Finite difference method accelerated with sparse solvers for structural analysis of the metal-organic complexes
Open Access
- 1 May 2016
- journal article
- research article
- Published by IOP Publishing in Journal of Physics: Conference Series
- Vol. 712 (1), 012004
- https://doi.org/10.1088/1742-6596/712/1/012004
Abstract
Finite difference method (FDM) implemented in the FDMNES software [Phys. Rev. B, 2001, 63, 125120] was revised. Thorough analysis shows, that the calculated diagonal in the FDM matrix consists of about 96% zero elements. Thus a sparse solver would be more suitable for the problem instead of traditional Gaussian elimination for the diagonal neighbourhood. We have tried several iterative sparse solvers and the direct one MUMPS solver with METIS ordering turned out to be the best. Compared to the Gaussian solver present method is up to 40 times faster and allows XANES simulations for complex systems already on personal computers. We show applicability of the software for metal-organic [Fe(bpy)3]2+ complex both for low spin and high spin states populated after laser excitation.Keywords
This publication has 15 references indexed in Scilit:
- Optimized Finite Difference Method for the Full-Potential XANES Simulations: Application to Molecular Adsorption Geometries in MOFs and Metal–Ligand Intersystem Crossing TransientsJournal of Chemical Theory and Computation, 2015
- DFT calculations of the structures and vibrational spectra of the [Fe(bpy)3]2+ and [Ru(bpy)3]2+ complexesChemical Physics, 2008
- Low-temperature lifetimes of metastable high-spin states in spin-crossover and in low-spin iron(II) compounds: The rule and exceptions to the ruleCoordination Chemistry Reviews, 2006
- Hybrid scheduling for the parallel solution of linear systemsParallel Computing, 2006
- Algorithm 832ACM Transactions on Mathematical Software, 2004
- Ligand Field Theoretical ConsiderationsPublished by Springer Science and Business Media LLC ,2004
- Spin Crossover—An Overall PerspectivePublished by Springer Science and Business Media LLC ,2004
- X-ray absorption near-edge structure calculations beyond the muffin-tin approximationPhysical Review B, 2001
- A Fully Asynchronous Multifrontal Solver Using Distributed Dynamic SchedulingSIAM Journal on Matrix Analysis and Applications, 2001
- A Fast and High Quality Multilevel Scheme for Partitioning Irregular GraphsSIAM Journal on Scientific Computing, 1998