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Update Jupyter notebooks

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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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142
python/examples/pylammps/interface_usage.ipynb
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@ -4,71 +4,29 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using LAMMPS with iPython and Jupyter"
"# Example 2: Using the PyLammps interface"
]
},
{
"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 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"
@ -90,7 +48,6 @@
"outputs": [],
"source": [
"# 3d Lennard-Jones melt\n",
"\n",
"L.units(\"lj\")\n",
"L.atom_style(\"atomic\")\n",
"L.atom_modify(\"map array\")\n",
@ -116,6 +73,13 @@
"L.run(10)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Visualize the initial state"
]
},
{
"cell_type": "code",
"execution_count": null,
@ -205,9 +169,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"a index 2\")"
@ -225,9 +187,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"t equal temp\")"
@ -283,9 +243,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"b index a b c\")"
@ -321,9 +279,16 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.lmp.command('variable i loop 10')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"i loop 10\")"
@ -379,7 +344,7 @@
"metadata": {},
"outputs": [],
"source": [
"[x for x in dir(L.atoms[0]) if not x.startswith('__')]"
"dir(L.atoms[0])"
]
},
{
@ -479,6 +444,15 @@
"L.runs[0].thermo"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"dir(L.runs[0].thermo)"
]
},
{
"cell_type": "markdown",
"metadata": {},
@ -486,14 +460,48 @@
"## Saving session to as LAMMPS input file"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"PyLammps can keep track of all LAMMPS commands that are executed. This allows you to prototype a script and then later on save it as a regular input script:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L = IPyLammps()\n",
"\n",
"# enable command history\n",
"L.enable_cmd_history = True\n",
"\n",
"# 3d Lennard-Jones melt\n",
"L.units(\"lj\")\n",
"L.atom_style(\"atomic\")\n",
"L.atom_modify(\"map array\")\n",
"\n",
"L.lattice(\"fcc\", 0.8442)\n",
"L.region(\"box block\", 0, 4, 0, 4, 0, 4)\n",
"L.create_box(1, \"box\")\n",
"L.create_atoms(1, \"box\")\n",
"L.mass(1, 1.0)\n",
"\n",
"L.velocity(\"all create\", 1.44, 87287, \"loop geom\")\n",
"\n",
"L.pair_style(\"lj/cut\", 2.5)\n",
"L.pair_coeff(1, 1, 1.0, 1.0, 2.5)\n",
"\n",
"L.neighbor(0.3, \"bin\")\n",
"L.neigh_modify(\"delay 0 every 20 check no\")\n",
"\n",
"L.fix(\"1 all nve\")\n",
"\n",
"L.run(10)\n",
"\n",
"# write LAMMPS input script with all commands executed so far (including implicit ones)\n",
"L.write_script(\"in.output\")"
]
},
@ -503,7 +511,7 @@
"metadata": {},
"outputs": [],
"source": [
"dir(L.runs[0].thermo)"
"!cat in.output"
]
},
{
@ -530,7 +538,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.2"
"version": "3.9.2"
}
},
"nbformat": 4,