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<p>Dear Jonathan,<br>
</p>
<p></p>
Thank you for your reply. I’m not sure to understand, what do you
mean by log call ? I don't see conditions to limit a certain value
in the files you pointed out.<br>
<br>
I started looking on your suggestions and what I can say for now is:<br>
<br>
(1) I copy the two files for ocean at the end of this message.<br>
<br>
(2a) By only checking available outputs every half-an-hour, it seems
the atmospheric pCO2 concentration becomes equals to zero first.
Unfortunately, as this is a homogeneous value for the whole
atmosphere I cannot identify a local point where the problem occur.
But following your suggestion (4) it seems the problem do not
directly coming from here. <br>
<br>
(2b) For the moment, I haven’t observe the problem but both
atmospheric and oceanic pCO2 concentration are increasing. My
simulation is still running so I will see if this solve the problem
after spin-up time or not.<br>
<br>
(3) Yes, I tried and it also turn to the same problem.<br>
<br>
(4) Thank you for this suggestion. Looking on the additional prints,
especially those related to dic_atmos.F file, leads me to believe
that the problem first occur with the fluxCO2 variable in ocean -
which is shared with atmosphere. Here I copy the relevant lines of
debug output. <br>
<pre class="western" style="font-style: normal; font-weight: normal; text-decoration: none" lang="en-US"><font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span style="background: transparent"> QQ atmos C, total, pCo2 NaN NaN</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="font-style: normal"><span style="text-decoration: none"><span style="font-weight: normal"><span style="background: transparent"> QQ total C, current, old, dif</span></span></span></span></span></font></font></font><font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="font-style: normal"><span style="text-decoration: none"><span style="font-weight: normal"><span style="background: transparent">f </span></span></span></span></span></font></font></font><font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="font-style: normal"><span style="text-decoration: none"><span style="font-weight: normal"><span style="background: transparent"> NaN 1.3077058455813389E+018 NaN</span></span></span></span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> QQ ocean C, current, old, diff NaN 1.2264261974040456E+018 NaN</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> QQ air-sea flux, addition diff NaN NaN</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: atpco2 (DIC_ATMOS) min= 0.00000000000000E+00</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: atpco2 (DIC_ATMOS) max= 0.00000000000000E+00</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: atpco2 (DIC_ATMOS) mean= 0.00000000000000E+00</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: atpco2 (DIC_ATMOS) S.D.= 0.00000000000000E+00</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: co2atmos (DIC_ATMOS) min= 0.00000000000000E+00</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: co2atmos (DIC_ATMOS) max= 0.00000000000000E+00</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: co2atmos (DIC_ATMOS) mean= 0.00000000000000E+00</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: co2atmos (DIC_ATMOS) S.D.= 0.00000000000000E+00</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_WRITE: atm_pCO2 val= NaN</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_WRITE: dic_pCO2 val= 3.20000000000000E-04</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_WRITE: tile_flux val= 1.07455380469069E+09</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_WRITE: total_atmos_carbon val= NaN</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_WRITE: total_flux val= NaN</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: dTtracerLev min= -2.00000000000000E+03</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: dTtracerLev max= 4.65311520000000E+09</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: dTtracerLev mean= 2.39551968956715E+07</span></span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"><span style="background: transparent"> DEBUG_STATS_RL: dTtracerLev S.D.= 3.18669211791863E+08</span></span></font></font></font></pre>
<style type="text/css">pre { background: transparent }pre.western { font-family: "Liberation Mono", monospace; font-size: 10pt }pre.cjk { font-family: "Noto Sans Mono CJK SC", monospace; font-size: 10pt }pre.ctl { font-family: "Liberation Mono", monospace; font-size: 10pt }p { margin-bottom: 0.25cm; line-height: 115%; background: transparent }</style><br>
There is points with fluxCO2 around -6.10⁻⁴ (so two order of
magnitude smaller than elsewhere) at the limit between two faces
(note there is no ice into this simulation). If I fix a lower limit
for fluxCO2 then there is not anymore appearance of zeros, and
atmospheric pCO2 stay in reasonable range. But, the oceanic pCO2 is
largely increasing (up to 8000 ppm!) and there is still “NaN” in
standard output related to oceanic carbon. I put below the
corresponding lines of standard outputs: <br>
<pre class="western" style="font-style: normal; font-weight: normal; text-decoration: none" lang="en-US"><font color="#000000"><span style="background: transparent"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"> QQ atmos C, total, pCo2 81393757432549728. 4.5985173690706060E-004</font></font></span></font>
<font color="#000000"><span style="background: transparent"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">QQ total C, current, old, diff NaN 1.3077629004370186E+018 NaN</span></font></font></span></font>
<font color="#000000"><span style="background: transparent"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">QQ ocean C, current, old, diff NaN 1.2264261974040456E+018 NaN</span></font></font></span></font>
<font color="#000000"><span style="background: transparent"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">QQ air-sea flux, addition diff -57054399576804.773 NaN</span></font></font></span></font></pre>
<style type="text/css">pre { background: transparent }pre.western { font-family: "Liberation Mono", monospace; font-size: 10pt }pre.cjk { font-family: "Noto Sans Mono CJK SC", monospace; font-size: 10pt }pre.ctl { font-family: "Liberation Mono", monospace; font-size: 10pt }p { margin-bottom: 0.25cm; line-height: 115%; background: transparent</style>Is
this flux can really be the initial source of the problem or am I
wrong? Is make sense to limit it? I would have a look on it
computation to better understand the problem and solve it but I
can't found it, do you not in which file I should look?<br>
<br>
Best regards,<br>
<br>
Charline<br>
<br>
<br>
<br>
Here are the files:<br>
<br>
data.dic:<br>
<pre class="western" style="font-style: normal; font-weight: normal; text-decoration: none" lang="en-US"><font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"># DIC parameters </font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">&ABIOTIC_PARMS</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">selectPHsolver=1</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">&</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">&BIOTIC_PARMS</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">alphaUniform = 0.97e-10,</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">rainRatioUniform = 5.e-2,</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">KRemin = 0.95,</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">&</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">&DIC_FORCING</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">dic_int1 = 3,</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">dic_pCO2 = 320.E-6,</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">DIC_iceFile=' ',</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">DIC_windFile=' ',</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">DIC_silicaFile=' ',</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">DIC_atmospFile=' ',</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">&</span></font></font></font></pre>
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data.cpl:<br>
<br>
<pre class="western" style="font-style: normal; font-weight: normal; text-decoration: none" lang="en-US"><font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"># Coupling package parameters, OCN component: </font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># cpl_earlyExpImpCall :: call coupler early in the time stepping call sequence</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># useImportHFlx :: True => use the Imported HeatFlux from couler</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># useImportFW :: True => use the Imported Fresh Water flux fr cpl</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># useImportTau :: True => use the Imported Wind-Stress from couler</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># useImportSLP :: True => use the Imported Sea-level Atmos. Pressure</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># useImportSIce :: True => use the Imported Sea-Ice loading</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># cpl_taveFreq :: Frequency^-1 for time-Aver. output (s)</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">&CPL_OCN_PARAM</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># cpl_earlyExpImpCall=.FALSE.,</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># useImportHFlx=.FALSE.,</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># useImportFW =.FALSE.,</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">useImportTau =.TRUE.,</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">useImportSLP =.FALSE.,</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># useImportSIce=.FALSE.,</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># 1 month average</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># cpl_taveFreq=2592000.,</span></font></font></font>
<font color="#000000"><font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US"># 10 year average</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">cpl_taveFreq=31104000000.,</span></font></font></font>
<font color="#000000"> <font face="Liberation Mono, monospace"><font style="font-size: 10pt" size="2"><span lang="en-US">&</span></font></font></font>
</pre>
<br>
<pre class="moz-quote-pre" wrap="">--
Charline RAGON
PhD Student
Group of Applied Physics & Institute for Environmental Sciences
University of Geneva, Switzerland
</pre>
<br>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">Dear Charline,
Thanks for your email, I?ll reply here for posterity.
I?m not as familiar with the coupled set up as I would like, however we should be able to diagnose what?s going on. In my experience, abrupt NaNs in output like this are usually the result of illegal values in a log call. There?s one in ?pkg/aim_v23/phy_driver.F? and another in the pH solver for oceanic pCO2 in ?pkg/dic/carbon_chem.F? that I would target. I can see how the former could be the issue if aim_pco2 is invalid (negative or zero), which could happen if there is an issue in ?pkg/aim_v23/aim_do_co2.F?...I think you?d get warnings/errors or immediate crashes if your variable choices were an issue, and also the pCO2 appears to be increasing in your run with ?aim_select_pcO2 = 3?, not trending to zero, but it wouldn?t hurt to check that the DIC package is indeed talking to the AIM package (for example, do you have "#define COMPONENT_MODULE? in your CPP_EEOPTIONS.h file?) On the other hand, the latter log-call is often at the root of many issues like this so I am wondering if th
e problem instead lies in the DIC package itself.
So, a couple of things to test:
(1) Can you post your "data.cpl" and "data.dic" files?
(2a) Have a look at the ocean DIC/surface pCO2 and see if there are NaNs propogating there too. If you have fine enough output frequency around the crash you observe, you may be able to narrow down where geographically the issue is coming from (possibly a sea-ice region?).
(2b) If you are using the default pCO2 solver (which can be bit finicky), I would recompile with "#define CARBONCHEM_SOLVESAPHE" in ?DIC_OPTIONS.h? and set "selectPHsolver=1? in the ?ABIOTIC_PARMS? section of ?data.dic?. This uses a more robust (although possibly more expensive) pH/pCO2 solver.
(3) Have you tried restarting the model with variable absorption coefficient from the end of the run with constant absorption coefficient? I think sometimes there are too many moving parts which causes hard to pin-down erratic behavior as the model adjusts to the initial conditions.
(4) If the above doesnt work you could use the debug framework (#define ALLOW_DEBUG in CPP_OPTIONS.h, set debugMode = .TRUE. in ?eedata? file, and set "debugLevel=5? in PARM01 section of your ?data? file ? lots of messages), plus adding a few print statements for identifying where the NaN first appears, such as maybe print out the relevant variables in ?pkg/aim_v23/aim_do_co2.F? and ?pkg/aim_v23/phy_driver.F?, as well as in ?pkg/dic/dic_atmos.F? and ?hnew?, ?gam? and ?stuff? variables in ?pkg/dic/carbon_chem.F? subroutine "CALC_PCO2_APPROX?.
Hope that helps!
Jonathan
___________________________________________________________________________
Dr. Jonathan M. Lauderdale
Research Scientist
Department of Earth, Atmosphere and Planetary Sciences
Massachusetts Institute of Technology
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</pre>
<blockquote type="cite" style="color: #007cff;">
<pre class="moz-quote-pre" wrap="">On Jul 19, 2021, at 8:09 AM, Charline Ragon <a class="moz-txt-link-rfc2396E" href="mailto:Charline.Ragon@unige.ch"><Charline.Ragon@unige.ch></a> wrote:
Dear all,
I'm performing simulations in a coupled atmosphere, ocean and sea-ice configuration, using the biogeochemical packages GCHEM, DIC and PTRACERS.
I would like to allow a CO2-flux between atmosphere and ocean but I have troubles as all diagnostics are suddenly moving to zero (NaN are appearing in standard outputs). I set parameters dic_int1 = 3 and aim_select_pCO2 = 3, but if I change the value of aim_select_pCO2, this problem is not appearing (at least, I haven't observed it).
I had a look on, and attached to this e-mail, the evolution of atmospheric pCO2 in three similar simulations where I only change the aim_select_pCO2 value to 1, 2 or 3. These runs start from nIter0=0 and tracers are initialized by files. Note that, in my case aim_pCO2 = aim_ref_pCO2 = 320 ppm so it seems the absorption in CO2-band is constant and equals 4 also when aim_select_pCO2 = 1 (so, similar to aim_select_pCO2 = 0).
As I understand it, when the absorption in CO2-band is prescribed the simulation no exhibits the problem even if partial pressure of CO2 is largely increasing in both atmosphere and ocean. So, the zero-appearing should be related to this coefficient but I'm unable to understand exactly what the problem is nor to solve it.
I'm wondering if someone know more about this, and maybe have suggestions for me ?
Thanks in advance for your help!
Best,
Charline
--
Charline RAGON
PhD Student
Group of Applied Physics & Institute for Environmental Sciences
University of Geneva, Switzerland</pre>
</blockquote>
</blockquote>
<br>
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