arXiv subjects

Stefan Goedecker

Publications and source records attributed to Stefan Goedecker.

At least 37 records · Page 2Linked to original sources

arXiv2020

Maximum volume simplex method for automatic selection and classification of atomic environments and environment descriptor compression

Fingerprint distances, which measure the similarity of atomic environments, are commonly calculated from atomic environment fingerprint vectors. In this work we present the simplex method which can perform the inverse operation, i.e. calculating fingerprint vectors from fingerprint distances. The fingerprint vectors found in this way point to the corners of a simplex. For a large data set of fingerprints, we can find a particular largest volume simplex, whose dimension gives the effective dimension of the fingerprint vector space. We show that the corners of this simplex correspond to landmark environments that can by used in a fully automatic way to analyse structures. In this way we can for instance detect atoms in grain boundaries or on edges of carbon flakes without any human input about the expected environment. By projecting fingerprints on the largest volume simplex we can also obtain fingerprint vectors that are considerably shorter than the original ones but whose information content is not significantly reduced.

physics.comp-ph↗

arXiv2020

Detecting non-local effects in the electronic structure of a simple covalent system with machine learning methods

Using methods borrowed from machine learning we detect in a fully algorithmic way long range effects on local physical properties in a simple covalent system of carbon atoms. The fact that these long range effects exist for many configurations implies that atomistic simulation methods, such as force fields or modern machine learning schemes, that are based on locality assumptions, are limited in accuracy. We show that the basic driving mechanism for the long range effects is charge transfer. If the charge transfer is known, locality can be recovered for certain quantities such as the band structure energy.

cond-mat.mtrl-sci↗

arXiv2020

An assessment of the structural resolution of various fingerprints commonly used in machine learning

Atomic environment fingerprints are widely used in computational materials science, from machine learning potentials to the quantification of similarities between atomic configurations. Many approaches to the construction of such fingerprints, also called structural descriptors, have been proposed. In this work, we compare the performance of fingerprints based on the Overlap Matrix(OM), the Smooth Overlap of Atomic Positions (SOAP), Behler-Parrinello atom-centered symmetry functions (ACSF), modified Behler-Parrinello symmetry functions (MBSF) used in the ANI-1ccx potential and the Faber-Christensen-Huang-Lilienfeld (FCHL) fingerprint under various aspects. We study their ability to resolve differences in local environments and in particular examine whether there are certain atomic movements that leave the fingerprints exactly or nearly invariant. For this purpose, we introduce a sensitivity matrix whose eigenvalues quantify the effect of atomic displacement modes on the fingerprint. Further, we check whether these displacements correlate with the variation of localized physical quantities such as forces. Finally, we extend our examination to the correlation between molecular fingerprints obtained from the atomic fingerprints and global quantities of entire molecules.

physics.comp-ph↗

arXiv2020

Funnel Hopping Monte Carlo: An efficient method to overcome broken ergodicity

Monte Carlo simulations are a powerful tool to investigate the thermodynamic properties of atomic systems. In practice however, sampling of the complete configuration space is often hindered by high energy barriers between different regions of configuration space which can make ergodic sampling completely infeasible within accessible simulation times. Although several extensions to the conventional Monte Carlo scheme have been developed, that enable the treatment of such systems, these extensions often entail substantial computational cost or rely on the harmonic approximation. In this work we propose an exact method called Funnel Hopping Monte Carlo (FHMC) that is inspired by the the ideas of smart darting but is more efficient. Gaussian mixtures are used to approximate the Boltzmann distribution around local energy minima which are then used to propose high quality Monte Carlo moves that enable the Monte Carlo simulation to directly jump between different funnels. To fit the Gaussian mixtures we developed an extended version of the expectation-maximization algorithm that is able to take advantage of the high symmetry present in many low energy configurations. We demonstrate the methods performance on the example of the 38 as well as the 75 atom Lennard-Jones clusters which are well known for their double funnel energy landscapes that prevent ergodic sampling with conventional Monte Carlo simulations. By integrating FHMC into the parallel tempering scheme we were able to reduce the number of steps required until convergence of the simulation significantly.

cond-mat.stat-mech↗

arXiv2019

Finding reaction pathways with optimal atomic index mappings

Finding complex reaction and transformation pathways, involving many intermediate states, is in general not possible on the DFT level with existing simulation methods due to the very large number of required energy and force evaluations. This is due to a large extent to the fact that for complex reactions, it is not possible to determine which atom in the educt is mapped onto which atom in the product. Trying out all possible atomic index mappings is not feasible because of the factorial increase in the number of possible mappings. By using a penalty function that is invariant under index permutations, we can bias the potential energy surface in such a way that it obtains the characteristics of a structure seeker whose global minimum is the product. By performing a Minima Hopping based global optimization on this biased potential energy surface we can rapidly find intermediate states that lead into the global minimum. Based on this information we can then extract the full reaction pathway. We first demonstrate for a benchmark system, namely LJ38 that our method allows to preferentially find intermediate states that are relevant for the lowest energy reaction pathway and that we, therefore, need a much smaller number of intermediate states than previous methods to find the lowest energy reaction pathway. Finally, we apply the method to two real systems, C60 and C20H20 and show that the found reaction pathway contains valuable information on how the system can be synthesized.

physics.comp-ph↗

arXiv2019

Solvent-aware Interfaces in Continuum Solvation

Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key ingredient of continuum models is the choice of the solute cavity, i.e. the definition of the sharp or smooth boundary between the regions of space occupied by the quantum-mechanical (QM) system and the continuum embedding environment. Although most of the solute-based approaches developed lead to models with comparable and high accuracy when applied to small organic molecules, they can introduce significant artifacts when complex systems are considered. As an example, condensed-matter simulations often deal with supports that present open structures. Similarly, unphysical pockets of continuum solvent may appear in systems featuring multiple molecular components. Here, we introduce a solvent-aware approach to eliminate the unphysical effects where regions of space smaller than the size of a single solvent molecule could still be filled with a continuum environment. We do this by defining a smoothly varying solute cavity that overcomes several of the limitations of straightforward solute-based definitions. This new approach applies to any smooth local definition of the continuum interface, being it based on the electronic density or the atomic positions of the QM system. It produces boundaries that are continuously differentiable with respect to the QM degrees of freedom, leading to accurate forces and/or Kohn-Sham potentials. Benchmarks on semiconductor substrates and on explicit water substrates confirm the flexibility and the accuracy of the approach and provide a general set of parameters for condensed-matter systems featuring open structures and/or explicit liquid components.

physics.chem-ph↗

arXiv2018

Emergence of hidden phases of methylammonium lead-iodide (CH$_3$NH$_3$PbI$_3$) upon compression

We perform a thorough structural search with the minima hopping method (MHM) to explore low-energy structures of methylammonium lead iodide. By combining the MHM with a forcefield, we efficiently screen vast portions of the configurational space with large simulation cells containing up to 96 atoms. Our search reveals two structures of methylammonium iodide perovskite (MAPI) that are substantially lower in energy than the well-studied experimentally observed low-temperature $Pnma$ orthorhombic phase according to density functional calculations. Both structures have not yet been reported in the literature for MAPI, but our results show that they could emerge as thermodynamically stable phases via compression at low temperatures. In terms of the electronic properties, the two phases exhibit larger band gaps than the standard perovskite-type structures. Hence, pressure induced phase selection at technologically achievable pressures (i.e., via thin-film strain) is a route towards the synthesis of several MAPI polymorph with variable band gaps.

cond-mat.mtrl-sci↗

arXiv2018

Comment on the stability of decorated C 48 B 12 heterofullerene

A good hydrogen storage material should adsorb hydrogen in high concentrations and with optimal binding energies. Numerous mixed carbon boron fullerenes which are decorated with metal atoms were previously constructed by hand and proposed as a promising material in this context. We present a fully ab-initio, unbiased structure search in the configurational space of decorated C48B12 and find that most of the hitherto postulated ground state structures are not ground states. We determine the energetically lowest configurations for Be, Ca, Li and Sc decorated C48B12 clusters.

cond-mat.mtrl-sci↗

arXiv2017

Accurate, Large-Scale and Affordable Hybrid-PBE0 Calculations with GPU-Accelerated Supercomputers

Performing high accuracy hybrid functional calculations for condensed matter systems containing a large number of atoms is at present computationally very demanding - when not out of reach - if high quality basis sets are used. We present a highly efficient multiple GPU implementation of the exact exchange operator which allows hybrid functional density-functional theory calculations with systematic basis sets without additional approximations for up to a thousand atoms. This method is implemented in a portable real-space-based algorithm, released as an open-source package. With such a framework hybrid DFT calculations of high quality become accessible on state-of-the-art supercomputers within a time-to-solution of the same order of magnitude as traditional semilocal-GGA functionals.

cond-mat.mtrl-sci↗

arXiv2017

A two-dimensional hexagonal sheet of TiO$_2$

We report on the ab initio discovery of a novel putative ground state for quasi two-dimensional TiO$_2$ through a structural search using the minima hopping method with an artificial neural network potential. The structure is based on a honeycomb lattice and is energetically lower than the experimentally reported lepidocrocite sheet by 7~meV/atom, and merely 13~meV/atom higher in energy than the ground state rutile bulk structure. According to our calculations, the hexagonal sheet is stable against mechanical stress, it is chemically inert and can be deposited on various substrates without disrupting the structure. Its properties differ significantly from all known TiO$_2$ bulk phases with a large gap of 5.05~eV that can be tuned through strain engineering.

cond-mat.mtrl-sci↗

arXiv2017

Elemental Phosphorus: structural and superconducting phase diagram under pressure

Pressure-induced superconductivity and structural phase transitions in phosphorous (P) are studied by resistivity measurements under pressures up to 170 GPa and fully $ab-initio$ crystal structure and superconductivity calculations up to 350 GPa. Two distinct superconducting transition temperature (T$_{c}$) vs. pressure ($P$) trends at low pressure have been reported more than 30 years ago, and for the first time we are able to reproduce them and devise a consistent explanation founded on thermodynamically metastable phases of black-phosphorous. Our experimental and theoretical results form a single, consistent picture which not only provides a clear understanding of elemental P under pressure but also sheds light on the long-standing and unsolved $anomalous$ superconductivity trend. Moreover, at higher pressures we predict a similar scenario of multiple metastable structures which coexist beyond their thermodynamical stability range. Metastable phases of P experimentally accessible at pressures above 240 GPa should exhibit T$_{c}$'s as high as 15 K, i.e. three times larger than the predicted value for the ground-state crystal structure. We observe that all the metastable structures systematically exhibit larger transition temperatures than the ground-state ones, indicating that the exploration of metastable phases represents a promising route to design materials with improved superconducting properties.

cond-mat.supr-con↗

arXiv2017

The Elephant in the Room of Density Functional Theory Calculations

Using multiwavelets, we have obtained total energies and corresponding atomization energies for the GGA-PBE and hybrid-PBE0 density functionals for a test set of 211 molecules with an unprecedented and guaranteed $μ$Hartree accuracy. These quasi-exact references allow us to quantify the accuracy of standard all-electron basis sets that are believed to be highly accurate for molecules, such as Gaussian-type orbitals (GTOs), all-electron numeric atom-centered orbitals (NAOs) and full-potential augmented plane wave (APW) methods. We show that NAOs are able to achieve the so-called chemical accuracy (1 kcal/mol) for the typical basis set sizes used in applications, for both total and atomization energies. For GTOs, a triple-zeta quality basis has mean errors of ~10kcal/mol in total energies, while chemical accuracy is almost reached for a quintuple-zeta basis. Due to systematic error cancellations, atomization energy errors are reduced by almost an order of magnitude, placing chemical accuracy within reach also for medium to large GTO bases, albeit with significant outliers. In order to check the accuracy of the computed densities, we have also investigated the dipole moments, where in general, only the largest NAO and GTO bases are able to yield errors below 0.01 Debye. The observed errors are similar across the different functionals considered here.

physics.comp-ph↗

arXiv2016

Emergence of superconductivity in doped H$_2$O ice at high pressure

We investigate the possibility of achieving high-temperature superconductivity in hydrides under pressure by inducing metallization of otherwise insulating phases through doping, a path previously used to render standard semiconductors superconducting at ambient pressure. Following this idea, we study H$_2$O, one of the most abundant and well-studied substances, we identify nitrogen as the most likely and promising substitution/dopant. We show that for realistic levels of doping of a few percent, the phase X of ice becomes superconducting with a critical temperature of about 60 K at 150GPa. In view of the vast number of hydrides that are strongly covalent bonded, but that remain insulating until rather large pressures, our results open a series of new possibilities in the quest for novel high-temperature superconductors.

cond-mat.supr-con↗

arXiv2016

Computationally Efficient Characterization of Potential Energy Surfaces Based on Fingerprint Distances

An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic, dynamic and structural properties. Unfortunately computing the transition states and reaction pathways in addition to the significant energetically low-lying local minima is a computationally demanding task. We here introduce a computationally efficient method that is based on a combination of the minima hopping global optimization method and the insight that uphill barriers tend to increase with increasing structural distances of the educt and product states. This method allows to replace the exact connectivity information and transition state energies with alternative and approximate concepts. Without adding any significant additional cost to the minima hopping global optimization approach, this method allows to generate an approximate network of the minima, their connectivity and a rough measure for the energy needed for their interconversion. This can be used to obtain a first qualitative idea on important physical and chemical properties by means of a disconnectivity graph analysis. Besides the physical insight obtained by such an analysis, the gained knowledge can be used to make a decision if it is worthwhile or not to invest computational resources for an exact computation of the transition states and the reaction pathways. Furthermore it is demonstrated that the here presented method can be used for finding physically reasonable interconversion pathways that are promising input pathways for methods like transition path sampling or discrete path sampling.

cond-mat.mtrl-sci↗

arXiv2016

Ultralow Thermal Conductivity in Full-Heusler Semiconductors

Semiconducting half- and, to a lesser extent, full-Heusler compounds are promising thermoelectric materials due to their compelling electronic properties with large power factors. However, intrinsically high thermal conductivity resulting in a limited thermoelectric efficiency has so far impeded their widespread use in practical applications. Here, we report the computational discovery of a class of hitherto unknown stable semiconducting full-Heusler compounds with ten valence electrons ($X_2YZ$, $X$=Ca, Sr, and Ba; $Y$= Au and Hg; $Z$=Sn, Pb, As, Sb, and Bi) through high-throughput $ab-initio$ screening. These new compounds exhibit ultralow lattice thermal conductivity $κ_{\text{L}}$ close to the theoretical minimum due to strong anharmonic rattling of the heavy noble metals, while preserving high power factors, thus resulting in excellent phonon-glass electron-crystal materials.

cond-mat.mtrl-sci↗

arXiv2015

Superconductivity in metastable phases of phosphorus-hydride compounds under high pressure

Hydrogen-rich compounds have been extensively studied both theoretically and experimentally in the quest for novel high-temperature superconductors. Reports on sulfur-hydride attaining metallicity under pressure and exhibiting superconductivity at temperatures as high as 200 K have spurred an intense search for room-temperature superconductors in hydride materials. Recently, compressed phosphine was reported to metallize at pressures above 45 GPa, reaching a superconducting transition temperature (T$_{c}$) of 100 K at 200 GPa. However, neither the exact composition nor the crystal structure of the superconducting phase have been conclusively determined. In this work the phase diagram of PH$_n$ ($n=1,2,3,4,5,6$) was extensively explored by means of {\it ab initio} crystal structure predictions using the Minima Hopping Method (MHM). The results do not support the existence of thermodynamically stable PH$_n$ compounds, which exhibit a tendency for elemental decomposition at high pressure even when vibrational contributions to the free energies are taken into account. Although the lowest energy phases of PH$_{1,2,3}$ display T$_{c}$'s comparable to experiments, it remains uncertain if the measured values of T$_{c}$ can be fully attributed to a phase-pure compound of PH$_n$.

cond-mat.supr-con↗

arXiv2015

A fingerprint based metric for measuring similarities of crystalline structures

Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell we introduce crystal fingerprints that can be calculated easily and allow to define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures. The new method is an useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms and high-throughput screenings.

physics.comp-ph↗

arXiv2015

Low-density silicon allotropes for photovoltaic applications

Silicon materials play a key role in many technologically relevant fields, ranging from the electronic to the photovoltaic industry. A systematic search for silicon allotropes was performed by employing a modified ab initio minima hopping crystal structure prediction method. The algorithm was optimized to specifically investigate the hitherto barely explored low-density regime of the silicon phase diagram by imitating the guest-host concept of clathrate compounds. In total 44 metastable phases are presented, of which 11 exhibit direct or quasi-direct band-gaps in the range of $\approx$1.0-1.8 eV, close to the optimal Shockley-Queisser limit of $\approx$1.4 eV, with a stronger overlap of the absorption spectra with the solar spectrum compared to conventional diamond silicon. Due to the structural resemblance to known clathrate compounds it is expected that the predicted phases can be synthesized.

cond-mat.mtrl-sci↗