The hiphive package for the extraction of high-order force constants by machine learning

The efficient extraction of force constants (FCs) is crucial for the analysis of many thermodynamic materials properties. Approaches based on the systematic enumeration of finite differences scale poorly with system size and can rarely extend beyond third order when input data is obtained from first-principles calculations. Methods based on parameter fitting in the spirit of interatomic potentials, on the other hand, can extract FC parameters from semi-random configurations of high information density and advanced regularized regression methods can recover physical solutions from a limited amount of data. Here, we present the hiPhive Python package, that enables the construction of force constant models up to arbitrary order. hiPhive exploits crystal symmetries to reduce the number of free parameters and then employs advanced machine learning algorithms to extract the force constants. Depending on the problem at hand both over and underdetermined systems are handled efficiently. The FCs can be subsequently analyzed directly and or be used to carry out e.g., molecular dynamics simulations. The utility of this approach is demonstrated via several examples including ideal and defective monolayers of MoS$_2$ as well as bulk nickel

A window to the past through modern urban environments: Developing a photogrammetric workflow for the orientation parameter estimation of historical images

The ongoing process of digitization in archives is providing access to ever-increasing historical image collections. In many of these repositories, images can typically be viewed in a list or gallery view. Due to the growing number of digitized objects, this type of visualization is becoming increasingly complex. Among other things, it is difficult to determine how many photographs show a particular object and spatial information can only be communicated via metadata. Within the scope of this thesis, research is conducted on the automated determination and provision of this spatial data. Enhanced visualization options make this information more eas- ily accessible to scientists as well as citizens. Different types of visualizations can be presented in three-dimensional (3D), Virtual Reality (VR) or Augmented Reality (AR) applications. However, applications of this type require the estimation of the photographer’s point of view. In the photogrammetric context, this is referred to as estimating the interior and exterior orientation parameters of the camera. For determination of orientation parameters for single images, there are the established methods of Direct Linear Transformation (DLT) or photogrammetric space resection. Using these methods requires the assignment of measured object points to their homologue image points. This is feasible for single images, but quickly becomes impractical due to the large amount of images available in archives. Thus, for larger image collections, usually the Structure-from-Motion (SfM) method is chosen, which allows the simultaneous estimation of the interior as well as the exterior orientation of the cameras. While this method yields good results especially for sequential, contemporary image data, its application to unsorted historical photographs poses a major challenge. In the context of this work, which is mainly limited to scenarios of urban terrestrial photographs, the reasons for failure of the SfM process are identified. In contrast to sequential image collections, pairs of images from different points in time or from varying viewpoints show huge differences in terms of scene representation such as deviations in the lighting situation, building state, or seasonal changes. Since homologue image points have to be found automatically in image pairs or image sequences in the feature matching procedure of SfM, these image differences pose the most complex problem. In order to test different feature matching methods, it is necessary to use a pre-oriented historical dataset. Since such a benchmark dataset did not exist yet, eight historical image triples (corresponding to 24 image pairs) are oriented in this work by manual selection of homologue image points. This dataset allows the evaluation of frequently new published methods in feature matching. The initial methods used, which are based on algorithmic procedures for feature matching (e.g., Scale Invariant Feature Transform (SIFT)), provide satisfactory results for only few of the image pairs in this dataset. By introducing methods that use neural networks for feature detection and feature description, homologue features can be reliably found for a large fraction of image pairs in the benchmark dataset. In addition to a successful feature matching strategy, determining camera orientation requires an initial estimate of the principal distance. Hence for historical images, the principal distance cannot be directly determined as the camera information is usually lost during the process of digitizing the analog original. A possible solution to this problem is to use three vanishing points that are automatically detected in the historical image and from which the principal distance can then be determined. The combination of principal distance estimation and robust feature matching is integrated into the SfM process and allows the determination of the interior and exterior camera orientation parameters of historical images. Based on these results, a workflow is designed that allows archives to be directly connected to 3D applications. A search query in archives is usually performed using keywords, which have to be assigned to the corresponding object as metadata. Therefore, a keyword search for a specific building also results in hits on drawings, paintings, events, interior or detailed views directly connected to this building. However, for the successful application of SfM in an urban context, primarily the photographic exterior view of the building is of interest. While the images for a single building can be sorted by hand, this process is too time-consuming for multiple buildings. Therefore, in collaboration with the Competence Center for Scalable Data Services and Solutions (ScaDS), an approach is developed to filter historical photographs by image similarities. This method reliably enables the search for content-similar views via the selection of one or more query images. By linking this content-based image retrieval with the SfM approach, automatic determination of camera parameters for a large number of historical photographs is possible. The developed method represents a significant improvement over commercial and open-source SfM standard solutions. The result of this work is a complete workflow from archive to application that automatically filters images and calculates the camera parameters. The expected accuracy of a few meters for the camera position is sufficient for the presented applications in this work, but offer further potential for improvement. A connection to archives, which will automatically exchange photographs and positions via interfaces, is currently under development. This makes it possible to retrieve interior and exterior orientation parameters directly from historical photography as metadata which opens up new fields of research.:1 Introduction 1 1.1 Thesis structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Historical image data and archives . . . . . . . . . . . . . . . . . . . . . . . . 2 1.3 Structure-from-Motion for historical images . . . . . . . . . . . . . . . . . . . 4 1.3.1 Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.3.2 Selection of images and preprocessing . . . . . . . . . . . . . . . . . . 5 1.3.3 Feature detection, feature description and feature matching . . . . . . 6 1.3.3.1 Feature detection . . . . . . . . . . . . . . . . . . . . . . . . 7 1.3.3.2 Feature description . . . . . . . . . . . . . . . . . . . . . . . 9 1.3.3.3 Feature matching . . . . . . . . . . . . . . . . . . . . . . . . 10 1.3.3.4 Geometric verification and robust estimators . . . . . . . . . 13 1.3.3.5 Joint methods . . . . . . . . . . . . . . . . . . . . . . . . . . 16 1.3.4 Initial parameterization . . . . . . . . . . . . . . . . . . . . . . . . . . 19 1.3.5 Bundle adjustment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 1.3.6 Dense reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 1.3.7 Georeferencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 1.4 Research objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 2 Generation of a benchmark dataset using historical photographs for the evaluation of feature matching methods 29 2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 2.1.1 Image differences based on digitization and image medium . . . . . . . 30 2.1.2 Image differences based on different cameras and acquisition technique 31 2.1.3 Object differences based on different dates of acquisition . . . . . . . . 31 2.2 Related work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 2.3 The image dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 2.4 Comparison of different feature detection and description methods . . . . . . 35 2.4.1 Oriented FAST and Rotated BRIEF (ORB) . . . . . . . . . . . . . . . 36 2.4.2 Maximally Stable Extremal Region Detector (MSER) . . . . . . . . . 36 2.4.3 Radiation-invariant Feature Transform (RIFT) . . . . . . . . . . . . . 36 2.4.4 Feature matching and outlier removal . . . . . . . . . . . . . . . . . . 36 2.5 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 2.6 Conclusions and future work . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 3 Photogrammetry as a link between image repository and 4D applications 45 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 IX Contents 3.2 Multimodal access on repositories . . . . . . . . . . . . . . . . . . . . . . . . . 47 3.2.1 Conventional access . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 3.2.2 Virtual access using online collections . . . . . . . . . . . . . . . . . . 48 3.2.3 Virtual museums . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 3.3 Workflow and access strategies . . . . . . . . . . . . . . . . . . . . . . . . . . 52 3.3.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 3.3.2 Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 3.3.3 Photogrammetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 3.3.4 Browser access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 3.3.5 VR and AR access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 3.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 4 An adapted Structure-from-Motion Workflow for the orientation of historical images 69 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 4.2 Related Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 4.2.1 Historical images for 3D reconstruction . . . . . . . . . . . . . . . . . 72 4.2.2 Algorithmic Feature Detection and Matching . . . . . . . . . . . . . . 73 4.2.3 Feature Detection and Matching using Convolutional Neural Networks 74 4.3 Feature Matching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 4.4 Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 4.4.1 Step 1: Data preparation . . . . . . . . . . . . . . . . . . . . . . . . . 78 4.4.2 Step 2.1: Feature Detection and Matching . . . . . . . . . . . . . . . . 78 4.4.3 Step 2.2: Vanishing Point Detection and Principal Distance Estimation 80 4.4.4 Step 3: Scene Reconstruction . . . . . . . . . . . . . . . . . . . . . . . 80 4.4.5 Comparison with Three Other State-of-the-Art SfM Workflows . . . . 81 4.5 Datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 4.6 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 4.7 Conclusions and Future Work . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 4.8 Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 4.A Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 5 Fully automated pose estimation of historical images 97 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 5.2 Related Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 5.2.1 Image Retrieval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 5.2.2 Feature Detection and Matching . . . . . . . . . . . . . . . . . . . . . 101 5.3 Data Preparation: Image Retrieval . . . . . . . . . . . . . . . . . . . . . . . . 102 5.3.1 Experiment and Data . . . . . . . . . . . . . . . . . . . . . . . . . . . 103 5.3.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 5.3.2.1 Layer Extraction Approach (LEA) . . . . . . . . . . . . . . . 104 5.3.2.2 Attentive Deep Local Features (DELF) Approach . . . . . . 105 5.3.3 Results and Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . 106 5.4 Camera Pose Estimation of Historical Images Using Photogrammetric Methods 110 5.4.1 Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 5.4.1.1 Benchmark Datasets . . . . . . . . . . . . . . . . . . . . . . . 111 5.4.1.2 Retrieval Datasets . . . . . . . . . . . . . . . . . . . . . . . . 113 5.4.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115 5.4.2.1 Feature Detection and Matching . . . . . . . . . . . . . . . . 115 5.4.2.2 Geometric Verification and Camera Pose Estimation . . . . . 116 5.4.3 Results and Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . 117 5.5 Conclusions and Future Work . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 5.A Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124 6 Related publications 129 6.1 Photogrammetric analysis of historical image repositores for virtual reconstruction in the field of digital humanities . . . . . . . . . . . . . . . . . . . . . . . 130 6.2 Feature matching of historical images based on geometry of quadrilaterals . . 131 6.3 Geo-information technologies for a multimodal access on historical photographs and maps for research and communication in urban history . . . . . . . . . . 132 6.4 An automated pipeline for a browser-based, city-scale mobile 4D VR application based on historical images . . . . . . . . . . . . . . . . . . . . . . . . . . 133 6.5 Software and content design of a browser-based mobile 4D VR application to explore historical city architecture . . . . . . . . . . . . . . . . . . . . . . . . 134 7 Synthesis 135 7.1 Summary of the developed workflows . . . . . . . . . . . . . . . . . . . . . . . 135 7.1.1 Error assessment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137 7.1.2 Accuracy estimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139 7.1.3 Transfer of the workflow . . . . . . . . . . . . . . . . . . . . . . . . . . 141 7.2 Developments and Outlook . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 8 Appendix 149 8.1 Setup for the feature matching evaluation . . . . . . . . . . . . . . . . . . . . 149 8.2 Transformation from COLMAP coordinate system to OpenGL . . . . . . . . 150 References 151 List of Figures 165 List of Tables 167 List of Abbreviations 169Der andauernde Prozess der Digitalisierung in Archiven ermöglicht den Zugriff auf immer größer werdende historische Bildbestände. In vielen Repositorien können die Bilder typischerweise in einer Listen- oder Gallerieansicht betrachtet werden. Aufgrund der steigenden Zahl an digitalisierten Objekten wird diese Art der Visualisierung zunehmend unübersichtlicher. Es kann u.a. nur noch schwierig bestimmt werden, wie viele Fotografien ein bestimmtes Motiv zeigen. Des Weiteren können räumliche Informationen bisher nur über Metadaten vermittelt werden. Im Rahmen der Arbeit wird an der automatisierten Ermittlung und Bereitstellung dieser räumlichen Daten geforscht. Erweiterte Visualisierungsmöglichkeiten machen diese Informationen Wissenschaftlern sowie Bürgern einfacher zugänglich. Diese Visualisierungen können u.a. in drei-dimensionalen (3D), Virtual Reality (VR) oder Augmented Reality (AR) Anwendungen präsentiert werden. Allerdings erfordern Anwendungen dieser Art die Schätzung des Standpunktes des Fotografen. Im photogrammetrischen Kontext spricht man dabei von der Schätzung der inneren und äußeren Orientierungsparameter der Kamera. Zur Bestimmung der Orientierungsparameter für Einzelbilder existieren die etablierten Verfahren der direkten linearen Transformation oder des photogrammetrischen Rückwärtsschnittes. Dazu muss eine Zuordnung von gemessenen Objektpunkten zu ihren homologen Bildpunkten erfolgen. Das ist für einzelne Bilder realisierbar, wird aber aufgrund der großen Menge an Bildern in Archiven schnell nicht mehr praktikabel. Für größere Bildverbände wird im photogrammetrischen Kontext somit üblicherweise das Verfahren Structure-from-Motion (SfM) gewählt, das die simultane Schätzung der inneren sowie der äußeren Orientierung der Kameras ermöglicht. Während diese Methode vor allem für sequenzielle, gegenwärtige Bildverbände gute Ergebnisse liefert, stellt die Anwendung auf unsortierten historischen Fotografien eine große Herausforderung dar. Im Rahmen der Arbeit, die sich größtenteils auf Szenarien stadträumlicher terrestrischer Fotografien beschränkt, werden zuerst die Gründe für das Scheitern des SfM Prozesses identifiziert. Im Gegensatz zu sequenziellen Bildverbänden zeigen Bildpaare aus unterschiedlichen zeitlichen Epochen oder von unterschiedlichen Standpunkten enorme Differenzen hinsichtlich der Szenendarstellung. Dies können u.a. Unterschiede in der Beleuchtungssituation, des Aufnahmezeitpunktes oder Schäden am originalen analogen Medium sein. Da für die Merkmalszuordnung in SfM automatisiert homologe Bildpunkte in Bildpaaren bzw. Bildsequenzen gefunden werden müssen, stellen diese Bilddifferenzen die größte Schwierigkeit dar. Um verschiedene Verfahren der Merkmalszuordnung testen zu können, ist es notwendig einen vororientierten historischen Datensatz zu verwenden. Da solch ein Benchmark-Datensatz noch nicht existierte, werden im Rahmen der Arbeit durch manuelle Selektion homologer Bildpunkte acht historische Bildtripel (entspricht 24 Bildpaaren) orientiert, die anschließend genutzt werden, um neu publizierte Verfahren bei der Merkmalszuordnung zu evaluieren. Die ersten verwendeten Methoden, die algorithmische Verfahren zur Merkmalszuordnung nutzen (z.B. Scale Invariant Feature Transform (SIFT)), liefern nur für wenige Bildpaare des Datensatzes zufriedenstellende Ergebnisse. Erst durch die Verwendung von Verfahren, die neuronale Netze zur Merkmalsdetektion und Merkmalsbeschreibung einsetzen, können für einen großen Teil der historischen Bilder des Benchmark-Datensatzes zuverlässig homologe Bildpunkte gefunden werden. Die Bestimmung der Kameraorientierung erfordert zusätzlich zur Merkmalszuordnung eine initiale Schätzung der Kamerakonstante, die jedoch im Zuge der Digitalisierung des analogen Bildes nicht mehr direkt zu ermitteln ist. Eine mögliche Lösung dieses Problems ist die Verwendung von drei Fluchtpunkten, die automatisiert im historischen Bild detektiert werden und aus denen dann die Kamerakonstante bestimmt werden kann. Die Kombination aus Schätzung der Kamerakonstante und robuster Merkmalszuordnung wird in den SfM Prozess integriert und erlaubt die Bestimmung der Kameraorientierung historischer Bilder. Auf Grundlage dieser Ergebnisse wird ein Arbeitsablauf konzipiert, der es ermöglicht, Archive mittels dieses photogrammetrischen Verfahrens direkt an 3D-Anwendungen anzubinden. Eine Suchanfrage in Archiven erfolgt üblicherweise über Schlagworte, die dann als Metadaten dem entsprechenden Objekt zugeordnet sein müssen. Eine Suche nach einem bestimmten Gebäude generiert deshalb u.a. Treffer zu Zeichnungen, Gemälden, Veranstaltungen, Innen- oder Detailansichten. Für die erfolgreiche Anwendung von SfM im stadträumlichen Kontext interessiert jedoch v.a. die fotografische Außenansicht des Gebäudes. Während die Bilder für ein einzelnes Gebäude von Hand sortiert werden können, ist dieser Prozess für mehrere Gebäude zu zeitaufwendig. Daher wird in Zusammenarbeit mit dem Competence Center for Scalable Data Services and Solutions (ScaDS) ein Ansatz entwickelt, um historische Fotografien über Bildähnlichkeiten zu filtern. Dieser ermöglicht zuverlässig über die Auswahl eines oder mehrerer Suchbilder die Suche nach inhaltsähnlichen Ansichten. Durch die Verknüpfung der inhaltsbasierten Suche mit dem SfM Ansatz ist es möglich, automatisiert für eine große Anzahl historischer Fotografien die Kameraparameter zu bestimmen. Das entwickelte Verfahren stellt eine deutliche Verbesserung im Vergleich zu kommerziellen und open-source SfM Standardlösungen dar. Das Ergebnis dieser Arbeit ist ein kompletter Arbeitsablauf vom Archiv bis zur Applikation, der automatisch Bilder filtert und diese orientiert. Die zu erwartende Genauigkeit von wenigen Metern für die Kameraposition sind ausreichend für die dargestellten Anwendungen in dieser Arbeit, bieten aber weiteres Verbesserungspotential. Eine Anbindung an Archive, die über Schnittstellen automatisch Fotografien und Positionen austauschen soll, befindet sich bereits in der Entwicklung. Dadurch ist es möglich, innere und äußere Orientierungsparameter direkt von der historischen Fotografie als Metadaten abzurufen, was neue Forschungsfelder eröffnet.:1 Introduction 1 1.1 Thesis structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Historical image data and archives . . . . . . . . . . . . . . . . . . . . . . . . 2 1.3 Structure-from-Motion for historical images . . . . . . . . . . . . . . . . . . . 4 1.3.1 Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.3.2 Selection of images and preprocessing . . . . . . . . . . . . . . . . . . 5 1.3.3 Feature detection, feature description and feature matching . . . . . . 6 1.3.3.1 Feature detection . . . . . . . . . . . . . . . . . . . . . . . . 7 1.3.3.2 Feature description . . . . . . . . . . . . . . . . . . . . . . . 9 1.3.3.3 Feature matching . . . . . . . . . . . . . . . . . . . . . . . . 10 1.3.3.4 Geometric verification and robust estimators . . . . . . . . . 13 1.3.3.5 Joint methods . . . . . . . . . . . . . . . .

토카막 통합 시뮬레이션 코드의 개발과 여러 장치에 대한 적용 연구

학위논문(박사) -- 서울대학교대학원 : 공과대학 에너지시스템공학부, 2022. 8. 나용수.The in-depth design and implementation of a newly developed integrated suite of codes, TRIASSIC (tokamak reactor integrated automated suite for simulation and computation), are reported. The suite comprises existing plasma simulation codes, including equilibrium solvers, 1.5D and 2D plasma transport solvers, neoclassical and anomalous transport models, current drive and heating (cooling) models, and 2D grid generators. The components in TRIASSIC could be fully modularized, by adopting a generic data structure as its internal data. Due to a unique interfacing method that does not depend on the generic data itself, legacy codes that are no longer maintained by the original author were easily interfaced. The graphical user interface and the parallel computing of the framework and its components are also addressed. The verification of TRIASSIC in terms of equilibrium, transport, and heating is also shown. Following the data model and definition of the data structure, a declarative programming method was adopted in the core part of the framework. The method was used to keep the internal data consistency of the data by enforcing the reciprocal relations between the data nodes, contributing to extra flexibility and explicitness of the simulations. TRIASSIC was applied on various devices including KSTAR, VEST, and KDEMO, owing to its flexibility in composing a workflow. TRIASSIC was validated against KSTAR plasmas in terms of interpretive and predictive modelings. The prediction and validation on the VEST device using TRIASSIC are also shown. For the applications to the upcoming KDEMO device, the machine design parameters were optimized, targeting an economical fusion demonstration reactor.본 연구에서는 TRIASSIC (tokamak reactor integrated automated suite for simulation and computation) 코드의 자세한 디자인과 실행 결과에 대해 소개합니다. 이 시뮬레이션 코드는 기존에 존재하던 플라즈마 평형, 1.5차원 및 2차원 플라즈마 수송, 신고전 및 난류 수송 모델, 전류 구동 및 가열 (냉각) 모델, 그리고 2차원 격자 생성기 등의 코드를 구성하여 만들어졌습니다. 프레임워크 내 데이터 구조로써 일반 데이터 구조를 채택함으로써 TRIASSIC의 코드 구성요소들은 완전한 모듈화 방식으로 결합될 수 있었습니다. 일반 데이터 구조에 의존하지 않는 독특한 코드 결합 방식으로 인해, 더 이상 유지보수되지 않는 레거시 코드들 또한 쉽게 결합될 수 있었습니다. 본 코드의 그래피컬 유저 인터페이스, 프레임워크와 코드 구성 요소들의 병렬 컴퓨팅에 관한 내용도 다뤄집니다. 평형, 수송, 그리고 가열 측면에서의 TRIASSIC 시뮬레이션의 검증 내용도 소개됩니다. 시뮬레이션 프레임워크 내 일반 데이터 구조의 데이터 모델과 데이터 정의를 만족시키기 위해, 데이터를 관리하는 프레임워크의 중심부에는 선언적 프로그래밍이 도입되었습니다. 선언적 프로그래밍을 통해 일반 데이터의 데이터 노드 간 관계식을 만족시킴으로써 데이터 간 내부 일관성을 확보하고, 코드의 유연성과 명시성을 추가적으로 확보할 수 있었습니다. TRIASSIC은 해석적, 예측적 모델링 측면에서 KSTAR 플라즈마를 대상으로 검증되었습니다. VEST 장치를 대상으로 한 예측 및 이에 대한 검증 내용 또한 서술됩니다. 경제적인 핵융합 실증로 건설을 목표로 KDEMO 장치에 대한 적용 및 장치 설계 최적화 연구도 소개됩니다.Abstract １ Table of Contents ２ List of Figures ４ List of Tables １０ Chapter 1. Introduction １１ 1.1. Background １１ 1.1.1. Fusion Reactor and Modeling １１ 1.1.2. Interpretive Analysis and Predictive Modeling １７ 1.1.3. Modular Approach ２１ 1.1.4. The Standard Data Structure ２４ 1.1.5. The Internal Data Consistency in a Generic Data ２８ 1.1.6. Integration of Physics Codes into IDS ２９ 1.2. Overview of the Research ３１ Chapter 2. Development of Integrated Suite of Codes ３３ 2.1. Development of TRIASSIC ３３ 2.1.1. Design Requirements ３３ 2.1.2. Overview of TRIASSIC ３５ 2.1.3. Comparison of Integrated Simulation Codes ４０ 2.2. Components in the Framework ４３ 2.2.1. Physics Codes Interfaced with the Framework ４３ 2.2.2. Physics Code Interfacings ４６ 2.2.3. Graphical User Interface ５２ 2.2.4. Jobs Scheduler and MPI ５５ 2.3. Verifications ５７ 2.3.1. The Coordinate Conventions ５７ 2.3.2. Coupling of Equilibrium-Transport ５９ 2.3.3. Neoclassical Transport and Bootstrap Current ６３ 2.3.4. Heating and Current Drive ６５ Chapter 3. Improvements in Keeping the Internal Data Consistency ６８ 3.1. Background ６８ 3.2. Possible Implementations of a Component ７１ 3.3. A Method Adopted in the Framework ７３ 3.3.1. Prerequisites and Relation Definitions ７３ 3.3.2. Adding Relations in the Framework ７８ 3.3.3. Applying Relations ８０ 3.4. Performance and Flexibility of the Framework ８３ 3.4.1. Performance Enhancement ８３ 3.4.2. Flexibility and Maintenance of the Framework ８５ Chapter 4. Applications to Various Devices ９１ 4.1. Applications to KSTAR ９１ 4.1.1. Kinetic equilibrium workflow and its validation ９１ 4.1.2. Stationary-state predictive modeling workflow ９５ 4.2. Application to VEST １０２ 4.2.1. Time-dependent predictive modeling workflow １０３ 4.3. Application to KDEMO １０６ 4.3.1. Predictive simulation workflow for optimization １０６ Chapter 5. Summary and Conclusion １１２ 5.1. Summary and Conclusion １１２ Appendix １１６ A. Code Snippet of the Relation Definition １１６ Bibliography １１８ Abstract in Korean １２６박

Climate-Invariant Machine Learning

Data-driven algorithms, in particular neural networks, can emulate the effects of unresolved processes in coarse-resolution climate models when trained on high-resolution simulation data; however, they often make large generalization errors when evaluated in conditions they were not trained on. Here, we propose to physically rescale the inputs and outputs of machine learning algorithms to help them generalize to unseen climates. Applied to offline parameterizations of subgrid-scale thermodynamics in three distinct climate models, we show that rescaled or "climate-invariant" neural networks make accurate predictions in test climates that are 4K and 8K warmer than their training climates. Additionally, "climate-invariant" neural nets facilitate generalization between Aquaplanet and Earth-like simulations. Through visualization and attribution methods, we show that compared to standard machine learning models, "climate-invariant" algorithms learn more local and robust relations between storm-scale convection, radiation, and their synoptic thermodynamic environment. Overall, these results suggest that explicitly incorporating physical knowledge into data-driven models of Earth system processes can improve their consistency and ability to generalize across climate regimes.Comment: 12+18 pages, 8+12 figures, 2+2 tables in the main text + supplementary information. Submitted to PNAS on December 14th, 202

CoCalc as a Learning Tool for Neural Network Simulation in the Special Course "Foundations of Mathematic Informatics"

The role of neural network modeling in the learning content of the special course "Foundations of Mathematical Informatics" was discussed. The course was developed for the students of technical universities - future IT-specialists and directed to breaking the gap between theoretic computer science and it's applied applications: software, system and computing engineering. CoCalc was justified as a learning tool of mathematical informatics in general and neural network modeling in particular. The elements of technique of using CoCalc at studying topic "Neural network and pattern recognition" of the special course "Foundations of Mathematic Informatics" are shown. The program code was presented in a CoffeeScript language, which implements the basic components of artificial neural network: neurons, synaptic connections, functions of activations (tangential, sigmoid, stepped) and their derivatives, methods of calculating the network's weights, etc. The features of the Kolmogorov-Arnold representation theorem application were discussed for determination the architecture of multilayer neural networks. The implementation of the disjunctive logical element and approximation of an arbitrary function using a three-layer neural network were given as an examples. According to the simulation results, a conclusion was made as for the limits of the use of constructed networks, in which they retain their adequacy. The framework topics of individual research of the artificial neural networks is proposed.Comment: 16 pages, 3 figures, Proceedings of the 13th International Conference on ICT in Education, Research and Industrial Applications. Integration, Harmonization and Knowledge Transfer (ICTERI, 2018

A machine learning framework for quantifying chemical segregation and microstructural features in atom probe tomography data

Atom probe tomography (APT) is ideally suited to characterize and understand the interplay of chemical segregation and microstructure in modern multicomponent materials. Yet, the quantitative analysis typically relies on human expertise to define regions of interest. We introduce a computationally efficient, multistage machine learning strategy to identify chemically distinct domains in a semi automated way, and subsequently quantify their geometric and compositional characteristics. In our algorithmic pipeline, we first coarse grain the APT data into voxels, collect the composition statistics, and decompose it via clustering in composition space. The composition classification then enables the real space segmentation via a density based clustering algorithm, thus revealing the microstructure at voxel resolution. Our approach is demonstrated for a Sm(Co,Fe)ZrCu alloy. The alloy exhibits two precipitate phases with a plate-like, but intertwined morphology. The primary segmentation is further refined to disentangle these geometrically complex precipitates into individual plate like parts by an unsupervised approach based on principle component analysis, or a U-Net based semantic segmentation trained on the former. Following the chemical and geometric analysis, detailed chemical distribution and segregation effects relative to the predominant plate-like geometry can be readily mapped without resorting to the initial voxelization