Merge pull request #30 from nvaytet/new_test_data

Update notebooks for new test data
osyris-project · Oct 2, 2021 · d1b6670 · d1b6670
2 parents e9064a8 + 17b9155
commit d1b6670
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diff --git a/docs/basics.ipynb b/docs/basics.ipynb
@@ -17,7 +17,9 @@
    "source": [
     "## Reading a RAMSES output\n",
     "\n",
-    "Import the `osyris` module and load the output of your choice (this will be output number `71` in this example)."
+    "Import the `osyris` module and load the output of your choice.\n",
+    "We are loading output number `8` from a simulation of a collapsing system of gas,\n",
+    "that is forming young stars in its core."
    ]
   },
   {
@@ -53,7 +55,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(71, scale=\"au\", path=\"osyrisdata\")"
+    "data = osyris.Dataset(8, scale=\"au\", path=\"osyrisdata/starformation\")"
    ]
   },
   {
@@ -127,9 +129,9 @@
     "\n",
     "## Creating a 2D histogram\n",
     "\n",
-    "We now wish to plot a 2d histogram of the logarithm of density versus logarithm of gas temperature,\n",
+    "We now wish to plot a 2d histogram of the logarithm of density versus logarithm of magnetic field magnitude,\n",
     "for all the cells inside the computational domain.\n",
-    "We also use a logarithmic colormap which represents the cell counts in the $(\\rho,T)$ plane"
+    "We also use a logarithmic colormap which represents the cell counts in the $(\\rho,B)$ plane"
    ]
   },
   {
@@ -138,7 +140,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram(data[\"hydro\"][\"density\"], data[\"hydro\"][\"temperature\"],\n",
+    "osyris.histogram(data[\"hydro\"][\"density\"], data[\"hydro\"][\"B_field\"],\n",
     "                 norm=\"log\", loglog=True)"
    ]
   },
@@ -148,7 +150,7 @@
    "source": [
     "## Simple cut plane\n",
     "\n",
-    "The goal here is to create a 2D gas density slice, 100 au wide, through the plane normal to `z`,\n",
+    "The goal here is to create a 2D gas density slice, 2000 au wide, through the plane normal to `z`,\n",
     "that passes through the center of the young star forming system.\n",
     "\n",
     "We first need to define where the center of the system is.\n",
@@ -180,7 +182,7 @@
    "outputs": [],
    "source": [
     "osyris.plane({\"data\": data[\"hydro\"][\"density\"], \"norm\": \"log\"},\n",
-    "             dx=100 * osyris.units('au'),\n",
+    "             dx=2000 * osyris.units('au'),\n",
     "             origin=center,\n",
     "             direction=\"z\")"
    ]

diff --git a/docs/data_structures.ipynb b/docs/data_structures.ipynb
@@ -40,7 +40,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(71, scale=\"au\", path=\"osyrisdata\").load()"
+    "data = osyris.Dataset(8, scale=\"au\", path=\"osyrisdata/starformation\").load()"
    ]
   },
   {

diff --git a/docs/loading_data.ipynb b/docs/loading_data.ipynb
@@ -32,7 +32,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(71, scale=\"au\", path=\"osyrisdata\").load()"
+    "path = \"osyrisdata/starformation\"\n",
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load()"
    ]
   },
   {
@@ -62,7 +63,7 @@
     "\n",
     "It is possible to load only a subset of the cells, by using custom functions to perform the selection.\n",
     "\n",
-    "As an example, to load all the cells with $\\rho > 10^{-13}~{\\rm g~cm}^{-3}$, we use a selection criterion"
+    "As an example, to load all the cells with $\\rho > 10^{-15}~{\\rm g~cm}^{-3}$, we use a selection criterion"
    ]
   },
   {
@@ -71,8 +72,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(71, scale=\"au\", path=\"osyrisdata\").load(\n",
-    "    select={\"hydro\": {\"density\": lambda d : d > 1.0e-13 * osyris.units('g/cm**3')}})"
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load(\n",
+    "    select={\"hydro\": {\"density\": lambda d : d > 1.0e-15 * osyris.units('g/cm**3')}})"
    ]
   },
   {
@@ -105,9 +106,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(71, scale=\"au\", path=\"osyrisdata\").load(\n",
-    "    select={\"hydro\": {\"density\": lambda d : d > 1.0e-13 * osyris.units('g/cm**3')},\n",
-    "            \"amr\": {\"xyz_x\": lambda x : x > 5500. * osyris.units('au')}})"
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load(\n",
+    "    select={\"hydro\": {\"density\": lambda d : d > 1.0e-16 * osyris.units('g/cm**3')},\n",
+    "            \"amr\": {\"xyz_x\": lambda x : x > 1500. * osyris.units('au')}})"
    ]
   },
   {
@@ -117,7 +118,7 @@
    "outputs": [],
    "source": [
     "osyris.plane({\"data\": data[\"hydro\"][\"density\"], \"norm\": \"log\"},\n",
-    "             dx=200 * osyris.units('au'),\n",
+    "             dx=1000 * osyris.units('au'),\n",
     "             origin=data[\"amr\"][\"xyz\"][np.argmax(data[\"hydro\"][\"density\"]).values],\n",
     "             direction='z')"
    ]
@@ -137,7 +138,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(71, scale=\"au\", path=\"osyrisdata\").load(\n",
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load(\n",
     "    select={\"hydro\": {\"density\": False}})\n",
     "\"density\" in data[\"hydro\"]"
    ]
@@ -158,7 +159,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(71, scale=\"au\", path=\"osyrisdata\").load(\n",
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load(\n",
     "    select={\"hydro\": False})\n",
     "data"
    ]
@@ -184,16 +185,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(71, scale=\"au\", path=\"osyrisdata\").load(\n",
-    "    select={\"amr\": {\"level\": lambda l : l < 10}})\n",
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load(\n",
+    "    select={\"amr\": {\"level\": lambda l : l < 7}})\n",
     "data[\"amr\"][\"level\"]"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "will only read levels 1 to 9, while"
+    "will only read levels 1 to 6, while"
    ]
   },
   {
@@ -202,16 +203,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(71, scale=\"au\", path=\"osyrisdata\").load(\n",
-    "    select={\"amr\": {\"level\": lambda l : np.logical_and(l > 9, l < 13)}})\n",
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load(\n",
+    "    select={\"amr\": {\"level\": lambda l : np.logical_and(l > 5, l < 9)}})\n",
     "data[\"amr\"][\"level\"]"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "will read levels 1 to 12, but will then discard all cells with `level` < 10.\n",
+    "will read levels 1 to 8, but will then discard all cells with `level` < 6.\n",
     "\n",
     "### Loading only selected CPU outputs\n",
     "\n",
@@ -224,7 +225,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(71, scale=\"au\", path=\"osyrisdata\").load(\n",
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load(\n",
     "    cpu_list=[1, 2, 10, 4, 5])"
    ]
   },
@@ -235,7 +236,7 @@
    "outputs": [],
    "source": [
     "osyris.plane({\"data\": data[\"hydro\"][\"density\"], \"norm\": \"log\"},\n",
-    "             dx=400 * osyris.units(\"au\"),\n",
+    "             dx=2000 * osyris.units(\"au\"),\n",
     "             origin=data[\"amr\"][\"xyz\"][np.argmax(data[\"hydro\"][\"density\"]).values],\n",
     "             direction='z')"
    ]