Table of Contents:
This section describes how to install Virtual NanoLab (VNL) with Atomistix ToolKit (ATK) 2017 on Windows and Linux.
In principle, it’s very easy:
WARNING: Feature Not Licensed to Work on a Virtual Machine and is Ignored; libGL Warning: 3D Driver Claims to Not Support 0x5b (Err:20) Feature Not Allowed to Run on a Virtual Machine (Err:19) Feature Not Allowed to Run on Terminal Server Clients (Err: 10) Hostid Does Not Match License (Err: 6) Unable to Read File; glibc Detected. H2020,VNL,SMEInst-02-2016-2017,QUANTUMWISE A/S(DK) Objective. BUSINESS MODEL: QuantumWise (QW) has developed a new cross-disciplinary platform – Virtual NanoLab (VNL) – which integrates materials/nanotechnology simulation simulation engines through a plug-in mechanism. The latest version of Virtual NanoLab is 2016.2 on Mac Informer. It is a perfect match for Viewers & Editors in the Design & Photo category. The app is developed by QuantumWise.
- There are many damaging, virus-infected applications on the Internet. Only download applications onto your computer from trusted, verified sources! System requirements. You can find the system requirements for the Virtual NanoLab application on the application's website and the application's manual.
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- Download the installer from the QuantumWise website.
- Run it, and follow the step-by-step instructions.
- Start VNL and follow the step-by-step instructions to obtain/install/configure the license.
Below you will find a few more details on each topic.
Note
It is recommended to uninstall previous versions of VNL and ATK before installing a new version. This is mainly to avoid confusion;two versions can be installed alongside each other without problems, but you will have to take care which version you run, especially from the command line.
Installing on Windows and Linux¶
Virtual NanoLab is distributed as a binary installer package which also includes Atomistix ToolKit (ATK), the calculation engine.╾◉ INSTALLING VNL-ATK ON WINDOWS | ╾◉ INSTALLING VNL-ATK ON LINUX |
---|
The installation process has the following simple steps (watch also the videos above for more details):
Download the installer for your platform from the QuantumWise website.
Double-click the downloaded file, or (on Linux) run it from the command line as
./VNL-ATK-2017.0-Linux64.bin
in the directory where you saved the file. You may first need to add the execute permission to the downloaded file by typingchmod+x./VNL-ATK-2017.0-Linux64.bin
.Follow the step-by-step instructions to read and approve the license agreement, choose the installation directory, etc.
From the final page of the installer you can open VNL, which will assist you in configuring the license.
Note
It is not necessary to have administrator rights to install on Windows.However, if you do not have administrative rights you will need to install the program in a differentdirectory than the default location (C:ProgramFiles(x86)QuantumWise
).
Launching the program¶
The installer simplifies the process of launching VNL/ATK in several ways:
- On Windows and Linux, a shortcut icon is added to the Desktop, which you can double-click to start Virtual NanoLab.
- On Windows, shortcuts are also placed in the Start Menu, under QuantumWise ‣ Virtual NanoLab 2017.
Note
- On Windows, you should allow VNL to access the network, when prompted.
Running ATK from the command line¶
Running calculations with ATK, both in serial and parallel, can either be done from within VNL, using the Job Manager, or from the command line, which is typically the choice when you work on a cluster.
You execute a Python script with ATK like this:
To run in parallel from the command line, you also need to use mpiexec
, as described in the separate Parallel Guide to ATK.
Note
- On Windows and Linux, the binary directory for the ATK command-line interpreter (
atkpython
) and Virtual NanoLab (vnl
) are added to the system PATH, so that you can issue these commands from anywhere on your system. - On Linux, before you can start VNL or ATK from the command line after the installation, you need to open a new terminal window for the new PATH to take effect.
Tip
If you start atkpython
without any command line argument, you will enter interactive mode where you can issue Python commands directly on the command line (like, for instance, in Matlab).Press Ctrl+D
to quit the interactive mode.
The first time you run atkpython in interactive mode, it will display some configuration information.
Unattended installation¶
It is possible to run the installer in so-called unattended mode, for instance for automatedinstallations of a network of computers.In this mode, the installer will not prompt the user for any information but will insteaduse default settings for each parameter (like installation directory) or values givenas command-line arguments.
We will call the installer binary VNL-ATK-2017.0-Linux64.bin
in the example below;running in unattended mode can only be done from the command line.
To install VNL in unattended mode, run:
Tip
Custom parameters can be defined through command line switches; for a full list of these, type
For example, to to specify another installation location than default, use the option --prefix
.
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For more information, see the BitRock documentation.
Uninstalling ATK and VNL¶
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To uninstall ATK and VNL on
- Linux: run the binary
uninstall
in the installation directory, or just delete the installation directory (you will only have to remove the PATH manually from your.bashrc
and.profile
files to clean up completely); - Windows: either use the Control Panel, or launch the uninstaller from the Start Menu, under QuantumWise ‣ Virtual NanoLab 2017;
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