ThirdYearMgOExpt-1415

Thermal Expansion of MgO

This is the welcome page for the elective MgO component of the third year computational chemistry labs for 2018/19.

The computational lab will be from 10:00 to 17:00 on Monday, Tuesday, Thursday and Friday. During these 4 days demonstrators will be available in the computer room to answer all your questions.

The start date is given in the table below according to the session.

There is an introductory lecture to the lab in Room 235 at 10:00 on the Start Date of your session.

The deadline is at 12:00 of the day indicated in the table below ("Report Deadline").

Work submitted late will be penalised.

There's a link set up on Blackboard for submitting the report and the Jupyter notebooks in the folder 3rd Year Chemistry Laboratories (2018 - 2019) / Y3C Third Year Computaqtional Laboratory/.

In each exercise there are a number of explicit Questions and often also an opportunity to Speculate on the results obtained. The final report will be expected to contain answers to these questions and, where you feel able, further speculation.

Questions related to this computational experiment can be directed to Prof. Nicholas Harrison and Dr Giuseppe Mallia.

Introduction

The properties of materials (solids, liquids, gasses) are a statistical average over the many different energy states of the molecules making up the material. The vibrational free energy of H2 can be computed analytically by summing over the harmonic vibrations of the molecule. This cannot be done by hand for a real material containing many atoms.

In this laboratory you will use a simple model of atomic interactions to calculate the energy and vibrations of a crystal of MgO. These vibrational energy levels will then be used to compute the free energy of the crystal and to predict how the material expands when heated. In the last final stage you will go beyond the harmonic (and quasi-harmonic) approximation and expand the crystal using a technique called molecular dynamics - essentially reproducing the actual vibration motions of the atoms. Fortunately the computer will do most of the work !

Instructions

- Download the Jupyter Notebooks: Here

- Open Jupyter Notebook.

- Run the The_lab.ipynb

- Follow the instructions in the notebook.

Please, make a copy of the Jupyter notebooks, just in case you mess up with the code.

Previous years related contents

- Maths and Physics for Chemist

- Thermodynamics

- Statistical thermodynamics

- Python

Good skills on python is not a requirement. All the scripts are written in a way where you only need to write an input value (e.g. Temperature = 300 K). However, feel free to edit and play with the scripts.

New contents

- Phonons and reciprocal space

- Quasi-Harmonic approximation

- Molecular dynamics

Submission

The report will be written with a scientific report style in a Jupyter notebook.

Please, submit all the files (including the lab notebooks) via Blackboard.

Write up

Some guidelines about writing a scientific report:

Scientific report structure:

• Title
• Abstract
• Introduction
• Methodology
• Results and discussion
• Conclusions
• Bibliography
• Appendices (optional)

Tips:

• The golden rule: Aim for clarity
  • Structured statements that flow in a logical manner.
  • Good use of diagrams and appropriate level of theory.
  • Careful choice of content.

• Keep your language clear and simple.
• Correctly label all tables and figures. This should be self-contained, which means that it should be interpretable by itself.
• Appropriate referencing of figures and tables.
• Cite previous works (with an accepted citation style) whenever is appropriate.

Abstract:

• The Abstract is an informative summary of what you did and what you found out. It should be self-contained, which means that it should contain a very short description of the objectives, methodology, results and conclusions.

Introduction:

• The purpose of the Introduction is to put the reader in the context of the research. It may contain a brief review of previous research, why the research was undertaken, an explanation of the techniques and why they are used and why it is important in a broader context.

Methodology:

• The Methodology is a description of the materials, techniques and procedures used. It is not necessary to include every single detail of the experiment but there has to be enough information so that someone can reproduce the study.

Results and discussion:

• The Results and Discussion tells what it has been found in the research and the interpretation of the findings. It includes figures and tables whenever practical.
• Compared or contrast the results with the literature.
• Described and explain possible sources of errors.

Conclusions:

• This is a summarise of the arguments and findings of the research and it should be related back to the Introduction. If appropriate, suggest improvements or additional experiments.

Suggested Time Frame

Try to finish all the calculations by Thursday. All the calculations takes seconds, however, it takes time to analyse the results and understand all the new concepts that you will learn in this lab.

Mark Scheme

The break-down for the marks for this lab are as follows:

Presentation	10%
Introduction and Methodology	25%
Results and Discussion	55%
Conclusions	10%

Plagiarism

Submissions are checked for plagiarism. External images may be used if correctly cited, but it's always better to create your own.

Demonstrators

The demonstrators will be Victor Chang and Carles Rafols i Belles . They will be available in the computer room from 10:00 to 11:00 and from 2:00 to 3:00.

Feel free to contact them in the lab or via email.

Related literature

How Chemistry and Physics meet in the Solid State by Roald Hoffman

Introduction to Lattice Dynamics. Dove, Martin T. (ebook available in the library)

Installation of the lab in your personal computer

The lab uses Gulp for all the calculations. Jupyter Notebook and python is used as interface between the user and Gulp. This is optional and is under your responsibility. People in charge of the lab or ICT will not provide support for this.

To install the lab in Windows:

1. If you do have anaconda installed you can go to point 3.

2. Download and install Anaconda

3. Download the ASE package.

4. Download GULP from the website. Download version 4.3 which has the executable for Windows ready to download.

5. Copy Gulp to c:\gulp-4.3.

6. Sets a system environment variable for GULP_LIB to C:\gulp-4.3\Libraries and add C:\gulp-4.3\Exe to the PATH system variable.

7. Copy the ionic.lib file that you will find in the library folder you downloaded to the $GULP_LIB folder

To install the lab in Linux/Unix:

1. If you do have conda installed you can go to point 6.

2. Open a terminal and create a new conda environment: conda create -n TE_lab

3. Activate the environment: source activate TE_lab

4. Install ASE: conda install -c conda-forge ase

5. Install Jupyter: conda install -c anaconda notebook

6. Download GULP from the website. The version 5.0 only has the source files. Download this one if you feel comfortable with compiling it by yourself. Otherwise, download version 4.3 which has the executable ready to download.

7. Set $GULP_LIB and $ASE_GULP_COMMAND in your ~/.bashrc or ~/.bash_profile (see this page for more information)

8. Copy the ionic.lib file that you will find in the library folder you downloaded to the $GULP_LIB folder