software for modelling catalytic materials and chemical ... · 06/12/2018 · deployment of...

PRODUCTS ON MARKETPLACES – SWO

Software for modelling catalytic materials and chemical processes at the molecular and mesoscopic scales:

current status and broader vision

Michail StamatakisUniversity College London (UCL)

EMMC IntOP2018

Stan van GisbergenSoftware for Chemistry & Materials (SCM)

Tuesday, November 6, 2018

Catalysis & Chemical Reaction Engineering1

1 Freedonia, World Catalysts - Demand and Sales Forecasts, Market Share, Market Size, Market Leaders. (The Freedonia Group, Inc., 2014).

2 D. G. Vlachos and S. Caratzoulas. Chem. Eng. Sci. 65, 18 (2009); G. A. Olah, Angew. Chem. Int. Edit. 44, 2636 (2005).

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Year

• At the heart of chemical industry:1

Petroleum

Chemicals production

Energy generation

Food production …

• Tackling challenges in the energy, environmental and sustainability fields2

Biomass, methane, CO2 conversion

Emissions control …

Diffusion through the porous network of the catalytic pellet

Convection/diffusion of reactants towards (or products from) the surface of the pellet

Materials Design Aspects2

Adsorption and surface reactionson the catalytically active phase

Possible bulk phase reactions…

Materials modelling opportunities:• Property prediction• Materials discovery/engineering• Unit (reactor) & process design

Software Indispensable for Materials Modelling3

However, most of it is “trapped” in TRL of about 1-4…

Outline4

Zacros software application

• Kinetic Monte Carlo for reactions on heterogeneous catalysts

• Licensing via XIP portal developed at UCL

ADF Modelling Suite

• Molecular mechanics with ADF

• Experimenting with Marketplaces

Towards multi-equation modelling…

Outline5




ADF Modelling Suite




Multiscale Computational Catalysis & Materials Science Lab

• Method and Software development.

Fundamental understanding of reactivity trends and prediction of catalytic performance of novel materials…

• Applications: emissions control, biomass reforming (HDO, coupling), methane activation. Materials of interest: pure metals, alloys, dichalcogenides, carbon-based materials.

http://zacros.org

Michail StamatakisAssociate Professor

in Chemical Engineering

The Kinetic Monte Carlo Approach7

reactants

products

Potential Energy Surface

Metal surface

CO(gas) + OH∗ COOH∗→←

1 M. Neurock and E. W. Hansen, Comput. Chem. Eng. 22, S1045 (1998); K. Reuter and M. Scheffler, Phys. Rev. Lett. 90: 046103 (2003); M. Stamatakis, J. Phys. Condens. Matter. 27: 013001 (2015).

2 J. A. Dumesic et al., The Microkinetics of Heterogeneous Catalysis. (American Chemical Society, 1993).

• Instead of simulating dynamics, KMC1 focuses on rare events

• Simulates reactions much faster than Molecular Dynamics

• Incorporates spatial information contrary to micro-kinetic models2

The Kinetic Monte Carlo Approach8

• Instead of simulating dynamics, KMC1 focuses on rare events

• Simulates reactions much faster than Molecular Dynamics

• Incorporates spatial information contrary to micro-kinetic models2

reactants

productstransition

state

‡

B

E‡k TB

rxnrxn

k T Qk eh Q

∆−

⋅⋅= κ ⋅ ⋅ ⋅

Metal surface

Potential Energy Surface

CO(gas) + OH∗ COOH∗→←

1 M. Neurock and E. W. Hansen, Comput. Chem. Eng. 22, S1045 (1998); K. Reuter and M. Scheffler, Phys. Rev. Lett. 90: 046103 (2003); M. Stamatakis, J. Phys. Condens. Matter, 27: 013001 (2015).

2 J. A. Dumesic et al., The Microkinetics of Heterogeneous Catalysis. (American Chemical Society, 1993).

Zacros: Modular Software Architecture9

General input(conditions,

KMC options)

Lattice generator

Reaction Mechanism Parser

O2** krxn

O*

O*

Energetics Parser

120o 3εGraph-Theoretical KMC

simulator

Catalytic activity & selectivity…Active sites &

pathways…

…from lower-level molecular-mechanics models

( ) ( ) ( )dPW P W P

dt ′ ′→ →′

′= ⋅ − ⋅ ∑ σ σ σ σσ

σσ σ

Marketing Approach10

http://zacros.org

• XIP licensing portal powered by e-lucid:– Licensing & transactions for anything from biological materials to software

– Customized licenses as well as approval and notification processes

– Keeps track of licences distributed

Licensing Approach and User Statistics11

Three types of licenses:

• Academic License (290 active)– Free of charge, prohibits modifications and re-selling

– Perpetual, covers future versions

– Fortran source code provided along with compilation scripts, test-suite, manual, and example input files.

• Commercial (1 current, 1 in progress)– As academic but with a fee…

• Commercial evaluation (5 granted)– 30-day demo/trial, free of charge

– Windows executable provided along with manual and examples.

Resources Made Available12

http://zacros.org

• Dedicated website (separate from XIP) providing information, tutorials and links to scientific publications

• Users can email [email protected] for support

mailto:[email protected]

Outline13




ADF Modelling Suite




SCM: Company Profile14

Software for Chemistry & Materials (SCM) strong academic background

approximately 15 in-house developers

global academic developer network

research highlights: catalytic research, biochemical research, drug design, semiconductors, materials design, battery design, ...

several collaborations with European Research & Training Networks (QuasiNano, AutoCheMo, Fortissimo,…)

Amsterdam

The ADF Modelling SuiteBridging Scales Under a Single Interface

15

Software for Reactive Materials Modelling16

Molecular DFT with ADF• All electrons, all elements, relativistic effects• Many spectroscopic properties + analysis

BAND AO-based• Polarizable 2D systems• Easy orbital & density analysis• NEGF: Charge and spin transport

DFTB: faster more approximate• Spectroscopy, reactivity, dynamics• NEGF: transmission, charge transport

ReaxFF: reactive MD large, complex systems• Monte Carlo methods to speed up time / equilibrium• New: eReaxFF for batteries / Redox reactions

COSMO-RS/COSMO-SAC/UNIFAC• Quick thermodynamic predictions fluids/gas

(Python) scripting and GUI for all modules

Customers: a diverse, global community17

Academic researchers & research institutions• “free” access to computing resources• ease of software access (teaching),

extra resources of interest• IP/data protection secondary• ranging from one-man groups to

whole universities (or countries!)

Commercial and industry• computing resources expensive• disused computing resources not

acceptable• IP/data protection crucial• ranging from small specialists to

largest chemical companies

the cloud:a one-size-fits-all solution?

The FORTISSIMO HPC-Cloud Infrastructure18

The FORTISSIMO Marketplace

Simulation-as-a-Service

HPC Platform-as-a-Service

HPC Infrastructure

Support Consultancy Business Container

Code Verification

Matchmaking Registry

• FORTISSIMO: permanent, simple & cost-effective access to hardware, software, and know-how for intensive simulations.

• On-demand, pay-per-use model (pre-pay also possible).

• Platform for solution providers to offer products and services.

19

Engagement with Fortissimo Marketplace20

• Case study with Albemarle and SCM demonstrating the low costs of Cloud-based-HPC on a pay-per-use basis

• Cost: half that of owning & maintaining a sufficiently powerful in-house system, representing a yearly saving of €38,000

Albemarle: a prototypical customer21

…as a company• chemical company: flame retardants, fluid catalytic cracking, ...• head quartered in Baton Rouge, Louisiana, USA• research and production sites in the USA, China, and Europe• 4260 employees, 2.869 billion $ revenue (2011)• long-term licensee of SCM (via modelling team at Dutch site)

as a fortissimo end user• experienced ADF user, unexperienced HPC user• limited to small local resources (and small-scale simulations)

(How) does access to cloud-resources change the game for them?

High-Performance Computing: the Classic Way22

fetch results/data

submit job

(supported) client setup, visualization

and analysis

Computing resources well-

defined hardware and software stack

• Problems:– user must install client-side software (and dependencies)

– interaction with computing resources highly formalized & non-portable

ADF Cloud Implementations on FORTISSIMO23

Cloud

fast, easy

ClientVNC client software

VNC server with custom extensions

ADFsimulation

environment

SURFsaraCartesius, GPU island

• fast remote access to ADF analysis & visualization

• tight integration with SURFsara’s resources

Cloud

fast, easy

Clientbrowser

SSL encryption, HTML5 technology,

VNC server

ADFsimulation

environment

Arbitrary computing resources (CPU, GPU, MIC)

• full ADF simulation environment in the browser

• deployment automated…“your private ADF cloud in 30 min”

ADF in the Browser24

New Business Model: Cooperation with HPC Providers

25

Advantages of HPC vs Generic Cloud Providers, for Material Modellers:• Better pricing options for intense, peak computing power demanded by HPC

applications (heavy “number crunching”, as opposed e.g. to running web services).

• Fewer technical limitations: scientific applications such as ours require fast interconnects, high bandwidth and low latency ⇒ better parallel scalability.

• (Typically) higher level of HPC expertise of support staff.

• Software in standard clouds is normally run in virtual machines, while HPC alternatives allow running software directly “on the metal” ⇒ more aggressive optimization, shorter run-times.

New Business Model: Benefits of Cloud Setup26

Benefits associated with using a HPC cloud:• In general, end-users of cloud services avoid hardware licenses or hardware

maintenance and upgrade costs, and have reduced up-front software license costs.

• The cloud-based HPC setup allows the industrial end user to easily scale up simulations and reach system sizes that would have demanded too long computation times with their in-house resources.

• Cloud computing vendors manage all of their customers on a single instance of the software, which allows to amortize costs over many customers and yields substantial economies of scale and skill.

• In our particular experiment, Albemarle’s area of expertise is in chemical engineering, not hardware and software deployment and maintenance. The company can cut significant costs by outsourcing the latter to HPC specialists.

…reduced costs, increased flexibility…

Outline27




ADF Modelling Suite




Broader Vision – Future Developments…28

Mesoscopic Frameworks

Repositories, Marketplaces

Ab initio dataMolecular structuresBinding/activation energiesInteraction energiesVibrational frequencies

Coupling interfaces

KMC+metamodelsCoarse-grained mesosc. models

Kinetic data and ModelsCatalytic pathwaysActivation energiesReaction energies Pre-exponentials

Electronic/Atomistic Frameworks

Ab initio packagesTransition state finders

Continuum Frameworks

Design equationsComputational Fluid Dynamics

Reactor-scale ModelsReactor geometryCatalyst loadingActivity, selectivity, yieldEnergy consumption

Atom, Molecule (Å-nm) Catalytic Nanoparticle (nm) Pellet (μm-mm) Reactor (cm-m)

Coupling interfaces

Linking and coupling of software for multi-equation modelling of reactors

Deployment of solution to European Materials Modelling Marketplace

Integrated services: training, cloud computing resources, data repositories, …

Conclusions and Perspective29

• Simulation of reactive materials and catalytic processes requires high-quality software– Zacros is a popular “light-touch” commercialized academic code for

kinetic Monte Carlo simulations of catalysts with a growing userbase

– ADF Modelling Suite is a versatile framework for molecular mechanics with an established userbase

• Both software applications can benefit by engaging with Materials Modelling Marketplace(s)– Engagement with and marketing to broad userbase

– Cloud-based services that cut costs for the end-user

– Software coupling for marketing complete solutions

30

Thank you for your attention!

software for modelling catalytic materials and chemical ... · 06/12/2018 · deployment of...

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