Software for scientific simulations

Several codes developed by Action participants are available through the AMOS Gateway, a Portal for Research and Education in Atomic, Molecular, and Optical Science: https://amosgateway.org/. This Science Gateway is an international effort to collect and make available to the community a set of advanced com-tools that are actively being used to study atomic and molecular collisions and the interaction of radiation with atoms and molecules.
Main actors involved are: Barry I. Schneider Klaus Bartschat (Drake University) Kathryn Hamilton (Drake University) Igor Bray (Curtin University, Australia)Armin Scrinzi (Ludwig-Maximilians U., Germany) Fernando Martiın (U. Autonoma de Madrid, Spain) Jesus Gonzalez Vasquez(U. Autonoma de Madrid) Jimena Gorfinkiel (Open University, UK) Jonathan Tennyson (University College London,UK) Sudhakar Pamidighantam (Indiana University)

Some of the codes developed by AttoChem participants are:

R-Matrix with Time Dependence (RMT)

RMT is a programme which solves the time-dependent Schrödinger equation for general, multielectron atoms, ions and molecules interacting with laser light. As such it can be used to model ionization (single-photon, multiphoton and strong-field), recollision (high-harmonic generation, strong-field rescattering) and, more generally, absorption or scattering processes with a full account of the multielectron correlation effects in a time-dependent manner. Calculations can be performed for targets interacting with ultrashort, intense laser pulses of long wavelength and arbitrary polarization. Calculations for atoms can optionally include the Breit–Pauli correction terms for the description of relativistic (in particular, spin–orbit) effects.The code is written in Fortran, and invokes both distributed and shared memory parallelism via MPI and OpenMP.

License: GNU General Public License 3

Acknowledgements: RMT is part of the UK-AMOR suite, and can be obtained for free from https://gitlab.com/Uk-amor/RMT/rmt/. The development of RMT has benefited from computational support from CoSeC, the Computational Science Centre for Research Communities, through CCPQ. Funding from the EPSRC under Grants No. EP/P022146/1, No. EP/P013953/1, No. EP/R029342/1, and No. EP/T019530/1.

Bibliography

Time-dependent Recursive IndeXing (TRECX)

The time-dependent Recursive indeXing method for strong-field interactions with atoms and molecules. tRecX is a C++ code for solving generalized inhomogeneous time-dependent Schrödinger-type equations idΨ /dt = H[t, Ψ ] + Φ in arbitrary dimensions and in a variety of coordinate systems. The operator H[t, Ψ] may have simple non-linearities, as in Gross-Pitaevskii and Hartree(-Fock) problems.

Primary application of tRecX has been for non-perturbative strong-field single and double photo-electron emission in atomic and molecular physics. The code is designed for large-scale ab initio calculations, for exploring models, and for advanced teaching in computational physics.

License: GNU General Public License 2

Bibliography

UK Molecular R-Matrix (UKRMOL+)

UKRmol+ is an implementation of the time-independent R-matrix method for molecules. The suite determines scattering data (e.g. integral cross sections, resonance parameters, vibrational excitation cross sections for diatomic molecules) for low energy electron and positron collisions, photoionization observables, and permanent and transition dipole moments between bound and continuum states that can be used to model further photon-induced processes, for example, by means of the R-matrix with time approach and software.

UKRmol+ requires external quantum chemistry codes (e.g. Molpro) to provide target molecular orbitals used to build multi-configurational, multicentric wavefunctions. Gaussian and/or B-spline basis functions are used to represent the continuum; all integral operations (evaluation, transformation, etc.) in the mixed basis are carried out using the GBTOlib, a high-performance library for evaluation of molecular integrals.

The suite contains about a dozen programs, some serial, some multi-threaded, and some employing MPI. The source codes together with CMake scripts for the configuration, compilation, testing and installation of the suite are freely available as a tarball from Zenodo.

  • Main Developers: Zdeněk Mašín, Jakub Benda, Jimena D. Gorfinkiel, Jonathan Tennyson, Alex G. Harvey and many colleagues who have contributed to the development of the UK Molecular R-matrix codes over many years
  • The code is written in Fortran 95 with use of some Fortran 2003 features and uses OpenMP and optionally MPI.
  • Contact: J.Gorfinkiel@open.ac.uk
  • Source code
  • CPC UKRmol+ paper
  • Performance
  • Examples from the NIST AMPGateway Workshop, December 2019
  • Further information

Bibliography

XChem

XChem is a solution for an all-electron ab-initio calculation of the electronic continuum of molecular systems. XChem combines the tools of quantum chemistry (as implemented in Molcas) and scattering theory to accurately account for electron correlation in the single-ionization continuum of atoms, small and medium-size molecules.

  • Developers: C. Marante, M. Klinker, L. Argenti, V. Borrás, I. Corral, J. González-Vázquez and F. Martín.
  • XChem website
  • Performance

Bibliography

Octopus

Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation.
For optimal execution performance Octopus is parallelized using MPI and OpenMP and can scale to tens of thousands of processors. It also has support for graphical processing units (GPUs) through OpenCL and CUDA.
Octopus is free software, released under the GPL license, so you are free to download it, use it and modify it.

Sharc

The SHARC (Surface Hopping including ARbitrary Couplings) molecular dynamics program suite is a software package developed by the González group in Vienna to study the excited-state dynamics of molecules. Learn more about the magic of SHARC…

Documentation

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