Virtual Nanolab
VNL offers a wide range of tools for building atomic geometry for molecules, crystals, nanostructures, and devices. These tools include a surface cleaver and interface builder, a polycrystalline builder, a molecular builder, and a passivation tool for surfaces. Moreover, thanks to a high-performance shader-based rendering engine for very large data sets, 1M atoms and bonds can be drawn and managed very easily. One of the characteristic examples of VNL plugins is the VASP Scripter.
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It provides an effective machinery that works in two directions: on the one hand, you can build your structures in VNL and export them with your input files, and on the other, you can analyze the results of your VASP calculations in VNL. Features:.
Input file generation via interactive scripter, supporting most VASP functionality. Read data files for plotting and data analysis (OUTCAR, CONTCAR, CHGCAR, DOSCAR, EIGENVAL, CHG, PARCHG, ELFCAR, XDATCAR). Plot band structures, DOS, etc. Generate initial NEB paths using the IDPP method. Visualize NEB paths and barriers.
Import and analyze MD trajectories. Visualize vibrational modes. VNL is available for Linux, Windows, and Mac OS through self-contained binary installers – no compilation needed, and no external library dependencies beyond standard OS packages.
If you work as an academic researcher at a university, high school, or similar (but not including government labs), you can obtain a free, perpetual license for Virtual NanoLab by filling out. Aggiornamento software galaxy s plus i9001. Free VNL does not include the VASP functionalities, and for that, you must purchase a license. More information can be found.
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Downloads & Links There are two different ways to start up VNL:. by clicking the VNL icon on the Desktop;. by executing the vnl command in a terminal. When doing one of these, the Open Project window will appear. It allows you to manage projects and open one of them.
Each project must be given a suitable title and a local path for storing project files. Use the Create New button to add a new project. Once you have selected a project and clicked Open, the VNL main window will show up.
Virtual Nano Laboratory
The following sections will introduce the main parts of Virtual NanoLab and the functionalities each part offers. Building atomistic structures The Builder is a graphical interface for building any desired nanoscale structure. The Stash contains the configurations you have built in the current project, and an ever expanding list of tools and plugins can be used to manipulate the structures. A Stash item must be active in order to apply an operation by one of the Builder tools. Once an item is activated, it is visualized in the 3D View. You can also apply operations on a Stash item such as rename, copy, and delete. When you have finished building your configuration, use the Send to button (located in the lower-right corner of the Builder window) to transfer it to the Script Generator and set up the desired calculations.
This is the topic of the next section. Script Generator ATK is executed using Python scripting, and the Script Generator is a graphical interface for generating ATK Python scripts – it allows you to graphically add blocks of Python code to the script and edit relevant settings if needed. Simply double-clik a block in the left-hand panel (named Blocks) to add it to the Script in the right-hand panel. The order of the blocks, from top to bottom, defines the workflow of the ATK calculation. All data from the ATK calculation is saved in the Default output file. It should have file extension.nc, indicating that it is a NetCDF file type.
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Once you have finished setting up the ATK Python script, you can save it with file extension.py and then execute it on a supercomputing cluster or in a terminal on your local machine. Analyzing the results Data analysis and visualization is the final step in the most basic VNL-ATK workflow: You have built a nanostructure, calculated the electronic structure at some level of theory, and have most likely performed some post-SCF analysis, e.g. Computed the electron density and band structure. It is time to visualize the results and perhaps perform further analysis. The Project Files panel shows at all times the contents of the project folder you specified when creating the project (unless filtering is used). This includes ATK scripts (.py), ATK data files (.nc), log files, images, and any other standard file type. Next, the LabFloor shows the contents of the selected (ticked).nc data files.
VNL reads the data as individual Python objects, and displays each object as an easily recognizable item on the LabFloor. In the figure below, the data file GaAs(100).nc contains three saved data items: The band structure, the bulk configuration, and the electron density. Finally, the Panel Bar offers an extensive list of analysis and visualization tools that can be applied to the selected LabFloor item(s).
This way, the LabFloor and Panel Bar constitute in total a graphical interface for analyzing and visualizing the data generated by running simulations. Note The LabFloor will show all the objects saved in a.nc data file, and the contents of newly generated files are automatically added to the LabFloor. Ticking/unticking a file in the Project Files list adds/removes its contents from the LabFloor. A LabFloor item must be selected in order to apply an analysis tool to it. Panel Bar tools that cannot be applied to a selected item type are greyed out. The Viewer is one possible analysis tool – it is used to visualize configurations as well as grid quantities (e.g.
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Electron density). Please proceed to the next chapter.