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| Job Manager | Energy Spectrometer |
Table of Contents
The Result Browser tool is used to browse the
contents of VNLFiles, i.e. files with
the extension .vnl.
Generally speaking, a VNLFile contains one or more objects that have been saved from a VNL session and/or from the execution of a script by ATK. These objects can be of the following kinds:
Samples: A sample contains one configuration (a molecule, bulk, or two-probe system) and it may as well contain any number of numerical data sets. These data sets are typically a physical property calculated with one of the “calculate” functions in ATK using the configuration stored in the same sample.
![[Note]](images/icons/note.png){kind=icon}
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There is no restriction for a user who wants to store data sets that are not correlated -- it is not a recommended practice but it is possible to store in the same sample, e.g., a given configuration, the electron density corresponding to a different configuration, and the energy spectrum of yet another configuration. |
Methods: The Method containing the definition of all the parameters needed to set up a computation with the exception of the configuration and the analysis options (only used for backwards compatibility with VNL 2.0).
NanoLanguage Scripts.
Tools: In previous versions of VNL, it has been possible to save so called “instruments” into VNLFiles. This practice is obsolete.
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The current version of VNL does not allow saving instruments (or tools) into VNL files. When reading old VNLFiles, the Result Browser will ignore any “instrument” found. Therefore, if an old VNLFile only contains tools, it would appear empty in the Result Browser. |
![[Important]](images/icons/important.png){kind=icon}
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With the mentioned exception of not reading “instruments” in a VNLFile, the Result Browser has full support for opening any VNLFile. |
To open the Result Browser tool, simply double click the corresponding icon in the Virtual NanoLab Toolbar. It will open in the state it was before it was closed, or empty if it hasn't been used in this session previously. It can also be opened by directly dropping a VNLFile from your file browser onto the Result Browser icon.
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If the VNLFile has been created with the current version of VNL, using the NanoLanguage Scripter, the name and location of the VNLFile is specified in the Analysis tab of the NanoLanguage Scripter, and can also be found and edited in the actual script. |
Therefore, to access the contents of a VNLFile, first locate the VNLFile on the file system, and do either of the following:
Drag-and-drop the VNLFile onto the Result Browser icon on the VNL Toolbar. The Result Browser opens and displays the contents of the file.
Double-click the Result Browser icon in the Toolbar. The Result Browser window opens. Then, drag-and-drop the VNLFile onto the left panel of the open Result Browser. The contents of the VNLFile will be displayed.
Simply drag-and-drop a file onto the Result Browser, or its icon, to load it in. What happens next depends on the kind of file that has been loaded:
If the loaded file is a NanoLanguage Script file, a corresponding new entry will appear on the left panel of the Result Browser. It presents information in two columns: the left column, labeled as Sample, presents the path and file name; while the right column, labeled as Description, shows the string: “NanoLanguage Script”.
If the loaded file is a VNLFile, a corresponding new entry will appear on the left panel of the Result Browser. In the left column, labeled as Sample, a sample label appears. A tree structure can be expanded by left-clicking at the left of that label. Once expanded, each numerical data set stored under that sample name is listed and can be selected individually. Note that each of these numerical data sets has a corresponding label, in the Sample column, and a corresponding description in the Description column.
Figure 56: The open Result Browser window. The frame to the left shows which samples and properties are present in the Result Browser - in this case a water molecule sample labeled H2O and a small two probe system labeled lih2li. In the right panel, you can see the configuration of the H2O sample represented as a script.
The Result Browser adds new samples as you drag-and-drop new VNLFiles to it. If you want to remove some of the samples from the Result Browser, you select the sample you want to remove and left-click the clear selected button. Note that you can only remove entire samples from the Result Browser, and not individual physical properties. Note also that this will not remove the property from the VNLFile. Similarly, you can clear all samples from the Result Browser by left-click the clear all button.
Once you have loaded one or more files into the Result Browser, its left panel will show a list of entries as described above. To visualize the contents of each of these entries, you only have to select them by left-clicking on them. The right panel of the Result Browser will react displaying information related to the selected entry in the left panel. The information shown in the right panel depends on what has been selected on the left, as follows:
If the selected entry on the left panel is a NanoLanguage Script, the right panel will present the corresponding text that is the script itself. Right-clicking on the text will trigger a context menu with the following entries:
Select All
Copy Ctrl+C
If the selected entry on the left panel is a numerical data set corresponding to an Energy Spectrum, the right panel will present a graphical representation of the energy spectrum as a 2D plot. Each of the graphically represented energy levels can be pointed at with the mouse cursor, to obtain its numerical value in a pop-up information text. Left-click to select a zoom area. Right-clicking on the right panel will trigger a context menu with the following entries:
Zoom in
Zoom out
Zoom reset
Export plot
Print plot
Whose use is also self-explanatory.
If the selected entry on the left panel is a numerical data set corresponding to a Transmission Spectrum, the right panel will present a graphical representation of the transmission spectrum as a 2D plot, see Figure 57. Each of the graphically represented transmission values can be pointed at with the mouse cursor, to obtain its numerical value in a pop-up information text. Left-click to select a zoom area. Right-clicking on the right panel will trigger a context menu with the following entries:
Zoom in
Zoom out
Zoom reset
Export plot
Print plot
Whose use is also self-explanatory.
If the selected entry on the left panel is a numerical data set corresponding to a 3D grid, such as those sets corresponding to the following physical quantities:
A message appears in the right panel of the Result
Browser indicating that the Nanoscope tool should be used to see these results.
Thus, to visualize these in VNL, drag-and-drop the sample from the Result
Browser to the Nanoscope icon on the
Toolbar. Then right-click and choose
Insert Plot. If your sample contains 3D grid data,
the menu items Contour plot,
Isosurface, and Volume
plot appears. From any of these menu entries, select the desired
physical property. The selected property will be visualized in the Nanoscope
window using the chosen 3D representation.
Consult one of the subsequent links, for further information regarding fine-tuning of contour, isosurface, and volume plots.
Figure 57: The open Result Browser window. The frame to the right shows the 2D plot for the transmission spectrum of the lih2li sample.
You may notice than when you drag a sample entry from the Result Browser an icon appears that depends on what kind of sample you are dragging. The specific icon is chosen according to the configuration type present in the sample (molecule, bulk, or a two-probe configuration). A summary of the different icon types is shown in the table below
If the selected entry on the left panel is a file of another kind, you might be able to visualize its contents in the right panel if it is a plain text file, but otherwise it will not be parsed or correctly visualized.
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| It is not a recommendable practice to use the Result Browser to visualize file contents other than those for which it has been specifically designed. |
Older versions of VNL (version ≤ 2.0) used the VNLFile format exclusively for all data storage. If you have any configuration, NanoLanguage script, or Method set-up stored using this format, just drag-and-drop them to the Result Browser, and access the data from there. For example, to extract a molecule stored in a VNLFile:
drop the VNLFile on the Result Browser
drag-and-drop the extracted sample on the Molecular Builder.
press Save to store the configuration as a NanoLanguage script.
Older versions of VNL used to store each session as one big VNL file, which was written to the file system when the program was quit. Since the Result Browser is the tool to read VNL files with, it is also used to access the content of old session files:
Windows: To access your old session files under Windows
Locate the folder C:\Documents and
Settings\username\.vnl\saves
Double-click the save you want to access, e.g. 2_0_0-r11620.
Drag-and-drop the icon, e.g.
1192135448.vnl, to the Result Browser.
Linux: To access your old session files under LINUX
Open your Home directory with your local file browser, i.e. double-click the icon for your Home directory on your desktop.
Select Show Hidden Files from the View
menu (alternatively use the Ctrl-H
shortcut) to show all hidden files.
Locate and double-click .vnl.
Double-click “saves”.
Double-click the save you want to access, e.g. 2_0_0-r11620.
Drag-and-drop the icon, e.g.
1192135448.vnl, to the Result Browser.
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If the Result Browser is empty (or unchanged if you have something in the Result Browser since previous) after you have dropped the VNL file, it means that you have not saved that particular session of VNL when quitting the program. Select another, chances are that you have had the same items on your LabFloor also in the following sessions. |
Once you have the VNL session file in the Result Browser, you have access to them by drag-and-dropping them from the sample label in the Result Browser to the tool icons on the Toolbar. If you want to store them on the disk you can do the following:
Configurations: drag-and-drop molecular configurations onto the Molecular Builder, or bulk and two-probe configurations onto the Atomic Manipulator and press the Save or Save As button.
Methods: drag-and-drop “methods” on to the Method Editor and press the Save or Save As button.
NanoLanguage scripts: drag-and-drop “scripts” onto the text editor icon and press the Save or Save As button.
Samples: individual samples cannot be extracted from VNLFiles and saved on the disk, you can always, however, drop it on the Nanoscope and visualize its contents.
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Since the configurations, scripts, and methods are stored as NanoLanguage script sections, they appear in plain text in the right panel that can also be copied and pasted into a text editor. |
Since the LabFloor has been removed, the import of XYZ-files has been moved to the Result Browser. To open a file, left-click the Open button and select one of the following file extensions
Python files
VNL files
XYZ files
Select a file and left-click Open. At present, these are the file formats that are currently supported. There are, however, programs that can convert various file formats to an XYZ file.
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In case you open an XYZ file and it does not have a name in the Result Browser sample field, it is most likely because the title line (the second line) of the XYZ file is empty. You can still use drag-and-drop from the empty configuration label. |
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| Job Manager |
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Energy Spectrometer |
