OpenMD  2.5
Molecular Dynamics in the Open
OpenMD::SimCreator Class Reference

#include "brains/SimCreator.hpp"

Public Member Functions

virtual ~SimCreator ()
 
SimInfocreateSim (const std::string &mdFileName, bool loadInitCoords=true)
 

Private Member Functions

GlobalsparseFile (std::istream &rawMetaData, const std::string &mdFileName, int mdFileVersion, int metaDataStartingLine)
 
virtual void createMolecules (SimInfo *info)
 
int computeStorageLayout (SimInfo *info)
 
void setGlobalIndex (SimInfo *info)
 
void gatherParameters (SimInfo *info, const std::string &mdfile)
 
void divideMolecules (SimInfo *info)
 
void loadCoordinates (SimInfo *info, const std::string &mdFileName)
 

Private Attributes

std::string mdFileName_
 

Detailed Description

The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo instance based on the information returned by parser.

Definition at line 68 of file SimCreator.hpp.

Constructor & Destructor Documentation

◆ ~SimCreator()

virtual OpenMD::SimCreator::~SimCreator ( )
inlinevirtual

Member Function Documentation

◆ computeStorageLayout()

◆ createMolecules()

◆ createSim()

◆ divideMolecules()

◆ gatherParameters()

◆ loadCoordinates()

void OpenMD::SimCreator::loadCoordinates ( SimInfo info,
const std::string &  mdFileName 
)
private

◆ parseFile()

◆ setGlobalIndex()

void OpenMD::SimCreator::setGlobalIndex ( SimInfo info)
private

Sets the global index for atoms, rigidbodies and cutoff groups and fill up globalGroupMembership and globalMolMembership arrays which map atoms' global index to the global index of the groups (or molecules) they belong to. These array are never changed during the simulation.

Definition at line 815 of file SimCreator.cpp.

References OpenMD::CutoffGroup::beginAtom(), OpenMD::Molecule::beginAtom(), OpenMD::Molecule::beginBend(), OpenMD::Molecule::beginBond(), OpenMD::Molecule::beginCutoffGroup(), OpenMD::Molecule::beginIntegrableObject(), OpenMD::Molecule::beginInversion(), OpenMD::SimInfo::beginMolecule(), OpenMD::Molecule::beginRigidBody(), OpenMD::Molecule::beginTorsion(), OpenMD::StuntDouble::getGlobalIndex(), OpenMD::Molecule::getGlobalIndex(), OpenMD::CutoffGroup::getGlobalIndex(), OpenMD::SimInfo::getMoleculeByGlobalIndex(), OpenMD::SimInfo::getMoleculeStamp(), OpenMD::SimInfo::getMoleculeStampId(), OpenMD::SimInfo::getMolToProc(), OpenMD::MoleculeStamp::getNAtoms(), OpenMD::MoleculeStamp::getNBends(), OpenMD::MoleculeStamp::getNBonds(), OpenMD::MoleculeStamp::getNCutoffGroups(), OpenMD::MoleculeStamp::getNFreeAtoms(), OpenMD::SimInfo::getNGlobalAtoms(), OpenMD::SimInfo::getNGlobalIntegrableObjects(), OpenMD::SimInfo::getNGlobalMolecules(), OpenMD::SimInfo::getNGlobalRigidBodies(), OpenMD::Molecule::getNIntegrableObjects(), OpenMD::MoleculeStamp::getNInversions(), OpenMD::MoleculeStamp::getNRigidBodies(), OpenMD::MoleculeStamp::getNTorsions(), OpenMD::CutoffGroup::nextAtom(), OpenMD::Molecule::nextAtom(), OpenMD::Molecule::nextBend(), OpenMD::Molecule::nextBond(), OpenMD::Molecule::nextCutoffGroup(), OpenMD::Molecule::nextIntegrableObject(), OpenMD::Molecule::nextInversion(), OpenMD::SimInfo::nextMolecule(), OpenMD::Molecule::nextRigidBody(), OpenMD::Molecule::nextTorsion(), OpenMD::SimInfo::setGlobalGroupMembership(), OpenMD::ShortRangeInteraction::setGlobalIndex(), OpenMD::StuntDouble::setGlobalIndex(), OpenMD::CutoffGroup::setGlobalIndex(), OpenMD::SimInfo::setGlobalMolMembership(), OpenMD::SimInfo::setIOIndexToIntegrableObject(), and worldRank.

Referenced by createSim(), and ~SimCreator().

Member Data Documentation

◆ mdFileName_

std::string OpenMD::SimCreator::mdFileName_
private

Definition at line 123 of file SimCreator.hpp.


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