NAMD
Public Member Functions | List of all members
GlobalMasterTMD Class Reference

#include <GlobalMasterTMD.h>

Inheritance diagram for GlobalMasterTMD:
GlobalMaster

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 AtomIDListrequestedAtoms ()
 
bool changedForces ()
 
const AtomIDListforcedAtoms ()
 
const ForceListappliedForces ()
 
bool changedGroups ()
 
const ResizeArray< AtomIDList > & requestedGroups ()
 
const ForceListgroupForces ()
 
bool changedGridObjs ()
 
const IntListrequestedGridObjs ()
 
const BigRealListgridObjForces ()
 
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 ()
 
AtomIDListmodifyRequestedAtoms ()
 
AtomIDListmodifyForcedAtoms ()
 
ForceListmodifyAppliedForces ()
 
ResizeArray< AtomIDList > & modifyRequestedGroups ()
 
ForceListmodifyGroupForces ()
 
IntListmodifyRequestedGridObjects ()
 
BigRealListmodifyGridObjForces ()
 
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 Latticelattice
 
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< AtomIDListreqGroups
 
ForceList grpForces
 
bool reqGridObjsChanged
 
IntList reqGridObjs
 
BigRealList gridobjForces
 

Detailed Description

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

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.

81  {
82  DebugM(3,"initialize called\n");
84  outputFreq = params->TMDOutputFreq;
85  K = params->TMDk;
86 /* if (params->TMDInitialRMSD < 0){
87  initialRMS = -1; // get from first coordinates
88  }
89  else */
90  initialRMS = params->TMDInitialRMSD;
91  finalRMS = params->TMDFinalRMSD;
92 
93  currentStep = params->firstTimestep;
94  firstStep = params->TMDFirstStep;
95  lastStep = params->TMDLastStep;
96  qDiffRMSD=params->TMDDiffRMSD;
97  altloc = 0;
98  target = 0;
99  target2 = 0;
100  weight = 0;
101  if (qDiffRMSD) parseAtoms(params->TMDFile2,Node::Object()->molecule->numAtoms, 1);
102  parseAtoms(params->TMDFile,Node::Object()->molecule->numAtoms, 0);
103 
104  //iterate through all domains to see if altloc is used
105  map <int, vector<int> >::iterator it;
106  for (it = dmap.begin(); it != dmap.end(); ++it){
107  int refcount = 0;
108  int biascount = 0;
109  for(int i = 0; i<it->second.size(); i++){
110  char aloc = altloc[it->second[i]];
111  if ( aloc & 1 ) ++biascount;
112  if ( aloc & 2 ) ++refcount;
113  }
114  altlocmap[it->first] = ( refcount ? 1 : 0 );
115  if ( ! refcount ) refcount = it->second.size();
116  iout << iINFO << "TMD domain " << it->first <<
117  " has " << it->second.size() << " atoms " <<
118  refcount << " fitted " << biascount << " biased\n" << endi;
119  }
120 
121  // k /= numTMDatoms;
122  iout << iINFO << numTMDatoms << " TMD ATOMS\n" << endi;
123  DebugM(1,"done with initialize\n");
124 }
static Node * Object()
Definition: Node.h:86
BigReal TMDInitialRMSD
std::ostream & iINFO(std::ostream &s)
Definition: InfoStream.C:107
SimParameters * simParameters
Definition: Node.h:178
#define DebugM(x, y)
Definition: Debug.h:59
char TMDFile2[128]
#define iout
Definition: InfoStream.h:87
int numAtoms
Definition: Molecule.h:556
BigReal TMDFinalRMSD
infostream & endi(infostream &s)
Definition: InfoStream.C:38
char TMDFile[128]
Molecule * molecule
Definition: Node.h:176
GlobalMasterTMD::~GlobalMasterTMD ( )

Definition at line 227 of file GlobalMasterTMD.C.

227  {
228  delete [] target;
229  // delete [] target_aid;
230 // delete [] aidmap;
231  delete [] atompos;
232  delete [] atompos2;
233  delete [] altloc;
234  delete [] target2;
235 }

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