UK R-matrix Atomic and Molecular Physics HPC Code Development Project (UK-RAMP)

Lead Research Organisation: Science and Technology Facilities Council
Department Name: Computational Science & Engineering

Abstract

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Description EPSRC Software Development Project UK-RAMP is a four-site collaboration. The other three grants (QUB, UCL, OU) are listed as partners. Professor Hugo van der Hart (QUB) is overall PI. The scientific code developed by UK-RAMP at QUB, UCL and OU treats the interactions of atoms and molecules with collding electrons and with light (laser pulses on both the femtosecond and attosecond scales) in full detail, solving the full Schrodinger equation for many-electron systems using the 'R-matrix' method. The scientific applications range from astrophysics and atmospheric physics and chemistry to industrial plasmas (lighting, molecular resonance processes affecting engines engines) and biological processes including the detailed mechanisms occurring in radiation damage to DNA/RNA. In attosecond science laser light and the electrons of matter interact on the atto-second time-scale making possible, for example, the shortest-ever pulses of VUV light. One atto-second is only one millionth-millionth-millionth of a second but electrons driven by strong laser light collide violently with others and move distances large compared to the size of an atom on the atto-second time-scale of several hundred atto-seconds.
The UK-RAMP project has, at QUB developed from scratch a new 'R-matrix'-based code, RMT, that can treat laser atom interactions by solving the time-dependent Schroedinger equation. At UCL/OU, the molecular R-Matrix package UKRMol has been completely upgraded (and is currently in the process of being extended to even more ambitious applications as a result of this upgrade) and formed into a sustainable repository-based modern code on the UK academic sourceforge system CCPForge, along with much new coding (described in the OU/UCL key findings) and interface development to the appropriate part of the RMT code to allow future treatment molecules in laser pulses.
The main purpose of the DL part of UK-RAMP has been to assist with sustainable software development and to agree coding standards so that the codes will be future-proof, as well as assistence with use of the codes on parallel High Performance Computing platforms (and to be ready for new HPC computer technologies). Particular assistence was given to the UKRMol CCPForge repository, with UKRMol being accessed by a wide group of developers and users. DL also had a specific task to interface part of UKRMol, 'UKRMol-in', to 'PFARM', a massively parallel 'outer region' part of the of electron-atom R-matrix code PRMAT: R-matrix theory separates configuration space into two regions divided by a sphere. While the full mathematical solution of the Schrodinger equation is not affected by this division, computationally the inner and outer region codes are distinct and rely on separate methods with distinct opportunities for efficiency, parallelization, optimization etc.
Modified in March 2019: The CCPForge repository was very successful and its prinicples have been used and adapted by other, separate, projects in the overall atomic and molecular physics area, in particular the Tensor Network Theory (TNT) project which treats very strongly correlated many-body interactions. The PFARM interface to UKRMol is complete and has already resulted in scientifc studies and publications (science outputs of UK-RAMP are described in more detail in the QUB/UCL/OU key findings, as DL concentrated on computational matters). The diverse atomic and molecular R-Matric codes (PRMAT/PFARM, UKRMol, RMT) are in use on HPC platforms (with some modules already adapted for 'GPU' and 'Xeon-Phi' new technology: in particular now showing highly efficient use of Xeon-Phi technology), a further post-UK-RAMP code optimization 'eCSE' project for RMT (for use on the highest level 'Tier 0' platforms) has completed successfully and new coding work for higher energy electronic excitations 'to the continuum' is underway. The communities developing the codes are working together effcieintly as a team (before UK-RAMP, atomic and molecular code developments were becoming a little isolated from each other). A recent (2018-19) development is a working interface between the UKRMol+ molecular code and the RMT laser-atom code, allowing the ab initio study and simulation of molecules in laser fields.
Prior to the closure of CCPForge in December 2018, there were various URLs associated with the DL part of UK-RAMP. These included
http://ccpforge.cse.rl.ac.uk/gf/project/ukrmol-in http://ccpforge.cse.rl.ac.uk/gf/project/ukrmol-out http://ccpforge.cse.rl.ac.uk/gf/project/prmat-dcse/ as well as those associated with various outputs in the publications section. All projects have now moved to the UK-AMOR project (EPSRC grant EP/R029342/1, see the 'taken forward' section below) Gitlab site https://gitlab.com/Uk-amor . These are all active projects with ongoing further development and applications.
(Added in 2018: the 'PFARM Wiki' site https://hpcforge.org/plugins/mediawiki/wiki/pfarm/index.php/Main_Page, available for several years, is no longer available but the content is being transferred to be publicly accessible again)
Exploitation Route As of February 2016:
The CCPForge repository is very successful and its prinicples have been used and adapted by other, separate, projects in the overall atomic and molecular physics area, in particular the Tensor Network Theory (TNT) project which treats very strongly correlated many-body interactions. The PFARM interface to UKRMol is complete and has already resulted in scientifc studies and publications (science outputs of UK-RAMP are described in more detail in the QUB/UCL/OU key findings, as DL concentrated on computational matters). The diverse atomic and molecular R-Matric codes (PRMAT/PFARM, UKRMol, RMT) are in use on HPC platforms (with some modules already adapted for 'GPU' and 'Xeon-Phi' new technology, in particular now showing highly efficient use of Xeon-Phi technology); a further post-UK-RAMP code optimization 'eCSE' project for RMT (for use on the highest level 'Tier 0' platforms) has completed successfully and new coding work for higher energy electronic excitations 'to the continuum' is underway. The communities developing the codes are working well together. Many scientific applcations are underway and are better described by the QUB/OU/UCL sections of UK-RAMP.
Added February 2017: We note that PFARM is now part of the PRACE Accelerator Benchmark Suite. A parallel version of the UKRmol-out code TIMEDEL has been published in Computer Physics Communications. The UKRMol-in code is being / has been rewritten (by UK-RAMP's OU branch and collaborators), as UKRmol+, in fully object-oriented Fortran 2003 with some CCPQ core support from Daresbury.
Added February 2017: As a direct successor of the UK-RAMP grant a new CCP Software Flagship Grant EP/P022146/1 (2017-2019) has been awarded to QUB (van der Hart) with OU (Gorfinkiel) as co-investigator. This development builds on the unification of the atomic and molecular packages and will develop code for time-dependent laser pulse interactions with molecular electrons and arbitrary polarization of the pulse for atomic electrons. CCPQ SLA core support will assist this project. Further outputs from UK-RAMP in these areas will be associated with the new grant. Added March 2018: Building on the success of UK-RAMP and the above Flagship award, CCPQ has successfully applied for a new EPSRC High End Consortium (HEC). The new HEC, UK Atomic, Molecular and Optical physics R-matrix consortium, 'UK-AMOR', PI professor J Tennyson (UCL), EPSRC grant reference to be confirmed, is a 4-year consortium and involves M Plummer and AG Sunderland: outputs related to UK-RAMP work from this HEC consortium will be associated with the consortium.
Added March 2019: the UK-AMOR HEC grant has reference EP/R029342/1. Among ongoing developments associated with the DL-based part of UK-RAMP work, PFARM has been extended to be used in ultracold molecular collisions in addition to electron scattering. Following the closure of CCPForge in December 2018, the UK-RAMP-related code packages may now be found on the UK-AMOR collaboration (EPSRC grant EP/R029342/1) Gitlab site: https://gitlab.com/Uk-amor . We note (see above) the development by QUB and OU of a working interface between the UKRMol+ molecular code and the RMT laser-atom code, allowing the ab initio study and simulation of molecules in laser fields.
Sectors Digital/Communication/Information Technologies (including Software),Education,Energy,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology,Transport,Other
URL https://gitlab.com/Uk-amor
 
Description This update is February 2016 (see below for 2017-2019). Further updates will be made in the future. We note that the DL part of UK-RAMP was based on computational and best-practice developments, with science applications being discussed in the QUB/OU/UCL key findings and narrative impact. A particular non-academic impact is the use of UKRmol by the company Quantemol which provides companies with software to perform simulations relevant to industrial plasmas. The UKRmol software allows detailed ab initio data to be calculated as part of the various simulation packages offered by the company. Resonance-finding codes (such as TIMEDEL) have been used to provide resonance data which may be linked to (eg) strand-breaking in DNA. As of 2014 (the date recorded in the 'date' section of narrative impact): The CCPForge repository is very successful and its prinicples have been used and adapted by other, separate, projects in the overall atomic and molecular physics area, in particular the Tensor Network Theory (TNT) project which treats very strongly correlated many-body interactions. The PFARM interface to UKRMol is complete and has already resulted in scientifc studies and publications (science outputs of UK-RAMP are described in more detail in the QUB/UCL/OU key findings, as DL concentrated on computational matters). The diverse atomic and molecular R-Matric codes (PRMAT/PFARM, UKRMol, RMT) are in use on HPC platforms (with some modules already adapted for 'GPU' and 'Xeon-Phi' new technology), a further post-UK-RAMP code optimization 'eCSE' project underway for RMT (for use on the highest level 'Tier 0' platforms) and the communities developing them are working together. As of February 2016: The impact described above has continued. Work at DL, supported by EPSRC's Service Level Agreement for core support for the Collaborative Computational Projects, in this case CCPQ, has continued with further on-going ambitious code development and support for university-based code development in both the atomic and molecular areas of UK-RAMP. This work has also helped to maintain the contact and cross-fertilization between the communities. One immediate technical impact in this period is that one of the UK-RAMP codes has been 'properly' adapted for running on novel technology platform 'Xeon-Phi cluster' making full use of the properties of this heterogeneous ('host plus co-processor') system. Added February 2017: We note that PFARM is now part of the PRACE Accelerator Benchmark Suite for general performance benchmarking of HPC systems. A parallel version of the UKRmol-out code TIMEDEL has been published in Computer Physics Communications. The UKRMol-in code is being / has been rewritten (by UK-RAMP's OU branch and collaborators), as UKRmol+, in fully object-oriented Fortran 2003 with some CCPQ core support from Daresbury, and will be used by (eg) Quantemol. Added February 2017: As a direct successor of the UK-RAMP grant a new CCP Software Flagship Grant EP/P022146/1 (2017-2019) has been awarded to QUB (van der Hart) with OU (Gorfinkiel) as co-investigator. This development builds on the unification of the atomic and molecular packages and will develop code for time-dependent laser pulse interactions with molecular electrons and arbitrary polarization of the pulse for atomic electrons. CCPQ SLA core support will assist this project. Further outputs related to UK-RAMP in these areas will be associated with the new grant. Added March 2018: Building on the success of UK-RAMP and the above Flagship award, CCPQ has successfully applied for a new EPSRC High End Consortium (HEC). The new HEC, UK Atomic, Molecular and Optical physics R-matrix consortium, 'UK-AMOR', PI professor J Tennyson (UCL), EPSRC grant reference to be confirmed, is a 4-year consortium and involves M Plummer and AG Sunderland: outputs related to UK-RAMP work from this HEC consortium will be associated with the consortium. Added March 2019: The UK-AMOR grant reference is EPSRC EP/R029342/1. Following the closure of CCPForge in December 2018, all the code projects associated or developed from UK-RAMP may now be found on the UK-AMOR collaboration (EPSRC grant EP/R029342/1) Gitlab site: https://gitlab.com/Uk-amor . Nb at the time of writing, parts of the PFARM project are public and certain development areas are for Gitlab members only (the situation will be clarified during 2019).
First Year Of Impact 2014
Sector Education,Manufacturing, including Industrial Biotechology
Impact Types Societal
 
Description 3.5 months FTE from the STFC-SCD allocation of PRACE 3IP development effort to parallelise the UKRMol TIMEDEL module.
Amount £32,000 (GBP)
Organisation Science and Technologies Facilities Council (STFC) 
Sector Public
Country United Kingdom
Start 09/2013 
End 05/2014
 
Description HECToR NAG dCSE contract for code improvement: Combined-Multicore Parallelism for the UK electron-atom scattering Inner Region R-matrix codes on HECToR
Amount £85,000 (GBP)
Organisation Numerical Algorithms Group Ltd 
Sector Private
Country United Kingdom
Start 04/2011 
End 03/2012
 
Description ARCHER eCSE contract: eCSE02-6. PI: Prof Hugo van der Hart. Performance enhancement of RMT codes in preparation for the treatment of circular polarization. 
Organisation Queen's University Belfast
Country United Kingdom 
Sector Academic/University 
PI Contribution This is an ARCHER eCSE contract to further optimize and imnprove parallel efficiency of the parallel RMT codes developed at QUB under UK-RAMP, in particular to optimize the parallelism for large scale Tier-0 architectures and introduce full parallel I/O. The code will then be ready for the introduction of of circular polarized light interactions. MP was a co-author of the successful application for 9 months FTE (QUB UK-RAMP researcher J Parker). MP will also visit QUB at appropriate intervals to assist with interfacing to the statric PRMAT starter codes and for general advice.
Collaborator Contribution This is an ARCHER eCSE contract to further optimize and imnprove parallel efficiency of the parallel RMT codes developed at QUB under UK-RAMP, in particular to optimize the parallelism for large scale Tier-0 architectures and introduce full parallel I/O. The code will then be ready for the introduction of of circular polarized light interactions. The project is based at QUB and the work will be performed there. As part of the project MP will be funded for T&S for the visits to QUB described above.
Impact The project completed successfully with all milestones completed. The project report is available at the above URL. The work of the project has been incorporated into the main RMT code and already applied to complex calculations of ionized inert gases in laser fields (details and publications will be in the Queen's University team's ResearchFish portfolios).
Start Year 2014
 
Description CCPQ: Quantum Dynamics in Atomic, Molecular and Optical Physics (EPSRC Grant EP/M022544/1), renewal of previous CCPQ networks 
Organisation University of Birmingham
Country United Kingdom 
Sector Academic/University 
PI Contribution M Plummer provides 'core support' to CCPQ through the EPSRC Service Level Agreement with STFC Scientific Computing Department, SCD (this is allocated according to the CCPQ network panels but not paid by the Network Grant). This CCPQ network is a renewal of network EP/J010561 and the general description of that partnership applies here. The current network grant is from August 2015 to 2020. M Plummer (with A G Sunderland) continues to provide support for the atomic and molecular R-matrix packages and for antimatter work: other members of SCD provide support to the other aspects of CCPQ work. As noted in outputs below, the parallel molecular resonance code TIMEDEL has been published in Computer Physics Communications. Much optimization work has been performed on UKRMol+, the molecular inner region codes (a project to extend the UKRMol inner region basis sets to incorporate B-splines and use a more explicitly object-oriented approach to allow much more complexity in the target molecule descriptions). MP is continuing development work on a general inner region double-continuum atomic R-matrix code. He has also adapted the PFARM code for use in ultracold molecular collisions. The RMT code has been added to CCPForge (update 2019: since the closure of CCPForge in December 2018, RMT and other CCPQ codes have moved to a Gitlab site, with some SCD support). Various other publications and optimization support activities by SCD members at Daresbury and RAL (not directly related to the UK-RAMP award, eg in antimatter or strongly correlated systems) have taken place. The CCPQ website has been thoroughly revamped and relaunched.
Collaborator Contribution The new network is organized along similar lines to its predecessor CCPQ network (EP/J010561). The network coordinates joint activities among a large range of university-based members: SCD provides core support to these activities, as described above, through EPSRC's Service Level Agreement.
Impact One immediate output is the presentation at Supercomputing 2015 of a presentation on Xeon-Phi adaptation of the CCPQ/UK-RAMP code PFARM. This code was optimized to run as a fully heterogeneous (host and phi cores working simultaneously) application on a multi-node Xeon-Phi platform. The work was presented by M Lysaght (ICHEC Dublin) and is listed in the publications section (~50% contribution from M Plummer and AG Sunderland as part of CCPQ core support). In addition, the parallel molecular resonance code TIMEDEL has been published in Computer Physics Communications. Much optimization work has been performed on UKRMol+, the molecular inner region codes. The RMT code has been added to CCPForge. Various other publications and optimization support work (not directly related to the UK-RAMP award, eg in antimatter or strongly correlated systems) has taken place. Added February 2017: As a direct successor of the UK-RAMP grant a new CCP Software Flagship Grant EP/P022146/1 (2017-2019) has been awarded to QUB (van der Hart) with OU (Gorfinkiel) as co-investigator. This development builds on the unification of the atomic and molecular packages and will develop code for time-dependent laser pulse interactions with molecular electrons and arbitrary polarization of the pulse for atomic electrons. CCPQ SLA core support will assist this project. Further outputs from UK-RAMP in these areas will be associated with the new grant. Added March 2018 (updated March 2019): A new coding guide for the Flagship project, based on the UK-RAMP coding guide but updated, has been produced. Building on the success of UK-RAMP and the above Flagship award, CCPQ has successfully applied for a new EPSRC High End Consortium (HEC). The new HEC, UK Atomic, Molecular and Optical physics R-matrix consortium, 'UK-AMOR', PI professor J Tennyson (UCL), EPSRC grant reference EP/R029342/1, is a 4-year consortium and involves M Plummer and AG Sunderland: outputs related to UK-RAMP work from this HEC consortium will be associated with the consortium. (Outputs directly related to UK-RAMP work as a result of CCPQ support will continue to be reported here or under the CCPQ Network Grant report.)
Start Year 2015
 
Description Quantum dynamics in Atomic Molecular and Optical Physics (CCPQ: EPSRC Grant EP/J010561/1; previously CCP2, EPSRC grant EP/G003459/1) 
Organisation University College London
Department Department of Physics & Astronomy
Country United Kingdom 
Sector Academic/University 
PI Contribution CCPQ is an EPSRC collaborative computational project. The grant EP/J010561 is for a network and a particular flagship research project (based at Oxford and UCL). It also has associated core support from STFC SCD (Scientific Computing Department) provided through EPSRC's SLA (Service Level Agreement). All four UK-RAMP local PIs are on the CCPQ network Steering Panel. MP (local UK-RAMP PI at DL) is CCPQ secretary and is funded through the SLA to give core support to CCPQ. Since 2012 UK-RAMP MP was funded 0.85FTE through this core support and 0.15FTE as UK-RAMP investigator. MP was also funded through core support for the earlier network grant EP/G003459/1 prior to the current network. MP's CCPQ duties include general management of the electron atom collisions PRMAT code package, part of which (the PFARM code) was specifically adapted for electron molecule collisions during UK-RAMP. He is also responsible for managing the enhanced parallelization of the 'inner region' PRMAT codes and adapting them for double-continuum processes which will eventually feed into the QUB RMT codes. AG Sunderland of DL (short term researcher for UK-RAMP) also provides a fraction of CCPQ's core support.
Collaborator Contribution The CCPQ (and CCP2) networks have co-sponsored meetings at which the scientific developments of UK-RAMP (UCL, OU, QUB) have been presented. MP's work as CCPQ core support has shared interests with UK-RAMP's work in addition to the specific UK-RAMP tasks of general 'best practice' advice/management and overseeing the adaptation of PFARM for the UKRMol package. MP (with AGS and Hugo van der Hart, QUB PI) was respoinsible for obtaining a HECToR dCSE contract for enhnced parallelization of the PRMAT inner region package, which will feed into UK-RAMP: this is included as 'extra funding' and the report is included in the published outputs (and should be considered as weighted 0.15 UK-RAMP, 0.85 CCPQ). In summer 2014, he was co-applicant for an ARCHER eCSE contract lead by HvdH for optimized parallelization of the RMT code for Tier-0 architectures. This contract at QUB begins in October 2014 (this is a UK-RAMP success backed up withnh SCD expertise. As part of CCPQ support, AGS and MP successfully applied for PRACE 2IP funding for further optimization of PFARM and adaptation for GPU and Xeon-Phi clusters. This optimization and novel technology porting will feed back into UK-RAMP science (a CECAM workshop talk on this work is included in the publication outputs, to be weighted 0.9 CCPQ, 0.1 UK-RAMP). Further work on this, in a new informal collaboration with ICHEC Dublin, was reported at the 2015 EMIT conference (see publications) as a presentation and a report. MP and AGS also applied for PRACE 3IP funding of 3.5 months FTE to work on parallelization of the UKRMol TIMEDEL resonance-finding package. This is a direct follow-up to the UK-RAMP adaptation of PFARM to UKRMol: it is included as 'extra funding' and the resulting PRACE white paper is a UK-RAMP publication (~0.8 Uk-RAMP, 0.2 CCPQ). A more wide-ranging and very flexible extension of the parallelization of TIMEDEL took place over 2015.
Impact Specific to the collaboration with the DL part of the UK-RAMP project: a HECToR dCSE contract, an ARCHER eCSE contract, PRACE 3IP development funding (and influence on PRACE 2IP funding for CCPQ-related work). General shared expertise in HPC and novel technology: significant enhancement of PFARM, PRMAT, UKRMol and RMT. General: publicity and impact/awareness for UK-RAMP work through CCPQ network links. We note that the CCPForge-based 'best practice' code development and testing techniques that UK-RAMP put into practice have been embraced by the CCPQ Flagship 'Tensor Network Theory' (TNT): http://ccpforge.cse.rl.ac.uk/gf/project/tntlibrary/ .
Start Year 2009
 
Description SCD-ICHEC Novel Technology porting and optimization of R-matrix codes 
Organisation Irish Centre for High End Computing
Department Novel Technology
Country Ireland 
Sector Private 
PI Contribution An informal collaboration to port and optimize R-Matrix codes, in particular PFARM, on Novel Technology platforms, in particular Xeon-Phi clusters. Following a separate Daresbury Laboratory Technical Report (2015) examining the mixed-mode PRMAT RAD code as a follow-up to the dCSE project (see the further funding section), the extension to Novel Technology has resulted in a presentation and report at EMIT 2015, and a presentation at Supercomputing 2015 (IXPUG BoF). The PFARM propagation code has been ported and optimized on the ICHEC cluster by M Lysaght with guidance and debugging by M Plummer and AG Sunderland (from CCPQ core support). AGS has also diected work on porting the PFARM code to GPU-based systems.
Collaborator Contribution An informal collaboration to port and optimize R-Matrix codes, in particular PFARM, on Novel Technology platforms, in particular Xeon-Phi clusters. This has resulted in a presentation and report at EMIT 2015, and a presentation at Supercomputing 2015 (IXPUG BoF). The PFARM propagation code has been ported and optimized on the ICHEC cluster by M Lysaght with guidance and debugging by M Plummer and AG Sunderland (from CCPQ core support).
Impact A Daresbury Laboratory Technical Report on mixed-mode optimization, and then two presentation publications and a written report (with overall 50-60% contribution from CCPQ core support), listed in the publications. The PFARM Xeon-Phi port demonstrates proper efficient use of heterogeneous platforms, with host and phi working simultaneously on the same problem. A factor of 2 performance gain has been made so far with respect to running purely on the host network. Added February 2017: PFARM is now part of the PRACE Accelerator Benchmark Suite (a PRACE 4IP project) and a new publication detailing the benchmarks has been added. PFARM has been adapted for GPU platforms. PRACE white papers describing GPU and Xeon-Phi adaptations respectively are expected in 2017-2018. This work all builds on the UK-RAMP work. A revised and expanded version of the Accelerator Benchmark Suite paper and benchmarks was published in mid 2017. The collaboration with ICHEC was suspended in mid 2017 when Dr Lysaght left ICHEC, however the SCD development of novel architecture options for (former UK-RAMP codes will continue. For example, PFARM is now a member code of the PRACE European Accelerator Benchmark suite.
Start Year 2014
 
Description UK R-matrix Atomic and Molecular Physics HPC Code Development Project (UK-RAMP): EPSRC Grant EP/G055556/1 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution EPSRC Software Development Project. UK-RAMP is a four-site collaboration. The other three grants (apart from DL) are listed as partners. Professor Hugo van der Hart (QUB, grant EP/G055416/1), is the lead PI for the overall grant. Professor Jonathan Tennyson is local PI for grant EP/G055556/1 (UCL). The DL section provided general computational development and best practice support across all four sites particularly for repository develepment of 'UKRMol'. DL worked specifically to incorporate the atomic code 'PFARM' into the UKRMol molecular package (OU/UCL), allowing scientific outputs and papers. It also introduced further parallelization into UKRMol and QUB code RMT by obtaining related funding for relevant activities (via Daresbury's core support SLA for CCPQ, HECToR dCSE funding, ARCHER eCSE funding and through two short-term PRACE development projects) . nb While the official UK-RAMP partnership/collaboration has finished, general collaboration will continue through DL's EPSRC SLA core support and other routes/sources
Collaborator Contribution OU/UCL: Development of the UKRMol package and repository as described in the main UK-RAMP case for support, (detailed contributions in the OU and UCL UK-RAMP researchfish output reports). Support and advice on needs for the incorporation of PFARM into UKRMol and PRACE work parallelizing a time-delay resonance finding module.
Impact Professor Hugo van der Hart (QUB, grant EP/G055416/1), is the lead PI for the overall grant. Professor Jonathan Tennyson is local PI for grant EPSRC Software Development Project. UK-RAMP is a four-site collaboration. The other three grants (apart from DL) are listed as partners. Professor Hugo van der Hart (QUB, grant EP/G055416/1), is the lead PI for the overall grant. Professor Jonathan Tennyson is local PI for grant EP/G055556/1 (UCL). The DL section provided general computational development and best practice support across all four sites particularly for repository develepment of 'UKRMol'. DL worked specifically to incorporate the atomic code 'PFARM' into the UKRMol molecular package (OU/UCL), allowing scientific outputs and papers. It also introduced further parallelization into UKRMol and QUB code RMT by obtaining related funding for relevant activities (via Daresbury's core support SLA for CCPQ, HECToR dCSE funding, ARCHER eCSE funding and through two short-term PRACE development projects) . Main UCL outputs: a working UKRMol site and code: the paper describing this (Carr et al 2012) has, as of February 2016, had 43 citations. The PFARM adaptation to UKRMol has been used for electron-molecule calculations of resonances in RNA bases and electron methane collisions so far. The DL PRACE 3IP extra funding parallelized a resonance-finding module of UKRmol called TIMEDEL which was developed serially at UCL. A PRACE white paper has been published. Further development has greatly extended the parallelism, with much wider applications, and a joint paper on the serial and parallel TIMEDEL module is due to be submitted/published in 2016 (joint UCL-DL) . Note added February 2017: the TIMEDEL paper has been published in Computer Physics Communications (see publications list): this paper is a legacy of UK-RAMP and also due to continuing core support for CCPQ from the SLA. Added February 2017: As a direct successor of the UK-RAMP grant a new CCP Software Flagship Grant EP/P022146/1 (2017-2019) has been awarded to QUB (van der Hart) with OU (Gorfinkiel) as co-investigator. This development builds on the unification of the atomic and molecular packages and will develop code for time-dependent laser pulse interactions with molecular electrons and arbitrary polarization of the pulse for atomic electrons. CCPQ SLA core support will assist this project. Further outputs from UK-RAMP in these areas will be associated with the new grant.
Start Year 2009
 
Description UK R-matrix Atomic and Molecular Physics HPC Code Development Project (UK-RAMP): EPSRC Grant EP/G055599/1 
Organisation Open University
Country United Kingdom 
Sector Academic/University 
PI Contribution EPSRC Software Development Project. UK-RAMP is a four-site collaboration. The other three grants (apart from DL) are listed as partners. Professor Hugo van der Hart (QUB, grant EP/G055416/1), is the lead PI for the overall grant. Dr Jimena Gorfinkiel (EPSRC Grant EP/G055599/1) is local PI for OU. The DL section provided general computational development and best practice support across all four sites particularly for repository develepment of 'UKRMol'. DL worked specifically to incorporate the atomic code 'PFARM' into the UKRMol molecular package (OU/UCL), allowing scientific outputs and papers. It also introduced further parallelization into UKRMol and QUB code RMT by obtaining related funding for relevant activities (via Daresbury's core support SLA for CCPQ, HECToR dCSE funding, ARCHER eCSE funding and through two short-term PRACE development projects) . nb While the official UK-RAMP partnership/collaboration has finished, general collaboration will continue through DL's EPSRC SLA core support and other routes/sources.
Collaborator Contribution OU/UCL: Development of the UKRMol package and repository as described in the main UK-RAMP case for support, (detailed contributions in the OU and UCL UK-RAMP researchfish output reports). Support and advice on needs for the incorporation of PFARM into UKRMol.
Impact EPSRC Software Development Project. UK-RAMP is a four-site collaboration. The other three grants (apart from DL) are listed as partners. Professor Hugo van der Hart (QUB, grant EP/G055416/1), is the lead PI for the overall grant. Dr Jimena Gorfinkiel (EPSRC Grant EP/G055599/1) is local PI for OU. The DL section provided general computational development and best practice support across all four sites particularly for repository develepment of 'UKRMol'. DL worked specifically to incorporate the atomic code 'PFARM' into the UKRMol molecular package (OU/UCL), allowing scientific outputs and papers. It also introduced further parallelization into UKRMol and QUB code RMT by obtaining related funding for relevant activities (via Daresbury's core support SLA for CCPQ, HECToR dCSE funding, ARCHER eCSE funding and through two short-term PRACE development projects) . Main OU outputs: a working UKRMol site and code: the paper describing this (Carr et al 2012) has, as of February 2016, had 43 citations. The PFARM adaptation to UKRMol has been used for electron-molecule calculations of resonances in RNA bases and electron methane collisions so far. Further development of the UKRMol code, now called UKRMol+, is underway, supported at DL by EPSRC's Service Level Agreement for core support for CCPQ. Added February 2017: As a direct successor of the UK-RAMP grant a new CCP Software Flagship Grant EP/P022146/1 (2017-2019) has been awarded to QUB (van der Hart) with OU (Gorfinkiel) as co-investigator. This development builds on the unification of the atomic and molecular packages and will develop code for time-dependent laser pulse interactions with molecular electrons and arbitrary polarization of the pulse for atomic electrons. CCPQ SLA core support will assist this project. Further outputs from UK-RAMP in these areas will be associated with the new grant.
Start Year 2009
 
Description UK R-matrix Atomic and Molecular Physics HPC Code Development Project (UK-RAMP): EPSRC grant EP/G055416/1 
Organisation Queen's University Belfast
Country United Kingdom 
Sector Academic/University 
PI Contribution EPSRC Software Development Project. UK-RAMP is a four-site collaboration. The other three grants (apart from DL) are listed as partners. Professor Hugo van der Hart (QUB, grant EP/G055416/1), is the lead PI for the overall grant. The DL section provided general computational development and best practice support across all four sites particularly for repository develepment of 'UKRMol'. DL worked specifically to incorporate the atomic code 'PFARM' into the UKRMol molecular package (OU/UCL), allowing scientific outputs and papers. It also introduced further parallelization into UKRMol and QUB code RMT by obtaining related funding for relevant activities (via Daresbury's core support SLA for CCPQ, HECToR dCSE funding, ARCHER eCSE funding and through two short-term PRACE development projects) .
Collaborator Contribution QUB: Development of the RMT code as described in the main UK-RAMP case for support (other contributions in the QUB UK-RAMP researchfish output document). Joint dCSE application (DL/QUB), 2010-12 for parallelization and optimization of inner region atomic R-matrix codes (used as 'starter' codes by RMT). Joint eCSE application (QUB/DL, 2014-2015 for further parallelization/optimization work for 'RMT' for efficient use on 'Tier 0' facilities (completed successfully
Impact EPSRC Software Development Project. UK-RAMP is a four-site collaboration. The other three grants (apart from DL) are listed as partners. Professor Hugo van der Hart (QUB, grant EP/G055416/1), is the lead PI for the overall grant. The DL section provided general computational development and best practice support across all four sites particularly for repository develepment of 'UKRMol'. DL worked specifically to incorporate the atomic code 'PFARM' into the UKRMol molecular package (OU/UCL), allowing scientific outputs and papers. It also introduced further parallelization into UKRMol and QUB code RMT by obtaining related funding for relevant activities (via Daresbury's core support SLA for CCPQ, HECToR dCSE funding, ARCHER eCSE funding and through two short-term PRACE development projects) . Specific to QUB: Development of the RMT code as described in the main UK-RAMP case for support (other contributions in the QUB UK-RAMP researchfish output document). Joint dCSE application (DL/QUB), 2010-12 for parallelization and optimization of inner region atomic R-matrix codes (used as 'starter' codes by RMT) Joint eCSE application (QUB/DL, 2014-2015 for further parallelization/optimization work for 'RMT' for efficient use on 'Tier 0' facilities (completed successfully). Added February 2017: As a direct successor of the UK-RAMP grant a new CCP Software Flagship Grant EP/P022146/1 (2017-2019) has been awarded to QUB (van der Hart) with OU (Gorfinkiel) as co-investigator. This development builds on the unification of the atomic and molecular packages and will develop code for time-dependent laser pulse interactions with molecular electrons and arbitrary polarization of the pulse for atomic electrons. CCPQ SLA core support will assist this project. Further outputs from UK-RAMP in these areas will be associated with the new grant.
Start Year 2009
 
Title PRMAT (including PFARM) on Gitlab (previously CCPForge): an R-matrix ab initio electron atom collisions package including the general R-matrix outer region PFARM code. 
Description PRMAT is the (parallel) electron-atom collisions R-Matrix package developed at DL by core support for CCPQ (and previously CCP2) aand at QUB. The relevance to UK-RAMP is that the inner region PRMAT codes are used as 'starter' codes for the time-dependent (laser-atom) QUB R-matrix codes, in particular the UK-RAMP code RMT (developed as QUB's contribution to UK-RAMP), while a specific UK-RAMP task for DL was to adapt the PRMAT outer region code PFARM to interface to UKRMol. The CCPForge site was established at part of a CCPQ core support NAG HECToR dCSE project for optimization of PFARM which predated UK-RAMP: the site has grown significantly since. Further details on inner region PRMAT may be found in the (joint CCPQ-core and UK-RAMP) inner region dCSE report included as a publication, while further PFARM details may be found at https://hpcforge.org/plugins/mediawiki/wiki/pfarm/index.php/Main_Page . Nb: R-matrix theory separates configuration space into two regions divided by a sphere. While the full mathematical solution of the Schrodinger equation is not affected by this division, computationally the inner and outer region codes are distinct and rely on separate methods with distinct opportunities for efficiency, parallelization, optimization etc. Nb2: The user-release software is open source after (free) registration to the project on CCPForge, the project will eventually be moving to more formal open source public licensing. Note added March 2019: PFARM has now been adapted for use with ultracold molecular collisions: see the collaboration/partnership notes on CCPQ (and UK-AMOR). Note added March 2019: Following the closure of CCPForge in December 2018, PFARM (and PRMAT) may now be found on the UK-AMOR collaboration (EPSRC grant EP/R029342/1) Gitlab site: https://gitlab.com/Uk-amor . Parts of the project are public and certain development areas are for Gitlab members only (the situation will be clarified during 2019). 
Type Of Technology Software 
Year Produced 2009 
Open Source License? Yes  
Impact With respect to UK-RAMP, the UKRMol interface was sucessfully developed and the code has been used to enable massively parallel molecular calculations (already, two specific application papers as of autumn 2014 are included as UK-RAMP publication). The collaboration with CCPQ core support enabled a dCSE project on the PRMAT inner region codes and PRACE 2IP funding for further optimization of PFARM (the latter is considered a CCPQ-core extra funding but the output has relevance for UK-RAMP applications: publications/presentations describing PFARM on novel technology platforms are included in the portfolio, and PFARM has demonstrated efficient performance on a heterogeneous Xeon-Phi platform. PFARM has been added to the PRACE Accelerator Benchmarking Suite. The expertise will, post-UK-RAMP be extended to the rest of UKRMol. The PRMAT inner region developments were relevant to a QUB (with DL) ARCHER eCSE project for Tier-0 level optimization of RMT (see separate collaboration entry). As part of further CCPQ core support funded development, a double-continuum version of the inner region codes is being developed over the course of 2015-2019. PFARM is being benchmarked against a separate R-matrix package (PSTGF) for both performance and results. The results agreement is good for calculations in which PSTGF's approximations are considered valid, and performance is competitive although PFARM uses fewer approximations. 
URL https://gitlab.com/Uk-amor
 
Title UKRmol-in on Gitlab (previously CCPForge): the UK molecular R-matrix ab initio electron (positron) molecule collisions package (inner region codes). 
Description A CCPForge website for the inner region molecular R-matrix (UKRmol) codes, including code repositories for developers and users, bug-tracking, forums and newsgroups, official releases etc. A major aim of UK-RAMP was to apply best practice methodology to the legacy and then-current UKRmol codes, set up the repository, create proper standard interfaces between modules etc, and establish a sustainable codebase for both users and developers. The basic DL work on UKRMol-in was to support this best-practice technical upgrade carried out at OU and UCL. Nb: R-matrix theory separates configuration space into two regions divided by a sphere. While the full mathematical solution of the Schrodinger equation is not affected by this division, computationally the inner and outer region codes are distinct and rely on separate methods with distinct opportunities for efficiency, parallelization, optimization etc. The CCPForge site was established at the start of UK-RAMP and has grown significantly since. Nb2: The user-release software is open source after (free) registration to the project on CCPForge, the project is moving to GNU public licensing. From 2015 onwards, CCPQ core support (from DL) has been given in a project to extend the inner region basis sets to incorporate B-splines and use a more explicitly object-oriented approach to allow much more complexity in the target molecule descriptions. Note added March 2019: Following the closure of CCPForge in December 2018, the UKRMol (now UKRMol+) packages may now be found on the UK-AMOR collaboration (EPSRC grant EP/R029342/1) Gitlab site: https://gitlab.com/Uk-amor . 
Type Of Technology Software 
Year Produced 2009 
Open Source License? Yes  
Impact The main scientific code developments and scientific outputs will be described in the UCL and OU UK-RAMP grant outputs (publications particularly relevant to DL are included in the 'publications' outputs. We note here that the main paper describing the project (Carr et al 2012) has so far been referenced 43 times as of February 2015. The impacts have mainly been academic (with commercial use of UKRMol through the company Quantemol Ltd: see the UCL UK-RAMP outpus and the UK-RAMP case for support). The upgrading of the codebase is significant for future development of UKRMol (see the OU UK-RAMP outputs). One more general impact is that the CCPQ flagship project on Tensor Network Theory (TNT: http://ccpforge.cse.rl.ac.uk/gf/project/tntlibrary/) has fully embraced the 'best practice' outlook established for UKRMol and has developed substantially as a result. Other CCPQ projects have also taken on board these ideas. Added March 2018 (updated March 2019): further developments in UKRMol-in, now called UKRMol+, will be reported in the OU and UCL UK-RAMP outputs, the CCP Software Flagship Grant EP/P022146/1 (2017-2019) outputs, or the CCPQ Network (EP/M022544/2) and UK-AMOR HEC (EP/R029342/1) outputs as appropriate. One such notable development is the incorporation of molecular (UKRMol+) code into the laser atom (now molecule) RMT code. 
URL https://gitlab.com/Uk-amor
 
Title UKRmol-out on Gitlab (previously CCPForge): the UK molecular R-matrix ab initio electron (positron) molecule collisions package (outer region codes). 
Description A CCPForge website for the outer region molecular R-matrix (UKRmol) codes, including code repositories for developers and users, bug-tracking, forums and newsgroups, official releases etc. A major aim of UK-RAMP was to apply best practice methodology to the legacy and then-current UKRmol codes, set up the repository, create proper standard interfaces between modules etc, and establish a sustainable codebase for both users and developers. The basic DL work on UKRMol-out was to support this best-practice technical upgrade carried out at OU and UCL. Specific coding work was to adapt the atomic outer region package PFARM to be compatible with UKRMol-out: this is described in a separate software entry. In addition, the UK-RAMP work and expertise lead to further parallelization work of the UKRMol-out resonance-finding TIMEDEL module, funded by PRACE development effort. Nb: R-matrix theory separates configuration space into two regions divided by a sphere. While the full mathematical solution of the Schrodinger equation is not affected by this division, computationally the inner and outer region codes are distinct and rely on separate methods with distinct opportunities for efficiency, parallelization, optimization etc. The CCPForge site was established at the start of UK-RAMP and has grown significantly since. Nb2: The user-release software is open source after (free) registration to the project on CCPForge, the project is moving to GNU public licensing. Note added March 2019: Following the closure of CCPForge in December 2018, the UKRMol (now UKRMol+) packages may now be found on the UK-AMOR collaboration (EPSRC grant EP/R029342/1) Gitlab site: https://gitlab.com/Uk-amor . 
Type Of Technology Software 
Year Produced 2009 
Open Source License? Yes  
Impact The main scientific code developments and scientific outputs will be described in the UCL and OU UK-RAMP grant outputs (publications particularly relevant to DL are included in the 'publications' outputs. We note here that the main paper describing the project (Carr et al 2012) has so far been referenced 43 times as of February 2016. The impacts have mainly been academic (with commercial use of UKRMol through the company Quantemol Ltd: see the UCL UK-RAMP outpus and the UK-RAMP case for support). The upgrading of the codebase is significant for future development of UKRMol (see the OU UK-RAMP outputs). One more general impact is that the CCPQ flagship project on Tensor Network Theory (TNT: http://ccpforge.cse.rl.ac.uk/gf/project/tntlibrary/) has fully embraced the 'best practice' outlook established for UKRMol and has developed substantially as a result. Other CCPQ projects have also taken on board these ideas. In addition, the UK-RAMP work and expertise lead to further parallelization work of the UKRMol-out resonance-finding TIMEDEL module, funded by PRACE development effort. A PRACE white paper on this is included in the publications list: further development has greatly extended the parallelism, with much wider applications, and a joint paper on the serial and parallel TIMEDEL module has been published in Computer Physics Communications in early 2017 (TIMEDEL works within UKRmol-out and as a standalone package). Added March 2019: further developments in UKRMol-out will be reported in the OU and UCL UK-RAMP outputs, the CCP Software Flagship Grant EP/P022146/1 (2017-2019) outputs, or the CCPQ Network (EP/M022544/2) and UK-AMOR HEC (EP/R029342/1) outputs as appropriate. 
URL https://gitlab.com/Uk-amor