Introducing PROFESS 3.0: An advanced program for orbital-free density functional theory molecular dynamics simulations

Chen, Mohan; Xia, Junchao; Huang, Chen; Dieterich, Johannes M.; Hung, Linda; Shin, Ilgyou; Carter, Emily A.

doi:10.1016/j.cpc.2014.12.021

Cited by 81 publications

(75 citation statements)

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“…Conventionally, these extended interactions are computed in Fourier space to take advantage of the efficient evaluation of convolution integrals using Fourier transforms. For this reason, Fourier space formulations have been the most popular and widely used in orbital-free DFT calculations 27,28 . However, Fourier space formulations employing the plane-wave basis result in some significant limitations.…”

Section: A Local Real-space Formulationmentioning

confidence: 99%

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Real-space formulation of orbital-free density functional theory using finite-element discretization: The case for Al, Mg, and Al-Mg intermetallics

2015

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We propose a local real-space formulation for orbital-free DFT with density dependent kinetic energy functionals and a unified variational framework for computing the configurational forces associated with geometry optimization of both internal atomic positions as well as the cell geometry. The proposed real-space formulation, which involves a reformulation of the extended interactions in electrostatic and kinetic energy functionals as local variational problems in auxiliary potential fields, also readily extends to all-electron orbital-free DFT calculations that are employed in warm dense matter calculations. We use the local real-space formulation in conjunction with higher-order finite-element discretization to demonstrate the accuracy of orbital-free DFT and the proposed formalism for the Al-Mg materials system, where we obtain good agreement with Kohn-Sham DFT calculations on a wide range of properties and benchmark calculations. Finally, we investigate the cell-size effects in the electronic structure of point defects, in particular a mono-vacancy in Al. We unambiguously demonstrate that the cell-size effects observed from vacancy formation energies computed using periodic boundary conditions underestimate the extent of the electronic structure perturbations created by the defect. On the contrary, the bulk Dirichlet boundary conditions, accessible only through the proposed real-space formulation, which correspond to an isolated defect embedded in the bulk, show cell-size effects in the defect formation energy that are commensurate with the perturbations in the electronic structure. Our studies suggest that even for a simple defect like a vacancy in Al, we require cell-sizes of ∼ 10 3 atoms for convergence in the electronic structure.

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Section: A Local Real-space Formulationmentioning

confidence: 99%

“…The widely used numerical implementation of orbitalfree DFT is based on a Fourier space formalism using a plane-wave discretization 27,28 . A Fourier space formulation provides an efficient computation of the extended interactions arising in orbital-free DFT-electrostatics and kinetic energy functionals-through Fourier transforms.…”

Section: Introductionmentioning

confidence: 99%

Real-space formulation of orbital-free density functional theory using finite-element discretization: The case for Al, Mg, and Al-Mg intermetallics

2015

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“…The Perdew-Burke-Ernzerhof (PBE) [90] generalized gradient approximation (GGA) XC functional and previous GGA-PBE Si [84] and Li [44] BLPSs are used for direct comparison to previously published results [85] of KSDFT-PAW (projector augmented wave) [91], KSDFT-BLPS, and OFDFT-BLPS with the original WGCD KEDF. All OFDFT calculations are performed within PROFESS 3.0 [92][93][94]. The plane wave basis kinetic energy cutoff is 1600 eV to converge the total energy to within 1 meV/atom for all systems.…”

Section: Swgcd Testsmentioning

confidence: 99%

Orbital-free density functional theory study of amorphous Li–Si alloys and introduction of a simple density decomposition formalism

Xia¹,

Carter²

2016

Modelling Simul. Mater. Sci. Eng.

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We propose a simple density decomposition formalism within orbital-free (OF) density functional theory (DFT) based on the Wang-Govind-Carter-decomposition (WGCD) kinetic energy density functional (KEDF). The resulting simple-WGCD (sWGCD) KEDF provides efficient density optimization, full cell relaxation, reasonable bulk properties for various materials compared to both the original OFDFT-WGCD and the Kohn-Sham (KS) DFT values, and has various numerical benefits including more stable convergence and lower computational cost (twice as fast as the WGCD KEDF).We also study amorphous (a-) Li-Si alloys with KSDFT and OFDFT using the HuangCarter (HC), WGCD, and sWGCD KEDFs. The a-Li-Si alloy samples are prepared with the anneal-and-quench method using NVT molecular dynamics simulations. We report structural properties, equilibrium volumes, bulk moduli, and alloy formation energies for each a-alloy. The HC, WGCD, and sWGCD KEDFs within OFDFT all predict accurate equilibrium volumes compared against KSDFT benchmarks. The HC KEDF bulk moduli 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 2 agree with KSDFT benchmarks whereas the WGCD/sWGCD KEDFs generally overestimate the bulk moduli, especially for alloys with low Li concentrations. All three KEDFs show limited ability to predict alloy formation energies, which indicates the lack of transferability of these KEDFs among such systems and motivates future developments in OFDFT and KEDF formalisms.

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“…We will not attempt to reproduce the material covered therein, but rather summarise the state-of-the-art in terms of methods appropriate for high-accuracy calculations on biomolecules. For example, while orbital-free DFT is making significant progress in the description of metallic and simple semiconducting systems [85], it is not yet widely applied to biological systems except in the context of improving the description of the region surrounding an embedded system of interest [51] described with a higher-level method. It would appear that for the moment, given the limited accuracy of orbital-free representations of kinetic energy functionals based only on the density, the higher-accuracy representation of the kinetic energy that is possible within Kohn-Sham DFT is required to describe the variety of bonding present within a biological system.…”

Section: Feasibility Of Large-scale Simulationsmentioning

confidence: 99%

Applications of large-scale density functional theory in biology

Cole

Hine

2016

J. Phys.: Condens. Matter

139

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Abstract. Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.

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Introducing PROFESS 3.0: An advanced program for orbital-free density functional theory molecular dynamics simulations

Cited by 81 publications

References 0 publications

Real-space formulation of orbital-free density functional theory using finite-element discretization: The case for Al, Mg, and Al-Mg intermetallics

Real-space formulation of orbital-free density functional theory using finite-element discretization: The case for Al, Mg, and Al-Mg intermetallics

Orbital-free density functional theory study of amorphous Li–Si alloys and introduction of a simple density decomposition formalism

Applications of large-scale density functional theory in biology

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