XCrySDen --
(X-Window)
	      CRYstalline Structures and DENsities

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XCrySDen Scripting Documentation

Table of Contents
    Scripting/scripting::filter
    Scripting/scripting::filter::g98cube
    Scripting/scripting::filter::crystalInput
    Scripting/scripting::filter::pwscfInput
    Scripting/scripting::filter::pwscfOutput
    Scripting/scripting::filter::fhiInpini
    Scripting/scripting::filter::fhiCoord


Generated from scriptingFilter.tcl with ROBODoc v3.2.4 on Wed May 25 16:04:51 2005


Scripting/scripting::filter

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 
 

Scripting/scripting::filter::g98cube

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

Scripting/scripting::filter::crystalInput

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

Scripting/scripting::filter::pwscfInput

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

Scripting/scripting::filter::pwscfOutput

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


Scripting/scripting::filter::fhiInpini

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}

Scripting/scripting::filter::fhiCoord

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}

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This document was last modified on Wed Oct 7 16:12:19 CEST 2015