#!/usr/bin/env guile !# ;; Copyright © 2018 Urbain Vaes (use-modules (sxml simple)) ; To deal with records more easily (use-modules (srfi srfi-9)) ; Read files (use-modules (ice-9 popen)) (use-modules (ice-9 rdelim)) ; Directory of static content (define (static-url path) (string-append "/static/" path)) ; Auxiliary function to read html file (define (read-xml filename) (call-with-input-file filename (lambda (input-port) (xml->sxml input-port #:entities '((align . "ALIGNMENT")))))) (define (html-head title) `(head (title ,(string-append "Urbain Vaes - " title)) (meta (@ (charset "UTF-8"))) (meta (@ (name "author") (content "Urbain Vaes"))) (meta (@ (name "keywords") (content "contact,cv,work"))) (meta (@ (name "description") (content "My personal website"))) (meta (@ (name "viewport") (content "width=device-width, initial-scale=1.0"))) (link (@ (rel "stylesheet") (type "text/css") (href ,(static-url "css/base.css")))) (link (@ (rel "stylesheet") (type "text/css") (href "https://fonts.googleapis.com/css?family=Neuton&subset=latin") (media "screen") (charset "utf-8"))) (link (@ (rel "stylesheet") (type "text/css") (href "https://fonts.googleapis.com/css?family=Nobile:regular,italic,bold,bolditalic&subset=latin") (media "screen") (charset "utf-8"))) (script (@ (type "text/javascript") (src ,(static-url "js/common.js"))) "") (script (@ (type "text/javascript") (src "https://polyfill.io/v3/polyfill.min.js?features=es6")) "") (script (@ (id "MathJax-script") (type "text/javascript") (src "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js")) "") (link (@ (rel "icon") (type "image/x-icon") (href ,(static-url "img/airbender-favico.webp")))))) (define (site-menu) `(header (a (@ (id "avatar") (href "/hello/")) (img (@ (id "avatar_img") (src "https://s.gravatar.com/avatar/40bb63e5d0cfbe4ab1067d561ae08280?s=400") (alt "Main menu")))) (nav (a (@ (href "/contact/")) "Contact") (a (@ (href "/cv/")) "CV" " ") (a (@ (href "/research/")) "Research") (a (@ (href "/publications/")) "Publications") (a (@ (href "/software/")) "Software") (a (@ (href "/teaching/")) "Teaching")))) (define (site-footer) `(footer (p (a (@ (rel "licence") (href "http://creativecommons.org/licenses/by-nc-nd/4.0/")) (img (@ (alt "Creative Commons License") (style "border-width:0") ; (src "https://licensebuttons.net/l/by-nc-nd/4.0/88x31.png") ; (src "https://mirrors.creativecommons.org/presskit/buttons/88x31/svg/by-nc-nd.svg") (src "https://mirrors.creativecommons.org/presskit/buttons/80x15/svg/by-nc-nd.svg") ))) " Urbain Vaes, 2020. " (a (@ (href "https://git.vaes.uk/public/www-urbain.git/plain/site.scm")) "(Source code)") ))) (define (static-page head main) `(html (@ (lang "en")) ,(html-head head) (body ,(site-menu) ,main ,(site-footer)))) (define (contact-page) (static-page "Contact" `(main ,(read-xml "html/contact.html")))) (define-record-type (make-pub year title coauthors journal pdf-link journal-link arxiv-link bib-link) pub? (year pub-year) (title pub-title) (coauthors pub-coauthors) (journal pub-journal) (pdf-link pub-pdf-link) (journal-link pub-journal-link) (arxiv-link pub-arxiv-link) (bib-link pub-bib-link)) (define* (publication #:key year title coauthors journal pdf-link journal-link arxiv-link bib-link) (make-pub year title coauthors journal pdf-link journal-link arxiv-link bib-link)) (define* (get-links-publication p #:optional (show-bibtex #t) (class "logos")) `(,(if (pub-pdf-link p) `( (a (@ (href ,(pub-pdf-link p))) (img (@ (class ,class) (alt "PDF") (src ,(static-url "img/pdf.png"))))) " ") "") ,(if (pub-journal-link p) `( (a (@ (href ,(pub-journal-link p))) (img (@ (class ,class) (alt "url") (src ,(static-url "img/url-transparent.png"))))) " ") "") ,(if (pub-arxiv-link p) `( (a (@ (href ,(pub-arxiv-link p))) (img (@ (class ,class) (alt "arxiv") (src ,(static-url "img/arxiv.png"))))) " ") "") ,(if (and (pub-bib-link p) show-bibtex) `(a (@ (href ,(pub-bib-link p))) "Bibtex") ""))) (define (list-publication p) `((dt ,(pub-year p)) (dd (ul (@ (class "pub")) (li (@ (class "pub_title")) ,(string-append (pub-title p) ".")) (li (@ (class "pub_authors")) ,(string-append (pub-coauthors p) ".")) (li (@ (class "pub_journal")) ,(string-append (pub-journal p) ".")) ,(if (pub-pdf-link p) `(li (@ (class "pub_links")) ,(get-links-publication p)) ""))))) (define (highlight-publication p) `(div (@ (class "highlight")) (ul (@ (class "pub")) (li (@ (class "pub_title")) ,(string-append (pub-title p) ".")) (li (@ (class "pub_authors")) ,(string-append (pub-coauthors p) ", " (pub-year p) ".")) (li (@ (class "pub_journal")) ,(string-append (pub-journal p) ".") (span (@ (style "float: right; text-align: right; width: 10%")) ,(get-links-publication p #f "biglogos")))))) (define my_publications `(("UV_2013" . ,(publication #:year "2013" #:title "Discontinuous Galerkin method for 4th order elliptic PDEs (in French)" #:coauthors "MSc thesis supervised by J-F Remacle" #:journal "Unpublished" #:pdf-link (static-url "pub/msc_thesis.pdf"))) ("AAGPUV_2017" . ,(publication #:year "2017" #:title "Spectral methods for multiscale stochastic differential equations" #:coauthors "With A. Abdulle and G. A. Pavliotis" #:journal "SIAM/ASA J. Uncertain. Quantif" #:pdf-link "https://epubs.siam.org/doi/pdf/10.1137/16M1094117" #:journal-link "https://doi.org/10.1137/16M1094117" #:arxiv-link "https://arxiv.org/abs/1609.05097" #:bib-link "/static/bib/AAGPUU-2017.txt")) ("BAUVMPSK_2019" . ,(publication #:year "2019" #:title "A linear, second-order, energy stable, fully adaptive finite-element method for phase-field modelling of wetting phenomena" #:coauthors "With B. Aymard, M. Pradas and S. Kalliadasis" #:journal "J. Comput. Phys. X" #:pdf-link "https://arxiv.org/pdf/1901.06190" #:journal-link "https://doi.org/10.1016/j.jcpx.2019.100010" #:arxiv-link "https://arxiv.org/abs/1901.06190" #:bib-link "/static/bib/BAUVMPSK-2019.txt")) ("SGGPUV_2019" . ,(publication #:year "2019" #:title "The Desai-Zwanzig mean field model with colored noise" #:coauthors "With S. N. Gomes and G. A. Pavliotis" #:journal "Accepted for publication in SIAM Multiscale Modeling and Simulation (MMS)" #:pdf-link "https://arxiv.org/pdf/1904.05973" #:arxiv-link "https://arxiv.org/abs/1904.05973")) ("UV_2019" . ,(publication #:year "2019" #:title "Topics in multiscale modeling: numerical analysis and applications" #:coauthors "PhD thesis supervised by G. Pavliotis and S. Kalliadasis" #:journal "Unpublished" #:pdf-link "https://spiral.imperial.ac.uk/bitstream/10044/1/73890/3/Vaes-U-2019-PhD-Thesis.pdf" #:journal-link "https://spiral.imperial.ac.uk/handle/10044/1/73890")) ("JCUV_2019" . ,(publication #:year "2019" #:title "Wasserstein stability estimates for covariance-preconditioned Fokker-Planck equations" #:coauthors "With J. Carrillo" #:journal "Submitted for publication in Nonlinearity" #:pdf-link "https://arxiv.org/pdf/1910.07555" #:arxiv-link "https://arxiv.org/abs/1910.07555")) ("GPGSUV_2020" . ,(publication #:year "2020" #:title "Generalized Langevin equation: effective diffusion in a periodic potential and long-time behavior" #:coauthors "With G. A. Pavliotis and G. Stoltz" #:journal "Submitted to the Journal of Nonlinear Science" #:pdf-link "https://arxiv.org/pdf/2007.16087" #:arxiv-link "https://arxiv.org/abs/2007.16087")) ("JCGPASUV_2020" . ,(publication #:year "2020" #:title "A derivative-free multiscale method for Bayesian inverse problems" #:coauthors "With J. A. Carrillo, G. A. Pavliotis and A. M. Stuart" #:journal "In preparation")) ("DKGPUV_2020" . ,(publication #:year "2020" #:title "Optimal control of the Fokker-Planck equation: spectral methods and a reduced gradient approach" #:coauthors "With D. Kalise and G. A. Pavliotis" #:journal "In preparation")) )) (define (research-page) (static-page "Research" `(main (h1 "Research") (h2 "Summary") ,(read-xml "html/research/summary.html") (h2 "Main research interests") (h3 "Mean field limit of interacting particle systems") ,(read-xml "html/research/mckean.html") ,(highlight-publication (assoc-ref my_publications "SGGPUV_2019")) ,(read-xml "html/research/enkf.html") ,(highlight-publication (assoc-ref my_publications "JCUV_2019")) (h3 "The generalized Langevin equation: effective diffusion and long-time behavior") ,(read-xml "html/research/gle.html") ,(highlight-publication (assoc-ref my_publications "GPGSUV_2020")) (h3 "Spectral methods for Poisson and Fokker-Planck-Kolmogorov equations") ,(read-xml "html/research/spectral.html") ,(highlight-publication (assoc-ref my_publications "AAGPUV_2017")) (h3 "Finite element methods for elliptic partial differential equations") ,(read-xml "html/research/kirchoff.html") ,(highlight-publication (assoc-ref my_publications "UV_2013")) ,(read-xml "html/research/cahn.html") ,(highlight-publication (assoc-ref my_publications "BAUVMPSK_2019")) ))) (define* (link-files desc link #:key pdf py ipynb html special) (let ((url (static-url (string-append (if pdf "teaching/lectures/" "teaching/codes/") link)))) `(li ,(if special `(@ (class "special")) "") ,desc ": " ,(if pdf `("[" (a (@ (href ,(string-append url ".pdf"))) "pdf") "] ") "") ,(if py `("[" (a (@ (href ,(string-append url ".py")) (download)) "Python") "] ") "") ,(if ipynb `("[" (a (@ (href ,(string-append url ".ipynb")) (download)) "Jupyter") "] ") "") ,(if html `("[" (a (@ (href ,(string-append url ".html"))) "HTML") "] ") "") (p (em "Last modified: " ,(let* ((date (string-append "date -r " (if pdf "/www/computational_stochastic_processes/lectures/" "/www/codes/") link (if pdf ".pdf" ".py ") " +\"%d %b %Y\"")) (port (open-input-pipe date)) (str (read-line port))) (close-pipe port) str) ".")) ))) (define (teaching-page) (static-page "Teaching" `(main (h1 "Teaching activities") (ul (li "2020: " (a (@ (href "/teaching/2020-csp/")) "Computational Stochastic Processes")))) )) (define (teaching-page/2020-csp) (static-page "Computational Stochastic Processes" `(main (h1 "Computational Stochastic Processes") (p "This page contains some of the material for the course MATH97016/MATH97094: Computational Stochastic Processes. The course material was initially developed by " (a (@ (href "http://wwwf.imperial.ac.uk/~pavl/")) "Grigorios Pavliotis") ", and it later received improvements from " (a (@ (href "http://wwwf.imperial.ac.uk/~aduncan/")) "Andrew Duncan") " and " (a (@ (href "https://warwick.ac.uk/fac/sci/maths/people/staff/gomes/")) "Susana Gomes") ". In particular, the lecture notes linked below were assembled by Andrew Duncan, and the handwritten part of the notes distributed weekly were written by Susana Gomes." ; (dl ; (dt "Lectures") (dd (br "")) ; (ul (@ (style "list-style-type:none;padding-left:0;")) ; (li "Monday 13:00-14:00 (Huxley 145)") ; (li "Tuesday 12:00-13:00 (Huxley 140)") ; (li "Friday 17:00-18:00 (Huxley 213)")) ; (dt "Office hours") ; (dd "Tuesday 15:00-16:00, or by email appointment.")) ) (h2 "Lecture notes") (ul (@ (id codes)) ,(link-files "Lecture notes (from 2016)" "notes_2016" #:pdf #t #:special #t) ,(link-files "List of examinable proofs" "build/list_of_proofs" #:pdf #t #:special #t) ,(link-files "Introduction (based on slides by Susana Gomes)" "build/intro" #:pdf #t) ,(link-files "W1: Random number generation and introduction to Monte Carlo simulation" "build/lectures-w1" #:pdf #t) ,(link-files "W2: Variance reduction techniques for Monte Carlo simulation" "build/lectures-w2" #:pdf #t) ,(link-files "W3: Simulation of continuous-time Markov processes" "build/lectures-w3" #:pdf #t) ,(link-files "W4: Simulation of Gaussian processes (cont'd) and SDEs" "build/lectures-w4" #:pdf #t) ,(link-files "W5: Numerical methods for SDEs" "build/lectures-w5" #:pdf #t) ,(link-files "W6: Numerical methods for SDEs (cont'd)" "build/lectures-w6" #:pdf #t) ,(link-files "W7: Inference for SDEs" "build/lectures-w7" #:pdf #t) ,(link-files "W8: Inference (cont'd) and markov chains" "build/lectures-w8" #:pdf #t) ,(link-files "W9: Markov chain Monte Carlo" "build/lectures-w9" #:pdf #t) ) (h2 "Problem sheets and coursework") (ul (@ (id codes)) ,(link-files "Problem sheet 1: questions" "build/problem_sheet_1_questions" #:pdf #t) ,(link-files "Problem sheet 1: solutions" "build/problem_sheet_1_answers" #:pdf #t) ,(link-files "Problem sheet 1: codes" "w4_problem_sheet" #:py #t #:ipynb #t #:html #t) ,(link-files "Problem sheet 2: questions" "build/problem_sheet_2_questions" #:pdf #t) ,(link-files "Problem sheet 2: solutions" "build/problem_sheet_2_answers" #:pdf #t) ,(link-files "Problem sheet 2: codes" "w10_problem_sheet" #:py #t #:ipynb #t #:html #t) ,(link-files "Assessed coursework" "build/coursework_problems" #:pdf #t) ,(link-files "Assessed coursework: solution to Problem 1" "coursework_problem_1" #:py #t #:ipynb #t #:html #t) ,(link-files "Assessed coursework: solution to Problem 2" "coursework_problem_2" #:py #t #:ipynb #t #:html #t) ,(link-files "Assessed coursework: solution to Problem 3" "coursework_problem_3" #:py #t #:ipynb #t #:html #t) ,(link-files "Mock exam" "mock_exam" #:pdf #t) ,(link-files "Mock exam: brief solutions" "build/mock_exam-solutions" #:pdf #t) ) ,(read-xml "html/hint.html") (h2 "Python examples") (p "If you find bugs in the codes, or if you worked on a code example that that could benefit the class, do not hesitate to drop me an email. Alternatively, you can open an issue or a pull request at the " (a (@ (href "https://github.com/urbainvaes/computational_stochastic_processes")) "git repository") ".") (ul (@ (id codes)) ,(link-files "Introduction - Calculating Pi" "introduction_calculate_pi" #:py #t) ,(link-files "Introduction: Simulation of Langevin dynamics" "introduction_langevin" #:py #t) ,(link-files "W1 - Linear congruential generator" "w1_linear_congruential_generator" #:py #t #:ipynb #t #:html #t) ,(link-files "W1 - Generating nonuniform random numbers" "w1_generate_nonuniform_random_numbers" #:py #t #:ipynb #t #:html #t) ,(link-files "W2 - Monte Carlo simulation" "w2_monte_carlo" #:py #t #:ipynb #t #:html #t) ,(link-files "W2 - Variance reduction" "w2_variance_reduction" #:py #t #:ipynb #t #:html #t) ,(link-files "W3 - Simulation of Gaussian processes" "w3_gaussian_processes" #:py #t #:ipynb #t #:html #t) ,(link-files "W4 - Fast simulation of stationary Gaussian processes" "w4_dft_gaussian_processes" #:py #t #:ipynb #t #:html #t) ,(link-files "W5 - Numerical methods for SDEs" "w5_numerical_solution_of_sdes" #:py #t #:ipynb #t #:html #t) ,(link-files "W6 - Some applications of numerical methods for SDEs" "w6_applications_of_sdes" #:py #t #:ipynb #t #:html #t) ,(link-files "W7 - Inference for SDEs" "w7_inference_for_sdes" #:py #t #:ipynb #t #:html #t) ,(link-files "W8 - Introduction to Markov chains" "w8_markov_chains" #:py #t #:ipynb #t #:html #t) ,(link-files "W9 - Markov chain Monte Carlo" "w9_metropolis-hastings" #:py #t #:ipynb #t #:html #t) )))) (define (publications-page) (static-page "Publications" `(main (h1 "Publications") (h2 "Published and submitted papers") (dl ,(list-publication (assoc-ref my_publications "GPGSUV_2020")) ,(list-publication (assoc-ref my_publications "JCUV_2019")) ,(list-publication (assoc-ref my_publications "SGGPUV_2019")) ,(list-publication (assoc-ref my_publications "BAUVMPSK_2019")) ,(list-publication (assoc-ref my_publications "AAGPUV_2017"))) (h2 "Preprints in preparation") (dl ,(list-publication (assoc-ref my_publications "JCGPASUV_2020")) ,(list-publication (assoc-ref my_publications "DKGPUV_2020"))) (h2 "Unpublished work") (dl ,(list-publication (assoc-ref my_publications "UV_2019")) ,(list-publication (assoc-ref my_publications "UV_2013"))) ))) (define (git-page) (static-page "Software" `(main (h1 "Software") (p "Most of the git repositories I work(ed) on are available " (a (@ (href "https://git.vaes.uk")) "here") " or on my " (a (@ (href "https://github.com/urbainvaes")) "github page.")) (h2 "Scientific software") (p "During the course of my PhD, I was involved in two programming projects related to my research.") ; (p (div (@ (class "github-card") (data-github "urbainvaes/hermipy") (data-width "400") (data-height "") (data-theme "default")) "") ; (script (@ (src "//cdn.jsdelivr.net/github-cards/latest/widget.js")) "")) (h3 "Hermipy") (p (a (@ (href "https://github.com/urbainvaes/hermipy")) "Hermipy") " is a thin Python library that allows automating most of the operations involved in implementing a Hermite spectral method. The library uses the data structures provided by the " (a (@ (href "https://en.wikipedia.org/wiki/NumPy")) "Numpy") " library for linear algebra, and it also depends on " (a (@ (href "https://en.wikipedia.org/wiki/SymPy")) "Sympy") " for symbolic calculations. Computationally intensive parts of the computations, such as Hermite transforms, are handed over to a C++ compiled component, and " (a (@ (href "https://en.wikipedia.org/wiki/Boost_(C%2B%2B_libraries)")) "Boost") " is used for efficient exchange of data with Python. For more information, read the " (a (@ (href "https://hermipy.readthedocs.io/en/latest/")) "documentation") ".") (h3 "Cahn-Hilliard solver") (p (a (@ (href "https://github.com/urbainvaes/cahn-hilliard")) "This") " is a high-level framework for the numerical solution of the " (a (@ (href "https://en.wikipedia.org/wiki/Cahn%E2%80%93Hilliard_equation")) "Cahn-Hilliard equation") ", implementing a number of semi-implicit numerical methods in " (a (@ (href "https://freefem.org")) "FreeFem++") " and offering users the means to rapidly " (strong "(i)") " define the initial and boundary conditions of the problem, " (strong "(ii)") " run a particular numerical method with appropriate parameters, and " (strong "(iii)") " post-process the solution. Both two and three-dimensional settings are supported, and the geometry of the domain is read in files generated by the " (a (@ (href "http://gmsh.info/")) "Gmsh") " mesh-generator.") (h2 "Vim plugins") (p (div (@ (class "github-card") (data-github "urbainvaes/vim-remembrall") (data-width "400") (data-height "") (data-theme "default")) "") (script (@ (src "//cdn.jsdelivr.net/github-cards/latest/widget.js")) "")) (p (div (@ (class "github-card") (data-github "urbainvaes/vim-tmux-pilot") (data-width "400") (data-height "") (data-theme "default")) "") (script (@ (src "//cdn.jsdelivr.net/github-cards/latest/widget.js")) "")) (h2 "Bash/Zsh plugin") (p (div (@ (class "github-card") (data-github "urbainvaes/fzf-marks") (data-width "400") (data-height "") (data-theme "default")) "") (script (@ (src "//cdn.jsdelivr.net/github-cards/latest/widget.js")) "")) ))) (define (cv-page) (static-page "CV" `(main (h1 "Curriculum Vitæ") (p (a (@ (id "download") (href ,(static-url "doc/short_cv.pdf"))) "▶ Download PDF version")) ,(read-xml "html/cv.html")))) (define (hello-page) (static-page "Welcome" `(main (h1 "Hello, world!")))) ; Deploy website (define site-directory "site") (system (string-append "rm -rf " site-directory)) (system (string-append "mkdir -p " site-directory)) (system (string-append "cp -r static " site-directory)) (for-each ; Write resource to output file (lambda (resource) (let* ((path (string-append site-directory "/" (car resource)))) (begin (system (string-append "mkdir -p " (dirname path))) (call-with-output-file path (lambda (output-port) (sxml->xml (cdr resource) output-port)))))) ; List of web resources (list (cons "index.html" (hello-page)) (cons "cv/index.html" (cv-page)) (cons "hello/index.html" (hello-page)) (cons "contact/index.html" (contact-page)) (cons "research/index.html" (research-page)) (cons "publications/index.html" (publications-page)) (cons "software/index.html" (git-page)) (cons "teaching/index.html" (teaching-page)) (cons "teaching/2020-csp/index.html" (teaching-page/2020-csp)) ))