#include <GlobalMasterFreeEnergy.h>

Inheritance diagram for GlobalMasterFreeEnergy:

Public Member Functions
	GlobalMasterFreeEnergy ()

	~GlobalMasterFreeEnergy ()

int	getAtomID (const char segid, int resid, const char aname)

int	getNumAtoms (const char *segid, int resid)

int	getAtomID (const char *segid, int resid, int index)

double	getMass (int atomid)

int	requestAtom (int atomid)

int	getPosition (int atomid, Position &position)

int	addForce (int atomid, Force force)

Public Member Functions inherited from GlobalMaster
void	processData (AtomIDList::iterator a_i, AtomIDList::iterator a_e, PositionList::iterator p_i, PositionList::iterator g_i, PositionList::iterator g_e, BigRealList::iterator gm_i, BigRealList::iterator gm_e, ForceList::iterator gtf_i, ForceList::iterator gtf_e, IntList::iterator goi_i, IntList::iterator goi_e, BigRealList::iterator gov_i, BigRealList::iterator gov_e, AtomIDList::iterator last_atoms_forced_i, AtomIDList::iterator last_atoms_forced_e, ForceList::iterator last_forces_i, AtomIDList::iterator, AtomIDList::iterator, ForceList::iterator)

bool	changedAtoms ()

const AtomIDList &	requestedAtoms ()

bool	changedForces ()

const AtomIDList &	forcedAtoms ()

const ForceList &	appliedForces ()

bool	changedGroups ()

const ResizeArray< AtomIDList > &	requestedGroups ()

const ForceList &	groupForces ()

bool	changedGridObjs ()

const IntList &	requestedGridObjs ()

const BigRealList &	gridObjForces ()

bool	requestedTotalForces ()

void	clearChanged ()

virtual	~GlobalMaster ()

void	check () const

void	setLattice (const Lattice *lat)

Additional Inherited Members
Public Attributes inherited from GlobalMaster
int	step

int	globalMasterStep

int	old_num_groups_requested

Protected Member Functions inherited from GlobalMaster
	GlobalMaster ()

AtomIDList &	modifyRequestedAtoms ()

AtomIDList &	modifyForcedAtoms ()

ForceList &	modifyAppliedForces ()

ResizeArray< AtomIDList > &	modifyRequestedGroups ()

ForceList &	modifyGroupForces ()

IntList &	modifyRequestedGridObjects ()

BigRealList &	modifyGridObjForces ()

AtomIDList::const_iterator	getAtomIdBegin ()

AtomIDList::const_iterator	getAtomIdEnd ()

PositionList::const_iterator	getAtomPositionBegin ()

PositionList::const_iterator	getGroupPositionBegin ()

PositionList::const_iterator	getGroupPositionEnd ()

ForceList::const_iterator	getGroupTotalForceBegin ()

ForceList::const_iterator	getGroupTotalForceEnd ()

IntList::const_iterator	getGridObjIndexBegin ()

IntList::const_iterator	getGridObjIndexEnd ()

BigRealList::const_iterator	getGridObjValueBegin ()

BigRealList::const_iterator	getGridObjValueEnd ()

AtomIDList::const_iterator	getLastAtomsForcedBegin ()

AtomIDList::const_iterator	getLastAtomsForcedEnd ()

ForceList::const_iterator	getLastForcesBegin ()

AtomIDList::const_iterator	getForceIdBegin ()

AtomIDList::const_iterator	getForceIdEnd ()

ForceList::const_iterator	getTotalForce ()

void	requestTotalForce (bool yesno=true)

BigRealList::const_iterator	getGroupMassBegin ()

BigRealList::const_iterator	getGroupMassEnd ()

Protected Attributes inherited from GlobalMaster
bool	totalForceRequested

const Lattice *	lattice

AtomIDList::iterator	atomIdBegin

AtomIDList::iterator	atomIdEnd

PositionList::iterator	atomPositionBegin

PositionList::iterator	groupPositionBegin

PositionList::iterator	groupPositionEnd

BigRealList::iterator	groupMassBegin

BigRealList::iterator	groupMassEnd

ForceList::iterator	groupTotalForceBegin

ForceList::iterator	groupTotalForceEnd

IntList::iterator	gridObjIndexBegin

IntList::iterator	gridObjIndexEnd

BigRealList::iterator	gridObjValueBegin

BigRealList::iterator	gridObjValueEnd

AtomIDList::iterator	lastAtomsForcedBegin

ForceList::iterator	lastForcesBegin

AtomIDList::iterator	lastAtomsForcedEnd

AtomIDList::iterator	forceIdBegin

AtomIDList::iterator	forceIdEnd

ForceList::iterator	totalForceBegin

bool	reqAtomsChanged

AtomIDList	reqAtoms

bool	appForcesChanged

AtomIDList	fAtoms

ForceList	appForces

bool	reqGroupsChanged

ResizeArray< AtomIDList >	reqGroups

ForceList	grpForces

bool	reqGridObjsChanged

IntList	reqGridObjs

BigRealList	gridobjForces

Detailed Description

Definition at line 17 of file GlobalMasterFreeEnergy.h.

Constructor & Destructor Documentation

◆ GlobalMasterFreeEnergy()

GlobalMasterFreeEnergy::GlobalMasterFreeEnergy ( )

Definition at line 189 of file GlobalMasterFreeEnergy.C.

References DebugM, Node::molecule, Node::Object(), and Node::simParameters.

 : GlobalMaster() {
   DebugM(3,"Constructing GlobalMasterFreeEnergy\n");
   molecule = Node::Object()->molecule;
   simParams = Node::Object()->simParameters;
 
   // now set up the free energy stuff
   initialize();
 }

◆ ~GlobalMasterFreeEnergy()

GlobalMasterFreeEnergy::~GlobalMasterFreeEnergy ( )

Definition at line 199 of file GlobalMasterFreeEnergy.C.

References DebugM.

                                                 {
   DebugM(3,"Destructing GlobalMasterFreeEnergy\n");
   delete config;
 }

Member Function Documentation

◆ addForce()

int GlobalMasterFreeEnergy::addForce	(	int	atomid,
		Force	force
	)

Definition at line 179 of file GlobalMasterFreeEnergy.C.

References ResizeArray< Elem >::add(), DebugM, GlobalMaster::modifyAppliedForces(), GlobalMaster::modifyForcedAtoms(), and Molecule::numAtoms.

Referenced by ARestraint::DistributeForce().

 {
   DebugM(2,"Forcing "<<atomid<<" with "<<force<<"\n");
   if ( atomid < 0 || atomid >= molecule->numAtoms ) return -1;  // failure
   modifyForcedAtoms().add(atomid);
   modifyAppliedForces().add(force);
   return 0;  // success
 }

◆ getAtomID() [1/2]

int GlobalMasterFreeEnergy::getAtomID	(	const char *	segid,
		int	resid,
		const char *	aname
	)

Definition at line 134 of file GlobalMasterFreeEnergy.C.

References Molecule::get_atom_from_name().

Referenced by AddAtom(), and AddResidues().

 {
   return molecule->get_atom_from_name(segid,resid,aname);
 }

◆ getAtomID() [2/2]

int GlobalMasterFreeEnergy::getAtomID	(	const char *	segid,
		int	resid,
		int	index
	)

Definition at line 146 of file GlobalMasterFreeEnergy.C.

References Molecule::get_atom_from_index_in_residue().

 {
   return molecule->get_atom_from_index_in_residue(segid,resid,index);
 }

◆ getMass()

double GlobalMasterFreeEnergy::getMass ( int atomid )

Definition at line 151 of file GlobalMasterFreeEnergy.C.

References Molecule::atommass(), and Molecule::numAtoms.

Referenced by ARestraint::DistributeForce(), and ARestraint::UpdateCOMs().

 {
   if ( atomid < 0 || atomid >= molecule->numAtoms ) return -1.;  // failure
   return molecule->atommass(atomid);
 }

◆ getNumAtoms()

int GlobalMasterFreeEnergy::getNumAtoms	(	const char *	segid,
		int	resid
	)

Definition at line 140 of file GlobalMasterFreeEnergy.C.

References Molecule::get_residue_size().

Referenced by AddResidues().

 {
   return molecule->get_residue_size(segid,resid);
 }

◆ getPosition()

int GlobalMasterFreeEnergy::getPosition	(	int	atomid,
		Position &	position
	)

Definition at line 165 of file GlobalMasterFreeEnergy.C.

References GlobalMaster::getAtomIdBegin(), GlobalMaster::getAtomIdEnd(), and GlobalMaster::getAtomPositionBegin().

Referenced by ARestraint::UpdateCOMs().

 {
   AtomIDList::const_iterator a_i = getAtomIdBegin();
   AtomIDList::const_iterator a_e = getAtomIdEnd();
   PositionList::const_iterator p_i = getAtomPositionBegin();
   for ( ; a_i != a_e; ++a_i, ++p_i ) {
     if ( *a_i == atomid ) {
       position = *p_i;
       return 0;  // success
     }
   }
   return -1;  // failure
 }

◆ requestAtom()

int GlobalMasterFreeEnergy::requestAtom ( int atomid )

Definition at line 158 of file GlobalMasterFreeEnergy.C.

References ResizeArray< Elem >::add(), GlobalMaster::modifyRequestedAtoms(), and Molecule::numAtoms.