lammps/python/examples/pylammps/interface_usage_bonds.ipynb

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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Using LAMMPS with iPython and Jupyter"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "LAMMPS can be run interactively using iPython easily. This tutorial shows how to set this up."
   ]
  },
  {
   "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",
    "   python Make.py -m mpi -png -s exceptions -a file\n",
    "   make mode=shlib auto\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",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from lammps import IPyLammps"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L = IPyLammps()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# 2d circle of particles inside a box with LJ walls\n",
    "import math\n",
    "\n",
    "b = 0\n",
    "x = 50\n",
    "y = 20\n",
    "d = 20\n",
    "\n",
    "# careful not to slam into wall too hard\n",
    "\n",
    "v = 0.3\n",
    "w = 0.08\n",
    "                \n",
    "L.units(\"lj\")\n",
    "L.dimension(2)\n",
    "L.atom_style(\"bond\")\n",
    "L.boundary(\"f f p\")\n",
    "\n",
    "L.lattice(\"hex\", 0.85)\n",
    "L.region(\"box\", \"block\", 0, x, 0, y, -0.5, 0.5)\n",
    "L.create_box(1, \"box\", \"bond/types\", 1, \"extra/bond/per/atom\", 6)\n",
    "L.region(\"circle\", \"sphere\", d/2.0+1.0, d/2.0/math.sqrt(3.0)+1, 0.0, d/2.0)\n",
    "L.create_atoms(1, \"region\", \"circle\")\n",
    "L.mass(1, 1.0)\n",
    "\n",
    "L.velocity(\"all create 0.5 87287 loop geom\")\n",
    "L.velocity(\"all set\", v, w, 0, \"sum yes\")\n",
    "\n",
    "L.pair_style(\"lj/cut\", 2.5)\n",
    "L.pair_coeff(1, 1, 10.0, 1.0, 2.5)\n",
    "\n",
    "L.bond_style(\"harmonic\")\n",
    "L.bond_coeff(1, 10.0, 1.2)\n",
    "\n",
    "L.create_bonds(\"all\", \"all\", 1, 1.0, 1.5)\n",
    "\n",
    "L.neighbor(0.3, \"bin\")\n",
    "L.neigh_modify(\"delay\", 0, \"every\", 1, \"check yes\")\n",
    "\n",
    "L.fix(1, \"all\", \"nve\")\n",
    "\n",
    "L.fix(2, \"all wall/lj93 xlo 0.0 1 1 2.5 xhi\", x, \"1 1 2.5\")\n",
    "L.fix(3, \"all wall/lj93 ylo 0.0 1 1 2.5 yhi\", y, \"1 1 2.5\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.image(zoom=1.8)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.thermo_style(\"custom step temp epair press\")\n",
    "L.thermo(100)\n",
    "output = L.run(40000)\n",
    "L.image(zoom=1.8)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Queries about LAMMPS simulation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.system"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.system.natoms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.system.nbonds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.system.nbondtypes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.communication"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.fixes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.computes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.dumps"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.groups"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Working with LAMMPS Variables"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.variable(\"a index 2\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.variables"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.variable(\"t equal temp\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.variables"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "\n",
    "if sys.version_info < (3, 0):\n",
    "    # In Python 2 'print' is a restricted keyword, which is why you have to use the lmp_print function instead.\n",
    "    x = float(L.lmp_print('\"${a}\"'))\n",
    "else:\n",
    "    # In Python 3 the print function can be redefined.\n",
    "    # x = float(L.print('\"${a}\"')\")\n",
    "    \n",
    "    # To avoid a syntax error in Python 2 executions of this notebook, this line is packed into an eval statement\n",
    "    x = float(eval(\"L.print('\\\"${a}\\\"')\"))\n",
    "x"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.variables['t'].value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.eval(\"v_t/2.0\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.variable(\"b index a b c\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.variables['b'].value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.eval(\"v_b\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.variables['b'].definition"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.variable(\"i loop 10\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.variables['i'].value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.next(\"i\")\n",
    "L.variables['i'].value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.eval(\"ke\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Accessing Atom data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.atoms[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "[x for x in dir(L.atoms[0]) if not x.startswith('__')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.atoms[0].position"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.atoms[0].id"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.atoms[0].velocity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.atoms[0].force"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.atoms[0].type"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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