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New efficient integral algorithms for quantum chemistry
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0002-7906-2946
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The contents of this thesis are centered in the developement of new efficient algorithms for molecular integral evaluation in quantum chemistry, as well as new design and implementation strategies for such algorithms aimed at maximizing their performance and the utilization of modern hardware.

This thesis introduces the K4+MIRROR algorithm for 2-electron repulsion integrals, a new ERI integral scheme effective for both segmented and general contraction, which surpasses the performance of all previous ERI analytic algorithms published in the literature. The performance of the K4 kernel contraction schemeis further boosted by the use of some new recurrence relations, CDR/AERR family of recurrences, and the algorithms is further refined for spherical GTOs with the also new SKS method.

New prescreening methods for two-electron integrals are also derived, allowing a more consistent methodology for discarding negligible ERI batches. This thesis introduces new techniques useful to pack integrals efficiently and better exploit the underlying modern SIMD or stream processing hardware. These algorithms and methods are implemented in a new library, the Echidna Fock Solver, a hybrid parallelized module for computing Coulomb and Exchange matrices which has been interfaced to the Dalton suite of quantum chemistry programs. Self-Consistent Field and Response Theory calculations in Dalton using the new EFS library are substantially accelerated, also enabling for the first time the use of general contraction basis sets as default basis for extended calculations.

The thesis further describes the derivation and implementation of an integral algorithm for evaluating the matrix elements needed for the recently introduced QM/CMM method, for which many of the techniques previously derived are also used, along with a suitable prescreening method for the matrix elements. The implementation is also interfaced to the Dalton quantum chemistry program, and used in production calculations.

The last chapter of the thesis is devoted to the derivation of a general analytic solution for type-II Effective Core Potential integrals, arguably one of the most troublesome molecular integrals in quantum chemistry. A new recurrence is introduced for the integrals, and a screening method is presented. Based on these results, a new efficient algorithm for computing type-II ECPs is also described.

 

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2014. , xi, 103 p.
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2014:13
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
URN: urn:nbn:se:kth:diva-149572ISBN: 978-91-7595-237-6 (print)OAI: oai:DiVA.org:kth-149572DiVA: diva2:740301
Public defence
2014-09-15, FB53, AlbaNova, Roslagstullsbacken, Stockholm, 14:00 (English)
Opponent
Supervisors
Note

QC 20140826

Available from: 2014-08-26 Created: 2014-08-24 Last updated: 2014-08-26Bibliographically approved
List of papers
1. An algorithm for the efficient evaluation of two-electron repulsion integrals over contracted Gaussian-type basis functions
Open this publication in new window or tab >>An algorithm for the efficient evaluation of two-electron repulsion integrals over contracted Gaussian-type basis functions
2012 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 137, no 23, 234105- p.Article in journal (Refereed) Published
Abstract [en]

A new algorithm for the evaluation of two-electron repulsion integrals optimized for high contraction degrees is derived. Both the segmented and general contraction versions of the algorithm show significant theoretical performance gains over the asymptotically fastest algorithms published in the literature so far. A preliminary implementation of the algorithm shows good agreement with the theoretical results and demonstrates substantial average speedups in the evaluation of two-electron repulsion integrals over commonly used basis sets with varying degrees of contraction with respect to a mature, highly optimized quantum chemical code.

Keyword
chemistry computing, electric potential, integration, numerical analysis, potential energy functions, quantum chemistry
National Category
Physical Sciences Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-116652 (URN)10.1063/1.4769730 (DOI)000312780300007 ()2-s2.0-84871955075 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note

QC 20130123

Available from: 2013-01-23 Created: 2013-01-22 Last updated: 2017-12-06Bibliographically approved
2. A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments
Open this publication in new window or tab >>A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments
Show others...
2014 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 3, 989-1003 p.Article in journal (Refereed) Published
Abstract [en]

We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.

Keyword
Molecular-Dynamics Simulations, Particle Mesh Ewald, Qm/Mm Approach, Force-Fields, Gas-Phase, Energies, Systems, Model, Polarizabilities, Proteins
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-144555 (URN)10.1021/ct400897s (DOI)000332913500013 ()2-s2.0-84896288202 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note

QC 20140425

Available from: 2014-04-25 Created: 2014-04-24 Last updated: 2017-12-05Bibliographically approved
3. Non-linear optical properties of molecules in heterogeneous environments: a quadratic density functional/molecular mechanics response theory
Open this publication in new window or tab >>Non-linear optical properties of molecules in heterogeneous environments: a quadratic density functional/molecular mechanics response theory
2014 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 19, 8981-8989 p.Article in journal (Refereed) Published
Abstract [en]

We generalize a density functional theory/molecular mechanics approach for heterogeneous environments with an implementation of quadratic response theory. The updated methodology allows us to address a variety of non-linear optical, magnetic and mixed properties of molecular species in complex environments, such as combined metallic, solvent and confined organic environments. Illustrating calculations of para-nitroaniline on gold surfaces and in solution reveals a number of aspects that come into play when analyzing second harmonic generation of such systems - such as surface charge flow, coupled surface-solvent dynamics and induced geometric and electronic structure effects of the adsorbate. Some ramifications of the methodology for applied studies are discussed.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2014
Keyword
Enhanced Raman-Scattering, Para-Nitroaniline, 2nd-Harmonic Generation, Force-Fields, Hyperpolarizabilities, Polarizabilities, Nanoclusters, Model
National Category
Other Physics Topics Other Chemistry Topics
Identifiers
urn:nbn:se:kth:diva-145620 (URN)10.1039/c4cp00992d (DOI)000335015700033 ()2-s2.0-84898812949 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note

QC 20140523

Available from: 2014-05-23 Created: 2014-05-23 Last updated: 2017-12-05Bibliographically approved
4. Efficient time dependent density functional theory calculations using general contraction basis sets
Open this publication in new window or tab >>Efficient time dependent density functional theory calculations using general contraction basis sets
(English)Manuscript (preprint) (Other academic)
National Category
Other Physics Topics Other Chemistry Topics
Identifiers
urn:nbn:se:kth:diva-149681 (URN)
Note

QS 2014

Available from: 2014-08-26 Created: 2014-08-26 Last updated: 2014-08-26Bibliographically approved
5. New recurrence relations for analytic evaluationof two-electron repulsion integrals over highly contracted gaussian-type orbitals
Open this publication in new window or tab >>New recurrence relations for analytic evaluationof two-electron repulsion integrals over highly contracted gaussian-type orbitals
(English)Manuscript (preprint) (Other academic)
National Category
Other Physics Topics Other Chemistry Topics
Identifiers
urn:nbn:se:kth:diva-149683 (URN)
Note

QS 2014

Available from: 2014-08-26 Created: 2014-08-26 Last updated: 2014-08-26Bibliographically approved

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