initmol.c File Reference

Functions to retrieve fragments data from Fortran90
Functions to retrieve molecules data from Fortran90
Functions to analyze molecule topology. More...

#include "global.h"
#include "interface.h"
#include "bind.h"
#include "color_box.h"
#include "glwindow.h"
#include "initcoord.h"

Include dependency graph for initmol.c:

Go to the source code of this file.

Data Structures
struct	search_molecule

Typedefs
typedef struct search_molecule	search_molecule

Functions
void	duplicate_molecule (molecule *new_mol, search_molecule *old_mol)
	create a copy of a molecule data structure
search_molecule *	duplicate_search_molecule (search_molecule *old_mol)
	create a copy of a search molecule data structure
void	allocate_mol_for_step_ (int *sid, int *mol_in_step)
	allocate the data to store molecule information for a MD step
void	allocate_mol_data_ ()
	allocate data to store molecule information
void	send_mol_neighbors_ (int *stp, int *mol, int *aid, int *nvs, int neigh[*nvs])
	update molecule typology information from Fortran90
void	update_mol_details (search_molecule *mol, int sp, int cp)
	update molecule information
void	send_mol_details_ (int *stp, int *mol, int *ats, int *sps, int spec_in_mol[*sps], int atom_in_mol[*ats])
	overall molecule information from Fortran90
gboolean	are_identical_molecules (search_molecule *mol_a, search_molecule *mol_b)
	test if 2 molecules are identicals
int *	merge_mol_data (int val_a, int val_b, int table_a[val_a], int table_b[val_b])
	merge molecule a and molecule b data
void	free_search_molecule_data (search_molecule *smol)
	free search molecule data structure
void	setup_molecules_ (int *stepid)
	setup molecule data
void	setup_menu_molecules_ ()
	prepare the menu elements related to molecule(s)
void	setup_fragments_ (int *sid, int coord[active_project -> natomes])

Variables
int *	pgeo
search_molecule *	tmp_search = NULL
search_molecule **	in_calc_mol = NULL
molecule *	tmp_mol

Detailed Description

Functions to retrieve fragments data from Fortran90
Functions to retrieve molecules data from Fortran90
Functions to analyze molecule topology.

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 initmol.c.

Typedef Documentation

search_molecule

typedef struct search_molecule search_molecule

Definition at line 63 of file initmol.c.

Function Documentation

allocate_mol_data_()

void allocate_mol_data_

(

)

allocate data to store molecule information

Definition at line 184 of file initmol.c.

allocate_mol_for_step_()

void allocate_mol_for_step_	(	int *	sid,
		int *	mol_in_step )

allocate the data to store molecule information for a MD step

Parameters

sid	the MD step
mol_in_step	the number of molecule(s) for this MD step

Definition at line 173 of file initmol.c.

are_identical_molecules()

gboolean are_identical_molecules	(	search_molecule *	mol_a,
		search_molecule *	mol_b )

test if 2 molecules are identicals

Parameters

mol_a	the 1st molecule
mol_b	the 2nd molecule

Definition at line 349 of file initmol.c.

duplicate_molecule()

void duplicate_molecule	(	molecule *	new_mol,
		search_molecule *	old_mol )

create a copy of a molecule data structure

Parameters

new_mol	the new molecule
old_mol	the molecule to copy

Definition at line 96 of file initmol.c.

duplicate_search_molecule()

search_molecule * duplicate_search_molecule

(

search_molecule *

old_mol

)

create a copy of a search molecule data structure

Parameters

old_mol

the search molecule data structure to copy

Definition at line 114 of file initmol.c.

free_search_molecule_data()

void free_search_molecule_data

(

search_molecule *

smol

)

free search molecule data structure

Parameters

smol	the search molecule data structure to free

Definition at line 437 of file initmol.c.

merge_mol_data()

int * merge_mol_data	(	int	val_a,
		int	val_b,
		int	table_a[val_a],
		int	table_b[val_b] )

merge molecule a and molecule b data

Parameters

val_a	multiplicity, or multiplicity x atoms, for molecule a
val_b	multiplicity, or multiplicity x atoms, for molecule b
table_a	the list of molecular fragment(s) or atoms for molecule a
table_b	the list of molecular fragment(s) or atoms for molecule b

Definition at line 414 of file initmol.c.

send_mol_details_()

void send_mol_details_	(	int *	stp,
		int *	mol,
		int *	ats,
		int *	sps,
		int	spec_in_mol[ *sps],
		int	atom_in_mol[ *ats] )

overall molecule information from Fortran90

Parameters

stp	the MD step
mol	the molecule id
ats	the number of atom(s) in the molecule
sps	the number of chemical species in the molecule
spec_in_mol	the number of atom(s) by chemical species in the molecule
atom_in_mol	the list of atom(s) in the molecule

Definition at line 302 of file initmol.c.

send_mol_neighbors_()

void send_mol_neighbors_	(	int *	stp,
		int *	mol,
		int *	aid,
		int *	nvs,
		int	neigh[ *nvs] )

update molecule typology information from Fortran90

Parameters

stp	the MD step
mol	the molecule id
aid	the atom id
nvs	the number of neighbor(s) for this atom
neigh	the list of neighbor(s) for this atom

Definition at line 223 of file initmol.c.

setup_fragments_()

void setup_fragments_	(	int *	sid,
		int	coord[active_project -> natomes] )

Definition at line 625 of file initmol.c.

setup_menu_molecules_()

void setup_menu_molecules_

(

)

prepare the menu elements related to molecule(s)

Definition at line 600 of file initmol.c.

setup_molecules_()

void setup_molecules_

(

int *

stepid

)

setup molecule data

Parameters

stepid

the MD step

Definition at line 505 of file initmol.c.

update_mol_details()

void update_mol_details	(	search_molecule *	mol,
		int	sp,
		int	cp )

update molecule information

Parameters

mol	the molecule to update
sp	the chemical species
cp	the partial coordination id

Definition at line 268 of file initmol.c.

Variable Documentation

in_calc_mol

search_molecule** in_calc_mol = NULL

Definition at line 85 of file initmol.c.

pgeo

int* pgeo

Definition at line 83 of file initmol.c.

tmp_mol

molecule* tmp_mol

extern

Definition at line 1046 of file dlp_field.c.

tmp_search

search_molecule* tmp_search = NULL

Definition at line 84 of file initmol.c.