Functions to build a crystal using space group, crystallographic position(s) and object(s) to insert. More...

#include "global.h"
#include "callbacks.h"
#include "interface.h"
#include "glview.h"
#include "bind.h"
#include "project.h"
#include "workspace.h"
#include "atom_edit.h"
#include "cbuild_edit.h"
#include "readers.h"
#include <ctype.h>

Include dependency graph for cbuild_action.c:

Go to the source code of this file.

Functions
int	get_crystal_id (int spg)
	get the bravais lattice id from space group id

double	get_val_from_setting (gchar pos, gchar sval)
	get value from space group setting

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

void	get_origin (space_group *spg)
	get space group origin matrices

void	compute_lattice_properties (cell_info *cell)
	compute lattice parameters following cell description

int	test_lattice (builder_edition cbuilder, cell_info cif_cell)
	test lattice parameters

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

void	clean_this_proj (project *this_proj, gboolean newp)
	clean project and/or associated cell parameters

gboolean	same_coords (float a, float b)
	test if values are similar, allowing a 0.0001 difference

gboolean	are_equal_vectors (vec3_t u, vec3_t v)
	comparing atomic coordinates vectors

int	pos_not_saved (vec3_t *all_pos, int num_pos, vec3_t pos)
	was this position already saved ?

space_group *	duplicate_space_group (space_group *spg)
	duplicate space ground information

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

gboolean	pos_not_taken (int pos, int dim, int *tab)
	is this position already taken ?

gboolean	adjust_object_occupancy (crystal_data *cryst, int occupying, int tot_cell)
	adjust the crystallograpĥic sites occupancy

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

Variables
atomic_object *	cif_object

gchar *	tmp_pos = NULL

Detailed Description

Functions to build a crystal using space group, crystallographic position(s) and object(s) to insert.

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_action.c.

Function Documentation

◆ adjust_object_occupancy()

gboolean adjust_object_occupancy	(	crystal_data *	cryst,
		int	occupying,
		int	tot_cell )

adjust the crystallograpĥic sites occupancy

Parameters

cryst	the crystal
occupying	how to adjust occupancy: 0 = Random for the initial cell only, 1 = Random cell by cell, 2 = Completely random 3 = Successively 4 = Alternatively
tot_cell	the total number of cell to build

Definition at line 665 of file cbuild_action.c.

◆ allocate_crystal_data()

crystal_data * allocate_crystal_data	(	int	objects,
		int	species )

allocate crystal data pointer

Parameters

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

Definition at line 590 of file cbuild_action.c.

◆ are_equal_vectors()

gboolean are_equal_vectors	(	vec3_t	u,
		vec3_t	v )

comparing atomic coordinates vectors

Parameters

u	1st vector
v	2nd vector

Definition at line 530 of file cbuild_action.c.

◆ build_crystal()

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

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.

◆ clean_this_proj()

void clean_this_proj	(	project *	this_proj,
		gboolean	newp )

clean project and/or associated cell parameters

Parameters

this_proj	the target project
newp	is this a new project ?

Definition at line 485 of file cbuild_action.c.

◆ compute_lattice_properties()

void compute_lattice_properties ( cell_info * cell )

compute lattice parameters following cell description

Parameters

cell	the target cell description

Definition at line 193 of file cbuild_action.c.

◆ duplicate_space_group()

space_group * duplicate_space_group ( space_group * spg )

duplicate space ground information

Parameters

spg	the space group to duplicate

Definition at line 565 of file cbuild_action.c.

◆ free_crystal_data()

crystal_data * free_crystal_data ( crystal_data * cryst )

free crystal data pointer

Parameters

cryst the data pointer to free

Definition at line 617 of file cbuild_action.c.

◆ get_crystal_id()

int get_crystal_id ( int spg )

extern

get the bravais lattice id from space group id

Parameters

spg	the target space group id

Definition at line 127 of file cbuild_edit.c.

◆ get_origin()

void get_origin ( space_group * spg )

get space group origin matrices

Parameters

spg	the target space group

Definition at line 146 of file cbuild_action.c.

◆ get_val_from_setting()

double get_val_from_setting	(	gchar *	pos,
		gchar *	sval )

get value from space group setting

Parameters

pos	the position "a", "b" or "c"
sval	the space group setting

Definition at line 82 of file cbuild_action.c.

◆ get_val_from_wyckoff()

double get_val_from_wyckoff	(	gchar *	pos,
		gchar *	wval )

get point value from wyckoff position

Parameters

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

Definition at line 446 of file cbuild_action.c.

◆ get_value_from_pos()

double get_value_from_pos ( gchar * pos )

get position double value from string description

Parameters

pos	the string description

Definition at line 121 of file cbuild_action.c.

◆ pos_not_saved()

int pos_not_saved	(	vec3_t *	all_pos,
		int	num_pos,
		vec3_t	pos )

was this position already saved ?

Parameters

all_pos	the list of saved atomic coordinates
num_pos	the number of saved atomic coordinates
pos	the vector to test

Definition at line 548 of file cbuild_action.c.

◆ pos_not_taken()

gboolean pos_not_taken	(	int	pos,
		int	dim,
		int *	tab )

is this position already taken ?

Parameters

pos	position id
dim	number of position(s)
tab	the list of position(s)

Definition at line 644 of file cbuild_action.c.

◆ same_coords()

gboolean same_coords	(	float	a,
		float	b )

test if values are similar, allowing a 0.0001 difference

Parameters

a	1st value
b	2nd value

Definition at line 515 of file cbuild_action.c.

◆ test_lattice()

int test_lattice	(	builder_edition *	cbuilder,
		cell_info *	cif_cell )

test lattice parameters

Parameters

cbuilder	the builder edition with the lattice parameters
cif_cell	the cell information when testing CIF file

Definition at line 312 of file cbuild_action.c.

Variable Documentation

◆ cif_object

atomic_object* cif_object

extern

Definition at line 282 of file read_cif.c.

◆ tmp_pos

gchar* tmp_pos = NULL

Definition at line 72 of file cbuild_action.c.

Functions

Variables

Detailed Description

Function Documentation

◆ adjust_object_occupancy()

◆ allocate_crystal_data()

◆ are_equal_vectors()

◆ build_crystal()

◆ clean_this_proj()

◆ compute_lattice_properties()

◆ duplicate_space_group()

◆ free_crystal_data()

◆ get_crystal_id()

◆ get_origin()

◆ get_val_from_setting()

◆ get_val_from_wyckoff()

◆ get_value_from_pos()

◆ pos_not_saved()

◆ pos_not_taken()

◆ same_coords()

◆ test_lattice()

Variable Documentation

◆ cif_object

◆ tmp_pos