votca::csg::LAMMPSDataReader Class Reference

class for reading lammps data files More...

#include <lammpsdatareader.h>

Inheritance diagram for votca::csg::LAMMPSDataReader:

Collaboration diagram for votca::csg::LAMMPSDataReader:

Public Member Functions
	LAMMPSDataReader ()=default
	~LAMMPSDataReader () override=default
bool	ReadTopology (std::string file, Topology &top) override
	open, read and close topology file
bool	Open (const std::string &file) override
	open a trajectory file
bool	FirstFrame (Topology &top) override
	read in the first frame of trajectory file
bool	NextFrame (Topology &top) override
	read in the next frame of trajectory file
void	Close () override
	close the topology file
Public Member Functions inherited from votca::csg::TrajectoryReader
virtual	~TrajectoryReader ()=default
virtual bool	Open (const std::string &file)=0
	open a trejectory file
virtual void	Close ()
virtual bool	FirstFrame (Topology &top)=0
	read in the first frame
virtual bool	NextFrame (Topology &top)=0
	read in the next frame
Public Member Functions inherited from votca::csg::TopologyReader
virtual	~TopologyReader ()=default
virtual bool	ReadTopology (std::string file, Topology &top)=0
	open, read and close topology file

Public Attributes
const tools::DistanceUnit	distance_unit = tools::DistanceUnit::angstroms
const tools::TimeUnit	time_unit = tools::TimeUnit::femtoseconds
const tools::MassUnit	mass_unit = tools::MassUnit::grams_per_mole
const tools::MolarEnergyUnit	energy_unit
const tools::ChargeUnit	charge_unit = tools::ChargeUnit::e
const tools::MolarForceUnit	force_unit

Private Types
enum	lammps_format { style_angle_bond_molecule = 0 , style_atomic = 1 , style_full = 2 }

Private Member Functions
bool	MatchOneFieldLabel_ (std::vector< std::string > fields, Topology &top)
bool	MatchTwoFieldLabels_ (std::vector< std::string > fields, Topology &top)
bool	MatchThreeFieldLabels_ (std::vector< std::string > fields)
bool	MatchFourFieldLabels_ (std::vector< std::string > fields, Topology &top)
void	ReadBox_ (std::vector< std::string > fields, Topology &top)
void	SortIntoDataGroup_ (std::string tag)
void	ReadNumTypes_ (std::vector< std::string > fields, std::string type)
void	ReadNumOfAtoms_ (std::vector< std::string > fields, Topology &top)
void	ReadNumOfBonds_ (std::vector< std::string > fields)
void	ReadNumOfAngles_ (std::vector< std::string > fields)
void	ReadNumOfDihedrals_ (std::vector< std::string > fields)
void	ReadNumOfImpropers_ (std::vector< std::string > fields)
void	ReadAtoms_ (Topology &top)
void	ReadBonds_ (Topology &top)
void	ReadAngles_ (Topology &top)
void	ReadDihedrals_ (Topology &top)
void	SkipImpropers_ ()
void	RenameMolecules (MoleculeContainer &molecules) const
lammps_format	determineDataFileFormat_ (std::string line)
void	InitializeAtomAndBeadTypes_ ()
	Determines atom and bead types based on masses in lammps files.

Private Attributes
std::ifstream	fl_
std::string	fname_
bool	topology_
std::map< std::string, std::vector< std::vector< std::string > > >	data_
std::map< Index, std::string >	atomtypes_
std::map< std::string, Index >	numberOfDifferentTypes_
std::map< std::string, Index >	numberOf_
std::map< Index, Molecule * >	molecules_
std::map< Index, Index >	atomIdToMoleculeId_
std::map< Index, Index >	atomIdToIndex_

Additional Inherited Members
Static Public Member Functions inherited from votca::csg::TrajectoryReader
static void	RegisterPlugins (void)
Static Public Member Functions inherited from votca::csg::TopologyReader
static void	RegisterPlugins (void)

Detailed Description

class for reading lammps data files

This class provides the TrajectoryReader + Topology reader interface for lammps data files

Definition at line 45 of file lammpsdatareader.h.

Member Enumeration Documentation

lammps_format

enum votca::csg::LAMMPSDataReader::lammps_format

private

Enumerator
style_angle_bond_molecule
style_atomic
style_full

Definition at line 125 of file lammpsdatareader.h.

Constructor & Destructor Documentation

LAMMPSDataReader()

votca::csg::LAMMPSDataReader::LAMMPSDataReader ( )

default

~LAMMPSDataReader()

votca::csg::LAMMPSDataReader::~LAMMPSDataReader ( )

overridedefault

Member Function Documentation

Close()

void votca::csg::LAMMPSDataReader::Close ( )

overridevirtual

close the topology file

Reimplemented from votca::csg::TrajectoryReader.

Definition at line 113 of file lammpsdatareader.cc.

determineDataFileFormat_()

LAMMPSDataReader::lammps_format votca::csg::LAMMPSDataReader::determineDataFileFormat_ ( std::string  line )

private

Definition at line 377 of file lammpsdatareader.cc.

FirstFrame()

bool votca::csg::LAMMPSDataReader::FirstFrame ( Topology &  top )

overridevirtual

read in the first frame of trajectory file

Implements votca::csg::TrajectoryReader.

Definition at line 115 of file lammpsdatareader.cc.

InitializeAtomAndBeadTypes_()

void votca::csg::LAMMPSDataReader::InitializeAtomAndBeadTypes_ ( )

private

Determines atom and bead types based on masses in lammps files.

The purpose of this function is to take lammps output where there are more than a single atom type of the same element. For instance there may be 4 atom types with mass of 12.01. Well this means that they are all carbon but are treated differently in lammps. It makes sense to keep track of this. If a mass cannot be associated with an element we will assume it is pseudo atom or course grained watom which we will represent as a bead. So when creating the atom names we will take this into account. So say we have the following masses in the lammps .data file:

Masses

1 1.0 2 12.01 3 12.01 4 16.0 5 12.01 6 15.2 7 12.8 8 15.2

Then we would translate this to the following atom names 1 H 2 C1 3 C2 4 O 5 C3 6 Bead1 BeadType 1 7 Bead2 BeadType 8 Bead1 BeadType 2

Note that we do not append a number if it is singular, in such cases the element and the atom name is the same.

Definition at line 291 of file lammpsdatareader.cc.

MatchFourFieldLabels_()

bool votca::csg::LAMMPSDataReader::MatchFourFieldLabels_ ( std::vector< std::string >  fields, Topology &  top  )

private

Definition at line 280 of file lammpsdatareader.cc.

MatchOneFieldLabel_()

bool votca::csg::LAMMPSDataReader::MatchOneFieldLabel_ ( std::vector< std::string >  fields, Topology &  top  )

private

Definition at line 207 of file lammpsdatareader.cc.

MatchThreeFieldLabels_()

bool votca::csg::LAMMPSDataReader::MatchThreeFieldLabels_ ( std::vector< std::string >  fields )

private

Definition at line 262 of file lammpsdatareader.cc.

MatchTwoFieldLabels_()

bool votca::csg::LAMMPSDataReader::MatchTwoFieldLabels_ ( std::vector< std::string >  fields, Topology &  top  )

private

Definition at line 233 of file lammpsdatareader.cc.

NextFrame()

bool votca::csg::LAMMPSDataReader::NextFrame ( Topology &  top )

overridevirtual

read in the next frame of trajectory file

Implements votca::csg::TrajectoryReader.

Definition at line 121 of file lammpsdatareader.cc.

Open()

bool votca::csg::LAMMPSDataReader::Open ( const std::string &  file )

overridevirtual

open a trajectory file

Implements votca::csg::TrajectoryReader.

Definition at line 104 of file lammpsdatareader.cc.

ReadAngles_()

void votca::csg::LAMMPSDataReader::ReadAngles_ ( Topology &  top )

private

Definition at line 613 of file lammpsdatareader.cc.

ReadAtoms_()

void votca::csg::LAMMPSDataReader::ReadAtoms_ ( Topology &  top )

private

Definition at line 396 of file lammpsdatareader.cc.

ReadBonds_()

void votca::csg::LAMMPSDataReader::ReadBonds_ ( Topology &  top )

private

Definition at line 548 of file lammpsdatareader.cc.

ReadBox_()

void votca::csg::LAMMPSDataReader::ReadBox_ ( std::vector< std::string >  fields, Topology &  top  )

private

Definition at line 316 of file lammpsdatareader.cc.

ReadDihedrals_()

void votca::csg::LAMMPSDataReader::ReadDihedrals_ ( Topology &  top )

private

Definition at line 681 of file lammpsdatareader.cc.

ReadNumOfAngles_()

void votca::csg::LAMMPSDataReader::ReadNumOfAngles_ ( std::vector< std::string >  fields )

private

Definition at line 365 of file lammpsdatareader.cc.

ReadNumOfAtoms_()

void votca::csg::LAMMPSDataReader::ReadNumOfAtoms_ ( std::vector< std::string >  fields, Topology &  top  )

private

Definition at line 353 of file lammpsdatareader.cc.

ReadNumOfBonds_()

void votca::csg::LAMMPSDataReader::ReadNumOfBonds_ ( std::vector< std::string >  fields )

private

Definition at line 361 of file lammpsdatareader.cc.

ReadNumOfDihedrals_()

void votca::csg::LAMMPSDataReader::ReadNumOfDihedrals_ ( std::vector< std::string >  fields )

private

Definition at line 369 of file lammpsdatareader.cc.

ReadNumOfImpropers_()

void votca::csg::LAMMPSDataReader::ReadNumOfImpropers_ ( std::vector< std::string >  fields )

private

Definition at line 373 of file lammpsdatareader.cc.

ReadNumTypes_()

void votca::csg::LAMMPSDataReader::ReadNumTypes_ ( std::vector< std::string >  fields, std::string  type  )

private

Definition at line 348 of file lammpsdatareader.cc.

ReadTopology()

bool votca::csg::LAMMPSDataReader::ReadTopology ( std::string  file, Topology &  top  )

overridevirtual

open, read and close topology file

Implements votca::csg::TopologyReader.

Definition at line 66 of file lammpsdatareader.cc.

RenameMolecules()

void votca::csg::LAMMPSDataReader::RenameMolecules ( MoleculeContainer &  molecules ) const

private

Definition at line 176 of file lammpsdatareader.cc.

SkipImpropers_()

void votca::csg::LAMMPSDataReader::SkipImpropers_ ( )

private

Definition at line 672 of file lammpsdatareader.cc.

SortIntoDataGroup_()

void votca::csg::LAMMPSDataReader::SortIntoDataGroup_ ( std::string  tag )

private

Definition at line 334 of file lammpsdatareader.cc.

Member Data Documentation

atomIdToIndex_

std::map<Index, Index> votca::csg::LAMMPSDataReader::atomIdToIndex_

private

Definition at line 100 of file lammpsdatareader.h.

atomIdToMoleculeId_

std::map<Index, Index> votca::csg::LAMMPSDataReader::atomIdToMoleculeId_

private

Definition at line 97 of file lammpsdatareader.h.

atomtypes_

std::map<Index, std::string> votca::csg::LAMMPSDataReader::atomtypes_

private

Definition at line 82 of file lammpsdatareader.h.

charge_unit

const tools::ChargeUnit votca::csg::LAMMPSDataReader::charge_unit = tools::ChargeUnit::e

Definition at line 52 of file lammpsdatareader.h.

data_

std::map<std::string, std::vector<std::vector<std::string> > > votca::csg::LAMMPSDataReader::data_

private

Definition at line 76 of file lammpsdatareader.h.

distance_unit

const tools::DistanceUnit votca::csg::LAMMPSDataReader::distance_unit = tools::DistanceUnit::angstroms

Definition at line 47 of file lammpsdatareader.h.

energy_unit

const tools::MolarEnergyUnit votca::csg::LAMMPSDataReader::energy_unit

Initial value:

=
      tools::MolarEnergyUnit::kilocalories_per_mole

Definition at line 50 of file lammpsdatareader.h.

fl_

std::ifstream votca::csg::LAMMPSDataReader::fl_

private

Definition at line 72 of file lammpsdatareader.h.

fname_

std::string votca::csg::LAMMPSDataReader::fname_

private

Definition at line 73 of file lammpsdatareader.h.

force_unit

const tools::MolarForceUnit votca::csg::LAMMPSDataReader::force_unit

Initial value:

=
      tools::MolarForceUnit::kilocalories_per_mole_angstrom

Definition at line 53 of file lammpsdatareader.h.

mass_unit

const tools::MassUnit votca::csg::LAMMPSDataReader::mass_unit = tools::MassUnit::grams_per_mole

Definition at line 49 of file lammpsdatareader.h.

molecules_

std::map<Index, Molecule *> votca::csg::LAMMPSDataReader::molecules_

private

Definition at line 94 of file lammpsdatareader.h.

numberOf_

std::map<std::string, Index> votca::csg::LAMMPSDataReader::numberOf_

private

Definition at line 90 of file lammpsdatareader.h.

numberOfDifferentTypes_

std::map<std::string, Index> votca::csg::LAMMPSDataReader::numberOfDifferentTypes_

private

Definition at line 86 of file lammpsdatareader.h.

time_unit

const tools::TimeUnit votca::csg::LAMMPSDataReader::time_unit = tools::TimeUnit::femtoseconds

Definition at line 48 of file lammpsdatareader.h.

topology_

bool votca::csg::LAMMPSDataReader::topology_

private

Definition at line 74 of file lammpsdatareader.h.

---

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

• csg/src/libcsg/modules/io/lammpsdatareader.h
• csg/src/libcsg/modules/io/lammpsdatareader.cc