situated @: bath; birkbeck; cambridge; cclrc daresbury reading the royal institution
DESCRIPTION
eMinerals one of NERCs eScience testbed projects. eMinerals: Science Outcomes enabled by new Grid Tools. Maria Alfredsson Nottingham 21/9/2005. The eMinerals team: Environmental scientists; Chemists; Physicists; Computational and Grid scientists. PI: Martin Dove - PowerPoint PPT PresentationTRANSCRIPT
Situated @:
Bath;Birkbeck; Cambridge;CCLRC DaresburyReadingThe Royal InstitutionUniversity College London (UCL)
eMinerals one of NERCs eScience testbed projects
The eMinerals team:
Environmental scientists;Chemists; Physicists;Computational andGrid scientists.
PI:Martin Dove ([email protected])
Web:www.eminerals.org
eMinerals: Science Outcomes enabled by new Grid ToolseMinerals: Science Outcomes enabled by new Grid Tools
Maria AlfredssonMaria AlfredssonNottingham 21/9/2005Nottingham 21/9/2005
eMinerals one of NERCs eScience testbed projects
Research undertaken by:Bath group:A. Marmier, D.J. Cooke, S.C. ParkerBirkbeck group:Z. Du and N.H. de LeeuwCambridge group:K. Trachenko, E. Artacho, J.M Pruneda,M.T. DoveDaresbury group:I. Todorov and W. SmithRI group:M. Blanchard and K. WrightUCL group:M. Alfredsson, J.P. Brodholt andG.D. Price
eMinerals one of NERCs eScience testbed projects
Environmental ProcessesEnvironmental ProcessesAIM:we use computational modelling to research mineralogical processes at an atomistic level, providing information on transport and immobilisation processes of pollutants, including both toxic elements (.i.e. As, Cd, Pb and organic molecules) as well as radioactive waste.We have also looked alternative energy resources to fossil fuels.
Sources of pollution e.g.:• Acid mine drainage• Land filling sites• Industries and farming• Accidents with toxics• Natural catastrophes or mineralogical properties
eMinerals one of NERCs eScience testbed projects
Environmental ProcessesEnvironmental Processes
Problem:Relastic models of mineral process are computationally very expensive.
Layout:Layout:• Grid ResourcesGrid Resources• Data ManagementData Management• Science OutcomesScience Outcomes
Solution:GRID COMPUTING
• LLaakekess (Bath, Cambridge, UCL): (Bath, Cambridge, UCL): 4 linux-based clusters4 linux-based clusters 88 nodes in total with 2Gb memory per node88 nodes in total with 2Gb memory per node
• Pond (Cambridge): 1 Pond (Cambridge): 1 Apple Xserve cluster Apple Xserve cluster 8 nodes with 8Gb memory per node8 nodes with 8Gb memory per node
• 24-node IBM cluster (Reading)24-node IBM cluster (Reading)
• 33 CCoonnddoorr--ppoooollss:: UCL > 900 machinesUCL > 900 machines Cambridge (25 machines)Cambridge (25 machines) BathBath
NNGGSS –– CCSSAARR -- HHPPCCxx
Grid Resources:
Resources marked in red suitablefor first principles code green represents resources suitable forinter-atomic potential codes.
• Storage Resource Broker (SRB)Storage Resource Broker (SRB)Bath, Cambridge, Reading and the central MCAT at Bath, Cambridge, Reading and the central MCAT at DaresburyDaresbury
• Chemical Markup Language (CML)Chemical Markup Language (CML)-version of XML adapted for chemical applications-version of XML adapted for chemical applications-All codes developed in eMinerals support CML-All codes developed in eMinerals support CML
• Personal Interface Grid (PIG)Personal Interface Grid (PIG)
• MAST MAST
Data Management
• WIKIWIKI
• RcommandsRcommands
• MetadataMetadata
Job Submission:
• Globus Globus (GSI/X.509-certificaes)(GSI/X.509-certificaes)
• Condor-GCondor-G
• SeagullSeagull
Computer Codes:
Submit jobs from all machines fromour work station.
Maintained and developed with eMinerals:• DL_Poly• Metadise – Monte Carlo implemented• Siesta• Casino Other Codes:
• Gulp • Marvin
• AbInit• Casino• VASP• Crystal
automatic meta-scheduler to submit to the “most appropriate”machine in the mini-grid.
Dagman and Perl scripts
eMinerals one of NERCs eScience testbed projects
Science Outcome:Science Outcome:• Surface and InterfacesSurface and InterfacesDetermine water exchange and diffusion coefficientDetermine water exchange and diffusion coefficientEffect of impuritesEffect of impurites
• Phase TransitionsPhase Transitionsdue to compositional and pressure effectsdue to compositional and pressure effectsLattice dynamics calculations to determine most stableLattice dynamics calculations to determine most stablepolymorphpolymorph
• Radioactive wasteRadioactive waste
Aim:To fully understand transport and immobilisation processes of contaminants we need an accurate description of the mineral/solvent interfaces.
Solution:We perform Molecular Dynamics simulations using the DL_POLY code.
Snapshot of Goethite/Solvent interface using MD-simulation on the HPCx. A. Marmier, D. Cooke, S. Kerisit and S.C. Parker Bath University.
Mineral/Solvent Interfaces
Computer resources:Condor-pool - distributing many independent calculations over the machines available, using Dagman or Perl scripts good statistical data, which can be used to determine diffusion and water exchange coefficients.NGSHPCx – larger jobs
Mineral/Solvent Interfaces
Result: • Ordering of the water molecules close to mineral surface.• Cl- ions order closer to the mineral surface than Na+ ions
• The classical modelsof the electrical doublelayer do not describecorrectly the ion distribution close to thesurface.
A. Marmier, D.J. Cooke, S. Kerisit and S.C. Parker
Bath University.
Pt/Graphite interfacePt/Graphite interface
• Graphite: Model for Graphite: Model for organic substrateorganic substrate
• Pt/Graphite: Alternative Pt/Graphite: Alternative (renewable) energy (renewable) energy resource to fossil fuels resource to fossil fuels know to generate green know to generate green house gases.house gases.
• Graphite: Model for Graphite: Model for organic substrateorganic substrate
• Pt/Graphite: Alternative Pt/Graphite: Alternative (renewable) energy (renewable) energy resource to fossil fuels resource to fossil fuels know to generate green know to generate green house gases.house gases.A. Marmier and
S.C. Parker at University of Bath
Pt/Graphite interfacePt/Graphite interface
Aim: Derive highly quality empirical potentialsfrom density functional theory (DFT) calcualtions.
Problem: Computational costly
Solution: Grid computing - NGS
Aim: Derive highly quality empirical potentialsfrom density functional theory (DFT) calcualtions.
Problem: Computational costly
Solution: Grid computing - NGS
A. Marmier andS.C. Parker at University of Bath
Conclusions:• Most stable site is located on a
bridge site
• The activation barrier is 0.5 eV
• The adsorption sites and energiesare different for inter-atomicpotential
calculations
Conclusions:• Most stable site is located on a
bridge site
• The activation barrier is 0.5 eV
• The adsorption sites and energiesare different for inter-atomicpotential
calculations
Pt/Graphite interfacePt/Graphite interface
A. Marmier andS.C. Parker at University of Bath
CaO-termimated
TiO2-termimated
{001} surfaces of CaTiO3
Mineral Surfaces
M. Alfredsson, J.P. Brodholt and G.D. PriceUCL
Calculations:• investigate 10-20 surfaces• 2 to 5 surface terminations• 4 to 16 impurity positions• > 4 concentrations
Total number of calculationsper impurity: 120-2440
Computer Resources:• Condor Cluster • SRB
We defined a new methodto calculate surface energies which allow us to determine crystal particle shape. We find particle shapes change with concentration of the impurity and the type of dopant.
Important to understand the reactivity and inter- actions between pollutants and minerals.
Mineral Surfaces
increasing concentration
In all mineral processes we are dealing with impurities, which may changes the crystal structures
Phyllosilicates (layered silicate minerals, including clays) are known to adsorb and store toxic elements.
Here we show how the crystal structure of layeredLi2Si2O5 transforms (‘breaks up’) in the presence of different elements, e.g. Cs.
Z. Du and N. H. de LeeuwBirkbeck College and UCL
Compositional Phase Transitions
LiCs
Na
Computational Resources:• Condor Pools• Eminerals mini-grid• SRB
Z. Du and N. H. de Leeuw: Birkbeck College and UCL
Compositional Phase Transitions
Li
Na
Processes Entalphy
(kJ/mol)
-30.9
-26.2
-37.9
-40.9
2084420844 OSiLiMOSiLiK
)()( 2084320844 aqKOSiNaLiKaqNaOSiLiK
)()( 20842220843 aqKOSiLiNaKaqNaOSiNaLiK
)()( 20843208422 aqKOSiLiKNaaqNaOSiLiNaK
)()( 2084420843 aqKOSiLiNaaqNaOSiLiKNa
Results:Solid solutions of guest ions in silicates are often thermodynamically stable.• Cation exchange from solution is an endothermic process; only K-Na exchange expected to occur
Pyrite (Fools gold): Pyrite (Fools gold): FeSFeS22Fe-bearing minerals active role in the control of acid mine
drainage and transport of heavy metals like As.
Transport and imobilisation process:• Pyrite may contain ca. 10wt% of As• Adsorption of As on Pyrite surface
Aim: understanding electronicstructure and bonding propertiesof pure pyrite. Possible phasetransitions?
Method: linear respons phononcalculations, using DFT
Computational resources:HPCx linking back to the SRBs
M. Blanchard and K. Wrightat the RI
Pyrite (Fools gold): Pyrite (Fools gold): FeSFeS22Results:
• Pyrite is an insulator (in agreement with experiment)• Pyrite is described by S2 molecules interacting with Fe ions
Conclusions: • Calculated frequencies are in good agreement with experiment• All vibrational modes show non-linear pressure dependence• Mode Grüneisen parameters give information about thermodynamical properties
M. Blanchard and K. Wrightat the RI
Pressure Induced Phase diagrams: MgO and FeO
Expt.1) HF-AE* HF-PP** QMC-PP**
a (Å)
B0 (GPa)
4.194.19
157157
4.1954.195
184184
4.0894.089
196196
4.0944.094
178178
1) M. I. McCarthy et al PRB (1994) and ref. therein
*AE=All-electron**PP=Pseudo-potential
Note: The PP used in the HF and QMCNote: The PP used in the HF and QMCcalculations is the same.calculations is the same.
Problem:QMC calculations are ca. 1000 times more computer intensive than traditional first principles calculations.
Solution:HPCx – the CASINO code show excellent scaling
Problem:Traditional DFT techniques often fail in reproducing Fe-bearing minerals
Solution:Quantum Monte Carlo (QMC) calculationsHybrid-DFT calculations
by UCL-team
PPTT calculated from H calculated from HB1B1=H=HB2B2; Birch-Murnaghan 3; Birch-Murnaghan 3rdrd order EOS order EOS
Transition Pressure (PTransition Pressure (PTT) B1 to B2: QMC) B1 to B2: QMC
Result:QMC and LDA (with the same PP) give similar results
PPTT ~ 597GPa ~ 597GPa
B1B1
Method
GGA-PAWGGA-PP(PW)GGA-PP(PW)LDA-LAPWLDA-PP(PW)
QMC-PPQMC-PPLDA-PP (PW)LDA-PP (PW)
5975972020569569
509489664510451
P(GPa)
Oganov et al JPC 2003 and ref. thereinThis work
PP=Pseudo-potential
B2B2
Observeration: We consumed ca. 200.000 Cpu Hrs
by UCL-team
P(GPa)
r-B1(AFM)r-B1(AFM) i-B8(AFM)i-B8(AFM) B8(NM)B8(NM)
83 145insulatorinsulator insulatorinsulator metallicmetallic
Phase Diagram and Crystal StructuresPhase Diagram and Crystal Structures
TNéel =193 K
P~115 GPaat T=0K
Fei & Mao, Science (1994)
To determine phase To determine phase transitions we need transitions we need to:to:• optimise the optimise the geometries for all the geometries for all the possible crystal possible crystal structures at various structures at various pressures. pressures. ~ 240 ~ 240 calculations for FeOcalculations for FeO• for up to 10 for up to 10 computational computational methods methods (Hamiltonians)(Hamiltonians) ~240 x 10 = ~2400 ~240 x 10 = ~2400 calculationscalculations
Solution:Solution:• Condor cluster @UCLCondor cluster @UCL• SRBSRB
Solution:Solution:• Condor cluster @UCLCondor cluster @UCL• SRBSRB
Aim: Find alternative to QMCSolution: Hybrid-DFT
by UCL-team
Radioactive WasteRadioactive WasteNuclear waste disposal – encapsulation in ceramic materials
Aim:Find the best waste form to be used to immobilise surplusPu and high-radiation waste (hrw)
Problem:Most of the currently considered waste forms are damaged(amorphorised) by irradiation from hrw
K. Trachenko, M.T. DoveI. Todorov and W. Smith
Radioactive WasteRadioactive WasteK. Trachenko, M.T. DoveI. Todorov and W. Smith
Observation of amorphisation in Zircon
Radioactive WasteRadioactive WasteNuclear waste disposal – encapsulation in ceramic materials
Aim:Find the best waste form to be used to immobilise surplusPu and high-radiation waste (hrw)
Problem:• Most of the currently considered waste forms are damaged(amorphorised) by irradiation from hrw.• Amorphisation requires large computational system sizes
Code development:DL_Poly5 million atoms using the HPCx
K. Trachenko, M.T. DoveI. Todorov and W. Smith
SiO2
GeO2
TiO2
Al2O3
MgO
Radioactive waste
Result: The more ionic properties the ceramics showthe faster healing processes are observed.
Increasing ionicity
Evolution of time
K. Trachenko, M.T. DoveI. Todorov and W. Smith
Snapshot of MD-generatedstructures caused by 40 keV U recoil.
Prior the eMinerals: • project the data presented here would take several years, involving many projects.
• many of the calculations on realistic systems were also out of reach, such as the modelling of the electrical double layer at the solvent/mineral interface, and the radiation damage, using more than 5 millions ions in the simulation.
Future:•“team projects”• automatic work flows for job submission and data analysis.
Level of theory
Adsorbing surface
Contaminant
Quantum Monte Carlo
Large empirical models
Linear-scaling quantum mechanics
Organic molecules
HalogensMetallic elements
Cla
ys,
mic
as
Alu
min
osili
cate
s
Nat
ura
l org
anic
mat
ter
Pho
sph
ates
Car
bona
tes
Oxi
des/
hydr
oxid
es
Sul
phi
des
Acknowledgement:Acknowledgement:The “Eminerals team”The “Eminerals team”
NERC for financial supportNERC for financial support
eMinerals one of NERCs eScience testbed projects
Web:
www.eminerals.org