Gator: a Python-driven program for spectroscopy simulations

A bit over a year ago we published our adcc code. In this work the aim was to develop a toolkit for computational spectroscopy methods focused on rapid development and interactive hands-on usage (see the blog article for details). Our target back then was to simplify method development involving the algebraic-diagrammatic construction approach (ADC) to compute excited states energies and properties. ADC has been a research focus both of myself as well as the group of Andreas Dreuw and the ADC family of methods have proven in the past to be greatly suited for describing photochemistry and spectroscopic results.

Employing mainly thread-based parallelism and (apart from our recent inclusion of libxm) basically no options for swapping stored tensors to disk, adcc is naturally restricted to problems that fit into the main memory of a single cluster node. This is fine for developing and testing new ADC methods, but can be limiting for employing ADC methods in practice: The code can currently only treat small-sized to medium-sized molecules.

In parallel to adcc we therefore started working on the Gator project in collaboration with the groups of Patrick Norman and Zilvinas Rinkevicius (both KTH Stockholm). We now release in a first version. Apart from an interface to adcc, Gator features a response library capable of the complex polarisation propagator (CPP) approach for simulating properties such as excited-states polarisabilities or enabling a direct computation of spectra including broadening. Additionally it contains a newly developed ADC(2) module with MPI-based distributed computing capabilities. For this the integral driver of the Veloxchem code from KTH is used, which allows the ADC(2) computation to be performed in a direct fashion (i.e. without storing the two-electron-integral tensor). This makes ADC(2) simulations in Gator more memory efficient and allows them to be distributed over a few cluster nodes. In this publication we provide an overview of Gator's current capabilities. The full abstract reads

The Gator program has been developed for computational spectroscopy and calculations of molecular properties using real and complex propagators at the correlated level of wave function theory. At present, the focus lies on methods based on the algebraic diagrammatic construction (ADC) scheme up to third-order of perturbation theory. A Fock matrix-driven implementation of the second-order ADC method for excitation energies has been realized with an underlying hybrid MPI/OpenMP parallelization scheme suitable for execution in high-performance computing cluster environments. With a modular and object-oriented program structure written in a Python/C++ layered fashion, Gator enables, in addition, time-efficient prototyping of novel scientific approaches as well as interactive notebook-driven training of students in quantum chemistry.

Recent developments in adcc
Since the publication of the adcc paper a few months back, there are a few updates to report briefly:
- adcc can now be interactively tried in the browser at try.adc-connect.org using the infrastructure from the binder project.
- Binary installation of adcc is now available via conda for Linux …
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Posted on Mi 03 Juni 2020 in Research.
Tags: electronic structure theory theoretical chemistry adcc and algebraic-diagrammatic construction
Quantifying the error of the core-valence separation approximation

After only a few months of publishing our adcc paper, which introduces the novel algebraic-diagrammatic construction (ADC) code adcc, the package has already found mention in a number of related articles. One example is a manuscript on updates in the Psi4 quantum chemistry package, which features adcc as one of …
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Posted on Mi 13 Mai 2020 in Publications.
Tags: electronic structure theory theoretical chemistry adcc algebraic-diagrammatic construction and core-valence separation
Talk in Toulouse: adcc and DFTK

A few weeks ago on 21st and 22nd November of this year Pierre-Francois Loos invited me for two days to the Laboratoire de Chimie et Physique Quantiques of the Université Paul Sabatier Toulouse. On Thursday the 21st I had the chance to present our current status in DFTK and adcc …
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Posted on Fr 06 Dezember 2019 in Research.
Tags: talk electronic structure theory Julia HPC molsturm DFTK theoretical chemistry adcc and algebraic-diagrammatic construction
adcc: A versatile toolkit for rapid development of algebraic-diagrammatic construction methods

Over the part year or so a side project I have been working off and on has been the adcc code. This python module allows to perform excited states calculation for simulating molecular spectra based on algebraic-diagrammatic construction (ADC) methods. The speciality of the adcc code is that (a) multiple …
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Posted on Mi 23 Oktober 2019 in Publications.
Tags: electronic structure theory theoretical chemistry adcc and algebraic-diagrammatic construction
Interdisciplinary software for electronic structure theory: adcc and DFTK

Last week, from Wednesday to Friday, I paid the Technical University of Munich (TUM) a short visit for two great opportunities to present my work: Once in the theoretical chemistry group of Professor Wolfgang Domcke and once at the annual meeting of the modeling, analysis and simulation of molecular systems …
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Posted on Mo 16 September 2019 in Research.
Tags: talk electronic structure theory Julia HPC molsturm DFTK theoretical chemistry adcc and algebraic-diagrammatic construction
Interdisciplinary software development in electronic structure theory (MQM Poster)

At the beginning of the month, from 30th June till 5th July, I attended the 9th Molecular Quantum Mechanics Conference in my old home Heidelberg. This occasion was a great opportunity to catch up with friends and colleges both in science and from my old circle in Heidelberg as well …
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Posted on Di 30 Juli 2019 in Research.
Tags: poster electronic structure theory Julia HPC molsturm DFTK theoretical chemistry MQM adcc and algebraic-diagrammatic construction
Franco-German Workshop 2018: Open problems related to the algebraic-diagrammatic construction scheme

In some of my recent projects, e.g. the PE-ADC paper, I got a little more into method development surrounding the algebraic-diagrammatic construction scheme (ADC). Even though quite a few people from the Dreuw group in Heidelberg are involved with ADC development and we have regular talks on ADC, I …
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Posted on Di 18 September 2018 in Research.
Tags: talk electronic structure theory theoretical chemistry algebraic-diagrammatic construction workshop and invited talk
Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems

Yesterday the journal of chemical theory and computation accepted our manuscript titled Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems. In this work we describe the combination of the polarisable embedding (PE) scheme for including environmental effects with the algebraic-diagrammatic construction (ADC) approach.

The …
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Posted on Mi 08 August 2018 in Publications.
Tags: electronic structure theory theoretical chemistry algebraic-diagrammatic construction and embedding