From 335285a3fe0ece5565c45c235b15852ab7d0b139 Mon Sep 17 00:00:00 2001
From: johannes wasmer <johannes.wasmer@gmail.com>
Date: Tue, 10 Sep 2024 03:06:55 +0200
Subject: [PATCH] update for hdslee retreat talk
---
bib/bibliography.bib | 22 +-
.../fig4-clip1.pdf | 3 +
.../fig4-clip2.pdf | 3 +
.../bosoniHowVerifyPrecision2024/fig4.pdf | 3 +
fig/logos/logos.tex | 394 +++++++++---------
...resentation-2023-02_02-emph-both_ktikz.pdf | 4 +-
...esentation-2023-02_02-emph-both_ktikz.tikz | 8 +-
.../industry-research/4-entries.pdf | 3 +
.../industry-research/5-entries.pdf | 3 +
.../industry-research/6-entries.pdf | 3 +
fig/tikz-tmp.pdf | 4 +-
fig/tikz-tmp.tex | 4 +-
12 files changed, 246 insertions(+), 208 deletions(-)
create mode 100644 fig/external/papers/bosoniHowVerifyPrecision2024/fig4-clip1.pdf
create mode 100644 fig/external/papers/bosoniHowVerifyPrecision2024/fig4-clip2.pdf
create mode 100644 fig/external/papers/bosoniHowVerifyPrecision2024/fig4.pdf
create mode 100644 fig/presentation-2024-09/industry-research/4-entries.pdf
create mode 100644 fig/presentation-2024-09/industry-research/5-entries.pdf
create mode 100644 fig/presentation-2024-09/industry-research/6-entries.pdf
diff --git a/bib/bibliography.bib b/bib/bibliography.bib
index a062061..76a2fa2 100644
--- a/bib/bibliography.bib
+++ b/bib/bibliography.bib
@@ -2147,6 +2147,26 @@ Subject\_term\_id: computational-chemistry;computational-science},
file = {/Users/wasmer/Nextcloud/Zotero/Bosoni et al_2023_How to verify the precision of density-functional-theory implementations via.pdf;/Users/wasmer/Zotero/storage/GIP5Z2MT/2305.html}
}
+@article{bosoniHowVerifyPrecision2024,
+ title = {How to Verify the Precision of Density-Functional-Theory Implementations via Reproducible and Universal Workflows},
+ author = {Bosoni, Emanuele and Beal, Louis and Bercx, Marnik and Blaha, Peter and Blügel, Stefan and Bröder, Jens and Callsen, Martin and Cottenier, Stefaan and Degomme, Augustin and Dikan, Vladimir and Eimre, Kristjan and Flage-Larsen, Espen and Fornari, Marco and Garcia, Alberto and Genovese, Luigi and Giantomassi, Matteo and Huber, Sebastiaan P. and Janssen, Henning and Kastlunger, Georg and Krack, Matthias and Kresse, Georg and Kühne, Thomas D. and Lejaeghere, Kurt and Madsen, Georg K. H. and Marsman, Martijn and Marzari, Nicola and Michalicek, Gregor and Mirhosseini, Hossein and Müller, Tiziano M. A. and Petretto, Guido and Pickard, Chris J. and Poncé, Samuel and Rignanese, Gian-Marco and Rubel, Oleg and Ruh, Thomas and Sluydts, Michael and Vanpoucke, Danny E. P. and Vijay, Sudarshan and Wolloch, Michael and Wortmann, Daniel and Yakutovich, Aliaksandr V. and Yu, Jusong and Zadoks, Austin and Zhu, Bonan and Pizzi, Giovanni},
+ date = {2024-01},
+ journaltitle = {Nature Reviews Physics},
+ shortjournal = {Nat Rev Phys},
+ volume = {6},
+ number = {1},
+ pages = {45--58},
+ publisher = {Nature Publishing Group},
+ issn = {2522-5820},
+ doi = {10.1038/s42254-023-00655-3},
+ url = {https://www.nature.com/articles/s42254-023-00655-3},
+ urldate = {2024-09-09},
+ abstract = {Density-functional theory methods and codes adopting periodic boundary conditions are extensively used in condensed matter physics and materials science research. In 2016, their precision (how well properties computed with different codes agree among each other) was systematically assessed on elemental crystals: a first crucial step to evaluate the reliability of such computations. In this Expert Recommendation, we discuss recommendations for verification studies aiming at further testing precision and transferability of density-functional-theory computational approaches and codes. We illustrate such recommendations using a greatly expanded protocol covering the whole periodic table from Z\,=\,1 to 96 and characterizing 10 prototypical cubic compounds for each element: four unaries and six oxides, spanning a wide range of coordination numbers and oxidation states. The primary outcome is a reference dataset of 960~equations of state cross-checked between two all-electron codes, then used to verify and improve nine pseudopotential-based approaches. Finally, we discuss the extent to which the current results for total energies can be reused for different goals.},
+ langid = {english},
+ keywords = {Condensed-matter physics,Electronic structure},
+ file = {/Users/wasmer/Nextcloud/Zotero/Bosoni et al. - 2024 - How to verify the precision of density-functional-theory implementations via reproducible and univer.pdf}
+}
+
@article{bouazizSpinDynamics3d2019,
title = {Spin Dynamics of 3d and 4d Impurities Embedded in Prototypical Topological Insulators},
shorttitle = {Spin Dynamics Of},
@@ -8204,7 +8224,7 @@ Subject\_term\_id: condensed-matter-physics;theory-and-computation},
urldate = {2024-09-09},
abstract = {Chiral magnets are an emerging class of topological matter harboring localized and topologically protected vortex-like magnetic textures called skyrmions, which are currently under intense scrutiny as an entity for information storage and processing. Here, on the level of micromagnetics we rigorously show that chiral magnets can not only host skyrmions but also antiskyrmions as least energy configurations over all non-trivial homotopy classes. We derive practical criteria for their occurrence and coexistence with skyrmions that can be fulfilled by (110)-oriented interfaces depending on the electronic structure. Relating the electronic structure to an atomistic spin-lattice model by means of density functional calculations and minimizing the energy on a mesoscopic scale by applying spin-relaxation methods, we propose a double layer of Fe grown on a W(110) substrate as a practical example. We conjecture that ultra-thin magnetic films grown on semiconductor or heavy metal substrates with C2vsymmetry are prototype classes of materials hosting magnetic antiskyrmions.},
langid = {english},
- keywords = {/unread,interfaces and thin films,Magnetic properties and materials,Spintronics,Surfaces},
+ keywords = {interfaces and thin films,Magnetic properties and materials,Spintronics,Surfaces},
file = {/Users/wasmer/Nextcloud/Zotero/Hoffmann et al. - 2017 - Antiskyrmions stabilized at interfaces by anisotropic Dzyaloshinskii-Moriya interactions.pdf}
}
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+% \includegraphics[height=2.0\fontcharht\font`\B]{../resources/fig/icons/fontawesome-selection-johannes/png/75_dpi/white/brain-solid_white.png}
% \endgroup
% }
% \newcommand{\logoNeuralNetworkSolidCircledHelmholtzdarkblueBgWhite}{%
-% \begingroup\normalfont
-% \includegraphics[height=2.0\fontcharht\font`\B]{fifth-paradigm/neural-network-solid-circled-helmholtzdarkblue-bg-white.pdf}
-% \endgroup
+% \begingroup\normalfont
+% \includegraphics[height=2.0\fontcharht\font`\B]{../resources/fig/fifth-paradigm/neural-network-solid-circled-helmholtzdarkblue-bg-white.pdf}
+% \endgroup
% }
% \newcommand{\logoJupyter}{%
% \begingroup\normalfont
-% \includegraphics[height=2.0\fontcharht\font`\B]{logos/jupyter/jupyter.pdf}%
+% \includegraphics[height=2.0\fontcharht\font`\B]{../resources/fig/logos/jupyter/jupyter.pdf}%
% \endgroup
% }
% \newcommand{\logoDocker}{%
% \begingroup\normalfont
-% \includegraphics[height=2.0\fontcharht\font`\B]{logos/docker/docker-vertical-mono-cropped-square.png}%
+% \includegraphics[height=2.0\fontcharht\font`\B]{../resources/fig/logos/docker/docker-vertical-mono-cropped-square.png}%
% \endgroup
% }
% \newcommand{\logoMljar}{%
% \begingroup\normalfont
-% \includegraphics[height=1.0\fontcharht\font`\B]{/logos/mljar/mljar-logo.pdf}%
+% \includegraphics[height=1.0\fontcharht\font`\B]{../resources/fig/logos/mljar/mljar-logo.pdf}%
% \endgroup
% }
% \newcommand{\logoMljarXTwo}{%
% \begingroup\normalfont
-% \includegraphics[height=2.0\fontcharht\font`\B]{/logos/mljar/mljar-logo.pdf}%
+% \includegraphics[height=2.0\fontcharht\font`\B]{../resources/fig/logos/mljar/mljar-logo.pdf}%
+% \endgroup
+% }
+% \newcommand{\logoMljarXThree}{%
+% \begingroup\normalfont
+% \includegraphics[height=3.0\fontcharht\font`\B]{../resources/fig/logos/mljar/mljar-logo.pdf}%
% \endgroup
% }
+
+
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% ktikz path-adapated code
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\newcommand{\logoCpp}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/cpp/iso-cpp-logo.pdf}%
+ \endgroup
+}
+\newcommand{\logoPython}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/python/python-logo.pdf}%
+ \endgroup
+}
+\newcommand{\logoPythonNotext}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/python/python-logo-notext.pdf}%
+ \endgroup
+}
+\newcommand{\logoPythonNotextNoshadow}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/python/python-logo-notext-noshadow.pdf}%
+ \endgroup
+}
+\newcommand{\logoGoogleScholar}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/google-scholar/google-scholar-logo.pdf}%
+ \endgroup
+}
+\newcommand{\logoOrcidId}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/orcid/orcid-id-icon-logo.pdf}%
+ \endgroup
+}
+\newcommand{\logoMastodon}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/mastodon/mastodon-logo.pdf}%
+ \endgroup
+}
+\newcommand{\logoAiida}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/aiida/aiida.png}
+ \endgroup
+}
+\newcommand{\logoAiidaXTwo}{%
+ \begingroup\normalfont
+ \includegraphics[height=2.0\fontcharht\font`\B]{logos/aiida/aiida.png}
+ \endgroup
+}
+\newcommand{\logoAiidalab}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/aiida/aiidalab.png}
+ \endgroup
+}
+\newcommand{\logoCostDaemon}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.25\fontcharht\font`\B]{logos/cost-daemon/cost-daemon-logo-cropped.png}%
+ \endgroup
+}
+\newcommand{\logoJuDFT}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.25\fontcharht\font`\B]{logos/juDFT/judft-cropped.png}
+ \endgroup
+}
+\newcommand{\logoJuDFTRectangled}{%
+\begingroup\normalfont
+\includegraphics[height=1.5\fontcharht\font`\B]{logos/juDFT/judft-rectangled.png}
+\endgroup
+}
+\newcommand{\logoJuDFTRectangledBgWhite}{%
+\begingroup\normalfont
+\includegraphics[height=1.5\fontcharht\font`\B]{logos/juDFT/judft-rectangled-bg-white.png}
+\endgroup
+}
+\newcommand{\logoFLEURNoURL}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/juDFT/FLEUR/fleur-cropped-no-url.png}
+ \endgroup
+}
+\newcommand{\logoFLEURNoURLXOnePointFive}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.5\fontcharht\font`\B]{logos/juDFT/FLEUR/fleur-cropped-no-url.png}
+ \endgroup
+}
+\newcommand{\logoJuKKR}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/juDFT/juKKR/jukkr-cropped.png}
+ \endgroup
+}
+\newcommand{\logoKKRimpCircled}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/juDFT/juKKR/logo-kkrimp-circled.png}
+ \endgroup
+}
+\newcommand{\logoKKRimpCircledXTwo}{%
+ \begingroup\normalfont
+ \includegraphics[height=2.0\fontcharht\font`\B]{logos/juDFT/juKKR/logo-kkrimp-circled.png}
+ \endgroup
+}
+\newcommand{\logoSpirit}{%
+ \begingroup\normalfont
+ \includegraphics[height=2.0\fontcharht\font`\B]{logos/juDFT/Spirit/logo-spirit-cropped.png}
+ \endgroup
+}
+\newcommand{\logoSpiritCircled}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{logos/juDFT/Spirit/logo-spirit-circled.png}
+ \endgroup
+}
+\newcommand{\logoSpiritCircledXTwo}{%
+ \begingroup\normalfont
+ \includegraphics[height=2.0\fontcharht\font`\B]{logos/juDFT/Spirit/logo-spirit-circled.png}
+ \endgroup
+}
+\newcommand{\logoSpiritWithText}{%
+ \begingroup\normalfont
+ \includegraphics[height=2.0\fontcharht\font`\B]{logos/juDFT/Spirit/spirit-original-with-text.png}
+ \endgroup
+}
+\newcommand{\logoFABrainSolidBlack}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.2\fontcharht\font`\B]{icons/fontawesome-selection-johannes/png/75_dpi/black/brain-solid_black.png}
+ \endgroup
+}
+\newcommand{\logoFABrainSolidWhite}{%
+ \begingroup\normalfont
+ \includegraphics[height=2.0\fontcharht\font`\B]{icons/fontawesome-selection-johannes/png/75_dpi/white/brain-solid_white.png}
+ \endgroup
+}
+\newcommand{\logoNeuralNetworkSolidCircledHelmholtzdarkblueBgWhite}{%
+ \begingroup\normalfont
+ \includegraphics[height=2.0\fontcharht\font`\B]{fifth-paradigm/neural-network-solid-circled-helmholtzdarkblue-bg-white.pdf}
+ \endgroup
+}
+\newcommand{\logoJupyter}{%
+ \begingroup\normalfont
+ \includegraphics[height=2.0\fontcharht\font`\B]{logos/jupyter/jupyter.pdf}%
+ \endgroup
+}
+\newcommand{\logoDocker}{%
+ \begingroup\normalfont
+ \includegraphics[height=2.0\fontcharht\font`\B]{logos/docker/docker-vertical-mono-cropped-square.png}%
+ \endgroup
+}
+\newcommand{\logoMljar}{%
+ \begingroup\normalfont
+ \includegraphics[height=1.0\fontcharht\font`\B]{/logos/mljar/mljar-logo.pdf}%
+ \endgroup
+}
+\newcommand{\logoMljarXTwo}{%
+ \begingroup\normalfont
+ \includegraphics[height=2.0\fontcharht\font`\B]{/logos/mljar/mljar-logo.pdf}%
+ \endgroup
+}
diff --git a/fig/presentation-2023-02/atomistic-ml/classification-of-atomistic-ml_presentation-2023-02_02-emph-both_ktikz.pdf b/fig/presentation-2023-02/atomistic-ml/classification-of-atomistic-ml_presentation-2023-02_02-emph-both_ktikz.pdf
index 80b7303..e3ec1b6 100644
--- a/fig/presentation-2023-02/atomistic-ml/classification-of-atomistic-ml_presentation-2023-02_02-emph-both_ktikz.pdf
+++ b/fig/presentation-2023-02/atomistic-ml/classification-of-atomistic-ml_presentation-2023-02_02-emph-both_ktikz.pdf
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:c3ddf0ec4fd6ff2ddf1825d7ebae0eddbb61fe19bc88117a451993ebeb379b20
-size 121532
+oid sha256:f9aab5fc7d8c51aa1020b8d17da12dea77a0ec77181fb3b35d1460eab29cc98d
+size 122532
diff --git a/fig/presentation-2023-02/atomistic-ml/classification-of-atomistic-ml_presentation-2023-02_02-emph-both_ktikz.tikz b/fig/presentation-2023-02/atomistic-ml/classification-of-atomistic-ml_presentation-2023-02_02-emph-both_ktikz.tikz
index f123c49..496a0fc 100644
--- a/fig/presentation-2023-02/atomistic-ml/classification-of-atomistic-ml_presentation-2023-02_02-emph-both_ktikz.tikz
+++ b/fig/presentation-2023-02/atomistic-ml/classification-of-atomistic-ml_presentation-2023-02_02-emph-both_ktikz.tikz
@@ -228,12 +228,12 @@
\begin{scope}[transform canvas={yshift=-7}]
% shift arrow st surrogate input arrows not overlaid
% \draw[/arr/ml1] (representation) -- (surrogate-2) node[midway,right=-4.4,yshift=-6.0] {\textit{\textcolor{mint}{invariant}}};
- \draw[/arr/ml1UnderpassOut] (representation) -- (surrogate-1) node[midway,right=-2.1,yshift=-6.0] {\textcolor{helmholtzhighlight!50!mint}{\textbf{\textit{invariant}}}};
+ \draw[/arr/ml1UnderpassOut] (representation) -- (surrogate-1) node[midway,right=-2.1,yshift=-6.0] {\textcolor{helmholtzhighlight!50!mint}{\textbf{\textit{vectors, tensors}}}};
\draw[/arr/ml1UnderpassIn] (surrogate-1) -- (surrogate-2);
\end{scope}
\begin{scope}[transform canvas={yshift=7}]
% shift arrow st surrogate input arrows not overlaid
- \draw[/arr/ml2] (representation) -- (surrogate-1) node[midway,right=-2.1,yshift=-7.5] {\textcolor{helmholtzhighlight!0!mint}{\textbf{\textit{equivariant}}}};
+ \draw[/arr/ml2] (representation) -- (surrogate-1) node[midway,right=-2.1,yshift=-7.5] {\textcolor{helmholtzhighlight!0!mint}{\textbf{\textit{symmetries}}}};
\end{scope}
% \draw[/arr/active] (dft) -- (surrogate-1) node[midway,right=-2.3,yshift=19,rotate=-22.5] {\textit{train}};
\begin{scope}[transform canvas={xshift=-18}]
@@ -242,7 +242,7 @@
\draw[/arr/ml2UnderpassOut] [color=mint] (surrogate-1) -- (primary);
%
\node[above=.7 of dft, minimum height=0] (dummypreserveheight) {}; % for arrow above in 6-kkr
- \draw[/arr/ml2UnderpassIn] (primary.north) -- ++(0,.7) -| (dft) node[midway,right=0.3,yshift=-10] {\textit{\textcolor{mint}{\logoAiida feedback}}};
+ \draw[/arr/ml2UnderpassIn] (primary.north) -- ++(0,.7) -| (dft) node[midway,right=0.3,yshift=-10] {\textit{\textcolor{mint}{\logoAiida HTC \& AL}}};
%
%\draw[/arr/active] (primary) -- (surrogate-2) node[midway,right=-2.3,yshift=19,rotate=-22.5] {\textit{train}};
\begin{scope}[transform canvas={xshift=-0}]
@@ -254,4 +254,4 @@
% % for now, not inserted here put directly in document via textblock env.
% \node[text width=4cm] at (13,-2) {};
-\end{tikzpicture}
\ No newline at end of file
+\end{tikzpicture}
diff --git a/fig/presentation-2024-09/industry-research/4-entries.pdf b/fig/presentation-2024-09/industry-research/4-entries.pdf
new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/fig/tikz-tmp.pdf b/fig/tikz-tmp.pdf
index 292bb64..e3ec1b6 100644
--- a/fig/tikz-tmp.pdf
+++ b/fig/tikz-tmp.pdf
@@ -1,3 +1,3 @@
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+oid sha256:f9aab5fc7d8c51aa1020b8d17da12dea77a0ec77181fb3b35d1460eab29cc98d
+size 122532
diff --git a/fig/tikz-tmp.tex b/fig/tikz-tmp.tex
index 72badbf..3d8216a 100644
--- a/fig/tikz-tmp.tex
+++ b/fig/tikz-tmp.tex
@@ -1,7 +1,7 @@
% Use this file to create, compile and edit TikZ figures
-% \newcommand{\pathtotikzfig}{presentation-2023-02/atomistic-ml/classification-of-atomistic-ml_presentation-2023-02_02-emph-both_ktikz.tikz}
+\newcommand{\pathtotikzfig}{presentation-2023-02/atomistic-ml/classification-of-atomistic-ml_presentation-2023-02_02-emph-both_ktikz.tikz}
% \newcommand{\pathtotikzfig}{external/fzj/scientific-it-systems/iffaiida-architecture/iffaiida-architecture-with-logos.tikz}
-\newcommand{\pathtotikzfig}{presentation-2024-09/the-most-important-problem/mip.tikz}
+% \newcommand{\pathtotikzfig}{presentation-2024-09/the-most-important-problem/mip.tikz}
\input{tikz-preamble.tex}
% % while editing the tikz figure, go to logos and switch the paths as described
% % there. for insertion into document, switch them back.
--
GitLab