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V_SIM(1) General Commands Manual V_SIM(1)

NAME

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

SYNOPSIS

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-column id ] [ fileToRender ]

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

OPTIONS

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

A complete list of options is included below.

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).

load the given resources file on startup instead of looking for a valid resources file in the standard locations.

show this little help.

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)

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.

policy used to show or not null modulus spins possible values are positives. (Default value: 0)

always draws atomic rendering on node position in addition to spin rendering.

the argument fileToRender must be called, then the given file of the option is used to colorize the elements.

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.

this option can be used with the '--colorize' one or the '--build-map' one. It chooses a preset color scheme. The id argument is an integer that corresponds to a defined color shade (ranging from 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.

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.

the argument fileToRender must be called, then the given file of the option is parsed as a list of planes and they are rendered.

the argument fileToRender must be called, then the given file of the option is parsed as a scalar field and loaded.

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).

the argument fileToRender must be given, then the given file of the option is parsed and surfaces are rendered.

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.

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

when positive, val isolines are plotted on the coloured map.

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])

if val is not TRUE, the surfaces use their own bounding box. (Default value: TRUE)

draw the given image on the background.

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).

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)

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)

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.

Give the precision in percent to render the coloured map. (Default value: 100)

Set the minimum and maximum values for the coloured map rendering. (Default value: auto)

Dump object signals and properties for introspection.

Range to adjust values into for colourisation. col specifiesthe column to apply the range to. Use -2, -1 and 0 for x, yand z directions respectively. (Default value: auto)

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

FILES

/usr/share/v_sim/v_sim.res specify all rendering informations from position of the camera to colour of the elements.
/usr/share/v_sim/v_sim.par specify all interface and non-rendering options 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.

AUTHOR

V_Sim was written by Luc Billard, Damien Caliste, Olivier D'Astier Aurélien Lherbier, Jérémy Blanc, Simon Planès, Thomas Jourdan and Yoann Ratao.

This manual page was written by Damien Caliste <damien.caliste@cea.fr>.

September 17, 2013