From b647db94a6b0663c13b2d543f124060c42b9ba84 Mon Sep 17 00:00:00 2001 From: Denis Kramer <d.kramer@soton.ac.uk> Date: Mon, 14 May 2018 16:08:23 +0100 Subject: [PATCH] Work on tutorial --- webpage/content/tutorials/cu-input-open.md | 20 +++++++++++++ webpage/content/tutorials/cu-input-run.md | 16 ++++++++++ .../tutorials/cu-input-walk-through.md | 29 +++++++++++++++++++ .../tutorials/first-dft-calculation.md | 13 +++++++++ webpage/content/tutorials/input-files.md | 24 +++++++++++++++ 5 files changed, 102 insertions(+) create mode 100644 webpage/content/tutorials/cu-input-open.md create mode 100644 webpage/content/tutorials/cu-input-run.md create mode 100644 webpage/content/tutorials/cu-input-walk-through.md create mode 100644 webpage/content/tutorials/input-files.md diff --git a/webpage/content/tutorials/cu-input-open.md b/webpage/content/tutorials/cu-input-open.md new file mode 100644 index 0000000..dfe3c36 --- /dev/null +++ b/webpage/content/tutorials/cu-input-open.md @@ -0,0 +1,20 @@ +--- +title: "Cu Input Walk Through" +date: 2018-05-14T14:29:26+01:00 +draft: true +position: 6 +--- + +# Copper example + +An example input for FCC copper is part of the examples. Let's have a look at it: + +```bash +cd exercises/Cu_bulk +``` + +The `cu.scf.in` file within this folder contains all that is needed to calculate the **total energy** of FCC copper. Let's have a look at it by starting a text editor + +```bash +subl cu.scf.in +``` diff --git a/webpage/content/tutorials/cu-input-run.md b/webpage/content/tutorials/cu-input-run.md new file mode 100644 index 0000000..41ce503 --- /dev/null +++ b/webpage/content/tutorials/cu-input-run.md @@ -0,0 +1,16 @@ +--- +title: "Cu run calculation" +date: 2018-05-14T15:34:14+01:00 +draft: true +position: 8 +--- + +# Running a DFT calculation + +OK. We are ready to do our first serious calculation: + +```bash +pw.x cu.scf.in | tee cu.scf.out +``` + +The first part of that command runs Quantum Espresso and feeds it the `cu.scf.in` input file. The second part deals with the output. `tee` is a little helper program that copies all output into a file. The `|` symbol is called a pipe and connects the output from `pw.x` to `tee`. diff --git a/webpage/content/tutorials/cu-input-walk-through.md b/webpage/content/tutorials/cu-input-walk-through.md new file mode 100644 index 0000000..991e236 --- /dev/null +++ b/webpage/content/tutorials/cu-input-walk-through.md @@ -0,0 +1,29 @@ +--- +title: "Cu Input Walk Through" +date: 2018-05-14T15:34:14+01:00 +draft: true +position: 7 +--- + +# Input file format + +You can find a detailed description of the file format on the [Quantum Espresso webpage](https://www.quantum-espresso.org/Doc/INPUT_PW.html). + + +## Namelists + +There are three **mandatory** `NAMELIST`s: + +- `&CONTROL` contains input variables that control the type of calculation performed and the amount of I/O +- `&SYSTEM` contains input variables that specify the system. Most notably the Bravais lattice +- `&ELECTRONS` describes the algorithm used to reach a self-consistent solution of the Kohn-Sham equations + +> Note: There are other (optional) `NAMELIST`s with more configuration variables. + +## Cards + +There are three *mandatory* `CARD`s: + +- `ATOMIC_SPECIES` contains information about the atoms. At the moment, this is only Cu. You will see the symbol for copper, it's atomic mass, and a filename describing the core electrons. More on this later. +- `ATOMIC_POSITIONS` holds the positions of all atoms in the unit cell as fractions of the lattice vectors. Note that we have only one atom specified although the FCC unit cell contains four atoms. We have already told the code that we have an FCC lattice (`ibrav=2` under `@SYSTEM`), and all atoms in an FCC unit cell are related by symmetry. So you only need to specify the unique atoms per unit cell. +- `K_POINTS` defines the number of points and weights used for the first [Brillouin zone](https://en.wikipedia.org/wiki/Brillouin_zone). Parts of the calculations are performed in reciprocal space, and the the `K_POINTS` card defines the accuracy (and cost) of these. diff --git a/webpage/content/tutorials/first-dft-calculation.md b/webpage/content/tutorials/first-dft-calculation.md index 9319d60..daa140f 100644 --- a/webpage/content/tutorials/first-dft-calculation.md +++ b/webpage/content/tutorials/first-dft-calculation.md @@ -8,3 +8,16 @@ draft: true # Time for Espresso Let's jump right into it. We will use an open-source DFT code called [Quantum Espresso](https://www.quantum-espresso.org/). This is a large code with many capabilities, developed by an international community. + +Let's start the code by typing + +```bash +pw.x +``` + +You will see in the terminal output from the code. It tells you which version of the code you are running and how to cite it should you choose to publish your results. + +> Please do cite the relevant papers if you do serious work. Without recognition, they will not be able to improve the code in the future! + +Finally, it is `Waiting for input...`. You now could give the code instructions by typing into the terminal. But it is much better to provide an input file. So let's quit the +program for now with ```Ctrl+c```. diff --git a/webpage/content/tutorials/input-files.md b/webpage/content/tutorials/input-files.md new file mode 100644 index 0000000..3c2422b --- /dev/null +++ b/webpage/content/tutorials/input-files.md @@ -0,0 +1,24 @@ +--- +title: "Input Files" +date: 2018-05-14T14:21:30+01:00 +draft: true +position: 5 +--- + +# Getting material + +You should be back in the command prompt. You should see your login name and the directory where you are to the left of the cursor. + +Let's get some material to work with. We will use `git`, a version control software for this. Type + +```bash +git clone https://git.soton.ac.uk/CHEM6136/exercises.git +``` + +What just happened? `git` fetched some pre-made files for us by checking out a repository from the universities version control system. Version control a great way to keep track of changes to text files etc. You are welcome to learn more about it. But not right now. + +You have a new directory called `exercises`. Check it: + +```bash +ls +``` -- GitLab