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| This is the homepage for the hands-on tutorial '''Laboratory of Quantum Simulation of Materials''' (LabQSM), | | This is the homepage for the hands-on tutorial '''Laboratory of Quantum Simulation of Materials''' (LabQSM), a university (master-level) class on electronic structure methods, with a particular focus on density functional theory (DFT). |
| a university (master-level) class on electronic structure methods, with a particular focus on density functional theory (DFT). | |
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| Starting from 2016/2017, this training material has been extensively used in Master degree in Physics of the University of Modena and Reggio Emilia (UniMoRe), fall term. | | Starting from 2016/2017, this training material has been extensively used in Master degree in Physics of the University of Modena and Reggio Emilia (UniMoRe), fall terms. |
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| | '''Authors and credits''': Andrea Ferretti and Daniele Varsano |
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| | * Next: [[Warming up with Unix commands]] |
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| == Getting Started == | | == Getting Started == |
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| In order to go through this tutorial you need to have access to a Unix/Linux machine, where you can run Unix terminals.
| | === Machine setup and Training material === |
| Software-wise, one needs the following:
| | * [[Getting Started#Machine setup| Machine setup]] |
| * One '''quantum engine''', i.e. a software able to run quantum mechanical DFT simulations. Here we consider [http://www.quantum-espresso.org Quantum ESPRESSO] (QE). During this class we'll be using QE-v6.5, though any version newer that 6.0 would do.
| | * [[Getting Started#Training material| Training material]] |
| * '''Structure visualization and builders''': applications like [http://www.xcrysden.org XcrySDen] or [https://jp-minerals.org/vesta/en/ VESTA](QE compatible structure visualization) and [https://avogadro.cc Avogadro] (molecular editor) will be used in the more advanced part of the class.
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| * General purpose '''scientific plotting tools'''. At least one of the following SW should be available: [https://plasma-gate.weizmann.ac.il/Grace/ (XM)Grace], [http://www.gnuplot.info Gnuplot], or python with [https://matplotlib.org matplotlib] support.
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| Several options are available:
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| * Opt1: Using the '''Quantum Mobile''' virtual machine (VM);
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| * Opt2: Connecting to '''existing machines''', compliant with the class, as provided by the tutors
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| * Opt3: Installing '''your own machine'''
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| === Opt1: Using Quantum Mobile ===
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| Quantum mobile is a ready-to-go VM, thought to provide all MaX flagship codes (incl QE) together with AiiDA seamlessly integrated in a plug-and-play linux (Ubuntu) environment. Quantum Mobile is [https://www.materialscloud.org/work/quantum-mobile available] on the [https://www.materialscloud.org MaterialsCloud] portal.
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| Step by step installation:
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| * Download the latest version of Quantum Mobile, following the link here: [ https://quantum-mobile.readthedocs.io/ https://quantum-mobile.readthedocs.io/]. By doing this you'll obtain a VM image.
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| * If not available, install [https://www.virtualbox.org VirtualBox] to run the Quantum Mobile VM.
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| * Double click on the Quantum Mobile to start the VM.
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| * At this point, you should see a virtualised Ubuntu OS. By opening a terminal you'll see that pw.x (and the other required executables) are available. Among others, all executables from the QE distribution, XcrySDen, Grace, gnuplot, and python are all pre-installed.
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| * The unix accounting within the VM is as follows:
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| user: max passwd: moritz
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| * Further information about Quantum Mobile installation can be found here: [https://github.com/marvel-nccr/quantum-mobile/releases/ https://github.com/marvel-nccr/quantum-mobile/releases/].
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| === Opt2: Connecting to existing machines ===
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| === Opt3: Installing the needed software in your own machine ===
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| If you want to use your desktop or laptop, be sure you have the following software installed:
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| * [http://www.quantum-espresso.org Quantum ESPRESSO] package | |
| * Structure visualization software ([http://www.xcrysden.org XcrySDen] or [https://jp-minerals.org/vesta/en/ VESTA])
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| * A molecular editor (e.g. [https://avogadro.cc Avogadro]) | |
| * General purpose '''scientific plotting tools'''. At least one of the following SW should be available: [https://plasma-gate.weizmann.ac.il/Grace/ (XM)Grace], [http://www.gnuplot.info Gnuplot], or python with [https://matplotlib.org matplotlib] support.
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| === Training material ===
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| In order to download the training material needed for this class, clone the [https://github.com/max-centre/LabCQM LabQSM] repository from [https://github.com/ GitHub], by issuing the command:
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| > git clone https://github.com/max-centre/LabCQM.git
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| No passed request is be prompted, and a folder called LabQSM is created locally. Inspect the contact of the folder by typing:
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| > ls LabQSM/
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| > LAB_1 LICENSE README.md docs tools
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| On every new lecture, or when mentioned by the tutors, update the repository by typing:
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| > cd LabQSM
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| > git pull
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| You are now all set and ready to start the hands-on part.
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| == Link to Selected Laboratories == | | == Link to Selected Laboratories == |
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| === Lecture 0: The Unix environment === | | === Module 0: The Unix environment (3h)=== |
| * [[Warming up with Unix commands]] | | * [[Warming up with Unix commands]] |
| * [[Bash scripting ]] | | * [[Scripting]] |
| | * [[Plotting and visualization tools]] |
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| | === Module 1: Basic DFT calculations and Convergences (9h) === |
| | * [[Structural and electronic properties of semiconductors and metals]] |
| | * [[Non self-consistent calculations: Band structures and Density Of States]] |
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| === Lecture 1: Basic DFT calculations and Convergences === | | === Module 2: DFT simulations of Molecules (6h) === |
| | *[[Electronic properties of isolated molecules]] |
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| === Lecture 2: DFT simulations of Molecules === | | === Module 3: Low dimensional structures (6h) === |
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| === Lecture 3: Surfaces and Low dimensional structures ===
| | *[[Electronic properties of 2D and 1D systems]] |