Function declarations for the crystal builder. More...

#include "global.h"
#include <libxml/xmlreader.h>

Include dependency graph for cbuild_edit.h:

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Data Structures
struct	crystal_data

Typedefs
typedef struct crystal_data	crystal_data

Functions
int	clean_xml_data (xmlDoc *doc, xmlTextReaderPtr reader)
	free XML data

xmlNodePtr	findnode (xmlNodePtr startnode, char *nname)
	find XML node

gboolean	test_vol (double box[2][3], double vect[3][3])
	is the cell properly described to use PBC ?

G_MODULE_EXPORT void	update_vect (GtkEntry *entry, gpointer data)
	update lattice vector component

G_MODULE_EXPORT void	update_box (GtkEntry *entry, gpointer data)
	update lattice parameters

double	get_value_from_pos (gchar *pos)
	get position double value from string description

double	get_val_from_wyckoff (gchar pos, gchar wval)
	get point value from wyckoff position

crystal_data *	allocate_crystal_data (int objects, int species)
	allocate crystal data pointer

crystal_data *	free_crystal_data (crystal_data *cryst)
	free crystal data pointer

G_MODULE_EXPORT gboolean	to_update_box (GtkWidget widg, GdkEventFocus event, gpointer data)

G_MODULE_EXPORT gboolean	to_update_vect (GtkWidget widg, GdkEventFocus event, gpointer data)

int	occupancy (double occ, int cif_occ)
	handle occupancy integer rouding

gchar *	replace_markup (char init, char key, char *rep)
	replace pattern in string

gchar *	substitute_string (gchar init, gchar o_motif, gchar *n_motif)
	substitute all patterns in string

space_group *	read_sg_xml_file (const char *filetoread)
	read space group data from XML file

GtkWidget *	create_atoms_tree (atom_search asearch, project this_proj, int na)
	create atom search tree view

atom_search *	allocate_atom_search (int proj, int action, int searchid, int tsize)
	allocate atom search data structure

GtkWidget *	create_action_combo (int id, project *this_proj)
	create action combo box

void	prepare_atom_edition (gpointer data, gboolean visible)
	prepare atom edition

void	clean_all_trees (atom_search asearch, project this_proj)
	clean all tree models in the 'model edition' window

void	prepare_opengl_menu_bar (glwin *view)
	update the OpenGL window menu bar

void	allocatoms (project *this_proj)
	allocate project data

chemical_data *	alloc_chem_data (int spec)
	allocate chemistry data

void	setup_default_lights (project this_proj, image img)
	initialize lightning for an image data structure

void	setup_image_spec_data (project this_proj, image img)
	initialize the chemical species related pointers in an image data structure

void	glwin_init_spec_data (project *this_proj, int nspec)
	initialize the glwin chemical species related pointers

G_MODULE_EXPORT void	set_mode (GtkWidget *widg, gpointer data)
	set mouse mode callback

void	shift_it (vec3_t shift, int refresh, int proj)
	shift atomic coordinates

G_MODULE_EXPORT void	close_edit (GtkWidget *widg, gpointer data)

int	insert_this_project_from_lib (int id, gboolean visible, project this_proj, atom_search asearch)
	insert object from the library

void	to_insert_in_project (int stat, int orig, project this_proj, atom_search asearch, gboolean visible)
	to insert object in project

Variables
gchar *	groups [230]

gchar *	hmsymbols [230]

dint	t_box [9]

double	tmp_box [2][3]

double	tmp_vect [3][3]

char *	vect_name [3]

char *	vect_comp [3]

char *	box_p [2]

char *	box_prop [2][3]

gchar *	cif_occupancies [3]

gchar *	cif_occ [3]

gchar *	cif_sites [2]

atom_search *	insert_search

gboolean	crystal_low_warning

gboolean	crystal_crowded

gboolean	crystal_dist_chk

Detailed Description

Function declarations for the crystal builder.

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 cbuild_edit.h.

Typedef Documentation

◆ crystal_data

typedef struct crystal_data crystal_data

Definition at line 37 of file cbuild_edit.h.

Function Documentation

◆ alloc_chem_data()

chemical_data * alloc_chem_data ( int spec )

extern

allocate chemistry data

Parameters

spec	the number of chemical species

Definition at line 189 of file open_p.c.

◆ allocate_atom_search()

atom_search * allocate_atom_search	(	int	proj,
		int	action,
		int	searchid,
		int	tsize )

extern

allocate atom search data structure

Parameters

proj	the target project id
action	the edition action
searchid	the atom search id
tsize	the atom search object list size

Definition at line 386 of file atom_edit.c.

◆ allocate_crystal_data()

crystal_data * allocate_crystal_data	(	int	objects,
		int	species )

extern

allocate crystal data pointer

Parameters

objects	the number of object(s)
species	the number of chemical species

Definition at line 621 of file cbuild_action.c.

◆ allocatoms()

void allocatoms ( project * this_proj )

extern

allocate project data

Parameters

this_proj the target project

Definition at line 163 of file open_p.c.

◆ clean_all_trees()

void clean_all_trees	(	atom_search *	asearch,
		project *	this_proj )

extern

clean all tree models in the 'model edition' window

Parameters

asearch	the target atom search
this_proj	the target project

Definition at line 1024 of file atom_action.c.

◆ clean_xml_data()

int clean_xml_data	(	xmlDoc *	doc,
		xmlTextReaderPtr	reader )

extern

free XML data

Parameters

doc	the XML doc pointer to free
reader	the XML reader to free

Definition at line 322 of file w_library.c.

◆ close_edit()

G_MODULE_EXPORT void close_edit	(	GtkWidget *	widg,
		gpointer	data )

extern

◆ create_action_combo()

GtkWidget * create_action_combo	(	int	id,
		project *	this_proj )

extern

create action combo box

Parameters

id	the action id
this_proj	the target project

Definition at line 206 of file atom_search.c.

◆ create_atoms_tree()

GtkWidget * create_atoms_tree	(	atom_search *	asearch,
		project *	this_proj,
		int	nats )

extern

create atom search tree view

Parameters

asearch	the target atom search
this_proj	the target project
nats	the total number of atom(s)

Definition at line 3582 of file w_search.c.

◆ findnode()

xmlNodePtr findnode	(	xmlNodePtr	startnode,
		char *	nname )

extern

find XML node

Parameters

startnode	Starting node
nname	Node name to find

Definition at line 546 of file read_isaacs.c.

◆ free_crystal_data()

crystal_data * free_crystal_data ( crystal_data * cryst )

extern

free crystal data pointer

Parameters

cryst the data pointer to free

Definition at line 648 of file cbuild_action.c.

◆ get_val_from_wyckoff()

double get_val_from_wyckoff	(	gchar *	pos,
		gchar *	wval )

extern

get point value from wyckoff position

Parameters

pos	"x", "y" or "z"
wval	wyckoff position vector

Definition at line 462 of file cbuild_action.c.

◆ get_value_from_pos()

double get_value_from_pos ( gchar * pos )

extern

get position double value from string description

Parameters

pos	the string description

Definition at line 136 of file cbuild_action.c.

◆ glwin_init_spec_data()

void glwin_init_spec_data	(	project *	this_proj,
		int	nspec )

extern

initialize the glwin chemical species related pointers

Parameters

this_proj	the target project
nspec	the number of chemical species

Definition at line 1637 of file glview.c.

◆ insert_this_project_from_lib()

int insert_this_project_from_lib	(	int	id,
		gboolean	visible,
		project *	this_proj,
		atom_search *	asearch )

extern

insert object from the library

Parameters

id	object id to insert
visible	is the 'model edition window' visible
this_proj	the target project
asearch	the target atom search

Definition at line 1160 of file w_library.c.

◆ occupancy()

int occupancy	(	double	occ,
		int	cif_occ )

extern

handle occupancy integer rouding

Parameters

occ	value to round
cif_occ	how to round

Definition at line 690 of file cbuild_action.c.

◆ prepare_atom_edition()

void prepare_atom_edition	(	gpointer	data,
		gboolean	visible )

extern

prepare atom edition

Parameters

data	the associated data pointer
visible	is the window visible (1/0)

Definition at line 453 of file atom_edit.c.

◆ prepare_opengl_menu_bar()

void prepare_opengl_menu_bar ( glwin * view )

extern

update the OpenGL window menu bar

Parameters

view	the target glwin

Definition at line 615 of file glwindow.c.

◆ read_sg_xml_file()

space_group * read_sg_xml_file ( const char * filetoread )

extern

read space group data from XML file

Parameters

filetoread the file to read

Definition at line 652 of file cbuild_sg.c.

◆ replace_markup()

gchar * replace_markup	(	char *	init,
		char *	key,
		char *	rep )

extern

replace pattern in string

Parameters

init	the string
key	the pattern to replace
rep	the new pattern

Definition at line 339 of file w_library.c.

◆ set_mode()

G_MODULE_EXPORT void set_mode	(	GtkWidget *	widg,
		gpointer	data )

extern

set mouse mode callback

Parameters

widg	the GtkWidget sending the signal
data	the associated data pointer

Definition at line 172 of file m_tools.c.

◆ setup_default_lights()

void setup_default_lights	(	project *	this_proj,
		image *	img )

extern

initialize lightning for an image data structure

Parameters

this_proj	the target project
img	the target image

Definition at line 1305 of file glview.c.

◆ setup_image_spec_data()

void setup_image_spec_data	(	project *	this_proj,
		image *	img )

extern

initialize the chemical species related pointers in an image data structure

Parameters

this_proj	the target project
img	the target image

Definition at line 1264 of file glview.c.

◆ shift_it()

void shift_it	(	vec3_t	shift,
		int	refresh,
		int	proj )

extern

shift atomic coordinates

Parameters

shift	the shift vector
refresh	refresh rendering data
proj	the target project id

Definition at line 206 of file cell_shift.c.

◆ substitute_string()

gchar * substitute_string	(	gchar *	init,
		gchar *	o_motif,
		gchar *	n_motif )

extern

substitute all patterns in string

Parameters

init	the initial string
o_motif	the pattern to replace
n_motif	the new pattern

Definition at line 372 of file w_library.c.

◆ test_vol()

gboolean test_vol	(	double	box[2][3],
		double	vect[3][3] )

extern

is the cell properly described to use PBC ?

Parameters

box	lattice parameters
vect	lattice vectors

Definition at line 487 of file edit_menu.c.

◆ to_insert_in_project()

void to_insert_in_project	(	int	stat,
		int	orig,
		project *	this_proj,
		atom_search *	asearch,
		gboolean	visible )

extern

to insert object in project

Parameters

stat	in enum object_types
orig	- (fragmol id/species id +1), -1, or, orgin atom id
this_proj	the target project
asearch	the target atom search
visible	is the model edition window visible ?

Definition at line 1214 of file atom_object.c.

◆ to_update_box()

G_MODULE_EXPORT gboolean to_update_box	(	GtkWidget *	widg,
		GdkEventFocus *	event,
		gpointer	data )

extern

◆ to_update_vect()

G_MODULE_EXPORT gboolean to_update_vect	(	GtkWidget *	widg,
		GdkEventFocus *	event,
		gpointer	data )

extern

◆ update_box()

G_MODULE_EXPORT void update_box	(	GtkEntry *	entry,
		gpointer	data )

extern

update lattice parameters

Parameters

entry	the GtkEntry sending the signal
data	the associated data pointer

Definition at line 108 of file edit_menu.c.

◆ update_vect()

G_MODULE_EXPORT void update_vect	(	GtkEntry *	entry,
		gpointer	data )

extern

update lattice vector component

Parameters

entry	the GtkEntry sending the signal
data	the associated data pointer

Definition at line 188 of file edit_menu.c.

Variable Documentation

◆ box_p

char* box_p[2]

extern

Definition at line 73 of file edit_menu.c.

◆ box_prop

char* box_prop[2][3]

extern

Definition at line 74 of file edit_menu.c.

◆ cif_occ

gchar* cif_occ[3]

extern

Definition at line 478 of file interface.c.

◆ cif_occupancies

gchar* cif_occupancies[3]

extern

Definition at line 460 of file interface.c.

◆ cif_sites

gchar* cif_sites[2]

extern

Definition at line 481 of file interface.c.

◆ crystal_crowded

gboolean crystal_crowded

extern

Definition at line 956 of file cbuild_action.c.

◆ crystal_dist_chk

gboolean crystal_dist_chk

extern

Definition at line 957 of file cbuild_action.c.

◆ crystal_low_warning

gboolean crystal_low_warning

extern

Definition at line 955 of file cbuild_action.c.

◆ groups

gchar* groups[230]

extern

Definition at line 43 of file cbuild_sg.c.

◆ hmsymbols

gchar* hmsymbols[230]

extern

Definition at line 274 of file cbuild_sg.c.

◆ insert_search

atom_search* insert_search

extern

Definition at line 175 of file popup.c.

◆ t_box

dint t_box[9]

extern

Definition at line 95 of file edit_menu.c.

◆ tmp_box

double tmp_box[2][3]

extern

Definition at line 262 of file preferences.c.

◆ tmp_vect

double tmp_vect[3][3]

extern

Definition at line 92 of file edit_menu.c.

◆ vect_comp

char* vect_comp[3]

extern

Definition at line 83 of file edit_menu.c.

◆ vect_name

char* vect_name[3]

extern

Definition at line 82 of file edit_menu.c.

Data Structures

Typedefs

Functions

Variables

Detailed Description

Typedef Documentation

◆ crystal_data

Function Documentation

◆ alloc_chem_data()

◆ allocate_atom_search()

◆ allocate_crystal_data()

◆ allocatoms()

◆ clean_all_trees()

◆ clean_xml_data()

◆ close_edit()

◆ create_action_combo()

◆ create_atoms_tree()

◆ findnode()

◆ free_crystal_data()

◆ get_val_from_wyckoff()

◆ get_value_from_pos()

◆ glwin_init_spec_data()

◆ insert_this_project_from_lib()

◆ occupancy()

◆ prepare_atom_edition()

◆ prepare_opengl_menu_bar()

◆ read_sg_xml_file()

◆ replace_markup()

◆ set_mode()

◆ setup_default_lights()

◆ setup_image_spec_data()

◆ shift_it()

◆ substitute_string()

◆ test_vol()

◆ to_insert_in_project()

◆ to_update_box()

◆ to_update_vect()

◆ update_box()

◆ update_vect()

Variable Documentation

◆ box_p

◆ box_prop

◆ cif_occ

◆ cif_occupancies

◆ cif_sites

◆ crystal_crowded

◆ crystal_dist_chk

◆ crystal_low_warning

◆ groups

◆ hmsymbols

◆ insert_search

◆ t_box

◆ tmp_box

◆ tmp_vect

◆ vect_comp

◆ vect_name