"We can now inspect the data in this dataset quite easily"
...
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@@ -1171,7 +1171,7 @@
{
"cell_type": "code",
"execution_count": 17,
"id": "difficult-cartoon",
"id": "starting-dress",
"metadata": {},
"outputs": [],
"source": [
...
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@@ -1181,7 +1181,7 @@
{
"cell_type": "code",
"execution_count": 18,
"id": "analyzed-bargain",
"id": "massive-wheat",
"metadata": {},
"outputs": [],
"source": [
...
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@@ -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"
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@@ -1199,7 +1199,7 @@
{
"cell_type": "code",
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"id": "simple-packet",
"id": "standard-organic",
"metadata": {},
"outputs": [],
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...
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%% Cell type:markdown id:previous-lotus tags:
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# [**Workflows for atomistic simulations**](http://potentials.rub.de/)
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## **Day 1 - Atomistic simulations with [pyiron](https://pyiron.org)**
### **Exercise 2: Creating and working with structure databases**
Before the excercise, you should:
* Finish exercise 1
The aim of this exercise is to make you familiar with:
* Creating structure databases and working with them for potential fitting (day 2)
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## **Importing necessary modules and creating a project**
This is done the same way as shown in the first exercise
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``` python
importnumpyasnp
%matplotlibinline
importmatplotlib.pylabasplt
```
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``` python
frompyironimportProject
```
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``` python
pr=Project("creating_datasets")
```
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## Creating a structure "container" from the data
We now go over the jobs generated in the first notebook to store structures, energies, and forces into a structure container which will later be used for potential fitting
**Note**: Usually these datasets are created using highly accurate DFT calculations. But for practical reasons, we only demonstrate how to do this using data from LAMMPS calculations (the workflow remain the same)
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%% Cell type:code id:contrary-spider tags:
``` python
# Access the project created in exercise 1
pr_fs=pr["../first_steps"]
```
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``` python
# Create a TrainingContainer job (to store structures and databases)
