Density Functional Theory calculation on many-cores hybrid CPU-GPU architectures

The implementation of a full electronic structure calculation code on a hybrid parallel architecture with Graphic Processing Units (GPU) is presented. The code which is on the basis of our implementation is a GNU-GPL code based on Daubechies wavelets. It shows very good performances, systematic convergence properties and an excellent efficiency on parallel computers. Our GPU-based acceleration fully preserves all these properties. In particular, the code is able to run on many cores which may or may not have a GPU associated. It is thus able to run on parallel and massive parallel hybrid environment, also with a non-homogeneous ratio CPU/GPU. With double precision calculations, we may achieve considerable speedup, between a factor of 20 for some operations and a factor of 6 for the whole DFT code.Comment: 14 pages, 8 figure

Particle-Particle, Particle-Scaling function (P3S) algorithm for electrostatic problems in free boundary conditions

An algorithm for fast calculation of the Coulombic forces and energies of point particles with free boundary conditions is proposed. Its calculation time scales as N log N for N particles. This novel method has lower crossover point with the full O(N^2) direct summation than the Fast Multipole Method. The forces obtained by our algorithm are analytical derivatives of the energy which guarantees energy conservation during a molecular dynamics simulation. Our algorithm is very simple. An MPI parallelised version of the code can be downloaded under the GNU General Public License from the website of our group.Comment: 19 pages, 11 figures, submitted to: Journal of Chemical Physic

Daubechies wavelets as a basis set for density functional pseudopotential calculations

Daubechies wavelets are a powerful systematic basis set for electronic structure calculations because they are orthogonal and localized both in real and Fourier space. We describe in detail how this basis set can be used to obtain a highly efficient and accurate method for density functional electronic structure calculations. An implementation of this method is available in the ABINIT free software package. This code shows high systematic convergence properties, very good performances and an excellent efficiency for parallel calculations.Comment: 15 pages, 11 figure

Brownian dynamics simulation of linear polymers under elongational flow: Bead–rod model with hydrodynamic interactions

Brownian dynamics (BD) simulations of a linear freely jointed bead–rod polymer chain with excluded volume (EV) interaction have been performed under elongational flow with and without the use of fluctuating hydrodynamic interactions (HI). The dependence of the chain size, shape and intrinsic elongational viscosity on the elongational rate are reported. A sharp coil–stretch transition is observed when exceeds a critical value, c. The inclusion of the HI leads to a shift in the coil–stretch transition to higher flow values. Chain deformation due to elongational flow is observed to first consist of the alignment of the chain with the direction of flow without significant chain extension followed by additional alignment of the bond vectors with the flow direction and chain extension as flow rate is increased further. The distribution function for the chain's radius of gyration becomes significantly broader within the transition region which implies an increase in fluctuations in the chain size in this region. The structure factors parallel and perpendicular to the flow direction illustrate different elongational rate dependencies. At high rates, the structure factor in the direction of the flow exhibits an oscillating dependence which corresponds to the theoretically predicted shape for a rigid-rod model. The mean squared orientation of each bond within the chain with respect to the flow direction as function of bond number is nearly parabolic in shape with the highest degree of orientation found within the chain's interior. The dependence of the critical elongational rate, c, on the chain length, N, is observed to be c~N–1.96 when hydrodynamic interactions are not employed and c~N–1.55 when they are invoked. These scaling exponents agree well with those obtained in previous BD simulations of bead-FENE (i.e., finitely extensible nonlinear elastic) spring chains as well as with the theoretical predictions of c~N–2 and c~N–1.5 without and with hydrodynamic interactions based on the Rouse and Zimm models, respectivel

Structure of large gold clusters obtained by global optimization using the minima hopping method

The energetic ground state of gold clusters with up to 318 atoms consists of complex geometries that have only a limited resemblance to the perfect icosahedra, decahedra, and octahedra that are encountered for some magic numbers. The structure changes in most cases completely by the addition of a single atom. Other low-energy structures are so close in energy that their Boltzmann weight is not negligible at room temperature

Efficient solution of Poisson’s equation with free boundary conditions

Interpolating scaling functions give a faithful representation of a localized charge distribution by its values on a grid. For such charge distributions, using a Fast Fourier method, we obtain highly accurate electrostatic potentials for free boundary conditions at the cost of O(N logN) operations, where N is the number of grid points. Thus, with our approach, free boundary conditions are treated as efficiently as the periodic conditions via plane wave methods. PACS numbers: I