Generated from scriptingFilter.tcl with ROBODoc v3.2.4 on Wed May 25 16:04:51 2005
NAME
scripting::filter
PURPOSE
This namespace provide the filter functions for loading crystal
(molecular) structures from various formats. The filter functions
are similar to "scripting::open --format file.format". However for
some formats using the latter form will query interactively some
parameters, for instance, atomic numbers are usually not known in
I/O files of pseudopotential-codes and are therefore
queried. Instead by using the filter functions, the necessary
information is supplied in function call, thus avoiding interactive
querying. This makes the filter functions suitable for use in
scripts. For example, if one wants to make 100 figures, the 100
interactive queries would be very cumbersome, therefore one can use
the filter functions instead.
COMMANDS
scripting::filter::g98cube -- loads the Gaussian98 CUBE file
scripting::filter::crystalInput -- loads the CRYSTAL input file
scripting::filter::pwscfInput -- loads the PWSCF input file
scripting::filter::pwscfOutput -- loads the PWSCF output file
scripting::filter::fhiInpini -- loads the FHI98MD inp.ini file
scripting::filter::fhiCoord -- loads the FHI98MD coord.out file
NAME
scripting::filter::g98cube
USAGE
scripting::filter::g98cube cube_file mo_index
PURPOSE
This proc is used in XCRYSDEN scripts to display a particular
molecular orbital (MO) from Gaussian cube-file by specifying the
"mo_index", which is the ID of the MO as specified in the Gaussian
cube-file. Using instead the "scripting::open --g98_cube cube_file"
proc will result in querying the mo_index. Hence this proc differs
from "scripting::open --g98_cube cube_file" in that the mo_index is
already specified explicitly and is therefore not queried.
ARGUMENTS
cube_file -- name of Gaussian cube file.
mo_index -- which Molecular Orbital to display
RETURN VALUE
Undefined.
EXAMPLE
scripting::filter::g98cube molecular_orbitals.cube 11
NAME
scripting::filter::crystalInput
USAGE
scripting::filter::crystalInput crystalInput_file
PURPOSE
This proc is used in XCRYSDEN scripts to display a the structure
from the CRYSTAL input file. Using instead the "scripting::open
--crystal_inp file" call will result in interactive query of some
action. Instead this proc immediately displays the structure and the
interactive query is turned off.
ARGUMENTS
crystalInput_file -- name of CRYSTAL input file.
RETURN VALUE
Undefined.
EXAMPLE
scripting::filter::crystalInput urea.c98
NAME
scripting::filter::pwscfInput -- Filter for PWscf-Input files
USAGE
scripting::filter::pwscfInput pwscfInput_file reduce ?itypNatList?
PURPOSE
This proc is used in XCRYSDEN scripts to display crystal structure
from PWSCF input file. It is similar to "scripting::open --pw_inp
file" call. The latter call will result in querying the atomic
numbers for PWscf version < 1.3, while this information is supplied
in the function call by itypNatList argument. One can also specify a
possible reduction of the structure dimensionality. For example, if
the structure is a molecule, then one can get rid of 3D unit cell,
by reducing the dimensionality to 0D.
ARGUMENTS
pwscfInput_file -- name of PWSCF input file.
reduce -- reduce dimenionality to "reduce"-D.
itypNatList -- used for PWSCF < 1.2 only.
PWSCF's ityp --> atomic-number (i.e. nat) mapping list.
The format of the list is the following:
{ityp1 nat1 ityp2 nat2 ...}
RETURN VALUE
Undefined.
EXAMPLE
scripting::filter::pwscfInput water.inp 0 {1 8 2 1} ; # for PWSCF < 1.2
scripting::filter::pwscfInput water.inp 0 ; # for PWSCF >= 1.2
NAME
scripting::filter::pwscfOutput -- Filter for PWscf-Output files
USAGE
scripting::filter::pwscfOutput option pwscfOutput_file reduce ?itypNatList?
PURPOSE
This proc is used in XCRYSDEN scripts to display crystal structure
from PWSCF output file. It is similar to "scripting::open --pw_out
file" call. The latter call will result in querying the atomic
numbers, ... Contrary, this information is supplied in the function
call by itypNatList argument (used only for PWSCF outputs <
1.2). One can also specify possible reduction of the structure
dimensionality. For example, if the structure is a molecule, then
one can get rid of 3D unit cell, by reducing the dimensionality to
0D. Since PWSCF output file may contains several structures, one
should specify which one to display using the option argument.
ARGUMENTS
option -- which structure to render. Possibilities:
--initcoor or -ic ... render initial structure
--latestcoor or -lc ... latest structure in the file
--optcoor or -oc ... optimized structure
--animxsf or -a ... extract all structure (animation)
pwscfOutput_file -- name of PWSCF output file
reduce -- reduce dimenionality to "reduce"-D
itypNatList -- used for PWSCF < 1.2 only.
PWSCF's ityp --> atomic-number (i.e. nat) mapping list.
The format of the list is the following:
{ityp1 nat1 ityp2 nat2 ...}
RETURN VALUE
Undefined.
EXAMPLE
scripting::filter::pwscfOutput --optcoor water.out 0 {1 8 2 1} ; # for PWSCF < 1.2
scripting::filter::pwscfOutput --optcoor water.out 0 ; # for PWSCF >= 1.2
NAME
scripting::filter::fhiInpini
USAGE
scripting::filter::fhiInpini fhiInpini_file reduce itypNatList
PURPOSE
This proc is used in XCRYSDEN scripts to display crystal structure
from FHI98MD inp.ini file. It is similar to "scripting::open
--fhi_inpini file" call. The latter call will result in querying the
atomic numbers. Contrary, this information is supplied in function
call of the scripting::filter::fhiInpini. Also one can specify
possible reduction of the structure dimensionality. For example, if
the structure is a molecule, then one can get rid of 3D unit cell,
by reducing the dimensionality to 0D.
ARGUMENTS
fhiInpini_file -- name of FHI98MD input file.
reduce -- reduce dimenionality to "reduce"-D
itypNatList -- FHI98MD's atomic-name --> atomic-number (i.e. nat)
mapping list. The format of the list is the following:
{name1 nat1 name2 nat2 ...}
RETURN VALUE
Undefined.
EXAMPLE
scripting::filter::fhiInpini inp.ini 0 {oxygen 8 hydrogen 1}
NAME
scripting::filter::fhiCoord
USAGE
scripting::filter::fhiCoord fhiCoord_file reduce itypNatList
PURPOSE
This proc is used in XCRYSDEN scripts to display crystal structure
from FHI98MD coord.out file. It is similar to "scripting::open
--fhi_coord file" call. The latter call will result in querying the
atomic numbers. Contrary, this information is supplied in function
call of the scripting::filter::fhiCoord. Also one can specify
possible reduction of the structure dimensionality. For example, if
the structure is a molecule, then one can get rid of 3D unit cell,
by reducing the dimensionality to 0D.
ARGUMENTS
fhiCoord_file -- name of FHI98MD input file.
reduce -- reduce dimenionality to "reduce"-D
itypNatList -- FHI98MD's atomic-name --> atomic-number (i.e. nat)
mapping list. The format of the list is the following:
{name1 nat1 name2 nat2 ...}
RETURN VALUE
Undefined.
EXAMPLE
scripting::filter::fhiCoord coord.out 0 {oxygen 8 hydrogen 1}
![[Figure]](img/xcrysden-picture-small-new.jpg)