diff --git a/README.md b/README.md
index 8122fac..3ee2f46 100644
--- a/README.md
+++ b/README.md
@@ -8,6 +8,7 @@
* [JARVIS-School](#school)
* [AI tutorial](#ai)
* [QC tutorial](#qc)
+* [NanoHub tutorial](#nanohub)
* [References](#refs)
* [How to contribute](#contrib)
* [Correspondence](#corres)
@@ -112,10 +113,13 @@ AI models for chemical formula, atomic structures, image and text for both forwa
27) [AtomVision_Example](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/AtomVisionExample.ipynb)
28) [ChemNLP example](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/ChemNLP_Example.ipynb)
29) [ChemNLP HuggingFace example](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/ChemNLP_TitleToAbstract.ipynb)
-30) [AtomGPT example](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/atomgpt_example.ipynb)
-31) [Open catalyst project load model](https://github.com/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/ocp_load_pretrained_models.ipynb)
-32) [Vacancy formation ML](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/vacancy_ml.ipynb)
-33) [Basic external tutorial on linear models](training_linear_models)
+30) [AtomGPT training example](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/atomgpt_example.ipynb)
+31) [AtomGPT HuggingFace inference example](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/atomgpt_example_huggingface.ipynb)
+32) [Open catalyst project load model](https://github.com/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/ocp_load_pretrained_models.ipynb)
+33) [Vacancy formation ML](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/vacancy_ml.ipynb)
+34) [Interface Materials Design/InterMat example](https://colab.research.google.com/gist/knc6/0d9aa89f671687c6e925eea2be9b824a/intermat_gettingstarted.ipynb)
+35) [ALIGNN-FF Unified force-field structure relaxation](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/Train_ALIGNNFF_Mlearn.ipynb)
+36) [Basic external tutorial on linear models](training_linear_models)
@@ -124,6 +128,52 @@ AI models for chemical formula, atomic structures, image and text for both forwa
1) [With new qiskit package version: Quantum computation and Qiskit based electronic bandstructure](https://github.com/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/Qiskit_based_electronic_bandstructure_latest_qiskit.ipynb)
2) [With old qiskit package version: Quantum computation and Qiskit based electronic bandstructure](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/Qiskit_based_electronic_bandstructure_.ipynb)
+
+
+
+
+# Nanohub Purdue university FAIR workflow workshop/JARVIS-School
+
+[https://nanohub.org/FAIR_workshop_2024](https://nanohub.org/FAIR_workshop_2024)
+
+1. Learn a basic DFT calculation
+
+[Basic quantum espresso run](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/JARVIS_QuantumEspressoColab_Basic_Example.ipynb)
+
+2. Once you run a lot of these, you can make a database, and analyze trends (Exploratory Data Analysis)
+
+[Analyzing_data_in_the_JARVIS_DFT_dataset](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/Analyzing_data_in_the_JARVIS_DFT_dataset.ipynb)
+
+3. These datasets can also be used to develop fast surrogate machine learning models
+
+[JARVIS_Leaderboard_contribution_ALIGNN](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/alignn_jarvis_leaderboard.ipynb)
+
+4. Beyond single property prediction models, they can be used to train machine-learning force-fields as well
+
+[ALIGNN-FF for energy and forces](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/Train_ALIGNNFF_Mlearn.ipynb)
+
+5. While the above MLFF was trained for single element system, a more generalized model was developed with JARVIS-DFT diverse dataset, and the developed model can be used for fast atomic structure optimization and phonon etc. property predicions
+
+[ALIGNN-FF Unified force-field structure relaxation](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/Train_ALIGNNFF_Mlearn.ipynb)
+
+6. While the above ML models were for forward design, we can use somthing like AtomGPT for inverse design as well
+
+[AtomGPT training example](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/atomgpt_example.ipynb)
+
+[AtomGPT HuggingFace inference example](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/atomgpt_example_huggingface.ipynb)
+
+7. Other optional notebooks for the tutorial session
+
+[AtomVision_Example](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/AtomVisionExample.ipynb)
+
+[JARVIS_LAMMPS](https://colab.research.google.com/github/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/JARVIS_LAMMPS.ipynb)
+
+[With new qiskit package version: Quantum computation and Qiskit based electronic bandstructure](https://github.com/knc6/jarvis-tools-notebooks/blob/master/jarvis-tools-notebooks/Qiskit_based_electronic_bandstructure_latest_qiskit.ipynb)
+
+# AIMS2024 tutorial and presentation slides
+
+[https://github.com/usnistgov/aims2024_workshop](https://github.com/usnistgov/aims2024_workshop)
+
# JARVIS-School
diff --git a/jarvis-tools-notebooks/JARVIS_QuantumEspressoColab_Basic_Example.ipynb b/jarvis-tools-notebooks/JARVIS_QuantumEspressoColab_Basic_Example.ipynb
index 5ceb26d..7e1e4d9 100644
--- a/jarvis-tools-notebooks/JARVIS_QuantumEspressoColab_Basic_Example.ipynb
+++ b/jarvis-tools-notebooks/JARVIS_QuantumEspressoColab_Basic_Example.ipynb
@@ -5,7 +5,7 @@
"colab": {
"name": "JARVIS_QuantumEspressoColab_Basic_Example.ipynb",
"provenance": [],
- "authorship_tag": "ABX9TyOwGykC/F5K/rh0qaUltmpb",
+ "authorship_tag": "ABX9TyN9/mlO1yVG93WhAMxGAPkR",
"include_colab_link": true
},
"kernelspec": {
@@ -30,12 +30,36 @@
{
"cell_type": "markdown",
"source": [
- "# This example shows how to run a Quantum espresso calculations with JARVIS-Tools for silicon and add the contribution to the JARVIS-Leaderboard."
+ "# This example shows how to run a Quantum espresso calculation with JARVIS-Tools for silicon and add the contribution to the JARVIS-Leaderboard.\n",
+ "\n",
+ "# Table of contents\n",
+ "\n",
+ "1. Installing [Quantum Espresso](https://www.quantum-espresso.org/), [JARVIS-Tools](https://github.com/usnistgov/jarvis) and [JARVIS-Leaderboard](https://github.com/usnistgov/jarvis_leaderboard).\n",
+ "2. Obtain and example atomic structure such as Silicon\n",
+ "3. Setup and run job\n",
+ "4. Analyze data\n",
+ "5. Upload to JARVIS-Leaderboard\n",
+ "\n",
+ "Author: Kamal Choudhary (kamal.choudhary@nist.gov)\n",
+ "\n",
+ "Refereces where such workflows were used:\n",
+ "1. https://www.nature.com/articles/s41524-022-00933-1\n",
+ "2. https://pubs.acs.org/doi/full/10.1021/acs.nanolett.2c04420\n",
+ "3. https://pubs.acs.org/doi/full/10.1021/acs.jpclett.4c01126\n"
],
"metadata": {
"id": "JIugyjg85Eep"
}
},
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 1. Installing Quantum Espresso, JARVIS-Tools and JARVIS-Leaderboard."
+ ],
+ "metadata": {
+ "id": "yITVOUQZc0T-"
+ }
+ },
{
"cell_type": "code",
"execution_count": 1,
@@ -44,36 +68,33 @@
"base_uri": "https://localhost:8080/"
},
"id": "9CNO-RGBxCqi",
- "outputId": "e1a48224-c691-400a-988e-031353bdff5c"
+ "outputId": "dbc3234c-51ab-43c6-c5d7-47205424d64a"
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
- "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m4.2/4.2 MB\u001b[0m \u001b[31m22.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
- "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m1.1/1.1 MB\u001b[0m \u001b[31m19.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
- "\u001b[?25h"
+ " Preparing metadata (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m4.2/4.2 MB\u001b[0m \u001b[31m24.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m72.1/72.1 MB\u001b[0m \u001b[31m7.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.9/3.9 MB\u001b[0m \u001b[31m22.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m8.8/8.8 MB\u001b[0m \u001b[31m33.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m1.1/1.1 MB\u001b[0m \u001b[31m16.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m251.0/251.0 kB\u001b[0m \u001b[31m10.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m82.9/82.9 kB\u001b[0m \u001b[31m5.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+ "\u001b[?25h Building wheel for paginate (setup.py) ... \u001b[?25l\u001b[?25hdone\n"
]
}
],
"source": [
- "!pip install -q jarvis-tools"
+ "!pip install -q jarvis-tools jarvis-leaderboard"
]
},
{
"cell_type": "markdown",
"source": [
- "# JARVIS-Tools +Quantum Espresso workflow used in: https://www.nature.com/articles/s41524-022-00933-1 and https://pubs.acs.org/doi/abs/10.1021/acs.nanolett.2c04420"
- ],
- "metadata": {
- "id": "YYF-iR3aUOY3"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- "It takes about 7 minutes to install QE."
+ "It takes about 8 minutes to install QE."
],
"metadata": {
"id": "HjbUWNz14VTC"
@@ -102,7 +123,7 @@
"base_uri": "https://localhost:8080/"
},
"id": "wnTJPQJyxE0r",
- "outputId": "f7f4a427-1d16-4cd8-d5fd-cd5e3500ba7d"
+ "outputId": "54c56e5c-6a1d-49c8-d552-b8c4cfa706d1"
},
"execution_count": 2,
"outputs": [
@@ -129,7 +150,7 @@
"Get:6 http://archive.ubuntu.com/ubuntu jammy/main amd64 libfftw3-bin amd64 3.3.8-2ubuntu8 [35.5 kB]\n",
"Get:7 http://archive.ubuntu.com/ubuntu jammy/main amd64 libfftw3-dev amd64 3.3.8-2ubuntu8 [2,101 kB]\n",
"Get:8 http://archive.ubuntu.com/ubuntu jammy/main amd64 libfftw3-doc all 3.3.8-2ubuntu8 [262 kB]\n",
- "Fetched 4,918 kB in 1s (4,869 kB/s)\n",
+ "Fetched 4,918 kB in 1s (4,897 kB/s)\n",
"Selecting previously unselected package libfftw3-double3:amd64.\n",
"(Reading database ... 123594 files and directories currently installed.)\n",
"Preparing to unpack .../0-libfftw3-double3_3.3.8-2ubuntu8_amd64.deb ...\n",
@@ -165,23 +186,23 @@
"Setting up libfftw3-dev:amd64 (3.3.8-2ubuntu8) ...\n",
"Processing triggers for man-db (2.10.2-1) ...\n",
"Processing triggers for libc-bin (2.35-0ubuntu3.4) ...\n",
- "/sbin/ldconfig.real: /usr/local/lib/libur_adapter_opencl.so.0 is not a symbolic link\n",
+ "/sbin/ldconfig.real: /usr/local/lib/libur_loader.so.0 is not a symbolic link\n",
"\n",
- "/sbin/ldconfig.real: /usr/local/lib/libur_adapter_level_zero.so.0 is not a symbolic link\n",
+ "/sbin/ldconfig.real: /usr/local/lib/libtbb.so.12 is not a symbolic link\n",
"\n",
- "/sbin/ldconfig.real: /usr/local/lib/libtbbmalloc_proxy.so.2 is not a symbolic link\n",
+ "/sbin/ldconfig.real: /usr/local/lib/libtbbmalloc.so.2 is not a symbolic link\n",
"\n",
- "/sbin/ldconfig.real: /usr/local/lib/libtbbbind.so.3 is not a symbolic link\n",
+ "/sbin/ldconfig.real: /usr/local/lib/libur_adapter_level_zero.so.0 is not a symbolic link\n",
"\n",
"/sbin/ldconfig.real: /usr/local/lib/libtbbbind_2_5.so.3 is not a symbolic link\n",
"\n",
- "/sbin/ldconfig.real: /usr/local/lib/libtbbmalloc.so.2 is not a symbolic link\n",
+ "/sbin/ldconfig.real: /usr/local/lib/libtbbbind.so.3 is not a symbolic link\n",
"\n",
"/sbin/ldconfig.real: /usr/local/lib/libtbbbind_2_0.so.3 is not a symbolic link\n",
"\n",
- "/sbin/ldconfig.real: /usr/local/lib/libtbb.so.12 is not a symbolic link\n",
+ "/sbin/ldconfig.real: /usr/local/lib/libtbbmalloc_proxy.so.2 is not a symbolic link\n",
"\n",
- "/sbin/ldconfig.real: /usr/local/lib/libur_loader.so.0 is not a symbolic link\n",
+ "/sbin/ldconfig.real: /usr/local/lib/libur_adapter_opencl.so.0 is not a symbolic link\n",
"\n",
"test -d bin || mkdir bin\n",
"( cd UtilXlib ; make TLDEPS= all || exit 1 )\n",
@@ -280,7 +301,7 @@
"remote: Counting objects: 100% (117/117), done.\u001b[K\n",
"remote: Compressing objects: 100% (68/68), done.\u001b[K\n",
"remote: Total 77 (delta 41), reused 26 (delta 8), pack-reused 0 (from 0)\u001b[K\n",
- "Unpacking objects: 100% (77/77), 94.95 KiB | 1.79 MiB/s, done.\n",
+ "Unpacking objects: 100% (77/77), 94.95 KiB | 1.28 MiB/s, done.\n",
"From https://gitlab.com/max-centre/components/devicexlib\n",
" * branch a6b89ef77b1ceda48e967921f1f5488d2df9226d -> FETCH_HEAD\n",
"Submodule path 'external/devxlib': checked out 'a6b89ef77b1ceda48e967921f1f5488d2df9226d'\n",
@@ -2488,12 +2509,21 @@
"( cd ../../bin ; ln -fs ../PW/tools/rism1d.x . )\n",
"make[2]: Leaving directory '/content/q-e/PW/tools'\n",
"make[1]: Leaving directory '/content/q-e/PW'\n",
- "CPU times: user 4.94 s, sys: 574 ms, total: 5.52 s\n",
- "Wall time: 9min 34s\n"
+ "CPU times: user 5.22 s, sys: 588 ms, total: 5.81 s\n",
+ "Wall time: 9min 52s\n"
]
}
]
},
+ {
+ "cell_type": "markdown",
+ "source": [
+ "List files/folders"
+ ],
+ "metadata": {
+ "id": "KhLIwMoifXV-"
+ }
+ },
{
"cell_type": "code",
"source": [
@@ -2504,7 +2534,7 @@
"colab": {
"base_uri": "https://localhost:8080/"
},
- "outputId": "835b0255-f3ef-487a-9a6d-1cf3e15f36b8"
+ "outputId": "59675797-9408-4197-8b7c-b8bb98885516"
},
"execution_count": 3,
"outputs": [
@@ -2534,6 +2564,15 @@
"execution_count": null,
"outputs": []
},
+ {
+ "cell_type": "markdown",
+ "source": [
+ "Compute info"
+ ],
+ "metadata": {
+ "id": "LucgMttcfZyh"
+ }
+ },
{
"cell_type": "code",
"source": [
@@ -2544,7 +2583,7 @@
"base_uri": "https://localhost:8080/"
},
"id": "CtFkbRdT2Frw",
- "outputId": "2edeb6f3-902d-431c-9914-001d36084b3d"
+ "outputId": "6f0330a1-3dfe-4225-b37b-7d0b6aff4175"
},
"execution_count": 4,
"outputs": [
@@ -2566,7 +2605,7 @@
" Core(s) per socket: 1\n",
" Socket(s): 1\n",
" Stepping: 0\n",
- " BogoMIPS: 4399.99\n",
+ " BogoMIPS: 4400.43\n",
" Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 cl\n",
" flush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc re\n",
" p_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni pclmulqdq ssse3\n",
@@ -2606,6 +2645,15 @@
}
]
},
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 2. Obtain and example atomic structure such as Silicon"
+ ],
+ "metadata": {
+ "id": "xwZ6IBkCdENc"
+ }
+ },
{
"cell_type": "code",
"source": [
@@ -2626,6 +2674,7 @@
" else:\n",
" return np.nan\n",
"\n",
+ "# Searching for Silicon systems only\n",
"df['el'] = df['atoms'].apply(lambda x: has_elements(atoms_dict = x, my_element = ['Si']))\n",
"df1 = df.dropna()\n",
"df_eform_filter = df1[df1['formation_energy_peratom']==0]\n",
@@ -2638,7 +2687,7 @@
"height": 335
},
"id": "FuLEmYXq9CKn",
- "outputId": "c5f9e40c-5562-47c5-8fe7-92e687ab57bb"
+ "outputId": "7cfa47b5-92af-4e6b-80f4-8d92c59a4986"
},
"execution_count": 5,
"outputs": [
@@ -2655,7 +2704,7 @@
"output_type": "stream",
"name": "stderr",
"text": [
- "100%|██████████| 40.8M/40.8M [00:01<00:00, 21.4MiB/s]\n"
+ "100%|██████████| 40.8M/40.8M [00:02<00:00, 15.2MiB/s]\n"
]
},
{
@@ -2698,7 +2747,7 @@
],
"text/html": [
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- "type": "dataframe",
- "variable_name": "df",
- "summary": "{\n \"name\": \"df\",\n \"rows\": 1,\n \"fields\": [\n {\n \"column\": \"id\",\n \"properties\": {\n \"dtype\": \"string\",\n \"num_unique_values\": 1,\n \"samples\": [\n \"JVASP-1002\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"prediction\",\n \"properties\": {\n \"dtype\": \"number\",\n \"std\": null,\n \"min\": 0.4883900939631527,\n \"max\": 0.4883900939631527,\n \"num_unique_values\": 1,\n \"samples\": [\n 0.4883900939631527\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n }\n ]\n}"
- }
+ "['run.sh',\n",
+ " 'ES-SinglePropertyPrediction-bandgap_JVASP_1002_Si-dft_3d-test-mae.csv.zip',\n",
+ " 'metadata.json']"
+ ]
},
"metadata": {},
- "execution_count": 21
+ "execution_count": 40
}
]
},
- {
- "cell_type": "markdown",
- "source": [
- "Now lets make a benchmark json.zip file"
- ],
- "metadata": {
- "id": "g_uuxlV270gP"
- }
- },
{
"cell_type": "code",
"source": [
- "from jarvis.db.jsonutils import dumpjson\n",
- "content = {\"train\": {}, \"test\": {\"JVASP-1002\": 1.17}}\n",
- "dumpjson(content, \"dft_3d_bandgap_JVASP_1002_Si.json\")"
+ "!jarvis_upload.py --your_contribution_directory knc6_silicon_test"
],
"metadata": {
- "id": "71Nct1ba794_"
+ "id": "wMfDgnjmpCSV"
},
- "execution_count": 22,
+ "execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"source": [
- "The `dft_3d_bandgap_JVASP_1002_Si.json.zip` file can go to folders such as this [link](https://github.com/usnistgov/jarvis_leaderboard/blob/main/jarvis_leaderboard/benchmarks/ES/SinglePropertyPrediction/dft_3d_bandgap_JVASP_1002_Si.json.zip)\n",
- "\n",
- "The `ES-SinglePropertyPrediction-bandgap_JVASP_1002_Si-dft_3d-test-mae.csv` can go to folder such as [this link](https://github.com/usnistgov/jarvis_leaderboard/blob/main/jarvis_leaderboard/contributions/vasp_optb88vdw/ES-SinglePropertyPrediction-bandgap_JVASP_1002_Si-dft_3d-test-mae.csv.zip)"
+ "Replace knc6 with your username"
],
"metadata": {
- "id": "xgFb9qzC8TDE"
+ "id": "4A_isCmtpHZB"
}
},
{
"cell_type": "markdown",
"source": [
- "# Now you can\n",
- "\n",
- "1) [Fork](https://github.com/usnistgov/jarvis_leaderboard/fork) the jarvis-leaderboard GitHub repository\n",
- "\n",
- "2) Add a new folder in the `jarvis_leaderboard/jarvis_leaderboard\n",
- "/contributions/` folder, e.g., `qe_pbe_test`\n",
- "\n",
- "3) In the folder, add the `ES-SinglePropertyPrediction-bandgap_JVASP_1002_Si-dft_3d-test-mae.csv.zip` file, an example `metadata.json` file, e.g. [this](https://github.com/usnistgov/jarvis_leaderboard/blob/main/jarvis_leaderboard/contributions/gpaw_lda/metadata.json) one, add a `run.sh` file, e.g. this [one](https://github.com/usnistgov/jarvis_leaderboard/blob/main/jarvis_leaderboard/contributions/gpaw_lda/run.sh)\n",
- "\n",
- "4) Make a pull request from your forked repo to the main jarvis-leaderboard"
+ "Now, the benchmark for silicon bandgap was already in the jarvis_leaderboard so we didnt have to create a json.zip. To create a new benchmark (must have a peer reviewed DOI), we can follow a process like the following.\n"
],
"metadata": {
- "id": "1cRWuI_6MdKY"
+ "id": "g_uuxlV270gP"
}
},
{
"cell_type": "code",
- "source": [],
- "metadata": {
- "id": "liQSlOGPMa2x"
- },
- "execution_count": null,
- "outputs": []
- },
- {
- "cell_type": "code",
- "source": [],
+ "source": [
+ "from jarvis.db.jsonutils import dumpjson\n",
+ "content = {\"train\": {}, \"test\": {\"JVASP-1002\": 1.17}}\n",
+ "dumpjson(content, \"dft_3d_bandgap_JVASP_1002_Si.json\")"
+ ],
"metadata": {
- "id": "dTwhFRaUMa0g"
+ "id": "71Nct1ba794_"
},
"execution_count": null,
"outputs": []
@@ -3787,62 +3807,31 @@
{
"cell_type": "markdown",
"source": [
- "Further analysis"
+ "The `dft_3d_bandgap_JVASP_1002_Si.json.zip` file can go to folders such as this [link](https://github.com/usnistgov/jarvis_leaderboard/blob/main/jarvis_leaderboard/benchmarks/ES/SinglePropertyPrediction/dft_3d_bandgap_JVASP_1002_Si.json.zip)\n",
+ "\n",
+ "The `ES-SinglePropertyPrediction-bandgap_JVASP_1002_Si-dft_3d-test-mae.csv` can go to folder such as [this link](https://github.com/usnistgov/jarvis_leaderboard/blob/main/jarvis_leaderboard/contributions/vasp_optb88vdw/ES-SinglePropertyPrediction-bandgap_JVASP_1002_Si-dft_3d-test-mae.csv.zip)"
],
"metadata": {
- "id": "O5UPzLXO9AIG"
+ "id": "xgFb9qzC8TDE"
}
},
{
"cell_type": "code",
- "source": [
- "import numpy as np\n",
- "%matplotlib inline\n",
- "energies, DOS = ds.dos(smearing=0.2)"
- ],
+ "source": [],
"metadata": {
- "id": "Ep7_3jDgMPNd"
+ "id": "liQSlOGPMa2x"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
- "source": [
- "%matplotlib inline\n",
- "import matplotlib.pyplot as plt\n",
- "plt.plot(energies, DOS)\n",
- "plt.xlabel('E-$E_F$ (eV)')\n",
- "plt.ylabel('Density of states (arb. unit)')\n",
- "plt.fill_between(energies, 0, DOS, where=(energies < 0), facecolor='blue', alpha=0.25)\n",
- "plt.axvline(x=0,linestyle='-.',color='green')\n",
- "\n",
- "plt.xlim([-5,5])\n",
- "plt.ylim([0,3])\n",
- "plt.show()\n",
- "\n"
- ],
+ "source": [],
"metadata": {
- "id": "anfNRjlNMO39",
- "colab": {
- "base_uri": "https://localhost:8080/",
- "height": 458
- },
- "outputId": "cfb90943-e88d-4d64-fb77-b26ebe442e4c"
+ "id": "dTwhFRaUMa0g"
},
"execution_count": null,
- "outputs": [
- {
- "output_type": "display_data",
- "data": {
- "text/plain": [
- "