Fokke Dijkstra - Academia.edu (original) (raw)

Papers by Fokke Dijkstra

The effects of atomic and molecular electron correlation and Gaunt interaction on the transition ... more The effects of atomic and molecular electron correlation and Gaunt interaction on the transition energies between the âµDâ and â·F{sub 1,2} levels, arising from the 4fâ¶ state of the europium ion, have been studied for the ion and for the [EuOâ]â¹â» cluster as it is found in the BaâGdNbOâ crystal. The calculations were performed using the MOLFDIR program package. The results are compared to work previously done by Visser et al. in which correlation effects had not been taken into account. The effect of the Gaunt interaction is to be small. An important contribution to the correlation energy emerges from the configuration represented by the double excitations from 4d to 4f. This in agreement with work performed by Jankowski and Sokolwski on Pr{sup 3+}. The results are now in better agreement with experiment but are still not satisfactory. 13 refs., 1 fig., 4 tabs.

In this report we describe the integration of the parallel direct selected multireference CI code... more In this report we describe the integration of the parallel direct selected multireference CI code Diesel into GAMESSUK. This has been done in order to introduce a parallel version of this method into GAMESSUK. Most of the time has been spent on updating the C++ code in which Diesel has been written. The scaling of the resulting code is shown to be satisfactorily, but expected to be very good for large calculations. The project has been funded by NCF, project number NRG2004.06.

The Target infrastructure has been specially built as a storage and compute infrastructure for th... more The Target infrastructure has been specially built as a storage and compute infrastructure for the information systems derived from Astro-WISE. This infrastructure will be used by several applications that collaborate in the area of information systems within the Target project. It currently consists of 10 PB of storage and thousands of computational cores. The infrastructure has been constructed based on the requirements of the applications. The storage is controlled by the Global Parallel File System of IBM. This file system takes care of the required flexibility by combining storage hardware with different characteristics into a single file system. It is also very scalable, which allows the system to be extended into the future, while replacing old hardware with new technology.

The LOFAR Long Term Archive (LTA) is a distributed information system that provides integrated se... more The LOFAR Long Term Archive (LTA) is a distributed information system that provides integrated services for data analysis as well as long term preservation of astronomical datasets and their provenance. The data analysis capabilities are provided by a federated system that integrates a central catalog and client user interfaces provided by Astro-Wise with processing pipelines running on Grid based and University HPC clusters. The framework used for data analysis ensures that proper authorization and access rules are applied and that generated data products are ingested into the storage part of the Long Term Archive. The ingest process includes information about data provenance. This paper presents the architecture of the processing framework of the LTA.

Theoretical and Computational Chemistry, 2002

The Ab Initio Valence Bond program TURTLE has been under development for about 12 years and is no... more The Ab Initio Valence Bond program TURTLE has been under development for about 12 years and is now becoming useful for the non-specialist computational chemist as is exemplified by its incorporation in the GAMESS-UK program. We describe here the principles of the matrix evaluation and orbital optimisation algorithms and the extensions required to use the Valence Bond wavefunctions in analytical (nuclear) gradient calculations. For the applications, the emphasis is on the selective use of restrictions on the orbitals in the Valence Bond wavefunctions, to investigate chemical concepts, in particular resonance in aromatic systems.

Arxiv preprint arXiv: …, 2011

Abstract: The LOFAR Long-Term Archive (LTA) is a multi-Petabyte scale data storage for the proces... more Abstract: The LOFAR Long-Term Archive (LTA) is a multi-Petabyte scale data storage for the processed data of LOFAR telescope. We describe the adaptation of the WISE concept implemented by Target consortium for the LOFAR LTA and changes we introduced to it to ...

The Journal of Physical Chemistry A, 2001

The effect of cyclopentafusion on the aromatic properties of pyrene and its cyclopentafused conge... more The effect of cyclopentafusion on the aromatic properties of pyrene and its cyclopentafused congeners has been studied by calculating resonance energies, using the valence bond (VB) method, and nucleus independent chemical shifts using DIGLO. The VB resonance energy is only ...

Molecular Physics, 1999

The interacting correlated fragments (ICF) method proposed by Liu and McLean is employed using no... more The interacting correlated fragments (ICF) method proposed by Liu and McLean is employed using non-orthogonal orbital spaces for the interacting fragments. This way orthogonalization schemes may be avoided and the orbitals may be optimized separately at each internuclear distance. This approach is illustrated using a calculation on the He dimer, which is one of the ® rst systems to which ICF was applied. It is found that the use of non-orthog onal orbitals gives a more attractive potential. Although the orbital basis inconsistency is avoided completely, the con® guration basis inconsistency still gives rise to a considerable basis set superposition error.

Journal of Physical Organic Chemistry, 2003

epoc ABSTRACT: C m H m (m ¼ 4, 6, 8) species are analyzed in D mh and D (1/2)mh geometries by mea... more epoc ABSTRACT: C m H m (m ¼ 4, 6, 8) species are analyzed in D mh and D (1/2)mh geometries by means of valence bond (VB) calculations. The fundamental factors that distinguish aromatic and antiaromatic modes of electron delocalization are elucidated by analysis of the mixing between the covalent-state and ionic structures that distribute the electrons in all possible modes available in the cycle. The major difference found is that, by contrast to the aromatic species where all the ionic structures mix into the covalent state, in the antiaromatic species the set of diagonal-ionic structures is excluded from mixing with the covalent-state, owing to its fundamental symmetry features. This exclusion of covalent-ionic mixing is expressed at the most fundamental building blocks of the wavefunction; the spin-alternant state. The spin-alternant state is a resonance hybrid of the two spin-alternant determinants. This resonance hybrid will support a collective motion of the p -electrons around the perimeter of the ring only if ionic structures can mix to mediate the electronic flow. It is shown that in aromatic species all the ionic structures mix and sustain a continuous electronic flow around the ring perimeter. By contrast, owing to the exclusion of the diagonal-ionic structures in antiaromatic compounds, the electronic flow in antiaromatic species is interrupted. Symmetry and angular momentum analyses of the ground state in the presence of an external magnetic field show that the properties of the spin-alternant state can qualitatively describe the magnetic properties of the two classes. The continuous flow of -electrons mediated by the ionic structures of aromatic species is responsible for the enhanced diamagnetism of these species. By contrast, paramagnetic -ring current in antiaromatic species becomes possible only in the presence of the magnetic field that allows the mixing of the otherwise excluded ionic structures.

Journal of Grid Computing, 2010

these problems. We give examples of applications running on Astro-WISE and EGEE and review future... more these problems. We give examples of applications running on Astro-WISE and EGEE and review future development of the merged system.

Journal of Computational Chemistry, 2001

A parallel version of the valence bond program TURTLE has been developed. In this version the cal... more A parallel version of the valence bond program TURTLE has been developed. In this version the calculation of matrix elements is distributed over the processors. The implementation has been done using the message-passing interface (MPI), and is, therefore, portable. The parallel version of the program is shown to be quite efficient with a speed-up of 55 at 64 processors.

International Journal of Quantum Chemistry, 1995

ABSTRACT The effects of atomic and molecular electron correlation and Gaunt interaction on the tr... more ABSTRACT The effects of atomic and molecular electron correlation and Gaunt interaction on the transition energies between the 5D0 and 7F1,2 levels, arising from the 4f6 state of the europium ion, have been studied for the ion and for the [EuO6]9− cluster as it is found in the Ba2GdNbO6 crystal. The calculations were performed using the MOLFDIR program package. The results are compared to work previously done by Visser et al. in which correlation effects had not been taken into account. The effect of the Gaunt interaction is found to be small. An important contribution to the correlation energy emerges from the configuration represented by the double excitations from 4d to 4f. This in agreement with work performed by Jankowski and Sokolowski on Pr3+. The results are now in better agreement with experiment but are still not satisfactory. © 1995 John Wiley & Sons, Inc.

International Journal of Quantum Chemistry, 1998

The calculation of matrix elements involving nonorthogonal orbitals is speeded up by recognizing ... more The calculation of matrix elements involving nonorthogonal orbitals is speeded up by recognizing the orthogonalities between orbitals, leading to generalized Slater rules. The block structure present in the overlap matrix makes an efficient evaluation of its cofactors possible. These cofactors are calculated per subblock, each with its own parity sign. An adjustment parity sign has to be evaluated, which is added to the combined local signs, to give the correct total sign for the matrix element. An algorithm for the evaluation of this adjustment sign has been developed, making an easy and correct evaluation possible. The current scheme is shown to be very efficient, but possibilities for further improvement remain.

International Journal of Quantum Chemistry, 2003

Geometry optimizations have been performed for benzene and cyclobutadiene and for the correspondi... more Geometry optimizations have been performed for benzene and cyclobutadiene and for the corresponding moieties with nonresonating double bonds, viz. 1,3,5-cyclohexatriene and 1,3-cyclobutadiene. The calculations were done using the valence bond self-consistent field method including orbital optimization. Both strictly local and delocalized p-like orbitals were used for the π system, which influences the strengths of the π bonds. The calculations result

International Journal of Quantum Chemistry, 1999

The effect of ring deformation on aromaticity has been studied for bent benzene molecules in whic... more The effect of ring deformation on aromaticity has been studied for bent benzene molecules in which two carbon atoms have been bent out of plane, resulting in Ž . a boat conformation. Valence-bond self-consistent field VBSCF calculations have been performed on these molecules to obtain insight into the aromaticity of bent benzenes. Results for total energy, structure energies, weights, and orbital overlaps show that the molecule keeps its aromatic nature up to 55Њ. After 55Њ a transition to Dewar benzene occurs. The valence-bond model, by showing the weights of both Dewar and Kekulé structures, is an excellent tool to study deformed benzene.

Experimental Astronomy, 2013

The Astro-WISE information system was developed to handle data processing for the KIDS survey. In... more The Astro-WISE information system was developed to handle data processing for the KIDS survey. In this paper we describe the adaptation of the WISE concept to allow scaling to support archives containing tens of petabytes of stored data and the changes we introduced to accommodate the system for the LOFAR Long Term Archive. With this we provide an example of how

Concurrency and Computation: Practice and Experience, 2006

ABSTRACT We describe our experiences with the integration of two ocean models (THCM and MOM4) wit... more ABSTRACT We describe our experiences with the integration of two ocean models (THCM and MOM4) within a computational framework, in this case Cactus. The use of a framework like Cactus offers many advantages to computational scientists. When integrating existing code some problems are still encountered. The main problems are structural ones caused by mismatches between data structures and parallelization models. We discuss these problems and try to offer directions for improvement of the available frameworks. Copyright © 2005 John Wiley & Sons, Ltd.

Chemical Physics Letters, 1999

A gradient method for very general valence bond VB wavefunctions is presented. This method introd... more A gradient method for very general valence bond VB wavefunctions is presented. This method introduces the electronic energy as a Lagrange multiplier, and evaluates the contributions of the derivatives of the normalisation and of the first-and second-order cofactors present in the VB energy expression. The correctness of the method is illustrated with classic and breathing-orbital VB calculations on the HF molecule. q 1999 Elsevier Science B.V. All rights reserved.

Chemical Physics Letters, 2002

The geometry and energy of 1,3,5-cyclohexatriene, the reference molecule for the determination of... more The geometry and energy of 1,3,5-cyclohexatriene, the reference molecule for the determination of the extra stabilization of benzene, have been calculated using an Ab Initio Valence Bond method. The theoretical resonance energy, according to Dewar, calculated as the energy difference between two-structure benzene and single-structure 1,3,5-cyclohexatriene, both with completely optimized geometries and orbitals, is only )12.05 kcal/mol. Resonance energies of )25.37 (local orbitals), )19.82 (delocal orbitals) and )44.13 (breathing orbitals) kcal/mol are found using the Pauling definition. The concept of the vertical resonance energy, however, is proven to be not tenable beyond a minimal basis. Ó