Logo: to the web site of Uppsala University

uu.sePublications from Uppsala University
Change search
Link to record
Permanent link

Direct link
Souvatzis, Petros
Publications (10 of 27) Show all publications
Grånäs, O., Timneanu, N., Eliah Dawod, I., Ragazzon, D., Trygg, S., Souvatzis, P., . . . Caleman, C. (2019). Femtosecond bond breaking and charge dynamics in ultracharged amino acids. Journal of Chemical Physics, 151(14), Article ID 144307.
Open this publication in new window or tab >>Femtosecond bond breaking and charge dynamics in ultracharged amino acids
Show others...
2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 151, no 14, article id 144307Article in journal (Refereed) Published
Abstract [en]

Historically, structure determination of nanocrystals, proteins, and macromolecules required the growth of high-quality crystals sufficiently large to diffract X-rays efficiently while withstanding radiation damage. The development of the X-ray free-electron laser has opened the path toward high resolution single particle imaging, and the extreme intensity of the X-rays ensures that enough diffraction statistics are collected before the sample is destroyed by radiation damage. Still, recovery of the structure is a challenge, in part due to the partial fragmentation of the sample during the diffraction event. In this study, we use first-principles based methods to study the impact of radiation induced ionization of six amino acids on the reconstruction process. In particular, we study the fragmentation and charge rearrangement to elucidate the time scales involved and the characteristic fragments occurring.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-395440 (URN)10.1063/1.5116814 (DOI)000500356200030 ()31615216 (PubMedID)
Funder
Swedish National Infrastructure for Computing (SNIC), SNIC 2019/8-30Swedish National Infrastructure for Computing (SNIC), SNIC 2018/3-221Swedish Research Council, 637-2013-7303Swedish Research Council, 2013-3940Swedish Foundation for Strategic Research , ICA16-0037
Available from: 2019-10-18 Created: 2019-10-18 Last updated: 2024-01-09Bibliographically approved
Souvatzis, P. & Niklasson, A. M. N. (2014). First principles molecular dynamics without self-consistent field optimization. Journal of Chemical Physics, 140(4), 044117
Open this publication in new window or tab >>First principles molecular dynamics without self-consistent field optimization
2014 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 140, no 4, p. 044117-Article in journal (Refereed) Published
Abstract [en]

We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations. (C) 2014 AIP Publishing LLC.

National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-220813 (URN)10.1063/1.4862907 (DOI)000331211700025 ()
Available from: 2014-03-21 Created: 2014-03-20 Last updated: 2017-12-05Bibliographically approved
Isaeva, L., Souvatzis, P., Eriksson, O. & Lashley, J. C. (2014). Lattice dynamics of cubic AuZn from first principles. Physical Review B. Condensed Matter and Materials Physics, 89(10), 104101
Open this publication in new window or tab >>Lattice dynamics of cubic AuZn from first principles
2014 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 89, no 10, p. 104101-Article in journal (Refereed) Published
Abstract [en]

We study the mechanism of the B2 -> R martensitic transformation in the shape memory alloy AuZn by means of first-principles theory. Phonon anomalies in the TA(2) acoustic branch along the Gamma-M [xi,xi,0] direction associated with a structural transformation are observed. The calculated Fermi surface of the B2 phase of AuZn reveals large portions nested with each other by a translation through a vector q = 1/3[1,1,0] associated with the soft mode. In addition, we find that the B2 phase can be stabilized by pressure in the low-temperature limit. The energetic barrier for the B2 -> R transition is 2 mRy and appears to be near a critical point.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-222732 (URN)10.1103/PhysRevB.89.104101 (DOI)000332453700003 ()
Available from: 2014-04-14 Created: 2014-04-14 Last updated: 2017-12-05Bibliographically approved
Souvatzis, P. (2014). Uquantchem: A versatile and easy to use quantum chemistry computational software. Computer Physics Communications, 185(1), 415-421
Open this publication in new window or tab >>Uquantchem: A versatile and easy to use quantum chemistry computational software
2014 (English)In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 185, no 1, p. 415-421Article in journal (Refereed) Published
Abstract [en]

In this paper we present the Uppsala Quantum Chemistry package (UQUANTCHEM), a new and versatile computational platform with capabilities ranging from simple Hartree-Fock calculations to state of the art First principles Extended Lagrangian Born-Oppenheimer Molecular Dynamics (XL-BOMD) and diffusion quantum Monte Carlo (DMC). The UQUANTCHEM package is distributed under the general public license and can be directly downloaded from the code web-site (http://www.anst.uu.se/pesou087/DOWNLOADUQUANTCHEM/DOWNLOAD-UQUANTCHEM/DOWNLOAD-SITE-UQUANTCHEM.html) [1]. Together with a presentation of the different capabilities of the uquantchem code and a more technical discussion on how these capabilities have been implemented, a presentation of the user-friendly aspect of the package on the basis of the large number of default settings will also be presented. Furthermore, since the code has been parallelized within the framework of the message passing interface (MPI), the timing of some benchmark calculations are reported to illustrate how the code scales with the number of computational nodes for different levels of chemical theory. Program summary Program title: Uquantchem Catalogue identifier: AEQY_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEQY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 2082722. No. of bytes in distributed program, including test data, etc.: 15501085 Distribution format: tar.gz Programming language: Fortran90. Computer: The program should work on any system with a F90 compiler. The code has been tested with the Intel and gfortran compilers. Operating system: Unix/Linux. Has the code been vectorized or parallelized?: The distribution file contains both a serial and a parallel version of the program. Number of processors used, 2-2000. RAM: 2 GB for molecules consisting of <10 atoms. Classification: 16.10. External routines: The Lapack and Bias libraries are required but are included in the distribution file. MP1 is required for the parallel version. Nature of problem:. Electronic structure, total energy and force calculation of molecules. Solution method: Basis-set expansion in terms of contracted Gaussian functions is used to solve the Hartree-Fock or the Kohn-Sham equations self consistently. Running time: From a couple of seconds up to several days depending on the size of the molecule, the level of theory used and the number of Processors used.

Keywords
Quantum chemistry, DFT, Molecular Dynamics, Software
National Category
Natural Sciences Engineering and Technology
Identifiers
urn:nbn:se:uu:diva-216051 (URN)10.1016/j.cpc.2013.09.014 (DOI)000328666100042 ()
Available from: 2014-01-20 Created: 2014-01-17 Last updated: 2017-12-06Bibliographically approved
Souvatzis, P. & Niklasson, A. M. N. (2013). Extended Lagrangian Born-Oppenheimer molecular dynamics in the limit of vanishing self-consistent field optimization. Journal of Chemical Physics, 139(21), 214102
Open this publication in new window or tab >>Extended Lagrangian Born-Oppenheimer molecular dynamics in the limit of vanishing self-consistent field optimization
2013 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 139, no 21, p. 214102-Article in journal (Refereed) Published
Abstract [en]

We present an efficient general approach to first principles molecular dynamics simulations based on extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The reduction of the optimization requirement reduces the computational cost to a minimum, but without causing any significant loss of accuracy or long-term energy drift. The optimization-free first principles molecular dynamics requires only one single diagonalization per time step, but is still able to provide trajectories at the same level of accuracy as "exact," fully converged, Born-Oppenheimer molecular dynamics simulations. The optimization-free limit of extended Lagrangian Born-Oppenheimer molecular dynamics therefore represents an ideal starting point for robust and efficient first principles quantum mechanical molecular dynamics simulations.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-215917 (URN)10.1063/1.4834015 (DOI)000328636400004 ()
Available from: 2014-01-20 Created: 2014-01-17 Last updated: 2017-12-06Bibliographically approved
Söderlind, P., Grabowski, B., Yang, L., Landa, A., Björkman, T., Souvatzis, P. & Eriksson, O. (2012). High-temperature phonon stabilization of γ-uranium from relativistic first-principles theory. Physical Review B. Condensed Matter and Materials Physics, 85(6), 060301
Open this publication in new window or tab >>High-temperature phonon stabilization of γ-uranium from relativistic first-principles theory
Show others...
2012 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 85, no 6, p. 060301-Article in journal (Refereed) Published
Abstract [en]

A microscopic explanation for temperature stabilization of the body-centered cubic (bcc) phase in the actinide metals is proposed. We show that for a prototype actinide, uranium, phonon-phonon interaction promotes bcc gamma-U when heated, even though at low temperatures, it is mechanically a strongly unstable phase. Utilizing the recently developed self-consistent ab initio lattice dynamics (SCAILD) scheme in conjunction with highly accurate and fully relativistic density functional theory we obtain phonon dispersion and density of states that compare well with data acquired from inelastic neutron-scattering experiments. The investigation thus establishes that high-temperature lattice dynamics can be modeled from ab initio theory even for complex materials with substantial electron correlation including the actinides.

National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-171668 (URN)10.1103/PhysRevB.85.060301 (DOI)000300934300001 ()
Available from: 2012-03-27 Created: 2012-03-25 Last updated: 2017-12-07Bibliographically approved
Råsander, M., Souvatzis, P., Höglund, A. & Eriksson, O. (2011). Elasticity model for the evaluation of structural parameters in multilayer systems with applications to transition metal and Si-based multilayers. Physical Review B. Condensed Matter and Materials Physics, 84(12), 125424
Open this publication in new window or tab >>Elasticity model for the evaluation of structural parameters in multilayer systems with applications to transition metal and Si-based multilayers
2011 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 84, no 12, p. 125424-Article in journal (Refereed) Published
Abstract [en]

In this paper we present and evaluate a model based on elasticity theory for the calculation of in- and out-of-plane lattice parameters in multilayer systems, which can be used for a wide selection of multilayers. The model assumes perfect lattice matching at the interface between the different components in the multilayer. The only input is the knowledge of the elastic and lattice constants of the different components in the bulk as well as the relative thickness between the components in the multilayer. We show that the model is in good agreement when compared to first-principles theory calculations and also that there is good agreement between the model and experimental structures for several multilayer systems. The model is also shown to be more appropriate in describing thicker multilayers with larger periodicities such that the lattice constants in the system are independent on the periodicity. Furthermore, we provide results for the lattice parameters for a large body of multilayers based on transition metals and semiconducting materials.

National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-159232 (URN)10.1103/PhysRevB.84.125424 (DOI)000294777400017 ()
Available from: 2011-09-27 Created: 2011-09-26 Last updated: 2022-01-28Bibliographically approved
Souvatzis, P. (2011). Phonon lifetimes from first-principles self-consistent lattice dynamics. Journal of Physics: Condensed Matter, 23(44), 445401
Open this publication in new window or tab >>Phonon lifetimes from first-principles self-consistent lattice dynamics
2011 (English)In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 23, no 44, p. 445401-Article in journal (Refereed) Published
Abstract [en]

Phonon lifetime calculations from first principles usually rely on time-consuming molecular dynamics calculations, or density functional perturbation theory where the zero-temperature crystal structure is assumed to be dynamically stable. Here is presented a new and effective method for calculating phonon lifetimes from first principles. This method is not limited to crystallographic phases stable at 0 K and provides a scheme more effective than most corresponding molecular dynamics calculations. The method is based on the recently developed self-consistent ab initio lattice dynamical method and is here tested by calculating the bcc phase phonon lifetimes of Li, Na, Ti and Zr as representative examples.

National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-162687 (URN)10.1088/0953-8984/23/44/445401 (DOI)000296714100005 ()
Available from: 2011-12-07 Created: 2011-12-05 Last updated: 2017-12-08Bibliographically approved
Souvatzis, P., Arapan, S., Eriksson, O. & Katsnelson, M. I. (2011). Temperature-driven alpha-to-beta phase transformation in Ti, Zr and Hf from first-principles theory combined with lattice dynamics. Europhysics letters, 96(6), 66006
Open this publication in new window or tab >>Temperature-driven alpha-to-beta phase transformation in Ti, Zr and Hf from first-principles theory combined with lattice dynamics
2011 (English)In: Europhysics letters, ISSN 0295-5075, E-ISSN 1286-4854, Vol. 96, no 6, p. 66006-Article in journal (Refereed) Published
Abstract [en]

Lattice dynamical methods used to predict phase transformations in crystals typically deal with harmonic phonon spectra and are therefore not applicable in important situations where one of the competing crystal structures is unstable in the harmonic approximation, such as the bcc structure involved in the hcp-to-bcc martensitic phase transformation in Ti, Zr and Hf. Here we present an expression for the free energy that does not suffer from such shortcomings, and we show by self-consistent ab initio lattice dynamical calculations (SCAILD), that the critical temperature for the hcp-to-bcc phase transformation in Ti, Zr and Hf, can be effectively calculated from the free-energy difference between the two phases. This opens up the possibility to study quantitatively, from first-principles theory, temperature-induced phase transitions.

National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-168756 (URN)10.1209/0295-5075/96/66006 (DOI)000298561600033 ()
Available from: 2012-02-16 Created: 2012-02-15 Last updated: 2017-12-07Bibliographically approved
Souvatzis, P., Legut, D., Eriksson, O. & Katsnelson, M. I. (2010). Ab initio study of interacting lattice vibrations and stabilization of the beta phase in Ni-Ti shape-memory alloy. Physical Review B. Condensed Matter and Materials Physics, 81(9), 092201
Open this publication in new window or tab >>Ab initio study of interacting lattice vibrations and stabilization of the beta phase in Ni-Ti shape-memory alloy
2010 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 81, no 9, p. 092201-Article in journal (Refereed) Published
Abstract [en]

Lattice dynamical methods used to predict phase transformations in crystals typically evaluate the harmonic phonon spectra and therefore do not work in frequent and important situations where the crystal structure is unstable in the harmonic approximation, such as the beta structure when it appears as a high-temperature phase of the shape memory alloy Ni-Ti. Here it is shown by self-consistent ab initio lattice dynamical calculations that the critical temperature for the premartensitic R-to-beta phase transformation in Ni-Ti can be effectively calculated with good accuracy, and that the beta phase is a result primarily of the stabilizing interaction between different lattice vibrations.

National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-137111 (URN)10.1103/PhysRevB.81.092201 (DOI)000276207300005 ()
Available from: 2010-12-15 Created: 2010-12-15 Last updated: 2017-12-11Bibliographically approved
Organisations

Search in DiVA

Show all publications