D. Van Neck

Subsystem constraints in variational second order density matrix optimization: Curing the dissociative behavior

B. Verstichel, H. van Aggelen, D. Van Neck, P.W. Ayers, P. Bultinck
Journal of Chemical Physics
132, 114113
2010
A1

Abstract 

A previous study of diatomic molecules revealed that variational second-order density matrix theory has serious problems in the dissociation limit when the N-representability is imposed at the level of the usual two-index (P,Q,G) or even three-index (T1,T2) conditions [ H. Van Aggelen et al., Phys. Chem. Chem. Phys. 11, 5558 (2009) ]. Heteronuclear molecules tend to dissociate into fractionally charged atoms. In this paper we introduce a general class of N-representability conditions, called subsystem constraints, and show that they cure the dissociation problem at little additional computational cost. As a numerical example the singlet potential energy surface of Be B+ is studied. The extension to polyatomic molecules, where more subsystem choices can be identified, is also discussed.

Open Access version available at UGent repository

Partitioning of the molecular density matrix over atoms and bonds

D. Vanfleteren, D. Van Neck, P. Bultinck, P.W. Ayers, M. Waroquier
Journal of Chemical Physics
132, 164111
2010
A1

Abstract 

A double-index atomic partitioning of the molecular first-order density matrix is proposed. Contributions diagonal in the atomic indices correspond to atomic density matrices, whereas off-diagonal contributions carry information about the bonds. The resulting matrices have good localization properties, in contrast to single-index atomic partitioning schemes of the molecular density matrix. It is shown that the electron density assigned to individual atoms, when derived from the density matrix partitioning, can be made consistent with well-known partitions of the electron density over atom in the molecule basins, either with sharp or with fuzzy boundaries. The method is applied to a test set of about 50 molecules, representative for various types of chemical binding. A close correlation is observed between the trace of the bond matrices and the shared electron density index.

Comparative study of various normal mode analysis techniques based on partial Hessians

A. Ghysels, V. Van Speybroeck, E. Pauwels, S. Catak, B.R. Brooks, D. Van Neck, M. Waroquier
Journal of Computational Chemistry
31 (5), 994-1007
2010
A1

Abstract 

Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of information when the full Hessian matrix is used. Several partial Hessian methods have been proposed in the literature, yielding approximate normal modes. These methods aim at reducing the computational load and/or calculating only the relevant normal modes of interest in a specific application. Each method has its own (dis)advantages and application field but guidelines for the most suitable choice are lacking. We have investigated several partial Hessian methods, including the Partial Hessian Vibrational Analysis (PHVA), the Mobile Block Hessian (MBH), and the Vibrational Subsystem Analysis (VSA). In this article, we focus on the benefits and drawbacks of these methods, in terms of the reproduction of localized modes, collective modes, and the performance in partially optimized structures. We find that the PHVA is suitable for describing localized modes, that the MBH not only reproduces localized and global modes but also serves as an analysis tool of the spectrum, and that the VSA is mostly useful for the reproduction of the low frequency spectrum. These guidelines are illustrated with the reproduction of the localized amine-stretch, the spectrum of quinine and a bis-cinchona derivative, and the low frequency modes of the LAO binding protein. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010

Nonlocal extension of the dispersive optical model to describe data below the Fermi energy

W.H. Dickhoff, D. Van Neck, S.J. Waldecker, R.J. Charity, L.G. Sobotka
Physical Review C
82, 054306
2010
A1

Abstract 

Present applications of the dispersive-optical-model analysis are restricted by the use of a local but energy-dependent version of the generalized Hartree-Fock potential. This restriction is lifted by the introduction of a corresponding nonlocal potential without explicit energy dependence. Such a strategy allows for a complete determination of the nucleon propagator below the Fermi energy with access to the expectation value of one-body operators (like the charge density), the one-body density matrix with associated natural orbits, and complete spectral functions for removal strength. The present formulation of the dispersive optical model (DOM) therefore allows the use of elastic electron-scattering data in determining its parameters. Application to 40Ca demonstrates that a fit to the charge radius leads to too much charge near the origin using the conventional assumptions of the functional form of the DOM. A corresponding incomplete description of high-momentum components is identified, suggesting that the DOM formulation must be extended in the future to accommodate such correlations properly. Unlike the local version, the present nonlocal DOM limits the location of the deeply bound hole states to energies that are consistent with (e,e′p) and (p,2p) data.

Communication: Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors

D. Vanfleteren, D. Van Neck, P. Bultinck, P.W. Ayers, M. Waroquier
Journal of Chemical Physics
133, 231103
2010
A1

Abstract 

A double-atom partitioning of the molecular one-electron density matrix is used to describe atoms and bonds. All calculations are performed in Hilbert space. The concept of atomic weight functions (familiar from Hirshfeld analysis of the electron density) is extended to atomic weight matrices. These are constructed to be orthogonal projection operators on atomic subspaces, which has significant advantages in the interpretation of the bond contributions. In close analogy to the iterative Hirshfeld procedure, self-consistency is built in at the level of atomic charges and occupancies. The method is applied to a test set of about 67 molecules, representing various types of chemical binding. A close correlation is observed between the atomic charges and the Hirshfeld-I atomic charges.

Open Access version available at UGent repository

Variational density matrix optimization using semidefinite programming

B. Verstichel, H. van Aggelen, D. Van Neck, P.W. Ayers, P. Bultinck
Computer Physics Communications
182 (9), 2025-2028
2011
A1

Abstract 

We discuss how semidefinite programming can be used to determine the second-order density matrix directly through a variational optimization. We show how the problem of characterizing a physical or N-representable density matrix leads to matrix-positivity constraints on the density matrix. We then formulate this in a standard semidefinite programming form, after which two interior point methods are discussed to solve the SDP. As an example we show the results of an application of the method on the isoelectronic series of Beryllium.

Open Access version available at UGent repository

Stockholder Projector Analysis: a Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors

D. Vanfleteren, D. Van Neck, P. Bultinck, P.W. Ayers, M. Waroquier
Journal of Chemical Physics
136, 014107
2012
A1

Abstract 

A previously introduced partitioning of the molecular one-electron density matrix over atoms and bonds [D. Vanfleteren et al., J. Chem. Phys. 133, 231103 (2010)] is investigated in detail. Orthogonal projection operators are used to define atomic subspaces, as in Natural Population Analysis. The orthogonal projection operators are constructed with a recursive scheme. These operators are chemically relevant and obey a stockholder principle, familiar from the Hirshfeld-I partitioning of the electron density. The stockholder principle is extended to density matrices, where the orthogonal projectors are considered to be atomic fractions of the summed contributions. All calculations are performed as matrix manipulations in one-electron Hilbert space. Mathematical proofs and numerical evidence concerning this recursive scheme are provided in the present paper. The advantages associated with the use of these stockholder projection operators are examined with respect to covalent bond orders, bond polarization, and transferability.

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian

A. Ghysels, H. Lee Woodcock III, J.D. Larkin, B.T. Miller, Y. Shao, J. Kong, D. Van Neck, V. Van Speybroeck, M. Waroquier, B.R. Brooks
Journal of Chemical Theory and Computation (JCTC)
7 (2), 496–514
2011
A1

Abstract 

The calculation of the analytical second derivative matrix (Hessian) is the bottleneck for vibrational analysis in QM/MM systems when an electrostatic embedding scheme is employed. Even with a small number of QM atoms in the system, the presence of MM atoms increases the computational cost dramatically: the long-range Coulomb interactions require that additional coupled perturbed self-consistent field (CPSCF) equations need to be solved for each MM atom displacement. This paper presents an extension to the Mobile Block Hessian (MBH) formalism for QM/MM calculations with blocks in the MM region and its implementation in a parallel version of the Q-Chem/CHARMM interface. MBH reduces both the CPU time and the memory requirements compared to the standard full Hessian QM/MM analysis, without the need to use a cutoff distance for the electrostatic interactions. Special attention is given to the treatment of link atoms which are usually present when the QM/MM border cuts through a covalent bond. Computational efficiency improvements are highlighted using a reduced chorismate mutase enzyme system, consisting of 24 QM atoms and 306 MM atoms, as a test example. In addition, the drug bortezomib, used for cancer treatment of myeloma, has been studied as a test case with multiple MBH block choices and both a QM and QM/MM description. The accuracy of the calculated Hessians is quantified by imposing Eckart constraints, which allows for the assessment of numerical errors in second derivative procedures. The results show that MBH within the QM/MM description not only is a computationally attractive method but also produces accurate results.

Variational second order density matrix study of F3−: Importance of subspace constraints for size-consistency

H. van Aggelen, B. Verstichel, P. Bultinck, D. Van Neck, P.W. Ayers, D.L. Cooper
Journal of Chemical Physics
134, 054115
2011
A1

Abstract 

Variational second order density matrix theory under “two-positivity” constraints tends to dissociate molecules into unphysical fractionally charged products with too low energies. We aim to construct a qualitatively correct potential energy surface for F3− by applying subspace energy constraints on mono- and diatomic subspaces of the molecular basis space. Monoatomic subspace constraints do not guarantee correct dissociation: the constraints are thus geometry dependent. Furthermore, the number of subspace constraints needed for correct dissociation does not grow linearly with the number of atoms. The subspace constraints do impose correct chemical properties in the dissociation limit and size-consistency, but the structure of the resulting second order density matrix method does not exactly correspond to a system of noninteracting units. © 2011 American Institute of Physics

Open Access version available at UGent repository

A primal-dual semidefinite programming algorithm tailored to the variational determination of the two-body density matrix

B. Verstichel, H. van Aggelen, D. Van Neck, P. Bultinck, S. De Baerdemacker
Computer Physics Communications
182 (6), 1235-1244
2011
A1

Abstract 

The quantum many-body problem can be rephrased as a variational determination of the two-body reduced density matrix, subject to a set of N-representability constraints. The mathematical problem has the form of a semidefinite program. We adapt a standard primal–dual interior point algorithm in order to exploit the specific structure of the physical problem. In particular the matrix-vector product can be calculated very efficiently. We have applied the proposed algorithm to a pairing-type Hamiltonian and studied the computational aspects of the method. The standard N-representability conditions perform very well for this problem.
Keywords: Density matrix; Variational; Semidefinite programming

Open Access version available at UGent repository

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