Environment from the molecular level:

1. Environment from the molecular level: An e-science project for modelling the atomistic processes involved in environmental issues – Martin Dove – Department of Earth Sciences, University of Cambridge www.eminerals.org

2. Scales of Earth modelling From global ... … to molecular

3. Molecular environmental issues Radioactive waste disposal Pollution: molecules and atoms on mineral surfaces Crystal dissolution and weathering Crystal growth and scale inhibition

4. Molecular environmental issues Radioactive waste disposal Pollution: molecules and atoms on mineral surfaces Crystal dissolution and weathering Crystal growth and scale inhibition

5. University of Reading Royal Institution

7. Plan of work High-requirement science High-performance codes Collaborative environment

8. Plan of work High-requirement science High-performance codes Collaborative environment

9. Studies of radiation damage for nuclear containment

10. Studies of radiation damage for nuclear containment Short-term solutions: long term planning now essential with potential increase use of nuclear power and arms reductions

11. Studies of radiation damage for nuclear containment Nature is known to have encapsulated radioactive isotopes in minerals such as zircon (ZrSiO4) over geological time scales

12. Studies of radiation damage for nuclear containment Large-scale Molecular Dynamics simulations show the structural damage caused by radioactive decay Information can be related to macroscopic properties (swelling, leaching etc)

13. Studies of radiation damage for nuclear containment Simulation of repeated radioactive decay events Note large deflection of recoil atom and damage

14. Studies of radiation damage for nuclear containment Ratio (r) of number of damaged regions in surface cluster to the total of damaged regions as function of concentration (p), giving percolation point Volume swelling (f) calculated from percolation model

15. Adsorption of organic molecules on mineral surfaces Aim is to investigate microscopic basis for binding of organic pollutant molecules (e.g. PCB, DDTs, dioxins) on solid matter of soils (minerals)

16. Adsorption of organic molecules on mineral surfaces

17. Adsorption of organic molecules on mineral surfaces Calculation of binding energy for different positions of molecule on surface

18. Adsorption of organic molecules on mineral surfaces Calculation of binding energy for different numbers of chlorine atoms in molecule

19. Hydration energies of quartz surfaces Quantum mechanics calculations are being used to determine the hydration energies of quartz surfaces and to investigate the preferred state of water on the surfaces of quartz

20. Plan of work High-requirement science High-performance codes Collaborative environment

21. Molecular simulation models QMC Quantum mechanics with plane-wave basis functions SIESTA, CRYSTAL Quantum mechanics with localised basis functions Detailed accuracy DL_POLY, METADISE Models with empirical potentials Integration of methodologies can combine all advantages GUESS Achievable length/time scale

22. Examples of codes DL_POLY3: parallel molecular dynamics code. Modifications aimed at running efficient simulations with millions of atoms for simulations of radiation damage (Daresbury) SIESTA: Order-N quantum mechanics code. Objective to run with large samples and realistic fluids (Cambridge) SURFACE SIMULATIONS: New developments aimed at efficient scanning of many configurations of complex fluid-mineral interfaces, for studies of crystal growth and dissolution (Bath)

23. Method developments EMBEDDED CLUSTERS: linking different simulations with varying sophistication, Aiming to solve the problem of various length scales (RI) QUANTUM MONTE CARLO: goes beyond standard quantum mechanics methods (DFT). This will be the first use of this tool in mineral sciences (UCL)

24. XML for exchange of data Collaboration with Peter Murray-Rust to develop the computational chemistry extension to the Chemical Markup Language The idea is to convert codes to read/write XML (CMLcomp) files for ready exchange of data, with parsers for legacy codes

25. Plan of work High-requirement science High-performance codes Collaborative environment

26. Areas of grid activity • Use of condor technologies • Web Portal Development • eMinerals Minigrid • Data Management Tools • Collaboratory tools

27. Condor technologies Mature-ish technology to build small or large distributed computing systems from standard desktop computers Now being used as production tool in our research groups with heterogeneous clusters of PCs (windows & linux) and unix workstations – we have developed some web-based tools to assist researchers We are now developing large condor pool based on UCL teaching clusters

29. The UCL windows condor pool • Runs Windows Terminal Server • Approximately 750 cpu’s in 30 clusters. • Most are 1GHz Pentium 4, with 256/512Mb RAM and 40Gb hard disks. • All 90%+ underutilised and running 24/7… • We are building this as a large condor pool with UCL Information Systems group to use as a massive distributed computing system

30. eMinerals minigrid and portal Minigrid makes the shared computing resources available to the project through the UK escience grid (built using globus, incorporating storage resource broker) The eminerals minigrid is accessed through the eminerals portal, based on the HPC and data portals developed at the Daresbury Laboratory The eminerals minigrid links to a storage resource broker to store the outputs of simulation runs

31. eMinerals Portal First fully integrated custom instance of CCLRC Data Portal and CCLRC HPC Portal

32. CCLRC Data Portal CLRC DataPortal Server Other Instances of the CLRC DataPortal Server XML wrapper XML wrapper XML wrapper Local metadata Local metadata Local metadata Local data Local data Local data Facility N Facility 1 Facility 1 ...

33. eMinerals minigrid and portal Login window Metadata entry

34. CCLRC HPC Portal • Web portal for HPC over the Grid • Encapsulates the core pillars of Globus Toolkit 2: • User Authentication and Authorisation • Resource Discovery and Interrogation • File Management and Transfer • Job Submission

35. eMinerals minigrid GIIS GIIS GIIS GIIS GRIS GRIS GRIS GRIS UK e-Science GIIS e-Minerals GIIS … UCL Cambridge CCLRC UK e-Science Grid e-Minerals Mini Grid

36. Storage Resource Broker Facilitates distributed data management across virtual organisation

37. Collaboratory tools CCF toolkit to facilitate scientific collaboration across virtual organisation; coupled with personal access grid (both multicast technologies)

38. Plan of work: summary High-requirement science High-performance codes Collaborative environment

39. Summary Science: attack on environmental problems from the molecular level, including radiation damage and surfaces Code developments: range of empirical and ab initio approaches, with aim to take advantage of grid technologies for running larger and more complex systems Grid: development of eminerals minigrid, including use of condor & portal technologies (also developing use of other collaboration tools)