read_coord.c File Reference

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 "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 86 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 196 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 116 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 322 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 1728 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 250 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 440 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 217 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 251 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 244 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 303 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 101 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 142 of file read_coord.c.

Variable Documentation

cif_object

atomic_object* cif_object

extern

Definition at line 282 of file read_cif.c.

cif_search

atom_search* cif_search

extern

Definition at line 281 of file read_cif.c.

coord_line

gchar** coord_line = NULL

Definition at line 72 of file read_coord.c.

coordf

FILE* coordf

Definition at line 70 of file read_coord.c.

dfi

const gchar* dfi[2]

extern

Definition at line 74 of file main.c.

head

line_node* head = NULL

Definition at line 75 of file read_coord.c.

tail

line_node* tail = NULL

Definition at line 76 of file read_coord.c.

this_line

gchar* this_line = NULL

Definition at line 73 of file read_coord.c.

this_reader

coord_file* this_reader

Definition at line 71 of file read_coord.c.

this_word

char* this_word

Definition at line 74 of file read_coord.c.