atomes 1.1.14
atomes: an atomic scale modeling tool box
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Functions to handle the output of the DL-POLY FIELD file
Functions to handle the output of the DL-POLY CONTROL file
Functions to handle the output of the DL-POLY CONFIG file
Functions to fill the structural element(s) tree models in the assistant.
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Go to the source code of this file.
Data Structures | |
struct | imp_inv |
Typedefs | |
typedef struct imp_inv | imp_inv |
Functions | |
gboolean | in_bond (int at, int bd[2]) |
is atom at in bond bd | |
int | get_num_vdw_max () |
Get the number of field shell interactions. | |
gchar * | get_body_element_name (field_nth_body *body, int aid, int nbd) |
get field body potential element name | |
void | print_field_prop (field_prop *pro, int st, field_molecule *mol) |
print force field property | |
void | print_field_struct (field_struct *stru, field_molecule *mol) |
print force field structural element | |
void | print_all_field_struct (field_molecule *mol, int str) |
print all field structural element(s) | |
gboolean | print_this_imp_inv (imp_inv *inv, int di, int a, int b, int c, int d) |
print this improper / inversion structure or not (already printed) ? | |
gboolean | member_of_atom (field_atom *fat, int id) |
is the id atom from the model in target field atom | |
void | print_dlp_improper_inversion (int di, GtkTextBuffer *buf, field_struct *dhii, int fi, GtkTreeStore *store, GtkTreeIter *iter) |
print / fill tree store with force field improper(s)/inversion(s) information | |
void | print_dlp_dihedral (int dih, 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 | |
void | print_dlp_rigid (GtkTextBuffer *buf, field_rigid *rig) |
print force field rigid | |
void | print_dlp_tet (GtkTextBuffer *buf, field_tethered *tet) |
print force field tethered potential | |
void | print_dlp_pmf (GtkTextBuffer *buf, field_pmf *pmf) |
print force field mean force potential | |
void | print_dlp_cons (GtkTextBuffer *buf, field_constraint *cons) |
print force field constraint | |
void | print_dlp_shell (GtkTextBuffer *buf, field_molecule *fmol, field_shell *shell) |
print force field core shell | |
void | print_dlp_atom (GtkTextBuffer *buf, int at, int numat) |
print force field atom | |
int | get_num_struct_to_print (field_molecule *fmol, int sid) |
find the number of structural element(s) to print | |
void | print_dlp_molecule (GtkTextBuffer *buf, field_molecule *fmol) |
print force field molecule | |
void | print_dlp_body (GtkTextBuffer *buf, field_nth_body *body) |
print force field non bonded potential | |
void | print_dlp_tersoff_cross (GtkTextBuffer *buf, field_nth_body *body_a, field_nth_body *body_b) |
print Tersoff potential cross term | |
void | print_dlp_tersoff (GtkTextBuffer *buf, field_nth_body *body) |
print force field Tersoff potential | |
void | print_dlp_field (GtkTextBuffer *buf) |
print DL-POLY classical force field | |
int | get_pbc () |
get the PBC DL-POLY lattice type | |
void | print_dlp_config (GtkTextBuffer *buf) |
print DL-POLY CONFIG file | |
gboolean | print_ana () |
determine if the analysis information section is required | |
void | print_int (GtkTextBuffer *buf, int data) |
print integer value | |
void | print_control_int (GtkTextBuffer *buf, int data, gchar *info_a, gchar *info_b, gchar *key) |
print CONTROL file print integer value | |
void | print_float (GtkTextBuffer *buf, double data) |
print float value | |
void | print_control_float (GtkTextBuffer *buf, double data, gchar *info_a, gchar *info_b, gchar *key) |
print CONTROL file print float value | |
void | print_sci (GtkTextBuffer *buf, double data) |
print float in scientific format | |
void | print_control_sci (GtkTextBuffer *buf, double data, gchar *info_a, gchar *info_b, gchar *key) |
print CONTROL file print float value in scientific format | |
void | print_string (GtkTextBuffer *buf, gchar *string) |
print string | |
void | print_control_string (GtkTextBuffer *buf, gchar *string, gchar *info_a, gchar *info_b, gchar *key) |
print CONTROL file print string | |
void | print_control_key (GtkTextBuffer *buf, gchar *info, gchar *key) |
print CONTROL file print key | |
void | print_dlp_control (GtkTextBuffer *buf) |
print DL-POLY CONTROL file | |
Variables | |
gchar * | ens_keyw [4] = {"nve", "nvt", "npt", "nst"} |
gchar * | thermo_keyw [10] = {"evans", "lang", "ander", "ber", "hoover", "gst", "dpd", "mtk", "ttm", "inhomo"} |
gchar * | pseudo_thermo [3] = {"langevin", "gauss", "direct"} |
gchar * | area_keyw [5] ={"area", "tens", "tens", "orth", "orth"} |
gchar * | md_keyw [4] ={"temp ", "steps ", "integrat ", "pres "} |
gchar * | md_text [4] ={"# Target temperature in K\n", "# Number of MD steps\n", "# Integration time step in ps\n", "# Target presssure in k atms\n"} |
gchar * | min_key [3] ={"force", "energy", "distance"} |
gchar * | eval_m [10] |
gchar * | eval_vdw [6] |
gchar * | io_rw_m [4] |
gchar * | io_pres [2] |
gchar * | elec_key [10] |
gchar * | vdw_key [6] |
gchar * | sys_info [8] |
gchar * | sys_key [8] ={NULL, NULL, NULL, NULL, "rlxtol ", "subcell ", "nfold ", "restart "} |
gchar * | sys_string [8] ={"ind", "str", "top", "vom", NULL, NULL, NULL, NULL} |
gchar * | rest_inf [3] |
gchar * | rest_key [3] ={NULL, "noscale", "scale"} |
gchar * | time_inf [2] ={"\n\n# Set job time to ", "\n\n# Set job closure time to "} |
gchar * | time_key [2] ={"job time ", "close time "} |
gchar * | io_inf [2] ={"\n# I/O read interface, with:\n", "\n# I/O write interface, with:\n"} |
gchar * | io_key [2] ={"\nio read ", "\nio writ "} |
gchar * | io_meth [4] ={"mpiio", "direct", "master", "netcdf"} |
gchar * | io_pec [2] ={"off", "on"} |
gchar * | io_typ [2] ={"sorted", "unsorted"} |
Functions to handle the output of the DL-POLY FIELD file
Functions to handle the output of the DL-POLY CONTROL file
Functions to handle the output of the DL-POLY CONFIG file
Functions to fill the structural element(s) tree models in the assistant.
Definition in file dlp_print.c.
typedef struct imp_inv imp_inv |
Definition at line 216 of file dlp_print.c.
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extern |
get field body potential element name
body | the field body potential |
aid | the atom id, if any |
nbd | the body potential id |
Definition at line 1934 of file dlp_edit.c.
int get_num_struct_to_print | ( | field_molecule * | fmol, |
int | sid ) |
find the number of structural element(s) to print
fmol | the target field molecule |
sid | the type of structural element |
Definition at line 1026 of file dlp_print.c.
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extern |
Get the number of field shell interactions.
Definition at line 2002 of file dlp_edit.c.
int get_pbc | ( | ) |
get the PBC DL-POLY lattice type
Definition at line 1536 of file dlp_print.c.
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extern |
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.
gboolean member_of_atom | ( | field_atom * | fat, |
int | id ) |
is the id atom from the model in target field atom
fat | the target field atom |
id | the atom id in the model |
Definition at line 277 of file dlp_print.c.
void print_all_field_struct | ( | field_molecule * | mol, |
int | str ) |
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.
gboolean print_ana | ( | ) |
determine if the analysis information section is required
Definition at line 1674 of file dlp_print.c.
void print_control_float | ( | GtkTextBuffer * | buf, |
double | data, | ||
gchar * | info_a, | ||
gchar * | info_b, | ||
gchar * | key ) |
print CONTROL file print float value
buf | the GtkTextBuffer to print into |
data | the float value to print |
info_a | 1st string to print |
info_b | 2nd string to print, if any |
key | DL-POLY key |
Definition at line 1790 of file dlp_print.c.
void print_control_int | ( | GtkTextBuffer * | buf, |
int | data, | ||
gchar * | info_a, | ||
gchar * | info_b, | ||
gchar * | key ) |
print CONTROL file print integer value
buf | the GtkTextBuffer to print into |
data | the integer value to print |
info_a | 1st string to print |
info_b | 2nd string to print, if any |
key | DL-POLY key |
Definition at line 1752 of file dlp_print.c.
void print_control_key | ( | GtkTextBuffer * | buf, |
gchar * | info, | ||
gchar * | key ) |
print CONTROL file print key
buf | the GtkTextBuffer to print into |
info | the information string, if any |
key | DL-POLY key to print |
Definition at line 1883 of file dlp_print.c.
void print_control_sci | ( | GtkTextBuffer * | buf, |
double | data, | ||
gchar * | info_a, | ||
gchar * | info_b, | ||
gchar * | key ) |
print CONTROL file print float value in scientific format
buf | the GtkTextBuffer to print into |
data | the float value to print |
info_a | 1st string to print |
info_b | 2nd string to print, if any |
key | DL-POLY key |
Definition at line 1828 of file dlp_print.c.
void print_control_string | ( | GtkTextBuffer * | buf, |
gchar * | string, | ||
gchar * | info_a, | ||
gchar * | info_b, | ||
gchar * | key ) |
print CONTROL file print string
buf | the GtkTextBuffer to print into |
string | the string to print |
info_a | 1st string to print, if any |
info_b | 2nd string to print, if any |
key | DL-POLY key |
Definition at line 1865 of file dlp_print.c.
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
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.
void print_dlp_atom | ( | GtkTextBuffer * | buf, |
int | at, | ||
int | numat ) |
print force field atom
buf | the GtkTextBuffer to print into |
at | the list id in the target field atom |
numat | the atom id in the fragment / molecule |
Definition at line 1003 of file dlp_print.c.
void print_dlp_body | ( | GtkTextBuffer * | buf, |
field_nth_body * | body ) |
print force field non bonded potential
buf | the GtkTextBuffer to print into |
body | the non bonded potential to print |
Definition at line 1292 of file dlp_print.c.
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
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.
void print_dlp_config | ( | GtkTextBuffer * | buf | ) |
print DL-POLY CONFIG file
buf | the GtkTextBuffer to print into |
Definition at line 1575 of file dlp_print.c.
void print_dlp_cons | ( | GtkTextBuffer * | buf, |
field_constraint * | cons ) |
print force field constraint
buf | the GtkTextBuffer to print into |
cons | the field constraint to print |
Definition at line 969 of file dlp_print.c.
void print_dlp_control | ( | GtkTextBuffer * | buf | ) |
print DL-POLY CONTROL file
buf | the GtkTextBuffer to print into |
Definition at line 1897 of file dlp_print.c.
void print_dlp_dihedral | ( | int | dih, |
GtkTextBuffer * | buf, | ||
field_struct * | dh, | ||
int | fi, | ||
GtkTreeStore * | store, | ||
GtkTreeIter * | iter ) |
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.
void print_dlp_field | ( | GtkTextBuffer * | buf | ) |
print DL-POLY classical force field
buf | the GtkTextBuffer to print into |
Definition at line 1401 of file dlp_print.c.
void print_dlp_improper_inversion | ( | int | di, |
GtkTextBuffer * | buf, | ||
field_struct * | dhii, | ||
int | fi, | ||
GtkTreeStore * | store, | ||
GtkTreeIter * | iter ) |
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.
void print_dlp_molecule | ( | GtkTextBuffer * | buf, |
field_molecule * | fmol ) |
print force field molecule
buf | the GtkTextBuffer to print into |
fmol | the field molecule to print |
Definition at line 1058 of file dlp_print.c.
void print_dlp_pmf | ( | GtkTextBuffer * | buf, |
field_pmf * | pmf ) |
print force field mean force potential
buf | the GtkTextBuffer to print into |
pmf | the field PMF to print |
Definition at line 939 of file dlp_print.c.
void print_dlp_rigid | ( | GtkTextBuffer * | buf, |
field_rigid * | rig ) |
print force field rigid
buf | the GtkTextBuffer to print into |
rig | the field rigid to print |
Definition at line 877 of file dlp_print.c.
void print_dlp_shell | ( | GtkTextBuffer * | buf, |
field_molecule * | fmol, | ||
field_shell * | shell ) |
print force field core shell
buf | the GtkTextBuffer to print into |
fmol | the target field molecule |
shell | the field shell to print |
Definition at line 986 of file dlp_print.c.
void print_dlp_tersoff | ( | GtkTextBuffer * | buf, |
field_nth_body * | body ) |
print force field Tersoff potential
buf | the GtkTextBuffer to print into |
body | the non bonded (Tersoff potential) to print |
Definition at line 1351 of file dlp_print.c.
void print_dlp_tersoff_cross | ( | GtkTextBuffer * | buf, |
field_nth_body * | body_a, | ||
field_nth_body * | body_b ) |
print Tersoff potential cross term
buf | the GtkTextBuffer to print into |
body_a | 1st non bonded potential |
body_b | 2nd non bonded potential |
Definition at line 1326 of file dlp_print.c.
void print_dlp_tet | ( | GtkTextBuffer * | buf, |
field_tethered * | tet ) |
print force field tethered potential
buf | the GtkTextBuffer to print into |
tet | the field tethered potential to print |
Definition at line 915 of file dlp_print.c.
void print_field_prop | ( | field_prop * | pro, |
int | st, | ||
field_molecule * | mol ) |
print force field property
pro | the field property to print |
st | the type of structural element |
mol | the target field molecule |
Definition at line 94 of file dlp_print.c.
void print_field_struct | ( | field_struct * | stru, |
field_molecule * | mol ) |
print force field structural element
stru | the target field structural element |
mol | the target field molecule |
Definition at line 154 of file dlp_print.c.
void print_float | ( | GtkTextBuffer * | buf, |
double | data ) |
print float value
buf | the GtkTextBuffer to print into |
data | the float value to print |
Definition at line 1772 of file dlp_print.c.
void print_int | ( | GtkTextBuffer * | buf, |
int | data ) |
print integer value
buf | the GtkTextBuffer to print into |
data | the integer value to print |
Definition at line 1734 of file dlp_print.c.
void print_sci | ( | GtkTextBuffer * | buf, |
double | data ) |
print float in scientific format
buf | the GtkTextBuffer to print into |
data | the float value to print |
Definition at line 1810 of file dlp_print.c.
void print_string | ( | GtkTextBuffer * | buf, |
gchar * | string ) |
print string
buf | the GtkTextBuffer to print into |
string | the string to print |
Definition at line 1848 of file dlp_print.c.
gboolean print_this_imp_inv | ( | imp_inv * | inv, |
int | di, | ||
int | a, | ||
int | b, | ||
int | c, | ||
int | d ) |
print this improper / inversion structure or not (already printed) ?
inv | the improper / inversion structure to check |
di | 6 = improper, 7 = inversion |
a | 1st atom id |
b | 2nd atom id |
c | 3rd atom id |
d | 4th atom id |
Definition at line 239 of file dlp_print.c.
gchar* area_keyw[5] ={"area", "tens", "tens", "orth", "orth"} |
Definition at line 1663 of file dlp_print.c.
gchar* elec_key[10] |
Definition at line 1691 of file dlp_print.c.
gchar* ens_keyw[4] = {"nve", "nvt", "npt", "nst"} |
Definition at line 1660 of file dlp_print.c.
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Definition at line 1868 of file dlp_control.c.
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extern |
Definition at line 2181 of file dlp_control.c.
gchar* io_inf[2] ={"\n# I/O read interface, with:\n", "\n# I/O write interface, with:\n"} |
Definition at line 1720 of file dlp_print.c.
gchar* io_key[2] ={"\nio read ", "\nio writ "} |
Definition at line 1721 of file dlp_print.c.
gchar* io_meth[4] ={"mpiio", "direct", "master", "netcdf"} |
Definition at line 1722 of file dlp_print.c.
gchar* io_pec[2] ={"off", "on"} |
Definition at line 1723 of file dlp_print.c.
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Definition at line 1566 of file dlp_control.c.
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extern |
Definition at line 1563 of file dlp_control.c.
gchar* io_typ[2] ={"sorted", "unsorted"} |
Definition at line 1724 of file dlp_print.c.
gchar* md_keyw[4] ={"temp ", "steps ", "integrat ", "pres "} |
Definition at line 1664 of file dlp_print.c.
gchar* md_text[4] ={"# Target temperature in K\n", "# Number of MD steps\n", "# Integration time step in ps\n", "# Target presssure in k atms\n"} |
Definition at line 1665 of file dlp_print.c.
gchar* min_key[3] ={"force", "energy", "distance"} |
Definition at line 1666 of file dlp_print.c.
gchar* pseudo_thermo[3] = {"langevin", "gauss", "direct"} |
Definition at line 1662 of file dlp_print.c.
gchar* rest_inf[3] |
Definition at line 1713 of file dlp_print.c.
gchar* rest_key[3] ={NULL, "noscale", "scale"} |
Definition at line 1716 of file dlp_print.c.
gchar* sys_info[8] |
Definition at line 1703 of file dlp_print.c.
gchar* sys_key[8] ={NULL, NULL, NULL, NULL, "rlxtol ", "subcell ", "nfold ", "restart "} |
Definition at line 1711 of file dlp_print.c.
gchar* sys_string[8] ={"ind", "str", "top", "vom", NULL, NULL, NULL, NULL} |
Definition at line 1712 of file dlp_print.c.
gchar* thermo_keyw[10] = {"evans", "lang", "ander", "ber", "hoover", "gst", "dpd", "mtk", "ttm", "inhomo"} |
Definition at line 1661 of file dlp_print.c.
gchar* time_inf[2] ={"\n\n# Set job time to ", "\n\n# Set job closure time to "} |
Definition at line 1718 of file dlp_print.c.
gchar* time_key[2] ={"job time ", "close time "} |
Definition at line 1719 of file dlp_print.c.
gchar* vdw_key[6] |
Definition at line 1701 of file dlp_print.c.