From 0371660a6ec236ecf39e3fb0fb39756979c264a5 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Thu, 14 Sep 2023 11:19:41 +0200 Subject: [PATCH] fix doc build --- _toc.yml | 19 +++++++++---------- intro.md | 11 ++++++----- .../01_Introduction_Pyiron.ipynb | 12 +++++++++--- .../02_Visualizing_Training_Data.ipynb | 6 +++--- .../03_Creating_Training_Data.ipynb | 12 +++++++++--- .../02_phase_diagram/tutorial_1.ipynb | 4 ++-- .../02_phase_diagram/tutorial_2.ipynb | 2 +- .../03_continuum/damask_tutorial.ipynb | 13 ++++++++++--- 8 files changed, 49 insertions(+), 30 deletions(-) diff --git a/_toc.yml b/_toc.yml index 2db59f8..eb28f6e 100644 --- a/_toc.yml +++ b/_toc.yml @@ -4,13 +4,12 @@ format: jb-book root: intro chapters: - sections: - - file: matwerk_workshop/01_introduction/01_Introduction_Pyiron.ipynb - - file: matwerk_workshop/01_introduction/02_Visualizing_Training_Data.ipynb - - file: matwerk_workshop/01_introduction/03_Creating_Training_Data.ipynb - - file: matwerk_workshop/02_phase_diagram/exercise_1.ipynb - - file: matwerk_workshop/02_phase_diagram/exercise_2.ipynb - - file: matwerk_workshop/03_continuum/atomistic_elastic_constants.ipynb - - file: matwerk_workshop/03_continuum/calculation.ipynb - - file: matwerk_workshop/03_continuum/damask_tutorial.ipynb - - file: matwerk_workshop/03_continuum/submitter.ipynb + - file: matwerk_workshop/01_introduction/01_Introduction_Pyiron.ipynb + - file: matwerk_workshop/01_introduction/02_Visualizing_Training_Data.ipynb + - file: matwerk_workshop/01_introduction/03_Creating_Training_Data.ipynb + - file: matwerk_workshop/02_phase_diagram/tutorial_1.ipynb + - file: matwerk_workshop/02_phase_diagram/tutorial_2.ipynb + #- file: matwerk_workshop/03_continuum/atomistic_elastic_constants.ipynb + #- file: matwerk_workshop/03_continuum/calculation.ipynb + - file: matwerk_workshop/03_continuum/damask_tutorial.ipynb + #- file: matwerk_workshop/03_continuum/submitter.ipynb diff --git a/intro.md b/intro.md index 6893c02..5aeeabe 100644 --- a/intro.md +++ b/intro.md @@ -1,12 +1,13 @@ -# From Electrons to Phase Diagrams 2022 +# Workflows for materials science simulations with pyiron -Phase diagrams are of ubiquitous importance for materials design. Current materials design workflows in industry and academia employ CALPHAD-computed phase diagrams that to a large extent rely on assessed experimental data. +Hickel, T. (Speaker)¹; Menon, S. (Speaker)¹; Waseda, O. (Speaker)¹ +¹Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf -Today the computation of large numbers of DFT data are becoming a routine task, due to efficient DFT codes, efficient workflow management and powerful high-performance computing. Together with progress in interatomic potentials, in particular the development of machine learning potentials as well as efficient implementations and parameterization codes, this means that interatomic potentials with near-DFT accuracy are now available. When combined with efficient sampling for the computation of free energies, it is therefore possible to estimate phase diagrams directly from DFT data and to supplement and assess experimental input. +Presented at the NFDI-Matwerk conference on 29.06.2023 -At the three-day workshop we will provide tutorials and hands-on classes that cover the complete chain from high-throughput electronic structure calculations to the computation of phase diagrams. Day 1 will focus on automated workflows for the generation of DFT data. On day 2 we will discuss the parameterization and validation of interatomic potentials from DFT reference data. Day 3 will then introduce the methods and tools for the computation of thermodynamic properties and phase diagrams. - +Advanced computational simulations in materials science have reached a maturity that allows one to accurately describe and predict materials properties and processes. The underlying simulation tasks often involve several different models and software that requires expert knowledge to set up a project and to vary input parameters. The accompanying increasing complexity of simulation protocols means that the workflow along the simulation chain becomes an integral part of research. Effective workflow management therefore is important for efficient research and transparent and reproducible results. In this hands-on tutorial we will provide an interactive hands-on introduction into managing workflows with pyiron (www.pyiron.org). Pyiron is an integrated development environment for materials science built on python and Jupyter notebooks that may be used for a wide variety of simulation tasks, from rapid prototyping to high performance computing. + ```{tableofcontents} diff --git a/matwerk_workshop/01_introduction/01_Introduction_Pyiron.ipynb b/matwerk_workshop/01_introduction/01_Introduction_Pyiron.ipynb index 09c465d..084c0d5 100644 --- a/matwerk_workshop/01_introduction/01_Introduction_Pyiron.ipynb +++ b/matwerk_workshop/01_introduction/01_Introduction_Pyiron.ipynb @@ -1,12 +1,18 @@ { "cells": [ + { + "cell_type": "markdown", + "id": "82c220b1-6252-4e2d-b4ae-df7ccb496634", + "metadata": {}, + "source": [ + "# Introduction to Atomistic Simulations with Pyiron " + ] + }, { "cell_type": "markdown", "id": "growing-detective", "metadata": {}, "source": [ - "# Introduction to Atomistic Simulations with Pyiron\n", - "\n", "Before the excercise, you should:\n", "\n", "* Be familiar with python especially with numerical libraries like numpy and plotting tools like matplotlib\n", @@ -1148,7 +1154,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.16" + "version": "3.11.5" }, "toc-autonumbering": false, "toc-showcode": false, diff --git a/matwerk_workshop/01_introduction/02_Visualizing_Training_Data.ipynb b/matwerk_workshop/01_introduction/02_Visualizing_Training_Data.ipynb index 04989c9..2e73e22 100644 --- a/matwerk_workshop/01_introduction/02_Visualizing_Training_Data.ipynb +++ b/matwerk_workshop/01_introduction/02_Visualizing_Training_Data.ipynb @@ -2,10 +2,10 @@ "cells": [ { "cell_type": "markdown", - "id": "b58fa431-18d0-444c-a0c0-b07d8f70fbb4", + "id": "fcc322bb-212c-4f53-b99e-31cb4e32e589", "metadata": {}, "source": [ - "# Exercise 3: Visualizing Training Data" + "# Visualizing Training Data " ] }, { @@ -415,7 +415,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.15" + "version": "3.11.5" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/matwerk_workshop/01_introduction/03_Creating_Training_Data.ipynb b/matwerk_workshop/01_introduction/03_Creating_Training_Data.ipynb index 2010107..022cff8 100644 --- a/matwerk_workshop/01_introduction/03_Creating_Training_Data.ipynb +++ b/matwerk_workshop/01_introduction/03_Creating_Training_Data.ipynb @@ -1,12 +1,18 @@ { "cells": [ + { + "cell_type": "markdown", + "id": "00012453-0e62-4fa0-8c11-6fcce55f1b33", + "metadata": {}, + "source": [ + "# Creating and working with structure databases " + ] + }, { "cell_type": "markdown", "id": "brutal-healing", "metadata": {}, "source": [ - "# Exercise 2: Creating and working with structure databases\n", - "\n", "Before the excercise, you should:\n", "\n", "* Run the 01_Introduction_Pyiron.ipynb notebook\n", @@ -1205,7 +1211,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.15" + "version": "3.11.5" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/matwerk_workshop/02_phase_diagram/tutorial_1.ipynb b/matwerk_workshop/02_phase_diagram/tutorial_1.ipynb index 74369ac..a4305d8 100644 --- a/matwerk_workshop/02_phase_diagram/tutorial_1.ipynb +++ b/matwerk_workshop/02_phase_diagram/tutorial_1.ipynb @@ -5,7 +5,7 @@ "id": "26a98d00", "metadata": {}, "source": [ - "# Phase diagrams and how to calculate them " + "# Phase diagrams and how to calculate them " ] }, { @@ -1116,7 +1116,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.16" + "version": "3.11.5" } }, "nbformat": 4, diff --git a/matwerk_workshop/02_phase_diagram/tutorial_2.ipynb b/matwerk_workshop/02_phase_diagram/tutorial_2.ipynb index 6253c9b..2223fac 100644 --- a/matwerk_workshop/02_phase_diagram/tutorial_2.ipynb +++ b/matwerk_workshop/02_phase_diagram/tutorial_2.ipynb @@ -5,7 +5,7 @@ "id": "e6829c50-ea89-4b95-b76b-5d61dd4a122a", "metadata": {}, "source": [ - "# AlLi phase diagram " + "# AlLi phase diagram " ] }, { diff --git a/matwerk_workshop/03_continuum/damask_tutorial.ipynb b/matwerk_workshop/03_continuum/damask_tutorial.ipynb index 416419f..6e73af4 100644 --- a/matwerk_workshop/03_continuum/damask_tutorial.ipynb +++ b/matwerk_workshop/03_continuum/damask_tutorial.ipynb @@ -1,11 +1,18 @@ { "cells": [ + { + "cell_type": "markdown", + "id": "0496718c-0919-4117-b677-54cc5bd9a8cb", + "metadata": {}, + "source": [ + "# DAMASK tutorial " + ] + }, { "cell_type": "markdown", "id": "sealed-session", "metadata": {}, "source": [ - "# DAMASK tutorial\n", "- creating necessary inputs for damask\n", "- runing the damask jobs\n", "\n", @@ -408,7 +415,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -422,7 +429,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.6" + "version": "3.11.5" } }, "nbformat": 4,