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  • 1.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A linear scaling study of solvent-solute interaction energy of drug molecules in aqua solution2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 34, p. 10320-10328Article in journal (Refereed)
    Abstract [en]

    Solvent-solute interaction energies for three well-known drug molecules in water solution are computed at the Hartree-Fock and B3LYP density functional theory levels using a linear scaling technique, which allows one to explicitly include in the model water molecules up to 14 A away from the solute molecule. The dependence of calculated interaction energies on the amount of included solvent has been examined. It is found that it is necessary to account for water molecules within an 8 A radius around the drug molecule to reach the saturated solvent interaction level. Effects of electron correlation and basis set on solvent-solute interaction energies are discussed.

  • 2.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Basis set dependence of solute-solvent interaction energy of benzene in water: a HF/DFT study2008In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 11, p. 1725-1732Article in journal (Refereed)
    Abstract [en]

    Solute-solvent interaction energies for the benzene molecule dissolved in water are computed using Hartree-Fock and B3LYP density functional theories. Explicit solvent molecules up to 14-angstrom away from the dissolved benzene molecule are included in the calculation of interaction energies. Both basis set dependence and basis Set Superposition errors are carefully examined. It is found that the use of a larger basis set for the region near the solute together with a smaller basis set for the outer region gives results very close to what would have been obtained if the larger basis set had been used for the whole system. It is also shown that a correction for the basis Set superposition error is a necessary component in this kind of calculations. With this correction, results obtained with different tested basis sets converge to within 1 kcal/mol.

  • 3.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Basis set dependence of solvent-solute interaction energy of benzene in water: a linear scaling ab initio studyArticle in journal (Refereed)
  • 4.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Erratum to: Basis set dependence of solute-solvent interaction energy of benzene in waterA HF/DFT study (vol 29, pg 1725, 2008)2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 3, p. 354-354Article in journal (Refereed)
  • 5.
    Rubensson, Emanuel H.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A hierarchic sparse matrix data structure for large-scale Hartree-Fock/Kohn-Sham calculations2007In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, no 16, p. 2531-2537Article in journal (Refereed)
    Abstract [en]

    A hierarchic sparse matrix data structure for Hartree-Fock/Kohn-Sham calculations is presented. The data structure makes the implementation of matrix manipulations needed for large systems faster, easier, and more maintainable without loss of performance. Algorithms for symmetric matrix square and inverse Cholesky decomposition within the hierarchic framework are also described. The presented data structure is general; in addition to its use in HartreeFock/Kohn-Sham calculations, it may also be used in other research areas where matrices with similar properties are encountered. The applicability of the data structure to ab initio calculations is shown with help of benchmarks on water droplets and graphene nanoribbons.

  • 6.
    Rubensson, Emanuel H.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Density matrix purification with rigorous error control2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 7Article in journal (Refereed)
    Abstract [en]

    Density matrix purification, although being a powerful tool for linear scaling construction of the density matrix in electronic structure calculations, has been limited by uncontrolled error accumulation. In this article, a strategy for the removal of small matrix elements in density matrix purification is proposed with which the forward error can be rigorously controlled. The total forward error is separated into two parts, the error in eigenvalues and the error in the occupied invariant subspace. We use the concept of canonical angles to measure and control differences between exact and approximate occupied subspaces. We also analyze the conditioning of the density matrix construction problem and propose a method for calculation of interior eigenvalues to be used together with density matrix purification. (C) 2008 American Institute of Physics.

  • 7.
    Rubensson, Emanuel H.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rotations of occupied invariant subspaces in self-consistent field calculations2008In: Journal of Mathematical Physics, ISSN 0022-2488, E-ISSN 1089-7658, Vol. 49, no 3, p. 032103-Article in journal (Refereed)
    Abstract [en]

    In this article, the self-consistent field (SCF) procedure as used in Hartree-Fock and Kohn-Sham calculations is viewed as a sequence of rotations of the so-called occupied invariant subspace of the potential and density matrices. Computational approximations are characterized as erroneous rotations of this subspace. Differences between subspaces are measured and controlled by the canonical angles between them. With this approach, a first step is taken toward a method where errors from computational approximations are rigorously controlled and threshold values are directly related to the accuracy of the current trial density, thus eliminating the use of ad hoc threshold values. Then, the use of computational resources can be kept down as much as possible without impairment of the SCF convergence. (C) 2008 American Institute of Physics.

  • 8.
    Rubensson, Emanuel H.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Truncation of Small Matrix Elements Based on the Euclidean Norm for Blocked Data Structures2009In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 30, no 6, p. 974-977Article in journal (Refereed)
    Abstract [en]

    Methods for the removal of small symmetric matrix elements based on the Euclidean norm of the error matrix are presented in this article. In large scale Hartree-Fock and Kohn-Sham calculations it is important to be able to enforce matrix sparsity while keeping errors under control. Truncation based on some unitary-invariant norm allows for control of errors in the occupied subspace as described in (Rubensson et al. J Math Phys 49, 032103). The Euclidean norm is unitary-invariant and does not grow intrinsically with system size and is thus suitable for error control in large scale calculations. The presented truncation schemes repetitively use the Lanczos method to compute the Euclidean norms of the error matrix candidates. Ritz value convergence patterns are utilized to reduce the total number of Lanczos iterations.

  • 9.
    Rubensson, Emanuel
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Near-Idempotent MatricesManuscript (Other academic)
  • 10.
    Rubensson, Emanuel
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Sparse matrix algebra for quantum modeling of large systems2007In: Applied Parallel Computing - STATE OF THE ART IN SCIENTIFIC COMPUTING     / [ed] Kagstrom B, Elmroth E, Dongarra J, Wasniewski J, Berlin, Germany: Springer-Verlag , 2007, p. 90-99Conference paper (Refereed)
    Abstract [en]

    Matrices appearing in Hartree-Fock or density functional theory coming from discretization with help of atom-centered local basis sets become sparse when the separation between atoms exceeds some system-dependent threshold value. Efficient implementation of sparse matrix algebra is therefore essential in large-scale quantum calculations. We describe a unique combination of algorithms and data representation that provides high performance and strict error control in blocked sparse matrix algebra. This has applications to matrix-rnatrix multiplication, the Trace-Correcting Purification algorithm and the entire self-consistent field calculation.

  • 11.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO).
    Fock Matrix Construction for Large Systems2006Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    This licentiate thesis deals with quantum chemistry methods for large systems. In particular, the thesis focuses on the efficient construction of the Coulomb and exchange matrices which are important parts of the Fock matrix in Hartree--Fock calculations.The methods described are also applicable in Kohn--Sham Density FunctionalTheory calculations, where the Coulomb and exchange matrices areparts of the Kohn--Sham matrix. Screening techniques for reducing the computational complexity of bot Coulomb and exchange computations are discussed, as well as the fast multipole method, used for efficient computation of the Coulomb matrix.

    The thesis also discusses how sparsity in the matrices occurring in Hartree--Fock and Kohn--Sham Density Functional Theory calculations can be used to achieve more efficient storage of matrices as well as more efficient operations on them.

    As an example of a possible type of application, the thesis includes a theoretical study of Heisenberg exchange constants, using unrestricted Kohn--Sham Density Functional Theory calculations.

    Download full text (pdf)
    FULLTEXT01
  • 12.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO).
    Quantum Chemistry for Large Systems2007Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    This thesis deals with quantum chemistry methods for large systems. In particular, the thesis focuses on the efficient construction of the Coulomb and exchange matrices which are important parts of the Fock matrix in Hartree-Fock calculations. Density matrix purification, which is a method used to construct the density matrix for a given Fock matrix, is also discussed.

    The methods described are not only applicable in the Hartree-Fock case, but also in Kohn-Sham Density Functional Theory calculations, where the Coulomb and exchange matrices are parts of the Kohn-Sham matrix. Screening techniques for reducing the computational complexity of both Coulomb and exchange computations are discussed, including the fast multipole method, used for efficient computation of the Coulomb matrix.

    The thesis also discusses how sparsity in the matrices occurring in Hartree-Fock and Kohn-Sham Density Functional Theory calculations can be used to achieve more efficient storage of matrices as well as more efficient operations on them.

    Download full text (pdf)
    FULLTEXT01
  • 13.
    Rudberg, Elias
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Computation of Franck-Condon factors for many-atom systems: simulated photoelectron spectra of formic acid isotopologues2004In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 302, no 1-3, p. 217-228Article in journal (Refereed)
    Abstract [en]

    Simulated photoelectron spectra of the four formic acid isotopologues HCOOH, HCOOD, DCOOH and DCOOD are reported. The simulations are based on computed multidimensional harmonic Franck-Condon factors (FCFs) for transitions from the ground state of the neutral molecule to the two lowest electronic states of the cation. The geometrical parameters and force constants used in the Franck-Condon analysis have been obtained at the B3LYP/6-311 +G(3df,2p) level of theory. The results are compared with well-resolved experimental spectra, and good agreement between simulated and experimental spectra is found, in particular for the first PES band. Using the computed FCFs, the vibrational fine structure of the first two bands of the experimental spectra is analyzed, and vibrational frequencies for the two cationic states are extracted from the experimental data.

  • 14.
    Rudberg, Elias
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rubensson, Emanuel H.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Automatic Selection of Integral Thresholds by Extrapolation in Coulomb and Exchange Matrix Constructions2009In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 5, no 1, p. 80-85Article in journal (Refereed)
    Abstract [en]

    We present a method to compute Coulomb and exchange matrices with predetermined accuracy as measured by a matrix norm. The computation of these matrices is fundamental in Hartree-Fock and Kohn-Sham electronic structure calculations. We show numerically that, when modern algorithms for Coulomb and exchange matrix evaluation are applied, the Euclidean norm of the error matrix e is related to the threshold value tau as epsilon C tau(alpha). The presented extrapolation method automatically selects the integral thresholds so that the Euclidean norm of the error matrix is at the requested accuracy. This approach is demonstrated for a variety of systems, including protein-like systems, water clusters, and graphene sheets. The proposed method represents an important step toward complete error control throughout the self-consistent field calculation as described in [J. Math. Phys. 2008, 49, 032103].

  • 15.
    Rudberg, Elias
    et al.
    KTH, School of Biotechnology (BIO).
    Rubensson, Emanuel H.
    KTH, School of Biotechnology (BIO).
    Salek, Pawel
    KTH, School of Biotechnology (BIO).
    Estimation of errors in Coulomb and exchange matrix constructionManuscript (Other academic)
  • 16.
    Rudberg, Elias
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rubensson, Emanuel H.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hartree-Fock calculations with linearly scaling memory usage2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 18Article in journal (Refereed)
    Abstract [en]

    We present an implementation of a set of algorithms for performing Hartree-Fock calculations with resource requirements in terms of both time and memory directly proportional to the system size. In particular, a way of directly computing the Hartree-Fock exchange matrix in sparse form is described which gives only small addressing overhead. Linear scaling in both time and memory is demonstrated in benchmark calculations for system sizes up to 11 650 atoms and 67 204 Gaussian basis functions on a single computer with 32 Gbytes of memory. The sparsity of overlap, Fock, and density matrices as well as band gaps are also shown for a wide range of system sizes, for both linear and three-dimensional systems. (C) 2008 American Institute of Physics.

  • 17.
    Rudberg, Elias
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Efficient implementation of the fast multipole method2006In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 125, no 8, p. 084106-Article in journal (Refereed)
    Abstract [en]

    A number of computational techniques are described that reduce the effort related to the continuous fast multipole method, used for the evaluation of Coulomb matrix elements as needed in Hartree-Fock and density functional theories. A new extent definition for Gaussian charge distributions is proposed, as well as a new way of dividing distributions into branches. Also, a new approach for estimating the error caused by truncation of multipole expansions is presented. It is found that the use of dynamically truncated multipole expansions gives a speedup of a factor of 10 in the work required for multipole interactions, compared to the case when all interactions are computed using a fixed multipole expansion order. Results of benchmark calculations on three-dimensional systems are reported, demonstrating the usefulness of our present implementation of the fast multipole method.

  • 18.
    Rudberg, Elias
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Nonlocal exchange interaction removes half-metallicity in graphene nanoribbons2007In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 7, no 8, p. 2211-2213Article in journal (Refereed)
    Abstract [en]

    Band gap studies of zigzag-edge graphene ribbons are presented. While earlier calculations at LDA level show that zigzag-edge graphene ribbons become half-metallic when cross-ribbon electric fields are applied, our calculations with hybrid density functional demonstrate that finite graphene ribbons behave as half-semiconductors. The spin-dependent band gap can be changed in a wide range, making possible many applications in spintronics.

  • 19.
    Rudberg, Elias
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Heisenberg Exchange in Dinuclear Manganese Complexes:  A Density Functional Theory Study2006In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 2, no 4, p. 981-989Article in journal (Refereed)
    Abstract [en]

    This work presents a systematic investigation of the performance of broken symmetry density functional theory for the evaluation of Heisenberg exchange constants. We study dinuclear MnIV-MnIV complexes with bis(μ-oxo), bis(μ-oxo)(μ-carboxylato), and tris(μ-oxo) cores for this purpose, as these are of fundamental biological interest as well as being potential precursors for molecular magnets based on manganese complexes, the so-called Mn12 magnets. The obtained results indicate that quantitative agreement with available experimental data for the Heisenberg exchange constants can be achieved for most of the investigated complexes but also that there are significant failures for some compounds. We evaluate factors influencing the accuracy of obtained results and examine effects of different mappings between broken symmetry and Heisenberg Hamiltonian states in an attempt to formulate a reliable recipe for the evaluation of magnetic coupling in these complexes. An assessment of the bonding situation in the molecular system under investigation is found crucial in choosing the appropriate scheme for evaluation of the Heisenberg exchange constants.

1 - 19 of 19
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