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Jolien128 committed Oct 22, 2024
2 parents cf5bc65 + 1ff1a9c commit b1f5633
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183 changes: 84 additions & 99 deletions docs/src/1_examples/3_3Dplots/plotModel3D.ipynb
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@@ -1,16 +1,31 @@
{
"cells": [
{
"cell_type": "markdown",
"id": "bb5e9049",
"metadata": {},
"source": [
"# Make a 3D plot of your model, that you can rotate, where you can zoom in, etc."
]
},
{
"cell_type": "markdown",
"id": "68b2f3fe",
"metadata": {},
"source": [
"### Importing packages"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "1aa00683-8e08-4c67-9fc2-e5d3cf73f385",
"id": "7f3f6af5",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"import numpy as np\n",
"\n",
"import plons\n",
"import plons.ConversionFactors_cgs as cgs\n",
"import plons.PhysicalQuantities as pq\n",
Expand All @@ -26,79 +41,68 @@
},
{
"cell_type": "markdown",
"id": "d8f69b7c-acb3-49f2-9b7a-20102e5598d7",
"id": "84c675d3",
"metadata": {},
"source": [
"EXAMPLE"
"### Retrieve the data of the example model"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "6a3ce4aa-0da4-443e-9fd3-e75c1fc9385a",
"metadata": {
"tags": []
},
"execution_count": 9,
"id": "e435d46a",
"metadata": {},
"outputs": [],
"source": [
"'''\n",
"Load in data\n",
"'''\n",
"model = 'v20e00'\n",
"run = '/lhome/jolienm/Documents/TierModels/R_Aql/cooling/binariesInPaper/finalAccrDisks/'+str(model)+'_T3000_res8_racc01/'\n",
"dump = 292\n",
" \n",
"setup = plons.LoadSetup(run, \"wind\")\n",
"dumpData = plons.LoadFullDump(os.path.join(run, f\"wind_%05d\" % dump), setup)\n",
"pos = dumpData['position']/cgs.au"
"prefix = 'wind'\n",
"model = 'v10e00'\n",
"loc = str(model)\n",
"dumpnumber = 584\n",
"dump = os.path.join(loc, f\"{prefix}_{dumpnumber:05d}\")\n"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "4a77e6e9-8e5c-47aa-8b6f-836696ea0c98",
"metadata": {
"tags": []
},
"execution_count": 10,
"id": "9b26a061",
"metadata": {},
"outputs": [],
"source": [
"'''\n",
"Load in data\n",
"'''\n",
"model = 'v20e00'\n",
"run = '/lhome/jolienm/Documents/TierModels/finalModelsHIcooling/'+str(model)+'/'\n",
"dump = 600\n",
" \n",
"setup = plons.LoadSetup(run, \"wind\")\n",
"dumpData = plons.LoadFullDump(os.path.join(run, f\"wind_%05d\" % dump), setup)\n",
"pos = dumpData['position']/cgs.au"
"!mkdir -p $loc"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "bddfdd1b-078a-41f1-b46b-5c05c15435fd",
"metadata": {
"tags": []
},
"execution_count": 12,
"id": "38f9fd84",
"metadata": {},
"outputs": [],
"source": [
"'''\n",
"Load in data\n",
"'''\n",
"run = '/STER/hydroModels/jolienm/modelsSlurm/planets/P40slowSilke_c/'\n",
"# run = '/lhome/jolienm/Documents/TierModels/R_Aql/cooling/binariesInPaper/bin_v20a06e00_c_MR/'\n",
"dump = 888\n",
" \n",
"setup = plons.LoadSetup(run, \"wind\")\n",
"dumpData = plons.LoadFullDump(os.path.join(run, f\"wind_%05d\" % dump), setup)\n",
"pos = dumpData['position']/cgs.au"
"%%capture\n",
"if not os.path.exists(dump):\n",
" # !wget \"https://github.com/Ensor-code/phantom-models/raw/refs/heads/main/Esseldeurs+2023/BinaryHighLucy/wind_00600?download=\" --output-document $dump\n",
" !wget 'https://raw.githubusercontent.com/Ensor-code/phantom-models/main/Malfait%2B2024a/v10e00/wind_v10e00' --output-document $dump\n",
"\n",
"infile = os.path.join(loc, f\"{prefix}.in\")\n",
"if not os.path.exists(infile):\n",
" !wget 'https://raw.githubusercontent.com/Ensor-code/phantom-models/main/Malfait%2B2024a/v10e00/wind.in' --output-document $infile\n",
"\n",
"setupfile = os.path.join(loc, f\"{prefix}.setup\")\n",
"if not os.path.exists(setupfile):\n",
" !wget 'https://raw.githubusercontent.com/Ensor-code/phantom-models/main/Malfait%2B2024a/v10e00/wind.setup' --output-document $setupfile\n"
]
},
{
"cell_type": "markdown",
"id": "f3ef2edb",
"metadata": {},
"source": [
"### Load in the data of your model"
]
},
{
"cell_type": "code",
"execution_count": 22,
"id": "fbc44d90-1823-437e-b0e9-aa120bb4731a",
"execution_count": 15,
"metadata": {
"tags": []
},
Expand All @@ -107,27 +111,34 @@
"'''\n",
"Load in data\n",
"'''\n",
"run = '/STER/hydroModels/matse/Binary6Lucy/'\n",
"# run = '/lhome/jolienm/Documents/TierModels/R_Aql/cooling/binariesInPaper/bin_v20a06e00_c_MR/'\n",
"dump = 600\n",
" \n",
"setup = plons.LoadSetup(run, \"wind\")\n",
"dumpData = plons.LoadFullDump(os.path.join(run, f\"wind_%05d\" % dump), setup)\n",
"setup = plons.LoadSetup(loc, prefix)\n",
"dumpData = plons.LoadFullDump(dump, setup)\n",
"pos = dumpData['position']/cgs.au"
]
},
{
"cell_type": "markdown",
"id": "7bf88093",
"metadata": {},
"source": [
"### Make the interactive 3D plot of the full data\n",
"(if the widget can't load, do pip install ipympl)\n",
"\n",
"In the interactive plot, you can change the point_size, opacity, colorbar min and max value in '> Points' "
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "cfe4d2ca-3de1-4505-ac8b-00aa82791804",
"execution_count": 16,
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "a0c966e15b8f46909cddb42b14515172",
"model_id": "db898d1843744a2392822488892faddd",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -141,7 +152,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "b02cc0c63fe54abcb8a2dcc30886c3d0",
"model_id": "6cd2ccfe9b9343d3b14999f9c786a113",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -154,8 +165,6 @@
}
],
"source": [
"## Make 3D plot of full data\n",
"\n",
"#choose colorbar limits (can also be changed interactively)\n",
"colMin = -20\n",
"colMax = -12\n",
Expand All @@ -164,41 +173,25 @@
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7b25800a-4392-4ff7-92ac-f730083d18bd",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "5afab499-2263-4f65-b77c-0baddd747797",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "2dc3d072-e954-47e3-b625-f9df80f8de67",
"cell_type": "markdown",
"id": "46af1461",
"metadata": {},
"outputs": [],
"source": []
"source": [
"### Make the same plot, but only include that within a certain range of projected velocities\n",
"This is usefull when you want to compare to channel maps, that only include data with a certain projected velocity (absolute value of velocity, so - and + side are plot)"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "326df486-96aa-4f93-9940-8d965a046810",
"execution_count": 7,
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "f79f3178c1d5411cb539a0f928ef8a5d",
"model_id": "89281a157b65447c8fb82baad0742635",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -212,7 +205,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "7385a20f0e6a406894856b120b5bfb5f",
"model_id": "16427dfb27b74d93ab6eb083f0f31474",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -225,25 +218,17 @@
}
],
"source": [
"# Make 3D plot of data within certain velocity (now absolute value) range to get dat in certain channel map\n",
"vmin = 0\n",
"# Make 3D plot of data within certain velocity (absolute value) range to get dat in certain channel map\n",
"vmin = 4\n",
"vmax = 7\n",
"#Fill in v_y, v_z, v_x or other v_array depending on inclincation\n",
"p3.makePlot_vDir(dumpData['vz'], dumpData['r'], dumpData['rho'], pos, vmin, vmax,pt_size =1,opty=0.5)"
"p3.makePlot_vDir(dumpData['vz'], dumpData['r'], dumpData['rho'], pos, vmin, vmax,pt_size =2,opty=0.7)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6450e529-3412-487e-b5f5-caaba05499e1",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
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