Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Workflows in ComputationalHeterogeneous Catalysis
Antonio M. Marquez
Departamento de Quımica Fısica
Universidad de Sevilla
11 de diciembre de 2006
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Summary
1 InfrastructureHardwareSoftwareQC packages
2 Heterogeneous Catalysis
3 Metals adsorption in oxides
4 Metal Nitrides
5 Concluding remarks
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Hardware
Beowulf type Cluster including as front-end
1 Intel based Pentium IV, @ 1.8 GHz, 1 Gb RAM
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Hardware
Beowulf type Cluster including as compute nodes
16 Intel Pentium IV, @ 2.4 GHz, 1 Gb RAM
24 Intel Pentium IV, @ 3.0-3.3 GHz, 1 Gb RAM
8 Sun V60X nodes with two Intel Xeon PentiumIV, @ 3.0 GHz, 2 Gb RAM
2 SunFire V20z Servers with two AMD dualOpteron 248 processors, @ 1 GHz, 2 Gb RAM
3 SunFire V40z Servers with four dual-coreOpteron 880 processors, @ 2.4 GHz, 16 Gb RAM
Connected by a 1 Gbit/s switched Ethernet
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Operating systems and contact
Linux Operating System
RedHat 9.0 (front-end) - to be upgraded by next
January
Fedora Core 2 (Intel Based compute nodes)
Fedora Core 4 (v20z) and 5 (v40z) 64-bits kernel
Contact person
Antonio M. Marquez ( [email protected] )
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Quantum Chemistry packages
In use
VASP 4.6
Crystal06
CPMD 3.11.1
HONDO
Gaussian 98 (serial version only)
To be installed
NWChem
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
QC packages
VASP
Plane-wave based code
Pseudopotentials
GGA density functionals
Ground state molecular dynamics
Good parallel efficiency up to 16 nodes (dependingon system size)
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
QC packages
Crystal06
Atom-centered gaussian basis set
RHF, B3LYP
Tools to analyze the adsorbate/substrateinteraction
Reasonable efficiency for up to 8 nodes
Post Hartree-Fock methods
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
QC packages
CPMD
Plane wave based code
Pseudopotentials
Excited state molecular dynamics
Incorporated a month ago, not fully tested
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Auxiliary programs/packages
Queue system
TORQUE: very simple instalation, only a queue on theserver, simple scheduler, home-made program used toredistribute the jobs between the compute nodes,home-made shells used to submit jobs, no graphicalinterface
F90 compiler
Intel Fortran Compiler: version 7.0 and 9.0 installed
C compiler
GNU C compiler
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Auxiliary programs/packages
MPI environment
LAM 7.1.1: good performance and well integrated withTORQUE
xmakemol
Simple graphical of molecules and solids
Open Data Explorer
Visualization of electron densities from VASPRequires data conversion and some utility program
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Software we are exploring
NWChem
GridChem
PathScale
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Catalysis
Catalysis is one of the main tools in chemicalsynthesis to the efficient conversion of rawmaterials into high added-value chemicals
Catalysis-based synthesis accounts for about 90 %of chemical processes
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Catalysis: Challenges
Develop new synthetic techniques
incorporating the approaches of other
disciplines
This includes the use of new computationaltechniques to guide synthesis by theory andmolecular modelling
Develop new catalysts and reaction systems
to prepare environmentally safe processes
This includes viable solid acid and base catalyststo replace the toxic and corrosive mineral acidsand bases
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Computational Heterogeneous Catalysis
Very complex problem both experimentally andcomputationally
Characterization of active sites is challenging
Rarely possible to perform discrete and systematicadjustement of the active sites
In the worst case the active site and/or the activephase of the catalyst is poorly characterized
Simulation allows specific questions to be askedand focus experimental work on solving particularproblems
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Metals on α-Al2O3
Metal deposition on surfaces is used to producematerials with modified surface properties
Enormous interest in heterogeneous catalysis: COoxidation, NOx reduction, hidrogenation, olefinepolimerization, . . .
Aluminum oxide is particularly importantsubstrate: mechanical and thermal resistance,highly dispersed powder
Many phases exists: α-Al2O3 is the bestcharacterized and very well studied
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Metals on α-Al2O3
Adsorption of transition metals on aluminaextensively studied
Catalytic properties influenced by
Electronic structure of the atom(s) at the surfaceCluster size effects
Bonding features of single atoms and smallclusters interacting with metal oxide surfaces areof interest
Amount and direction of charge transfer at theinterfase
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Metals on α-Al2O3
Strong relaxation at thesurface (requieres PCBcode)
Many possible adsorptionsites
In depth analysys of thebonding situation requires
Analysis of DOSextracted from periodiccalculationsExamination of DensityDifference mapsCluster models to allowfor more sophisticatedbonding analysis tools
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Coinage metal atoms on α-Al2O3
Change of preferred adsorption site
Cu and Ag prefer Al-hollow siteAu prefers on-top O site
Weak interaction energies (-0.6 to -1.1 eV),following the order Cu ¿ Au ¿ Ag
Strong effect of surface relaxation (up to 30 % ofbinding energy)
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Coinage metal atoms on α-Al2O3
Bonding analysis from CSOV indicates change ofbonding mechanism
N.C.Hernandez, J. Graciani, A, Marquez and J.Fernandez Sanz,
Surf. Sci. 2005, 575, 189
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Bonding analysis: tools
Constrained Space Orbital Variations (CSOV) method
allows to partition the adsorbate/substrateinteraction into physically meaningfull interactions
Limited to orbital based approaches
HONDO: requires development of a cluster modelfor the system of interest, not allways evident
Crystal: very recent implementation of PBCapproachN.C.Hernandez, J.Fernandez Sanz, C.M. Zicovich-Wilson,
J. Chem. Phys., 2006, 124, 194105
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Next steps
Metal cluster deposition
Dynamics: cluster grow mechanism, incorporationof metal atoms into the subsurface
Reactivity: CO oxidation
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Metals nitrides and oxides
Early transition metal nitrides show an unusualcombination of metallic, covalent and ionicproperties
High termal and mechanical resistance
High electronic conductivity: they are metals
All those properties may change dramatically withthe oxidation process
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Metals nitrides and oxidesComputationally challenging
Very important rippling atthe surface
Requires a large model tobe reproduced
Metal character best suitedto be reproduced withplane-wave codes
Presence of defects and localoxidation process best to bedeal with MO based codes
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Deposition of O2 on TiN and ScN
O2 adsorbs molecularly in different sites
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Deposition of O2 on TiN and ScN
O2 dissociation is easy
further incorporation of O atoms into the subsurface isdifficult
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Next steps
Surface oxidation: in colaboration with BNL
TiON phases or TiO + TiN segregated phases ?
Metal deposition on TiN (on going work)
Metal deposition on oxided phases
Workflows in
Computational
Heterogeneous
Catalysis
Infrastructure
Heterogeneous
Catalysis
Metals adsorption
in oxides
Metal Nitrides
Concluding remarks
Concluding remarks
Computational Heterogeneous Catalysis is a complexsubject that requires
Computationally intensive applications
Sophisticated tools to analyze bonding interactions
Interplay of many applications transferingstructure, and electron density data
Manipulation of many files by the user, storageand retrieval of results
Generation of many different structures incomplex problems