Unverified Commit 643bd27e authored by Jan Janssen's avatar Jan Janssen Committed by GitHub
Browse files

Merge pull request #64 from pyiron/execute_all_notebooks_in_the_cloud

Executed all the notebooks again on workshop.pyiron.org
parents c2a2b7f6 a83c58d6
This diff is collapsed.
......@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
"id": "previous-lotus",
"id": "expired-green",
"metadata": {},
"source": [
"# [**Workflows for atomistic simulations**](http://potentials.rub.de/) "
......@@ -10,7 +10,7 @@
},
{
"cell_type": "markdown",
"id": "solid-explosion",
"id": "brutal-healing",
"metadata": {},
"source": [
"## **Day 1 - Atomistic simulations with [pyiron](https://pyiron.org)**\n",
......@@ -29,7 +29,7 @@
},
{
"cell_type": "markdown",
"id": "apparent-assembly",
"id": "cheap-chick",
"metadata": {},
"source": [
"## **Importing necessary modules and creating a project**\n",
......@@ -40,7 +40,7 @@
{
"cell_type": "code",
"execution_count": 1,
"id": "fitting-testing",
"id": "married-kidney",
"metadata": {},
"outputs": [],
"source": [
......@@ -52,7 +52,7 @@
{
"cell_type": "code",
"execution_count": 2,
"id": "mature-bearing",
"id": "academic-print",
"metadata": {},
"outputs": [],
"source": [
......@@ -62,7 +62,7 @@
{
"cell_type": "code",
"execution_count": 3,
"id": "considered-karma",
"id": "comparable-creation",
"metadata": {},
"outputs": [],
"source": [
......@@ -71,7 +71,7 @@
},
{
"cell_type": "markdown",
"id": "controlled-david",
"id": "focal-percentage",
"metadata": {},
"source": [
"## Creating a structure \"container\" from the data\n",
......@@ -84,7 +84,7 @@
{
"cell_type": "code",
"execution_count": 4,
"id": "wrong-pickup",
"id": "contrary-spider",
"metadata": {},
"outputs": [],
"source": [
......@@ -95,7 +95,7 @@
{
"cell_type": "code",
"execution_count": 5,
"id": "current-vanilla",
"id": "superior-prospect",
"metadata": {},
"outputs": [],
"source": [
......@@ -105,7 +105,7 @@
},
{
"cell_type": "markdown",
"id": "dominican-northwest",
"id": "verified-lancaster",
"metadata": {},
"source": [
"## **Add structures from the E-V curves**\n",
......@@ -116,7 +116,7 @@
{
"cell_type": "code",
"execution_count": 6,
"id": "concrete-background",
"id": "false-flexibility",
"metadata": {},
"outputs": [],
"source": [
......@@ -127,7 +127,7 @@
},
{
"cell_type": "markdown",
"id": "worse-scheduling",
"id": "boolean-reply",
"metadata": {},
"source": [
"We can obtain this data as a `pandas` table"
......@@ -136,7 +136,7 @@
{
"cell_type": "code",
"execution_count": 7,
"id": "changed-shame",
"id": "introductory-latitude",
"metadata": {},
"outputs": [
{
......@@ -268,7 +268,7 @@
},
{
"cell_type": "markdown",
"id": "ultimate-duncan",
"id": "indirect-sellers",
"metadata": {},
"source": [
"## **Add structures from the MD**\n",
......@@ -279,7 +279,7 @@
{
"cell_type": "code",
"execution_count": 8,
"id": "disabled-computer",
"id": "applied-spank",
"metadata": {},
"outputs": [],
"source": [
......@@ -290,7 +290,7 @@
{
"cell_type": "code",
"execution_count": 9,
"id": "aggregate-wilderness",
"id": "operating-academy",
"metadata": {},
"outputs": [],
"source": [
......@@ -305,7 +305,7 @@
},
{
"cell_type": "markdown",
"id": "welsh-commercial",
"id": "consecutive-arbitration",
"metadata": {},
"source": [
"## **Add some defect structures (vacancies, surfaces, etc)**\n",
......@@ -316,14 +316,14 @@
{
"cell_type": "code",
"execution_count": 10,
"id": "continuing-upset",
"id": "certified-eligibility",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The job lammps_job_vac was saved and received the ID: 303\n"
"The job lammps_job_vac was saved and received the ID: 52\n"
]
}
],
......@@ -340,14 +340,14 @@
{
"cell_type": "code",
"execution_count": 11,
"id": "listed-occurrence",
"id": "eleven-intermediate",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The job lammps_job_surf was saved and received the ID: 304\n"
"The job lammps_job_surf was saved and received the ID: 53\n"
]
}
],
......@@ -363,7 +363,7 @@
{
"cell_type": "code",
"execution_count": 12,
"id": "sound-bathroom",
"id": "accepted-silly",
"metadata": {},
"outputs": [
{
......@@ -383,7 +383,7 @@
},
{
"cell_type": "markdown",
"id": "processed-liability",
"id": "diverse-stability",
"metadata": {},
"source": [
"We now add these structures to the dataset"
......@@ -391,8 +391,8 @@
},
{
"cell_type": "code",
"execution_count": 19,
"id": "trained-target",
"execution_count": 13,
"id": "single-treasure",
"metadata": {},
"outputs": [],
"source": [
......@@ -408,14 +408,14 @@
{
"cell_type": "code",
"execution_count": 14,
"id": "attended-drama",
"id": "widespread-homework",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The job dataset_example was saved and received the ID: 306\n"
"The job dataset_example was saved and received the ID: 54\n"
]
},
{
......@@ -438,7 +438,7 @@
{
"cell_type": "code",
"execution_count": 15,
"id": "signal-establishment",
"id": "professional-change",
"metadata": {},
"outputs": [
{
......@@ -482,17 +482,17 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>303</td>\n",
" <td>52</td>\n",
" <td>finished</td>\n",
" <td>Cu107</td>\n",
" <td>lammps_job_vac</td>\n",
" <td>/lammps_job_vac</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>day_1/creating_datasets/</td>\n",
" <td>2021-03-09 09:38:28.337496</td>\n",
" <td>2021-03-09 09:38:33.222851</td>\n",
" <td>2021-03-09 09:56:52.116789</td>\n",
" <td>2021-03-09 09:56:56.507766</td>\n",
" <td>4.0</td>\n",
" <td>pyiron@jupyter-sudarsan#1</td>\n",
" <td>pyiron@jupyter-janssen#1</td>\n",
" <td>Lammps</td>\n",
" <td>0.1</td>\n",
" <td>None</td>\n",
......@@ -500,17 +500,17 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>304</td>\n",
" <td>53</td>\n",
" <td>finished</td>\n",
" <td>Cu128</td>\n",
" <td>lammps_job_surf</td>\n",
" <td>/lammps_job_surf</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>day_1/creating_datasets/</td>\n",
" <td>2021-03-09 09:38:34.181033</td>\n",
" <td>2021-03-09 09:38:39.609826</td>\n",
" <td>5.0</td>\n",
" <td>pyiron@jupyter-sudarsan#1</td>\n",
" <td>2021-03-09 09:56:57.326228</td>\n",
" <td>2021-03-09 09:57:02.004791</td>\n",
" <td>4.0</td>\n",
" <td>pyiron@jupyter-janssen#1</td>\n",
" <td>Lammps</td>\n",
" <td>0.1</td>\n",
" <td>None</td>\n",
......@@ -518,17 +518,17 @@
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>306</td>\n",
" <td>54</td>\n",
" <td>finished</td>\n",
" <td>None</td>\n",
" <td>dataset_example</td>\n",
" <td>/dataset_example</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>day_1/creating_datasets/</td>\n",
" <td>2021-03-09 09:38:48.660175</td>\n",
" <td>2021-03-09 09:57:10.376230</td>\n",
" <td>NaT</td>\n",
" <td>NaN</td>\n",
" <td>pyiron@jupyter-sudarsan#1</td>\n",
" <td>pyiron@jupyter-janssen#1</td>\n",
" <td>TrainingContainer</td>\n",
" <td>0.4</td>\n",
" <td>None</td>\n",
......@@ -539,20 +539,20 @@
"</div>"
],
"text/plain": [
" id status chemicalformula job subjob \\\n",
"0 303 finished Cu107 lammps_job_vac /lammps_job_vac \n",
"1 304 finished Cu128 lammps_job_surf /lammps_job_surf \n",
"2 306 finished None dataset_example /dataset_example \n",
" id status chemicalformula job subjob \\\n",
"0 52 finished Cu107 lammps_job_vac /lammps_job_vac \n",
"1 53 finished Cu128 lammps_job_surf /lammps_job_surf \n",
"2 54 finished None dataset_example /dataset_example \n",
"\n",
" projectpath project timestart \\\n",
"0 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:38:28.337496 \n",
"1 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:38:34.181033 \n",
"2 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:38:48.660175 \n",
"0 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:56:52.116789 \n",
"1 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:56:57.326228 \n",
"2 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:57:10.376230 \n",
"\n",
" timestop totalcputime computer \\\n",
"0 2021-03-09 09:38:33.222851 4.0 pyiron@jupyter-sudarsan#1 \n",
"1 2021-03-09 09:38:39.609826 5.0 pyiron@jupyter-sudarsan#1 \n",
"2 NaT NaN pyiron@jupyter-sudarsan#1 \n",
" timestop totalcputime computer \\\n",
"0 2021-03-09 09:56:56.507766 4.0 pyiron@jupyter-janssen#1 \n",
"1 2021-03-09 09:57:02.004791 4.0 pyiron@jupyter-janssen#1 \n",
"2 NaT NaN pyiron@jupyter-janssen#1 \n",
"\n",
" hamilton hamversion parentid masterid \n",
"0 Lammps 0.1 None None \n",
......@@ -571,7 +571,7 @@
},
{
"cell_type": "markdown",
"id": "lyric-blair",
"id": "technological-partner",
"metadata": {},
"source": [
"## **Reloading the dataset**\n",
......@@ -582,7 +582,7 @@
{
"cell_type": "code",
"execution_count": 16,
"id": "swiss-catering",
"id": "processed-samuel",
"metadata": {},
"outputs": [
{
......@@ -1162,7 +1162,7 @@
},
{
"cell_type": "markdown",
"id": "premier-least",
"id": "julian-helena",
"metadata": {},
"source": [
"We can now inspect the data in this dataset quite easily"
......@@ -1171,7 +1171,7 @@
{
"cell_type": "code",
"execution_count": 17,
"id": "difficult-cartoon",
"id": "starting-dress",
"metadata": {},
"outputs": [],
"source": [
......@@ -1181,7 +1181,7 @@
{
"cell_type": "code",
"execution_count": 18,
"id": "analyzed-bargain",
"id": "massive-wheat",
"metadata": {},
"outputs": [],
"source": [
......@@ -1190,7 +1190,7 @@
},
{
"cell_type": "markdown",
"id": "serious-carry",
"id": "suited-blank",
"metadata": {},
"source": [
"The datasets used in the potential fitting procedure for day 2 (obtained from accurate DFT calculations) will be accessed in the same way"
......@@ -1199,7 +1199,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "simple-packet",
"id": "standard-organic",
"metadata": {},
"outputs": [],
"source": []
......
......@@ -2,6 +2,7 @@
"cells": [
{
"cell_type": "markdown",
"id": "infectious-lingerie",
"metadata": {},
"source": [
"# Day 2 - Parameterization of interatomic potentials"
......@@ -9,6 +10,7 @@
},
{
"cell_type": "markdown",
"id": "destroyed-simulation",
"metadata": {},
"source": [
"In this tutorial we will do simple fits for three different interatomic potentials.\n",
......@@ -21,6 +23,7 @@
},
{
"cell_type": "markdown",
"id": "prescribed-campbell",
"metadata": {},
"source": [
"## Embedded Atom Method Potential"
......@@ -28,6 +31,7 @@
},
{
"cell_type": "markdown",
"id": "dress-gauge",
"metadata": {},
"source": [
"* Atomic descriptors: pair functions\n",
......@@ -45,6 +49,7 @@
},
{
"cell_type": "markdown",
"id": "tribal-intro",
"metadata": {},
"source": [
"## Neural Network Potential"
......@@ -52,6 +57,7 @@
},
{
"cell_type": "markdown",
"id": "imported-answer",
"metadata": {},
"source": [
"* Atomic descriptors: pair and three-body symmetry functions\n",
......@@ -69,6 +75,7 @@
},
{
"cell_type": "markdown",
"id": "obvious-finish",
"metadata": {},
"source": [
"## Atomic Cluster Expansion"
......@@ -76,6 +83,7 @@
},
{
"cell_type": "markdown",
"id": "successful-maine",
"metadata": {},
"source": [
"* Atomic descriptors: pair, three-body, ... many-body basis functions\n",
......@@ -93,6 +101,7 @@
},
{
"cell_type": "markdown",
"id": "deluxe-recording",
"metadata": {},
"source": [
"# Reference data"
......@@ -100,6 +109,7 @@
},
{
"cell_type": "markdown",
"id": "accessible-criminal",
"metadata": {},
"source": [
"The potentials are parameterized by fitting to reference data. Here we use DFT data for Cu that we generated with the FHI-aims code. In the following we summarize key properties of the dataset."
......@@ -108,6 +118,7 @@
{
"cell_type": "code",
"execution_count": 1,
"id": "literary-discovery",
"metadata": {},
"outputs": [
{
......@@ -125,6 +136,7 @@
{
"cell_type": "code",
"execution_count": 2,
"id": "sunrise-siemens",
"metadata": {},
"outputs": [],
"source": [
......@@ -134,6 +146,7 @@
{
"cell_type": "code",
"execution_count": 3,
"id": "educational-toddler",
"metadata": {},
"outputs": [],
"source": [
......@@ -143,6 +156,7 @@
{
"cell_type": "code",
"execution_count": 4,
"id": "recorded-guitar",
"metadata": {},
"outputs": [],
"source": [
......@@ -155,6 +169,7 @@
{
"cell_type": "code",
"execution_count": 5,
"id": "infinite-genesis",
"metadata": {},
"outputs": [],
"source": [
......@@ -164,6 +179,7 @@
{
"cell_type": "code",
"execution_count": 6,
"id": "social-recycling",
"metadata": {},
"outputs": [
{
......@@ -207,87 +223,274 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>286</td>\n",
" <td>1</td>\n",
" <td>finished</td>\n",
" <td>None</td>\n",
" <td>df1_A1_A2_A3_EV_elast_phon</td>\n",
" <td>/df1_A1_A2_A3_EV_elast_phon</td>\n",
" <td>/home/yury/PycharmProjects/pyiron-2021/</td>\n",
" <td>pyiron_potentialfit/datasets/imported_datasets/Cu_database/</td>\n",
" <td>2021-02-08 10:33:52.341472</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>datasets/Cu_database/</td>\n",
" <td>2021-02-18 19:49:53.061360</td>\n",
" <td>NaT</td>\n",
" <td>NaN</td>\n",
" <td>zora@cmti001#1</td>\n",
" <td>TrainingContainer</td>\n",
" <td>0.4</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>287</td>\n",
" <td>2</td>\n",
" <td>finished</td>\n",
" <td>None</td>\n",
" <td>df3_10k</td>\n",
" <td>/df3_10k</td>\n",
" <td>/home/yury/PycharmProjects/pyiron-2021/</td>\n",
" <td>pyiron_potentialfit/datasets/imported_datasets/Cu_database/</td>\n",
" <td>2021-02-08 10:33:53.993230</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>datasets/Cu_database/</td>\n",
" <td>2021-02-18 19:49:55.496691</td>\n",
" <td>NaT</td>\n",
" <td>NaN</td>\n",
" <td>zora@cmti001#1</td>\n",
" <td>TrainingContainer</td>\n",
" <td>0.4</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>288</td>\n",
" <td>3</td>\n",
" <td>finished</td>\n",
" <td>None</td>\n",
" <td>df2_1k</td>\n",
" <td>/df2_1k</td>\n",
" <td>/home/yury/PycharmProjects/pyiron-2021/</td>\n",
" <td>pyiron_potentialfit/datasets/imported_datasets/Cu_database/</td>\n",
" <td>2021-02-08 10:33:54.435308</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>datasets/Cu_database/</td>\n",
" <td>2021-02-18 19:49:56.101883</td>\n",
" <td>NaT</td>\n",
" <td>NaN</td>\n",
" <td>zora@cmti001#1</td>\n",
" <td>TrainingContainer</td>\n",
" <td>0.4</td>\n",
" <td>None</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>4</td>\n",
" <td>finished</td>\n",
" <td>None</td>\n",
" <td>df4_2_5eV_25A3_8K</td>\n",
" <td>/df4_2_5eV_25A3_8K</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>datasets/Cu_database/</td>\n",
" <td>2021-02-18 19:49:57.547918</td>\n",
" <td>NaT</td>\n",
" <td>NaN</td>\n",
" <td>zora@cmti001#1</td>\n",
" <td>TrainingContainer</td>\n",
" <td>0.4</td>\n",
" <td>None</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>5</td>\n",
" <td>finished</td>\n",
" <td>Cu108</td>\n",
" <td>lammps_job</td>\n",
" <td>/lammps_job</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>day_1/first_steps/</td>\n",
" <td>2021-03-09 08:58:10.515085</td>\n",
" <td>2021-03-09 08:58:14.811278</td>\n",
" <td>4.0</td>\n",
" <td>pyiron@jupyter-janssen#1</td>\n",
" <td>Lammps</td>\n",
" <td>0.1</td>\n",
" <td>None</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>302</th>\n",
" <td>303</td>\n",
" <td>finished</td>\n",
" <td>Cu</td>\n",
" <td>lammps_struct_7</td>\n",
" <td>/lammps_struct_7</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>day_3/validation/Cu-atomicrex-df1-107-25/</td>\n",
" <td>2021-03-09 09:40:07.733451</td>\n",
" <td>2021-03-09 09:40:08.166608</td>\n",
" <td>0.0</td>\n",
" <td>pyiron@jupyter-janssen#1</td>\n",
" <td>Lammps</td>\n",
" <td>0.1</td>\n",
" <td>None</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>303</th>\n",
" <td>304</td>\n",