cbuild_action.c File Reference

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, int box_id)
	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 ?
int	occupancy (double occ, int cif_occ)
	handle occupancy integer rouding
gboolean	adjust_object_occupancy (crystal_data *cryst, int occupying, int rounding, int tot_cell)
	adjust the crystallograpĥic sites occupancy
int	build_crystal (gboolean visible, project *this_proj, int c_step, gboolean to_wrap, gboolean show_clones, cell_info *cell, GtkWidget *widg)
	build crystal

Variables
atomic_object *	cif_object
gchar *	tmp_pos = NULL
gboolean	crystal_low_warning
gboolean	crystal_crowded
gboolean	crystal_dist_chk

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	rounding,
		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
rounding	how to round the number of occupied site(s)
tot_cell	the total number of cell to build

Definition at line 721 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 621 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 561 of file cbuild_action.c.

build_crystal()

int build_crystal	(	gboolean	visible,
		project *	this_proj,
		int	c_step,
		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
c_step	the MD step if multiple CIF configurations
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 972 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 516 of file cbuild_action.c.

compute_lattice_properties()

void compute_lattice_properties	(	cell_info *	cell,
		int	box_id )

compute lattice parameters following cell description

Parameters

cell	the target cell description
box_id	the target box description to fill

Definition at line 209 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 596 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 648 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 128 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 161 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 83 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 462 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 136 of file cbuild_action.c.

occupancy()

int occupancy	(	double	occ,
		int	cif_occ )

handle occupancy integer rouding

Parameters

occ	value to round
cif_occ	how to round

Definition at line 690 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 579 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 675 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 546 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 328 of file cbuild_action.c.

Variable Documentation

cif_object

atomic_object* cif_object

extern

Definition at line 313 of file read_cif.c.

crystal_crowded

gboolean crystal_crowded

Definition at line 956 of file cbuild_action.c.

crystal_dist_chk

gboolean crystal_dist_chk

Definition at line 957 of file cbuild_action.c.

crystal_low_warning

gboolean crystal_low_warning

Definition at line 955 of file cbuild_action.c.

tmp_pos

gchar* tmp_pos = NULL

Definition at line 73 of file cbuild_action.c.