Barry I. Schneider
ABSTRACT
We document recent progress made in the development and deployment of a science gateway for atomic and molecular physics (AMP) [10]. The molecular scattering applications supported in the gateway and the early phase of the project were described in a preliminary report [33]. Here, we present recent advances in both the platform’s capabilities and in its adoption for additional software suites and new possibilities for further development. The past year has seen substantial progress, with the addition of two new software suites and additional authors. A very successful workshop, supported by the MOLSSI, NSF, and NIST, was held at NIST from Dec 11-13, 2019. The agenda contained discussions of the science as well as demonstrations of the codes both in production and learning modes. More than 30 scientists participated in the workshop. Over the past few months, the number of registered gateway users has grown to over 60.
The applications being deployed provide users with a number of state-of-the-art computational techniques to treat electron scattering from atomic and molecular targets, as well as the interaction of radiation with such systems. One may view all of these approaches as generalized close-coupling methods, where the inclusion of electron correlation is accomplished via the addition of generalized pseudostates. A number of the methods can also be employed to compute high-quality bound-state wave functions by closing the channels and imposing exponentially decaying boundary conditions. The application software suites are deployed on a number of NSF and DoE supercomputing systems. These deployments are brought to the user community through the science gateway with user interfaces, post-processing, and visualization tools. Below we outline our efforts in deploying the Django web framework for the AMPGateway using the Apache Airavata gateway middleware, discuss the new advanced capabilities available, and provide an outlook for future directions for the gateway and the AMP community.
Supplemental Material
- [1] Luca Argenti, Inés Corral, Jesús González-Vázquez, Markus Klinker, Carlos Marante, and Fernando Martín.2017. https://www.xchem.uam.es/xchem/?tag=xchemGoogle Scholar
- The Molcas Authors. 2016. Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table. Journal of Computational Chemistry 37, 5 (2016), 506–541. https://doi.org/10.1002/jcc.24221Google ScholarCross Ref
- [3] The OpenMolcas Authors.2019. https://gitlab.com/Molcas/OpenMolcasGoogle Scholar
- Jim Basney, Heather Flanagan, Terry Fleury, Jeff Gaynor, Scott Koranda, and Benn Oshrin. 2019. CILogon: Enabling Federated Identity and Access Management for Scientific Collaborations. In International Symposium on Grids & Clouds 2019 (ISGC2019) - Network, Security, Infrastructure & Operations, Vol. 351. https://doi.org/10.22323/1.351.0031Google Scholar
- Igor Bray. 1994. Convergent close-coupling method for the calculation of electron scattering on hydrogenlike targets. Phys. Rev. A 49, 2 (1994), 1066–1082. https://doi.org/10.1103/PhysRevA.49.1066Google ScholarCross Ref
- Igor Bray and Andris T. Stelbovics. 1992. Convergent close-coupling calculations of electron-hydrogen scattering. Phys. Rev. A 46, 11 (1992), 6995–7011. https://doi.org/10.1103/PhysRevA.46.6995Google ScholarCross Ref
- Igor Bray and Andris T. Stelbovics. 1995. Calculation of Electron Scattering on Hydrogenic Targets. In Advances In Atomic, Molecular, and Optical Physics. Vol. 35. 209 – 254. https://doi.org/10.1016/S1049-250X(08)60164-0Google Scholar
- Philip G. Burke. 2011. R-Matrix Theory of Atomic Collisions. Springer Series on Atomic, Optical, and Plasma Physics, Vol. 61. https://doi.org/10.1007/978-3-642-15931-2Google Scholar
- Marcus Christie, Anuj Bhandar, Supun Nakandala, Suresh Marru, Eroma Abeysinghe, Sudhakar Pamidighantam, and Marlon Pierce. 2017. Using Keycloak for Gateway Authentication and Authorization. https://doi.org/10.6084/m9.figshare.5483557.v1Google Scholar
- [10] The AMP Gateway Community.2019. https://ampgateway.org/Google Scholar
- [11] The AMP Gateway Community.2019. https://ampgateway.org/workshops/Google Scholar
- [12] Daniel T. Crawford, Cecilia Clementi, Robert Harrison, Teresa Head-Gordon, Shantenu Jha, Anna Krylov, and Theresa Windus.2016. https://molssi.org/Google Scholar
- Andrew C. Brown et al.2020. RMT: R-matrix with time-dependence. Solving the semi-relativistic, time-dependent Schrödinger equation for general, multi-electron atoms and molecules in intense, ultrashort, arbitrarily polarized laser pulses. Comput. Phys. Commun.(2020). https://doi.org/10.1016/j.cpc.2019.107062Google Scholar
- [14] Armin Scrinzi et al.2016. https://gitlab.physik.uni-muenchen.de/AG-ScrinziGoogle Scholar
- Joanne M. Carr et al.2012. UKRmol: a low-energy electron- and positron-molecule scattering suite. The European Physical Journal D 66, 3 (2012), 58. https://doi.org/10.1140/epjd/e2011-20653-6Google ScholarCross Ref
- John Towns et al.2014. XSEDE: Accelerating Scientific Discovery. Computing in Science Engineering 16, 5 (2014), 62–74. https://doi.org/10.1109/MCSE.2014.80Google ScholarCross Ref
- Lou Barreau et al.2019. Disentangling Spectral Phases of Interfering Autoionizing States from Attosecond Interferometric Measurements. Phys. Rev. Lett. 122, 25 (2019), 253203. https://doi.org/10.1103/PhysRevLett.122.253203Google ScholarCross Ref
- Marlon E. Pierce et al.2015. Apache Airavata: design and directions of a science gateway framework. Concurrency and Computation: Practice and Experience 27, 16(2015), 4282–4291. https://doi.org/10.1002/cpe.3534Google ScholarCross Ref
- Dmitry V. Fursa and Igor Bray. 1995. Calculation of electron-helium scattering. Phys. Rev. A 52, 2 (1995), 1279–1297. https://doi.org/10.1103/PhysRevA.52.1279Google ScholarCross Ref
- Dmitry V. Fursa and Igor Bray. 1997. Convergent close-coupling calculations of electron scattering on helium-like atoms and ions: electron - beryllium scattering. Journal of Physics B: Atomic, Molecular and Optical Physics 30, 24(1997), 5895–5913. https://doi.org/10.1088/0953-4075/30/24/023Google ScholarCross Ref
- Franco A. Gianturco, Robert R. Lucchese, and Nico Sanna. 1994. Calculation of low-energy elastic cross sections for electron-CF4 scattering. The Journal of Chemical Physics 100, 9 (1994), 6464–6471. https://doi.org/10.1063/1.467237Google ScholarCross Ref
- Markus Klinker, Carlos Marante, Luca Argenti, Jesús González-Vázquez, and Fernando Martín. 2018. Electron Correlation in the Ionization Continuum of Molecules: Photoionization of N2 in the Vicinity of the Hopfield Series of Autoionizing States. The Journal of Physical Chemistry Letters 9, 4 (2018), 756–762. https://doi.org/10.1021/acs.jpclett.7b03220Google ScholarCross Ref
- Vinay P. Majety, Alejandro Zielinski, and Armin Scrinzi. 2015. Photoionization of few electron systems: a hybrid coupled channels approach. New Journal of Physics 17, 6 (2015), 063002. https://doi.org/10.1088/1367-2630/17/6/063002Google ScholarCross Ref
- Carlos Marante, Luca Argenti, and Fernando Martín. 2014. Hybrid Gaussian–B-spline basis for the electronic continuum: Photoionization of atomic hydrogen. Phys. Rev. A 90, 1 (2014), 012506. https://doi.org/10.1103/PhysRevA.90.012506Google ScholarCross Ref
- Carlos Marante, Markus Klinker, Inés Corral, Jesús González-Vázquez, Luca Argenti, and Fernando Martín. 2017. Hybrid-Basis Close-Coupling Interface to Quantum Chemistry Packages for the Treatment of Ionization Problems. Journal of Chemical Theory and Computation 13, 2 (2017), 499–514. https://doi.org/10.1021/acs.jctc.6b00907Google ScholarCross Ref
- Carlos Marante, Markus Klinker, Tor Kjellsson, Eva Lindroth, Jesús González-Vázquez, Luca Argenti, and Fernando Martín. 2017. Photoionization using the xchem approach: Total and partial cross sections of Ne and resonance parameters above the 2s22p5 threshold. Phys. Rev. A 96, 2 (2017), 022507. https://doi.org/10.1103/PhysRevA.96.022507Google ScholarCross Ref
- Sonia Marggi Poullain, Markus Klinker, Jesús González-Vázquez, and Fernando Martín. 2019. Resonant photoionization of O2 up to the fourth ionization threshold. Phys. Chem. Chem. Phys. 21, 30 (2019), 16497–16504. https://doi.org/10.1039/C9CP02150GGoogle ScholarCross Ref
- Zdeněk Mašín, Jakub Benda, Jimena D. Gorfinkiel, Alex G. Harvey, and Jonathan Tennyson. 2020. UKRmol+: A suite for modelling electronic processes in molecules interacting with electrons, positrons and photons using the R-matrix method. Comput. Phys. Commun. 249 (2020), 107092. https://doi.org/10.1016/j.cpc.2019.107092Google ScholarCross Ref
- Alexandra P. P. Natalense and Robert R. Lucchese. 1999. Cross section and asymmetry parameter calculation for sulfur 1s photoionization of SF6. The Journal of Chemical Physics 111, 12 (1999), 5344–5348. https://doi.org/10.1063/1.479794Google ScholarCross Ref
- Marlon. E. Pierce, Suresh Marru, Eroma Abeysinghe, Sudhakar Pamidighantam, Marcus Christie, and Dimuthu Wannipurage. 2018. Supporting Science Gateways Using Apache Airavata and SciGaP Services. In PEARC ’18: Proceedings of the Practice and Experience on Advanced Research Computing.Google ScholarDigital Library
- Thomas N. Rescigno, C. William McCurdy, Ann E. Orel, and Byron. H. Lengsfield III. 1995. The Complex Kohn Variational Method. https://doi.org/10.1007/978-1-4757-9797-8_1Google Scholar
- [32] Paul W. Saxe, Byron H. Lengsfield III, Richard L. Martin, Miles Page, Barry I. Schneider, and P. Jeffrey Hay.1985. The MESA code was developed at LANL as a pure quantum chemistry code. A number of features were added to include those parts of the molecular short-range continuum that could be described using Gaussian basis sets.Google Scholar
- Barry I. Schneider, Klaus Bartschat, Oleg Zatsarinny, Igor Bray, Armin Scrinzi, Fernando Martín, Markus Klinker, Jonathan Tennyson, Jimena D. Gorfinkiel, and Sudhakar Pamidighantam. 2020. A Science Gateway for Atomic and Molecular Physics. arxiv:2001.02286Google Scholar
- [34] Barry I. Schneider, Robert Forrey, and Naduvalath Balakrishnan.2018. https://www.cfa.harvard.edu/itamp-event/developing-flexible-and-robust.-software-computational-atomic-and-molecular-physics-0Google Scholar
- Armin Scrinzi. 2010. Infinite-range exterior complex scaling as a perfect absorber in time-dependent problems. Phys. Rev. A 81, 5 (2010), 053845. https://doi.org/10.1103/PhysRevA.81.053845Google ScholarCross Ref
- Armin Scrinzi. 2012. t-SURFF: fully differential two-electron photo-emission spectra. New Journal of Physics 14, 8 (2012), 085008. https://doi.org/10.1088/1367-2630/14/8/085008Google ScholarCross Ref
- [37] Armin Scrinzi.2016. https://trecx.physik.uni-muenchen.de/index.htmlGoogle Scholar
- [38] C. David Sherrill, T. Daniel Crawford, Francesco Evangelista, Henry F. Schaefer III, Justin Turney, Andy Simmonett, Rollin King, and Lori Burns.2009. http://www.psicode.orgGoogle Scholar
- Jonathan Tennyson. 2010. Electron - molecule collision calculations using the R-matrix method. Phys. Rep. 491(2010), 29–76.Google ScholarCross Ref
- Oleg Zatsarinny. 2006. BSR: B-spline atomic R-matrix codes. Computer Physics Communications 174, 4 (2006), 273 – 356. https://doi.org/10.1016/j.cpc.2005.10.006Google ScholarCross Ref
- Oleg Zatsarinny and Klaus Bartschat. 2013. The B-spline R-matrix method for atomic processes: application to atomic structure, electron collisions and photoionization. Journal of Physics B: Atomic, Molecular and Optical Physics 46, 11(2013), 112001. https://doi.org/10.1088/0953-4075/46/11/112001Google ScholarCross Ref
- [42] Zenodo.2020. https://zenodo.orgGoogle Scholar
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