Home >> Forums >> Configuration of natural mortality

Configuration of natural mortality

Dear Sir or Madam,
I found that the "mortality.natural.rate.byDt.file.sp#" was not available in V3U2 with warning the model couldn't find file path. After a careful check, I make sure the path is correct.
Would you please tell me how to configurate this parameter? 
Thank you.
Best, 
Lei
 

Hi Lei

Could you please send me your Osmose configuration files (in an archive for instance)?

I will have a look at it.

Cheers,

Nicolas

Hi Nicolas,
I found the function "mortality.natural.rate.byDt.byAge.file.sp#" worked in the model. In other words, the model could read the path provided by it.
Therefore, I guess that whether some codes regarding to "mortality.natural.rate.byDt.file.sp#" missed.
The partial configuration of natural mortality was listed as follows: 
Path: mortality.natural.rate.byDt.file.sp0;setMnatural/1/Mnatural-byDt-Oratosquilla.csv
Warnings:  Could not find any parameters for natural mortality (mortality.natural.rate.byDt.byAge.file.sp# or mortality.natural.rate.byDt.bySize.file.sp mortality.natural.rate.byDt.file.sp or mortality.natural.rate.sp#) for species Oratosquilla
Thank you.
Best,
Lei

Hi Lei

Could you please send me your full configuration files? Because I can't see clearly what the problem is.

Could you also tell me version you are using?

Thanks.

Nicolas

Hi Nicolas,
Please find the attached zip file modified based on the example given in OSMOSE web.
The same warning arose again when I ran the model (V3U2).
Best,
Lei

Attachments: 

Hi Lei

I don't find the species Oratosquilla in the configuration file you sent me (and which seem to cause the problem).

I only have

osm_param-species.csv:# Species name
osm_param-species.csv:species.name.sp0;smallpelagic1
osm_param-species.csv:species.name.sp1;macrozooplankton
osm_param-species.csv:species.name.sp2;demersal1
osm_param-species.csv:species.name.sp3;demersal2
osm_param-species.csv:species.name.sp4;demersal3
osm_param-species.csv:species.name.sp5;mesopelagic
osm_param-species.csv:species.name.sp6;smallpelagic2
osm_param-species.csv:species.name.sp7;smallpelagic3
osm_param-species.csv:species.name.sp8;largepelagic1
osm_param-species.csv:species.name.sp9;largepelagic2
 

Did you send the right files?

Nicolas

Hi Nicolas,
I modified the configuration of Benguela OSMOSE model presented in the website, and took it as an example. 
The same problem will happen when we run the modified model provided in my last message.
The warnings is " Could not find any parameters for natural mortality (mortality.natural.rate.byDt.byAge.file.sp# or mortality.natural.rate.byDt.bySize.file.sp mortality.natural.rate.byDt.file.sp or mortality.natural.rate.sp#) for species smallpelagic1".
Thus, I guess the function "mortality.natural.rate.byDt.file.sp#" was not available in the V3U2.
Thank you.
Lei
 

Hi Lei

Ok I think I have found the problem...

To use byDt mortality, the code expects osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp0 instead of osm_param-natural-mortality.csv:mortality.natural.rate.byDt.file.sp0.

This is due to what might be a typo in the part of the code that reads the configuration. So you have to put that in your osm_param-natural-mortality.csv file

osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp0;Mnatural/Mnatural-byDt-sp0.csv
osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp1;Mnatural/Mnatural-byDt-sp1.csv
osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp2;Mnatural/Mnatural-byDt-sp2.csv
osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp3;Mnatural/Mnatural-byDt-sp3.csv
osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp4;Mnatural/Mnatural-byDt-sp4.csv
osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp5;Mnatural/Mnatural-byDt-sp5.csv
osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp6;Mnatural/Mnatural-byDt-sp6.csv
osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp7;Mnatural/Mnatural-byDt-sp7.csv
osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp8;Mnatural/Mnatural-byDt-sp8.csv
osm_param-natural-mortality.csv:mortality.natural.rate.bytDt.file.sp9;Mnatural/Mnatural-byDt-sp9.csv
 

I was able to run the code.

Please tell me if it worked.

Nicolas