1. O. Čertík, J.E. Pask, I. Fernando, R. Goswami, N. Sukumar, L.A. Collins, G. Manzini, J. Vackář
    High-order finite element method for atomic structure calculations
    Computer Physics Communications 297 (2024) 109051(1)-109051(17).
  2. M. Novák, J. Vackář, R. Cimrman, O. Šipr
    Adaptive Anderson mixing for electronic structure calculations
    Computer Physics Communications 292 (2023) 108865(1)-108865(18).
  3. O. Šipr, S. Mankovsky, J. Vackář, H. Ebert, A. Marmodoro
    Temperature-induced changes in the magnetism of Laves phase rare-earth-iron intermetallics by ab initio calculations
    Physical Review B 106 (2022) 144416-1-144416-6.
  4. M. Novák, J. Vackář, Robert Cimrman
    Evaluating Hellmann–Feynman forces within non-local pseudopotentials
    Computer Physics Communications 250 (2020) 107034(1)-107034(10).
  5. O. Šipr, J. Vackář, Ján Minár
    Finite lifetime broadening of calculated X-ray absorption spectra: possible artefacts close to the edge
    Journal of Synchrotron Radiation 25 (2018) 523-528.
  6. R.Cimrman, M. Novák, R.Kolman, M.Tůma, J. Vackář
    Isogeometric analysis in electronic structure calculations
    Mathematics and Computers in Simulation 145 (2018) 125-135.
  7. R.Cimrman, M. Novák, R.Kolman, M.Tůma, J.Plešek, J. Vackář
    Convergence study of isogeometric analysis based on Bézier extraction in electronic structure calculations
    Applied Mathematics and Computation 319 (2018) 138-152.
  8. O. Šipr, J. Vackář, A. Kuzmin
    Effect of atomic vibrations in XANES: polarization-dependent damping of the fine structure at the Cu K -edge of (creat)2CuCl4
    Journal of Synchrotron Radiation 23 (2016) 1433-1439.
  9. O. Šipr, S. Bornemann, H. Ebert, S. Mankovsky, J. Vackář, J. Minár
    Co monolayers and adatoms on Pd(100), Pd(111), and Pd(110): Anisotropy of magnetic properties
    Physical Review B 88 (2013) 064411(1)-064411(14).
  10. Robert Cimrman, Miroslav Tůma, M. Novák, Ondřej Čertík, Jiří Plešek, J. Vackář
    Python-based finite element code used as a universal and modular tool for electronic structure calculation
    American Institute of Physics Conference Proceedings 1558 (2013) 1532 -1535.
  11. O. Čertík, J.E. Pask, J. Vackář
    A robust and general Schrödinger and Dirac solver for atomic structure calculations
    Computer Physics Communications 184 (2013) 1777-1791.
  12. O. Šipr, J. Vackář, P.S. Vachhani, R.K. Ramamoorthy, G. Dalba, A.K. Bhatnagar, F. Rocca
    Local structure and magnetism of Cu-doped ZnO via Cu K-edge XAS and XMCD: theory and experiment
    Journal of Physics: Conference Series 430 (2013) 012128-1-012128-6.
  13. J. Vackář, O. Čertík, R. Cimrman, M. Novák, O. Šipr, J. Plešek
    Finite Element Method in Density Functional Theory Electronic Structure Calculations
    Chapter 12 in Advances in the Theory of Quantum Systems in Chemistry and Physics, eds. P.E.Hoggan, E.J.Brändas, J.Maruani, P.Piecuch, G.Delgado-Barrio, in series: Progress in Theoretical Chemistry and Physics, Vol. 22, Springer 2012, pp.199-217, ISBN 978-94-007-2075-6, 978-94-007-2076-3, ISSN: 1567-7354
  14. J. Vackář, O. Šipr, A. Šimůnek
    Relationship between atomically related core levels and ground-state properties of solids: First-principles calculations
    Physical Review B 77 (2008) 045112-1-045112-6.
  15. O.Čertík, J. Vackář, J. Plešek
    Density functional theory calculations using the finite element method
    Proceedings of the Estonian Academy of Sciences 57 (2008) 155-178.
  16. A. Šimůnek, J. Vackář
    A Reply to the Comment by Z. Y. Liu et al.
    Physical Review Letters 98 (2007) 109602-109602.
  17. O. Šipr, J. Minár, J. Vackář, H. Ebert
    Influence of interdiffusion on the magnetic moments in Co/Au multilayers
    Physical Review B 75 (2007) 134422-1-134422-10.
  18. A. Šimůnek, J. Vackář
    Hardness of Covalent and Ionic Crystals: First-Principle Calculations
    Physical Review Letters 96 (2006) 085501/1-085501/4.
  19. O. Šipr, A. Šimůnek, J. Vackář, G. Daba, F. Rocca
    Connection between spectral features of B K edge XANES of minerals and the local structure
    Physics and Chemistry of Glasses 47 (2006) 412-418.
  20. Kolektiv autorů, J. Vackář, L. Navrátil, J. Rosina, T. Blažek, I. Dylevský, J. Jakuš, V. Hlavatý, J. Hanuš, R. Havránková, J. Heřmanská, H. Kolářová, E. Kukurová, P. Kuna, J. Kymplová, N. Pilecká, F. Podzimek, J. Sabo, A. Stránsky, J. Vackářová, K. Volenec
    Medicínská biofyzika
    Ed. Navrátil L., Rosina J., GRADA (2005), ISBN: 80-247-1152-4
  21. A. Šimůnek, J. Vackář, K. Kunc
    Core energy levels of Sc and N and their variation with coordination number in ScN
    Physical Review B 72 (2005) 045110(1)-045110(4).
  22. A. Šimůnek, J. Vackář
    Ab-initio calculation of graphite surface-bulk core-level splitting
    Phys. Rev. B 69 (2004) 073403
  23. T. Blažek, I. Dylevský, V. Hlavatý, J. Hanuš, H. Kolářová, P. Kuna, J. Kymplová, L. Navrátil, N. Pilecká, J. Rosina, J. Vackář, J. Vackářová, K. Volenec
    Lékařská biofyzika
    Manus, Praha 2003, ISBN 80-86571-03-3
  24. J. Vackář, A. Šimůnek
    Adaptability and accuracy of all-electron pseudopotentials
    Phys. Rev. B 67 (2003) 125113
  25. A. Šimůnek, J. Vackář
    Correlation between core-level shift and bulk modulus in transition-metal carbides and nitrides
    Phys. Rev. B 64 (2001) 235115
  26. J. Vackář, A. Simunek
    All-electron pseudopotentials with pseudocore
    Čs. čas. fyz. 10 (2001) 11
  27. A. Simunek, J. Vackář
    All-electron pseudopotentials
    Čs. čas. fyz. 2000 (2000) 19
  28. A. Simunek, J. Vackář, M. Polcik, J. Drahokoupil, W. Wolf, R. Podloucky
    Electronic structure and x-ray bands of CoSi${_2}$
    Phys. Rev. B 61 (2000) 4385
  29. A. Simunek, J. Vackář, K. Kunc, J. Hutter
    Soft norm-conserving pseudopotential for carbon
    Eur. Phys. J. B 14 (2000) 245
  30. R. Nietubyc, E. Sobczak, O. Sipr, J. Vackář, A. Simunek
    Electronic structure of silicon nitride
    J. Alloy. Compd. 286 (1999) 148
  31. J. Vackář, A. Simunek, M. Hytha
    All-electron pseudopotentials
    Phys. Rev. B 58 (1998) 12712
  32. R. Nietubyc, E. Sobczak, O. Sipr, J. Vackář, A. Simunek
    BIS study of silicon nitride: Experiment and theory
    J. Phys. IV France 7 , C2-583-584 (1997)
  33. R. Nietubyc, E. Sobczak, O. Sipr, J. Vackář, A. Simunek
    Partial probabilities of x-ray bremsstrahlung transitions
    Acta Phys. Polon. A 91 (1997) 841
  34. O. Sipr, P. Machek, A. Simunek, J. Vackář, J. Horak
    X-ray absorption near-edge structure of CuGaSe$_ 2 $ and ZnSe: Experiment and theory
    Phys. Rev. B 56 (1997) 13151
  35. G. Wiech, N. Auer, A. Simunek, J. Vackář, A. Hammerschmidt, G. Rittmayer
    Diamond-like hydrogenated amorphous carbon films studied bgy x-ray emission spectroscopy
    Diamond Relat. Mater. 6  (1997) 944
  36. A. Di Pomponio, A. Continenza, R. Podloucky, J. Vackář
    Symmetrization of atomic forces within the full-potential linearized augmented-plane-wave method
    Phys. Rev. B 53 (1996) 9505
  37. J. Vackář, A. Simunek, R. Podloucky
    Ab-initio pseudopotentials of interacting atoms
    Phys. Rev. B 53 (1996) 7727
  38. A. Di Pomponio, A. Continenza, R. Podloucky, J. Vackář
    Atomic forces within all-electron calculations
    Čs. čas. fyz. 7 (1995) 1995
  39. J. Vackář, A. Simunek
    Modelling the valence electronic structure of the core region of an atom in a solid within a local-density approximation pseudopotential framework: reintroduction of the full nodal form
    J. Phys.-Condens. Mat. 6 (1994) 3025
  40. A. Simunek, J. Vackář, G. Wiech
    Local s,p and d charge distributions and x-ray emission bands of SiO : $alpha$-quartz and stishovite
    J. Phys.-Condens. Mat. 5 (1993) 867
  41. J. Vackář, A. Simunek
    Phase-shift technique for generating generalized norm-conserving semilocal pseudopotentials
    Solid State Commun. 81 (1992) 837
  42. O. Sipr, J. Vackář, A. Simunek
    Finite-cluster multiple-scattering theory of X-ray bremsstrahlung isochromat spectra
    Phys. Rev. B 44 (1991) 4832
  43. A. Simunek, J. Vackář
    Selection rules and x-ray isochromat fine structure of Pd and Cu
    Physica B 158 (1989) 572
  44. A. Simunek, O. Sipr, J. Vackář
    Real-space, multiple-scattering theory method for the calculation of x-ray bremsstrahlung isochromat spectra
    Phys. Rev. Lett. 63 (1989) 2076
  45. A. Simunek, J. Vackář, E. Sobczak
    Selection rules and extended x-ray bremsstrahlung isochromat spectra of Cu and Pd
    Phys. Rev. B 38 (1988) 8515