Namespaces
namespace	Colors
	stores color codes for colorful help output

namespace	conv

namespace	EigenIO_MatrixMarket

namespace	filesystem

namespace	internal

namespace	topology_constants

Classes
class	AkimaSpline
	An Akima Spline Class. More...

class	Application

class	Average

class	Calculator
	Base class for all calculators. More...

class	Color

class	ColorScheme

class	ColorSchemeBase

class	Correlate
	class to calculate correlations of values More...

class	CrossCorrelate
	class to calculate cross correlations and autocorrelations More...

class	csDefault

class	csRGB

class	CubicSpline
	A cubic spline class. More...

class	DataCollection
	This class handles a set of arrays which can be identified by name tags. More...

class	Edge
	Connects to vertices. More...

class	EdgeContainer
	EdgeContainer is responsible for operations on groups of edges. More...

class	EigenSystem

class	Elements
	information about an element More...

struct	globals
	class to store global variables More...

class	Graph

class	Graph_BF_Visitor

class	Graph_DF_Visitor

class	GraphDistVisitor

class	GraphNode
	A graph node that will take a variety of different values. More...

class	GraphVisitor

class	Histogram
	class to generate histograms More...

class	HistogramNew
	class to generate histograms More...

class	Identity
	Information about Identity. More...

class	LinSpline
	A Linear Spline Class. More...

class	Mutex

class	Name
	Name object. More...

class	NDimVector
	N-Dim Vector. More...

class	ObjectFactory
	template class for object factory More...

class	OptionsHandler

class	Property
	class to manage program options with xml serialization functionality More...

class	PropertyIOManipulator
	Manipulates the format state of the output stream. More...

class	Random

class	RangeParser
	RangeParser. More...

class	ReducedEdge
	Connects two vertices, also stores the vertices between the endpoints. More...

class	ReducedGraph
	Contains a graph that consits of vertices with degree of 1 or greater than 3. More...

class	Spline
	Spline Class. More...

class	StructureParameters
	Provides a means to standardise the constructors of different classes. More...

class	Table
	class to store tables like rdfs, tabulated potentials, etc More...

class	Thread
	Framework for threaded execution. More...

class	Tokenizer
	break string into words More...

class	UnitConverter
	Class converts between different unit types. More...

Enumerations
enum	StructureParameter { Mass , Position , MoleculeId , ResidueId , Charge , Element , Symmetry , ResidueType , BeadId , BeadType , MoleculeType }
	Supported and Standardized parameter types. More...

enum	DistanceUnit { meters , centimeters , nanometers , angstroms , bohr }

enum	MassUnit { attograms , picograms , femtograms , atomic_mass_units , grams_per_mole , kilograms , grams }

enum	TimeUnit { seconds , microseconds , nanoseconds , femtoseconds , picoseconds }

enum	EnergyUnit { electron_volts , kilocalories , hartrees , joules , kilojoules }

enum	MolarEnergyUnit { kilojoules_per_mole , joules_per_mole , kilocalories_per_mole , electron_volts_per_mole , hartrees_per_mole }

enum	ChargeUnit { e , coulombs }

enum	VelocityUnit { angstroms_per_femtosecond , angstroms_per_picosecond , nanometers_per_picosecond }

enum	ForceUnit { kilocalories_per_angstrom , newtons , kilojoules_per_nanometer , kilojoules_per_angstrom , hatree_per_bohr }

enum	MolarForceUnit { kilocalories_per_mole_angstrom , newtons_per_mole , kilojoules_per_mole_nanometer , kilojoules_per_mole_angstrom , hatree_per_mole_bohr }

Functions
std::ostream &	operator<< (std::ostream &out, const Correlate &c)

std::ostream &	operator<< (std::ostream &out, const CrossCorrelate &c)

std::ostream &	operator<< (std::ostream &out, const DataCollection< double >::selection &sel)

const Edge	DUMMY_EDGE (std::numeric_limits< Index >::max(), std::numeric_limits< Index >::max())

template<typename T >
static bool	isApproximatelyEqual (T a, T b, T tolerance)

std::istream &	getline (std::istream &is, std::string &str)
	Wrapper for a getline function.

std::string	GetVotcaShare ()
	Retrieves VOTCASHARE environment variable. Throws std::runtime_error if not set.

bool	VotcaShareSet ()

bool	cmpVertNodePair (const std::pair< Index, GraphNode > &id_and_node1, const std::pair< Index, GraphNode > &id_and_node2)
	Compare function pair<Index ,GraphNode> object.

bool	singleNetwork (Graph &graph, GraphVisitor &graph_visitor)
	Determine if every vertex is connected to every other one through some combination of edges.

std::set< Edge >	exploreBranch (Graph g, Index starting_vertex, const Edge &edge)
	Explore one of the branches if exploration is initiated at vertex `starting_vertex`.

ReducedGraph	reduceGraph (Graph graph)
	Will take a graph and reduce it, by removing all vertices with degree of 2.

std::vector< Graph >	decoupleIsolatedSubGraphs (Graph graph)
	Break graph into smaller graph instances if the network is made up of isolated sub networks.

void	exploreGraph (Graph &graph, GraphVisitor &graph_visitor)
	Explore a graph with a graph visitor.

template<typename GV >
std::string	findStructureId (Graph &graph)
	Find a unique identifier that describes graph structure.

bool	cmpNode (GraphNode gn1, GraphNode gn2)
	Comparison function to be used with stl sort algorithm.

std::ostream &	operator<< (std::ostream &out, Histogram &h)

std::ostream &	operator<< (std::ostream &out, HistogramNew &h)

template<typename Target , typename Source >
Target	lexical_cast (const Source &arg, const std::string &error)

Eigen::VectorXd	linalg_constrained_qrsolve (const Eigen::MatrixXd &A, const Eigen::VectorXd &b, const Eigen::MatrixXd &constr)
	solves Ax=b under the constraint Bx = 0

template<class parent , class T , typename... args_t>
std::unique_ptr< parent >	create_policy_new (args_t &&...args)

std::ostream &	operator<< (std::ostream &out, const RangeParser &rp)

int	wildcmp (const char wild, const char string)

int	wildcmp (const std::string &wild, const std::string &string)

template<class T >
T	convertFromString (const std::string &s)

const std::string &	ToolsVersionStr ()

ostream &	operator<< (ostream &os, const Edge &ed)

ostream &	operator<< (ostream &os, const EdgeContainer edgecontainer)

bool	nodeForEveryVertex_ (vector< Index > vertices, unordered_map< Index, GraphNode > nodes)

ostream &	operator<< (ostream &os, const Graph graph)

bool	cmpVertNodePair (const pair< Index, GraphNode > &id_and_node1, const pair< Index, GraphNode > &id_and_node2)

string	sig_fig_ (double val, Index sf)

string	getIntStringId_ (const unordered_map< string, Index > int_vals)

string	getDoubleStringId_ (const unordered_map< string, double > double_vals)

string	getStrStringId_ (const unordered_map< string, string > str_vals)

ostream &	operator<< (ostream &os, const GraphNode gn)

template<typename T >
static bool	IsValidCast (const tools::Property &prop)

void	FixPath (tools::Property &prop, std::string path)

static void	start_hndl (void data, const char el, const char **attr)

static void	end_hndl (void data, const char )

void	char_hndl (void data, const char txt, int txtlen)

void	PrintNodeTXT (std::ostream &out, const Property &p, const Index start_level, Index level=0, string prefix="", string offset="")

void	PrintNodeXML (std::ostream &out, const Property &p, PropertyIOManipulator *piom, Index level=0, string offset="")

void	PrintNodeHLP (std::ostream &out, const Property &p, const Index start_level=0, Index level=0, const string &prefix="", const string &offset="")

std::ostream &	operator<< (std::ostream &out, const Property &p)

PropertyIOManipulator	XML (PropertyIOManipulator::XML)

PropertyIOManipulator	TXT (PropertyIOManipulator::TXT)

PropertyIOManipulator	HLP (PropertyIOManipulator::HLP)

void	moveVertexWithSmallestValueToEnds_ (vector< Index > &vertices)

bool	verticesShouldBeReversed_ (vector< Index > &vertices)

ostream &	operator<< (ostream &os, const ReducedEdge &edge)

bool	compareChainWithChains_ (const vector< Index > &chain, const vector< vector< Index > > &chains)
	Function will compare a chain with a vector of chains.

set< Index >	getVertexJunctions_ (const vector< ReducedEdge > &reduced_edges)
	Given a vector of Reduced Edges will find and return junctions if any exist.

void	addEdgeIfNotLoop_ (vector< Edge > &edges, const ReducedEdge reduced_edge, unordered_map< Edge, vector< vector< Index > > > &expanded_edges)
	function adds an edge to an unordered_map and a vector if it is found to not be a loop

void	orderChainAfterInitialVertex_ (vector< Index > &chain)
	This is a helper function used to help store the vertex chain in a reproducable order.

bool	reorderAndStoreChainIfDoesNotExist_ (vector< Edge > &edges, unordered_map< Edge, vector< vector< Index > > > &expanded_edges, vector< Index > chain, Index vertex, size_t &chain_index)

set< Index >	getAllVertices_ (const std::vector< ReducedEdge > &reduced_edges)

set< Index >	getAllConnectedVertices_ (const unordered_map< Edge, vector< vector< Index > > > &expanded_edges)

ostream &	operator<< (ostream &os, const ReducedGraph graph)

istream &	operator>> (istream &in, Table &t)

std::ostream &	operator<< (std::ostream &out, const Table &t)

void *	runwrapper (void *arg)

Variables
Color< csDefault >	DEFAULT_COLORS

PropertyIOManipulator	XML

PropertyIOManipulator	HLP

PropertyIOManipulator	TXT

static const std::string	version_str

Enumeration Type Documentation

◆ ChargeUnit

enum votca::tools::ChargeUnit

Enumerator
e
coulombs

Definition at line 59 of file unitconverter.h.

◆ DistanceUnit

enum votca::tools::DistanceUnit

Enumerator
meters
centimeters
nanometers
angstroms
bohr

Definition at line 27 of file unitconverter.h.

◆ EnergyUnit

enum votca::tools::EnergyUnit

Enumerator
electron_volts
kilocalories
hartrees
joules
kilojoules

Definition at line 42 of file unitconverter.h.

◆ ForceUnit

enum votca::tools::ForceUnit

Enumerator
kilocalories_per_angstrom
newtons
kilojoules_per_nanometer
kilojoules_per_angstrom
hatree_per_bohr

Definition at line 68 of file unitconverter.h.

◆ MassUnit

enum votca::tools::MassUnit

Enumerator
attograms
picograms
femtograms
atomic_mass_units
grams_per_mole
kilograms
grams

Definition at line 29 of file unitconverter.h.

◆ MolarEnergyUnit

enum votca::tools::MolarEnergyUnit

Enumerator
kilojoules_per_mole
joules_per_mole
kilocalories_per_mole
electron_volts_per_mole
hartrees_per_mole

Definition at line 51 of file unitconverter.h.

◆ MolarForceUnit

enum votca::tools::MolarForceUnit

Enumerator
kilocalories_per_mole_angstrom
newtons_per_mole
kilojoules_per_mole_nanometer
kilojoules_per_mole_angstrom
hatree_per_mole_bohr

Definition at line 77 of file unitconverter.h.

◆ StructureParameter

enum votca::tools::StructureParameter

Supported and Standardized parameter types.

Enumerator
Mass
Position
MoleculeId
ResidueId
Charge
Element
Symmetry
ResidueType
BeadId
BeadType
MoleculeType

Definition at line 34 of file structureparameters.h.

◆ TimeUnit

enum votca::tools::TimeUnit

Enumerator
seconds
microseconds
nanoseconds
femtoseconds
picoseconds

Definition at line 39 of file unitconverter.h.

◆ VelocityUnit

enum votca::tools::VelocityUnit

Enumerator
angstroms_per_femtosecond
angstroms_per_picosecond
nanometers_per_picosecond

Definition at line 61 of file unitconverter.h.

Function Documentation

◆ addEdgeIfNotLoop_()

void votca::tools::addEdgeIfNotLoop_	(	vector< Edge > &	edges,
		const ReducedEdge	reduced_edge,
		unordered_map< Edge, vector< vector< Index > > > &	expanded_edges
	)

function adds an edge to an unordered_map and a vector if it is found to not be a loop

A loop is an edge that essentially makes a circle. In an edge that is a loop will have both end points equal to the samve vertex. E.g. a reduced edge like this:

Edge Expanded edge (chain of vertices) 2, 2 : 2 - 4 - 3 - 5 - 2

Graph

2 - 4 | | 5 - 3

Reduced Graph

2 |_|

Parameters

[in,out]	edges	- vector of edges, an edge is added to the vector if it is not a loop
[in]	reduced_edge	- a reduced edge, the edge to be added
[in,out]	expanded_edges	- an unordered_map that stores the edge and its chain if it is found to not be a loop

Definition at line 154 of file reducedgraph.cc.

◆ char_hndl()

void votca::tools::char_hndl	(	void *	data,
		const char *	txt,
		int	txtlen
	)

Definition at line 230 of file property.cc.

◆ cmpNode()

bool votca::tools::cmpNode	(	GraphNode	gn1,
		GraphNode	gn2
	)

Comparison function to be used with stl sort algorithm.

Given a vector of graph node objects this function can be used to sort them they are sorted based on the contents of the graphnode which are summarized in the graph nodes string id. E.g.

vector<GraphNode> vec_gn = { gn1, gn2,...etc };

sort(vec_gn.begin(),vec_gn.end(),cmpNode);

Definition at line 198 of file graphnode.cc.

◆ cmpVertNodePair() [1/2]

bool votca::tools::cmpVertNodePair	(	const pair< Index, GraphNode > &	id_and_node1,
		const pair< Index, GraphNode > &	id_and_node2
	)

Definition at line 179 of file graph.cc.

◆ cmpVertNodePair() [2/2]

bool votca::tools::cmpVertNodePair	(	const std::pair< Index, GraphNode > &	id_and_node1,
		const std::pair< Index, GraphNode > &	id_and_node2
	)

Compare function pair<Index ,GraphNode> object.

This function is meant to be used with the stl sort algorithm. It will sort a vector of pairs containing the vertex ids and the graphnodes. Only the contetns of the graph node object are used to determine precidence e.g.

pair<Index ,GraphNode> pr_grn1{ 1, gn }; pair<Index ,GraphNode> pr_grn2{ 2, gn2 };

vector<pair<Index ,GraphNode> > vec_pr_gn = { pr_grn1, pr_grn2 , ... etc };

sort(vec_pr_gn.begin(),vec_pr_gn.end(),cmpVertNodePair);

◆ compareChainWithChains_()

bool votca::tools::compareChainWithChains_	(	const vector< Index > &	chain,
		const vector< vector< Index > > &	chains
	)

Function will compare a chain with a vector of chains.

If the one of the chains in the vector of chains is equivalent will return true. A chain is simply a vector of integers where each integer represents a vertex along an edge. The vertices appear in the chain in the same order as they exist in a graph.

Definition at line 47 of file reducedgraph.cc.

◆ convertFromString()

template<class T >

T votca::tools::convertFromString ( const std::string & s )

Definition at line 155 of file tokenizer.h.

◆ create_policy_new()

template<class parent , class T , typename... args_t>

std::unique_ptr< parent > votca::tools::create_policy_new ( args_t &&... args )

Definition at line 84 of file objectfactory.h.

◆ decoupleIsolatedSubGraphs()

vector< Graph > votca::tools::decoupleIsolatedSubGraphs ( Graph graph )

Break graph into smaller graph instances if the network is made up of isolated sub networks.

This algorithm will determine if there are groups of vertices that are connected, but where there are no connections shared between the groups. These groups will be brocken up into their own Graph instances. E.g. Take a graph with the following vertices and connections

Graph 1:

1 - 2 - 3 | | 8 - 9 - 10 11 4 - 5 - 6 -7

decoupling the graph into sub graphs will break the islands up into individual graphs:

Sub Graph 1 Sub Graph 2 Sub Graph 3

1 - 2 - 3 | | 8 - 9 - 10 11 4 - 5 - 6 -7

Parameters

[in] graph - Graph instance

Returns: - vector containing shared pointers to all the sub graphs if there are no subgraphs than the input graph is returned.

Definition at line 244 of file graphalgorithm.cc.

◆ DUMMY_EDGE()

const Edge votca::tools::DUMMY_EDGE	(	std::numeric_limits< Index >	::max(),
		std::numeric_limits< Index >	::max()
	)

◆ end_hndl()

static void votca::tools::end_hndl	(	void *	data,
		const char *
	)

static

Definition at line 224 of file property.cc.

◆ exploreBranch()

std::set< Edge > votca::tools::exploreBranch	(	Graph	g,
		Index	starting_vertex,
		const Edge &	edge
	)

Explore one of the branches if exploration is initiated at vertex starting_vertex.

The edge is used to determine which branch is to be explored. The edge must be an edge connected to the starting_vertex.

Take the following

1 - 2 - 3 - 4 - 5 | | 6 - 7 - 8

If our graph is reprsented by the above depiction and vertex 3 is chosen as our starting vertex, we are left with 3 edges to choose from Edges:

2 - 3 3 - 4 3 - 6

If we pick edge 3 - 4 or 3 - 6 the returned set of edges will consist of the loop

    3 - 4 - 5
    |       |
    6 - 7 - 8

If instead Edge 2 - 3 is picked, the following set of edges would be returned

1 - 2 - 3

Parameters

[in]	g	- Graph instance
[in]	starting_vertex	- Index starting vertex, where the exploration begins
[in]	edge	- the edge indicating which branch is to be explored

Returns: - set of edges in the branch that were explored

Definition at line 49 of file graphalgorithm.cc.

◆ exploreGraph()

void votca::tools::exploreGraph	(	Graph &	graph,
		GraphVisitor &	graph_visitor
	)

Explore a graph with a graph visitor.

This function will simply explore a graph, any information gained from the exploration will depend on the graph visitor used. Note that the Graph visitor is the base class which will not work on its own. The purpose of doing this is to make use of polymorphism.

Parameters

[in,out]	graph	- Graph reference instance
[in,out]	graph_visitor	- graph visitor

Definition at line 291 of file graphalgorithm.cc.

◆ findStructureId()

template<typename GV >

std::string votca::tools::findStructureId ( Graph & graph )

Find a unique identifier that describes graph structure.

This algorithm is designed to explore the topology of the graph and return an identifier in the form of the string that is unique to the topology. It does this by taking into account the contents of the graphnodes. How it does this is specific to the graph visitor specified.

Parameters

[in,out] graph - Graph reference instance

Returns: - string identifier

Definition at line 181 of file graphalgorithm.h.

◆ FixPath()

void votca::tools::FixPath	(	tools::Property &	prop,
		std::string	path
	)

Definition at line 131 of file property.cc.

◆ getAllConnectedVertices_()

set< Index > votca::tools::getAllConnectedVertices_ ( const unordered_map< Edge, vector< vector< Index > > > & expanded_edges )

Definition at line 249 of file reducedgraph.cc.

◆ getAllVertices_()

set< Index > votca::tools::getAllVertices_ ( const std::vector< ReducedEdge > & reduced_edges )

Definition at line 238 of file reducedgraph.cc.

◆ getDoubleStringId_()

string votca::tools::getDoubleStringId_ ( const unordered_map< string, double > double_vals )

Turns the map of doubles into a string that is sorted alphabetically by the keys

Definition at line 74 of file graphnode.cc.

◆ getIntStringId_()

string votca::tools::getIntStringId_ ( const unordered_map< string, Index > int_vals )

Turns the map of ints into a string that is sorted alphabetically by the keys

Definition at line 56 of file graphnode.cc.

◆ getline()

std::istream & votca::tools::getline	(	std::istream &	is,
		std::string &	str
	)

inline

Wrapper for a getline function.

Removes Windows end-of-line character

Definition at line 35 of file getline.h.

◆ getStrStringId_()

string votca::tools::getStrStringId_ ( const unordered_map< string, string > str_vals )

Turns the map of strings into a string that is sorted alphabetically by the keys

Definition at line 92 of file graphnode.cc.

◆ getVertexJunctions_()

set< Index > votca::tools::getVertexJunctions_ ( const vector< ReducedEdge > & reduced_edges )

Given a vector of Reduced Edges will find and return junctions if any exist.

A junction is a vertex in a graph that has 3 or more edges eminating from it.

Consider three reduced edges given by

Edge Reduced Edge when Expanded (chain of vertices) 1, 5 : 1 - 3 - 4 - 6 - 5 5, 10 : 5 - 2 - 10 5, 9 : 5 - 8 - 9

Graph:

1 - 3 - 4 - 6 - 5 - 2 - 10 | 8 - 9

Reduced Graph:

1 - 5 - 10 | 9

Here vertex 5 would be found to be a junction

Parameters

[in,out] reduced_edges - vector of reduced edges

Returns: - set of integers containing junctions

Definition at line 97 of file reducedgraph.cc.

◆ GetVotcaShare()

std::string votca::tools::GetVotcaShare ( )

Retrieves VOTCASHARE environment variable. Throws std::runtime_error if not set.

Definition at line 27 of file globals.cc.

◆ HLP()

PropertyIOManipulator votca::tools::HLP ( PropertyIOManipulator::HLP )

◆ isApproximatelyEqual()

template<typename T >

static bool votca::tools::isApproximatelyEqual	(	T	a,
		T	b,
		T	tolerance
	)

static

Definition at line 45 of file floatingpointcomparison.h.

◆ IsValidCast()

template<typename T >

static bool votca::tools::IsValidCast ( const tools::Property & prop )

static

Definition at line 30 of file optionshandler.cc.

◆ lexical_cast()

template<typename Target , typename Source >

Target votca::tools::lexical_cast	(	const Source &	arg,
		const std::string &	error
	)

inline

Wrapper for boost::lexical_cast with improved error messages

Parameters

arg	variable to convert
error	additional error text

Returns: converted value

Definition at line 38 of file lexical_cast.h.

◆ linalg_constrained_qrsolve()

Eigen::VectorXd votca::tools::linalg_constrained_qrsolve	(	const Eigen::MatrixXd &	A,
		const Eigen::VectorXd &	b,
		const Eigen::MatrixXd &	constr
	)

solves A*x=b under the constraint B*x = 0

Returns: x

Parameters

A	matrix for linear equation system
b	inhomogenity
constr	constrained condition

This function implements the qrsolver under constraints

Definition at line 28 of file linalg.cc.

◆ moveVertexWithSmallestValueToEnds_()

void votca::tools::moveVertexWithSmallestValueToEnds_ ( vector< Index > & vertices )

Given a chain of vertices where the end points are the same this method will rotate the chain so that the vertex with the smallest value is at the end points e.g.

3 - 4 - 5 - 9 - 2 - 8 - 3

The method will return the chain as

2 - 8 - 3 - 4 - 5 - 9 - 2

Notice that the order is preserved, because it is assumed that the chain makes a loop.

Definition at line 46 of file reducededge.cc.

◆ nodeForEveryVertex_()

bool votca::tools::nodeForEveryVertex_	(	vector< Index >	vertices,
		unordered_map< Index, GraphNode >	nodes
	)

Definition at line 35 of file graph.cc.

◆ operator<<() [1/14]

ostream & votca::tools::operator<<	(	std::ostream &	os,
		const Edge &	ed
	)

Definition at line 84 of file edge.cc.

◆ operator<<() [2/14]

ostream & votca::tools::operator<<	(	std::ostream &	os,
		const EdgeContainer	edgecontainer
	)

Definition at line 192 of file edgecontainer.cc.

◆ operator<<() [3/14]

ostream & votca::tools::operator<<	(	std::ostream &	os,
		const Graph	graph
	)

Definition at line 170 of file graph.cc.

◆ operator<<() [4/14]

ostream & votca::tools::operator<<	(	std::ostream &	os,
		const GraphNode	gn
	)

Definition at line 182 of file graphnode.cc.

◆ operator<<() [5/14]

ostream & votca::tools::operator<<	(	std::ostream &	os,
		const ReducedEdge &	edge
	)

Definition at line 183 of file reducededge.cc.

◆ operator<<() [6/14]

ostream & votca::tools::operator<<	(	std::ostream &	os,
		const ReducedGraph	graph
	)

Definition at line 398 of file reducedgraph.cc.

◆ operator<<() [7/14]

std::ostream & votca::tools::operator<<	(	std::ostream &	out,
		const Correlate &	c
	)

inline

Definition at line 53 of file correlate.h.

◆ operator<<() [8/14]

std::ostream & votca::tools::operator<<	(	std::ostream &	out,
		const CrossCorrelate &	c
	)

inline

Definition at line 50 of file crosscorrelate.h.

◆ operator<<() [9/14]

std::ostream & votca::tools::operator<<	(	std::ostream &	out,
		const DataCollection< double >::selection &	sel
	)

Definition at line 27 of file datacollection.cc.

◆ operator<<() [10/14]

std::ostream & votca::tools::operator<<	(	std::ostream &	out,
		const Property &	p
	)

Definition at line 440 of file property.cc.

◆ operator<<() [11/14]

std::ostream & votca::tools::operator<<	(	std::ostream &	out,
		const RangeParser &	rp
	)

inline

Definition at line 116 of file rangeparser.h.

◆ operator<<() [12/14]

std::ostream & votca::tools::operator<<	(	std::ostream &	out,
		const Table &	t
	)

Definition at line 207 of file table.cc.

◆ operator<<() [13/14]

std::ostream & votca::tools::operator<<	(	std::ostream &	out,
		Histogram &	h
	)

inline

Definition at line 84 of file histogram.h.

◆ operator<<() [14/14]

std::ostream & votca::tools::operator<<	(	std::ostream &	out,
		HistogramNew &	h
	)

inline

Definition at line 176 of file histogramnew.h.

◆ operator>>()

istream & votca::tools::operator>>	(	std::istream &	in,
		Table &	t
	)

Definition at line 94 of file table.cc.

◆ orderChainAfterInitialVertex_()

void votca::tools::orderChainAfterInitialVertex_ ( vector< Index > & chain )

This is a helper function used to help store the vertex chain in a reproducable order.

Ordering chains in a reproducable manner enable quicker comparison between chains.

E.g. Given a chain

End Point 1 v 1 - 4 - 3 - 5 - 6 - 2 - 1 ^ End Point 2

This function will ensure that it is reordered such that the next consecutive number in the chain after end point 2 is the lower number, in this case the two numbers that are compared are 4 and 2. The 2 is smaller so the chain is reordered.

1 - 2 - 6 - 5 - 3 - 4 - 1

Parameters

[in,out] chain - vector of integers containing the chain

Definition at line 195 of file reducedgraph.cc.

◆ PrintNodeHLP()

void votca::tools::PrintNodeHLP	(	std::ostream &	out,
		const Property &	p,
		const Index	start_level = `0`,
		Index	level = `0`,
		const string &	prefix = `""`,
		const string &	offset = `""`
	)

Definition at line 377 of file property.cc.

◆ PrintNodeTXT()

void votca::tools::PrintNodeTXT	(	std::ostream &	out,
		const Property &	p,
		const Index	start_level,
		Index	level = `0`,
		string	prefix = `""`,
		string	offset = `""`
	)

Definition at line 276 of file property.cc.

◆ PrintNodeXML()

void votca::tools::PrintNodeXML	(	std::ostream &	out,
		const Property &	p,
		PropertyIOManipulator *	piom,
		Index	level = `0`,
		string	offset = `""`
	)

Definition at line 300 of file property.cc.

◆ reduceGraph()

ReducedGraph votca::tools::reduceGraph ( Graph graph )

Will take a graph and reduce it, by removing all vertices with degree of 2.

The purpose of this algorithm is to introduce new functionality that reduces the complexity of a graph by removing any vertex that has a degree of 2. By exploring a reduced graph instead of a full graph insight can still be gained into the topology of the graph but with better performance. The edges of the reduced graph can be expanded if needed to determine how they correspond to the full graph. Take:

1 - 2 - 3 - 4 - 5 - 6 | | 7 - 8 - 9

This would be reduced to

1 - 2 - 4 - 6 | _ |

A total of 4 vertices with 4 edges as opposed to 9 vertices and 9 edges.

Parameters

[in] graph - graph instance

Returns: - a reduced graph

This class is to help keep track of which vertices have and have not been explored.

It is only used within the function and hence the encapsulation, it is not a public class and is not meant to be.

This class is to help keep track of which vertices have and have not been explored.

It is only used within the function and hence the encapsulation, it is not a public class and is not meant to be.

Definition at line 100 of file graphalgorithm.cc.

◆ reorderAndStoreChainIfDoesNotExist_()

bool votca::tools::reorderAndStoreChainIfDoesNotExist_	(	vector< Edge > &	edges,
		unordered_map< Edge, vector< vector< Index > > > &	expanded_edges,
		vector< Index >	chain,
		Index	vertex,
		size_t &	chain_index
	)

Definition at line 212 of file reducedgraph.cc.

◆ runwrapper()

void * votca::tools::runwrapper ( void * arg )

Definition at line 31 of file thread.cc.

◆ sig_fig_()

string votca::tools::sig_fig_	(	double	val,
		Index	sf
	)

Converts a double into a string with max number of significant figures indicated by sf

Definition at line 46 of file graphnode.cc.

◆ singleNetwork()

bool votca::tools::singleNetwork	(	Graph &	graph,
		GraphVisitor &	graph_visitor
	)

Determine if every vertex is connected to every other one through some combination of edges.

The purpose of this algorithm is to simply determine if the graph is one large network or not. If it is it means every vertex is connected to every other one by 1 or more series of edges.

Parameters

[in]	graph	- Graph instance
[in,out]	graph_visitor	- Graph visitor reference instance used to explore the graph

Returns: - Boolean value (true - if single network)

Definition at line 42 of file graphalgorithm.cc.

◆ start_hndl()

static void votca::tools::start_hndl	(	void *	data,
		const char *	el,
		const char **	attr
	)

static

Definition at line 210 of file property.cc.

◆ ToolsVersionStr()

const std::string & votca::tools::ToolsVersionStr ( )

Definition at line 33 of file version.cc.

◆ TXT()

PropertyIOManipulator votca::tools::TXT ( PropertyIOManipulator::TXT )

◆ verticesShouldBeReversed_()

bool votca::tools::verticesShouldBeReversed_ ( vector< Index > & vertices )

This function will determine if it is necessary to reverse the order of a chain of vertices. E.g.

1 - 2 - 4 - 5

This chain will not need to be reversed because the end points have end point 1 smaller than 5

This chain will need to be reversed

4 - 1 - 8 - 2

Because 2 is smaller than 4

If the chain has the same end points the next two vertices will be compared

1 - 2 - 3 - 4 - 1 ^ ^ | |

The 2 is smaller than the 4 so there is no need to reverse the order.

4 - 9 - 8 - 6 - 4

In this case th 6 is smaller than the 9 so the order will be reversed.

Definition at line 86 of file reducededge.cc.

◆ VotcaShareSet()

bool votca::tools::VotcaShareSet ( )

Definition at line 35 of file globals.cc.

◆ wildcmp() [1/2]

int votca::tools::wildcmp	(	const char *	wild,
		const char *	string
	)

Definition at line 28 of file tokenizer.cc.

◆ wildcmp() [2/2]

int votca::tools::wildcmp	(	const std::string &	wild,
		const std::string &	string
	)

Definition at line 24 of file tokenizer.cc.

◆ XML()

PropertyIOManipulator votca::tools::XML ( PropertyIOManipulator::XML )

Variable Documentation

◆ DEFAULT_COLORS

Color< csDefault > votca::tools::DEFAULT_COLORS

Definition at line 24 of file colors.cc.

◆ HLP

PropertyIOManipulator votca::tools::HLP(PropertyIOManipulator::HLP)

◆ TXT

PropertyIOManipulator votca::tools::TXT(PropertyIOManipulator::TXT)

◆ version_str

const std::string votca::tools::version_str

static

Initial value:

= std::string(TOOLS_VERSION) + " " +
                                       gitversion +
                                       " (compiled " __DATE__ ", " __TIME__ ")"

Definition at line 29 of file version.cc.

◆ XML

PropertyIOManipulator votca::tools::XML(PropertyIOManipulator::XML)

Namespaces

Classes

Enumerations

Functions

Variables

Enumeration Type Documentation

◆ ChargeUnit

◆ DistanceUnit

◆ EnergyUnit

◆ ForceUnit

◆ MassUnit

◆ MolarEnergyUnit

◆ MolarForceUnit

◆ StructureParameter

◆ TimeUnit

◆ VelocityUnit

Function Documentation

◆ addEdgeIfNotLoop_()

◆ char_hndl()

◆ cmpNode()

◆ cmpVertNodePair() [1/2]

◆ cmpVertNodePair() [2/2]

◆ compareChainWithChains_()

◆ convertFromString()

◆ create_policy_new()

◆ decoupleIsolatedSubGraphs()

◆ DUMMY_EDGE()

◆ end_hndl()

◆ exploreBranch()

◆ exploreGraph()

◆ findStructureId()

◆ FixPath()

◆ getAllConnectedVertices_()

◆ getAllVertices_()

◆ getDoubleStringId_()

◆ getIntStringId_()

◆ getline()

◆ getStrStringId_()

◆ getVertexJunctions_()

◆ GetVotcaShare()

◆ HLP()

◆ isApproximatelyEqual()

◆ IsValidCast()

◆ lexical_cast()

◆ linalg_constrained_qrsolve()

◆ moveVertexWithSmallestValueToEnds_()

◆ nodeForEveryVertex_()

◆ operator<<() [1/14]

◆ operator<<() [2/14]

◆ operator<<() [3/14]

◆ operator<<() [4/14]

◆ operator<<() [5/14]

◆ operator<<() [6/14]

◆ operator<<() [7/14]

◆ operator<<() [8/14]

◆ operator<<() [9/14]

◆ operator<<() [10/14]

◆ operator<<() [11/14]

◆ operator<<() [12/14]

◆ operator<<() [13/14]

◆ operator<<() [14/14]

◆ operator>>()

◆ orderChainAfterInitialVertex_()

◆ PrintNodeHLP()

◆ PrintNodeTXT()

◆ PrintNodeXML()

◆ reduceGraph()

◆ reorderAndStoreChainIfDoesNotExist_()

◆ runwrapper()

◆ sig_fig_()

◆ singleNetwork()

◆ start_hndl()

◆ ToolsVersionStr()

◆ TXT()

◆ verticesShouldBeReversed_()

◆ VotcaShareSet()

◆ wildcmp() [1/2]

◆ wildcmp() [2/2]

◆ XML()

Variable Documentation