Merge branch 'debug'

examples/.gitignore

@@ -0,0 +1 @@
+*/param.*

examples/Basic_Simulation/initial_conditions.ipynb

@@ -0,0 +1,155 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2c4f59ea-1251-49f6-af1e-5695d7e25500",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import swiftest\n",
+    "import numpy as np\n",
+    "from numpy.random import default_rng"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6054c7ab-c748-4b39-9fee-d8b27326f497",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Initialize the simulation object as a variable\n",
+    "sim = swiftest.Simulation(tstart=0.0, tstop=10.0, dt=0.005, tstep_out=1.0, fragmentation=True, minimum_fragment_mass = 2.5e-11, mtiny=2.5e-8)\n",
+    "sim.get_parameter()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1c122676-bacb-447c-bc37-5ef8019be0d0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Add the modern planets and the Sun using the JPL Horizons Database\n",
+    "sim.add_solar_system_body([\"Sun\",\"Mercury\",\"Venus\",\"Earth\",\"Mars\",\"Jupiter\",\"Saturn\",\"Uranus\",\"Neptune\",\"Pluto\"])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "97fe9f16-bc2e-443c-856b-7dacb1267f2d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Add 5 user-defined massive bodies\n",
+    "npl         = 5\n",
+    "density_pl  = 3000.0 / (sim.param['MU2KG'] / sim.param['DU2M'] ** 3)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "566a742e-3935-484d-9c7a-87310b6aaa3a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "name_pl     = [\"MassiveBody_01\", \"MassiveBody_02\", \"MassiveBody_03\", \"MassiveBody_04\", \"MassiveBody_05\"]\n",
+    "a_pl        = default_rng().uniform(0.3, 1.5, npl)\n",
+    "e_pl        = default_rng().uniform(0.0, 0.3, npl)\n",
+    "inc_pl      = default_rng().uniform(0.0, 90, npl)\n",
+    "capom_pl    = default_rng().uniform(0.0, 360.0, npl)\n",
+    "omega_pl    = default_rng().uniform(0.0, 360.0, npl)\n",
+    "capm_pl     = default_rng().uniform(0.0, 360.0, npl)\n",
+    "GM_pl       = (np.array([6e23, 8e23, 1e24, 3e24, 5e24]) / sim.param['MU2KG']) * sim.GU\n",
+    "R_pl        = np.full(npl, (3 * (GM_pl / sim.GU) / (4 * np.pi * density_pl)) ** (1.0 / 3.0))\n",
+    "Rh_pl       = a_pl * ((GM_pl) / (3 * sim.GU)) ** (1.0 / 3.0)\n",
+    "Ip1_pl      = [0.4, 0.4, 0.4, 0.4, 0.4]\n",
+    "Ip2_pl      = [0.4, 0.4, 0.4, 0.4, 0.4]\n",
+    "Ip3_pl      = [0.4, 0.4, 0.4, 0.4, 0.4]\n",
+    "rotx_pl     = [0.0, 0.0, 0.0, 0.0, 0.0]\n",
+    "roty_pl     = [0.0, 0.0, 0.0, 0.0, 0.0]\n",
+    "rotz_pl     = [0.0, 0.0, 0.0, 0.0, 0.0]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d2c14121-e5b4-45bd-99a7-acde0ee77955",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sim.add_body(name_pl, a_pl, e_pl, inc_pl, capom_pl, omega_pl, capm_pl, GMpl=GM_pl, Rpl=R_pl, rhill=Rh_pl, Ip1=Ip1_pl, Ip2=Ip2_pl, Ip3=Ip3_pl, rotx=rotx_pl, roty=roty_pl, rotz=rotz_pl)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b3f979b3-5238-492f-8589-0cf5d9a3c2bc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Add 10 user-defined test particles\n",
+    "ntp = 10"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5777c1bb-8c91-452a-8869-ce6f951b33a3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "name_tp     = [\"TestParticle_01\", \"TestParticle_02\", \"TestParticle_03\", \"TestParticle_04\", \"TestParticle_05\", \"TestParticle_06\", \"TestParticle_07\", \"TestParticle_08\", \"TestParticle_09\", \"TestParticle_10\"]\n",
+    "a_tp        = default_rng().uniform(0.3, 1.5, ntp)\n",
+    "e_tp        = default_rng().uniform(0.0, 0.3, ntp)\n",
+    "inc_tp      = default_rng().uniform(0.0, 90, ntp)\n",
+    "capom_tp    = default_rng().uniform(0.0, 360.0, ntp)\n",
+    "omega_tp    = default_rng().uniform(0.0, 360.0, ntp)\n",
+    "capm_tp     = default_rng().uniform(0.0, 360.0, ntp)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8df4bcb7-46a6-402a-b10f-f37c55a0fdee",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sim.add_body(name_tp, a_tp, e_tp, inc_tp, capom_tp, omega_tp, capm_tp)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fd30638b-6868-4162-bc05-1011bb255968",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Run the simulation\n",
+    "sim.run()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "swiftest",
+   "language": "python",
+   "name": "swiftest"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

python/swiftest/swiftest/simulation_class.py

@@ -2325,12 +2325,14 @@ def _combine_and_fix_dsnew(self,dsnew):
                 warnings.warn("Non-unique names detected for bodies. The Dataset will be dimensioned by integer id instead of name.")
                 warnings.warn("Consider using unique names instead.")
 
+        self.data = xr.combine_by_coords([self.data, dsnew])
+
         if self.param['OUT_TYPE'] == "NETCDF_DOUBLE":
             dsnew = io.fix_types(dsnew, ftype=np.float64)
+            self.data = io.fix_types(self.data, ftype=np.float64)
         elif self.param['OUT_TYPE'] == "NETCDF_FLOAT":
             dsnew = io.fix_types(dsnew, ftype=np.float32)
-
-        self.data = xr.combine_by_coords([self.data, dsnew])
+            self.data = io.fix_types(self.data, ftype=np.float32)
 
         def get_nvals(ds):
             if "name" in ds.dims:
@@ -2348,6 +2350,8 @@ def get_nvals(ds):
         dsnew = get_nvals(dsnew)
         self.data = get_nvals(self.data)
 
+        self.data = self.data.sortby("id")
+
         return dsnew
 
     def read_param(self,