atomes 1.1.14
atomes: an atomic scale modeling tool box
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Functions to initialize the creation of a classical force field. More...
Go to the source code of this file.
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) |
intialize 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) |
intialize 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) |
intialize new field non bonded interaction | |
field_external * | init_field_external (int bi) |
intialize 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 |
Functions to initialize the creation of a classical force field.
Definition in file dlp_init.c.
int angles_from_bonds | ( | int | n, |
field_atom * | at, | ||
field_atom * | bt, | ||
field_atom * | ct ) |
find, and initialize, angles using bonds
n | the number of different angle types already found |
at | 1st field atom |
bt | 2nd field atom |
ct | 3rd field atom |
Definition at line 1129 of file dlp_init.c.
gboolean are_in_bond | ( | atom | ato, |
int | at ) |
is at in ato neighbors ?
ato | the target atom |
at | the target atom id |
Definition at line 930 of file dlp_init.c.
gboolean are_neighbors | ( | field_neighbor * | ngb, |
int | at ) |
test if 2 atoms are neighbors
ngb | the neighbor data structure to test |
at | the target atom id in the model |
Definition at line 912 of file dlp_init.c.
int bonds_between_atoms | ( | int | n, |
field_atom * | at, | ||
field_atom * | bt, | ||
int | a, | ||
int | b ) |
search for bond(s) between two field atoms
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.
void clean_field_struct_list | ( | field_struct * | stru | ) |
clean force field structural property(ies)
stru |
Definition at line 2146 of file dlp_init.c.
int coord_sphere_multiplicity | ( | atom * | at, |
int | id, | ||
gboolean | set_atom_id ) |
get coord sphere multiplicity in the model
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 1420 of file dlp_init.c.
classical_field * create_force_field_data_structure | ( | int | ai | ) |
initialize classical force field
ai | how to initialize the force field (0 = atomic species, 1 = total coordination, 2 = partial coordination) |
Definition at line 2986 of file dlp_init.c.
int dihedrals_from_angles | ( | int | n, |
field_atom * | at, | ||
field_atom * | bt, | ||
field_atom * | ct, | ||
field_atom * | dt ) |
find, and initialize, dihedrals using angles
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 1240 of file dlp_init.c.
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extern |
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extern |
void find_atom_id_in_field_molecule | ( | ) |
find field atom id in field molecule (fragment multiplicity > 1)
Definition at line 1972 of file dlp_init.c.
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
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 1591 of file dlp_init.c.
int get_atom_id_in_fragment_from_model_id | ( | int | frag, |
int | at ) |
retrieve field atom id in fragment from model id
frag | the fragment id |
at | the atom id in the model |
Definition at line 197 of file dlp_init.c.
int get_field_atom_id_from_model_id | ( | field_molecule * | fmol, |
int | at ) |
retrieve field atom id using atom id in model
fmol | the target field molecule |
at | the target model atom id |
Definition at line 151 of file dlp_init.c.
int get_fragment_atom_id_from_model_id | ( | field_molecule * | fmol, |
int | at ) |
retrieve fragment atom id using atom id in model
fmol | the target field molecule |
at | the target model atom id |
Definition at line 174 of file dlp_init.c.
field_neighbor * get_init_neighbor | ( | int | a | ) |
retrieve neighbor data structure for atom a
a | the atom id in the fragment |
Definition at line 1483 of file dlp_init.c.
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
fat | the target field atom |
at | the target model atom id |
Definition at line 132 of file dlp_init.c.
int get_struct_id_from_atom_id | ( | int | ids, |
int * | aid ) |
retrieve field structural element id from a list of atom id
ids | the type of structural element |
aid | the list of atom id |
Definition at line 559 of file dlp_init.c.
void get_weight | ( | int | seq | ) |
compute field weigth for the atom(s) in the model
seq | weighting sequence |
Definition at line 1832 of file dlp_init.c.
gboolean id_atoms_in_fragment | ( | int | frag, |
int | seed ) |
find the atom field id in the fragment
frag | the fragment id |
seed | seed |
Definition at line 1789 of file dlp_init.c.
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
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 1638 of file dlp_init.c.
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
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 1301 of file dlp_init.c.
gboolean in_bond | ( | int | at, |
int | bd[2] ) |
is atom at in bond bd
at | the target atom id |
bd | the bond atoms id |
Definition at line 892 of file dlp_init.c.
void init_all_angles | ( | ) |
find, and intialiaze, all angle(s) using bonds
Definition at line 1145 of file dlp_init.c.
void init_all_atoms | ( | int | i | ) |
initialize all field atom(s)
i | the molecule id in the model, if any |
Definition at line 838 of file dlp_init.c.
void init_all_bonds | ( | ) |
find, and initialize all bond(s)
Definition at line 1031 of file dlp_init.c.
void init_all_dihedrals | ( | ) |
find, and intialiaze, all dihedral(s) using bonds
Definition at line 1259 of file dlp_init.c.
void init_all_field_struct | ( | gboolean | init | ) |
initialize the force field structural properties for a field molecule
init | search for the atom(s) force field id number(s) |
Definition at line 2170 of file dlp_init.c.
void init_all_impropers_inversions | ( | int | stru | ) |
initialize all impropers and inversions
stru | 6 = improper(s), 7 = inversion(s) |
Definition at line 1343 of file dlp_init.c.
void init_dlpoly_field | ( | classical_field * | new_field | ) |
initialize DL-POLY classical force field
new_field | the force field to initialize |
Definition at line 2407 of file dlp_init.c.
field_atom * init_field_atom | ( | int | id, |
int | type, | ||
int | at, | ||
int | nat, | ||
int | coo, | ||
int * | list ) |
intialize a new type of field atom
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.
field_constraint * init_field_constraint | ( | int | id, |
int | ia, | ||
int | ib ) |
initialize field bond constraint
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.
field_external * init_field_external | ( | int | bi | ) |
intialize new field external potential
bi | the id of the new field external potential |
Definition at line 790 of file dlp_init.c.
void init_field_molecule | ( | int | i | ) |
initialiaze of field molecule data structurre
i | the id of the field molecule to initialize |
Definition at line 2239 of file dlp_init.c.
field_nth_body * init_field_nth_body | ( | int | bi, |
int | bd, | ||
int * | na, | ||
int ** | ma, | ||
int ** | ba ) |
intialize new field non bonded interaction
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.
field_pmf * init_field_pmf | ( | int | id, |
int | num[2], | ||
int * | list[2], | ||
float * | w[2] ) |
initialize new field mean force potential
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.
field_prop * init_field_prop | ( | int | ti, |
int | key, | ||
gboolean | show, | ||
gboolean | use ) |
initialize new field molecule structural property
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.
field_rigid * init_field_rigid | ( | int | id, |
int | num, | ||
int * | list ) |
initialize new field rigid constraint
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.
field_shell * init_field_shell | ( | int | id, |
int | ia, | ||
int | ib ) |
initialize field core shell interaction
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.
field_struct * init_field_struct | ( | int | st, |
int | ai, | ||
int | an, | ||
int * | aid ) |
initialize field molecule new structural element
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.
field_tethered * init_field_tethered | ( | int | id, |
int | num ) |
intialize new field tethered potential
id | the new field tethered potential id |
num | the atom id in the field molecule |
Definition at line 510 of file dlp_init.c.
void init_lammps_field | ( | classical_field * | new_field | ) |
initialize a LAMMPS classical force field
new_field | the force field to initialize |
Definition at line 2697 of file dlp_init.c.
int init_vdw | ( | gboolean | init | ) |
initialize the VdW section of a classical force field
init |
Definition at line 2299 of file dlp_init.c.
gboolean is_numbering_possible | ( | int | frag | ) |
compare if the atom numbering of two fragment(s) are identical, and it should
frag | the fragment id |
Definition at line 1502 of file dlp_init.c.
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
frag | the fragment id |
ngma | the neigbbor data structure for this fragment |
atom | the atom id in the model |
Definition at line 1550 of file dlp_init.c.
int prepare_field_atom | ( | int | i, |
int | j, | ||
int | k, | ||
int | l, | ||
int | m ) |
initialiaze new type of field atom
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.
int prepare_field_struct | ( | int | ids, |
int | sid, | ||
int | yes_no_num, | ||
int * | aid ) |
prepare the creation of a field structural element
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.
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extern |
print all field structural element(s)
mol | the target field molecule |
str | the type of structural element |
Definition at line 195 of file dlp_print.c.
int set_atom_id | ( | field_atom * | at, |
int | c, | ||
int | p, | ||
int | id ) |
set new fragment/molecule atom 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.
gchar * set_field_atom_name | ( | field_atom * | ato, |
field_molecule * | mol ) |
get name string for field atom
ato | the target field atom |
mol | the target field molecule |
Definition at line 247 of file dlp_init.c.
int setup_atomic_weight | ( | int | seq | ) |
setup atom(s) field weight
seq | weighting sequencce |
Definition at line 1877 of file dlp_init.c.
int test_for_angles | ( | field_atom * | at, |
field_atom * | bt, | ||
field_atom * | ct ) |
search for angle(s) between these field atoms
at | 1st field atom |
bt | 2nd field atom |
ct | 3rd field atom |
Definition at line 1081 of file dlp_init.c.
int test_for_bonds | ( | field_atom * | at, |
field_atom * | bt ) |
search for bond(s) between 2 field atoms
at | 1st field atom |
bt | 2nd field atom |
Definition at line 948 of file dlp_init.c.
int test_for_dihedrals | ( | field_atom * | at, |
field_atom * | bt, | ||
field_atom * | ct, | ||
field_atom * | dt ) |
search for dihedral(s) between these field atoms
at | 1st field atom |
bt | 2nd field atom |
ct | 3rd field atom |
dt | 4th field atom |
Definition at line 1181 of file dlp_init.c.
gboolean was_not_created_struct | ( | int | ids, |
int | num, | ||
int * | aid ) |
was this structural element already created ?
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.
int a_multi |
Definition at line 122 of file dlp_init.c.
int assigned |
Definition at line 1471 of file dlp_init.c.
int* astr |
Definition at line 116 of file dlp_init.c.
int* i_weight |
Definition at line 1472 of file dlp_init.c.
int id_atom |
Definition at line 120 of file dlp_init.c.
field_neighbor* init_ngb = NULL |
Definition at line 1474 of file dlp_init.c.
int multi |
Definition at line 121 of file dlp_init.c.
int* n_weight |
Definition at line 1473 of file dlp_init.c.
float val |
Definition at line 117 of file dlp_init.c.