Scalable Quantum Chemistry with Flexible Embedding Stage 2

Lead Research Organisation: STFC - Laboratories
Department Name: Scientific Computing Department

Abstract

In stage two of the "Scalable Quantum Chemistry with Flexible Embedding" project we propose to refine the software we have developed in stage one for molecular modelling of reactivity in complex systems, in particular surface chemistry and heterogeneous catalysis in the presence of a solvent such as water. This software combines quantum chemistry (also known as first principles) techniques, which can treat the chemically reacting centres, embedded in an empirical (molecular mechanics) model for the rest of the system, i.e. the slab of material which models the surface and the solvent layers on top of it.

In stage one we are extending our embedding model to include new treatments for spin-polarised systems such as magnetically ordered materials, an implementation of a low-cost quantum method to describe anisotropic and spin-polarised environments and periodic boundary conditions in order to perform calculations on solvated surfaces. Examples of the science this software targets includes metal oxide catalysis that work in the presence or water; the binding of pollutant species (heavy metals or toxic organics) to natural minerals in the environment, or specially designed inorganic materials that could potentially remove them from the environment; catalysis by more complex minerals, not well treated by existing treatments but of great industrial importance; and the design of sensors and photoelectric materials by organic layers on inorganic surfaces.

The aim of stage two is to make it is as straightforward as possible for new users to set up and run flexible embedding calculations based on the methods developed in stage one, and for advanced users to adapt the code to their own needs. We will achieve this by replacing the user interface the stage one code, which is able to achieve the scientific goals of stage one but is many-layered and relies on a legacy software package, with a new direct user interface written in the popular scripting language Python. The new interface will radically simplify use and development of the code without compromising on the primary goal of stage one, namely achieving high performance for the new embedding models on large-scale parallel machines.

We will incorporate all the key functionality from our legacy codebase into the new version of the code, including utilities to set up embedded cluster calculations, an advanced geometry optimisation library, and the ability to interface to multiple quantum mechanical and molecular mechanical software packages, in particular the FHI-AIMS package which will be coupled to the code in collaboration with the FHI-AIMS developers. We also aim to make the new code as user-friendly as possible through the development of comprehensive documentation, tutorials and case studies from the demonstration applications program began in stage one.

By the end of stage two we will have a new version of the code that is ready for release to the community, with all the key functionality of the legacy version implemented, and we will be in a position to transition users to the new code and use it as our platform for all future QM/MM and multiscale developments.

Planned Impact

Materials research is an underpinning technology for a wide range of UK industries. In the chemicals industry economic and environmental sustainability of processes depends on innovation in the area of catalysis. The emerging area of supported nanoparticulate catalysts depends on the construction of specific metal/support combinations with the particle size and interface with the oxide playing an important role in catalyst performance. Advances in this field will require fundamental understanding of the connection between catalyst structure and activity for which modelling at the quantum level is an indispensible tool. The new software package developed as a result of stage 2 will help improve the range of problems that can be addressed by both academic and industrial researchers in this area, without needing the intimate knowledge of the methods and codes required to operate the transitional workflow in stage 1.

For systems of interest, new fundamental insights will be obtained. Materials are widely used in industrial context, including electronics, catalysis, energy materials, environmentally friendly materials and materials used as filters and sorbents tackling chemical and or radioactive waste. New classes of minerals will be addressed along with their interfaces with water thus impacting on our knowledge in earth sciences (calcite and water cycles) and biominerals (apatite in tooth enamel and bones etc.)

The partners are all active participants in the Collaborative Computational Projects, in particular CCP5 (SCP is chair and CRAC is a past chair). The developments described here are believed to be highly relevant to the use of condensed phase simulation techniques for systems of technological and commercial interest, and it is anticipated that many within the CCP5 network will be able to exploit the software within their own commercial interactions.
STFC and UCL have worked together on an earlier embedding scheme for solids and implemented it in ChemShell. Commercial interest in the model was the main motivation for Accelrys to licence ChemShell as the basis of their QMERA product, which they are now selling commercially. Once the ability of the stage 2 package to interface to multiple QM packages has been demonstrated, it should be straightforward to introduce the required additional functionality into the Accelrys QM code, DMol3, so that the new methods can be exploited by users of Materials Studio, which is widely used in industry.

Publications

10 25 50
 
Description The scientific developments from stage 1 of the Scalable Quantum Chemistry with Flexible Embedding project ( EP/I030662/1) have been taken forward into a new python-based computational chemistry environment for QM/MM calculations, the objective of which was to make the stage 1 models accessible to other researchers through the development of a robust, easy-to-use and flexible user interface. Key functionality from the old Tcl-based version of ChemShell to the new python version, such that the legacy code is no longer required to perform materials chemistry QM/MM simulations. The python-based version of ChemShell is now in beta testing by our collaborators and an initial release to the scientific community was made in December 2017.
Exploitation Route The python-based version of ChemShell will be of general applicability to all scientific projects involving solid state QM/MM calculations and we expect a quick uptake based on the existing ChemShell user community and the appeal of the open-source licencing model to new users outside the UK. Future work will include porting of features from the legacy code and new developments to support biomolecular QM/MM modelling and other multiscale methods.
Sectors Chemicals,Digital/Communication/Information Technologies (including Software),Energy,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL http://www.chemshell.org
 
Description Transition metal controlled nitrogen chemistry in zeolite and protein environments using a unified quantum embedding model
Amount £1,022,120 (GBP)
Funding ID EP/R001847/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 01/2018 
End 04/2021
 
Description Collaboration with Karsten Reuter, Technical University of Munich, Germany 
Organisation Technical University of Munich
Department Faculty of Medicine
Country Germany 
Sector Academic/University 
PI Contribution Development of an FHI-aims interface in Python-ChemShell
Collaborator Contribution In-depth experience of the FHI-aims package and the modelling of surface catalytic reactions in general, and resources from the SUPER-MUC HPC machine at the Leibniz Rechenzentrum in Garching
Impact Development of the FHI-aims interface in Python-ChemShell
Start Year 2014
 
Description Collaboration with Volker Blum, Fritz Haber Institute, Berlin 
Organisation Max Planck Society
Department Fritz Haber Institute
Country Germany 
Sector Academic/University 
PI Contribution Development of an interface to FHI-aims in Python ChemShell
Collaborator Contribution Time and computational resources at the Fritz Haber Institute and the Garching Computing Centre of the Max Planck Society
Impact Development of an interface to FHI-aims in Python-ChemShell
Start Year 2014
 
Title Py-ChemShell 
Description Py-ChemShell is the python-based version of the ChemShell multiscale computational chemistry environment, a leading package for combined quantum mechanical/molecular mechanical simulations. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact An initial alpha release of Py-ChemShell was made in December 2017 and is now being tested in preparation for the first full release. 
URL http://www.chemshell.org
 
Description Bristol Chemshell training Feb 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Tom Keal and You Lu gave a 2-day training course in the use of ChemShell for materials and biomolecular modelling to a group of 15 researchers at the University of Bristol
Year(s) Of Engagement Activity 2019
 
Description ChemShell presentation at DL_SOFTWARE training workshop, Guangzhou, China 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Tom Keal and You Lu gave a presentation on recent developments in ChemShell to over 50 students at the DL_SOFTWARE traininng workshop, Guangzhou, China on 27 October 2015.
Year(s) Of Engagement Activity 2015
 
Description ChemShell presentation at MCC conference, Lincoln, September 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Tom Keal gave a presentation on recent ChemShell developments at the Materials Chemistry Consortium conference at the University of Lincoln on 4 September 2018.
Year(s) Of Engagement Activity 2018
 
Description ChemShell presentation at MCC meeting, December 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Tom Keal gave a presentation on recent developments in ChemShell at the Materials Chemistry Consortium meeting at UCL, 21 December 2016.
Year(s) Of Engagement Activity 2016
 
Description ChemShell presentation at MCC meeting, July 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Tom Keal gave a presentation on recent ChemShell developments at the Materials Chemistry Consortium meeting at UCL on 6 July 2015
Year(s) Of Engagement Activity 2015
 
Description DL ChemShell training January 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Tom Keal and You Lu gave ChemShell training to a group of 6 researchers from UCL
Year(s) Of Engagement Activity 2019
 
Description Presentation at UK Catalysis Hub Summer Conference, July 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Matthew Farrow gave a presentation on "An introduction to ChemShell: A hybrid QM/MM embedded cluster approach for the computational modelling of heterogeneous catalysis" at the UK Catalysis Hub Summer Conference on 2 July 2015 to an audience of postgraduates and senior researchers, with questions and discussion afterwards.
Year(s) Of Engagement Activity 2015
URL http://www.ukcatalysishub.co.uk/events/highlights
 
Description Presentation at the Cardiff University, Cardiff, December 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact You Lu gave a talk on "Python-Based Redevelopment of ChemShell" at the Computational Chemistry Seminar of Cardiff University on 05/12/2017. More than twenty academic staff and students attended and raised questions after the talk. Tom Keal and You Lu visited Prof. David Willock and Dr. Andrew Logsdail of Cardiff University to discuss the future plan for collaboration and tutored a postdoctoral researcher Sachin Nanavati to set up and use Py-ChemShell.
Year(s) Of Engagement Activity 2017
 
Description Presentation at the University of Limpopo, South Africa, January 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact 30 mainly undergraduate students attended a talk given by Matthew Farrow on ChemShell entitled "Computational Modelling of Heterogeneous Catalysis" at the University of Limpopo, South Africa, 28 January 2016. A question and answer session followed and there was a great deal of interest among the students in using the code in future.
Year(s) Of Engagement Activity 2016
 
Description UCL Embedding Day workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Tom Keal was invited to speak at the UCL Embedding Workshop on the topic of recent developments in ChemShell. Alexey Sokol, Andrew Logsdail and You Lu also participated in the meeting.
Year(s) Of Engagement Activity 2014