRestraint::GetGradient(), AForcingDiheRestraint::GetGradient(), GetLambdaKf(), and SetLambdaKf().
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Definition at line 44 of file FreeEnergyRestrain.h.
Referenced by AForcingPosRestraint::Get_dU_dLambda(), AForcingDistRestraint::Get_dU_dLambda(), AForcingAngleRestraint::Get_dU_dLambda(), AForcingDiheRestraint::Get_dU_dLambda(), AForcingAngleRestraint::GetAngleTarget(), AForcingDiheRestraint::GetDiheTarget1(), AForcingPosRestraint::GetDistance(), AForcingDistRestraint::GetDistTarget(), AForcingPosRestraint::GetEnergy(), AForcingDistRestraint::GetEnergy(), AForcingAngleRestraint::GetEnergy(), AForcingDiheRestraint::GetEnergy(), AForcingPosRestraint::GetGradient(), AForcingDistRestraint::GetGradient(), AForcingAngleRestraint::GetGradient(), AForcingDiheRestraint::GetGradient(), GetLambdaRef(), AForcingPosRestraint::GetPosTarget(), and SetLambdaRef().
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Definition at line 38 of file FreeEnergyRestrain.h.
Referenced by ADiheRestraint::ADiheRestraint(), ADistRestraint::ADistRestraint(), AnAngleRestraint::AnAngleRestraint(), APosRestraint::APosRestraint(), ARestraint(), DistributeForce(), GetNumGroups(), SetGroup(), SetGroups(), and UpdateCOMs().
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Definition at line 40 of file FreeEnergyRestrain.h.
Referenced by ADiheRestraint::ADiheRestraint(), ADistRestraint::ADistRestraint(), AnAngleRestraint::AnAngleRestraint(), APosRestraint::APosRestraint(), ARestraint(), AForcingPosRestraint::Get_dU_dLambda(), AForcingDistRestraint::Get_dU_dLambda(), AForcingAngleRestraint::Get_dU_dLambda(), AForcingDiheRestraint::Get_dU_dLambda(), AFixedPosRestraint::GetDistance(), ABoundPosRestraint::GetDistance(), AForcingPosRestraint::GetDistance(), APosRestraint::GetE(), ADistRestraint::GetE(), AnAngleRestraint::GetE(), ADiheRestraint::GetE(), ABoundPosRestraint::GetEnergy(), ABoundDistRestraint::GetEnergy(), ABoundAngleRestraint::GetEnergy(), ABoundDiheRestraint::GetEnergy(), APosRestraint::GetGrad(), ADistRestraint::GetGrad(), AnAngleRestraint::GetGrad(), ADiheRestraint::GetGrad(), ABoundPosRestraint::GetGradient(), ABoundDistRestraint::GetGradient(), ABoundAngleRestraint::GetGradient(), ABoundDiheRestraint::GetGradient(), APosRestraint::PrintInfo(), ADistRestraint::PrintInfo(), AnAngleRestraint::PrintInfo(), ADiheRestraint::PrintInfo(), UpdateCOMs(), and ~ARestraint().
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Definition at line 39 of file FreeEnergyRestrain.h.
Referenced by ADiheRestraint::ADiheRestraint(), ADistRestraint::ADistRestraint(), AnAngleRestraint::AnAngleRestraint(), APosRestraint::APosRestraint(), ARestraint(), DistributeForce(), SetGroup(), SetGroups(), UpdateCOMs(), and ~ARestraint().