<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Aptos;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Aptos",sans-serif;
mso-ligatures:standardcontextual;
mso-fareast-language:EN-US;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:11.0pt;
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="NL" link="#467886" vlink="#96607D" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US">Dear MITgcm Community,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I am encountering an issue related to specifying a space-dependent (longitude-latitude-depth) vertical diffusivity coefficient for temperature in MITgcm. Based on my understanding, this should be possible by enabling
the ALLOW_3D_DIFFKR flag in the CPP_OPTIONS.h file. After changing #undef ALLOW_3D_DIFFKR to #define ALLOW_3D_DIFFKR and copying the modified file to my code directory, I recompiled the code using the following command:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">$base_dir/tools/genmake2 -mods $base_dir/$code_dir -mpi -of=$OPTFILE_PATH<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">This successfully generates the Makefile and the executable mitgcmuv. In my data script, I specify the variable diffusion coefficient with PARAMS05 as follows:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">diffKrFile='diffKrFile.bin'<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">However, when I run the model, I encounter the following error message:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">(PID.TID 0000.0001) *** ERROR *** CONFIG_CHECK: diffKrFile is set but never used.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">(PID.TID 0000.0001) *** ERROR *** CONFIG_CHECK: Re-compile with: "#define ALLOW_3D_DIFFKR"<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">(PID.TID 0000.0001) *** ERROR *** CONFIG_CHECK: detected 1 fatal error(s)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">(PID.TID 0000.0001) *** ERROR *** S/R ALL_PROC_DIE: ending the run<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">This suggests that the diffKrFile is not being loaded and the #define ALLOW_3D_DIFFKR flag is not being recognized. Despite verifying that the flag is correctly enabled (see attached), I still receive this error. Could
I be overlooking something? Is there any additional configuration or package that I need to include for this feature to work?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">For context, my PACKAGES section is as follows:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">&PACKAGES<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> useDiagnostics = .TRUE.,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> useGMRedi = .TRUE.,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> useRBCS = .TRUE.,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">&<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Finally, once the diffKrFile is loaded, will it only affect temperature as an active tracer, or could it also apply to other tracers if they are included in the model?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I look forward to any insights you may have.<o:p></o:p></span></p>
<p class="MsoNormal">Best regards,<o:p></o:p></p>
<p class="MsoNormal">Elian<o:p></o:p></p>
</div>
</body>
</html>