#include <GlobalMasterSymmetry.h>

Inheritance diagram for GlobalMasterSymmetry:

Public Member Functions
	GlobalMasterSymmetry ()

	~GlobalMasterSymmetry ()

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	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 16 of file GlobalMasterSymmetry.h.

Constructor & Destructor Documentation

GlobalMasterSymmetry::GlobalMasterSymmetry ( )

Definition at line 57 of file GlobalMasterSymmetry.C.

References Node::configList, StringList::data, DebugM, ConfigList::find(), SimParameters::firstTimestep, Node::molecule, NAMD_die(), StringList::next, Molecule::numAtoms, Node::Object(), Node::simParameters, SimParameters::symmetryFirstFullStep, SimParameters::symmetryFirstStep, SimParameters::symmetryk, SimParameters::symmetryLastFullStep, SimParameters::symmetryLastStep, and SimParameters::symmetryScaleForces.

                                            {
   DebugM(3,"initialize called\n");
   SimParameters *params = Node::Object()->simParameters;
   currentStep = params->firstTimestep;
   firstStep = params->symmetryFirstStep;
   lastStep = params->symmetryLastStep;
   firstFullStep = params->symmetryFirstFullStep;
   lastFullStep = params->symmetryLastFullStep;
   K = params->symmetryk;
 
   StringList *klist = Node::Object()->configList->find("symmetrykfile");
   if (!K){
     //if (!params->symmetrykfile){NAMD_die("A pdb file containing per-atom force constants must be specified if symmetryk is not in configuration file!");}
     if (!klist){NAMD_die("A pdb file containing per-atom force constants must be specified if symmetryk is not in configuration file!");}
     //symmetrykfile = params->symmetrykfile;
   }
   scaleForces = params->symmetryScaleForces;
   if (scaleForces && lastStep == -1){
     NAMD_die("symmetryLastStep must be specified if symmetryScaleForces is enabled!");
   }
   StringList *matrixList = Node::Object()->configList->find("symmetryMatrixFile");
   StringList *symmetryList = Node::Object()->configList->find("symmetryFile");
   int symfileindex = 0;
   if (!K) {symmetrykfile = klist->data;}
   for (; symmetryList; symmetryList = symmetryList->next) {  
     parseAtoms(symmetryList->data, Node::Object()->molecule->numAtoms, symfileindex);
     if(!K){
       klist = klist->next;
      if (klist){ symmetrykfile = klist->data;}
     }
   }
 
   map<int, vector<int> >::iterator it = simmap.begin();
   if (!matrixList) {initialTransform();}
   for (; matrixList; matrixList = matrixList->next, ++it){
       parseMatrix(it->first, matrixList->data);
   }
 
   DebugM(1,"done with initialize\n");
 }

GlobalMasterSymmetry::~GlobalMasterSymmetry ( )

Definition at line 395 of file GlobalMasterSymmetry.C.

                                             { 
   map <int, BigReal *>::iterator pit = posmap.begin();
   for (; pit != posmap.end(); ++pit){delete pit->second;}
 }

The documentation for this class was generated from the following files:

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation