Documentation updated and os part added to other plotscripts

Python_files/Code/plotscripts/plot_bgc.py

@@ -30,9 +30,15 @@ levelsbrine  = ([400,2000])
 import numpy
 import matplotlib.pyplot as plt
 from matplotlib import rc
+import os
 rc('font', size='10')
 rc('font', family='serif')
 
+# set wd to the directory of the script
+abspath = os.path.abspath(__file__)
+dname = os.path.dirname(abspath)
+os.chdir(dname)
+
 #Loading data
 bgc_br     = numpy.loadtxt("../../../output/dat_bgc"+tracernumber+".br.dat")
 bgc_bu     = numpy.loadtxt("../../../output/dat_bgc"+tracernumber+".bu.dat")

Python_files/Code/plotscripts/plot_profile.py

@@ -9,14 +9,21 @@
 #6. Run the script! (python plot_profile.py)
 #7. Open the outputfile in the imageviewer of your choice.
 
+
+
 #Loading modules and setting fonts
 import numpy
 import matplotlib.pyplot as plt
 from matplotlib import rc
+import os
 import matplotlib
 rc('font', size='10')
 rc('font', family='serif')
 
+# set wd to the directory of the script
+abspath = os.path.abspath(__file__)
+dname = os.path.dirname(abspath)
+os.chdir(dname)
 
 #Settings 
 dx           = 1.0 

Run_specifics/config.json

 {
-    "start_time": "2019-01-01 00:00:00",
-    "dt": 20,
+    "start_time": "2022-01-01 00:00:00",
+    "dt": 60,
     "time": 0.0,
-    "time_out": 86400,
-    "time_total": 55468800,
+    "time_out": 302400.0,
+    "time_total": 65318400.0,
+    "length_input": 1088640.0,
     "timestep_data": 60,
-    "length_input": 924481,
-    "thick_0": 0.02,
-    "Nlayer": 80,
+    "thick_0": 0.03,
+    "Nlayer": 20,
     "N_active": 1,
-    "N_top": 20,
-    "N_bottom": 20,
-    "N_middle": 40,
+    "N_top": 5,
+    "N_bottom": 5,
+    "N_middle": 10,
     "boundflux_flag": 2,
     "albedo_flag": 2,
     "grav_heat_flag": 1,
@@ -25,7 +25,7 @@
     "turb_flag": 2,
     "bottom_flag": 1,
     "tank_flag": 1,
-    "precip_flag": 1,
+    "precip_flag": 0,
     "freeboard_snow_flag": 0,
     "snow_flush_flag": 1,
     "styropor_flag": 0,
@@ -33,14 +33,14 @@
     "debug_flag": 1,
     "bgc_flag": 1,
     "initial_state_flag": 1,
-    "tank_depth": 0,
-    "alpha_flux_stable": 0,
-    "alpha_flux_instable": 0,
-    "N_bgc": 0,
-    "bgc_bottom_1": 0,
-    "bgc_bottom_2": 0,
-    "thick_1": 0.02,
-    "m_1": 20.56,
-    "S_abs_1": 699.04,
-    "H_abs_1": -69904.0
+    "tank_depth": 1,
+    "alpha_flux_stable": 15,
+    "alpha_flux_instable": 22,
+    "N_bgc": 2,
+    "bgc_bottom_1": 385,
+    "bgc_bottom_2": 385,
+    "thick_1": 0.03,
+    "m_1": 30.84,
+    "S_abs_1": 1048.56,
+    "H_abs_1": 0
 }
\ No newline at end of file

Run_specifics/description.txt

-Mosaic_run_1
\ No newline at end of file
+Testcase_3
\ No newline at end of file

documentation/Configuration_Guide.md

@@ -2,7 +2,7 @@
 How to configure SAMSIM3.0 with config.json files and the respective inputs
 
 ## Brief Description
-This Guide will show you an example run of SAMSIM3.0 with testcase. We go step-by-step through the python file build_config_1.py which is used to build the config.json file and
+This Guide will show you an example run of SAMSIM3.0 with testcase 1. We go step-by-step through the python file build_config_1.py which is used to build the config.json file and
 the input files needed to run SAMSIM3.0 for testcase 1. For a detailed documentation of the different variables, please look at
 reference manual and SAMISM3.md. 
 
@@ -12,15 +12,21 @@ We use the build_config_1.py file, which is used to create the config.json and t
 testcase 1 as an example. 
 
 The first section imports the json lbrary and the functions used to build the input files for the respective testcases.
-It also defines two constants used below. 
+It also defines two constants used below and sets the working directory to the directory of the build_config file. 
 
 ```python
 import json
-from Python_files.Code.build_config_files.func_bound_values import *
+from func_bound_values import *
+import os
+
+# set wd to the directory of the script
+abspath = os.path.abspath(__file__)
+dname = os.path.dirname(abspath)
 
 # set constants
 rho_l = 1028
 c_l = 3400
+os.chdir(dname)
 ```
 The second section initializes the config array which is converted into the config.json file in the end and sets the
 paths for the storage spaces of the input files and the config file.
@@ -43,11 +49,13 @@ file.write(description)
 file.close()
 ``` 
 In the fourth section, the time settings of the simulation are defined. Note that 'time_total' 
-should be a multiple of 'time_out'.
+should be a multiple of 'time_out'. 'start_time' sets the beginning of your run, which is important if you 
+want to have a realistic timeframe. For testcase 1-4 this is arbitrary. 
 ```python
 # **********************************************************************************************************************
 # Initial layer thickness, timestep, output time and simulation time
 # **********************************************************************************************************************
+config['start_time'] = '2022-01-01 00:00:00'  # start time in YYYY-mm-dd HH:MM:SS
 config['dt'] = 1  # time increment [s]]
 config['time'] = 0.0  # initial value of time [s]
 config['time_out'] = 3600  # time between outputs [s]
@@ -191,5 +199,45 @@ json_object = json.dumps(config, indent=4)
 
 with open(path_config + "config.json", "w") as outfile:
     outfile.write(json_object)
-
 ```
+### Run config script
+You can run the build_config_1 file to prepare testcase 1 by simpely typing 
+````shell
+python3 Python_files/Code/build_config_files/build_config_1.py
+````
+into your console. Note that the path can be different, depending on what folder you are in. 
+Running the script will put the needed input in the input folder and the config.json and the description.txt file
+in the Run_specifics folder. 
+
+### Run SAMSIM
+Now, you can run the model by going to the directory with the makefile in it (home directory of the repository) 
+and typing 
+````shell
+make
+````
+into the console. This will compile the fortran code and produce a .mod and a .o file for every module and an executable file 
+called samsim.x. 
+
+Having done that, you can now run SAMSIM by typing
+````shell
+./samsim.x
+````
+into the console, which will run the executable file. One good thing about SAMSIM3.0 is that you 
+don't have to recompile it after you changed the inputs or the config file. You can simpely type the above command again
+to rerun it for a different setting. 
+
+Runnig the SAMSIM will produce some output in your console, showing the progress and some other model variables.
+
+After SAMSIM finishes, you can find the model output in the output foler. 
+
+### Plotting the output
+The model output can simpely be plotted by running one of the plotscrips, depending on what you want to investigate. 
+For a good first overview I suggest using the plot_TPhiS.py script, which plots temperature, liquid fraction and salinity of the 
+sea ice profile over time. To do so, type
+````shell
+python3 Python_files/Code/plotscripts/plot_TPhiS.py
+````
+The path again depends on which folder you are currently in. This produces a nice plot which you can find in the folder 
+Python_files/Plots and should look like this for testcase 1:
+
+![Testcase1](Plots/pic_TPhiS.png?raw=true)
\ No newline at end of file

documentation/SAMSIM3.md

@@ -22,7 +22,7 @@ This warning have been removed by introducing an additional variable T_in:
 ````
 This improvement of the code caused minor changes in the output of the testcases which have a snow cover (3&4). For testcase 3, the changes look like this: 
 
-![testcase3_changes](C:\Users\jakob\OneDrive\Dokumente\Jobs\Sea ice Hiwi\Grotz3000\final_version\documentation\Plots\testcase3_v1_v2.png)
+![testcase3_changes](Plots\testcase3_v1_v2.png)
 
 There have been a lot of other warnings removed but these were the major ones. 
 
@@ -101,13 +101,13 @@ while reading the input data. The exact cause could not be identified but the di
 If you can find the cause for the errors, contact me (jakob.deutloff@gmail.com) and I invite you for a drink ;). 
 
 Differences testcase 1 (none):
-![testcase1_diff](C:\Users\jakob\OneDrive\Dokumente\Jobs\Sea ice Hiwi\Grotz3000\final_version\documentation\Plots\differeces_sam_final1.png)
+![testcase1_diff](Plots\differeces_sam_final1.png)
 Differences testcase 2:
-![testcase2_diff](C:\Users\jakob\OneDrive\Dokumente\Jobs\Sea ice Hiwi\Grotz3000\final_version\documentation\Plots\differeces_sam_final2.png)
+![testcase2_diff](Plots\differeces_sam_final2.png)
 Differences Testcase 3:
-![testcase3_diff](C:\Users\jakob\OneDrive\Dokumente\Jobs\Sea ice Hiwi\Grotz3000\final_version\documentation\Plots\differeces_sam_final3.png)
+![testcase3_diff](Plots\differeces_sam_final3.png)
 Differences Testcase 4:
-![testcase4_diff](C:\Users\jakob\OneDrive\Dokumente\Jobs\Sea ice Hiwi\Grotz3000\final_version\documentation\Plots\differeces_sam_final4.png)
+![testcase4_diff](Plots\differeces_sam_final4.png)
 ## List of New Variables
 - T2m_input - Input file for T2m
 - T_top_input - Input file for T_top

mo_init.f90

@@ -98,7 +98,7 @@ CONTAINS
         !Time settings needed when input is given
         !*************************************************************************************************************************
         CALL json%get('length_input', length_input, is_found)
-        IF (.not. is_found) THEN; PRINT*, 'n_time_output not found'; STOP; END IF
+        IF (.not. is_found) THEN; PRINT*, 'lenght_input not found'; STOP; END IF
         CALL json%get('timestep_data', timestep_data, is_found)
         IF (.not. is_found) THEN; PRINT*, 'timestep_data not found'; STOP; END IF