E. Neveu, D. Ritchie, P. Popov, and S. Grudinin, PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation, Bioinformatics, vol.32, pp.693-701, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01358645

G. S. Ho, V. L. Lignères, and E. A. Carter, Introducing profess: A new program for orbital-free density functional theory calculations, Computer Physics Communications, vol.179, pp.839-854, 2008.

A. K. Rappé, C. J. Casewit, K. Colwell, W. A. Goddard, I. et al., Uff, a full periodic table force field for molecular mechanics and molecular dynamics simulations, Journal of the American chemical society, vol.114, issue.25, pp.10024-10035, 1992.

H. Nakashima and H. Nakatsuji, Solving the schrödinger equation for helium atom and its isoelectronic ions with the free iterative complement interaction (ici) method, The Journal of chemical physics, vol.127, issue.22, p.224104, 2007.

D. Marx and J. Hutter, Ab initio molecular dynamics: basic theory and advanced methods, 2009.

J. Xia, C. Huang, I. Shin, and E. A. Carter, Can orbital-free density functional theory simulate molecules?, The Journal of chemical physics, vol.136, issue.8, p.84102, 2012.

G. S. Ho and E. A. Carter, Mechanical response of aluminum nanowires via orbitalfree density functional theory, Journal of Computational and Theoretical Nanoscience, vol.6, issue.6, pp.1236-1246, 2009.

P. Suryanarayana and D. Phanish, Augmented lagrangian formulation of orbital-free density functional theory, Journal of Computational Physics, vol.275, pp.524-538, 2014.

S. Artemova and S. Redon, Adaptively Restrained Particle Simulations, Physical Review Letters, vol.109, pp.190201-190202, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00756121

S. Artemova, Adaptive algorithms for molecular simulation, 2012.
URL : https://hal.archives-ouvertes.fr/tel-00846690

M. Bosson, C. Richard, A. Plet, S. Grudinin, and S. Redon, Interactive quantum chemistry: A divide-and-conquer ASED-MO method, Journal of Computational Chemistry, vol.33, pp.779-790, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00755498

M. Bosson, S. Grudinin, and S. Redon, Block-Adaptive Quantum Mechanics: An Adaptive Divide-and-Conquer Approach to Interactive Quantum Chemistry, Journal of Computational Chemistry, vol.34, pp.492-504, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00755521

S. P. Edorh and S. Redon, Incremental update of electrostatic interactions in adaptively restrained particle simulations, Journal of Computational Chemistry, vol.39, pp.1455-1469, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01761906

K. K. Singh, D. F. Marin, and S. Redon, Parallel Adaptively Restrained Molecular Dynamics, 2017 International Conference on High Performance Computing & Simulation (HPCS), pp.308-314, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01591466

K. K. Singh and S. Redon, Adaptively Restrained Molecular Dynamics in LAMMPS, Modelling and Simulation in Materials Science and Engineering, vol.25, p.55013, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01525253

S. Redon, G. Stoltz, and Z. Trstanova, Error analysis of modified langevin dynamics, Journal of Statistical Physics, vol.164, issue.4, pp.735-771, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01263700

Z. Trstanova, Mathematical and Algorithmic Analysis of Modified Langevin Dynamics. Theses, 2016.
URL : https://hal.archives-ouvertes.fr/tel-01682721

D. Frenkel and B. Smit, Chapter 3 -monte carlo simulations, Understanding Molecular Simulation, pp.23-61, 2002.

M. Schütz and H. Werner, Low-order scaling local electron correlation methods. iv. linear scaling local coupled-cluster (lccsd), The Journal of Chemical Physics, vol.114, issue.2, p.661, 2001.

M. Schütz, A new, fast, semi-direct implementation of linear scaling local coupled cluster theory, Phys. Chem. Chem. Phys, vol.4, issue.16, pp.3941-3947, 2002.

P. Hohenberg and W. Kohn, Inhomogeneous electron gas, Physical Review, vol.136, pp.864-871, 1964.

P. E. Blöchl, Projector augmented-wave method, Physical review B, vol.50, issue.24, p.17953, 1994.

P. E. Blöchl, C. J. Först, and J. Schimpl, Projector augmented wave method: ab initio molecular dynamics with full wave functions, Bulletin of Materials Science, vol.26, issue.1, pp.33-41, 2003.

W. Kohn and L. J. Sham, Self-consistent equations including exchange and correlation effects, Physical Review, vol.140, pp.1133-1138, 1965.

L. H. Thomas, The calculation of atomic fields, Mathematical Proceedings of the Cambridge Philosophical Society, vol.23, p.542, 1927.

C. V. Weizsäcker, Zur theorie der kernmassen, Zeitschrift für Physik A Hadrons and Nuclei, vol.96, issue.7, pp.431-458, 1935.

L. Wang and M. P. Teter, Kinetic-energy functional of the electron density, Physical Review B, vol.45, pp.13196-13220, 1992.

J. Lindhard, On the properties of a gas of charged particles, Kgl. Danske Videnskab. Selskab Mat.-Fys. Medd, vol.28, 1954.

M. Foley and P. A. Madden, Further orbital-free kinetic-energy functionals for ab initio molecular dynamics, Physical Review B, vol.53, issue.16, p.10589, 1996.

Y. A. Wang, N. Govind, and E. A. Carter, Orbital-free kinetic-energy functionals for the nearly free electron gas, Physical Review B, vol.58, issue.20, p.13465, 1998.

Y. A. Wang, N. Govind, and E. A. Carter, Orbital-free kinetic-energy density functionals with a density-dependent kernel, Physical Review B, vol.60, issue.24, p.16350, 1999.

C. Huang and E. A. Carter, Toward an orbital-free density functional theory of transition metals based on an electron density decomposition, Physical Review B, vol.85, issue.4, p.45126, 2012.

V. Gavini, J. Knap, K. Bhattacharya, and M. Ortiz, Non-periodic finite-element formulation of orbital-free density functional theory, Journal of the Mechanics and Physics of Solids, vol.55, issue.4, pp.669-696, 2007.

S. Ghosh and P. Suryanarayana, Higher-order finite-difference formulation of periodic orbital-free density functional theory, Journal of Computational Physics, vol.307, pp.634-652, 2016.

P. Ziesche, S. Kurth, and J. P. Perdew, Density functionals from lda to gga, Computational materials science, vol.11, issue.2, pp.122-127, 1998.

X. Shao, Q. Xu, S. Wang, J. Lv, Y. Wang et al., Large-scale ab initio simulations for periodic system, Computer Physics Communications, vol.233, pp.78-83, 2018.

S. Wright and J. , Numerical optimization, vol.35, p.7, 1999.

C. Huang and E. A. Carter, Transferable local pseudopotentials for magnesium, aluminum and silicon, Physical Chemistry Chemical Physics, vol.10, issue.47, p.7109, 2008.

C. Huang and E. A. Carter, Nonlocal orbital-free kinetic energy density functional for semiconductors, Phys. Rev. B, vol.81, p.45206, 2010.

B. Zhou, Y. A. Wang, and E. A. Carter, Transferable local pseudopotentials derived via inversion of the kohn-sham equations in a bulk environment, Physical Review B, vol.69, issue.12, p.125109, 2004.

P. Viot, Méthode d'analyse numérique, Lecture, 2006.

W. Yang, Gradient correction in thomas-fermi theory, Physical Review A, vol.34, issue.6, p.4575, 1986.

R. G. Parr and Y. Weitao, Density-functional theory of atoms and molecules, vol.16, 1994.

N. Govind, J. Wang, and H. Guo, Total-energy calculations using a gradient-expanded kinetic-energy functional, Physical Review B, vol.50, pp.11175-11178, 1994.
DOI : 10.1103/physrevb.50.11175

J. P. Perdew and A. Zunger, Self-interaction correction to density-functional approximations for many-electron systems, Physical Review B, vol.23, pp.5048-5079, 1981.
DOI : 10.1103/physrevb.23.5048
URL : http://link.aps.org/pdf/10.1103/PhysRevB.23.5048

P. Motamarri, M. Iyer, J. Knap, and V. Gavini, Higher-order adaptive finite-element methods for orbital-free density functional theory, Journal of Computational Physics, vol.231, issue.20, pp.6596-6621, 2012.
DOI : 10.1016/j.jcp.2012.04.036
URL : http://arxiv.org/pdf/1110.1280

N. Choly and E. Kaxiras, Kinetic energy density functionals for non-periodic systems, Solid State Communications, vol.121, pp.281-286, 2002.
DOI : 10.1016/s0038-1098(01)00500-2
URL : http://arxiv.org/pdf/cond-mat/0112040

T. Guillet and R. Teyssier, A simple multigrid scheme for solving the poisson equation with arbitrary domain boundaries, Journal of Computational Physics, vol.230, issue.12, pp.4756-4771, 2011.
DOI : 10.1016/j.jcp.2011.02.044
URL : http://arxiv.org/pdf/1104.1703

D. Braess, On the combination of the multigrid method and conjugate gradients, pp.52-64, 1986.

C. Temperton, Direct methods for the solution of the discrete poisson equation: some comparisons, Journal of Computational Physics, vol.31, issue.1, pp.1-20, 1979.

W. Gander and G. H. Golub, Cyclic reduction-history and applications, pp.73-85, 1997.

L. Genovese, T. Deutsch, A. Neelov, S. Goedecker, and G. Beylkin, Efficient solution of poisson's equation with free boundary conditions, The Journal of chemical physics, vol.125, issue.7, p.74105, 2006.

J. F. Gibbons, Ion implantation in semiconductors-part ii: Damage production and annealing, Proceedings of the IEEE, vol.60, issue.9, pp.1062-1096, 1972.

L. Dagum and R. Menon, Openmp: an industry standard api for shared-memory programming, IEEE Computational Science and Engineering, vol.5, pp.46-55, 1998.

A. Borgoo, J. A. Green, and D. J. Tozer, Molecular binding in post-kohn-sham orbitalfree dft, Journal of chemical theory and computation, vol.10, issue.12, pp.5338-5345, 2014.