From e7f6e0f0d8289a135aaf471e56f5ed2e51eedba0 Mon Sep 17 00:00:00 2001 From: JaGeo Date: Tue, 18 Feb 2025 16:08:31 +0100 Subject: [PATCH 1/6] try to fix the doc --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index d1f8818f2..fb9b894df 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -82,6 +82,7 @@ docs = [ "sphinx-copybutton==0.5.2", "sphinx==8.1.3", "sphinx_design==0.6.1", + "jupyerlab==4.3.4", ] dev = ["pre-commit>=2.12.1"] tests = [ From e160bf98e45b7e5157d5a0bb90ff64214b5493b8 Mon Sep 17 00:00:00 2001 From: JaGeo Date: Tue, 18 Feb 2025 16:10:06 +0100 Subject: [PATCH 2/6] try to fix the doc --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index fb9b894df..3aafaeea1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -82,7 +82,7 @@ docs = [ "sphinx-copybutton==0.5.2", "sphinx==8.1.3", "sphinx_design==0.6.1", - "jupyerlab==4.3.4", + "jupyterlab==4.3.4", ] dev = ["pre-commit>=2.12.1"] tests = [ From fa3297c8bb41465d823c66b4901e182941bbcd2d Mon Sep 17 00:00:00 2001 From: JaGeo Date: Tue, 18 Feb 2025 16:49:19 +0100 Subject: [PATCH 3/6] add headlines to two tutorials --- tutorials/grueneisen_workflow.ipynb | 12 ++++++++---- tutorials/lobster_workflow.ipynb | 22 ++++++++++++---------- tutorials/qha_workflow.ipynb | 14 ++++++-------- 3 files changed, 26 insertions(+), 22 deletions(-) diff --git a/tutorials/grueneisen_workflow.ipynb b/tutorials/grueneisen_workflow.ipynb index 78cc45d2d..0ee75cf6c 100644 --- a/tutorials/grueneisen_workflow.ipynb +++ b/tutorials/grueneisen_workflow.ipynb @@ -1,12 +1,16 @@ { "cells": [ { + "metadata": {}, "cell_type": "markdown", - "id": "0", + "source": "# Grueneisen Workflow (VASP)", + "id": "11f88d7c79c6b901" + }, + { "metadata": {}, - "source": [ - "This part is needed for the execution in the notebook.\n" - ] + "cell_type": "markdown", + "source": "This part is needed for the execution in the notebook.\n", + "id": "0" }, { "cell_type": "code", diff --git a/tutorials/lobster_workflow.ipynb b/tutorials/lobster_workflow.ipynb index ac9ebc123..e8279381a 100644 --- a/tutorials/lobster_workflow.ipynb +++ b/tutorials/lobster_workflow.ipynb @@ -1,12 +1,16 @@ { "cells": [ { - "cell_type": "raw", - "id": "0", "metadata": {}, - "source": [ - "The first lines are needed to ensure that we can mock VASP and LOBSTER runs. The test files here might not belong to the same calculation but are good enough for testing." - ] + "cell_type": "markdown", + "source": "# LOBSTER Workflow Tutorial (Using VASP for DFT)", + "id": "7be337c7e641e197" + }, + { + "metadata": {}, + "cell_type": "markdown", + "source": "The first lines are needed to ensure that we can mock VASP and LOBSTER runs. The test files here might not belong to the same calculation but are good enough for testing.", + "id": "79249014870760ef" }, { "cell_type": "code", @@ -30,12 +34,10 @@ ] }, { - "cell_type": "markdown", - "id": "2", "metadata": {}, - "source": [ - "We first load a structure that we want to analyze with bonding analysis." - ] + "cell_type": "markdown", + "source": "We first load a structure that we want to analyze with bonding analysis.", + "id": "fb06cf07e2f77f48" }, { "cell_type": "code", diff --git a/tutorials/qha_workflow.ipynb b/tutorials/qha_workflow.ipynb index 7cfd64db2..8fde14156 100644 --- a/tutorials/qha_workflow.ipynb +++ b/tutorials/qha_workflow.ipynb @@ -1,12 +1,10 @@ { "cells": [ { - "cell_type": "markdown", - "id": "0", "metadata": {}, - "source": [ - "# Quasi-harmonic Workflow Tutorial with VASP" - ] + "cell_type": "markdown", + "source": "# Quasi-harmonic Workflow Tutorial with VASP", + "id": "84ab7b2bff387f8a" }, { "cell_type": "markdown", @@ -74,9 +72,8 @@ ] }, { - "cell_type": "markdown", - "id": "3", "metadata": {}, + "cell_type": "raw", "source": [ "This tutorial will make use of a quasi-harmonic workflow\n", " that allows to include volume-dependent anharmonicity \n", @@ -89,7 +86,8 @@ " to arrive at free energy-volume curves\n", " that are the starting point for the q\n", " uasi-harmonic approximation." - ] + ], + "id": "5d833f038f4f4a22" }, { "cell_type": "markdown", From 256deacf569132667cd323c659b103386abffb61 Mon Sep 17 00:00:00 2001 From: JaGeo Date: Tue, 18 Feb 2025 16:51:04 +0100 Subject: [PATCH 4/6] fix spelling --- tutorials/tutorials.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/tutorials.md b/tutorials/tutorials.md index 6f3b61d53..d2b33ddb0 100644 --- a/tutorials/tutorials.md +++ b/tutorials/tutorials.md @@ -3,7 +3,7 @@ # Tutorials The section includes tutorials for workflows in atomate2. -They can also be found in the form of jupyternotebooks in: +They can also be found in the form of jupyter notebooks in: [https://github.com/materialsproject/atomate2/tree/main/tutorials](https://github.com/materialsproject/atomate2/tree/main/tutorials) ```{toctree} From 61d0f5f98300656488e295b7d6ecdced8f4140f9 Mon Sep 17 00:00:00 2001 From: JaGeo Date: Tue, 18 Feb 2025 16:58:43 +0100 Subject: [PATCH 5/6] fix linting --- tutorials/grueneisen_workflow.ipynb | 44 ++++++++++++++++------------- tutorials/lobster_workflow.ipynb | 40 +++++++++++++++----------- tutorials/qha_workflow.ipynb | 14 +++++---- 3 files changed, 55 insertions(+), 43 deletions(-) diff --git a/tutorials/grueneisen_workflow.ipynb b/tutorials/grueneisen_workflow.ipynb index 0ee75cf6c..e5d1932d8 100644 --- a/tutorials/grueneisen_workflow.ipynb +++ b/tutorials/grueneisen_workflow.ipynb @@ -1,21 +1,25 @@ { "cells": [ { - "metadata": {}, "cell_type": "markdown", - "source": "# Grueneisen Workflow (VASP)", - "id": "11f88d7c79c6b901" + "id": "0", + "metadata": {}, + "source": [ + "# Grueneisen Workflow (VASP)" + ] }, { - "metadata": {}, "cell_type": "markdown", - "source": "This part is needed for the execution in the notebook.\n", - "id": "0" + "id": "1", + "metadata": {}, + "source": [ + "This part is needed for the execution in the notebook.\n" + ] }, { "cell_type": "code", "execution_count": null, - "id": "1", + "id": "2", "metadata": {}, "outputs": [], "source": [ @@ -36,7 +40,7 @@ }, { "cell_type": "markdown", - "id": "2", + "id": "3", "metadata": {}, "source": [ "Let's load all required Makers." @@ -45,7 +49,7 @@ { "cell_type": "code", "execution_count": null, - "id": "3", + "id": "4", "metadata": {}, "outputs": [], "source": [ @@ -58,7 +62,7 @@ { "cell_type": "code", "execution_count": null, - "id": "4", + "id": "5", "metadata": {}, "outputs": [], "source": [ @@ -78,7 +82,7 @@ { "cell_type": "code", "execution_count": null, - "id": "5", + "id": "6", "metadata": {}, "outputs": [], "source": [ @@ -116,7 +120,7 @@ { "cell_type": "code", "execution_count": null, - "id": "6", + "id": "7", "metadata": {}, "outputs": [], "source": [ @@ -152,7 +156,7 @@ }, { "cell_type": "markdown", - "id": "7", + "id": "8", "metadata": {}, "source": [ "Then one can use the `GruneisenMaker` to generate a `Flow`." @@ -161,7 +165,7 @@ { "cell_type": "code", "execution_count": null, - "id": "8", + "id": "9", "metadata": {}, "outputs": [], "source": [ @@ -186,7 +190,7 @@ { "cell_type": "code", "execution_count": null, - "id": "9", + "id": "10", "metadata": {}, "outputs": [], "source": [ @@ -195,7 +199,7 @@ }, { "cell_type": "markdown", - "id": "10", + "id": "11", "metadata": {}, "source": [ "We can then run the code with \"mock_vasp\"." @@ -204,7 +208,7 @@ { "cell_type": "code", "execution_count": null, - "id": "11", + "id": "12", "metadata": { "jupyter": { "is_executing": true @@ -224,7 +228,7 @@ }, { "cell_type": "markdown", - "id": "12", + "id": "13", "metadata": {}, "source": [ "Let's then analyze outputs from the workflow." @@ -233,7 +237,7 @@ { "cell_type": "code", "execution_count": null, - "id": "13", + "id": "14", "metadata": {}, "outputs": [], "source": [ @@ -253,7 +257,7 @@ { "cell_type": "code", "execution_count": null, - "id": "14", + "id": "15", "metadata": {}, "outputs": [], "source": [ diff --git a/tutorials/lobster_workflow.ipynb b/tutorials/lobster_workflow.ipynb index e8279381a..f5f5afefd 100644 --- a/tutorials/lobster_workflow.ipynb +++ b/tutorials/lobster_workflow.ipynb @@ -1,21 +1,25 @@ { "cells": [ { - "metadata": {}, "cell_type": "markdown", - "source": "# LOBSTER Workflow Tutorial (Using VASP for DFT)", - "id": "7be337c7e641e197" + "id": "0", + "metadata": {}, + "source": [ + "# LOBSTER Workflow Tutorial (Using VASP for DFT)" + ] }, { - "metadata": {}, "cell_type": "markdown", - "source": "The first lines are needed to ensure that we can mock VASP and LOBSTER runs. The test files here might not belong to the same calculation but are good enough for testing.", - "id": "79249014870760ef" + "id": "1", + "metadata": {}, + "source": [ + "The first lines are needed to ensure that we can mock VASP and LOBSTER runs. The test files here might not belong to the same calculation but are good enough for testing." + ] }, { "cell_type": "code", "execution_count": null, - "id": "1", + "id": "2", "metadata": {}, "outputs": [], "source": [ @@ -34,15 +38,17 @@ ] }, { - "metadata": {}, "cell_type": "markdown", - "source": "We first load a structure that we want to analyze with bonding analysis.", - "id": "fb06cf07e2f77f48" + "id": "3", + "metadata": {}, + "source": [ + "We first load a structure that we want to analyze with bonding analysis." + ] }, { "cell_type": "code", "execution_count": null, - "id": "3", + "id": "4", "metadata": {}, "outputs": [], "source": [ @@ -59,7 +65,7 @@ }, { "cell_type": "markdown", - "id": "4", + "id": "5", "metadata": {}, "source": [ "Then, we initialize a workflow:" @@ -68,7 +74,7 @@ { "cell_type": "code", "execution_count": null, - "id": "5", + "id": "6", "metadata": {}, "outputs": [], "source": [ @@ -93,7 +99,7 @@ }, { "cell_type": "markdown", - "id": "6", + "id": "7", "metadata": {}, "source": [ "We then run this workflow locally to show-case the capabilities. In real-life, you would omit the `mock*` parts." @@ -102,7 +108,7 @@ { "cell_type": "code", "execution_count": null, - "id": "7", + "id": "8", "metadata": {}, "outputs": [], "source": [ @@ -118,7 +124,7 @@ }, { "cell_type": "markdown", - "id": "8", + "id": "9", "metadata": {}, "source": [ "We can also analyze the data from the database" @@ -127,7 +133,7 @@ { "cell_type": "code", "execution_count": null, - "id": "9", + "id": "10", "metadata": {}, "outputs": [], "source": [ diff --git a/tutorials/qha_workflow.ipynb b/tutorials/qha_workflow.ipynb index 8fde14156..1aa39b966 100644 --- a/tutorials/qha_workflow.ipynb +++ b/tutorials/qha_workflow.ipynb @@ -1,10 +1,12 @@ { "cells": [ { - "metadata": {}, "cell_type": "markdown", - "source": "# Quasi-harmonic Workflow Tutorial with VASP", - "id": "84ab7b2bff387f8a" + "id": "0", + "metadata": {}, + "source": [ + "# Quasi-harmonic Workflow Tutorial with VASP" + ] }, { "cell_type": "markdown", @@ -72,8 +74,9 @@ ] }, { - "metadata": {}, "cell_type": "raw", + "id": "3", + "metadata": {}, "source": [ "This tutorial will make use of a quasi-harmonic workflow\n", " that allows to include volume-dependent anharmonicity \n", @@ -86,8 +89,7 @@ " to arrive at free energy-volume curves\n", " that are the starting point for the q\n", " uasi-harmonic approximation." - ], - "id": "5d833f038f4f4a22" + ] }, { "cell_type": "markdown", From e7f6e304ab7bab001b1079a074d2b837ed1632f0 Mon Sep 17 00:00:00 2001 From: JaGeo Date: Tue, 18 Feb 2025 17:00:39 +0100 Subject: [PATCH 6/6] remove one comment --- tutorials/qha_workflow.ipynb | 1 - 1 file changed, 1 deletion(-) diff --git a/tutorials/qha_workflow.ipynb b/tutorials/qha_workflow.ipynb index 1aa39b966..231437cd5 100644 --- a/tutorials/qha_workflow.ipynb +++ b/tutorials/qha_workflow.ipynb @@ -166,7 +166,6 @@ " \"GGA\": \"PE\",\n", " \"ISPIN\": 1,\n", " \"KSPACING\": 0.1,\n", - " # \"EDIFFG\": 1e-5,\n", " \"ALGO\": \"Normal\",\n", " \"LAECHG\": False,\n", " \"ISMEAR\": 0,\n",