Biomedical subjects

Matt Challacombe

Publications and source records attributed to Matt Challacombe.

13 recordsLinked to original sources

PubMed2006

Time-reversible Born-Oppenheimer molecular dynamics.

We present a time-reversible Born-Oppenheimer molecular dynamics scheme, based on self-consistent Hartree-Fock or density functional theory, where both the nuclear and the electronic degrees of freedom are propagated in time. We show how a time-reversible adiabatic propagation of the electronic degrees of freedom is possible despite the nonlinearity and incompleteness of the self-consistent field procedure. With a time-reversible lossless propagation the simulated dynamics is stabilized with respect to a systematic long-term energy drift and the number of self-consistency cycles can be kept low thanks to a good initial guess given from the electronic propagation. The proposed molecular dynamics scheme therefore combines a low computational cost with a physically correct time-reversible representation, which preserves a detailed balance between propagation forwards and backwards in time.

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PubMed2006

Parallel algorithm for the computation of the Hartree-Fock exchange matrix: gas phase and periodic parallel ONX.

In this paper we present an efficient parallelization of the ONX algorithm for linear computation of the Hartree-Fock exchange matrix [J. Chem. Phys. 106, 9708 (1997)]. The method used is based on the equal time (ET) partitioning recently introduced [J. Chem. Phys. 118, 9128 (2003)] and [J. Chem. Phys. 121, 6608 (2004)]. ET exploits the slow variation of the density matrix between self-consistent-field iterations to achieve load balance. The method is presented and some benchmark calculations are discussed for gas phase and periodic systems with up to 128 processors. The current parallel ONX code is able to deliver up to 77% overall efficiency for a cluster of 50 water molecules on 128 processors (2.56 processors per heavy atom) and up to 87% for a box of 64 water molecules (two processors per heavy atom) with periodic boundary conditions.

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PubMed2006

Energy gradients with respect to atomic positions and cell parameters for the Kohn-Sham density-functional theory at the Gamma point.

The application of theoretical methods based on density-functional theory is known to provide atomic and cell parameters in very good agreement with experimental values. Recently, construction of the exact Hartree-Fock exchange gradients with respect to atomic positions and cell parameters within the Gamma-point approximation has been introduced. In this article, the formalism is extended to the evaluation of analytical Gamma-point density-functional atomic and cell gradients. The infinite Coulomb summation is solved with an effective periodic summation of multipole tensors. While the evaluation of Coulomb and exchange-correlation gradients with respect to atomic positions are similar to those in the gas phase limit, the gradients with respect to cell parameters needs to be treated with some care. The derivative of the periodic multipole interaction tensor needs to be carefully handled in both direct and reciprocal space and the exchange-correlation energy derivative leads to a surface term that has its origin in derivatives of the integration limits that depend on the cell. As an illustration, the analytical gradients have been used in conjunction with the QUICCA algorithm to optimize one-dimensional and three-dimensional periodic systems at the density-functional theory and hybrid Hartree-Fock/density-functional theory levels. We also report the full relaxation of forsterite supercells at the B3LYP level of theory.

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PubMed2006

Exchange energy gradients with respect to atomic positions and cell parameters within the Hartree-Fock Gamma-point approximation.

Recently, linear scaling construction of the periodic exact Hartree-Fock exchange matrix within the Gamma-point approximation has been introduced [J. Chem. Phys. 122, 124105 (2005)]. In this article, a formalism for evaluation of analytical Hartree-Fock exchange energy gradients with respect to atomic positions and cell parameters at the Gamma-point approximation is presented. While the evaluation of exchange gradients with respect to atomic positions is similar to those in the gas phase limit, the gradients with respect to cell parameters involve the accumulation of atomic gradients multiplied by appropriate factors and a modified electron repulsion integral (ERI). This latter integral arises from use of the minimum image convention in the definition of the Gamma-point Hartree-Fock approximation. We demonstrate how this new ERI can be computed with the help of a modified vertical recurrence relation in the frame of the Obara-Saika and Head-Gordon-Pople algorithm. As an illustration, the analytical gradients have been used in conjunction with the QUICCA algorithm [K. Nemeth and M. Challacombe, J. Chem. Phys. 121, 2877 (2004)] to optimize periodic systems at the Hartree-Fock level of theory.

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PubMed2005

Geometry optimization of crystals by the quasi-independent curvilinear coordinate approximation.

The quasi-independent curvilinear coordinate approximation (QUICCA) method [K. Nemeth and M. Challacombe, J. Chem. Phys. 121, 2877 (2004)] is extended to the optimization of crystal structures. We demonstrate that QUICCA is valid under periodic boundary conditions, enabling simultaneous relaxation of the lattice and atomic coordinates, as illustrated by tight optimization of polyethylene, hexagonal boron nitride, a (10,0) carbon nanotube, hexagonal ice, quartz, and sulfur at the Gamma-point RPBE/STO-3G level of theory.

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PubMed2005

Higher-order response in O(N) by perturbed projection.

Perturbed projection for linear scaling solution of the coupled-perturbed self-consistent-field equations [V. Weber, A.M.N. Niklasson, and M. Challacombe, Phys. Rev. Lett. 92, 193002 (2004)] is extended to the computation of higher-order static response properties. Although generally applicable, perturbed projection is further developed here in the context of the self-consistent first and second electric hyperpolarizabilities at the Hartree-Fock level of theory. Nonorthogonal, density-matrix analogs of Wigner's 2n+1 rule valid for linear one-electron perturbations are given up to fourth order. Linear scaling and locality of the higher-order response densities under perturbation by a global electric field are demonstrated for three-dimensional water clusters.

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PubMed2005

Nonorthogonal density-matrix perturbation theory.

Recursive density-matrix perturbation theory [A.M.N. Niklasson and M. Challacombe, Phys. Rev. Lett. 92, 193001 (2004)] provides an efficient framework for the linear scaling computation of materials response properties [V. Weber, A.M.N. Niklasson, and M. Challacombe, Phys. Rev. Lett. 92, 193002 (2004)]. In this article, we generalize the density-matrix perturbation theory to include properties computed with a perturbation-dependent nonorthogonal basis. Such properties include analytic derivatives of the energy with respect to nuclear displacement, as well as magnetic response computed with a field-dependent basis. The theory is developed in the context of linear scaling purification methods, which are briefly reviewed.

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PubMed2005

Linear scaling computation of the Fock matrix. VII. Periodic density functional theory at the Gamma point.

Linear scaling quantum chemical methods for density functional theory are extended to the condensed phase at the Gamma point. For the two-electron Coulomb matrix, this is achieved with a tree-code algorithm for fast Coulomb summation [M. Challacombe and E. Schwegler, J. Chem. Phys. 106, 5526 (1997)], together with multipole representation of the crystal field [M. Challacombe, C. White, and M. Head-Gordon, J. Chem. Phys. 107, 10131 (1997)]. A periodic version of the hierarchical cubature algorithm [M. Challacombe, J. Chem. Phys. 113, 10037 (2000)], which builds a telescoping adaptive grid for numerical integration of the exchange-correlation matrix, is shown to be efficient when the problem is posed as integration over the unit cell. Commonalities between the Coulomb and exchange-correlation algorithms are discussed, with an emphasis on achieving linear scaling through the use of modern data structures. With these developments, convergence of the Gamma-point supercell approximation to the k-space integration limit is demonstrated for MgO and NaCl. Linear scaling construction of the Fockian and control of error is demonstrated for RBLYP6-21G* diamond up to 512 atoms.

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PubMed2005

Linear scaling computation of the Fock matrix. VIII. Periodic boundaries for exact exchange at the Gamma point.

A translationally invariant formulation of the Hartree-Fock (HF) Gamma-point approximation is presented. This formulation is achieved through introduction of the minimum image convention (MIC) at the level of primitive two-electron integrals, and implemented in a periodic version of the ONX algorithm [E. Schwegler, M. Challacombe, and M. Head-Gordon, J. Chem. Phys. 106, 9708 (1997)] for linear scaling computation of the exchange matrix. Convergence of the HF-MIC Gamma-point model to the HF k-space limit is demonstrated for fully periodic magnesium oxide, ice, and diamond. Computation of the diamond lattice constant using the HF-MIC model together with the hybrid PBE0 density functional [C. Adamo, M. Cossi, and V. Barone, THEOCHEM 493, 145 (1999)] yields a0=3.569 A with the 6-21G* basis set and a 3x3x3 supercell. Linear scaling computation of the HF-MIC exchange matrix is demonstrated for diamond and ice in the condensed phase.

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PubMed2004

Linear scaling computation of the Fock matrix. VII. Parallel computation of the Coulomb matrix.

We present parallelization of a quantum-chemical tree-code for linear scaling computation of the Coulomb matrix. Equal time partition is used to load balance computation of the Coulomb matrix. Equal time partition is a measurement based algorithm for domain decomposition that exploits small variation of the density between self-consistent-field cycles to achieve load balance. Efficiency of the equal time partition is illustrated by several tests involving both finite and periodic systems. It is found that equal time partition is able to deliver 91%-98% efficiency with 128 processors in the most time consuming part of the Coulomb matrix calculation. The current parallel quantum chemical tree code is able to deliver 63%-81% overall efficiency on 128 processors with fine grained parallelism (less than two heavy atoms per processor).

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PubMed2004

The quasi-independent curvilinear coordinate approximation for geometry optimization.

This paper presents an efficient alternative to well established algorithms for molecular geometry optimization. This approach exploits the approximate decoupling of molecular energetics in a curvilinear internal coordinate system, allowing separation of the 3N-dimensional optimization problem into an O(N) set of quasi-independent one-dimensional problems. Each uncoupled optimization is developed by a weighted least squares fit of energy gradients in the internal coordinate system followed by extrapolation. In construction of the weights, only an implicit dependence on topologically connected internal coordinates is present. This new approach is competitive with the best internal coordinate geometry optimization algorithms in the literature and works well for large biological problems with complicated hydrogen bond networks and ligand binding motifs.

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PubMed2004

Density matrix perturbation theory.

An orbital-free quantum perturbation theory is proposed. It gives the response of the density matrix upon variation of the Hamiltonian by quadratically convergent recursions based on perturbed projections. The technique allows treatment of embedded quantum subsystems with a computational cost scaling linearly with the size of the perturbed region, O(N(pert.)), and as O(1) with the total system size. The method allows efficient high order perturbation expansions, as demonstrated with an example involving a 10th order expansion. Density matrix analogs of Wigner's 2n+1 rule are also presented.

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PubMed2004

Ab initio linear scaling response theory: electric polarizability by perturbed projection.

A linear scaling method for calculation of the static ab initio response within self-consistent field theory is developed and applied to the calculation of the static electric polarizability. The method is based on the density matrix perturbation theory [Phys. Rev. Lett. 92, 193001 (2004)]], obtaining response functions directly via a perturbative approach to spectral projection. The accuracy and efficiency of the linear scaling method is demonstrated for a series of three-dimensional water clusters at the RHF/6-31G(**) level of theory. The locality of the response under a global electric field perturbation is numerically demonstrated by the approximate exponential decay of derivative density matrix elements.

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