Updating for error hunt results

docs/sources/modules/src/scaleup_model.md

@@ -74,7 +74,7 @@ growth numbers
 A dataframe with all important growth numbers
 
 ### .determine_average_productivity
-[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L200)
+[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L210)
 ```python
 .determine_average_productivity(
    growth_rate_fraction, days_to_run, percent_usable_for_growth,
@@ -104,7 +104,7 @@ per area and day and the harvest intervall
 
 
 ### self_shading
-[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L255)
+[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L265)
 ```python
 .self_shading(
    density
@@ -131,7 +131,7 @@ the growth rate fraction
 
 
 ### calculate_seaweed_need
-[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L274)
+[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L284)
 ```python
 .calculate_seaweed_need(
    global_pop, calories_per_person_per_day, food_waste,
@@ -162,7 +162,7 @@ limited by the iodine content of the seaweed
 
 
 ### seaweed_farm_area_per_day
-[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L305)
+[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L315)
 ```python
 .seaweed_farm_area_per_day(
    day
@@ -188,7 +188,7 @@ the area that can be built per day
 
 
 ### logistic_curve
-[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L326)
+[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L336)
 ```python
 .logistic_curve(
    x, max_L, k, x0, off
@@ -214,7 +214,7 @@ Returns
 
 
 ### run_model
-[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L341)
+[source](https://github.com/allfed/Seaweed-Upscaling-Model/blob/master/src/scaleup_model.py/#L351)
 ```python
 .run_model(
    optimal_growth_rate, days_to_run, global_pop, calories_per_person_per_day,

mkgendocs.yml

@@ -9,6 +9,17 @@ copyright: ALLFED
 
 #This specifies the autogeneration portion
 pages:
+  - page: "modules/src/scaleup_model.md"
+    source: "src/scaleup_model.py"
+    classes:
+      - SeaweedScaleUpModel
+    functions:
+      - self_shading
+      - calculate_seaweed_need
+      - seaweed_farm_area_per_day
+      - logistic_curve
+      - run_model
+
   - page: "modules/src/plotter.md"
     source: "src/plotter.py"
     functions:
@@ -23,14 +34,3 @@ pages:
     functions:
       - prep_data
 
-  - page: "modules/src/scaleup_model.md"
-    source: "src/scaleup_model.py"
-    classes:
-      - SeaweedScaleUpModel
-    functions:
-      - self_shading
-      - calculate_seaweed_need
-      - seaweed_farm_area_per_day
-      - logistic_curve
-      - run_model
-

scripts/Bug hunting.ipynb

@@ -0,0 +1,155 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Finding agreement with Vasco"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Import the model\n",
+    "from src.scaleup_model import run_model\n",
+    "from src.preprocessing import prep_data\n",
+    "from src.plotter import create_plots"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Go up one directory\n",
+    "import os\n",
+    "os.chdir(\"..\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Initialize the model\n",
+    "optimal_growth_rate = 30  # % per day\n",
+    "days_to_run = 3600 - 3 * 30  # 120 month at 30 days per month (and skip the first three months before the nuclear war)\n",
+    "global_pop = 7000000000\n",
+    "calories_per_person_per_day = 2250\n",
+    "harvest_loss = 20  # % of the harvest that is lost\n",
+    "food_waste = 13  # https://www.researchsquare.com/article/rs-1446444/v1\n",
+    "calories_per_t_seaweed_wet = 288200  # see Efficiency.ipynb\n",
+    "food_limit = 0.15  # amount of food that can be replaced by seaweed\n",
+    "# https://academic.oup.com/jcem/article/87/12/5499/2823602\n",
+    "feed_limit = 0.05  # amount of feed that can be replaced by seaweed\n",
+    "biofuel_limit = 0.5  # amount of biofuel that can be replaced by seaweed\n",
+    "# percent of the area of the module that can acutally be used for food production.\n",
+    "# Rest is needed for things like lanes for harvesting\n",
+    "percent_usable_for_growth = 50  # %\n",
+    "# Which scenario to run\n",
+    "scenarios = [\"150tg\"]\n",
+    "location = \"global\"\n",
+    "number_of_clusters = 3\n",
+    "consumption_aim = 70 # % of the global need is the aim for the building of the farms"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Start preprocessing for scenario 150tg\n"
+     ]
+    }
+   ],
+   "source": [
+    "# do the preprocessing to get the data in the right format\n",
+    "# Go through all nuclear war scenarios\n",
+    "for scenario in scenarios:\n",
+    "    print(\"Start preprocessing for scenario \" + scenario)\n",
+    "    path = \"data\"\n",
+    "    prep_data(scenario, location, number_of_clusters)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Running scenario 150tg\n",
+      "Cluster 0 has a mean growth rate (fraction of max growth rate) of 0.11368341430016159\n",
+      "stable_harvest_intervall 87.0\n",
+      "stable_harvest_for_food 1931.0029876298024\n",
+      "productivity_day_km2 22.195436639423015\n",
+      "calculating yield for cluster 0\n",
+      "Cluster 1 has a mean growth rate (fraction of max growth rate) of 0.0004594581205788031\n",
+      "stable_harvest_intervall None\n",
+      "stable_harvest_for_food None\n",
+      "productivity_day_km2 None\n",
+      "Not enough productivity in cluster for production 1, skipping it\n",
+      "Cluster 2 has a mean growth rate (fraction of max growth rate) of 0.43795151408829613\n",
+      "stable_harvest_intervall 23.0\n",
+      "stable_harvest_for_food 1926.66699609971\n",
+      "productivity_day_km2 83.76813026520479\n",
+      "calculating yield for cluster 2\n",
+      "done\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Run the model\n",
+    "run_model(\n",
+    "    optimal_growth_rate,\n",
+    "    days_to_run,\n",
+    "    global_pop,\n",
+    "    calories_per_person_per_day,\n",
+    "    harvest_loss,\n",
+    "    food_waste,\n",
+    "    calories_per_t_seaweed_wet,\n",
+    "    food_limit,\n",
+    "    feed_limit,\n",
+    "    biofuel_limit,\n",
+    "    percent_usable_for_growth,\n",
+    "    scenarios,\n",
+    "    location,\n",
+    "    number_of_clusters,\n",
+    ")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "seaweed-upscaling-model",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

scripts/Efficieny.ipynb

@@ -197,7 +197,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.12"
   },
   "vscode": {
    "interpreter": {