Update Jupyter notebooks

python/examples/pylammps/interface_usage_bonds.ipynb

@@ -4,72 +4,29 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Using LAMMPS with iPython and Jupyter"
+    "# Example 3: 2D circle of particles inside of box with LJ walls"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "LAMMPS can be run interactively using iPython easily. This tutorial shows how to set this up."
+    "## Prerequisites\n",
+    "\n",
+    "Before running this example, make sure your Python environment can find the LAMMPS shared library (`liblammps.so`) and the LAMMPS Python package is installed. If you followed the [README](README.md) in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a dedicated [PyLammps HowTo](https://lammps.sandia.gov/doc/Howto_pylammps.html)."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Installation"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "1. Download the latest version of LAMMPS into a folder (we will calls this `$LAMMPS_DIR` from now on)\n",
-    "2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n",
-    "   ```bash\n",
-    "   cd $LAMMPS_DIR/src\n",
-    "   make yes-molecule\n",
-    "   make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
-    "   ```\n",
-    "\n",
-    "3. Create a python virtualenv\n",
-    "   ```bash\n",
-    "   virtualenv testing\n",
-    "   source testing/bin/activate\n",
-    "   ```\n",
-    "\n",
-    "4. Inside the virtualenv install the lammps package\n",
-    "   ```\n",
-    "   (testing) cd $LAMMPS_DIR/python\n",
-    "   (testing) python install.py\n",
-    "   (testing) cd   # move to your working directory\n",
-    "   ```\n",
-    "\n",
-    "5. Install jupyter and ipython in the virtualenv\n",
-    "   ```bash\n",
-    "   (testing) pip install ipython jupyter\n",
-    "   ```\n",
-    "\n",
-    "6. Run jupyter notebook\n",
-    "   ```bash\n",
-    "   (testing) jupyter notebook\n",
-    "   ```"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Example"
+    "## Setup system"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from lammps import IPyLammps"
@@ -135,6 +92,13 @@
     "L.fix(3, \"all wall/lj93 ylo 0.0 1 1 2.5 yhi\", y, \"1 1 2.5\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Visualize initial state"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -144,6 +108,13 @@
     "L.image(zoom=1.8)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Run simulation and visualize new state"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -254,9 +225,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "L.variable(\"a index 2\")"
@@ -274,9 +243,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "L.variable(\"t equal temp\")"
@@ -332,9 +299,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "L.variable(\"b index a b c\")"
@@ -370,9 +335,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "L.variable(\"i loop 10\")"
@@ -428,7 +391,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "[x for x in dir(L.atoms[0]) if not x.startswith('__')]"
+    "dir(L.atoms[0])"
    ]
   },
   {
@@ -479,9 +442,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": []
   }
@@ -502,7 +463,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.9.2"
   }
  },
  "nbformat": 4,