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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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18
python/examples/pylammps/dihedrals/dihedral.ipynb
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@ -19,9 +19,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"import matplotlib.pyplot as plt" "import matplotlib.pyplot as plt"
@ -30,9 +28,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"from lammps import IPyLammps" "from lammps import IPyLammps"
@ -194,9 +190,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"K = 80.0\n", "K = 80.0\n",
@ -232,9 +226,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [] "source": []
} }
@ -255,7 +247,7 @@
"name": "python", "name": "python",
"nbconvert_exporter": "python", "nbconvert_exporter": "python",
"pygments_lexer": "ipython3", "pygments_lexer": "ipython3",
"version": "3.6.2" "version": "3.9.2"
} }
}, },
"nbformat": 4, "nbformat": 4,

140
python/examples/pylammps/interface_usage.ipynb
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@ -4,71 +4,29 @@
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"# Using LAMMPS with iPython and Jupyter" "# Example 2: Using the PyLammps interface"
] ]
}, },
{ {
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "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", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"## Installation" "## Setup system"
]
},
{
"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"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"from lammps import IPyLammps" "from lammps import IPyLammps"
@ -90,7 +48,6 @@
"outputs": [], "outputs": [],
"source": [ "source": [
"# 3d Lennard-Jones melt\n", "# 3d Lennard-Jones melt\n",
"\n",
"L.units(\"lj\")\n", "L.units(\"lj\")\n",
"L.atom_style(\"atomic\")\n", "L.atom_style(\"atomic\")\n",
"L.atom_modify(\"map array\")\n", "L.atom_modify(\"map array\")\n",
@ -116,6 +73,13 @@
"L.run(10)" "L.run(10)"
] ]
}, },
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Visualize the initial state"
]
},
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
@ -205,9 +169,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"a index 2\")" "L.variable(\"a index 2\")"
@ -225,9 +187,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"t equal temp\")" "L.variable(\"t equal temp\")"
@ -283,9 +243,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"b index a b c\")" "L.variable(\"b index a b c\")"
@ -321,9 +279,16 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true "outputs": [],
"source": [
"L.lmp.command('variable i loop 10')"
]
}, },
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"i loop 10\")" "L.variable(\"i loop 10\")"
@ -379,7 +344,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "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" "L.runs[0].thermo"
] ]
}, },
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"dir(L.runs[0].thermo)"
]
},
{ {
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
@ -486,14 +460,48 @@
"## Saving session to as LAMMPS input file" "## 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", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "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\")" "L.write_script(\"in.output\")"
] ]
}, },
@ -503,7 +511,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"dir(L.runs[0].thermo)" "!cat in.output"
] ]
}, },
{ {
@ -530,7 +538,7 @@
"name": "python", "name": "python",
"nbconvert_exporter": "python", "nbconvert_exporter": "python",
"pygments_lexer": "ipython3", "pygments_lexer": "ipython3",
"version": "3.6.2" "version": "3.9.2"
} }
}, },
"nbformat": 4, "nbformat": 4,

93
python/examples/pylammps/interface_usage_bonds.ipynb
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@ -4,72 +4,29 @@
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"# Using LAMMPS with iPython and Jupyter" "# Example 3: 2D circle of particles inside of box with LJ walls"
] ]
}, },
{ {
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "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", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"## Installation" "## Setup system"
]
},
{
"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"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"from lammps import IPyLammps" "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\")" "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", "cell_type": "code",
"execution_count": null, "execution_count": null,
@ -144,6 +108,13 @@
"L.image(zoom=1.8)" "L.image(zoom=1.8)"
] ]
}, },
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Run simulation and visualize new state"
]
},
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
@ -254,9 +225,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"a index 2\")" "L.variable(\"a index 2\")"
@ -274,9 +243,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"t equal temp\")" "L.variable(\"t equal temp\")"
@ -332,9 +299,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"b index a b c\")" "L.variable(\"b index a b c\")"
@ -370,9 +335,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [ "source": [
"L.variable(\"i loop 10\")" "L.variable(\"i loop 10\")"
@ -428,7 +391,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"[x for x in dir(L.atoms[0]) if not x.startswith('__')]" "dir(L.atoms[0])"
] ]
}, },
{ {
@ -479,9 +442,7 @@
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
"metadata": { "metadata": {},
"collapsed": true
},
"outputs": [], "outputs": [],
"source": [] "source": []
} }
@ -502,7 +463,7 @@
"name": "python", "name": "python",
"nbconvert_exporter": "python", "nbconvert_exporter": "python",
"pygments_lexer": "ipython3", "pygments_lexer": "ipython3",
"version": "3.6.2" "version": "3.9.2"
} }
}, },
"nbformat": 4, "nbformat": 4,

10
python/examples/pylammps/simple.ipynb
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@ -4,7 +4,7 @@
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"# Using LAMMPS with PyLammps" "# Example 1: Using LAMMPS with PyLammps"
] ]
}, },
{ {
@ -27,7 +27,7 @@
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"## Example\n", "## Creating a new simulation\n",
"\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:" "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", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"### Visualizing the initial state\n", "## Visualizing the initial state\n",
"\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." "`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", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"### Running simulations\n", "## Running simulations\n",
"\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." "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", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"### Post-processing thermo output\n", "## Post-processing thermo output\n",
"\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:" "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:"
] ]