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Update Jupyter notebooks

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This commit is contained in:
Richard Berger
2021-03-16 15:18:07 -04:00
parent 32a2ee6dc2
commit 45b01aba0c
4 changed files with 112 additions and 151 deletions
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10
python/examples/pylammps/simple.ipynb
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@ -4,7 +4,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using LAMMPS with PyLammps"
"# Example 1: Using LAMMPS with PyLammps"
]
},
{
@ -27,7 +27,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Example\n",
"## Creating a new simulation\n",
"\n",
"Once the LAMMPS shared library and the LAMMPS Python package are installed, you can create a new LAMMMPS instance in your Python interpreter as follows:"
]
@ -109,7 +109,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### Visualizing the initial state\n",
"## Visualizing the initial state\n",
"\n",
"`IPyLammps` allows you to visualize the current simulation state with the [image](https://lammps.sandia.gov/doc/Python_module.html#lammps.IPyLammps.image) command. Here we use it to create an image of the initial state of the system."
]
@ -127,7 +127,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### Running simulations\n",
"## Running simulations\n",
"\n",
"Use the `run` command to start the simulation. In Jupyter the return value of the last command will be displayed. The `run` command will return the output of the simulation."
]
@ -177,7 +177,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### Post-processing thermo output\n",
"## Post-processing thermo output\n",
"\n",
"Independent of whether or not you suppress or show the output of the `run` command, `PyLammps` will record the output. Each `run` command creates a new entry in the `L.runs` list. So far our PyLammps instance `L` executed two `run` commands:"
]