xref: /libCEED/examples/python/tutorial-6-shell.ipynb (revision edab612303ce5c583510db4ec9520fcda426d3c1)

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   "source": [
    "# Standalone libCEED examples\n",
    "\n",
    "This is a tutorial for [libCEED](https://github.com/CEED/libCEED/), the low-level API library for efficient high-order discretization methods developed by the co-design [Center for Efficient Exascale Discretizations](https://ceed.exascaleproject.org/) (CEED) of the [Exascale Computing Project](https://www.exascaleproject.org/) (ECP).\n",
    "\n",
    "While libCEED's focus is on high-order finite/spectral element method implementations, the approach is mostly algebraic and thus applicable to other discretizations in factored form, as explained in the [user manual](https://libceed.readthedocs.io/)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Common notation\n",
    "\n",
    "For most of our examples, the spatial discretization\n",
    "uses high-order finite elements/spectral elements, namely, the high-order Lagrange\n",
    "polynomials defined over $P$ non-uniformly spaced nodes, the\n",
    "Gauss-Legendre-Lobatto (GLL) points, and quadrature points $\\{q_i\\}_{i=1}^Q$, with\n",
    "corresponding weights $\\{w_i\\}_{i=1}^Q$ (typically the ones given by Gauss\n",
    "or Gauss-Lobatto quadratures, that are built in the library).\n",
    "\n",
    "We discretize the domain, $\\Omega \\subset \\mathbb{R}^d$ (with $d=1,2,3$,\n",
    "typically) by letting $\\Omega = \\bigcup_{e=1}^{N_e}\\Omega_e$, with $N_e$\n",
    "disjoint elements. For most examples we use unstructured meshes for which the elements\n",
    "are hexahedra (although this is not a requirement in libCEED).\n",
    "\n",
    "The physical coordinates are denoted by $\\mathbf{x}=(x,y,z)\\in\\Omega_e$,\n",
    "while the reference coordinates are represented as\n",
    "$\\boldsymbol{X}=(X,Y,Z) \\equiv (X_1,X_2,X_3) \\in I=[-1,1]^3$\n",
    "(for $d=3$).\n",
    "\n",
    "### Ex1-Volume\n",
    "\n",
    "#### Mathematical formulation\n",
    "\n",
    "This example is located in the subdirectory `examples/ceed`. It illustrates a\n",
    "simple usage of libCEED to compute the volume of a given body using a matrix-free\n",
    "application of the mass operator. Arbitrary mesh and solution orders in 1D, 2D and 3D\n",
    "are supported from the same code.\n",
    "\n",
    "This example shows how to compute line/surface/volume integrals of a 1D, 2D, or 3D\n",
    "domain $\\Omega$ respectively, by applying the mass operator to a vector of\n",
    "$1$s. It computes:\n",
    "\n",
    "$$\n",
    "   I = \\int_{\\Omega} 1 \\, dV .\n",
    "$$\n",
    "\n",
    "We write here the vector $u(x)\\equiv 1$ in the Galerkin approximation,\n",
    "and find the volume of $\\Omega$ as\n",
    "\n",
    "$$\n",
    "   \\sum_e \\int_{\\Omega_e} v(x) 1 \\, dV\n",
    "$$\n",
    "\n",
    "with $v(x) \\in \\mathcal{V}_p = \\{ v \\in H^{1}(\\Omega_e) \\,|\\, v \\in P_p(\\boldsymbol{I}), e=1,\\ldots,N_e \\}$,\n",
    "the test functions.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Executing the example\n",
    "\n",
    "Clone or download libCEED by running"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! git clone https://github.com/CEED/libCEED.git"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Then move to the libCEED folder"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd libCEED"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And compile the library by running"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! make"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Move to the examples folder "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd examples/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Then move to the standalone libCEED's examples folder"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd ceed/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And compile the examples by running"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! make"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now run `ex1-volume` by running"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Selected options: [command line option] : <current value>\n",
      "  Ceed specification [-c] : /cpu/self\n",
      "  Mesh dimension     [-d] : 3\n",
      "  Mesh order         [-m] : 4\n",
      "  Solution order     [-o] : 4\n",
      "  Num. 1D quadr. pts [-q] : 6\n",
      "  Approx. # unknowns [-s] : 262144\n",
      "  QFunction source   [-g] : gallery\n",
      "\n",
      "Mesh size: nx = 16, ny = 16, nz = 16\n",
      "Number of mesh nodes     : 274625\n",
      "Number of solution nodes : 274625\n",
      "Computing the quadrature data for the mass operator ... done.\n",
      "Computing the mesh volume using the formula: vol = 1^T.M.1 ... done.\n",
      "Exact mesh volume    :  2.3561944901923\n",
      "Computed mesh volume :  2.3561944901921\n",
      "Volume error         : -2.7444713168734e-13\n"
     ]
    }
   ],
   "source": [
    "! ./ex1-volume -d 3 -g"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This example shows how to compute line/surface/volume integrals of a 1D, 2D, or 3D domain Ω respectively, by applying the mass operator to a vector of 1s. The command line option `-d` specifies the dimensionality of the domain Ω. The option `-g` specifies that the mass operator is, in this case, selected from a gallery of available built-in operators in the library."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Ex2-Surface\n",
    "\n",
    "#### Mathematical formulation\n",
    "\n",
    "This example is located in the subdirectory `examples/ceed`. It computes the\n",
    "surface area of a given body using matrix-free application of a diffusion operator.\n",
    "Arbitrary mesh and solution orders in 1D, 2D and 3D are supported from the same code.\n",
    "\n",
    "Similarly to the Ex1-Volume example, it computes:\n",
    "\n",
    "\\begin{equation}\\label{eq-ex2-surface}\\tag{eq. 1}\n",
    "   I =  \\int_{\\partial \\Omega} 1 \\, dS ,\n",
    "\\end{equation}\n",
    "\n",
    "by applying the divergence theorem.\n",
    "In particular, we select $u(\\mathbf x) = x_0 + x_1 + x_2$, for which $\\nabla u = [1, 1, 1]^T$, and thus $\\nabla u \\cdot \\hat{\\mathbf n} = 1$.\n",
    "\n",
    "Given Laplace's equation,\n",
    "\n",
    "$$\n",
    "   \\nabla \\cdot \\nabla u = 0, \\textrm{ for  } \\mathbf{x} \\in \\Omega ,\n",
    "$$\n",
    "\n",
    "let us multiply by a test function $v$ and integrate by parts to obtain\n",
    "\n",
    "$$\n",
    "   \\int_\\Omega \\nabla v \\cdot \\nabla u \\, dV - \\int_{\\partial \\Omega} v \\nabla u \\cdot \\hat{\\mathbf n}\\, dS = 0 .\n",
    "$$\n",
    "\n",
    "Since we have chosen $u$ such that $\\nabla u \\cdot \\hat{\\mathbf n} = 1$, the boundary integrand is $v 1 \\equiv v$. Hence, similar to the previous example, we can evaluate the surface integral by applying the volumetric Laplacian as follows\n",
    "\n",
    "$$\n",
    "   \\int_\\Omega \\nabla v \\cdot \\nabla u \\, dV \\approx \\sum_e \\int_{\\partial \\Omega_e} v(x) 1 \\, dS .\n",
    "$$"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Executing the example\n",
    "\n",
    "Assuming the steps above, you should be in the `examples/ceed/` subdirectory and have already compiled the example.\n",
    "\n",
    "Now run `ex2-surface` by running "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Selected options: [command line option] : <current value>\n",
      "  Ceed specification [-c] : /cpu/self\n",
      "  Mesh dimension     [-d] : 3\n",
      "  Mesh order         [-m] : 4\n",
      "  Solution order     [-o] : 4\n",
      "  Num. 1D quadr. pts [-q] : 6\n",
      "  Approx. # unknowns [-s] : 262144\n",
      "  QFunction source   [-g] : gallery\n",
      "\n",
      "Mesh size: nx = 16, ny = 16, nz = 16\n",
      "Number of mesh nodes     : 274625\n",
      "Number of solution nodes : 274625\n",
      "Computing the quadrature data for the diffusion operator ... done.\n",
      "Computing the mesh surface area using the formula: sa = 1^T.|K.x| ... done.\n",
      "Exact mesh surface area    :  6\n",
      "Computed mesh surface area :  5.9773703490853\n",
      "Surface area error         : -0.022629650914673\n"
     ]
    }
   ],
   "source": [
    "! ./ex2-surface -d 3 -g"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This example computes the surface area of a given body using matrix-free application of a Laplace's (diffusion) operator. The command line option `-d` specifies the dimensionality of the domain Ω. The option `-g` specifies that the Laplace's operator is, in this case, selected from a gallery of available built-in operators in the library."
   ]
  }
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