Clarify upload expectations for BM 1 to 4

usnistgov · Aug 10, 2023 · ed9f832 · ed9f832
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diff --git a/benchmarks/benchmark1.ipynb b/benchmarks/benchmark1.ipynb
@@ -127,9 +127,7 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "source": [
     " \n",
     " * [Overview](#Overview)\n",
@@ -244,9 +242,7 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "source": [
     "Because $c$ must obey a continuity equation -- the flux of $c$ is conserved -- the evolution of $c$ is given by the Cahn-Hilliard equation [[1][cahn1961spinodal]], which is derived from an Onsager force-flux relationship <span data-proofer-ignore>[[2][balluffi2005kinetics]]</span>:\n",
     "$$\n",
@@ -315,9 +311,7 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "source": [
     "Several boundary conditions, initial conditions and computational domain geometries\n",
     "are used to challenge different aspects of the numerical solver implementation. We test four combinations that are increasingly difficult to solve: two\n",
@@ -404,9 +398,7 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "source": [
     "A T-shaped region with zero flux boundary conditions and with dimensions, $a=b=100$  and  $c=d=20$."
    ]
@@ -1127,9 +1119,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/benchmarks/benchmark1.ipynb.raw.html b/benchmarks/benchmark1.ipynb.raw.html
diff --git a/benchmarks/benchmark2.ipynb b/benchmarks/benchmark2.ipynb
@@ -263,7 +263,7 @@
     "isotropic. In addition, we again choose $c_{\\alpha}=0.3$ and\n",
     "$c_{\\beta}=0.7$, and further specify $\\kappa_{c}=\\kappa_{\\eta}=3$,\n",
     "$\\varrho=\\sqrt[]{2}$, $w=1$, and $\\alpha=5$.  For these values, the\n",
-    "diffuse interface between $0.1<\\eta<0.9$ has a width of of 4.2 units.\n",
+    "diffuse interface between $0.1<\\eta<0.9$ has a width of 4.2 units.\n",
     "\n",
     "[ZHU]: http://dx.doi.org/10.1016/j.actamat.2004.02.032\n",
     "[KKS]: https://doi.org/10.1103/PhysRevE.60.7186\n",
@@ -284,9 +284,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -476,9 +474,7 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "source": [
     "Several boundary conditions, initial conditions and computational domain geometries\n",
     "are used to challenge different aspects of the numerical solver implementation. We test four combinations that are increasingly difficult to solve: two\n",
@@ -566,9 +562,7 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "source": [
     "A T-shaped region with zero flux boundary conditions and with dimensions, $a=b=100$  and  $c=d=20$."
    ]
@@ -1291,9 +1285,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -1400,6 +1392,53 @@
     "plot_3d_sphere(eta_func)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Submission Guidelines\n",
+    "\n",
+    "Please follow these [upload instructions](https://github.com/usnistgov/pfhub/blob/master/upload.md).\n",
+    "\n",
+    "In addition to that specified, further data to upload can include a YouTube video, snapshots of the simulation at different times, or the field variable at each point in the entire domain at different times. This auxiliary data is not required, but will help others view your work.\n",
+    "\n",
+    "### Part (a)\n",
+    "\n",
+    "Part (a) requires running the simulation to equilibrium, and the following data should be collected.\n",
+    "\n",
+    "- The free energy integrated over the whole domain, $\\mathcal{F}$, at each timestep. \n",
+    "\n",
+    "  The free energy data should be recorded in a file named `free_energy_2a.csv`. This plain-text CSV file ([comma-separated values](https://en.wikipedia.org/wiki/Comma-separated_values)) must have the following format -- note the column headings and lack of spaces,\n",
+    "  and that there is no requirement to fix the number of digits for each column or row.\n",
+    "\n",
+    "  ```csv\n",
+    "  time,free_energy\n",
+    "  0.0,6400.005\n",
+    "  5.000000001,6300.1\n",
+    "  ...\n",
+    "  10000,199.8753480000002\n",
+    "  ...\n",
+    "  ```\n",
+    "\n",
+    "- The composition field, $c$, and each phase-field, $\\eta_i$, at each grid point in the domain at the following times (aspirational):\n",
+    "  - 1,000\n",
+    "  - 10,000\n",
+    "  - 100,000\n",
+    "  - 1,000,000\n",
+    "\n",
+    "  You may provide this data in whatever format you consider \"most useful,\" e.g. a checkpoint file in the format native to your phase-field simulation framework, and the PFHub operations team will attempt to handle it correctly.\n",
+    "  Optionally, please consider also uploading a VTK ImageData file. If your mesh is unstructured or irregular, this will require appropriate interpolation prior to export. This can be accomplished using common scientific visualization software, e.g. using the PointVolumeInterpolator filter in ParaView.<sup>&#8225;</sup>\n",
+    "\n",
+    "  The names of these data files should encode the time and problem, e.g.,\n",
+    "  `raw_data_2a.0001000.vti`, `raw_data_2a.0010000.vti`, `raw_data_2a.0100000.vti`, and `raw_data_2a.1000000.vti`.\n",
+    "\n",
+    "<sup>&#8225;</sup>: Any mention of commercial products within NIST web pages is for information only; it does not imply recommendation or endorsement by NIST.\n",
+    "\n",
+    "### Parts (b) through (d)\n",
+    "\n",
+    "The same data as in Part (a) are required, stored in appropriately named files: please follow the same instructions, modifying \"2a\" with the appropriate letter (\"2b\", \"2c\", etc.)."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1416,9 +1455,7 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "source": [
     "## Feedback\n",
     "\n",
@@ -1429,7 +1466,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "outputs": [],
    "source": []
@@ -1452,9 +1492,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.4"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }