1var store = [{ 2 "title": "An introduction to creating professional looking documents with Markdown", 3 "excerpt":"This is a tutorial on creating visually appealing documents with Markdown and then converting them into Latex for further processing or exporting them as Pdfâs. It uses the packages Pandoc and Pdflatex. Introduction Throughout the last couple of years Iâve been trying to figure out the best way to keep...","categories": [], 4 "tags": ["tutorials","markdown","latex"], 5 "url": "/Markdown-Tutorial/", 6 "teaser": "/assets/media/2020-01-03-Markdown-Tutorial/image.jpg" 7 },{ 8 "title": "Glazer notation for Octahedral Tilting in Perovskites", 9 "excerpt":"This tutorial explains how Glazer notation is used to identify Perovskites of different symmetries based on their atomic positioning. What are Perovskites? Perovskites are structures that take the form ABX$_3$ structure (E.g.- SrVO$_3$, CaTiO$_3$, CsSnI$_3$). The B cation has 6 fold coordination, surrounded by an octahedron of corner sharing anions....","categories": [], 10 "tags": ["tutorials","physics","condensed-matter-physics"], 11 "url": "/Glazer-Notation/", 12 "teaser": "/assets/media/2020-02-01-Glazer-Notation/c8na00416a-f3_hi-res.png" 13 },{ 14 "title": "Stay home and plot Density of States", 15 "excerpt":"This is a tutorial on plotting total and partial Density of States for electronic structure calculations performed with the DFT code VASP. Being a computational condensed matter physicist who spends most of his day on a computer, one might think that COVID-191 may not have made drastic changes to my...","categories": [], 16 "tags": ["tutorials","physics","python","condensed-matter-physics","density-functional-theory"], 17 "url": "/Plotting-Density-of-States/", 18 "teaser": "/assets/media/2020-03-31-Plotting-Density-of-States/dos_atomic_total.png" 19 },{ 20 "title": "Calculating the diffusion energy barrier of a single oxygen vacancy", 21 "excerpt":"This is a short tutorial on the calculation of the energy barrier of diffusion for a single oxygen vacancy. The calculations are done with SOD, VTST Tools and VASP. Introduction Diffusion in materials plays a vital role in a wide range of applications ranging from energy storage to spintronics. This...","categories": [], 22 "tags": ["tutorials","python","density-functional-theory","physics"], 23 "url": "/OV-diffusion-tutorial/", 24 "teaser": "/assets/media/2021-12-08-OV-diffusion-tutorial/vacancy-migration.png" 25 },{ 26 "title": "Hi again and Resolve Mathjax Latex rendering issues on Jekyll Markdown website", 27 "excerpt":"This post serves as a short catch-up and a quick fix to a Latex rendering issue I recently noticed on my web posts. Hey folks! Long time no see! Hope youâre all doing awesome! After about a 2 year hiatus, I thought I would try and get back into blogging...","categories": [], 28 "tags": ["markdown","tutorials","latex"], 29 "url": "/Resolve-Mathjax-Latex-Rendering-on-Jekyll-Markdown-Website/", 30 "teaser": "/assets/media/2024-08-18-Resolve-Mathjax-Latex-Rendering-on-Jekyll-Markdown-Website/2024-08-18-Resolve-Mathjax-Latex-Rendering-on-Jekyll-Markdown-Website-20240818234059807.jpg" 31 },{ 32 "title": "Cron-the Unix assistant you didn't know you had", 33 "excerpt":"A short tutorial on automating recurring tasks on Unix systems with Cron. Do you have recurring tasks that thus far you had to run on your Unix (Linux/ Mac) system manually? This could be anything from making scheduled backups of a folder to syncing the contents of a file with...","categories": [], 34 "tags": ["linux","tutorials"], 35 "url": "/Cron-the-unix-assistant-you-didn't-know-you-had/", 36 "teaser": "/assets/media/2024-09-15-Cron-the-unix-assistant-you-didn't-know-you-had/2024-09-15-Cron-the-unix-assistant-you-didn't-know-you-had-20240915122634371.png" 37 },{ 38 "title": "Atomate2 workflows for FHI-aims", 39 "excerpt":"This brief tutorial provides an introduction to using Atomate2 to set up DFT workflows with the FHI-aims code. With the increasing availability of High Performance Computing (HPC) and High Throughput Computing (HTC), the use of efficient tools to perform complex Density Functional Theory (DFT) calculations is critical for advancing materials...","categories": [], 40 "tags": ["fhiaims","density-functional-theory","python","condensed-matter-physics","materials-science"], 41 "url": "/Atomate2-workflows-for-FHI-aims/", 42 "teaser": "/assets/media/2024-09-20-Atomate2-workflows-for-FHI-aims/2024-09-20-Atomate2-workflows-for-FHI-aims-20240920121324117.png" 43 },{ 44 "title": "Embedding a video gallery in Jekyll websites", 45 "excerpt":"A simple tutorial on embedding a video gallery in a Minimal Mistakes themed Jekyll website. The Minimal Mistakes theme 1 for Jekyll websites by Michael Rose offers a great way to embed images in a gallery layout. I wanted to do the same for videos. In this post I will...","categories": [], 46 "tags": ["tutorials","jekyll","minimal-mistakes","html"], 47 "url": "/Embedding-a-video-gallery-in-Jekyll-websites/", 48 "teaser": "/assets/media/2024-09-22-Embedding-a-video-gallery-in-Jekyll-websites/2024-09-22-Embedding-a-video-gallery-in-Jekyll-websites-20240922105246495.png" 49 },{ 50 "title": "Carved a Pumpkin? Seed the Possibilities!", 51 "excerpt":"This is a quick and simple recipe to roast pumpkin
51seeds. Pumpkin carving season just ended so you may be wondering what to do with those leftover pumpkin seeds. Not only are they delicious, but theyâre also packed with nutrients such as magnesium, zinc, and healthy fats. So donât toss...","categories": [], 52 "tags": ["recipes","cooking","hobbies"], 53 "url": "/Carved-a-Pumpkin-Seed-the-Possibilities/", 54 "teaser": "/assets/media/2024-11-01-Carved-a-Pumpkin-Seed-the-Possibilities/2024-11-01-Carved-a-Pumpkin-Seed-the-Possibilities-20241103130440057.jpg" 55 },{ 56 "title": "Advanced resource monitoring on HPC clusters", 57 "excerpt":"Efficient resource monitoring is key to maximizing HPC performance. In this post, I explore techniques for advanced resource monitoring on HPC clusters and provide a script that utilizes seff, sstat, and sacct to track CPU and memory usage effectively. Happy 2025, everyone! Although it might feel a little late for...","categories": [], 58 "tags": ["hpc","bash","linux"], 59 "url": "/Advanced-resource-monitoring-on-HPC-clusters/", 60 "teaser": "/assets/media/2025-02-05-Advanced-resource-monitoring-on-HPC-clusters/2025-02-05-Advanced-resource-monitoring-on-HPC-clusters-20250206132157590.png" 61 },{ 62 "title": "Error estimation in band structures", 63 "excerpt":"Accurate error estimation is highly beneficial for quantifying differences in band structures of materials. This post explores utilizing the root-mean-square error (RMSE) for comparing band structures calculated with the FHI-aims code. This method can help us quickly gauge the agreement between two band structures and guide more informed decisions in...","categories": [], 64 "tags": ["condensed-matter-physics","density-functional-theory","fhiaims","python","physics"], 65 "url": "/Error-estimation-in-band-structures/", 66 "teaser": "/assets/media/2025-03-01-Error-estimation-in-band-structures/2025-03-01-Error-estimation-in-band-structures-20250302162329280.png" 67 },{ 68 "title": "Accelerating materials research with Duke Compute Cluster's (DCC) NVIDIA Tesla P100 GPUs", 69 "excerpt":"Leveraging DCCâs NVIDIAâ¯Teslaâ¯P100 GPUs, in this post I demonstrate how GPU acceleration within FHIâaims and ELPA can speed up all-electron DFT calculations by a factor of ~2x on systems exceedingâ¯3,000â¯atoms and 50,000â¯basis functions. Firstly, May the 4th be with you! As mentioned in an earlier post, this semester I had...","categories": [], 70 "tags": ["gpu","hpc","fhiaims","condensed-matter-physics","density-functional-theory","materials-science"], 71 "url": "/Accelerating-materials-research-with-Duke-Compute-Cluster's-NVIDIA-Tesla-P100-GPUs/", 72 "teaser": "/assets/media/2025-04-25-Accelerating-materials-research-with-Duke-Compute-Cluster's-NVIDIA-Tesla-P100-GPUs/2025-04-25-Accelerating-materials-research-with-Duke-Compute-Cluster's-NVIDIA-Tesla-P100-GPUs-20250504215917066.png" 73 },{ 74 "title": "Our latest Nature publication unveiling a new mechanism that explains superfluorescence at high temperatures", 75 "excerpt":"Publication announcement: our latest publication in Nature highlights our collaborative research that led to the discovery of a new mechanism explaining superfluorescence occurring at high temperatures. Perovskites show superfluorescence-quantum coherence from solitons-emerging at high temperatures. Image: Ella Maru Studios Our latest paper was just published in Nature, marking a major...","categories": [], 76 "tags": ["condensed-matter-physics","materials-science","computational-physics","nature","superfluorescence"], 77 "url": "/Our-latest-Nature-publication-unveiling-a-new-mechanism-explaining-superfluorescence-at-high-temperatures/", 78 "teaser": "/assets/media/2025-05-30-Our-latest-Nature-publication-unveiling-a-new-mechanism-explaining-superfluorescence-at-high-temperatures/2025-05-30-Our-latest-Nature-publication-unveiling-a-new-mechanism-explaining-superfluorescence-at-high-temperatures-20250530210324672.png" 79 },{ 80 "title": "Running LLMs on a HPC cluster", 81 "excerpt":"This is a guide on setting up an Ollama server to run LLM models on a HPC cluster with GPUs. The Ollama server is hosted on a GPU node, while the inferencing can be done from any other node on the cluster. Large Language Models (LLMs) have become ever so...","categories": [], 82 "tags": ["ai","hpc","gpu"], 83 "url": "/Running-LLMs-on-a-HPC-cluster/", 84 "teaser": "/assets/media/2025-12-17-Running-LLMs-on-a-HPC-cluster/2025-12-17-Running-LLMs-on-a-HPC-cluster-20251217211525532.jpg" 85 },{ 86 "title": "About", 87 "excerpt":"Hello! Iâm Uthpala, a computational physicist passionate about empowering researchers to push the boundaries of discovery through advanced computing. With over a decade of experience in condensed matter physics, research computing, data science, and high-performance computing, I help teams across disciplines turn ambitious ideas into scalable, high-impact research. My journey...","url": "https://www.uthpalaherath.com/about/" 88 },{ 89 "title": "à¶à¶ºà·à¶¶à·à·à¶±à·! (ÄyubÅvan!)", 90 "excerpt":"Hello and welcome! ð Iâm Uthpala, a computational physicist passionate about empowering researchers to push the boundaries of discovery through advanced computing. With over a decade of experience in condensed matter physics, research computing, data science, and high-performance computing, I help teams across disciplines turn ambitious ideas into scalable, high-impact...","url": "https://www.uthpalaherath.com/" 91 },{ 92 "title": "Projects", 93 "excerpt":"The following is a list of research projects I have contributed to. PyProcar A Python library for electronic structure pre/post-processing PyProcar is a robust, open-source Python library used for pre- and post-processing of the electronic structure data coming from DFT calculations. It provides a set of functions that manage data...","url": "https://www.uthpalaherath.com/projects/" 94 },{ 95 "title": "Publications", 96 "excerpt":"Submitted Abbott, J. W. et al. Roadmap on Advancements of the FHIâaims Software Package. arXiv (2025). Karpov, P., Marek, A., Melson, T., Pöppl, A., Yu, V. W.âz., Hourahine, B., Garcia, A., Dawson, W., Yao, Y., Huhn, W., Moussa, J., Hall, S., Maurer, R., Herath, U., Lion, K., Kokott, S., &...","url": "https://www.uthpalaherath.com/publications/" 97 },{ 98 "title": "Research", 99 "excerpt":"My postdoc and Ph.D. research focused on the development and application of beyond-DFT (Density Functional Theory) methods for the design, discovery and characterization of novel materials. Over the past decade, I have leveraged research computing, data science, and high-performance computing (HPC) to push the boundaries of electronic structure simulations from...","url": "https://www.uthpalaherath.com/research/" 100 },{ 101 "title": "CV", 102 "excerpt":" This browser does not support PDFs. Please download the PDF to view it: Download PDF. </embed> ","url": "https://www.uthpalaherath.com/cv/" 103 },{ 104 "title": "Posts by tag", 105 "excerpt":" Back to default view ","url": "https://www.uthpalaherath.com/tags/" 106 },{ 107 "title": "Talks", 108 "excerpt":"Please click on the location pins for more details. Blue pins represent oral presentations. Red pins represent workshops or seminars. Scroll down for a list of recorded talks. Recorded talks PyProcar: A Python library for electronic structure pre/post-processing Electronic Structure Workshop, University of California, Merced, CA June 2-5, 2020 (Virtual...","url": "https://www.uthpalaherath.com/talks/" 109 },{ 110 "title": "Blog", 111 "excerpt":"Posts by tag Posts by year ","url": "https://www.uthpalaherath.com/year-archive/" 112 },{ 113 "title": "à¶à¶ºà·à¶¶à·à·à¶±à·! (ÄyubÅvan!)", 114 "excerpt":"Hello and welcome! ð Iâm Uthpala, a computational physicist passionate about empowering researchers to push the boundaries of discovery through advanced computing. With over a decade of experience in condensed matter physics, research computing, data science, and high-performance computing, I help teams across disciplines turn ambitious ideas into scalable, high-impact...","url": "https://www.uthpalaherath.com/page2/" 115 },{ 116 "title": "à¶à¶ºà·à¶¶à·à·à¶±à·! (ÄyubÅvan!)", 117 "excerpt":"Hello and welcome! ð Iâm Uthpala, a computational physicist passionate about empowering researchers to push the boundaries of discovery through advanced computing. With over a decade of experience in condensed matter physics, research computing, data science, and high-performance computing, I help teams across disciplines turn ambitious ideas into scalable, high-impact...","url": "https://www.uthpalaherath.com/page3/" 118 }]
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