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• W3025349170 abstract "It has been drawn to the authors’ attention that our original article[1] did not appropriately attribute some figures that we had reused or adapted from our own previous work. The figure captions as they should have appeared follow. Figure 1. Self-consistent convergence in calculations with ONETEP for a variety of materials. The main plot shows the change in the total energy (in Hartrees per atom) as a function of the iteration number for NGWF optimisation as in Equation (3). The inset shows the root mean square value of the NWGF gradient at each such iteration. The images of the H-bond, crystalline silicon and protein systems have been adapted from Figures 3, 5 (right) and 8 (middle), respectively, of ref. 8. Adapted with permission.[8] Copyright 2005, IOP Publishing. Figure 6. Schematic example of the ONETEP parallelisation strategy for atomic and simulation cell data. On the left hand side a serial calculation is shown performed on one processor (0) which holds the data for all the atoms and for the entire simulation cell volume. On right hand side the same calculation is performed in parallel on four processors (numbered from 0 to 3). Each processor now holds only a cluster of closely-spaced atoms and a slab of the simulation cell volume. Reproduced with permission[7] (Figure 4 of ref. 7). Copyright 2005, American Institute of Physics. Figure 7. Example of the ONETEP communication model on four processors (numbered 0–3). On the left the seven super-steps that are performed are shown. These allow point-to-point communication between all pairs of processors. The processor pairs that are active in each super-step are shown as shaded blocks in a matrix of processor-processor blocks and the direction of communication is indicated by arrows next to them. On the right, the actual sparsity pattern of the NGWF overlap matrix of a 3000-atom protein is shown. Only about 1% of the total number of elements are non-zero (shown in black). Most of them are clustered along the diagonal of the matrix which in turn implies that the bulk of the communication and computation will be performed during super-steps which involve diagonal or near-diagonal processor-processor blocks. Adapted with permission[7] (from Figure 5 of ref. 7). Copyright 2005, American Institute of Physics. Figure 10. Speed-up in the total wall-clock time taken for one NGWF iteration. These calculations were run on a Sun Fire F15K parallel computer. Data from ref. 7. Figure 11. Parallel speed-ups per one NGWF iteration on a SUN V40z server with four AMD OPTERON processors for a 1000-atom block of crystalline silicon (left) and a 988-atom protein (right). The speed-up as a function of the number of processors is given for the generation of the local potential integrals according to Section 3.1, the electronic charge density according to Section 3.2, the NGWF gradient according to Section 3.3 and the total wall-clock time taken for one NGWF iteration. The images of the crystalline silicon (left) and protein systems (right) have been adapted from Figures 5 (right) and 8 (middle), respectively, of ref. 8. Adapted with permission.[8] Copyright 2005, IOP Publishing. Cited references from [1]:" @default.
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• W3025349170 date "2020-05-01" @default.
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• W3025349170 title "Implementation of linear‐scaling plane wave density functional theory on parallel computers (Phys. Status Solidi B 2006, 243 , 973–988)" @default.
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• W3025349170 doi "https://doi.org/10.1002/pssb.202000102" @default.
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