General functions to import atomic coordinates. More...

#include "global.h"
#include "glview.h"
#include "callbacks.h"
#include "interface.h"
#include "project.h"
#include "bind.h"
#include <omp.h>
#include "cbuild_edit.h"

Include dependency graph for read_coord.c:

Go to the source code of this file.

Functions
int	open_xyz_file (int linec)
	open XYZ file

int	open_c3d_file (int linec)
	open C3D file

int	open_pdb_file (int linec)
	open PDB file

int	open_trj_file (int linec)
	open CPMD file

int	open_vas_file (int linec)
	open VASP file

int	open_cif_file (int linec)
	open CIF file

int	open_hist_file (int linec)
	open DL-POLY history file

void	allocatoms (project *this_proj)
	allocate project data

chemical_data *	alloc_chem_data (int spec)
	allocate chemistry data

int	build_crystal (gboolean visible, project this_proj, gboolean to_wrap, gboolean show_clones, cell_info cell, GtkWidget *widg)
	build crystal

void	add_reader_info (gchar *info, int mid)
	append information message to the reader information

void	reader_info (gchar type, gchar sinf, int val)
	display reader information

void	format_error (int stp, int ato, gchar *mot, int line)
	Message to display an error message.

int	set_v_dummy (gchar *this_word)
	check if dummy is used for unknown species, if not then ask what to do

void	check_for_species (double v, int ato)
	Fill the species for each atom and the associated data.

int	open_coord_file (gchar *filename, int fti)
	open atomic coordinates file

Variables
const gchar *	dfi [2]

atom_search *	cif_search

atomic_object *	cif_object

FILE *	coordf

coord_file *	this_reader

gchar **	coord_line = NULL

gchar *	this_line = NULL

char *	this_word

line_node *	head = NULL

line_node *	tail = NULL

Detailed Description

General functions to import atomic coordinates.

Author: Sébastien Le Roux sebas.nosp@m.tien.nosp@m..lero.nosp@m.ux@i.nosp@m.pcms..nosp@m.unis.nosp@m.tra.f.nosp@m.r

Definition in file read_coord.c.

Function Documentation

◆ add_reader_info()

void add_reader_info	(	gchar *	info,
		int	mid )

append information message to the reader information

Parameters

info	the reader information message
mid	message type (0 = error, 1 = warning)

Definition at line 84 of file read_coord.c.

◆ alloc_chem_data()

chemical_data * alloc_chem_data ( int spec )

extern

allocate chemistry data

Parameters

spec	the number of chemical species

Definition at line 186 of file open_p.c.

◆ allocatoms()

void allocatoms ( project * this_proj )

extern

allocate project data

Parameters

this_proj the target project

Definition at line 160 of file open_p.c.

◆ build_crystal()

int build_crystal	(	gboolean	visible,
		project *	this_proj,
		gboolean	to_wrap,
		gboolean	show_clones,
		cell_info *	cell,
		GtkWidget *	widg )

extern

build crystal

Parameters

visible	is the crystal builder window visible ?
this_proj	the target project
to_wrap	wrap or not atomic coordinates in the unit cell
show_clones	show / hide clone(s)
cell	the cell info that contains the crystal description
widg	the GtkWidget sending the signal

Definition at line 907 of file cbuild_action.c.

◆ check_for_species()

void check_for_species	(	double	v,
		int	ato )

Fill the species for each atom and the associated data.

Parameters

v	Z
ato	the atom id

Definition at line 194 of file read_coord.c.

◆ format_error()

void format_error	(	int	stp,
		int	ato,
		gchar *	mot,
		int	line )

Message to display an error message.

Parameters

stp	the MD step id
ato	Atom id
mot	Message
line	Line with the error

Definition at line 114 of file read_coord.c.

◆ open_c3d_file()

int open_c3d_file ( int linec )

extern

open C3D file

Parameters

linec Number of lines in the file

Definition at line 320 of file read_c3d.c.

◆ open_cif_file()

int open_cif_file ( int linec )

extern

open CIF file

Parameters

linec Total number of lines

Definition at line 1725 of file read_cif.c.

◆ open_coord_file()

int open_coord_file	(	gchar *	filename,
		int	fti )

open atomic coordinates file

Parameters

filename	the file name
fti	the type of coordinates

Definition at line 248 of file read_coord.c.

◆ open_hist_file()

int open_hist_file ( int linec )

extern

open DL-POLY history file

Parameters

linec Number of lines in the file

Definition at line 438 of file read_hist.c.

◆ open_pdb_file()

int open_pdb_file ( int linec )

extern

open PDB file

Parameters

linec Number of lines in the file

Definition at line 216 of file read_pdb.c.

◆ open_trj_file()

int open_trj_file ( int linec )

extern

open CPMD file

Parameters

linec Number of lines in the file

Definition at line 249 of file read_trj.c.

◆ open_vas_file()

int open_vas_file ( int linec )

extern

open VASP file

Parameters

linec Number of lines in the file

Definition at line 242 of file read_vas.c.

◆ open_xyz_file()

int open_xyz_file ( int linec )

extern

open XYZ file

Parameters

linec Number of lines in the file

Definition at line 301 of file read_xyz.c.

◆ reader_info()

void reader_info	(	gchar *	type,
		gchar *	sinf,
		int	val )

display reader information

Parameters

type	File type
sinf	Information message
val	Value to present

Definition at line 99 of file read_coord.c.

◆ set_v_dummy()

int set_v_dummy ( gchar * this_word )

check if dummy is used for unknown species, if not then ask what to do

Parameters

this_word the chemical species label

Definition at line 140 of file read_coord.c.

Variable Documentation

◆ cif_object

atomic_object* cif_object

extern

Definition at line 280 of file read_cif.c.

◆ cif_search

atom_search* cif_search

extern

Definition at line 279 of file read_cif.c.

◆ coord_line

gchar** coord_line = NULL

Definition at line 70 of file read_coord.c.

◆ coordf

FILE* coordf

Definition at line 68 of file read_coord.c.

◆ dfi

const gchar* dfi[2]

extern

Definition at line 75 of file main-b.c.

◆ head

line_node* head = NULL

Definition at line 73 of file read_coord.c.

◆ tail

line_node* tail = NULL

Definition at line 74 of file read_coord.c.

◆ this_line

gchar* this_line = NULL

Definition at line 71 of file read_coord.c.

◆ this_reader

coord_file* this_reader

Definition at line 69 of file read_coord.c.

◆ this_word

char* this_word

Definition at line 72 of file read_coord.c.

Functions

Variables

Detailed Description

Function Documentation

◆ add_reader_info()

◆ alloc_chem_data()

◆ allocatoms()

◆ build_crystal()

◆ check_for_species()

◆ format_error()

◆ open_c3d_file()

◆ open_cif_file()

◆ open_coord_file()

◆ open_hist_file()

◆ open_pdb_file()

◆ open_trj_file()

◆ open_vas_file()

◆ open_xyz_file()

◆ reader_info()

◆ set_v_dummy()

Variable Documentation

◆ cif_object

◆ cif_search

◆ coord_line

◆ coordf

◆ dfi

◆ head

◆ tail

◆ this_line

◆ this_reader

◆ this_word