Biomedical subjects

C J Tymczak

Publications and source records attributed to C J Tymczak.

4 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.

Journal Article↗

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.

Journal Article↗

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.

Journal Article↗

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).

Journal Article↗