{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Running `vplanet`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:50.122924Z",
     "iopub.status.busy": "2023-08-23T23:27:50.122412Z",
     "iopub.status.idle": "2023-08-23T23:27:50.500538Z",
     "shell.execute_reply": "2023-08-23T23:27:50.499918Z"
    },
    "tags": [
     "hide_input"
    ]
   },
   "outputs": [],
   "source": [
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Overview"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:50.503644Z",
     "iopub.status.busy": "2023-08-23T23:27:50.503230Z",
     "iopub.status.idle": "2023-08-23T23:27:50.511792Z",
     "shell.execute_reply": "2023-08-23T23:27:50.511232Z"
    },
    "tags": [
     "hide_input"
    ]
   },
   "outputs": [],
   "source": [
    "# Tar up the example folder\n",
    "import glob\n",
    "import tarfile\n",
    "import os\n",
    "\n",
    "with tarfile.open(\"examples/CircumbinaryOrbit.tar.gz\", \"w:gz\") as tar:\n",
    "    for file in glob.glob(\"examples/CircumbinaryOrbit/*.in\"):\n",
    "        tar.add(file, arcname=os.path.basename(file))"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Let's run :py:class:`vplanet` on the :download:`CircumbinaryOrbit <examples/CircumbinaryOrbit.tar.gz>` example."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:50.514606Z",
     "iopub.status.busy": "2023-08-23T23:27:50.514293Z",
     "iopub.status.idle": "2023-08-23T23:27:50.699437Z",
     "shell.execute_reply": "2023-08-23T23:27:50.698777Z"
    }
   },
   "outputs": [],
   "source": [
    "import vplanet"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:50.702669Z",
     "iopub.status.busy": "2023-08-23T23:27:50.702324Z",
     "iopub.status.idle": "2023-08-23T23:27:51.348021Z",
     "shell.execute_reply": "2023-08-23T23:27:51.347328Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<vplanet.Output: kepler16>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "output = vplanet.run(\"examples/CircumbinaryOrbit/vpl.in\")\n",
    "output"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "The variable :py:obj:`output` is an instance of :py:class:`vplanet.Output`. We can peek at its contents by accessing the :py:class:`members <vplanet.Output.members>` attribute:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.351057Z",
     "iopub.status.busy": "2023-08-23T23:27:51.350630Z",
     "iopub.status.idle": "2023-08-23T23:27:51.355904Z",
     "shell.execute_reply": "2023-08-23T23:27:51.355333Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['sysname', 'bodies', 'log', 'path', 'primary', 'secondary', 'cbp', 'earth']"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "output.members"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "The properties :py:obj:`sysname`, :py:obj:`bodies`, and :py:obj:`path` are just strings, but :py:obj:`log` is a :py:class:`vplanet.Log` instance and the remaining four are :py:class:`vplanet.Body` instances."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## The log file"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Let's peek at :py:obj:`log`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.358443Z",
     "iopub.status.busy": "2023-08-23T23:27:51.358146Z",
     "iopub.status.idle": "2023-08-23T23:27:51.361861Z",
     "shell.execute_reply": "2023-08-23T23:27:51.361309Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<vplanet.Log: kepler16>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "log = output.log\n",
    "log"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Again, let's look at the :py:class:`members <vplanet.Log.members>` attribute:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.364710Z",
     "iopub.status.busy": "2023-08-23T23:27:51.364407Z",
     "iopub.status.idle": "2023-08-23T23:27:51.368113Z",
     "shell.execute_reply": "2023-08-23T23:27:51.367556Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['sysname', 'path', 'header', 'initial', 'final']"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "log.members"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "The :py:obj:`header`, :py:obj:`initial`, and :py:obj:`final` properties are instances of :py:class:`vplanet.LogStage`, containing information about specific stages of the simulation. Let's check out everything in the header of the log file:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.370904Z",
     "iopub.status.busy": "2023-08-23T23:27:51.370611Z",
     "iopub.status.idle": "2023-08-23T23:27:51.374409Z",
     "shell.execute_reply": "2023-08-23T23:27:51.373946Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Executable: /usr/share/miniconda/envs/vplot/bin/vplanet\n",
      "Version: Unknown\n",
      "SystemName: kepler16\n",
      "PrimaryInputFile: vpl.in\n",
      "BodyFile1: primary.in\n",
      "BodyFile2: secondary.in\n",
      "BodyFile3: cbp.in\n",
      "BodyFile4: earth.in\n",
      "AllowFilesToBeOverwitten: True\n",
      "MassUnits: Grams\n",
      "LengthUnits: Meters\n",
      "TimeUnits: Seconds\n",
      "AngleUnits: Radians\n",
      "VerbosityLevel: 5\n",
      "CrossoverDecadeForScientificNotation: 4\n",
      "NumberOfDigitsAfterDecimal: 6\n",
      "IntegrationMethod: Runge-Kutta4\n",
      "Direction: Forward\n",
      "TimeStep: 31557600.0\n",
      "StopTime: 3155760000.0\n",
      "OutputInterval: 315576.0\n",
      "UseVariableTimestep: True\n",
      "dEta: 0.01\n",
      "MinimumValueOfEccAndObl: 1e-10\n"
     ]
    }
   ],
   "source": [
    "for member in log.header.members:\n",
    "    print(\"{}: {}\".format(member, getattr(log.header, member)))"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Note that all of these can, of course, be accessed as regular properties:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.376835Z",
     "iopub.status.busy": "2023-08-23T23:27:51.376643Z",
     "iopub.status.idle": "2023-08-23T23:27:51.380265Z",
     "shell.execute_reply": "2023-08-23T23:27:51.379729Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/usr/share/miniconda/envs/vplot/bin/vplanet'"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "log.header.Executable"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Next, let's inspect the :py:obj:`initial` stage of the log file:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.383182Z",
     "iopub.status.busy": "2023-08-23T23:27:51.382742Z",
     "iopub.status.idle": "2023-08-23T23:27:51.386539Z",
     "shell.execute_reply": "2023-08-23T23:27:51.385969Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['system', 'primary', 'secondary', 'cbp', 'earth']"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "log.initial.members"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "There is one attribute per body, plus one for the system. Here's what's in :py:obj:`earth`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.389452Z",
     "iopub.status.busy": "2023-08-23T23:27:51.389012Z",
     "iopub.status.idle": "2023-08-23T23:27:51.394377Z",
     "shell.execute_reply": "2023-08-23T23:27:51.393824Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ActiveModules: BINARY\n",
      "ModuleBitSum: 1025\n",
      "Color: 0\n",
      "Mass: 5.972186e+24 kg\n",
      "Radius: 6378100.0 m\n",
      "RadGyra: 0.5\n",
      "RotAngMom: 4.416946e+33 kg m2 / sec\n",
      "BodyType: 0.0\n",
      "Density: 5495.038549 kg / m3\n",
      "HZLimitDryRunaway: -1.0 m\n",
      "HZLimRecVenus: -1.0\n",
      "HZLimRunaway: -1.0\n",
      "HZLimMoistGreenhouse: -1.0\n",
      "HZLimMaxGreenhouse: -1.0\n",
      "HZLimEarlyMars: -1.0\n",
      "Instellation: -1.0 kg / sec3\n",
      "Eccentricity: 0.009302\n",
      "OrbEnergy: 0.0 kg m2 / sec2\n",
      "MeanMotion: 1.877507e-07 1 / sec\n",
      "OrbPeriod: 33905420.0 sec\n",
      "SemiMajorAxis: 150905800000.0 m\n",
      "CriticalSemiMajorAxis: -1.0 m\n",
      "COPP: 0.0\n",
      "OrbAngMom: 0.0 kg m2 / sec\n",
      "ArgP: 3.970693 rad\n",
      "Inc: 0.005425 rad\n",
      "LongA: 3.112206 rad\n",
      "LongP: 0.799715 rad\n",
      "TotOrbEnergy: 0.0 kg m2 / sec2\n",
      "OrbPotEnergy: 0.0 kg m2 / sec2\n",
      "FreeEcc: 0.03\n",
      "FreeInc: 0.005381 rad\n",
      "LL13N0: 1.88385e-07 sec\n",
      "LL13K0: 1.870849e-07 sec\n",
      "LL13V0: 1.896763e-07 sec\n",
      "CBPR: 149950500000.0 m\n",
      "CBPZ: 0.03614 m\n",
      "CBPPhi: 6.253799 rad\n",
      "CBPRDot: -191.811805 m / sec\n",
      "CBPZDot: -152.682529 m / sec\n",
      "CBPPhiDot: 1.87673e-07 1 / sec\n",
      "R0: 149597900000.0 m\n",
      "CBPInsol: -1.0 F/F_Earth\n",
      "BinPriR: 8366404000.0 m\n",
      "BinPriPhi: 0.658853 rad\n",
      "BinSecR: 28406370000.0 m\n",
      "BinSecPhi: 3.800446 rad\n",
      "OutputOrder: Time[year] CBPR[au] ArgP[deg] LongA[deg] Eccentricity[] Inc[deg] LongP[deg]\n",
      "GridOutputOrder: None\n"
     ]
    }
   ],
   "source": [
    "for member in log.initial.earth.members:\n",
    "    print(\"{}: {}\".format(member, getattr(log.initial.earth, member)))"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "The other attributes similarly list all of the initial properties of each body (or the system)."
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Before we move on, note the type of each of these properties:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.397029Z",
     "iopub.status.busy": "2023-08-23T23:27:51.396612Z",
     "iopub.status.idle": "2023-08-23T23:27:51.401763Z",
     "shell.execute_reply": "2023-08-23T23:27:51.401234Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "vplanet.quantity.VPLANETQuantity"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(log.initial.earth.Inc)"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "This isn't a regular number, but an instance of :py:class:`vplanet.Quantity`, which is a subclasss of :py:class:`astropy.units.Quantity`. These objects have numerical values (either scalars or arrays) *and* units; plus, they automatically handle unit conversions when operated on."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.404567Z",
     "iopub.status.busy": "2023-08-23T23:27:51.404127Z",
     "iopub.status.idle": "2023-08-23T23:27:51.408668Z",
     "shell.execute_reply": "2023-08-23T23:27:51.408126Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.005425 rad\n",
      "0.31082960385847164 deg\n"
     ]
    }
   ],
   "source": [
    "inc = log.initial.earth.Inc\n",
    "print(inc)\n",
    "print(inc.to(\"deg\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.411275Z",
     "iopub.status.busy": "2023-08-23T23:27:51.410838Z",
     "iopub.status.idle": "2023-08-23T23:27:51.415411Z",
     "shell.execute_reply": "2023-08-23T23:27:51.414834Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "5.972186e+24 kg\n",
      "1.000003036118378 earthMass\n"
     ]
    }
   ],
   "source": [
    "mass = log.initial.earth.Mass\n",
    "print(mass)\n",
    "print(mass.to(\"Mearth\"))"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Check out the `astropy documentation <https://docs.astropy.org/en/stable/units/>`_ for more information on supported units."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## The bodies"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Going back to the :py:obj:`output` object, let's inspect its :py:obj:`earth` member:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.418047Z",
     "iopub.status.busy": "2023-08-23T23:27:51.417685Z",
     "iopub.status.idle": "2023-08-23T23:27:51.422656Z",
     "shell.execute_reply": "2023-08-23T23:27:51.422124Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<vplanet.Body: earth>"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "output.earth"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "This object contains the information of the arrays computed during the simulation, which are specified in the :py:obj:`saOutputOrder` line of the input files."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.425147Z",
     "iopub.status.busy": "2023-08-23T23:27:51.424857Z",
     "iopub.status.idle": "2023-08-23T23:27:51.428664Z",
     "shell.execute_reply": "2023-08-23T23:27:51.428214Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['name',\n",
       " 'infile',\n",
       " 'fwfile',\n",
       " 'bwfile',\n",
       " 'climfile',\n",
       " 'Time',\n",
       " 'CBPR',\n",
       " 'ArgP',\n",
       " 'LongA',\n",
       " 'Eccentricity',\n",
       " 'Inc',\n",
       " 'LongP']"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "output.earth.members"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "Let's check out one of them:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.430696Z",
     "iopub.status.busy": "2023-08-23T23:27:51.430503Z",
     "iopub.status.idle": "2023-08-23T23:27:51.436573Z",
     "shell.execute_reply": "2023-08-23T23:27:51.436026Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/latex": [
       "$[0.310855,~0.311045,~0.311036,~\\dots,~0.310957,~0.310998,~0.311019] \\; \\mathrm{{}^{\\circ}}$"
      ],
      "text/plain": [
       "<VPLANETQuantity [0.310855, 0.311045, 0.311036, ..., 0.310957, 0.310998,\n",
       "                  0.311019] deg>"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "output.earth.Inc"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "As before, these are :py:class:`vplanet.Quantity` instances, which behave like :py:class:`numpy` arrays except they have units attached."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-08-23T23:27:51.439216Z",
     "iopub.status.busy": "2023-08-23T23:27:51.438698Z",
     "iopub.status.idle": "2023-08-23T23:27:51.442869Z",
     "shell.execute_reply": "2023-08-23T23:27:51.442319Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[0.00542544 0.00542876 0.0054286  ... 0.00542722 0.00542794 0.00542831] rad\n"
     ]
    }
   ],
   "source": [
    "print(output.earth.Inc.to(\"rad\"))"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "That's it for this tutorial! Check out the `plotting tutorial <Plotting.ipynb>`_ for information on how to easily visualize all of these quantities."
   ]
  }
 ],
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