Add species specific initialization. Bug fixes.

docs/examples/Magnetized_OCP/Magnetized_Plasma.ipynb

@@ -441,46 +441,29 @@
     "\tsnapshot interval time = 5.5000e-17 [s] = 9.2153e-02 w_p = 1.4667e-02 plasma periods\n",
     "\tTotal number of snapshots = 14000\n",
     "\n",
-    "Bernu ran a simulation for 244 plasma periods. We decided to run for a time 5 times longer. This is because we want to show the time slicing option in the Postprocessing phase.\n",
-    "\n",
-    "The estimated times, on this machine, are \n",
-    "\n",
-    "    ----------------------- Total Estimated Times ------------------------ \n",
-    "\n",
-    "\n",
-    "    Equilibration Time: 0 hrs 2 min 20 sec\n",
-    "\n",
-    "    Magnetization Time: 0 sec 0 msec 0 usec 0 nsec\n",
-    "\n",
-    "    Production Time: 0 hrs 33 min 11 sec\n",
-    "\n",
-    "    Total Run Time: 0 hrs 35 min 31 sec\n",
-    "\n",
-    "and the entire run requires\n",
-    "\n",
-    "    Total minimum required space: 1 GB 43 MB 1009 KB 192 bytes\n",
-    "\n",
-    "We are ready to start the simulation."
+    "Bernu ran a simulation for 244 plasma periods. We decided to run for a time 5 times longer. This is because we want to show the time slicing option in the Postprocessing phase."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
    "id": "d585f2ca",
-   "metadata": {},
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-03-22T20:31:15.612765Z",
+     "iopub.status.busy": "2024-03-22T20:31:15.611857Z",
+     "iopub.status.idle": "2024-03-22T20:31:15.632210Z",
+     "shell.execute_reply": "2024-03-22T20:31:15.630891Z",
+     "shell.execute_reply.started": "2024-03-22T20:31:15.612697Z"
+    }
+   },
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "{'platform': 'Darwin',\n",
-       " 'platform-release': '22.6.0',\n",
-       " 'architecture': 'arm64',\n",
-       " 'processor': 'arm',\n",
-       " 'ram': '32 GB'}"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Running on an arm processor with 32 GB GB of RAM\n"
+     ]
     }
    ],
    "source": [
@@ -493,7 +476,32 @@
     "info['processor']=platform.processor()\n",
     "info['ram']=str(round(psutil.virtual_memory().total / (1024.0 **3)))+\" GB\"\n",
     "\n",
-    "display(info)\n"
+    "print(f\"Running on an {info['processor']} processor with {info['ram']} GB of RAM\")\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "efabcbd6-07c6-43fc-8bf0-c2bd7dc34549",
+   "metadata": {},
+   "source": [
+    "The estimated times, on this machine, are \n",
+    "\n",
+    "    ----------------------- Total Estimated Times ------------------------ \n",
+    "\n",
+    "\n",
+    "    Equilibration Time: 0 hrs 2 min 20 sec\n",
+    "\n",
+    "    Magnetization Time: 0 sec 0 msec 0 usec 0 nsec\n",
+    "\n",
+    "    Production Time: 0 hrs 33 min 11 sec\n",
+    "\n",
+    "    Total Run Time: 0 hrs 35 min 31 sec\n",
+    "\n",
+    "and the entire run requires\n",
+    "\n",
+    "    Total minimum required space: 1 GB 43 MB 1009 KB 192 bytes\n",
+    "\n",
+    "We are ready to start the simulation."
    ]
   },
   {
@@ -1336,7 +1344,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },

sarkas/core.py

@@ -769,6 +769,11 @@ def set_species_attributes(self, species: list):
             List of :class:`sarkas.plasma.Species`.
 
         """
+
+        # DEV NOTE: This method could be defined in the Particles class, however, it is more convenient to have it here because it uses the correct unit system. 
+        # If I were to move it to the Particles class, I would need to pass the units as an argument. 
+        # TODO: It could be moved in the future. 
+
         # Loop over species and assign missing attributes
         # Collect species properties in single arrays