arXiv subjects

Roman Martoňák

Publications and source records attributed to Roman Martoňák.

At least 19 recordsLinked to original sources

arXiv2025

From diamond to BC8 to simple cubic and back: kinetic pathways to post-diamond carbon phases from metadynamics

The experimental observation of elusive post-diamond carbon phases at extreme pressures remains a major challenge in high-pressure science. Using metadynamics with coordination-number-based collective variables and SNAP machine-learned interatomic potential, we uncover atomistic mechanisms governing the transformation of cubic and hexagonal diamond into post-diamond phases above 1.5 TPa. The transition initiates via homogeneous nucleation of nanoscale liquid droplets, which rapidly crystallize into either BC8 (below 1.8 TPa) or simple cubic phases (above 2.1 TPa), once the liquid nucleus surpasses a critical size. Favorable conditions for synthesizing BC8 are identified near 1.8 TPa and 3500--5000 K. Decompression pathways from simple cubic and BC8 phases were also simulated to study possible experimental recovery of post-diamond carbon allotropes at ambient conditions. We also find a new metastable low-enthalpy structure with four-coordinated carbon atoms and space group P222. Our insights provide a theoretical foundation for experimental discovery of ultra-dense carbon phases under extreme conditions.

cond-mat.mtrl-sci↗

arXiv2025

Kinetic pathways of coesite densification from metadynamics

We study compression of coesite to pressures above 35 GPa, substantially beyond the equilibrium transition pressure to octahedral phases (8 GPa to stishovite). Experiments at room temperature showed that up to 30 GPa the metastable coesite structure develops only minor displacive changes (coesite-II and coesite-III) while the Si atoms remain 4-coordinated. Beyond 30 GPa, reconstructive transformations start, following different pathways from the complex structure of coesite. Besides amorphization, two different crystalline outcomes were observed. One is formation of defective high-pressure octahedral phases (Hu et al., 2015) and another one is formation of unusual and complex dense phases coesite-IV and coesite-V with Si atoms in 4-fold, 5-fold and 6-fold coordination (Bykova et al., 2018). Capturing these structural transformations computationally represents a challenge. Here we show that employing metadynamics with Si-O coordination number and volume as generic collective variables in combination with a machine-learning based ACE potential (Erhard et al., 2024), one naturally observes all three mentioned pathways, resulting in the phases observed experimentally. We describe the atomistic mechanisms along the transformation pathways. While the pathway to coesite-IV is simpler, the transformation to octahedral phases involves two steps: first, a hcp sublattice of O atoms is formed where Si atoms occupy octahedral positions but the octahedra chains do not form a regular pattern. In the second step, the Si atoms order and the chains develop a more regular arrangement. We predict that the pathway to coesite-IV is preferred at room temperature, while at 600 K the formation of octahedral phases is more likely.

cond-mat.mtrl-sci↗

arXiv2022

Ge$_{136}$ type-II clathrate as precursor for the synthesis of metastable germanium polymorphs: a computational study

The response to compression of the clathrate type-II structure Ge(cF136) is investigated by means of \textit{ab initio} small-cell metadynamics at different temperatures and pressures. At lower pressure $p$=2.5 GPa the metastable metallic bct-5 phase competes against $β$-Sn Ge(tI4), which forms at higher pressures. On lowering temperature, the presence of amorphous intermediates obtained from Ge$_{136}$ is more pronounced and is instrumental to the formation of denser structural motifs, from which metallic bct-5 can form. Therein, anisotropic box fluctuations promote phase formation. The metadynamics runs are analysed in depth using a set of topological descriptors, including coordination sequence and ring statistics. Differences in the structural landscape history and amorphous intermediates are critical for the selective formation of particular metastable polymorphs, towards turning crystal structure predictions into actual materials.

cond-mat.mtrl-sci↗

arXiv2021

Pressure-induced structural transformation of clathrate Ge$_{136}$ via an ultrafast recrystallization of an amorphous intermediate

We study the pressure-induced structural transformation of Ge$_{136}$ clathrate by ab initio molecular dynamics and metadynamics. The system under pressure first undergoes amorphization followed by an ultrafast recrystallization to the $β$-tin structure on the time scale of 30 ps. The initial pressure-induced amorphization of clathrate is triggered by high pressure while the subsequent fast recrystallization to $β$-tin is driven by low temperature. Interestingly, the amorphous intermediate is still diffusive even at room temperature, in spite of very strong undercooling, making the ultrafast recrystallization possible. The system provides an explicit example of structural transformation between two crystalline phases proceeding via non-crystalline intermediate. Upon fast decompression of the amorphous structure with incipient crystalline order the recrystallization is blocked and the system instead proceeds to the tetrahedral LDA amorphous phase.

cond-mat.mtrl-sci↗

arXiv2021

Nucleating a Different Coordination in a Crystal under Pressure: A Study of the B1-B2 Transition in NaCl by Metadynamics

Here we propose an NPT metadynamics simulation scheme for pressure-induced structural phase transitions, using coordination number and volume as collective variables, and apply it to the reconstructive structural transformation $B1$-$B2$ in NaCl. By studying systems with size up to 64 000 atoms we reach a regime beyond collective mechanism and observe transformations proceeding via nucleation and growth. We also reveal the crossover of the transition mechanism from Buerger-like for smaller systems to Watanabe-Tolédano for larger ones. The scheme is likely to be applicable to a broader class of pressure-induced structural transitions, allowing study of complex nucleation effects and bringing simulations closer to realistic conditions.

cond-mat.mtrl-sci↗

arXiv2021

High-Pressure Structural Evolution of Disordered Polymeric CS$_2$

Carbon disulfide, CS$_2$, is an archetypal double-bonded molecular system belonging to the rich class of group IV-group VI, AB$_2$ compounds. It is widely and since long time believed that upon compression at several GPa a polymeric chain of type (-(C=S)-S-)$_n$ named Bridgman's black polymer will form. By combining optical spectroscopy and synchrotron X-ray diffraction data with ab initio simulations, we demonstrate that the structure of the Bridgman's black polymer is remarkably different. Solid molecular CS$_2$ undergoes a pressure-induced structural transformation at around 10-11 GPa, developing a disordered polymeric system. The polymer consists of 3-fold and 4-fold coordinated carbon atoms with an average carbon coordination continuously increasing upon further compression to 40 GPa. Polymerization also gives rise to some C=C double bonds. Upon decompression, the structural changes are partially reverted, a very small amount of molecular CS$_2$ is recovered, while the sample undergoes partial chemical disproportionation. Our work uncovers the non-trivial high-pressure structural evolution in one of the simplest molecular systems exhibiting molecular as well as polymeric phases.

cond-mat.other↗

arXiv2019

Molecular and polymeric amorphous forms in dense SO$_2$

We report here a study of reversible pressure-induced structural transformation between two amorphous forms of SO$_2$: molecular at pressures below 26 GPa and polymeric above this pressure, at temperatures of 77 - 300 K. The transformation was observed by Raman spectroscopy and x-ray diffraction in a diamond anvil cell. The same phenomenon was also observed in ab initio molecular dynamics simulations where both forward and reverse transitions were detected, allowing to analyze in detail the atomic structure of both phases. The high-pressure polymeric amorphous form was found to consist mainly of disordered polymeric chains made of 3-coordinated sulfur atoms connected via oxygen atoms, and few residual intact molecules. The simulation results are in good agreement with experimental data. Our observations suggest a possible existence of molecular liquid - polymeric liquid transition in SO$_2$ and show a case example of polyamorphism in system consisting of simple molecules with multiple bonds.

cond-mat.dis-nn↗

arXiv2018

Structural evolution of amorphous polymeric nitrogen from \textit{ab initio} molecular dynamics simulations and evolutionary search

Polymeric nitrogen with single bonds can be created from the molecular form at high pressure and due to large energy difference between triple and single bonds it is interesting as energetic material. Its structure and properties are, however, still not well understood. We studied amorphous nitrogen by \textit{ab initio} simulations, employing molecular dynamics and evolutionary algorithms. Amorphous nitrogen was prepared at pressure of 120 GPa by quenching from hot liquid, by pressure-induced amorphization of molecular crystal and by evolutionary search. All three amorphous forms were found to be structurally similar. We studied in detail the structural evolution of the system upon decompression from 120 GPa to zero pressure at 100 K. At pressures above 100 GPa, system consists mainly of 3-coordinated atoms (80 \%) connected by single bonds while some short chains made of 2-coordinated atoms are also present. Upon decompression, the number of 3-coordinated atoms rapidly decreases below 60 GPa and longer chains are created. At 20 GPa the system starts to create also N$_2$ molecules and the ultimate structure at $p=0$ contains molecules inside a polymeric network consisting dominantly of longer chains made of 2-coordinated atoms. Besides structure, we also study vibrational and electronic properties of the system and estimate the amount of energy that could be stored in amorphous nitrogen at ambient pressure.

cond-mat.mtrl-sci↗

arXiv2017

\textit{Ab initio} molecular dynamics study of the structural and electronic transition in VO$_2$

The temperature-induced structural and electronic transformation in VO$_2$ between the monoclinic M1 and tetragonal rutile phases was studied by means of \textit{ab initio} molecular dynamics, based on density functional theory with Hubbard correction (DFT+U). Analysis of the dynamical processes associated with the structural transformation was carried out on the atomic scale by following the time evolution of dimerization amplitudes of vanadium atom chains and the twisting angle of vanadium dimers. The electronic transition was studied by tracing the changes in projected densities of states and their correlation with the evolution of the structural transformation. Our results reveal a strong interconnection between the structural and electronic transformations and show that they take place on the same time scale.

cond-mat.mtrl-sci↗

arXiv2017

High-pressure phase diagram, structural transitions, and persistent non-metallicity of BaBiO$_3$: theory and experiment

BaBiO$_3$ is a mixed-valence perovskite which escapes the metallic state through a Bi valence (and Bi-O bond) disproportionation or CDW distortion, resulting in a semiconductor with a gap of 0.8 eV at zero pressure. The evolution of structural and electronic properties at high pressure is, however, largely unknown. Pressure, one might have hoped, could reduce the disproportionation, making the two Bi ions equivalent and bringing the system closer to metallicity or even to superconductivity, such as is attained at ambient pressure upon metal doping. We address the high-pressure phase diagram of pristine BaBiO$_3$ by ab initio DFT calculations based on GGA and hybrid functionals in combination with crystal structure prediction methods based on evolutionary algorithms, molecular dynamics and metadynamics. The calculated phase diagram from 0 to 50 GPa indicates that pristine BaBiO$_3$ resists metallization under pressure, undergoing instead at room temperature structural phase transitions from monoclinic \textit{I2/m} to nearly tetragonal \textit{P-1} at 7 GPa, possibly to monoclinic \textit{C2/m} at 27 GPa, and to triclinic \textit{P1} at 43 GPa. Remarkably, all these phases sustain and in fact increase the inequivalence of two Bi neighboring sites and of their Bi-O bonds and, in all cases except semimetallic \textit{C2/m}, the associated insulating character. We then present high-pressure resistivity data which generally corroborate these results, and show that the insulating character persists at least up to 80 GPa, suggesting that the \textit{C2/m} phase is probably an artifact of the small computational cell.

cond-mat.mtrl-sci↗

arXiv2017

New High-Pressure Phases of MoSe$_2$ and MoTe$_2$

Three Mo-based transition metal dichalcogenides MoS$_2$, MoSe$_2$ and MoTe$_2$ share at ambient conditions the same structure 2H$_c$, consisting of layers where Mo atoms are surrounded by six chalcogen atoms in trigonal prism coordination. The knowledge of their high-pressure behaviour is, however, limited, particularly in case of MoSe$_2$ and MoTe$_2$. The latter materials do not undergo a layer-sliding transition 2H$_c$ $\rightarrow$ 2H$_a$ known in MoS$_2$ and currently no other stable phase besides 2H$_c$ is known in these systems at room temperature. Employing evolutionary crystal structure prediction in combination with \textit{ab initio} calculations we study the zero-temperature phase diagram of both materials up to Mbar pressures. We find a tetragonal phase with space group \textit{P4/mmm}, previously predicted in MoS$_2$, to become stable in MoSe$_2$ at 118 GPa. In MoTe$_2$ we predict at 50 GPa a transition to a new layered tetragonal structure with space group \textit{I4/mmm}, similar to CaC$_2$, where Mo atoms are surrounded by eight Te atoms. The phase is metallic already at the transition pressure and becomes a good metal beyond 1 Mbar. We discuss chemical trends in the family of Mo-based transition metal dichalcogenides and suggest that MoTe$_2$ likely offers the easiest route towards the post-2H phases.

cond-mat.mtrl-sci↗

arXiv2016

Creating new layered structures at high pressures: SiS$_2$

Old and novel layered structures are attracting increasing attention for their physical, electronic, and frictional properties. SiS$_2$, isoelectronic to SiO$_2$, CO$_2$ and CS$_2$, is a material whose phases known experimentally up to 6 GPa exhibit 1D chain-like, 2D layered and 3D tetrahedral structures. We present highly predictive $ab$ $initio$ calculations combined with evolutionary structure search and molecular dynamics simulations of the structural and electronic evolution of SiS$_2$ up to 100 GPa. A highly stable CdI$_2$-type layered structure, which is octahedrally coordinated with space group $P\bar{3}m1$ surprisingly appears between 4 and up to at least 100 GPa. The tetrahedral-octahedral switch is naturally expected upon compression, unlike the layered character realized here by edge-sharing SiS$_6$ octahedral units connecting within but not among sheets. The predicted phase is semiconducting with an indirect band gap of about 2 eV at 10 GPa, decreasing under pressure until metallization around 40 GPa. The robustness of the layered phase suggests possible recovery at ambient pressure, where calculated phonon spectra indicate dynamical stability. Even a single monolayer is found to be dynamically stable in isolation, suggesting that it could possibly be sheared or exfoliated from bulk $P\bar{3}m1$-SiS$_2$.

physics.chem-ph↗

arXiv2016

Pressure-induced gap closing and metallization of MoSe$_{2}$ and MoTe$_{2}$

Layered molybdenum dichalchogenides are semiconductors whose gap is controlled by delicate interlayer interactions. The gap tends to drop together with the interlayer distance, suggesting collapse and metallization under pressure. We predict, based on first principles calculations, that layered semiconductors 2H$_c$-MoSe$_2$ and 2H$_c$-MoTe$_2$ should undergo metallization at pressures between 28 and 40 GPa (MoSe$_2$) and 13 and 19 GPa (MoTe$_2$). Unlike MoS$_2$ where a 2H$_c$ $\to$ 2H$_a$ layer sliding transition is known to take place, these two materials appear to preserve the original 2H$_c$ layered structure at least up to 100 GPa and to increasingly resist lubric layer sliding under pressure. Similar to metallized MoS$_2$ they are predicted to exhibit a low density of states at the Fermi level, and presumably very modest superconducting temperatures if any. We also study the $β$-MoTe$_2$ structure, metastable with a higher enthalpy than 2H$_c$-MoTe$_2$. Despite its ready semimetallic and (weakly) superconducting character already at zero pressure, metallicity is not expected to increase dramatically with pressure.

cond-mat.mtrl-sci↗

arXiv2015

Transformation pathways in high-pressure solid nitrogen: from molecular N$_2$ to polymeric cg-N

The transformation pathway in high-pressure solid nitrogen from N$_2$ molecular state to polymeric cg-N phase was investigated by means of \textit{ab initio} molecular dynamics and metadynamics simulations. In our study, we observed a transformation mechanism starting from molecular $Immm$ phase that initiated with formation of $trans$-$cis$ chains. These chains further connected within layers and formed a chain-planar state, which we describe as a mixture of two crystalline structures - $trans$-$cis$ chain phase and $planar$ phase, both with $Pnma$ symmetry. This mixed state appeared in molecular dynamics performed at 120 GPa and 1500 K and in the metadynamics run at 110 GPa and 1500 K, where the chains continued to reorganize further and eventually formed cg-N. During separate simulations, we also found two new phases - molecular $P2_1/c$ and two-three-coordinated chain-like $Cm$. The transformation mechanism heading towards cg-N can be characterized as a progressive polymerization process passing through several intermediate states of variously connected $trans$-$cis$ chains. In the final stage of the transformation chains in the layered form rearrange collectively and develop new intraplanar as well as interplanar bonds leading to the geometry of cg-N. Chains with alternating $trans$ and $cis$ conformation were found to be the key entity - structural pattern governing the dynamics of the simulated molecular-polymeric transformation in compressed nitrogen.

physics.chem-ph↗

arXiv2014

Structural transformation between long and short-chain form of liquid sulfur from \textit{ab initio} molecular dynamics

We present results of \textit{ab initio} molecular dynamics study of a structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the chain-breakage phenomenon recently observed experimentally by Liu \textit{et al.} [1] and to the electronic transition reported by Brazhkin \textit{et al.} [2,3]. We performed an extensive \textit{ab initio} study and confirmed the existence of one transformation separating two distinct liquid polymeric phases: one composed of short chain-like fragments and another one with very long chains. We have not observed additional transformations reported in Refs. [2,3] and in the recent theoretical study by Zhao and Mu [4] and our findings are in agreement with the most recent experiment [1]. We offer a structural description of this liquid-liquid transformation in terms of chain lengths, cross-linking and geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in configurational energy and entropy as well as in diffusion coefficient and electronic properties (semiconductor-metal transition), but no density discontinuity was found. We also describe analogy of the investigated phenomenon to similar processes present in two other chalcogenes selenium and tellurium. Finally, we discuss possibility of a critical point terminating the studied transition in relation to the long-known behavior of ambient-pressure heated sulfur melt.

physics.chem-ph↗

arXiv2014

High Pressure Structure and Decomposition of MoS$_{2}$

The high pressure structural and electronic evolution of bulk MoS$_2$, an important transition metal layered dichalchogenide, is currently under active investigation. Recent theoretical and experimental work predicted and verified a 2H$_c \to$ 2H$_a$ layer sliding structural transition at 20 GPa and a band overlap semiconductor-semimetal transition in the same pressure range. The 2H$_a$ structure is known to persist up to pressure of 81 GPa but properties at higher pressures remain experimentally unknown. Here we predict, with a reliable first-principles evolutionary search, that major structural transformations should take place in equilibrium at higher pressures near 130-140 GPa. The main motif is a decomposition into MoS + S, also heralded in a small bimolecular cell by the appearance of a metastable non-layered metallic MoS$_2$ structure with space group \textit{P4/mmm}. Unlike semimetallic 2H$_a$-MoS$_2$, both this phase and sulphur in the fully phase separated system are fully metallic and superconducting with higher critical temperatures than alkali-intercalated MoS$_2$.

cond-mat.mtrl-sci↗

arXiv2014

Study of pressure-induced amorphization in sulfur using \textit{ab initio} molecular dynamics

We report results of ab initio constant-pressure molecular dynamics simulations of sulfur compression leading to structural transition and pressure-induced amorphization. Starting from the orthorhombic S-I phase composed of S$_8$ ring molecules we find at room temperature and pressure of 20 GPa a transformation to monoclinic phase where half of the molecules develop a different conformation. Upon further compression, the monoclinic phase undergoes pressure-induced amorphization into an amorphous phase, in agreement with experiments. We study the dynamics of the amorphization transition and investigate the evolution of intra and intermolecular distances in the monoclinic phase in order to provide a microscopic insight into the rings disintegration process leading to amorphization. In the amorphous form we examine the structural properties and discuss its relation to the experimentally found amorphous form and to underlying crystal phases as well. The amorphous form we find appears to correspond to the experimentally observed low density amorphous form.

cond-mat.dis-nn↗

arXiv2014

Structural evolution in high-pressure amorphous CO$_2$ from \textit{ab initio} molecular dynamics

By employing $ab$ $initio$ molecular dynamics simulations at constant pressure, we investigated behavior of amorphous carbon dioxide between 0-100 GPa and 200-500 K and found several new amorphous forms. We focused on evolution of the high-pressure polymeric amorphous form known as a-carbonia on its way down to zero pressure, where it eventually converts into a molecular amorphous solid. During decompression, two nonmolecular amorphous forms with different proportion of three and four-coordinated carbons and two mixed molecular-nonmolecular forms were observed. Transformation from a-carbonia to the molecular state thus appears to proceed discontinuously via several intermediate stages suggesting that solid CO$_2$ might exhibit interesting polyamorphism. We also studied relations of the amorphous forms to their crystalline counterparts. The tetrahedral-like a-carbonia is most probably related to phase-V according to their structural properties, while presence of the mixed forms may reflect hypothetical existence of metastable three-coordinated polymeric phase that is composed of linear chains. Our molecular amorphous form seems to be related to phase-I according to molecular coordination and their relative bond orientations.

cond-mat.mtrl-sci↗