Commit 5061e307 authored by Jan Janssen's avatar Jan Janssen
Browse files

Executed all the notebooks again on workshop.pyiron.org

parent 4307dfbe
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"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",
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"id": "literary-discovery",
"metadata": {},
"outputs": [
{
......@@ -125,6 +136,7 @@
{
"cell_type": "code",
"execution_count": 2,
"id": "sunrise-siemens",
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"outputs": [],
"source": [
......@@ -134,6 +146,7 @@
{
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"execution_count": 3,
"id": "educational-toddler",
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"outputs": [],
"source": [
......@@ -143,6 +156,7 @@
{
"cell_type": "code",
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"id": "recorded-guitar",
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"outputs": [],
"source": [
......@@ -155,6 +169,7 @@
{
"cell_type": "code",
"execution_count": 5,
"id": "infinite-genesis",
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"outputs": [],
"source": [
......@@ -164,6 +179,7 @@
{
"cell_type": "code",
"execution_count": 6,
"id": "social-recycling",
"metadata": {},
"outputs": [
{
......@@ -207,87 +223,274 @@
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" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>307 rows × 15 columns</p>\n",
"</div>"
],
"text/plain": [
" id status chemicalformula job \\\n",
"0 286 finished None df1_A1_A2_A3_EV_elast_phon \n",
"1 287 finished None df3_10k \n",
"2 288 finished None df2_1k \n",
" id status chemicalformula job \\\n",
"0 1 finished None df1_A1_A2_A3_EV_elast_phon \n",
"1 2 finished None df3_10k \n",
"2 3 finished None df2_1k \n",
"3 4 finished None df4_2_5eV_25A3_8K \n",
"4 5 finished Cu108 lammps_job \n",
".. ... ... ... ... \n",
"302 303 finished Cu lammps_struct_7 \n",
"303 304 finished Cu lammps_struct_8 \n",
"304 305 finished Cu lammps_struct_9 \n",
"305 306 finished Cu lammps_struct_10 \n",
"306 307 finished Cu lammps_box \n",
"\n",
" subjob projectpath \\\n",
"0 /df1_A1_A2_A3_EV_elast_phon /home/pyiron/ \n",
"1 /df3_10k /home/pyiron/ \n",
"2 /df2_1k /home/pyiron/ \n",
"3 /df4_2_5eV_25A3_8K /home/pyiron/ \n",
"4 /lammps_job /home/pyiron/ \n",
".. ... ... \n",
"302 /lammps_struct_7 /home/pyiron/ \n",
"303 /lammps_struct_8 /home/pyiron/ \n",
"304 /lammps_struct_9 /home/pyiron/ \n",
"305 /lammps_struct_10 /home/pyiron/ \n",
"306 /lammps_box /home/pyiron/ \n",
"\n",
" subjob projectpath \\\n",
"0 /df1_A1_A2_A3_EV_elast_phon /home/yury/PycharmProjects/pyiron-2021/ \n",
"1 /df3_10k /home/yury/PycharmProjects/pyiron-2021/ \n",
"2 /df2_1k /home/yury/PycharmProjects/pyiron-2021/ \n",
" project timestart \\\n",
"0 datasets/Cu_database/ 2021-02-18 19:49:53.061360 \n",
"1 datasets/Cu_database/ 2021-02-18 19:49:55.496691 \n",
"2 datasets/Cu_database/ 2021-02-18 19:49:56.101883 \n",
"3 datasets/Cu_database/ 2021-02-18 19:49:57.547918 \n",
"4 day_1/first_steps/ 2021-03-09 08:58:10.515085 \n",
".. ... ... \n",
"302 day_3/validation/Cu-atomicrex-df1-107-25/ 2021-03-09 09:40:07.733451 \n",
"303 day_3/validation/Cu-atomicrex-df1-107-25/ 2021-03-09 09:40:25.020783 \n",
"304 day_3/validation/Cu-atomicrex-df1-107-25/ 2021-03-09 09:40:42.552932 \n",
"305 day_3/validation/Cu-atomicrex-df1-107-25/ 2021-03-09 09:41:00.324055 \n",
"306 day_3/validation/Cu-atomicrex-df1-107-25/ 2021-03-09 09:41:17.387798 \n",
"\n",
" project \\\n",
"0 pyiron_potentialfit/datasets/imported_datasets/Cu_database/ \n",
"1 pyiron_potentialfit/datasets/imported_datasets/Cu_database/ \n",
"2 pyiron_potentialfit/datasets/imported_datasets/Cu_database/ \n",
" timestop totalcputime computer \\\n",
"0 NaT NaN zora@cmti001#1 \n",
"1 NaT NaN zora@cmti001#1 \n",
"2 NaT NaN zora@cmti001#1 \n",
"3 NaT NaN zora@cmti001#1 \n",
"4 2021-03-09 08:58:14.811278 4.0 pyiron@jupyter-janssen#1 \n",
".. ... ... ... \n",
"302 2021-03-09 09:40:08.166608 0.0 pyiron@jupyter-janssen#1 \n",
"303 2021-03-09 09:40:25.465015 0.0 pyiron@jupyter-janssen#1 \n",
"304 2021-03-09 09:40:42.978853 0.0 pyiron@jupyter-janssen#1 \n",
"305 2021-03-09 09:41:00.761452 0.0 pyiron@jupyter-janssen#1 \n",
"306 2021-03-09 09:41:17.863638 0.0 pyiron@jupyter-janssen#1 \n",
"\n",
" timestart timestop totalcputime computer \\\n",
"0 2021-02-08 10:33:52.341472 None None zora@cmti001#1 \n",
"1 2021-02-08 10:33:53.993230 None None zora@cmti001#1 \n",
"2 2021-02-08 10:33:54.435308 None None zora@cmti001#1 \n",
" hamilton hamversion parentid masterid \n",
"0 TrainingContainer 0.4 None NaN \n",
"1 TrainingContainer 0.4 None NaN \n",
"2 TrainingContainer 0.4 None NaN \n",
"3 TrainingContainer 0.4 None NaN \n",
"4 Lammps 0.1 None NaN \n",
".. ... ... ... ... \n",
"302 Lammps 0.1 None NaN \n",
"303 Lammps 0.1 None NaN \n",
"304 Lammps 0.1 None NaN \n",
"305 Lammps 0.1 None NaN \n",
"306 Lammps 0.1 None NaN \n",
"\n",
" hamilton hamversion parentid masterid \n",
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"[307 rows x 15 columns]"
]
},
"execution_count": 6,
......@@ -302,6 +505,7 @@
{
"cell_type": "code",
"execution_count": 7,
"id": "documented-liberia",
"metadata": {},
"outputs": [],
"source": [
......@@ -313,6 +517,7 @@
{
"cell_type": "code",
"execution_count": 8,
"id": "tropical-revision",
"metadata": {},
"outputs": [],
"source": [
......@@ -326,6 +531,7 @@
{
"cell_type": "code",
"execution_count": 9,
"id": "everyday-anthropology",
"metadata": {},
"outputs": [],
"source": [
......@@ -336,6 +542,7 @@
{
"cell_type": "code",
"execution_count": 10,
"id": "suffering-following",
"metadata": {},
"outputs": [],
"source": [
......@@ -347,6 +554,7 @@
{
"cell_type": "code",
"execution_count": 11,
"id": "featured-coalition",
"metadata": {},
"outputs": [
{
......@@ -417,6 +625,7 @@
},
{
"cell_type": "markdown",
"id": "viral-bedroom",
"metadata": {},
"source": [
"* Dataset1 (df1): 105 structures: E-V, elastic matrix and phonopy deformations for fcc, bcc, hcp\n",
......@@ -427,6 +636,7 @@
{
"cell_type": "code",
"execution_count": 12,
"id": "greater-louisiana",
"metadata": {},
"outputs": [
{
......@@ -466,12 +676,13 @@
{
"cell_type": "code",
"execution_count": 13,
"id": "threaded-tomato",
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"outputs": [
{
"data": {
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"execution_count": 13,
......@@ -508,6 +719,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "hybrid-allowance",
"metadata": {},
"outputs": [],
"source": []
......@@ -529,7 +741,7 @@
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......
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