#include <GlobalMasterTMD.h>

Inheritance diagram for GlobalMasterTMD:

Public Member Functions
	GlobalMasterTMD ()

	~GlobalMasterTMD ()

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 17 of file GlobalMasterTMD.h.

Constructor & Destructor Documentation

GlobalMasterTMD::GlobalMasterTMD ( )

Definition at line 81 of file GlobalMasterTMD.C.

References DebugM, endi(), SimParameters::firstTimestep, iINFO(), iout, Node::molecule, Molecule::numAtoms, Node::Object(), Node::simParameters, SimParameters::TMDDiffRMSD, SimParameters::TMDFile, SimParameters::TMDFile2, SimParameters::TMDFinalRMSD, SimParameters::TMDFirstStep, SimParameters::TMDInitialRMSD, SimParameters::TMDk, SimParameters::TMDLastStep, and SimParameters::TMDOutputFreq.

                                  {
   DebugM(3,"initialize called\n");
   SimParameters *params = Node::Object()->simParameters;
   outputFreq = params->TMDOutputFreq;
   K = params->TMDk;
 /*  if (params->TMDInitialRMSD < 0){
     initialRMS = -1; // get from first coordinates
   }
   else */
     initialRMS = params->TMDInitialRMSD;
   finalRMS = params->TMDFinalRMSD;
   
   currentStep = params->firstTimestep;
   firstStep = params->TMDFirstStep;
   lastStep = params->TMDLastStep;
   qDiffRMSD=params->TMDDiffRMSD;
   altloc = 0;
   target = 0;
   target2 = 0;
   weight = 0;
   if (qDiffRMSD) parseAtoms(params->TMDFile2,Node::Object()->molecule->numAtoms, 1);
   parseAtoms(params->TMDFile,Node::Object()->molecule->numAtoms, 0);
 
   //iterate through all domains to see if altloc is used
   map <int, vector<int> >::iterator it;
   for (it = dmap.begin(); it != dmap.end(); ++it){  
     int refcount = 0;
     int biascount = 0;
     for(int i = 0; i<it->second.size(); i++){
       char aloc = altloc[it->second[i]];
       if ( aloc & 1 ) ++biascount;
       if ( aloc & 2 ) ++refcount;
     }
     altlocmap[it->first] = ( refcount ? 1 : 0 );
     if ( ! refcount ) refcount = it->second.size();
     iout << iINFO << "TMD domain " << it->first <<
       " has " << it->second.size() << " atoms " <<
       refcount << " fitted " << biascount << " biased\n" << endi;
   }
 
  // k /= numTMDatoms;
   iout << iINFO << numTMDatoms << " TMD ATOMS\n" << endi;
   DebugM(1,"done with initialize\n");
 }

GlobalMasterTMD::~GlobalMasterTMD ( )

Definition at line 227 of file GlobalMasterTMD.C.

                                   { 
   delete [] target;
  // delete [] target_aid;
 //  delete [] aidmap;
   delete [] atompos;
   delete [] atompos2;
   delete [] altloc;
   delete [] target2;
 }

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation