Commit 0c5d7c1f authored by Jan Janssen's avatar Jan Janssen
Browse files

Updated notebooks from Sudarsan

parent 5061e307
This diff is collapsed.
......@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
"id": "orange-treaty",
"id": "expired-green",
"metadata": {},
"source": [
"# [**Workflows for atomistic simulations**](http://potentials.rub.de/) "
......@@ -10,7 +10,7 @@
},
{
"cell_type": "markdown",
"id": "lasting-stick",
"id": "brutal-healing",
"metadata": {},
"source": [
"## **Day 1 - Atomistic simulations with [pyiron](https://pyiron.org)**\n",
......@@ -29,7 +29,7 @@
},
{
"cell_type": "markdown",
"id": "sharing-maldives",
"id": "cheap-chick",
"metadata": {},
"source": [
"## **Importing necessary modules and creating a project**\n",
......@@ -40,7 +40,7 @@
{
"cell_type": "code",
"execution_count": 1,
"id": "serial-slovak",
"id": "married-kidney",
"metadata": {},
"outputs": [],
"source": [
......@@ -52,7 +52,7 @@
{
"cell_type": "code",
"execution_count": 2,
"id": "departmental-certification",
"id": "academic-print",
"metadata": {},
"outputs": [],
"source": [
......@@ -62,7 +62,7 @@
{
"cell_type": "code",
"execution_count": 3,
"id": "french-darwin",
"id": "comparable-creation",
"metadata": {},
"outputs": [],
"source": [
......@@ -71,7 +71,7 @@
},
{
"cell_type": "markdown",
"id": "electoral-norman",
"id": "focal-percentage",
"metadata": {},
"source": [
"## Creating a structure \"container\" from the data\n",
......@@ -84,7 +84,7 @@
{
"cell_type": "code",
"execution_count": 4,
"id": "demanding-proxy",
"id": "contrary-spider",
"metadata": {},
"outputs": [],
"source": [
......@@ -95,7 +95,7 @@
{
"cell_type": "code",
"execution_count": 5,
"id": "alert-undergraduate",
"id": "superior-prospect",
"metadata": {},
"outputs": [],
"source": [
......@@ -105,7 +105,7 @@
},
{
"cell_type": "markdown",
"id": "comprehensive-sudan",
"id": "verified-lancaster",
"metadata": {},
"source": [
"## **Add structures from the E-V curves**\n",
......@@ -116,7 +116,7 @@
{
"cell_type": "code",
"execution_count": 6,
"id": "compatible-sight",
"id": "false-flexibility",
"metadata": {},
"outputs": [],
"source": [
......@@ -127,7 +127,7 @@
},
{
"cell_type": "markdown",
"id": "illegal-capture",
"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": "impressive-basin",
"id": "introductory-latitude",
"metadata": {},
"outputs": [
{
......@@ -268,7 +268,7 @@
},
{
"cell_type": "markdown",
"id": "signed-instrument",
"id": "indirect-sellers",
"metadata": {},
"source": [
"## **Add structures from the MD**\n",
......@@ -279,7 +279,7 @@
{
"cell_type": "code",
"execution_count": 8,
"id": "removed-consent",
"id": "applied-spank",
"metadata": {},
"outputs": [],
"source": [
......@@ -290,7 +290,7 @@
{
"cell_type": "code",
"execution_count": 9,
"id": "fewer-average",
"id": "operating-academy",
"metadata": {},
"outputs": [],
"source": [
......@@ -305,7 +305,7 @@
},
{
"cell_type": "markdown",
"id": "gentle-manufacturer",
"id": "consecutive-arbitration",
"metadata": {},
"source": [
"## **Add some defect structures (vacancies, surfaces, etc)**\n",
......@@ -316,7 +316,7 @@
{
"cell_type": "code",
"execution_count": 10,
"id": "leading-julian",
"id": "certified-eligibility",
"metadata": {},
"outputs": [
{
......@@ -340,7 +340,7 @@
{
"cell_type": "code",
"execution_count": 11,
"id": "adjacent-panama",
"id": "eleven-intermediate",
"metadata": {},
"outputs": [
{
......@@ -363,7 +363,7 @@
{
"cell_type": "code",
"execution_count": 12,
"id": "encouraging-credit",
"id": "accepted-silly",
"metadata": {},
"outputs": [
{
......@@ -383,7 +383,7 @@
},
{
"cell_type": "markdown",
"id": "humanitarian-effect",
"id": "diverse-stability",
"metadata": {},
"source": [
"We now add these structures to the dataset"
......@@ -392,23 +392,23 @@
{
"cell_type": "code",
"execution_count": 13,
"id": "floating-utility",
"id": "single-treasure",
"metadata": {},
"outputs": [],
"source": [
"for job_name in [\"lammps_job_vac\", \"lammps_job_surf\"]:\n",
" job_md = pr.load(job_name)\n",
"for job_md in pr.iter_jobs(status=\"finished\"):\n",
" pos = job_md[\"output/generic/positions\"]\n",
" traj_length = len(pos)\n",
" stride = 10\n",
" for i in range(0, traj_length, stride):\n",
" container.include_job(job_md, iteration_step=i)"
" if pos is not None:\n",
" traj_length = len(pos)\n",
" stride = 10\n",
" for i in range(0, traj_length, stride):\n",
" container.include_job(job_md, iteration_step=i)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "excited-digest",
"id": "widespread-homework",
"metadata": {},
"outputs": [
{
......@@ -438,7 +438,7 @@
{
"cell_type": "code",
"execution_count": 15,
"id": "western-frank",
"id": "professional-change",
"metadata": {},
"outputs": [
{
......@@ -489,8 +489,8 @@
" <td>/lammps_job_vac</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>day_1/creating_datasets/</td>\n",
" <td>2021-03-09 09:00:43.012322</td>\n",
" <td>2021-03-09 09:00:47.308799</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-janssen#1</td>\n",
" <td>Lammps</td>\n",
......@@ -507,8 +507,8 @@
" <td>/lammps_job_surf</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>day_1/creating_datasets/</td>\n",
" <td>2021-03-09 09:00:48.219183</td>\n",
" <td>2021-03-09 09:00:52.902683</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",
......@@ -525,7 +525,7 @@
" <td>/dataset_example</td>\n",
" <td>/home/pyiron/</td>\n",
" <td>day_1/creating_datasets/</td>\n",
" <td>2021-03-09 09:01:01.281092</td>\n",
" <td>2021-03-09 09:57:10.376230</td>\n",
" <td>NaT</td>\n",
" <td>NaN</td>\n",
" <td>pyiron@jupyter-janssen#1</td>\n",
......@@ -545,13 +545,13 @@
"2 54 finished None dataset_example /dataset_example \n",
"\n",
" projectpath project timestart \\\n",
"0 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:00:43.012322 \n",
"1 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:00:48.219183 \n",
"2 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:01:01.281092 \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 09:00:47.308799 4.0 pyiron@jupyter-janssen#1 \n",
"1 2021-03-09 09:00:52.902683 4.0 pyiron@jupyter-janssen#1 \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",
......@@ -571,7 +571,7 @@
},
{
"cell_type": "markdown",
"id": "valuable-procedure",
"id": "technological-partner",
"metadata": {},
"source": [
"## **Reloading the dataset**\n",
......@@ -582,7 +582,7 @@
{
"cell_type": "code",
"execution_count": 16,
"id": "exempt-sydney",
"id": "processed-samuel",
"metadata": {},
"outputs": [
{
......@@ -1162,7 +1162,7 @@
},
{
"cell_type": "markdown",
"id": "crazy-clerk",
"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": "third-comfort",
"id": "starting-dress",
"metadata": {},
"outputs": [],
"source": [
......@@ -1181,7 +1181,7 @@
{
"cell_type": "code",
"execution_count": 18,
"id": "magnetic-spring",
"id": "massive-wheat",
"metadata": {},
"outputs": [],
"source": [
......@@ -1190,7 +1190,7 @@
},
{
"cell_type": "markdown",
"id": "expired-savage",
"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": "regular-branch",
"id": "standard-organic",
"metadata": {},
"outputs": [],
"source": []
......
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