# &app; manual

# &app; Manual V&manrevision;

2006-2012
Jean Bréfort

&legal;

GNOME Documentation Project
Jean
Bréfort

     jean.brefort@normalesup.org

&app; Manual V&manrevision;
&date;

Jean Bréfort jean.brefort@normalesup.org

GNOME Documentation Project

&app; Manual V0.12.0
April 2010

Jean Bréfort jean.brefort@normalesup.org

GNOME Documentation Project

&app; Manual V0.10.0
October 2008

Jean Bréfort jean.brefort@normalesup.org

GNOME Documentation Project

&app; Manual V0.8.0
February 2007

Jean Bréfort jean.brefort@normalesup.org

GNOME Documentation Project

This manual describes version &appversion; of &app;.

## Feedback

To report a bug or make a suggestion regarding the &app; application or this manual, go to the &app; home page.

&app; is a chemistry elements periodic table application.

## Introduction

The &app; application is a chemical elements periodic table application. It provides scientific information on the elements and multiple table color schemes.

## Getting started

### To Start &app;

You can start &app; in the following ways:

Applications list

  Choose Periodic table of the elements. It might be listed either in the Education or Science category.

Command line

  Type `gchemtable`, then press Return.

### When You Start &app;

When you start &app;, the following window is displayed:

#### &app; window

Screenshot of the &app;window.

The &app; window contains the following elements:

Menubar

  The menus on the menubar contain all of the commands you need to work with &app;.

Periodic table

  A periodic table of the elements. The colors used for the buttons are conventional colors for the elements. Other color schemes are also available, as explained later.

When the mouse is moved over an element button, a popup window appears with some data about the element:

#### &app; window with an element tip.

Screenshot of the &app;window with an application tip.

## Usage

### Color Schemes

Several color schemes are available:

No colors

  All buttons are grey.

Default

  Conventional colors are used.

Physical state

  The color of the button depends on the physical state (solid, liquid, or gas) of the element at a given temperature. This temperature can be changed using the horizontal scale.

  #### Physical state color scheme

  Screenshot of the Main Page with Physical state color scheme.

  Elements with a black background indicate that the state is unknown at the given temperature.

Family

  The data used are the element family as given in the Blue Obelisk Data Repository.

  #### Family color scheme

  Screenshot of the Main Page with Physical state color scheme.

  If a family is selected, only elements of this family will be displayed with their family color used as a background. Other elements will have a black background.

Electronegativity

  The data used are the Pauling electronegativity as given in the Blue Obelisk Data Repository. Colors go from red (lowest electronegativity) to blue (highest electronegativity). If no data is available in the database, the element will have a black background.

  #### Electronegativity color scheme

  Screenshot of the Main Page with Electronegativity color scheme.

Atomic radius

  The data used are the atomic radii as given in the Blue Obelisk Data Repository. Colors go from red (lowest radius) to blue (largest radius). If no data is available in the database, the element will have a black background.

  #### Atomic radius color scheme

  Screenshot of the Main Page with Atomic radius color scheme.

Block

  Elements buttons are colored according to the block (s, p, d, or f) to which the element belongs

  #### Block color scheme

  Screenshot of the Main Page with Block color scheme.

### Element Window

This window shows the data for an element. To display it, press the corresponding element button in the periodic table. It is possible to display several element windows at once.

The data are spread over several pages, the following screenshots show the various pages for iron:

Main Page

  #### Main Page

  Screenshot of the Main Page.

Electronic Properties

  #### Electronic Properties Page

  Screenshot of the Electronic Properties Page.

Radii

  #### Radii Page

  Screenshot of the Radii Page.

Thermodynamic Properties

  #### Thermodynamic Properties Page

  Screenshot of the Thermodynamic Properties Page.

When a Show curve button appears on the same line as data, it is possible to display a chart of this data as a function of the element atomic number by clicking on the button.

## Charts

### Pre-defined Charts

When you click on the Show curve button in the element window you obtain a chart such as:

#### First ionization energy curve

Screenshot of the first ionization energy curve.

Some charts can also be displayed by selecting one of the items in Edit Element charts, except Custom which creates a custom chart.

Consecutive points are joined by a segment. The absence of a segment means that at least one data point is missing.

Charts can be customized as explained in the next section.

### Customize Charts

To customize a chart, choose File Properies in the chart window menu. The following dialog pops up:

#### Chart properties dialog.

Screenshot of the chart properties dialog.

The main elements in this dialog are:

The graph hierarchy tree.

  The graph hierarchy tree (top left) displays the current graph components and their hierarchy. The hierarchy can be modified using the buttons just below it.

The graph preview.

  The graph preview (top right) shows the result of the modifications and displays a scaled version of the graph you will get when you apply the changes.

The Add button.

  The Add button allows for insertion of new components into the hierarchy. Note that the list of available components to add depends on the object selected.

The arrow buttons.

  The arrow buttons can be used to modify the order of child objects of the same parent. These buttons are only available when ordering makes sense for the currently selected object. If you have, say, two charts in the graph, you can change the order in the hierarchy, and this will affect the order in which they are displayed.

The Delete button.

  Clicking the Delete button destroys the selected graph component and all its children. The button is not available when the component can't be removed.

  These deletions can't be undone, so be careful.

The component properties notebook.

  The component properties notebook (bottom) shows all the properties you can set for the current component.

The window title can't be changed, so if you customize a pre-defined chart, the title may no longer reflect what is displayed in the window.

&app; does not check the validity of the charts. It is possible add titles and labels not corresponding to the data actually used, in which case the resulting charts will not make sense.

Some features appearing in the dialog, such as error bars are not currently supported by &app;.

### User Defined Charts

A user can create a new empty plot, and then customize it as explained in the previous section.

To create a new empty plot, choose Edit Element charts Custom. This will open two new windows: one containing the new chart, and one containing the chart properties dialog.

#### New empty chart window

Screenshot of the new chart.

#### New empty chart properties dialog

Screenshot of the new chart properties dialog.

The graph contains just one empty chart. In most cases, the first thing to do is to add a new plot using the Add button as seen in next screenshot:

#### Adding a plot

Adding a plot to the chart.

This adds not only a plot, but also a backplane, the two needed axes, and a data series to the plot.

You can then select the data to use for the new series. Only predefined data vectors can be used. If X values are not selected, an integer series starting from 0 will be used; that is the atomic number minus one.

#### Data selection

Selecting data for the series.

Further customization is explained in the previous section.

### To Copy a Chart

To copy the chart, choose Edit Copy and then paste into the target application. Charts will be copied as native graphs to Abiword or as svg or png data to other applications which support such formats.

### To Export a Chart as an Image

To export the displayed chart to an image, use File Save As Image .

Available formats are SVG, EPS, PS, PDF, and formats that support writing in GdkPixbuf.

To choose a format, you can use an appropriate file name extension, or explicitly select a format in the combo box. With the first method, if &app; does not recognize an extension, the exported file will be a SVG file. &app; will add an extension to the file name if needed.

You might change the default width and height of the exported image using the appropriate entries.

Postscript and PDF files can also be produced using the File Print... command.

### To Print a Chart

To print the chart, choose File Print... .

File Preview opens a window with a preview of the printed output.

To tune the printed output, choose File Page setup... as explained below.

#### The page setup dialog.

The first tab of the dialog concerns the paper and margins setup. Headers and footers are not supported in the version of &app;

##### The Page Setup tab.

Screenshot of page setup dialog.

The second tab allows you to choose the scale of the output. With no scaling or scaling at 100%, the output will have the same size in points as the size in pixels on the screen. If you choose automatic scaling, you can make the output fill the available space either horizontally, vertically, or both (unchecking both options is equivalent to no scaling).

Printing to more than one page is not supported in this version of &app;

##### The Print Scale tab.

Screenshot of the printing scale page.

## Support.

### To Ask a Question

If you choose Help Ask a question, your mail client should pop up with a new message to the Gnome Chemistry Utils mailing list.

Another way to get some help is to connect on the #gchemutils IRC channel on the irc.gimp.net network and ask your question there (if you are not alone on the channel).

### To Find the Gnome Chemistry Utils on the Web.

If you choose Help Gnome Chemistry Utils on the web, the default web browser should pop up and display the main page for the Gnome Chemsitry Utils.

The main page is http://gchemutils.nongnu.org and the project page at Savannah http://savannah.nongnu.org/projects/gchemutils.

### To Report a Bug

To report a bug, you must use the bug page for the Gnome Chemistry Utils at Savannah. You can access it by choosing Help Report Bugs (hopefully you'll have only one at a time to report).

You can also use a web browser to go to the bug report page address directly. The bug repository is at https://savannah.nongnu.org/bugs/?group=gchemutils

## License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

A copy of the GNU General Public License is included as an appendix to the GNOME Users Guide. You may also obtain a copy of the GNU General Public License from the Free Software Foundation by visiting their Web site or by writing to

        Free Software Foundation, Inc.
        51 Franklin St - Fifth Floor
        Boston, MA 02111-1307
        USA