dlp_init.c File Reference

Functions to initialize the creation of a classical force field. More...

#include "dlp_field.h"
#include "interface.h"

Include dependency graph for dlp_init.c:

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Functions
void	print_all_field_struct (field_molecule *mol, int str)
	print all field structural element(s)
int *	duplicate_int (int num, int *old_val)
	copy a list of int
float *	duplicate_float (int num, float *old_val)
	copy a list of float
int	get_position_in_field_atom_from_model_id (int fat, int at)
	retrieve atom position id in field atom id using atom id in model
int	get_field_atom_id_from_model_id (field_molecule *fmol, int at)
	retrieve field atom id using atom id in model
int	get_fragment_atom_id_from_model_id (field_molecule *fmol, int at)
	retrieve fragment atom id using atom id in model
int	get_atom_id_in_fragment_from_model_id (int frag, int at)
	retrieve field atom id in fragment from model id
int	set_atom_id (field_atom *at, int c, int p, int id)
	set new fragment/molecule atom parameters
gchar *	set_field_atom_name (field_atom *ato, field_molecule *mol)
	get name string for field atom
field_atom *	init_field_atom (int id, int type, int at, int nat, int coo, int *list)
	initialize a new type of field atom
field_shell *	init_field_shell (int id, int ia, int ib)
	initialize field core shell interaction
field_constraint *	init_field_constraint (int id, int ia, int ib)
	initialize field bond constraint
field_pmf *	init_field_pmf (int id, int num[2], int *list[2], float *w[2])
	initialize new field mean force potential
field_rigid *	init_field_rigid (int id, int num, int *list)
	initialize new field rigid constraint
field_tethered *	init_field_tethered (int id, int num)
	initialize new field tethered potential
field_prop *	init_field_prop (int ti, int key, gboolean show, gboolean use)
	initialize new field molecule structural property
int	get_struct_id_from_atom_id (int ids, int *aid)
	retrieve field structural element id from a list of atom id
gboolean	was_not_created_struct (int ids, int num, int *aid)
	was this structural element already created ?
field_struct *	init_field_struct (int st, int ai, int an, int *aid)
	initialize field molecule new structural element
field_nth_body *	init_field_nth_body (int bi, int bd, int *na, int **ma, int **ba)
	initialize new field non bonded interaction
field_external *	init_field_external (int bi)
	initialize new field external potential
int	prepare_field_atom (int i, int j, int k, int l, int m)
	initialiaze new type of field atom
void	init_all_atoms (int i)
	initialize all field atom(s)
gboolean	in_bond (int at, int bd[2])
	is atom at in bond bd
gboolean	are_neighbors (field_neighbor *ngb, int at)
	test if 2 atoms are neighbors
gboolean	are_in_bond (atom ato, int at)
	is at in ato neighbors ?
int	test_for_bonds (field_atom *at, field_atom *bt)
	search for bond(s) between 2 field atoms
int	prepare_field_struct (int ids, int sid, int yes_no_num, int *aid)
	prepare the creation of a field structural element
int	bonds_between_atoms (int n, field_atom *at, field_atom *bt, int a, int b)
	search for bond(s) between two field atoms
void	init_all_bonds ()
	find, and initialize all bond(s)
int	test_for_angles (field_atom *at, field_atom *bt, field_atom *ct)
	search for angle(s) between these field atoms
int	angles_from_bonds (int n, field_atom *at, field_atom *bt, field_atom *ct)
	find, and initialize, angles using bonds
void	init_all_angles ()
	find, and intialiaze, all angle(s) using bonds
int	test_for_dihedrals (field_atom *at, field_atom *bt, field_atom *ct, field_atom *dt)
	search for dihedral(s) between these field atoms
int	dihedrals_from_angles (int n, field_atom *at, field_atom *bt, field_atom *ct, field_atom *dt)
	find, and initialize, dihedrals using angles
void	init_all_dihedrals ()
	find, and intialiaze, all dihedral(s) using bonds
int	impropers_inversion (int n, int stru, int at, int bt, int ct, int dt, int a, int b, int c, int d)
	prepare new improper / inversion
void	init_all_impropers_inversions (int stru)
	initialize all impropers and inversions
int	coord_sphere_multiplicity (atom *at, int id, gboolean set_atom_id)
	get coord sphere multiplicity in the model
field_neighbor *	get_init_neighbor (int a)
	retrieve neighbor data structure for atom a
gboolean	is_numbering_possible (int frag)
	compare if the atom numbering of two fragment(s) are identical, and it should
gboolean	is_this_numbering_possible_for_this_atom (int frag, field_neighbor *ngma, int atom)
	check if the id in fragment for this atom is possible or not
int	find_neighbor_loop (int frag, int aid, int fai, field_atom *fat, field_neighbor *ngmb, int sid, gboolean save_it)
	find / set up field atom data for a fragment
gboolean	id_n_fold_atoms_in_fragment (int frag, int limit, int num_ngb, int search_type, int init, field_neighbor *ngma_init)
	find atom id in fragment using the neighbor list
gboolean	id_atoms_in_fragment (int frag, int seed)
	find the atom field id in the fragment
void	get_weight (int seq)
	compute field weigth for the atom(s) in the model
int	setup_atomic_weight (int seq)
	setup atom(s) field weight
void	find_atom_id_in_field_molecule ()
	find field atom id in field molecule (fragment multiplicity > 1)
void	clean_field_struct_list (field_struct *stru)
	clean force field structural property(ies)
void	init_all_field_struct (gboolean init)
	initialize the force field structural properties for a field molecule
void	init_field_molecule (int i)
	initialiaze of field molecule data structurre
int	init_vdw (gboolean init)
	initialize the VdW section of a classical force field
void	init_dlpoly_field (classical_field *new_field)
	initialize DL-POLY classical force field
void	init_lammps_field (classical_field *new_field)
	initialize a LAMMPS classical force field
classical_field *	create_force_field_data_structure (int ai)
	initialize classical force field

Variables
int *	astr
float	val
int	id_atom
int	multi
int	a_multi
int	assigned
int *	i_weight
int *	n_weight
field_neighbor *	init_ngb = NULL

Detailed Description

Functions to initialize the creation of a classical force field.

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 dlp_init.c.

Function Documentation

angles_from_bonds()

int angles_from_bonds	(	int	n,
		field_atom *	at,
		field_atom *	bt,
		field_atom *	ct )

find, and initialize, angles using bonds

Parameters

n	the number of different angle types already found
at	1st field atom
bt	2nd field atom
ct	3rd field atom

Definition at line 1124 of file dlp_init.c.

are_in_bond()

gboolean are_in_bond	(	atom	ato,
		int	at )

is at in ato neighbors ?

Parameters

ato	the target atom
at	the target atom id

Definition at line 930 of file dlp_init.c.

are_neighbors()

gboolean are_neighbors	(	field_neighbor *	ngb,
		int	at )

test if 2 atoms are neighbors

Parameters

ngb	the neighbor data structure to test
at	the target atom id in the model

Definition at line 912 of file dlp_init.c.

bonds_between_atoms()

int bonds_between_atoms	(	int	n,
		field_atom *	at,
		field_atom *	bt,
		int	a,
		int	b )

search for bond(s) between two field atoms

Parameters

n	the number of different bond types already found
at	1st field atom
bt	2nd field atom
a	1st atom chemical species
b	2nd atom chemical species

Definition at line 1015 of file dlp_init.c.

clean_field_struct_list()

void clean_field_struct_list

(

field_struct *

stru

)

clean force field structural property(ies)

Parameters

stru

Definition at line 2134 of file dlp_init.c.

coord_sphere_multiplicity()

int coord_sphere_multiplicity	(	atom *	at,
		int	id,
		gboolean	set_atom_id )

get coord sphere multiplicity in the model

Parameters

at	the target atom in the model
id	the atom id in the fragment
set_atom_id	adjust field atom parameters (yes / no)

Definition at line 1408 of file dlp_init.c.

create_force_field_data_structure()

classical_field * create_force_field_data_structure

(

int

ai

)

initialize classical force field

Parameters

ai	how to initialize the force field (0 = atomic species, 1 = total coordination, 2 = partial coordination)

Definition at line 2974 of file dlp_init.c.

dihedrals_from_angles()

int dihedrals_from_angles	(	int	n,
		field_atom *	at,
		field_atom *	bt,
		field_atom *	ct,
		field_atom *	dt )

find, and initialize, dihedrals using angles

Parameters

n	the number of different dihedral types already found
at	1st field atom
bt	2nd field atom
ct	3rd field atom
dt	4th field atom

Definition at line 1228 of file dlp_init.c.

duplicate_float()

float * duplicate_float ( int num, float * old_val )

extern

copy a list of float

Parameters

num	number of elements in the list
old_val	the list to copy

Definition at line 592 of file global.c.

duplicate_int()

int * duplicate_int ( int num, int * old_val )

extern

copy a list of int

Parameters

num	number of elements in the list
old_val	the list to copy

Definition at line 560 of file global.c.

find_atom_id_in_field_molecule()

void find_atom_id_in_field_molecule

(

)

find field atom id in field molecule (fragment multiplicity > 1)

Definition at line 1960 of file dlp_init.c.

find_neighbor_loop()

int find_neighbor_loop	(	int	frag,
		int	aid,
		int	fai,
		field_atom *	fat,
		field_neighbor *	ngmb,
		int	sid,
		gboolean	save_it )

find / set up field atom data for a fragment

Parameters

frag	the fragment id
aid	the atom id in the model
fai	the atom id in the fragment
fat	the field atom
ngmb	the neighbor(s) list for the fragment
sid	iter to save
save_it	save field atom data (yes / no)

Definition at line 1579 of file dlp_init.c.

get_atom_id_in_fragment_from_model_id()

int get_atom_id_in_fragment_from_model_id	(	int	frag,
		int	at )

retrieve field atom id in fragment from model id

Parameters

frag	the fragment id
at	the atom id in the model

Definition at line 197 of file dlp_init.c.

get_field_atom_id_from_model_id()

int get_field_atom_id_from_model_id	(	field_molecule *	fmol,
		int	at )

retrieve field atom id using atom id in model

Parameters

fmol	the target field molecule
at	the target model atom id

Definition at line 151 of file dlp_init.c.

get_fragment_atom_id_from_model_id()

int get_fragment_atom_id_from_model_id	(	field_molecule *	fmol,
		int	at )

retrieve fragment atom id using atom id in model

Parameters

fmol	the target field molecule
at	the target model atom id

Definition at line 174 of file dlp_init.c.

get_init_neighbor()

field_neighbor * get_init_neighbor

(

int

a

)

retrieve neighbor data structure for atom a

Parameters

a	the atom id in the fragment

Definition at line 1471 of file dlp_init.c.

get_position_in_field_atom_from_model_id()

int get_position_in_field_atom_from_model_id	(	int	fat,
		int	at )

retrieve atom position id in field atom id using atom id in model

Parameters

fat	the target field atom
at	the target model atom id

Definition at line 132 of file dlp_init.c.

get_struct_id_from_atom_id()

int get_struct_id_from_atom_id	(	int	ids,
		int *	aid )

retrieve field structural element id from a list of atom id

Parameters

ids	the type of structural element
aid	the list of atom id

Definition at line 559 of file dlp_init.c.

get_weight()

void get_weight

(

int

seq

)

compute field weigth for the atom(s) in the model

Parameters

seq	weighting sequence

Definition at line 1820 of file dlp_init.c.

id_atoms_in_fragment()

gboolean id_atoms_in_fragment	(	int	frag,
		int	seed )

find the atom field id in the fragment

Parameters

frag	the fragment id
seed	seed

Definition at line 1777 of file dlp_init.c.

id_n_fold_atoms_in_fragment()

gboolean id_n_fold_atoms_in_fragment	(	int	frag,
		int	limit,
		int	num_ngb,
		int	search_type,
		int	init,
		field_neighbor *	ngma_init )

find atom id in fragment using the neighbor list

Parameters

frag	the fragment id
limit	the total number of atom(s) in the fragment
num_ngb	the neighbor(s) list for the fragment
search_type	search type (0 = browse field molecule atom list, 1 = browse field atom list)
init	the atom id in the model
ngma_init	the target

Definition at line 1626 of file dlp_init.c.

impropers_inversion()

int impropers_inversion	(	int	n,
		int	stru,
		int	at,
		int	bt,
		int	ct,
		int	dt,
		int	a,
		int	b,
		int	c,
		int	d )

prepare new improper / inversion

Parameters

n	the actual number of structural element
stru	the type of structural element, 6 = impropers, 7 = inversions
at	1st field atom id
bt	2nd field atom id
ct	3rd field atom id
dt	4th field atom id
a	1st atom id in molecule/fragment
b	2nd atom id in molecule/fragment
c	3rd atom id in molecule/fragment
d	4th atom id in molecule/fragment

Definition at line 1289 of file dlp_init.c.

in_bond()

gboolean in_bond	(	int	at,
		int	bd[2] )

is atom at in bond bd

Parameters

at	the target atom id
bd	the bond atoms id

Definition at line 892 of file dlp_init.c.

init_all_angles()

void init_all_angles

(

)

find, and intialiaze, all angle(s) using bonds

Definition at line 1140 of file dlp_init.c.

init_all_atoms()

void init_all_atoms

(

int

i

)

initialize all field atom(s)

Parameters

i	the molecule id in the model, if any

Definition at line 838 of file dlp_init.c.

init_all_bonds()

void init_all_bonds

(

)

find, and initialize all bond(s)

Definition at line 1031 of file dlp_init.c.

init_all_dihedrals()

void init_all_dihedrals

(

)

find, and intialiaze, all dihedral(s) using bonds

Definition at line 1247 of file dlp_init.c.

init_all_field_struct()

void init_all_field_struct

(

gboolean

init

)

initialize the force field structural properties for a field molecule

Parameters

init	search for the atom(s) force field id number(s)

Definition at line 2158 of file dlp_init.c.

init_all_impropers_inversions()

void init_all_impropers_inversions

(

int

stru

)

initialize all impropers and inversions

Parameters

stru	6 = improper(s), 7 = inversion(s)

Definition at line 1331 of file dlp_init.c.

init_dlpoly_field()

void init_dlpoly_field

(

classical_field *

new_field

)

initialize DL-POLY classical force field

Parameters

new_field

the force field to initialize

Definition at line 2395 of file dlp_init.c.

init_field_atom()

field_atom * init_field_atom	(	int	id,
		int	type,
		int	at,
		int	nat,
		int	coo,
		int *	list )

initialize a new type of field atom

Parameters

id	the new field atom id
type	the new field atom coordination type
at	the new field atom species
nat	the number of atom(s) of for this field atom type
coo	the coordination id in coordination type, if any
list	the list of atoms that match this type of field atom

Definition at line 304 of file dlp_init.c.

init_field_constraint()

field_constraint * init_field_constraint	(	int	id,
		int	ia,
		int	ib )

initialize field bond constraint

Parameters

id	the new field constraint id
ia	1st atom id in field molecule
ib	2nd atom id in field molecule

Definition at line 419 of file dlp_init.c.

init_field_external()

field_external * init_field_external

(

int

bi

)

initialize new field external potential

Parameters

bi	the id of the new field external potential

Definition at line 790 of file dlp_init.c.

init_field_molecule()

void init_field_molecule

(

int

i

)

initialiaze of field molecule data structurre

Parameters

i	the id of the field molecule to initialize

Definition at line 2227 of file dlp_init.c.

init_field_nth_body()

field_nth_body * init_field_nth_body	(	int	bi,
		int	bd,
		int *	na,
		int **	ma,
		int **	ba )

initialize new field non bonded interaction

Parameters

bi	the new non bonded interaction id
bd	the type of non bonded interaction
na	the list of field atom(s), if any
ma	the list of field molecule(s), if any
ba	the list of atom id in field molecule, if any

Definition at line 740 of file dlp_init.c.

init_field_pmf()

field_pmf * init_field_pmf	(	int	id,
		int	num[2],
		int *	list[2],
		float *	w[2] )

initialize new field mean force potential

Parameters

id	the id of the new field PMF
num	the numbers of atom(s)
list	the lists of atom(s)
w	the weight list

Definition at line 445 of file dlp_init.c.

init_field_prop()

field_prop * init_field_prop	(	int	ti,
		int	key,
		gboolean	show,
		gboolean	use )

initialize new field molecule structural property

Parameters

ti	the type of field structural element to initialize
key	the formalism to use
show	visualize in the 3D window (yes / no)
use	use to create the force field input file (yes / no)

Definition at line 535 of file dlp_init.c.

init_field_rigid()

field_rigid * init_field_rigid	(	int	id,
		int	num,
		int *	list )

initialize new field rigid constraint

Parameters

id	the id of the new field rigid
num	the number of atom(s) to fix
list	the list of atom(s) to fix

Definition at line 487 of file dlp_init.c.

init_field_shell()

field_shell * init_field_shell	(	int	id,
		int	ia,
		int	ib )

initialize field core shell interaction

Parameters

id	the new shell id
ia	1st atom id in field molecule
ib	2nd atom id in field molecule

Definition at line 394 of file dlp_init.c.

init_field_struct()

field_struct * init_field_struct	(	int	st,
		int	ai,
		int	an,
		int *	aid )

initialize field molecule new structural element

Parameters

st	the type of structural element (0 = bond, 1 = angle, 2 = dihedral)
ai	the id of the new structural property
an	the number of atoms
aid	the list of field atoms

Definition at line 704 of file dlp_init.c.

init_field_tethered()

field_tethered * init_field_tethered	(	int	id,
		int	num )

initialize new field tethered potential

Parameters

id	the new field tethered potential id
num	the atom id in the field molecule

Definition at line 510 of file dlp_init.c.

init_lammps_field()

void init_lammps_field

(

classical_field *

new_field

)

initialize a LAMMPS classical force field

Parameters

new_field

the force field to initialize

Definition at line 2685 of file dlp_init.c.

init_vdw()

int init_vdw

(

gboolean

init

)

initialize the VdW section of a classical force field

Parameters

init

Definition at line 2287 of file dlp_init.c.

is_numbering_possible()

gboolean is_numbering_possible

(

int

frag

)

compare if the atom numbering of two fragment(s) are identical, and it should

Parameters

frag	the fragment id

Definition at line 1490 of file dlp_init.c.

is_this_numbering_possible_for_this_atom()

gboolean is_this_numbering_possible_for_this_atom	(	int	frag,
		field_neighbor *	ngma,
		int	atom )

check if the id in fragment for this atom is possible or not

Parameters

frag	the fragment id
ngma	the neigbbor data structure for this fragment
atom	the atom id in the model

Definition at line 1538 of file dlp_init.c.

prepare_field_atom()

int prepare_field_atom	(	int	i,
		int	j,
		int	k,
		int	l,
		int	m )

initialiaze new type of field atom

Parameters

i	the new field atom id
j	the new field atom coordination type
k	the new field atom species
l	the number of atom(s) of for this field atom type
m	the coordination id in coordination type, if any

Definition at line 814 of file dlp_init.c.

prepare_field_struct()

int prepare_field_struct	(	int	ids,
		int	sid,
		int	yes_no_num,
		int *	aid )

prepare the creation of a field structural element

Parameters

ids	the type of structural element (0 to 7)
sid	the id of the new structural element
yes_no_num	is there data to save (1 or > 1) or not (0) ?
aid	the list of field atoms

Definition at line 981 of file dlp_init.c.

print_all_field_struct()

void print_all_field_struct ( field_molecule * mol, int str )

extern

print all field structural element(s)

Parameters

mol	the target field molecule
str	the type of structural element

Definition at line 195 of file dlp_print.c.

set_atom_id()

int set_atom_id	(	field_atom *	at,
		int	c,
		int	p,
		int	id )

set new fragment/molecule atom parameters

Parameters

at	the target field atom
c	the fragment id
p	the list id in field atom
id	the field atom id

Definition at line 224 of file dlp_init.c.

set_field_atom_name()

gchar * set_field_atom_name	(	field_atom *	ato,
		field_molecule *	mol )

get name string for field atom

Parameters

ato	the target field atom
mol	the target field molecule

Definition at line 247 of file dlp_init.c.

setup_atomic_weight()

int setup_atomic_weight

(

int

seq

)

setup atom(s) field weight

Parameters

seq	weighting sequencce

Definition at line 1865 of file dlp_init.c.

test_for_angles()

int test_for_angles	(	field_atom *	at,
		field_atom *	bt,
		field_atom *	ct )

search for angle(s) between these field atoms

Parameters

at	1st field atom
bt	2nd field atom
ct	3rd field atom

Definition at line 1079 of file dlp_init.c.

test_for_bonds()

int test_for_bonds	(	field_atom *	at,
		field_atom *	bt )

search for bond(s) between 2 field atoms

Parameters

at	1st field atom
bt	2nd field atom

Definition at line 948 of file dlp_init.c.

test_for_dihedrals()

int test_for_dihedrals	(	field_atom *	at,
		field_atom *	bt,
		field_atom *	ct,
		field_atom *	dt )

search for dihedral(s) between these field atoms

Parameters

at	1st field atom
bt	2nd field atom
ct	3rd field atom
dt	4th field atom

Definition at line 1173 of file dlp_init.c.

was_not_created_struct()

gboolean was_not_created_struct	(	int	ids,
		int	num,
		int *	aid )

was this structural element already created ?

Parameters

ids	the type of structural element
num	the number of atoms
aid	the list of atom id

Definition at line 603 of file dlp_init.c.

Variable Documentation

a_multi

int a_multi

Definition at line 122 of file dlp_init.c.

assigned

int assigned

Definition at line 1459 of file dlp_init.c.

astr

int* astr

Definition at line 116 of file dlp_init.c.

i_weight

int* i_weight

Definition at line 1460 of file dlp_init.c.

id_atom

int id_atom

Definition at line 120 of file dlp_init.c.

init_ngb

field_neighbor* init_ngb = NULL

Definition at line 1462 of file dlp_init.c.

multi

int multi

Definition at line 121 of file dlp_init.c.

n_weight

int* n_weight

Definition at line 1461 of file dlp_init.c.

val

float val

Definition at line 117 of file dlp_init.c.