#include <cif_io.h>

Collaboration diagram for ModuleIO::CifParser:

Public Member Functions
	CifParser ()=delete

	CifParser (const std::string &fcif)

	~CifParser ()

std::vector< std::string >	get (const std::string &key)
	get information by key from the stored information of cif file, if the key is not found, an empty vector will be returned.

Static Public Member Functions
static void	write (const std::string &fcif, const double abc_angles, const int natom, const std::string atom_site_labels, const double atom_site_fract_coords, const std::string &title="# generated by ABACUS", const std::string &data_tag="data_?", const int rank=0, const double atom_site_occups=nullptr, const std::string &cell_formula_units_z="1")
	Print the CIF file from the given information.

static void	write (const std::string &fcif, const std::vector< double > &abc_angles, const std::vector< std::string > &atom_site_labels, const std::vector< double > &atom_site_fract_coords, const std::string &title="# generated by ABACUS", const std::string &data_tag="data_?", const int rank=0, const std::vector< double > &atom_site_occups={}, const std::string &cell_formula_units_z="1")
	A Pybind wrapper for the static method write.

static void	write (const std::string &fcif, const UnitCell &ucell, const std::string &title="# generated by ABACUS", const std::string &data_tag="data_?", const int rank=0)
	Write CIF file with the whole UnitCell instance.

static void	read (const std::string &fcif, std::map< std::string, std::vector< std::string > > &out, const int rank=0)
	Read the CIF file and store the information in the map.

Static Private Member Functions
static void	_unpack_ucell (const UnitCell &ucell, std::vector< double > &veca, std::vector< double > &vecb, std::vector< double > &vecc, int &natom, std::vector< std::string > &atom_site_labels, std::vector< double > &atom_site_fract_coords)

Private Attributes
std::map< std::string, std::vector< std::string > >	raw_

Detailed Description

CifParser

INTRODUCTION

In short

Tools for CIF file I/O.

Supported structure of CIF

A example (official template of CIF) is shown here (https://www.iucr.org/__data/iucr/ftp/pub/form.cif), but present impl. is ONLY capable to parse a CIF with ONE structure. If there are multiple structures in the CIF file, unexpected behavior may occur.

A CIF file always contain two kinds of data structure, the first is simply the key-value pair, the second is table which is lead by a keyword "loop_".

Key-value pair

key-value pair can have two types:

Type 1: the most general _KEY1 VALUE1 _KEY2 VALUE2 ... Type 2: text box _KEY1 ; very long text VeRy LoNg TeXt ... ;

Table

The table in CIF must be lead by a keyword "loop_", and all titles of the columns will be list first, then all the rest are the values of the table. For example: loop_ _KEY1 _KEY2 _KEY3 ... VALUE11 VALUE21 VALUE31 VALUE12 VALUE22 VALUE32 ... Once the number of values cannot be divided by the number of keys, will cause an assertion error.

Usage of this "class"

Read CIF file and store the information in a map

type the following line: std::map<std::string, std::vector<std::string>> cif_info; ModuleIO::CifParser::read("test.cif", cif_info);

Information of the cif file will stored in key-value pair manner, like cif_info["_cell_length_a"] = {"2.46772428"}; cif_info["_cell_length_b"] = {"2.46772428"}; ... cif_info["_atom_site_label"] = {"C1", "C2", ...}; cif_info["_atom_site_fract_x"] = {"0.00000000", "0.33333300", ...}; ... NOTE1: only keys in table will have value with length larger than 1, otherwise all words will be saved in the only element in std::vector<std::string>. For example please see unittest of this class at source/source_io/test/cif_io_test.cpp. NOTE2: One should note that for some cif files, the number will be in the format like "0.00000000(1)", which means the uncertainty of the number is 1 in the last digit. In this case, user should be careful to convert the string to double by its own.

Write CIF file with the given information.

ModuleIO::CifParser::write("test.cif", ...); For detailed usage, see the static methods in the class. A to-be-deprecated usage is simple as: ModuleIO::CifParser cif("test.cif", ucell); , where ucell is an instance of UnitCell. This usage is not encouraged.

Pythonization information

function write it is recommended to pythonize the 2nd overload of this function, the 3rd one will be deprecated in the future.
function read this function can be directly pythonized.

Constructor & Destructor Documentation

◆ CifParser() [1/2]

ModuleIO::CifParser::CifParser ( )

delete

◆ CifParser() [2/2]

ModuleIO::CifParser::CifParser ( const std::string & fcif )

◆ ~CifParser()

ModuleIO::CifParser::~CifParser ( )

inline

Member Function Documentation

◆ _unpack_ucell()

void ModuleIO::CifParser::_unpack_ucell	(	const UnitCell &	ucell,
		std::vector< double > &	veca,
		std::vector< double > &	vecb,
		std::vector< double > &	vecc,
		int &	natom,
		std::vector< std::string > &	atom_site_labels,
		std::vector< double > &	atom_site_fract_coords
	)

staticprivate

◆ get()

std::vector< std::string > ModuleIO::CifParser::get ( const std::string & key )

get information by key from the stored information of cif file, if the key is not found, an empty vector will be returned.

Parameters

key	the key to search

Returns: std::vector<std::string>. Only columns in table will have more than one element, otherwise all the information will be stored in the only element (the first).

◆ read()

void ModuleIO::CifParser::read	(	const std::string &	fcif,
		std::map< std::string, std::vector< std::string > > &	out,
		const int	rank = `0`
	)

static

Read the CIF file and store the information in the map.

Parameters

fcif	the input cif file name
out	the output map containing the information
rank	the rank which reads the CIF file

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◆ write() [1/3]

void ModuleIO::CifParser::write	(	const std::string &	fcif,
		const double *	abc_angles,
		const int	natom,
		const std::string *	atom_site_labels,
		const double *	atom_site_fract_coords,
		const std::string &	title = `"# generated by ABACUS"`,
		const std::string &	data_tag = `"data_?"`,
		const int	rank = `0`,
		const double *	atom_site_occups = `nullptr`,
		const std::string &	cell_formula_units_z = `"1"`
	)

static

Print the CIF file from the given information.

Parameters

fcif	the output cif file name
abc_angles	cell A B C angles in the form of [a, b, c, alpha, beta, gamma]
natom	the number of atoms
atom_site_labels	the atom site labels in the form of [atom1, atom2, ...]
atom_site_fract_coords	the fractional coordinates of the atoms in the form of [x1, y1, z1, x2, y2, z2, ...]
title	the title of the CIF file
data_tag	the data tag of the CIF file
rank	the rank which writes the CIF file
atom_site_occups	the occupancies of the atoms in the form of [occup1, occup2, ...]
cell_formula_units_z	the cell formula units Z

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◆ write() [2/3]

void ModuleIO::CifParser::write	(	const std::string &	fcif,
		const std::vector< double > &	abc_angles,
		const std::vector< std::string > &	atom_site_labels,
		const std::vector< double > &	atom_site_fract_coords,
		const std::string &	title = `"# generated by ABACUS"`,
		const std::string &	data_tag = `"data_?"`,
		const int	rank = `0`,
		const std::vector< double > &	atom_site_occups = `{}`,
		const std::string &	cell_formula_units_z = `"1"`
	)

static

A Pybind wrapper for the static method write.

Parameters

fcif	the output cif file name
abc_angles	cell A B C angles in the form of [a, b, c, alpha, beta, gamma]
atom_site_labels	the atom site labels in the form of [atom1, atom2, ...]
atom_site_fract_coords	the fractional coordinates of the atoms in the form of [x1, y1, z1, x2, y2, z2, ...]
title	the title of the CIF file
data_tag	the data tag of the CIF file
rank	the rank which writes the CIF file
atom_site_occups	the occupancies of the atoms in the form of [occup1, occup2, ...]
cell_formula_units_z	the cell formula units Z

◆ write() [3/3]

void ModuleIO::CifParser::write	(	const std::string &	fcif,
		const UnitCell &	ucell,
		const std::string &	title = `"# generated by ABACUS"`,
		const std::string &	data_tag = `"data_?"`,
		const int	rank = `0`
	)

static

Write CIF file with the whole UnitCell instance.

Parameters

fcif	the output cif file name
ucell	the input UnitCell instance
title	the title of the CIF file
data_tag	the data tag of the CIF file
rank	the rank which writes the CIF file

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Member Data Documentation

◆ raw_

std::map<std::string, std::vector<std::string> > ModuleIO::CifParser::raw_

private

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

/home/runner/work/abacus-develop/abacus-develop/source/source_io/cif_io.h
/home/runner/work/abacus-develop/abacus-develop/source/source_io/cif_io.cpp

Public Member Functions

Static Public Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

CifParser

INTRODUCTION

In short

Supported structure of CIF

Key-value pair

Table

Usage of this "class"

Read CIF file and store the information in a map

Write CIF file with the given information.

Pythonization information

Constructor & Destructor Documentation

◆ CifParser() [1/2]

◆ CifParser() [2/2]

◆ ~CifParser()

Member Function Documentation

◆ _unpack_ucell()

◆ get()

◆ read()

◆ write() [1/3]

◆ write() [2/3]

◆ write() [3/3]

Member Data Documentation

◆ raw_