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V_SIM(1)		    General Commands Manual		      V_SIM(1)

       v_sim - a GTK program for 3D visualisation of atomic systems

       v_sim [-e file ]	[-r file ] [-h ] [-g _w_x_h_ ] [-s file	] [-m id ] [-a
       ] [-c file ] [-u	l:m:n ]	[-d id ] [-t x:y:z ] [-x x:y:z ]  [-p  file  ]
       [-f  file  ] [-v	v[:v] ]	[-i file ] [-b id[:id] ] [--log-scale id ] [-n
       val ] [--color-iso-lines	[R:G:B]	or auto	] [--fit-to-box	val  ]	[--bg-
       image  file ] [-o id=value ] [-w	mode ] [--i-set	i ] [--value-file file
       ] [--map-precision prec ] [--map-clamp min:max or auto ]	[--introspect-
       dump  fileToDump	] [--color-clamp col#min:max or	auto ] [--scaling-col-
       umn id ]	[ fileToRender ]

       This manual page	documents briefly the v_sim commands. It is a software
       to visualise atomic structures with OpenGl rendering.

       This  program  follows the usual	GNU command line syntax, with long op-
       tions starting with two dashes (`-').

       A complete list of options is included below.

       -e, --export file (from v3.0.0)
	      make an image from the  fileToRender  argument.  The  format  is
	      specified	 through  the  extension  of the argument or by	the -o
	      fileFormatId=id option (get the id  of  available	 file  formats
	      with -o list).

       -r, --resources file (from v3.4.0)
	      load  the	given resources	file on	startup	instead	of looking for
	      a	valid resources	file in	the standard locations.

       -h, --help (from	v3.0.0)
	      show this	little help.

       -g, --geometry <w>x<h> (from v3.0.0)
	      specify the size of the rendering	window,	the size argument must
	      have  the	 following  format: <width>x<height> with positive non
	      null values. (Default value: 600x600)

       -s, --spin-file file (from v3.1.0)
	      use the given argument as	a spin indicator. If  this  option  is
	      used,  V_Sim  switches  automatically to spin rendering whatever
	      method is	specified in the parameter file.

       -m, --hiding-mode id (from v3.2.0)
	      policy used to show or not null modulus  spins  possible	values
	      are positives. (Default value: 0)

       -a, --spin-and-atomic (from v3.3.0)
	      always  draws  atomic  rendering on node position	in addition to
	      spin rendering.

       -c, --colorize file (from v3.1.0)
	      the argument fileToRender	must be	called,	then the given file of
	      the option is used to colorize the elements.

       -u, --use-column	l:m:n (from v3.1.0)
	      it specifies the columns to use from the data file for the three
	      colour channels [l;m;n]. Columns are counted from	1. Use -3, -2,
	      -1 and 0 to use the special values, constant 1, coord. x,	coord.
	      y, and coord. z, respectively.

       -d, --color-preset id (from v3.1.0)
	      this option can  be  used	 with  the  '--colorize'  one  or  the
	      '--build-map'  one. It chooses a preset color scheme. The	id ar-
	      gument is	an integer that	corresponds to a defined  color	 shade
	      (ranging from 0).

       -t, --translate x:y:z (from v3.3.0)
	      a	 file must be loaded. It applies the given translations	to the
	      loaded file. The units are those of the file. This is  available
	      for periodic file	formats	only.

       -x, --expand x:y:z (from	v3.4.0)
	      a	 file  must  be	 loaded. It applies the	given expansion	to the
	      loaded file. The values are given	in box	coordinates.  This  is
	      available	for periodic file formats only.

       -p, --planes file (from v3.2.0)
	      the argument fileToRender	must be	called,	then the given file of
	      the option is parsed as a	list of	planes and they	are rendered.

       -f, --scalar-field file (from v3.3.0)
	      the argument fileToRender	must be	called,	then the given file of
	      the option is parsed as a	scalar field and loaded.

       -v, --iso-values	v[:v] (from v3.3.0)
	      must  be	used  with the '--scalar-field'	option,	then the given
	      surfaces are built and rendered. If a  name  is  appended	 to  a
	      value  using  '#'	 as a separator, this name is used as the name
	      for the iso-surface (i.e.	0.25#Blue).

       -i, --iso-surfaces file (from v3.2.0)
	      the argument fileToRender	must be	given, then the	given file  of
	      the option is parsed and surfaces	are rendered.

       -b, --build-map id[:id] (from v3.4.0)
	      the  argument  fileToRender  must	 be  given, as the '--planes',
	      '--color-preset' and '--scalar-field'  options  used,  then  the
	      given  plane  'id'  is  replaced	by  a coloured map using given
	      scalar field and shade. 'id' ranges from 0. If several  ids  are
	      given, several maps are built.

       --log-scale id (from v3.4.0)
	      select  the  scaling method to use with gradients	(0: linear, 1:
	      log scaled and 2 is zero-centred log scale), default  is	linear

       -n, --n-iso-lines val (from v3.4.0)
	      when positive, val isolines are plotted on the coloured map.

       --color-iso-lines [R:G:B] or auto (from v3.5.0)
	      when  given,  generated iso-lines	are colourised [R:G:B] or auto
	      with the values. The specific value 'auto'  will	produced  iso-
	      lines in inversed	colours. (Default value: [0:0:0])

       --fit-to-box val	(from v3.3.0)
	      if  val  is  not	TRUE, the surfaces use their own bounding box.
	      (Default value: TRUE)

       --bg-image file (from v3.4.0)
	      draw the given image on the background.

       -o, --option id=value (from v3.3.0)
	      this is a	generic	way to give extended option. to	V_Sim. As much
	      as  -o can be used. Each one store a key and its value (boolean,
	      integer or float).

       -w, --window-mode mode (from v3.5.0)
	      used to choose the windowing mode. By default the	command	 panel
	      and  the rendering window	are separated. In the 'oneWindow' mode
	      they are joined. In the 'renderOnly' mode, the command panel  is
	      not used.	(Default value:	classic)

       --i-set i (from v3.5.0)
	      this  flag  is  used  to choose the id of	the loaded file	if the
	      format has support for multiple ids in one file (see XYZ	format
	      or -posi.d3 ones). (Default value: 0)

       --value-file file (from v3.5.0)
	      specify  an XML file with	some value information for V_Sim, like
	      a	list of	planes,	highlighted nodes... It	 replaces  and	extend
	      the previous --planes option.

       --map-precision prec (from v3.5.0)
	      Give  the	 precision in percent to render	the coloured map. (De-
	      fault value: 100)

       --map-clamp min:max or auto (from v3.6.0)
	      Set the minimum and maximum values for the coloured map  render-
	      ing. (Default value: auto)

       --introspect-dump fileToDump (from v3.6.0)
	      Dump object signals and properties for introspection.

       --color-clamp col#min:max or auto (from v3.7.0)
	      Range  to	adjust values into for colourisation. col specifiesthe
	      column to	apply the range	to. Use	-2, -1 and 0 for x, yand z di-
	      rections respectively. (Default value: auto)

       --scaling-column	id (from v3.7.0)
	      used with	a data file (see -c), it specifies the column id to be
	      used to scale the	nodes.

       /usr/share/v_sim/v_sim.res specify all rendering	informations from  po-
       sition of the camera to colour of the elements.
       /usr/share/v_sim/v_sim.par  specify all interface and non-rendering op-
       tions such as the positions of the panels.
       ~/$XDG_CONFIG_DIR/v_sim a directory  where  overloading	v_sim.res  and
       v_sim.par can be	put.

       V_Sim  was  written  by	Luc  Billard, Damien Caliste, Olivier D'Astier
       AurA(C)lien Lherbier, JA(C)rA(C)my Blanc, Simon PlanA"s,	Thomas Jourdan
       and Yoann Ratao.

       This manual page	was written by Damien Caliste <>.

			      September	17, 2013		      V_SIM(1)


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