EUROPE school and Erasmus Mundus Master 'Chemical Nanoengineering': Wrocław University of Science and Technology (Politechnika Wrocławska), Wrocłow, Poland
Local organizers Wroclaw University of Science and Technology (Politechnika Wrocławska):
- prof. Bogdan Kuchta
- dr Elżbieta (Ela) Zienkiewicz
Organizers and lectures:
- Dr. David Dubbeldam
- Prof. Randall Q. Snurr
- Prof. Sofía Calero
- Prof. Thijs J.H. Vlugt
About the school
The school focuses on a practical understanding of molecular simulations of fluids, ionic liquids, and nanoporous materials and applying the RASPA molecular simulation code to practical examples. The duration is 3.5 days, with lectures in the morning and exercises in the afternoon.
Students will learn the theoretical foundations of Molecular Dynamics and Monte Carlo with the aim of understanding the benefits and limitations of the algorithms, as well as the practical side of performing molecular simulations: setting up the system, constructing input files for molecules and frameworks, choosing and setting up a force field, understanding input settings, and analyzing the results. We will use our publicly available code RASPA for the workshop, but the gained knowledge and understanding are also directly applicable to other software.
Program
Monday 1 July 2019
| Day 1 Time | Lecturer | Content |
|---|---|---|
| AM Lectures | ||
| 8.30-9.00 | Registration | |
| 9.00-10.00 | Sofia Calero | Introduction to the course, introduction to the field of molecular simulation. Introduction to simulations: classical simulations, periodic boundary conditions, force fields (electrostatics, VDW interactions, intramolecular interactions). |
| 10.00-10.30 | Coffee-break | |
| 10.30-11.30 | Randall Snurr | Simulation setup and measuring properties. Introduction to simulation research of nanoporous materials, description of frameworks (IZA, CoRE MOF), simple calculations of pore volume, surface area, blocking pockets. |
| 11.30-12.30 | David Dubbeldam | Overview of the RASPA code, showing the manual, demo running RASPA, iRASPA for linux, demo of the linux live-usb environment. |
| PM Practical Hands-on Exercises | ||
| 13.30-17.00 | David Dubbeldam | Monte Carlo of methane in a box. |
| Investigating framework structures. | ||
| Methane in LTA-type zeolite. | ||
| Energy distributions of methane and CO2 in LTA and MFI | ||
| Where is the CO2 located in LTA-type zeolite? | ||
| Ship cruise on the Odra river and the conference dinner | ||
| 18.45 | meeting at the entrance of the Main Building | |
| 19.00-19.30 | ship cruise | |
| 20.00-20.30 | start of the conference dinner at the Marina restaurant | |
Tuesday 2 July 2019
| Day 2 Time | Lecturer | Content |
|---|---|---|
| AM Lectures | ||
| 9.00-10.00 | Randall Snurr | Molecular dynamics (MD) simulation, solving Newton’s equations of motion, NVE and NVT (thermostats). |
| 10.00-10.30 | Coffee-break | |
| 10.30-11.30 | Sofia Calero | NPT-MD and other ensembles, computing dynamic properties (e.g. diffusion), TST-methodology for rare-events. |
| 11.30-12.30 | David Dubbeldam | Visualization (for RASPA with VTK), plotting (gnuplot, plotting output of RASPA), and custom input for RASPA. |
| PM Practical Hands-on Exercises | ||
| 13.30-17.00 | David Dubbeldam | Radial distribution functions (RDF) in a fluid. |
| Self-diffusion in a fluid. | ||
| Self- and collective diffusion of methane in MFI. | ||
| Self- and collective diffusion of methane in LTA. | ||
| Transition State Theory (TST) for slow diffusion (methane in LTA). | ||
Wednesday 3 July 2019
| Day 3 Time | Content | |
|---|---|---|
| AM Lectures | ||
| 9.00-10.00 | Randall Snurr | Monte Carlo (MC) simulation, NVT-MC, basic level, Markov chains. |
| 10.00-10.30 | Coffee-break | |
| 10.30-11.30 | Thijs Vlugt | Gibbs and grand-canonical MC, computing isotherms, mixtures, converting fugacity and pressure, IAST. |
| 11.30-12.30 | Thijs Vlugt | Advanced MC techniques, CBMC and CFCMC, use of biasing to enhanced sampling for “difficult systems”. |
| PM Practical Hands-on Exercises | ||
| 13.30-17.00 | David Dubbeldam | Gibbs simulation of Vapor-Liquid Equilibrium (VLE) of CO2. |
| Computing the helium void-fraction. | ||
| Computing adsorption isotherm of CO2 in LTA-type zeolite. | ||
| Computing adsorption isotherms of CO2 in LTA-type zeolite using advanced methods (CFCMC). | ||
| Advanced simulations of ionic liquids. | ||
Thursday 4 July 2019
| Day 4 Time | Lecturer | Content |
|---|---|---|
| AM Lectures | ||
| 9.00-9.45 | David Dubbeldam | Demo iRASPA for macOS, GPU-accelerated visualization software for material scientists. |
| 9.45-10.30 | Thijs Vlugt | Reactive MC in fluids and use of expanded ensembles. |
| 10.30-11.00 | Coffee-break | |
| 11.00-11.45 | Sofia Calero | Force field development. |
| 11.45-12.30 | Randall Snurr | Diffusion in nanoporous materials. |