ec-jrc · casadoj · Dec 15, 2022 · Dec 15, 2022 · Dec 15, 2022 · Dec 15, 2022
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,9 @@
 
 # User-specific stuff
 .idea/
+
+# ignore checkpoints
+*checkpoint.md
+*checkpoint.yml
+*checkpoint.ipynb
+*checkpoint.py
diff --git a/LF_ETRS89_UseCase/settings_ETRS89-PreRun.xml b/LF_ETRS89_UseCase/settings_ETRS89-PreRun.xml
@@ -126,22 +126,22 @@ The option "numberParallelThreadsKinematicWave" may take the following values:
     - "2", "3", ... : manual setting of the number of parallel threads.
                       (if exceeding the number of CPUs, the option is set to "0") -->
             <textvar name="numCPUs_parallelKinematicWave" value="0"/>
-            
+
             <comment>
             **************************************************************
             PARALLELISATION WITH NUMBA (USED IN SOILLOOP)
             **************************************************************
             </comment>
-            
+
             !-- Parallelisation of using Numba runtime compiled library .
             The option "numCPUs_parallelNumba" may take the following values:
-                - "0"           : set to NUMBA_NUM_THREADS Environment Variable 
+                - "0"           : set to NUMBA_NUM_THREADS Environment Variable
                                   (if NUMBA_NUM_THREADS is not set, will take the number of CPU cores determined by python's multiprocessing.cpu_count())
                 - "1"           : serial execution (not parallel)
                 - "2", "3", ... : manual setting of the number of parallel threads.
                                   (if exceeding NUMBA_NUM_THREADS, the value is set to NUMBA_NUM_THREADS) -->
             <textvar name="numCPUs_parallelNumba" value="0"/>
-            
+
             <comment>
                 **************************************************************
                 AREA AND OUTLETS
@@ -651,7 +651,7 @@ The option "numberParallelThreadsKinematicWave" may take the following values:
                     -9999 sets initial value to steady-state level
                 </comment>
             </textvar>
-            
+
             <textvar name="LakePrevInflowValue" value="-9999">
                  <comment>
                      Lake inflow at previous routing sub-step (ChanQ(t-1)) [m3/s]
@@ -1039,18 +1039,18 @@ The option "numberParallelThreadsKinematicWave" may take the following values:
                     More than the transpiration is added e.g to prevent salinisation
                 </comment>
             </textvar>
-            
-            <textvar name="IrrigationWaterReUseM3" value="0.0">           
-                <comment>           
-                    Annual amount (m3) of treated wastewater reused for irrigation                  
-                </comment>    
+
+            <textvar name="IrrigationWaterReUseM3" value="0.0">
+                <comment>
+                    Annual amount (m3) of treated wastewater reused for irrigation
+                </comment>
             </textvar>
-            
-           <textvar name="IrrigationWaterReUseNumDays" value="143">          
-               <comment>           
-               Number of days over which the annual amount of treated wastewater for irrigation is used                
-               </comment>           
-           </textvar>            
+
+           <textvar name="IrrigationWaterReUseNumDays" value="143">
+               <comment>
+               Number of days over which the annual amount of treated wastewater for irrigation is used
+               </comment>
+           </textvar>
 
             <textvar name="LivestockConsumptiveUseFraction" value="0.15">
                 <comment>
@@ -1528,7 +1528,7 @@ LFBINDING: MORE LOW-LEVEL CONTROL OVER MODEL IN- AND OUTPUT
                 Clone map
             </comment>
         </textvar>
-        
+
         <textvar name="NetCDFTimeChunks" value="auto">
         <comment>
                 Chunking in time dimension used when reading NetCDF forcings (or other NetCDF temporal inputs).
@@ -1537,13 +1537,28 @@ LFBINDING: MORE LOW-LEVEL CONTROL OVER MODEL IN- AND OUTPUT
                  "-1": load the whole time series in memory (fastest option but memory consuming)
            </comment>
         </textvar>
-      
+
         <textvar name="MapsCaching" value="False">
             <comment>
-                Option designed for the calibration. All the static maps and forcings will be stored in a cache so that they don't have to be loaded by each lisflood instance. 
+                Option designed for the calibration. All the static maps and forcings will be stored in a cache so that they don't have to be loaded by each lisflood instance.
                 This option sets the value of NetCDFTimeChunks to -1, meaning that the whole time series in the NetCDF inputs is loaded into memory.
-            </comment>       
-        </textvar> 
+            </comment>
+        </textvar>
+
+        <textvar name="OutputMapsChunks" value="1">
+          <comment>
+            The option "OutputMapsChunks" may take the following values:
+                - "[positive integer number]"  : Dump outputs to disk every X steps (default 1)
+          </comment>
+        </textvar>
+
+        <textvar name="OutputMapsDataType" value="float64">
+          <comment>
+            The option "OutputMapsDataType" sets the output data type and may take the following values:
+                - "float64"
+                - "float32"
+          </comment>
+        </textvar>
 
         <textvar name="netCDFtemplate" value="$(netCDFtemplate)">
             <comment>
@@ -2489,18 +2504,18 @@ LFBINDING: MORE LOW-LEVEL CONTROL OVER MODEL IN- AND OUTPUT
                     More than the transpiration is added e.g to prevent salinisation
                 </comment>
             </textvar>
-            
-            <textvar name="IrrigationWaterReUseM3" value="$(IrrigationWaterReUseM3)">           
-                <comment>           
-                Annual amount (m3) of treated wastewater reused for irrigation                  
-                </comment>    
+
+            <textvar name="IrrigationWaterReUseM3" value="$(IrrigationWaterReUseM3)">
+                <comment>
+                Annual amount (m3) of treated wastewater reused for irrigation
+                </comment>
             </textvar>
-               
-            <textvar name="IrrigationWaterReUseNumDays" value="$(IrrigationWaterReUseNumDays)">      
+
+            <textvar name="IrrigationWaterReUseNumDays" value="$(IrrigationWaterReUseNumDays)">
                 <comment>
-                Number of days over which the annual amount of treated wastewater for irrigation is used                
-                </comment>          
-            </textvar>             
+                Number of days over which the annual amount of treated wastewater for irrigation is used
+                </comment>
+            </textvar>
 
             <textvar name="MapIrrigationCropCoef" value="$(MapIrrigationCropCoef)">
                 <comment>
@@ -3686,12 +3701,12 @@ LFBINDING: MORE LOW-LEVEL CONTROL OVER MODEL IN- AND OUTPUT
                         Soil moisture lower layer [cu mm / cu mm]
                     </comment>
                 </textvar>
-                
+
                 <textvar name="Theta3TS" value="$(PathOut)/th2.tss">
                     <comment>
                         Soil moisture lower layer [cu mm / cu mm]
                     </comment>
-                </textvar>                
+                </textvar>
 
                 <textvar name="UZTS" value="$(PathOut)/uz.tss">
                     <comment>

diff --git a/LF_ETRS89_UseCase/settings_ETRS89-Run.xml b/LF_ETRS89_UseCase/settings_ETRS89-Run.xml
@@ -127,22 +127,22 @@ The option "numberParallelThreadsKinematicWave" may take the following values:
     - "2", "3", ... : manual setting of the number of parallel threads.
                       (if exceeding the number of CPUs, the option is set to "0") -->
             <textvar name="numCPUs_parallelKinematicWave" value="0"/>
-            
+
             <comment>
             **************************************************************
             PARALLELISATION WITH NUMBA (USED IN SOILLOOP)
             **************************************************************
             </comment>
-            
+
             !-- Parallelisation of using Numba runtime compiled library .
             The option "numCPUs_parallelNumba" may take the following values:
-                - "0"           : set to NUMBA_NUM_THREADS Environment Variable 
+                - "0"           : set to NUMBA_NUM_THREADS Environment Variable
                                   (if NUMBA_NUM_THREADS is not set, will take the number of CPU cores determined by python's multiprocessing.cpu_count())
                 - "1"           : serial execution (not parallel)
                 - "2", "3", ... : manual setting of the number of parallel threads.
                                   (if exceeding NUMBA_NUM_THREADS, the value is set to NUMBA_NUM_THREADS) -->
             <textvar name="numCPUs_parallelNumba" value="0"/>
-            
+
             <comment>
                 **************************************************************
                 AREA AND OUTLETS
@@ -206,7 +206,7 @@ The option "numberParallelThreadsKinematicWave" may take the following values:
              <textvar name="proj4_params" value="+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs">
             </textvar>
 
-          
+
             <comment>
                 **************************************************************
                 TIME-RELATED CONSTANTS
@@ -682,7 +682,7 @@ The option "numberParallelThreadsKinematicWave" may take the following values:
                     -9999 sets initial value to steady-state level
                 </comment>
             </textvar>
-            
+
             <textvar name="LakePrevInflowValue" value="-9999">
                  <comment>
                      Lake inflow at previous routing sub-step (ChanQ(t-1)) [m3/s]
@@ -1074,17 +1074,17 @@ The option "numberParallelThreadsKinematicWave" may take the following values:
                 </comment>
             </textvar>
 
-            <textvar name="IrrigationWaterReUseM3" value="0.0">           
-                <comment>           
-                    Annual amount (m3) of treated wastewater reused for irrigation                  
-                </comment>    
+            <textvar name="IrrigationWaterReUseM3" value="0.0">
+                <comment>
+                    Annual amount (m3) of treated wastewater reused for irrigation
+                </comment>
             </textvar>
 
-           <textvar name="IrrigationWaterReUseNumDays" value="143">          
-               <comment>           
-               Number of days over which the annual amount of treated wastewater for irrigation is used                
-               </comment>           
-           </textvar>                
+           <textvar name="IrrigationWaterReUseNumDays" value="143">
+               <comment>
+               Number of days over which the annual amount of treated wastewater for irrigation is used
+               </comment>
+           </textvar>
 
             <textvar name="LivestockConsumptiveUseFraction" value="0.15">
                 <comment>
@@ -1562,7 +1562,7 @@ LFBINDING: MORE LOW-LEVEL CONTROL OVER MODEL IN- AND OUTPUT
                 Clone map
             </comment>
         </textvar>
-        
+
         <textvar name="NetCDFTimeChunks" value="auto">
            <comment>
                 Chunking in time dimension used when reading NetCDF forcings (or other NetCDF temporal inputs).
@@ -1571,14 +1571,29 @@ LFBINDING: MORE LOW-LEVEL CONTROL OVER MODEL IN- AND OUTPUT
                  "-1": load the whole time series in memory (fastest option but memory consuming)
            </comment>
         </textvar>
-      
+
         <textvar name="MapsCaching" value="False">
             <comment>
-                Option designed for the calibration. All the static maps and forcings will be stored in a cache so that they don't have to be loaded by each lisflood instance. 
+                Option designed for the calibration. All the static maps and forcings will be stored in a cache so that they don't have to be loaded by each lisflood instance.
                 This option sets the value of NetCDFTimeChunks to -1, meaning that the whole time series in the NetCDF inputs is loaded into memory.
-            </comment>       
-        </textvar>         
-
+            </comment>
+        </textvar>
+
+        <textvar name="OutputMapsChunks" value="1">
+          <comment>
+            The option "OutputMapsChunks" may take the following values:
+                - "[positive integer number]"  : Dump outputs to disk every X steps (default 1)
+          </comment>
+        </textvar>
+
+        <textvar name="OutputMapsDataType" value="float64">
+          <comment>
+            The option "OutputMapsDataType" sets the output data type and may take the following values:
+                - "float64"
+                - "float32"
+          </comment>
+        </textvar>
+
         <textvar name="netCDFtemplate" value="$(netCDFtemplate)">
             <comment>
                 netcdf template used to copy metadata information for writing netcdf
@@ -2501,30 +2516,30 @@ LFBINDING: MORE LOW-LEVEL CONTROL OVER MODEL IN- AND OUTPUT
                     More than the transpiration is added e.g to prevent salinisation
                 </comment>
             </textvar>
-            
-            <textvar name="IrrigationWaterReUseM3" value="$(IrrigationWaterReUseM3)">           
-                <comment>           
-                Annual amount (m3) of treated wastewater reused for irrigation                  
-                </comment>    
+
+            <textvar name="IrrigationWaterReUseM3" value="$(IrrigationWaterReUseM3)">
+                <comment>
+                Annual amount (m3) of treated wastewater reused for irrigation
+                </comment>
             </textvar>
-               
-            <textvar name="IrrigationWaterReUseNumDays" value="$(IrrigationWaterReUseNumDays)">      
+
+            <textvar name="IrrigationWaterReUseNumDays" value="$(IrrigationWaterReUseNumDays)">
                 <comment>
-                Number of days over which the annual amount of treated wastewater for irrigation is used                
-                </comment>          
-            </textvar>                
+                Number of days over which the annual amount of treated wastewater for irrigation is used
+                </comment>
+            </textvar>
 
-            <textvar name="IrrigationWaterReUseM3" value="$(IrrigationWaterReUseM3)">           
-                <comment>           
-                Annual amount (m3) of treated wastewater reused for irrigation                  
-                </comment>    
+            <textvar name="IrrigationWaterReUseM3" value="$(IrrigationWaterReUseM3)">
+                <comment>
+                Annual amount (m3) of treated wastewater reused for irrigation
+                </comment>
             </textvar>
 
-            <textvar name="IrrigationWaterReUseNumDays" value="$(IrrigationWaterReUseNumDays)">      
+            <textvar name="IrrigationWaterReUseNumDays" value="$(IrrigationWaterReUseNumDays)">
                 <comment>
-                Number of days over which the annual amount of treated wastewater for irrigation is used                
-                </comment>          
-            </textvar>     
+                Number of days over which the annual amount of treated wastewater for irrigation is used
+                </comment>
+            </textvar>
 
             <textvar name="MapIrrigationCropCoef" value="$(MapIrrigationCropCoef)">
                 <comment>
@@ -5503,7 +5518,7 @@ LFBINDING: MORE LOW-LEVEL CONTROL OVER MODEL IN- AND OUTPUT
                     <textvar name="AreatotalIrrigationUseM3" value="$(PathOut)/ATIrgUse">
                         <comment>
                             AreatotalIrrigationUseM3
-                        </comment> 
+                        </comment>
                     </textvar>
 
                     <textvar name="FractionAbstractedFromChannels" value="$(PathOut)/FrChan">

diff --git a/LF_mekong_usecase/.ipynb_checkpoints/README-checkpoint.md b/LF_mekong_usecase/.ipynb_checkpoints/README-checkpoint.md
@@ -0,0 +1,3 @@
+# Use case 3: the Nam Ngum river, Laos
+
+As a third use case we will simulate the Nam Ngum river basin, a tributary of the Mekong River, for a period of 30 years. We provide both the basic data to run the model (input data, settings files, etc.) and a detailed explanation of how to build the model. This explanation is both in the shape of a Jupyter Book, or in the shape of Jupyter Notebooks, if you want to interact with the data on your own.
diff --git a/LF_mekong_usecase/README.md b/LF_mekong_usecase/README.md
@@ -0,0 +1,19 @@
+# Use case 3: the Nam Ngum river, Laos
+
+As a third use case we will simulate the Nam Ngum river basin, a tributary of the Mekong River, for a period of 30 years. We provide both the basic data to run the model (input data, settings files, etc.) and a detailed explanation of how to build the model. 
+
+## Model
+
+In this folder you can find all the necessary data you need to run the LISFLOOD model of this catchment, i.e., the static maps, the meteorological forcings and the settings files. 
+
+> **Important**. You need to unzip the [meteorological forcings](https://github.com/ec-jrc/lisflood-usecases/tree/mekong_usecase/LF_mekong_usecase/model/meteo) and the [population maps](https://github.com/ec-jrc/lisflood-usecases/tree/mekong_usecase/LF_mekong_usecase/model/maps/water_use/pop_daily.zip)
+
+To run the model you need to have LISFLOOD installed in a Conda environment on **Linux** (support is not provided for Windows or macOS users). Follow this [instructions to install LISFLOOD](https://github.com/ec-jrc/lisflood-code).
+
+
+## Tutorial
+
+We provide a detailed explanation of how to build the model, we explained the necessary input data, how to change the settings file and we visualize and comment on the results. You can follow this tutorial in two flavours:
+
+* A Jupyter [Book](https://ec-jrc.github.io/lisflood-usecases/), which is a simple and clean way of reading the tutorial.
+* [Jupyter Notebooks](https://github.com/ec-jrc/lisflood-usecases/tree/mekong_usecase/LF_mekong_usecase/docs/notebooks) that allow you to interact with the tutorial, explore the inputs and outputs, edit, etc.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		# Use case 3: the Nam Ngum river, Laos

		As a third use case we will simulate the Nam Ngum river basin, a tributary of the Mekong River, for a period of 30 years. We provide both the basic data to run the model (input data, settings files, etc.) and a detailed explanation of how to build the model. This explanation is both in the shape of a Jupyter Book, or in the shape of Jupyter Notebooks, if you want to interact with the data on your own.