atomes 1.1.14
atomes: an atomic scale modeling tool box
|
Variable declarations for the creation of the DL_POLY input file(s) More...
#include "global.h"
Go to the source code of this file.
Data Structures | |
struct | field_prop |
struct | field_atom |
struct | field_shell |
struct | field_constraint |
struct | field_pmf |
struct | field_rigid |
struct | field_tethered |
struct | field_struct |
struct | field_nth_body |
struct | field_external |
struct | field_neighbor |
struct | field_molecule |
struct | field_object_match |
struct | field_data |
Typedefs | |
typedef struct field_prop | field_prop |
typedef struct field_atom | field_atom |
typedef struct field_shell | field_shell |
typedef struct field_constraint | field_constraint |
typedef struct field_pmf | field_pmf |
typedef struct field_rigid | field_rigid |
typedef struct field_tethered | field_tethered |
typedef struct field_struct | field_struct |
typedef struct field_nth_body | field_nth_body |
typedef struct field_external | field_external |
typedef struct field_neighbor | field_neighbor |
typedef struct field_molecule | field_molecule |
typedef struct field_object_match | field_object_match |
typedef struct field_data | field_data |
Enumerations | |
enum | dlp_atom_types { SPEC_ONLY = 0 , TOTAL_COORD_AND_SPEC = 1 , PARTIAL_COORD_AND_SPEC = 2 , OTHER = 3 } |
Functions | |
GtkWidget * | vbox_control (int f) |
crerate DL-POLY option widgets | |
int | struct_id (int f) |
number of atoms in a structural element | |
int | body_at (int b) |
find the number of atom(s) in a non bonded interaction | |
int | prepare_field_struct (int ids, int sid, int yes_no_num, int *aid) |
prepare the creation of a field structural element | |
int | test_for_bonds (field_atom *at, field_atom *bt) |
search for bond(s) between 2 field atoms | |
int | test_for_angles (field_atom *at, field_atom *bt, field_atom *ct) |
search for angle(s) between these field atoms | |
int | test_for_dihedrals (field_atom *at, field_atom *bt, field_atom *ct, field_atom *dt) |
search for dihedral(s) between these field atoms | |
void | clean_field_struct_list (field_struct *stru) |
clean force field structural property(ies) | |
void | set_mol_num_label () |
classical force field prepare the molecule information widget | |
G_MODULE_EXPORT void | changed_mol_box (GtkComboBox *box, gpointer data) |
classical force field assistant change the target molecule for the page | |
void | update_field_trees () |
classical force field assistant update all tree models | |
GtkWidget * | create_combo_mol (int f) |
classical force field create molecule selection combo box | |
void | fill_field_model (GtkTreeStore *store, int f, int m) |
classical force field fill the tree store | |
GtkWidget * | create_field_tree (int f) |
classical force field create the list store selection widgets | |
classical_field * | create_force_field_data_structure (int ai) |
initialize classical force field | |
int * | duplicate_int (int num, int *old_val) |
copy a list of int | |
gboolean * | duplicate_bool (int num, gboolean *old_val) |
copy a list of gboolean | |
float * | duplicate_float (int num, float *old_val) |
copy a list of float | |
field_atom * | duplicate_field_atom (field_atom *old_fat) |
create copy of a field atom data structure | |
field_shell * | duplicate_field_shell (field_shell *old_shell) |
create copy of a field shell data structure | |
field_constraint * | duplicate_field_constraint (field_constraint *old_cons) |
create copy of a field constraint data structure | |
field_rigid * | duplicate_field_rigid (field_rigid *old_rig) |
create copy of a field rigid data structure | |
field_tethered * | duplicate_field_tethered (field_tethered *old_tet) |
create copy of a field tethered data structure | |
field_prop * | duplicate_field_prop (field_prop *old_prop, int ti) |
create a copy of a field property | |
void | duplicate_other_prop (int oid, field_struct *old_fstr, field_struct *new_fstr) |
create copy of a field property 'other' list | |
field_struct * | duplicate_field_struct (field_struct *old_fstr) |
create copy of a field structural element | |
field_struct * | duplicate_field_struct_list (field_struct *list_str, gboolean init) |
create copy of list of field structural element(s) | |
field_nth_body * | duplicate_field_nth_body (field_nth_body *old_nth_body) |
create copy of a field body property | |
field_molecule * | duplicate_field_molecule (field_molecule *old_fmol) |
create copy of a field molecule | |
classical_field * | duplicate_dlpoly_field (classical_field *init_field) |
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 | |
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 | |
void | init_all_field_struct (gboolean init) |
initialize the force field structural properties for a field molecule | |
int | init_vdw (gboolean init) |
initialize the VdW section of a classical force field | |
void | setup_field_molecule_neighbors (int i, project *this_proj) |
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 | |
field_molecule * | get_active_field_molecule_from_model_id (project *this_proj, int aid) |
retrieve field molecule from overall atom id in the model | |
int | get_fragment_atom_id_from_model_id (field_molecule *fmol, int at) |
retrieve fragment atom id using atom id in model | |
field_molecule * | get_active_field_molecule (int a) |
retrieve field molecule | |
field_nth_body * | get_active_body (int a, int b) |
retrieve field nth body interaction | |
field_external * | get_active_external (int a) |
retrieve external field property | |
field_atom * | get_active_atom (int a, int b) |
retrieve field atom | |
field_shell * | get_active_shell (int a, int b) |
retrieve shell property | |
field_constraint * | get_active_constraint (int a, int b) |
retrieve constraint property | |
field_pmf * | get_active_pmf (int a, int b) |
retrieve PMF property | |
field_rigid * | get_active_rigid (int a, int b) |
retrieve rigid property | |
field_tethered * | get_active_tethered (int a, int b) |
retrieve tethered property | |
field_prop * | get_active_prop (struct field_prop *pr, int a) |
the field molecule structural property id to retrieve | |
field_prop * | get_active_prop_using_atoms (struct field_prop *pr, int ti, int *ids) |
retrieve field molecule structural property using atoms | |
field_struct * | get_active_struct (int s, int a, int b) |
retrieve field structural property | |
int | get_struct_id_from_atom_id (int ids, int *aid) |
retrieve field structural element id from a list of atom id | |
int | get_field_objects (int id, int jd) |
get the number of this type of field object | |
gboolean | show_field_object (int id, int jd, int kd) |
is the field object visible ? | |
void | visualize_object (int id, int jd, int kd) |
visualize object and update OpenGL rendering | |
G_MODULE_EXPORT void | on_toggle_visualize_or_select_object (GtkCellRendererToggle *cell_renderer, gchar *string_path, gpointer data) |
on visualize force field object toggle callback | |
G_MODULE_EXPORT void | visualize_or_select_all_elements (GtkTreeViewColumn *col, gpointer data) |
select all element(s) in the column for visualization | |
void | adjust_field_prop (int fil, int sti, field_prop *tmp, int *ids, int key) |
adjust field property | |
gchar * | remove_text (int i, int j, gchar *str) |
get removal information text | |
G_MODULE_EXPORT void | select_atom_id_from_fied_molecule (GtkButton *but, gpointer data) |
select atom id from field molecule - creating the dialog | |
G_MODULE_EXPORT void | edit_field_prop (GSimpleAction *action, GVariant *parameter, gpointer data) |
edit field property callback | |
G_MODULE_EXPORT void | add_field_prop (GSimpleAction *action, GVariant *parameter, gpointer data) |
add field property callback | |
G_MODULE_EXPORT void | remove_field_prop (GSimpleAction *action, GVariant *parameter, gpointer data) |
remove field property callback | |
G_MODULE_EXPORT void | add_molecule_to_field (GSimpleAction *action, GVariant *parameter, gpointer data) |
add molecule to force field - creating the dialog | |
G_MODULE_EXPORT void | remove_molecule_from_field (GSimpleAction *action, GVariant *parameter, gpointer data) |
remove molecule from force field - creating the dialog | |
G_MODULE_EXPORT void | remove_atom_from_field_molecule (GSimpleAction *action, GVariant *parameter, gpointer data) |
remove atom from field molecule - creating the dialog | |
distance | distance_3d (cell_info *cell, int mdstep, atom *at, atom *bt) |
distance between atom a and b in 3D | |
angle | angle_3d (cell_info *cell, int mdstep, atom *at, atom *bt, atom *ct) |
angle between atom a, b and c in 3D | |
angle | dihedral_3d (cell_info *cell, int mdstep, atom *at, atom *bt, atom *ct, atom *dt) |
dihedral between atom a, b, c and d in 3D | |
angle | inversion_3d (cell_info *cell, int mdstep, atom *at, atom *bt, atom *ct, atom *dt) |
inversion angle between atom a, b, c and d in 3D | |
gchar * | parameters_info (int obj, int key, gchar **words, float *data) |
prepare classical force field parameter description string | |
void | print_dlp_field (GtkTextBuffer *buf) |
print DL-POLY classical force field | |
void | print_dlp_config (GtkTextBuffer *buf) |
print DL-POLY CONFIG file | |
void | print_dlp_control (GtkTextBuffer *buf) |
print DL-POLY CONTROL file | |
void | print_dlp_improper_inversion (int di, GtkTextBuffer *buf, field_struct *dh, int fi, GtkTreeStore *store, GtkTreeIter *iter) |
print / fill tree store with force field improper(s)/inversion(s) information | |
void | print_dlp_dihedral (int di, GtkTextBuffer *buf, field_struct *dh, int fi, GtkTreeStore *store, GtkTreeIter *iter) |
print / fill tree store with force field dihedral(s) information | |
void | print_dlp_angle (int ai, GtkTextBuffer *buf, field_struct *an, int fi, GtkTreeStore *store, GtkTreeIter *iter) |
print / fill tree store with force field angle(s) information | |
void | print_dlp_bond (int bi, GtkTextBuffer *buf, field_struct *bd, int fi, GtkTreeStore *store, GtkTreeIter *iter) |
print / fill tree store with force field bond(s) information | |
G_MODULE_EXPORT void | setup_this_force_field (int id) |
setup force field parameters | |
float | get_force_field_atom_mass (int sp, int num) |
get force field atomic mass | |
Variable declarations for the creation of the DL_POLY input file(s)
Definition in file dlp_field.h.
#define AMBER94 0 |
Definition at line 120 of file dlp_field.h.
#define AMBER96 1 |
Definition at line 121 of file dlp_field.h.
#define AMBER98 2 |
Definition at line 122 of file dlp_field.h.
#define AMBER99 3 |
Definition at line 123 of file dlp_field.h.
#define CFF91 16 |
Definition at line 136 of file dlp_field.h.
#define CHARMM22M 5 |
Definition at line 125 of file dlp_field.h.
#define CHARMM22P 4 |
Definition at line 124 of file dlp_field.h.
#define CHARMM35E 6 |
Definition at line 126 of file dlp_field.h.
#define CHARMM36C 7 |
Definition at line 127 of file dlp_field.h.
#define CHARMM36G 8 |
Definition at line 128 of file dlp_field.h.
#define CHARMM36L 9 |
Definition at line 129 of file dlp_field.h.
#define CHARMM36M 12 |
Definition at line 132 of file dlp_field.h.
#define CHARMM36N 10 |
Definition at line 130 of file dlp_field.h.
#define CHARMM36P 11 |
Definition at line 131 of file dlp_field.h.
#define CHARMMSI 13 |
Definition at line 133 of file dlp_field.h.
#define COMPASS 18 |
Definition at line 138 of file dlp_field.h.
#define CVFF 14 |
Definition at line 134 of file dlp_field.h.
#define CVFF_AUG 15 |
Definition at line 135 of file dlp_field.h.
#define DL_ANGLES 15 |
Definition at line 45 of file dlp_field.h.
#define DL_ANGLES_P 6 |
Definition at line 82 of file dlp_field.h.
#define DL_BONDS 11 |
Definition at line 44 of file dlp_field.h.
#define DL_BONDS_P 4 |
Definition at line 81 of file dlp_field.h.
#define DL_DIHEDRAL 8 |
Definition at line 46 of file dlp_field.h.
#define DL_DIHEDRAL_P 5 |
Definition at line 83 of file dlp_field.h.
#define DL_ENERGY 5 |
Definition at line 43 of file dlp_field.h.
#define DL_EXTERNAL 13 |
Definition at line 54 of file dlp_field.h.
#define DL_EXTERNAL_P 6 |
Definition at line 91 of file dlp_field.h.
#define DL_FOURBODY 3 |
Definition at line 53 of file dlp_field.h.
#define DL_FOURBODY_P 3 |
Definition at line 90 of file dlp_field.h.
#define DL_INVERS 6 |
Definition at line 47 of file dlp_field.h.
#define DL_INVERS_P 3 |
Definition at line 84 of file dlp_field.h.
#define DL_METALS 9 |
Definition at line 50 of file dlp_field.h.
#define DL_METALS_P 9 |
Definition at line 87 of file dlp_field.h.
#define DL_TERSOFFS 2 |
Definition at line 51 of file dlp_field.h.
#define DL_TERSOFFS_P 16 |
Definition at line 88 of file dlp_field.h.
#define DL_TETH 3 |
Definition at line 48 of file dlp_field.h.
#define DL_TETH_P 3 |
Definition at line 85 of file dlp_field.h.
#define DL_THREEBODY 6 |
Definition at line 52 of file dlp_field.h.
#define DL_THREEBODY_P 5 |
Definition at line 89 of file dlp_field.h.
#define DL_VDW 21 |
Definition at line 49 of file dlp_field.h.
#define DL_VDW_P 7 |
Definition at line 86 of file dlp_field.h.
Definition at line 71 of file dlp_field.h.
#define FANGLES_P max(DL_ANGLES_P,LA_ANGLES_P) |
Definition at line 107 of file dlp_field.h.
Definition at line 70 of file dlp_field.h.
#define FBONDS_P max(DL_BONDS_P,LA_BONDS_P) |
Definition at line 106 of file dlp_field.h.
#define FDIHEDRAL max(DL_DIHEDRAL,LA_DIHEDRAL) |
Definition at line 72 of file dlp_field.h.
#define FDIHEDRAL_P max(DL_DIHEDRAL_P,LA_DIHEDRAL_P) |
Definition at line 108 of file dlp_field.h.
#define FEXTERNAL max(DL_EXTERNAL,LA_EXTERNAL) |
Definition at line 79 of file dlp_field.h.
#define FEXTERNAL_P max(DL_EXTERNAL_P,LA_EXTERNAL_P) |
Definition at line 115 of file dlp_field.h.
#define FFOURBODY max(DL_FOURBODY,LA_FOURBODY) |
Definition at line 78 of file dlp_field.h.
#define FFOURBODY_P max(DL_FOURBODY_P,LA_FOURBODY_P) |
Definition at line 114 of file dlp_field.h.
Definition at line 73 of file dlp_field.h.
#define FINVERS_P max(DL_INVERS_P,LA_INVERS_P) |
Definition at line 109 of file dlp_field.h.
Definition at line 75 of file dlp_field.h.
#define FMETALS_P max(DL_METALS_P,LA_METALS_P) |
Definition at line 111 of file dlp_field.h.
#define FTERSOFFS max(DL_TERSOFFS,LA_TERSOFFS) |
Definition at line 76 of file dlp_field.h.
#define FTERSOFFS_P max(DL_TERSOFFS_P,LA_TERSOFFS_P) |
Definition at line 112 of file dlp_field.h.
Definition at line 69 of file dlp_field.h.
Definition at line 105 of file dlp_field.h.
#define FTHREEBODY max(DL_THREEBODY,LA_THREEBODY) |
Definition at line 77 of file dlp_field.h.
#define FTHREEBODY_P max(DL_THREEBODY_P,LA_THREEBODY_P) |
Definition at line 113 of file dlp_field.h.
Definition at line 74 of file dlp_field.h.
Definition at line 110 of file dlp_field.h.
#define LA_ANGLES 19 |
Definition at line 58 of file dlp_field.h.
#define LA_ANGLES_P 6 |
Definition at line 94 of file dlp_field.h.
#define LA_BONDS 16 |
Definition at line 57 of file dlp_field.h.
#define LA_BONDS_P 5 |
Definition at line 93 of file dlp_field.h.
#define LA_DIHEDRAL 14 |
Definition at line 59 of file dlp_field.h.
#define LA_DIHEDRAL_P 11 |
Definition at line 95 of file dlp_field.h.
#define LA_ENERGY 1 |
Definition at line 56 of file dlp_field.h.
#define LA_EXTERNAL 0 |
Definition at line 67 of file dlp_field.h.
#define LA_EXTERNAL_P 0 |
Definition at line 103 of file dlp_field.h.
#define LA_FOURBODY 0 |
Definition at line 66 of file dlp_field.h.
#define LA_FOURBODY_P 0 |
Definition at line 102 of file dlp_field.h.
#define LA_INVERS 11 |
Definition at line 60 of file dlp_field.h.
#define LA_INVERS_P 5 |
Definition at line 96 of file dlp_field.h.
#define LA_METALS 0 |
Definition at line 63 of file dlp_field.h.
#define LA_METALS_P 0 |
Definition at line 99 of file dlp_field.h.
#define LA_TERSOFFS 0 |
Definition at line 64 of file dlp_field.h.
#define LA_TERSOFFS_P 0 |
Definition at line 100 of file dlp_field.h.
#define LA_TETH 0 |
Definition at line 61 of file dlp_field.h.
#define LA_TETH_P 0 |
Definition at line 97 of file dlp_field.h.
#define LA_THREEBODY 0 |
Definition at line 65 of file dlp_field.h.
#define LA_THREEBODY_P 0 |
Definition at line 101 of file dlp_field.h.
#define LA_VDW 0 |
Definition at line 62 of file dlp_field.h.
#define LA_VDW_P 0 |
Definition at line 98 of file dlp_field.h.
#define MOLIMIT 15 |
Definition at line 117 of file dlp_field.h.
#define N_FIELDS 21 |
Definition at line 39 of file dlp_field.h.
#define OPLSAAP 19 |
Definition at line 139 of file dlp_field.h.
#define OPLSAAR 20 |
Definition at line 140 of file dlp_field.h.
#define PCFF 17 |
Definition at line 137 of file dlp_field.h.
#define SEXTERN 20 |
Definition at line 118 of file dlp_field.h.
typedef struct field_atom field_atom |
Definition at line 166 of file dlp_field.h.
typedef struct field_constraint field_constraint |
Definition at line 208 of file dlp_field.h.
typedef struct field_data field_data |
Definition at line 368 of file dlp_field.h.
typedef struct field_external field_external |
Definition at line 297 of file dlp_field.h.
typedef struct field_molecule field_molecule |
Definition at line 319 of file dlp_field.h.
typedef struct field_neighbor field_neighbor |
Definition at line 309 of file dlp_field.h.
typedef struct field_nth_body field_nth_body |
Definition at line 279 of file dlp_field.h.
typedef struct field_object_match field_object_match |
Definition at line 356 of file dlp_field.h.
typedef struct field_pmf field_pmf |
Definition at line 221 of file dlp_field.h.
typedef struct field_prop field_prop |
Definition at line 152 of file dlp_field.h.
typedef struct field_rigid field_rigid |
Definition at line 236 of file dlp_field.h.
typedef struct field_shell field_shell |
Definition at line 190 of file dlp_field.h.
typedef struct field_struct field_struct |
Definition at line 262 of file dlp_field.h.
typedef struct field_tethered field_tethered |
Definition at line 248 of file dlp_field.h.
enum dlp_atom_types |
Enumerator | |
---|---|
SPEC_ONLY | 0 |
TOTAL_COORD_AND_SPEC | 1 |
PARTIAL_COORD_AND_SPEC | 2 |
OTHER | 3 |
Definition at line 143 of file dlp_field.h.
|
extern |
add field property callback
action | the GAction sending the signal |
parameter | GVariant parameter of the GAction |
data | the associated data pointer |
Definition at line 3058 of file dlp_edit.c.
|
extern |
|
extern |
adjust field property
fil | the type of field property |
sti | the number of field atoms for this type of field property |
tmp | the pointer of the field property list |
ids | the list of field atoms |
key | the key value to adjust |
Definition at line 163 of file dlp_edit.c.
angle between atom a, b and c in 3D
cell | unit cell |
mdstep | the MD step |
at | atom a |
bt | atom b |
ct | atom c |
Definition at line 179 of file ogl_utils.c.
|
extern |
find the number of atom(s) in a non bonded interaction
b |
Definition at line 1022 of file dlp_field.c.
|
extern |
classical force field assistant change the target molecule for the page
box | the GtkComboBox sending the signal |
data | the associated data pointer |
Definition at line 1770 of file dlp_field.c.
|
extern |
clean force field structural property(ies)
stru |
Definition at line 2146 of file dlp_init.c.
|
extern |
classical force field create molecule selection combo box
f | the type of force field object |
Definition at line 2479 of file dlp_field.c.
|
extern |
classical force field create the list store selection widgets
f | the page number / type of field object(s) |
Definition at line 3544 of file dlp_field.c.
|
extern |
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.
|
extern |
dihedral between atom a, b, c and d in 3D
cell | unit cell |
mdstep | the MD step |
at | atom a |
bt | atom b |
ct | atom c |
dt | atom d |
Definition at line 204 of file ogl_utils.c.
distance between atom a and b in 3D
cell | unit cell |
mdstep | the MD step |
at | atom a |
bt | atom b |
Definition at line 81 of file ogl_utils.c.
|
extern |
|
extern |
|
extern |
create copy of a field atom data structure
old_fat | the field atom to duplicate |
Definition at line 67 of file dlp_copy.c.
|
extern |
create copy of a field constraint data structure
old_cons | the field constraint to duplicate |
Definition at line 127 of file dlp_copy.c.
|
extern |
create copy of a field molecule
old_fmol | the feld molecule to duplicate |
Definition at line 436 of file dlp_copy.c.
|
extern |
create copy of a field body property
old_fbody | the field body property to duplicate |
Definition at line 365 of file dlp_copy.c.
|
extern |
create a copy of a field property
old_prop | the field property to duplicate |
ti | the type of field property |
Definition at line 218 of file dlp_copy.c.
|
extern |
create copy of a field rigid data structure
old_rig | the field rigid to duplicate |
Definition at line 176 of file dlp_copy.c.
|
extern |
create copy of a field shell data structure
old_shell | the field shell to duplicate |
Definition at line 101 of file dlp_copy.c.
|
extern |
create copy of a field structural element
old_fstr | the field structural element to duplicate |
Definition at line 300 of file dlp_copy.c.
|
extern |
create copy of list of field structural element(s)
list_str | the list of field structural element(s) to duplicate |
init |
Definition at line 325 of file dlp_copy.c.
|
extern |
create copy of a field tethered data structure
old_tet | the field tethered to duplicate |
Definition at line 197 of file dlp_copy.c.
|
extern |
|
extern |
|
extern |
create copy of a field property 'other' list
oid | the target field atom id |
old_fstr | the field property to duplicate |
new_fstr | the field property to store the results |
Definition at line 269 of file dlp_copy.c.
|
extern |
edit field property callback
action | the GAction sending the signal |
parameter | GVariant parameter of the GAction |
data | the associated data pointer |
Definition at line 2993 of file dlp_edit.c.
|
extern |
classical force field fill the tree store
store | the tree store to fill |
f | the type of field object |
m | the target field molecule, if any |
Definition at line 1264 of file dlp_field.c.
|
extern |
retrieve field atom
a | the id of the field molecule |
b | the id of the field atom to retrieve |
Definition at line 145 of file dlp_active.c.
|
extern |
retrieve field nth body interaction
a | the id of the body interaction to retrieve |
b | the type of body interaction |
Definition at line 106 of file dlp_active.c.
|
extern |
retrieve constraint property
a | the id of the field molecule |
b | the id of the constraint to retrieve |
Definition at line 185 of file dlp_active.c.
|
extern |
retrieve external field property
a | the id of the external field property to retrieve |
Definition at line 125 of file dlp_active.c.
|
extern |
retrieve field molecule
a | the id of the field molecule to retrieve |
Definition at line 87 of file dlp_active.c.
|
extern |
retrieve field molecule from overall atom id in the model
this_proj | the target project |
aid | the target atom id |
Definition at line 59 of file dlp_active.c.
|
extern |
retrieve PMF property
a | the id of the field molecule |
b | the id of the PMF property to retrieve |
Definition at line 205 of file dlp_active.c.
|
extern |
the field molecule structural property id to retrieve
pr | the pointer on the field molecule properties to browse |
a | the id of the field molecule property to retrieve |
Definition at line 265 of file dlp_active.c.
|
extern |
retrieve field molecule structural property using atoms
pr | the pointer on the field molecule properties to browse |
ti | the number of atoms for this property |
ids | the atoms to search for |
Definition at line 286 of file dlp_active.c.
|
extern |
retrieve rigid property
a | the id of the field molecule |
b | the id of the rigid property to retrieve |
Definition at line 225 of file dlp_active.c.
|
extern |
retrieve shell property
a | the id of the field molecule |
b | the id of the shell property to retrieve |
Definition at line 165 of file dlp_active.c.
|
extern |
retrieve field structural property
s | the type of structural property |
a | the field molecule id |
b | the structural property id to retrieve |
Definition at line 318 of file dlp_active.c.
|
extern |
retrieve tethered property
a | the id of the field molecule |
b | the id of the tethered to retrieve |
Definition at line 245 of file dlp_active.c.
|
extern |
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.
|
extern |
|
extern |
get force field atomic mass
sp | the target chemical species |
num | the atom id |
Definition at line 2289 of file force_fields.c.
|
extern |
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.
|
extern |
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.
|
extern |
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.
|
extern |
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.
|
extern |
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.
|
extern |
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.
|
extern |
intialize new field external potential
bi | the id of the new field external potential |
Definition at line 790 of file dlp_init.c.
|
extern |
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.
|
extern |
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.
|
extern |
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.
|
extern |
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.
|
extern |
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.
|
extern |
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.
|
extern |
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.
|
extern |
initialize the VdW section of a classical force field
init |
Definition at line 2299 of file dlp_init.c.
|
extern |
inversion angle between atom a, b, c and d in 3D
cell | unit cell |
mdstep | the MD step |
at | atom a |
bt | atom b |
ct | atom c |
dt | atom d |
Definition at line 240 of file ogl_utils.c.
|
extern |
|
extern |
prepare classical force field parameter description string
obj | the type of field object |
key | the formalism key for this type of object |
words | the string description lists |
data | the value(s) to print |
Definition at line 1097 of file dlp_field.c.
|
extern |
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.
|
extern |
print / fill tree store with force field angle(s) information
ai | 2 = angle(s), 3 = angular restraint(s) |
buf | the GtkTextBuffer to print into, if input print |
an | the field angle / angle restraint structural element(s) to print |
fi | the target fragment id |
store | the target GtkTreeStore to store, if assistant tab creation / refresh |
iter | the target tree iter to store the data, if assistant tab creation / refresh |
Definition at line 649 of file dlp_print.c.
|
extern |
print / fill tree store with force field bond(s) information
bi | 0 = bond(s), 1 = bond restraint(s) |
buf | the GtkTextBuffer to print into, if input print |
bd | the field bond / bond restraint structural element(s) to print |
fi | the target fragment id |
store | the target GtkTreeStore to store, if assistant tab creation / refresh |
iter | the target tree iter to store the data, if assistant tab creation / refresh |
Definition at line 774 of file dlp_print.c.
|
extern |
print DL-POLY CONFIG file
buf | the GtkTextBuffer to print into |
Definition at line 1575 of file dlp_print.c.
|
extern |
print DL-POLY CONTROL file
buf | the GtkTextBuffer to print into |
Definition at line 1897 of file dlp_print.c.
|
extern |
print / fill tree store with force field dihedral(s) information
dih | 4 = dihderale(s), 5 = dihedral restraint(s) |
buf | the GtkTextBuffer to print into, if input print |
dh | the field dihedral / dihedral restraint structural element(s) to print |
fi | the target fragment id |
store | the target GtkTreeStore to store, if assistant tab creation / refresh |
iter | the target tree iter to store the data, if assistant tab creation / refresh |
Definition at line 499 of file dlp_print.c.
|
extern |
print DL-POLY classical force field
buf | the GtkTextBuffer to print into |
Definition at line 1401 of file dlp_print.c.
|
extern |
print / fill tree store with force field improper(s)/inversion(s) information
di | 6 = improper(s), 7 = inversion(s) |
buf | the GtkTextBuffer to print into, if input print |
dhii | the field improper / inversion structural element(s) to print |
fi | the target fragment id |
store | the target GtkTreeStore to store, if assistant tab creation / refresh |
iter | the target tree iter to store the data, if assistant tab creation / refresh |
Definition at line 299 of file dlp_print.c.
|
extern |
remove atom from field molecule - creating the dialog
action | the GAction sending the signal |
parameter | GVariant parameter of the GAction |
data | the associated data pointer |
Definition at line 731 of file dlp_atom.c.
|
extern |
remove field property callback
action | the GAction sending the signal |
parameter | GVariant parameter of the GAction |
data | the associated data pointer |
Definition at line 3298 of file dlp_edit.c.
|
extern |
|
extern |
|
extern |
select atom id from field molecule - creating the dialog
but | the GtkButton sending the signal |
data | the associated data pointer |
Definition at line 1172 of file dlp_edit.c.
|
extern |
classical force field prepare the molecule information widget
Definition at line 1045 of file dlp_field.c.
|
extern |
|
extern |
setup force field parameters
id | the force field id |
Definition at line 2823 of file force_fields.c.
|
extern |
|
extern |
number of atoms in a structural element
f | the type of structural element |
Definition at line 999 of file dlp_field.c.
|
extern |
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.
|
extern |
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.
|
extern |
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.
|
extern |
classical force field assistant update all tree models
Definition at line 1786 of file dlp_field.c.
|
extern |
crerate DL-POLY option widgets
f | the page number in the CONTROL file section of the DL-POLY input file(s) creation assistant |
Definition at line 2570 of file dlp_control.c.
|
extern |
|
extern |
select all element(s) in the column for visualization
col | the target GtkTreeViewColumn |
data | the associated data pointer |
|
extern |
|
extern |
Definition at line 112 of file dlp_control.c.
|
extern |
Definition at line 944 of file dlp_field.c.
|
extern |
Definition at line 44 of file dlp_comp.c.
|
extern |
Definition at line 240 of file force_fields.c.
|
extern |
Definition at line 1946 of file force_fields.c.
|
extern |
Definition at line 1945 of file force_fields.c.
|
extern |
Definition at line 1947 of file force_fields.c.
|
extern |
Definition at line 1948 of file force_fields.c.
|
extern |
Definition at line 1949 of file force_fields.c.
|
extern |
Definition at line 1952 of file force_fields.c.
|
extern |
Definition at line 1950 of file force_fields.c.
|
extern |
Definition at line 200 of file force_fields.c.
|
extern |
Definition at line 940 of file dlp_field.c.
|
extern |
Definition at line 980 of file dlp_field.c.
|
extern |
Definition at line 948 of file dlp_field.c.
|
extern |
Definition at line 947 of file dlp_field.c.
|
extern |
Definition at line 979 of file dlp_field.c.
|
extern |
Definition at line 1939 of file force_fields.c.
|
extern |
Definition at line 945 of file dlp_field.c.
|
extern |
Definition at line 830 of file dlp_field.c.
|
extern |
Definition at line 185 of file dlp_field.c.
|
extern |
Definition at line 218 of file dlp_field.c.
|
extern |
Definition at line 255 of file dlp_field.c.
Definition at line 372 of file dlp_field.c.
Definition at line 306 of file dlp_field.c.
|
extern |
Definition at line 450 of file dlp_field.c.
|
extern |
Definition at line 762 of file dlp_field.c.
|
extern |
Definition at line 776 of file dlp_field.c.
Definition at line 522 of file dlp_field.c.
Definition at line 688 of file dlp_field.c.
|
extern |
Definition at line 736 of file dlp_field.c.
|
extern |
Definition at line 726 of file dlp_field.c.
Definition at line 292 of file dlp_field.c.
Definition at line 602 of file dlp_field.c.
|
extern |
Definition at line 938 of file dlp_field.c.
|
extern |
Definition at line 943 of file dlp_field.c.
|
extern |
Definition at line 974 of file dlp_field.c.
|
extern |
Definition at line 981 of file dlp_field.c.
|
extern |
Definition at line 982 of file dlp_field.c.
|
extern |
Definition at line 3912 of file dlp_field.c.
|
extern |
Definition at line 954 of file dlp_field.c.
|
extern |
Definition at line 957 of file dlp_field.c.
|
extern |
Definition at line 965 of file dlp_field.c.
field_atom * tmp_fbt |
Definition at line 406 of file dlp_field.h.
|
extern |
Definition at line 959 of file dlp_field.c.
field_atom * tmp_fct |
Definition at line 406 of file dlp_field.h.
field_atom * tmp_fdt |
Definition at line 406 of file dlp_field.h.
|
extern |
Definition at line 967 of file dlp_field.c.
|
extern |
Definition at line 951 of file dlp_field.c.
|
extern |
Definition at line 955 of file dlp_field.c.
|
extern |
Definition at line 960 of file dlp_field.c.
|
extern |
Definition at line 963 of file dlp_field.c.
|
extern |
Definition at line 961 of file dlp_field.c.
|
extern |
Definition at line 958 of file dlp_field.c.
|
extern |
Definition at line 964 of file dlp_field.c.
|
extern |
Definition at line 962 of file dlp_field.c.
|
extern |
Definition at line 956 of file dlp_field.c.
|
extern |
Definition at line 1940 of file force_fields.c.
|
extern |
Definition at line 953 of file dlp_field.c.
|
extern |
Definition at line 952 of file dlp_field.c.