add a comment and minor edits

Author: SarahAlidoost

notebooks/run_model_in_notebook.ipynb

@@ -22,14 +22,23 @@
     "import time"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Path to STEMMUS_SCOPE\n",
+    "\n",
+    "STEMMUS_SCOPE executable file is located in the **private** repository on GitHub https://github.com/EcoExtreML/STEMMUS_SCOPE. You need to clone the repository locally and specify the path to it in the cell below. Make sure you have right access to the repository. "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
     "# path to executable\n",
-    "root_path_to_model = Path(Path.home(), \"STEMMUS_SCOPE\")"
+    "path_to_model = Path(\"path_to_STEMMUS_SCOPE_repository\")"
    ]
   },
   {
@@ -41,13 +50,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
     "# the user must provide the correct path\n",
     "# path to config file\n",
-    "config_file_path = root_path_to_model / \"config_file_snellius.txt\"\n",
+    "config_file_path = path_to_model / \"config_file_snellius.txt\"\n",
     "# create an empty dict\n",
     "config = {}\n",
     "with open(config_file_path, \"r\") as f:\n",
@@ -58,7 +67,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -73,7 +82,7 @@
        " 'DurationSize': '17520'}"
       ]
      },
-     "execution_count": 16,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -84,22 +93,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "{'SoilPropertyPath': '/projects/0/einf2480/model_parameters/soil_property/',\n",
-       " 'InputPath': '/scratch-shared/ecoextreml/stemmus_scope/input/',\n",
-       " 'OutputPath': '/scratch-shared/ecoextreml/stemmus_scope/output/',\n",
-       " 'ForcingPath': '/projects/0/einf2480/forcing/plumber2_data/',\n",
+       "{'SoilPropertyPath': '/home/sarah/temp/ecoextreml/data/model_parameters/soil_property/',\n",
+       " 'InputPath': '/home/sarah/temp/ecoextreml/input/',\n",
+       " 'OutputPath': '/home/sarah/temp/ecoextreml/output/',\n",
+       " 'ForcingPath': '/home/sarah/temp/ecoextreml/data/forcing/plumber2_data/',\n",
        " 'ForcingFileName': 'FI-Hyy_1996-2014_FLUXNET2015_Met.nc',\n",
-       " 'VegetationPropertyPath': '/projects/0/einf2480/model_parameters/vegetation_property/',\n",
+       " 'VegetationPropertyPath': '/home/sarah/temp/ecoextreml/data/model_parameters/vegetation_property/',\n",
        " 'DurationSize': '20'}"
       ]
      },
-     "execution_count": 17,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -119,7 +128,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -152,15 +161,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Prepare work directory /scratch-shared/ecoextreml/stemmus_scope/input/NL-Hor_20220511_1608 for the station: NL-Hor\n",
-      "Prepare work directory /scratch-shared/ecoextreml/stemmus_scope/input/ZA-Kru_20220511_1608 for the station: ZA-Kru\n"
+      "Prepare work directory /home/sarah/temp/ecoextreml/input/NL-Hor_20220513_1256 for the station: NL-Hor\n",
+      "Prepare work directory /home/sarah/temp/ecoextreml/input/ZA-Kru_20220513_1256 for the station: ZA-Kru\n"
      ]
     }
    ],
@@ -190,38 +199,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Run STEMMUS-SCOPE with the forcing: NL-Hor_2008-2011_FLUXNET2015_Met.nc\n",
-      "Opening log file:  /scratch-shared/ecoextreml/stemmus_scope/input/NL-Hor_20220511_1608/java.log.8335\n",
-      "Reading config from /scratch-shared/ecoextreml/stemmus_scope/input/NL-Hor_20220511_1608/NL-Hor_20220511_1608_config.txt\n",
-      "\n",
-      " The calculations start now \n",
-      "Run STEMMUS-SCOPE with the forcing: ZA-Kru_2000-2002_FLUXNET2015_Met.nc\n",
-      "Opening log file:  /scratch-shared/ecoextreml/stemmus_scope/input/ZA-Kru_20220511_1608/java.log.9161\n",
-      "Reading config from /scratch-shared/ecoextreml/stemmus_scope/input/ZA-Kru_20220511_1608/ZA-Kru_20220511_1608_config.txt\n",
-      "\n",
-      " The calculations start now \n",
-      " The calculations end now \r"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# generate a text file\n",
-    "root_path = Path().resolve().parent\n",
     "str.split(\"/\")[-1]\n",
     "for ncfile in forcing_filenames_list:\n",
     "    path_to_config = config_path_dict[ncfile]\n",
     "    # set matlab log dir to slurm, otherwise java.log files are created in user home dir\n",
     "    os.environ['MATLAB_LOG_DIR'] = str(work_dir_dict[ncfile])\n",
     "    # run the model\n",
     "    print(f\"Run STEMMUS-SCOPE with the forcing: {ncfile}\")\n",
-    "    result = subprocess.run([f\"exe/STEMMUS_SCOPE {path_to_config}\"], cwd = root_path_to_model, shell=True)\n",
+    "    result = subprocess.run([f\"exe/STEMMUS_SCOPE {path_to_config}\"], cwd = path_to_model, shell=True)\n",
     "    result.check_returncode()"
    ]
   },
@@ -268,7 +258,7 @@
    ],
    "source": [
     "# convert csv files to nc files\n",
-    "path_to_utils = Path(root_path_to_model, \"utils/csv_to_nc\")\n",
+    "path_to_utils = Path(path_to_model, \"utils/csv_to_nc\")\n",
     "for ncfile in forcing_filenames_list:\n",
     "    path_to_config = config_path_dict[ncfile]\n",
     "    result = subprocess.run([\"python\", Path(path_to_utils, \"generate_netcdf_files.py\"),\n",