atomes 1.1.16
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dlp_print.c File Reference

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. More...

#include "dlp_field.h"
#include "interface.h"
+ Include dependency graph for dlp_print.c:

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"}
 

Detailed Description

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.

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_print.c.

Typedef Documentation

◆ imp_inv

typedef struct imp_inv imp_inv

Definition at line 216 of file dlp_print.c.

Function Documentation

◆ get_body_element_name()

gchar * get_body_element_name ( field_nth_body * body,
int aid,
int nbd )
extern

get field body potential element name

Parameters
bodythe field body potential
aidthe atom id, if any
nbdthe body potential id

Definition at line 1934 of file dlp_edit.c.

◆ get_num_struct_to_print()

int get_num_struct_to_print ( field_molecule * fmol,
int sid )

find the number of structural element(s) to print

Parameters
fmolthe target field molecule
sidthe type of structural element

Definition at line 1026 of file dlp_print.c.

◆ get_num_vdw_max()

int get_num_vdw_max ( )
extern

Get the number of field shell interactions.

Definition at line 2002 of file dlp_edit.c.

◆ get_pbc()

int get_pbc ( )

get the PBC DL-POLY lattice type

Definition at line 1536 of file dlp_print.c.

◆ in_bond()

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

is atom at in bond bd

Parameters
atthe target atom id
bdthe bond atoms id

Definition at line 892 of file dlp_init.c.

◆ member_of_atom()

gboolean member_of_atom ( field_atom * fat,
int id )

is the id atom from the model in target field atom

Parameters
fatthe target field atom
idthe atom id in the model

Definition at line 277 of file dlp_print.c.

◆ print_all_field_struct()

void print_all_field_struct ( field_molecule * mol,
int str )

print all field structural element(s)

Parameters
molthe target field molecule
strthe type of structural element

Definition at line 195 of file dlp_print.c.

◆ print_ana()

gboolean print_ana ( )

determine if the analysis information section is required

Definition at line 1674 of file dlp_print.c.

◆ print_control_float()

void print_control_float ( GtkTextBuffer * buf,
double data,
gchar * info_a,
gchar * info_b,
gchar * key )

print CONTROL file print float value

Parameters
bufthe GtkTextBuffer to print into
datathe float value to print
info_a1st string to print
info_b2nd string to print, if any
keyDL-POLY key

Definition at line 1790 of file dlp_print.c.

◆ print_control_int()

void print_control_int ( GtkTextBuffer * buf,
int data,
gchar * info_a,
gchar * info_b,
gchar * key )

print CONTROL file print integer value

Parameters
bufthe GtkTextBuffer to print into
datathe integer value to print
info_a1st string to print
info_b2nd string to print, if any
keyDL-POLY key

Definition at line 1752 of file dlp_print.c.

◆ print_control_key()

void print_control_key ( GtkTextBuffer * buf,
gchar * info,
gchar * key )

print CONTROL file print key

Parameters
bufthe GtkTextBuffer to print into
infothe information string, if any
keyDL-POLY key to print

Definition at line 1883 of file dlp_print.c.

◆ print_control_sci()

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

Parameters
bufthe GtkTextBuffer to print into
datathe float value to print
info_a1st string to print
info_b2nd string to print, if any
keyDL-POLY key

Definition at line 1828 of file dlp_print.c.

◆ print_control_string()

void print_control_string ( GtkTextBuffer * buf,
gchar * string,
gchar * info_a,
gchar * info_b,
gchar * key )

print CONTROL file print string

Parameters
bufthe GtkTextBuffer to print into
stringthe string to print
info_a1st string to print, if any
info_b2nd string to print, if any
keyDL-POLY key

Definition at line 1865 of file dlp_print.c.

◆ print_dlp_angle()

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

Parameters
ai2 = angle(s), 3 = angular restraint(s)
bufthe GtkTextBuffer to print into, if input print
anthe field angle / angle restraint structural element(s) to print
fithe target fragment id
storethe target GtkTreeStore to store, if assistant tab creation / refresh
iterthe target tree iter to store the data, if assistant tab creation / refresh

Definition at line 649 of file dlp_print.c.

◆ print_dlp_atom()

void print_dlp_atom ( GtkTextBuffer * buf,
int at,
int numat )

print force field atom

Parameters
bufthe GtkTextBuffer to print into
atthe list id in the target field atom
numatthe atom id in the fragment / molecule

Definition at line 1003 of file dlp_print.c.

◆ print_dlp_body()

void print_dlp_body ( GtkTextBuffer * buf,
field_nth_body * body )

print force field non bonded potential

Parameters
bufthe GtkTextBuffer to print into
bodythe non bonded potential to print

Definition at line 1292 of file dlp_print.c.

◆ print_dlp_bond()

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

Parameters
bi0 = bond(s), 1 = bond restraint(s)
bufthe GtkTextBuffer to print into, if input print
bdthe field bond / bond restraint structural element(s) to print
fithe target fragment id
storethe target GtkTreeStore to store, if assistant tab creation / refresh
iterthe target tree iter to store the data, if assistant tab creation / refresh

Definition at line 774 of file dlp_print.c.

◆ print_dlp_config()

void print_dlp_config ( GtkTextBuffer * buf)

print DL-POLY CONFIG file

Parameters
bufthe GtkTextBuffer to print into

Definition at line 1575 of file dlp_print.c.

◆ print_dlp_cons()

void print_dlp_cons ( GtkTextBuffer * buf,
field_constraint * cons )

print force field constraint

Parameters
bufthe GtkTextBuffer to print into
consthe field constraint to print

Definition at line 969 of file dlp_print.c.

◆ print_dlp_control()

void print_dlp_control ( GtkTextBuffer * buf)

print DL-POLY CONTROL file

Parameters
bufthe GtkTextBuffer to print into

Definition at line 1897 of file dlp_print.c.

◆ print_dlp_dihedral()

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

Parameters
dih4 = dihderale(s), 5 = dihedral restraint(s)
bufthe GtkTextBuffer to print into, if input print
dhthe field dihedral / dihedral restraint structural element(s) to print
fithe target fragment id
storethe target GtkTreeStore to store, if assistant tab creation / refresh
iterthe target tree iter to store the data, if assistant tab creation / refresh

Definition at line 499 of file dlp_print.c.

◆ print_dlp_field()

void print_dlp_field ( GtkTextBuffer * buf)

print DL-POLY classical force field

Parameters
bufthe GtkTextBuffer to print into

Definition at line 1401 of file dlp_print.c.

◆ print_dlp_improper_inversion()

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

Parameters
di6 = improper(s), 7 = inversion(s)
bufthe GtkTextBuffer to print into, if input print
dhiithe field improper / inversion structural element(s) to print
fithe target fragment id
storethe target GtkTreeStore to store, if assistant tab creation / refresh
iterthe target tree iter to store the data, if assistant tab creation / refresh

Definition at line 299 of file dlp_print.c.

◆ print_dlp_molecule()

void print_dlp_molecule ( GtkTextBuffer * buf,
field_molecule * fmol )

print force field molecule

Parameters
bufthe GtkTextBuffer to print into
fmolthe field molecule to print

Definition at line 1058 of file dlp_print.c.

◆ print_dlp_pmf()

void print_dlp_pmf ( GtkTextBuffer * buf,
field_pmf * pmf )

print force field mean force potential

Parameters
bufthe GtkTextBuffer to print into
pmfthe field PMF to print

Definition at line 939 of file dlp_print.c.

◆ print_dlp_rigid()

void print_dlp_rigid ( GtkTextBuffer * buf,
field_rigid * rig )

print force field rigid

Parameters
bufthe GtkTextBuffer to print into
rigthe field rigid to print

Definition at line 877 of file dlp_print.c.

◆ print_dlp_shell()

void print_dlp_shell ( GtkTextBuffer * buf,
field_molecule * fmol,
field_shell * shell )

print force field core shell

Parameters
bufthe GtkTextBuffer to print into
fmolthe target field molecule
shellthe field shell to print

Definition at line 986 of file dlp_print.c.

◆ print_dlp_tersoff()

void print_dlp_tersoff ( GtkTextBuffer * buf,
field_nth_body * body )

print force field Tersoff potential

Parameters
bufthe GtkTextBuffer to print into
bodythe non bonded (Tersoff potential) to print

Definition at line 1351 of file dlp_print.c.

◆ print_dlp_tersoff_cross()

void print_dlp_tersoff_cross ( GtkTextBuffer * buf,
field_nth_body * body_a,
field_nth_body * body_b )

print Tersoff potential cross term

Parameters
bufthe GtkTextBuffer to print into
body_a1st non bonded potential
body_b2nd non bonded potential

Definition at line 1326 of file dlp_print.c.

◆ print_dlp_tet()

void print_dlp_tet ( GtkTextBuffer * buf,
field_tethered * tet )

print force field tethered potential

Parameters
bufthe GtkTextBuffer to print into
tetthe field tethered potential to print

Definition at line 915 of file dlp_print.c.

◆ print_field_prop()

void print_field_prop ( field_prop * pro,
int st,
field_molecule * mol )

print force field property

Parameters
prothe field property to print
stthe type of structural element
molthe target field molecule

Definition at line 94 of file dlp_print.c.

◆ print_field_struct()

void print_field_struct ( field_struct * stru,
field_molecule * mol )

print force field structural element

Parameters
struthe target field structural element
molthe target field molecule

Definition at line 154 of file dlp_print.c.

◆ print_float()

void print_float ( GtkTextBuffer * buf,
double data )

print float value

Parameters
bufthe GtkTextBuffer to print into
datathe float value to print

Definition at line 1772 of file dlp_print.c.

◆ print_int()

void print_int ( GtkTextBuffer * buf,
int data )

print integer value

Parameters
bufthe GtkTextBuffer to print into
datathe integer value to print

Definition at line 1734 of file dlp_print.c.

◆ print_sci()

void print_sci ( GtkTextBuffer * buf,
double data )

print float in scientific format

Parameters
bufthe GtkTextBuffer to print into
datathe float value to print

Definition at line 1810 of file dlp_print.c.

◆ print_string()

void print_string ( GtkTextBuffer * buf,
gchar * string )

print string

Parameters
bufthe GtkTextBuffer to print into
stringthe string to print

Definition at line 1848 of file dlp_print.c.

◆ print_this_imp_inv()

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) ?

Parameters
invthe improper / inversion structure to check
di6 = improper, 7 = inversion
a1st atom id
b2nd atom id
c3rd atom id
d4th atom id

Definition at line 239 of file dlp_print.c.

Variable Documentation

◆ area_keyw

gchar* area_keyw[5] ={"area", "tens", "tens", "orth", "orth"}

Definition at line 1663 of file dlp_print.c.

◆ elec_key

gchar* elec_key[10]
Initial value:
={"coul ",
"distan ",
"ewald precision ",
"ewald ",
"reaction ",
"reaction damp ",
"reaction precision ",
"shift ",
"shift damp ",
"shift precision "}

Definition at line 1691 of file dlp_print.c.

◆ ens_keyw

gchar* ens_keyw[4] = {"nve", "nvt", "npt", "nst"}

Definition at line 1660 of file dlp_print.c.

◆ eval_m

gchar* eval_m[10]
extern

Definition at line 1868 of file dlp_control.c.

◆ eval_vdw

gchar* eval_vdw[6]
extern

Definition at line 2181 of file dlp_control.c.

◆ io_inf

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.

◆ io_key

gchar* io_key[2] ={"\nio read ", "\nio writ "}

Definition at line 1721 of file dlp_print.c.

◆ io_meth

gchar* io_meth[4] ={"mpiio", "direct", "master", "netcdf"}

Definition at line 1722 of file dlp_print.c.

◆ io_pec

gchar* io_pec[2] ={"off", "on"}

Definition at line 1723 of file dlp_print.c.

◆ io_pres

gchar* io_pres[2]
extern

Definition at line 1566 of file dlp_control.c.

◆ io_rw_m

gchar* io_rw_m[4]
extern

Definition at line 1563 of file dlp_control.c.

◆ io_typ

gchar* io_typ[2] ={"sorted", "unsorted"}

Definition at line 1724 of file dlp_print.c.

◆ md_keyw

gchar* md_keyw[4] ={"temp ", "steps ", "integrat ", "pres "}

Definition at line 1664 of file dlp_print.c.

◆ md_text

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.

◆ min_key

gchar* min_key[3] ={"force", "energy", "distance"}

Definition at line 1666 of file dlp_print.c.

◆ pseudo_thermo

gchar* pseudo_thermo[3] = {"langevin", "gauss", "direct"}

Definition at line 1662 of file dlp_print.c.

◆ rest_inf

gchar* rest_inf[3]
Initial value:
={"\n# Continue current simulation - require REVOLD file",
"\n# Start new simulation from older run without temperature reset",
"\n# Start new simulation from older run with temperature reset"}

Definition at line 1713 of file dlp_print.c.

◆ rest_key

gchar* rest_key[3] ={NULL, "noscale", "scale"}

Definition at line 1716 of file dlp_print.c.

◆ sys_info

gchar* sys_info[8]
Initial value:
={"\n# Ignore particle indices from CONFIG file and set indices by order of reading",
"\n# Ignore strict checks when reading CONFIG file, warning messages and assume safe simulation parameters",
"\n# Skip detailed topology reporting when reading FIELD file",
"\n# Ignore center of mass momentum removal during the simulation",
"\n# Tolerance for the relaxed shell model\n",
"\n# Subcelling threshold density of particle per link cell\n",
"\n# Create an expanded version of the current model\n",
"\n# Restart job from previous run: "}

Definition at line 1703 of file dlp_print.c.

◆ sys_key

gchar* sys_key[8] ={NULL, NULL, NULL, NULL, "rlxtol ", "subcell ", "nfold ", "restart "}

Definition at line 1711 of file dlp_print.c.

◆ sys_string

gchar* sys_string[8] ={"ind", "str", "top", "vom", NULL, NULL, NULL, NULL}

Definition at line 1712 of file dlp_print.c.

◆ thermo_keyw

gchar* thermo_keyw[10] = {"evans", "lang", "ander", "ber", "hoover", "gst", "dpd", "mtk", "ttm", "inhomo"}

Definition at line 1661 of file dlp_print.c.

◆ time_inf

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.

◆ time_key

gchar* time_key[2] ={"job time ", "close time "}

Definition at line 1719 of file dlp_print.c.

◆ vdw_key

gchar* vdw_key[6]
Initial value:
={"lor ", "fend", "hoge",
"halg", "tang", "func"}

Definition at line 1701 of file dlp_print.c.