Computational Physics · Cross-listed from cond-mat.mes-hall
Bend Contour Electron Tomography (BCET): Quantitative strain and topography mapping
Henry G. Bell, Chenhang Xu, Arthur McCray et al. (+5 more)
Freestanding thin films of
quantum materials naturally develop sub-micrometer, nonuniform strain fields that strongly affect their electronic,
magnetic, and structural properties in both
equilibrium and nonequilibrium conditions. However, current methods to quantitatively resolve these mesoscopic features are primarily restricted to scanning probes, making it challenging for dynamical measurements such as single-shot imaging and femtosecond microscopy. Here, we present a new computational framework which we denote as bend contour electron
tomography (BCET), which efficiently converts bend contours in transmission electron microscope images into quantitative two-dimensional maps of strain and topography. By iteratively minimizing a designed loss function between experimental and simulated bend contour images, BCET retrieves both surface morphology and in-plane strain tensor fields without requiring scanning or diffraction mapping. We applied BCET to freestanding SrTiO$_3$ thin films, demonstrating the successful reconstruction of the local strain distribution and
curvature field with high fidelity. Our approach provides a quantitative framework for characterizing mesoscale structures in freestanding films using wide-field imaging, opening new avenues to investigate how spatial inhomogeneity governs phase transitions and nonequilibrium dynamics in two-dimensional
quantum materials.
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All authors Henry G. Bell, Chenhang Xu, Arthur McCray, Minyong Han, Yicheng Zhuang, Harold Y. Hwang, Colin Ophus, Alfred Zong
Computational Physics
Warp-Geo: Differentiable Geometry Representation for Dynamic-Boundary Simulation and Shape Optimization
Weijie Zhang, Xiantao Fan and Jian-Xun Wang
Modern inverse problems and adaptive simulations require efficient and differentiable representations of complex geometries that can be updated frequently for gradient-based optimization. Existing methods cannot simultaneously achieve both. We present Warp-Geo, a differentiable GPU-accelerated framework for reconstructing signed distance fields and evaluating surface normals from point clouds of complex 3D geometries. Warp-Geo combines uniform grids for GPU parallelism with implicit differentiation through the Poisson solve, enabling frequent geometry recomputation while maintaining full differentiability. We demonstrate Warp-Geo on forward SDF reconstruction, dynamic fluid–structure interaction with moving boundaries, and inverse shape optimization via automatic differentiation with gradient validation. GPU scalability analysis confirms practical feasibility for frequent geometry updates. The framework, implemented in Warp and JAX, enables seamless integration with differentiable physics solvers for end-to-end shape optimization.
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Computational Physics
How Does Distribution Shift Shape Pretraining Gains in Neural PDE Surrogates?
Pochinapeddi Sai Bhargav, Nithin Somasekharan, Rohit Sunil Kanchi et al. (+2 more)
Pretraining a neural PDE surrogate can reduce the amount of new CFD data needed when geometry or modeled physics changes. However, it remains unclear how different components of distribution shift affect this benefit. We pretrain a surrogate on 254,909 RANS solutions from one airfoil family and fine-tune it on a new family under two target settings with matched freestream ranges: the same Spalart-Allmaras (SA) modeling and SA with added $e^N$ transition modeling. At $N=1000$, the pretrained model matches the accuracy of a model trained from scratch on $3.25\times$ as many samples for the same-SA target, but $2.58\times$ as many for the transition-modeled target. By $N=5000$, this ordering reverses ($1.56\times$ versus $1.86\times$). At $N=1000$, sampling more distinct airfoils lowers error on both targets, but only for the same-SA target is the gain increase larger than the observed draw-to-draw variation ($3.3\times$ to $4.0\times$). These results show that pretraining value depends jointly on target-data budget, target-data coverage, and whether source and target differ in modeled physics.
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All authors Pochinapeddi Sai Bhargav, Nithin Somasekharan, Rohit Sunil Kanchi, Sicheng He, Shaowu Pan
Computational Physics · Cross-listed from cond-mat.stat-mech
Global Minima of the Thomson Problem in a Disk: A Molecular Dynamics Approach with Fixed Border Charges
Georgiy K. Lavrov and Eduard G. Nikonov
We report improved global-minimum configurations for the classical Thomson problem of $N=60$, $61$, $92$, and $99$ repulsive Coulomb charges confined to a disk. By combining the quenched molecular dynamics (QMD) method with the fixed-border heuristic introduced by Amore and Zarate, we systematically obtain configurations with energies $E_{\mathrm{QMD}}(60)=2159.3584240930$, $E_{\mathrm{QMD}}(61)=2237.19264190$, $E_{\mathrm{QMD}}(92)=5358.35353314$, and $E_{\mathrm{QMD}}(99)=6254.83029083$, which improve upon the previously best-known values. For $N=60$, the Voronoi diagram of our configuration differs from the one reported earlier. The
symmetries for $N=61$ $(C_{2})$ and $N=99$ $(D_{1})$ are confirmed and are consistent with the known
symmetry patterns for these configurations. For $N=92$, whereas the previously reported Voronoi diagram has lower
symmetry, our solution exhibits a clear $D_{1}$ (axial)
symmetry of defects. The results are highly reproducible across multiple independent runs, providing strong evidence that these configurations are robust global-minimum candidates.
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Computational Physics
Mechanical resilience of ultra-low-density racing-shoe foams
Jeremy A. McCulloch and Ellen Kuhl
High-performance racing shoes rely on ultra-low-density elastomeric foams that undergo large, repeated deformations during running. Yet little is known about how their mechanical properties vary throughout the shoe or change with repeated use. Here, we characterize the midsole foam in an elite-level racing shoe from the heel, midfoot, and toe of a new shoe and a shoe worn for 300 miles. Microscopy reveals a characteristic pore length scale of 128+/-18 um and supports an approximately isotropic continuum description. We then quantify the mechanical response under tension, compression, and shear. Remarkably, despite 300 miles of real-world use, the foam retains its mechanical response across all three loading modes and shoe regions. Energy return remains largely unchanged, with values of 85-93% in tension and compression and 64-71% in shear. At the same time, we observe strong regional variations, with tensile and compressive stiffnesses 38-51% lower in the toe than in the heel. The foam also exhibits a pronounced tension-compression asymmetry in Poisson's ratio. Together, these findings reveal a spatially structured and mode-dependent mechanical response that remains largely preserved after 300 miles of use. This mechanical resilience may extend the functional lifetime of racing shoes, with implications for runners, replacement recommendations, and sustainability.
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Computational Physics
Correlation-Free Transition Path Sampling through Shooting Point Generation Guided by Committor Learning
Maximilian Negedly, Sebastian Falkner, Alessandro Coretti et al. (+1 more)
Studying the dynamical behavior of a system often depends on characterizing how it transitions between long-lived states. Because such transitions are rare, observing them usually requires specialized enhanced sampling techniques. Transition Path Sampling (TPS) is a well-established method for generating reactive trajectories, which is simple to implement and does not require the definition of a preconceived reaction coordinate. However, its efficiency is limited by its sequential nature and the resulting correlations between sampled paths. Previous work addressed this limitation by combining TPS with a sampling scheme based on conditioned Boltzmann Generators, a generative machine learning model capable of sampling a given target probability distribution. This approach produces uncorrelated transition paths but relies on an accurate reaction coordinate, which is rarely known in advance. Building on recent advances in committor learning, specifically on the Artificial Intelligence for Molecular Mechanism Discovery (AIMMD) method, in this work we introduce GenAIMMD, an iterative
algorithm that actively and self-consistently learns the ideal reaction coordinate (the committor) and trains a conditioned Boltzmann Generator to sample from arbitrary bias windows along it. GenAIMMD thereby provides a correlation-free and fully parallelizable path sampling scheme that does not require prior knowledge of the system's transition mechanism. We apply GenAIMMD to a two-dimensional toy model and a higher-dimensional
polymer system. In both cases, GenAIMMD succeeds in training the Boltzmann Generator and learning the committor.
Benchmark results show a substantial increase in performance compared to standard TPS.
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All authors Maximilian Negedly, Sebastian Falkner, Alessandro Coretti, Christoph Dellago
Computational Physics · Cross-listed from cond-mat.mtrl-sci
Anharmonic Phonon Renormalization and Defect Tolerance of the Thermoelectric Power Factor in Monolayer SnSe
Nguyen Tran Gia Bao, Thang Bach Phan, Vu Thi Hanh Thu et al. (+1 more)
Monolayer tin selenide (SnSe) exhibits phase-dependent anharmonic
lattice dynamics, yet their consequences for the thermoelectric power factor (PF) and point-defect tolerance remain unresolved. We combine density functional theory, the
stochastic self-consistent harmonic approximation (SSCHA), and Boltzmann transport calculations including electron-
phonon and electron-defect scattering to investigate monolayer $\alpha$-SnSe (Pnma) and $\beta$-SnSe (Cmcm). In dynamically stable $\alpha$-SnSe, SSCHA renormalizes the finite-temperature
phonons without changing the qualitative n-type transport picture. In $\beta$-SnSe, SSCHA removes the harmonic soft-mode instability of the Cmcm phase at 800-1000 K, and thereby enables high-temperature transport calculations; LO/TO-2 is the principal electron-scattering channel. In the lower-density window near $10^{12}$ cm$^{-2}$, the n-type PF reaches 15-19 $\mu\mathrm{W}/(\mathrm{K}^{2}\cdot\mathrm{cm})$ at 800-900 K and exceeds the p-type PF primarily because of the higher electrical conductivity. Se vacancies ($V_{\mathrm{Se}}$) produce weaker electron-defect scattering than Sn vacancies ($V_{\mathrm{Sn}}$), and p-type transport is less defect tolerant than n-type transport in both phases. We define an operational critical defect concentration, $C_{\mathrm{crit}}$, at which the PF decreases by 15% relative to the corresponding defect-free value. The lowest $C_{\mathrm{crit}}$ is $8.841\times10^{-5}$ (approximately 88 ppm) for p-type $\alpha$-SnSe with $V_{\mathrm{Sn}}$; for n-type $\beta$-SnSe with $V_{\mathrm{Se}}$, the 15% threshold is not reached up to $5\times10^{-3}$ (5000 ppm). These results distinguish finite-temperature
phonon renormalization in stable $\alpha$-SnSe from anharmonic stabilization in $\beta$-SnSe and provide defect-concentration limits for preserving the PF.
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All authors Nguyen Tran Gia Bao, Thang Bach Phan, Vu Thi Hanh Thu, Nguyen Tuan Hung
Computational Physics · Cross-listed from cond-mat.mtrl-sci
The Roadmap of Inorganic Computational Materials Databases: Capabilities, Credibility, Coverage, and the Open Frontier
Miao Liu, Jianghao Jin, Tenglong Lu et al. (+4 more)
Computational materials databases have become central infrastructure for data-driven discovery of inorganic materials, yet their growth remains strikingly uneven across property families. This perspective synthesizes a systematic survey of mainstream density functional theory (DFT) software, the computational cost and credibility of nineteen material-property families, and the coverage of existing computational databases, into a coherent picture of where the field stands and where it should go. We show that the ecosystem of first-principles codes is methodologically mature: for nearly every property of technological interest, at least one production-grade code can compute it.The binding constraint is no longer methodological capability but the economics of trust - which properties can be computed cheaply enough, and accurately enough, to be harvested at database scale. Mapping database coverage onto a Gartner-style readiness cycle reveals a sharp divide: ground-state structure, energetics, elasticity, and
topology have reached routine production, while nine property families - including NMR/EPR parameters, core-level spectra, electron-
phonon properties, thermal conductivity, and
quantum transport - remain without any systematic computational database. We argue that these blank zones define the scientific opportunity of the next decade, and we propose a three-horizon roadmap: consolidating coverage and interoperability in the near term, industrializing mid-cost properties through surrogate-accelerated workflows in the medium term, and conquering the high-cost frontier through machine-learned interatomic potentials, autonomous computing infrastructure, and community governance in the long term.
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All authors Miao Liu, Jianghao Jin, Tenglong Lu, Jianguo Si, Yin Shi, Sheng Meng, Weihua Wang
Computational Physics
Exergy-Anergy Representation of Turbomachine Performance Characteristics
Tihomir Varchev, Yiwen Yuan, Tobias Schateikis et al. (+1 more)
The performance synthesis calculation of aircraft engines relies on tabulated
datasets for the simulation of the complex turbomachinery components at acceptable runtimes. Typically, these so-called performance maps express the change of the fluid's energetic state over the component in terms of the total pressure ratio and the isentropic efficiency of the process. However, the definitions of both parameters are different for compressors and turbines and the isentropic efficiency is in both cases not defined for a unity pressure ratio. Moreover, this parameter combination is not directly applicable when modelling the engine at the aircraft level, which is required for modern highly integrated aircraft design. As exergy analysis is an established tool for aircraft design asessment, novel performance maps are proposed that describe the change in exergy and anergy over a given turbomachine component. Both changes are expressed as non-dimensional parameters whose definition is consistent for compressors and turbines, and is compatible with a unity pressure ratio. It is shown that the presented exergy-anergy maps are obtainable on a standard turbomachine test bed or through transformation of existing maps. It is highlighted using examples, that the conversion between existing maps and exergy-anergy maps is completely lossless. The different operating regimes of the turbomachines are clearly distinguishable in the novel map representation, which allows an assessment of the map's physical consistency. It is therefore concluded, that the exergy-anergy maps are an important alternative to the performance map variants established today.
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All authors Tihomir Varchev, Yiwen Yuan, Tobias Schateikis, Stephan Staudacher
Computational Physics · Cross-listed from physics.chem-ph
Efficient tensorized evaluation of permutation invariant polynomials for representing potential energy surfaces
Junhong Li, Kaisheng Song, Hua Guo et al. (+1 more)
Permutation invariant
polynomials (PIPs), together with related
polynomial-based invariant descriptors such as fundamental invariants (FIs), are widely used in constructing high-fidelity global potential energy surfaces (PESs) of molecules that contain identical atoms. Although the monomial symmetrization approach (MSA) enables fast evaluation of PIPs through recursive factorization, it leads to deeply nested computational graphs that may require large
memory and are inefficient in modern automatic differentiation frameworks. In this work, we introduce JaxPIP, a JAX-based implementation that reformulates PIP/FI evaluation into tensorized linear
algebra operations. By replacing recursive factorization with dense
matrix operations combined with log-exp transformation and segmented summation, the evaluation becomes regular and GPU-friendly. This allows efficient execution with just-in-time compilation and enables large-scale batch evaluation of energies and forces (as well as higher-order derivatives). The resulting architecture supports ensemble simulations such as quasi-classical trajectory (QCT), path-integral molecular dynamics (PIMD), and
diffusion Monte Carlo (DMC) in a fully vectorized manner. As demonstrated in examples, JaxPIP provides a practical route for efficient simulations of molecular systems with scalable GPU execution.
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All authors Junhong Li, Kaisheng Song, Hua Guo, Jun Li
Computational Physics
Mollified-sharp decomposition: a probabilistic regularization of parametric POD for shock-bearing flows
Oliver T. Schmidt
This paper introduces the mollified-sharp decomposition, a probabilistic regularization of moving shocks in parametric reduced-order models. Each detected shock location is treated as a random variable with a prescribed probability density. Averaging over this artificial distribution replaces the localized pressure change by a smooth transition whose spatial extent is set by the density width, rather than by direct filtering of the pressure field. Each snapshot is decomposed exactly into a regularized mollified field and a local sharp correction that restores the shock. This probabilistic construction and exact additive split define the general method; the detector, kernel, treatment of multiple shocks,
alignment coordinates, and regression are implementation choices. In the present realization, a calibrated indicator detects shocks, a compactly supported Wendland kernel mollifies them, and a peak-normalized and, where necessary, partitioned weight derived from each shock-location probability density defines the centroid, principal axes, and scales of its local
alignment domain. Separate POD-GPR models represent the mollified field and aligned corrections, with additional regressions for shock presence and
alignment. The method is demonstrated on the transonic airfoil pressure data of Catalani et al. (2023) and compared with a standard POD-GPR model constructed from the same data and POD-energy criterion. The mollified-sharp model reduces the mean test-set relative $L^2$ pressure error by 31.2% and the mean test-set surface-pressure-coefficient error by 33.2%, while also improving the predicted shock locations and pressure changes; the trade-off is a median online evaluation time 2.24 times as long. The construction is applicable in principle to other parameter-dependent fields with moving sharp features, such as moving material interfaces in multiphase flows.
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