<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Charline,<div class=""><br class=""></div><div class="">Without knowing exactly what your set up is, your approach sounds reasonable. You can also initialize the physical model from binary files so you don’t need to start entirely from rest/scratch (see for example the input file list for “data” file here: <a href="https://github.com/MITgcm/MITgcm/blob/master/model/src/ini_parms.F#L286" class="">https://github.com/MITgcm/MITgcm/blob/master/model/src/ini_parms.F#L286</a>).</div><div class=""><br class=""></div><div class="">The input files in data.dic (ice, wind, silica, atmospheric pressure) are for prescribed forcing of pkg/dic (i.e. not something that requires pickups). “DIC_iceFile" is prescribed sea ice fraction that affects light and gas fluxes, “DIC_windFile" is for prescribed wind speed that also affects gas transfer, same with pressure. The frequency and periodicity of the forcing is controlled by either the main model forcing cycle or by setting “DIC_forcingPeriod” or "DIC_forcingCycle”. If you’re using other packages that compute these things (such as pkg/seaice, or atmospheric model), then they are probably overwritten in dic_fields_update.F. However, DIC_silicaFile is different, because it’s not computed elsewhere or carried as a tracer in pkg/dic. Nevertheless, the silicate concentration is initialized to a constant value if you don’t supply anything and that is then used in the pH/pCO2 routines. You may need to consider if this is ok or what value(s) fit your needs better. </div><div class=""><br class=""></div><div class=""><div class="">Indeed, if PTRACERS_initialFile is not set, then your tracer fields are initialized to the values set in PTRACERS_ref, your tracer concentrations will be zero.</div></div><div class=""><br class=""></div><div class="">Certain tracers that have a freshwater influence are sensitive to PTRACERS_EvPrRn like DIC and ALK, so yes, setting those (to zero excludes any dissolved concentrations in rainwater/evaporate) allows dilution/concentration. Others you may want to enforce conservation (PO4/DOP) so leaving PTRACERS_EvPrRn unset does no FW forcing for that tracer. Your values for PTRACERS_ref may also affect concentration/dilution here, depending on your options for freshwater forcing and surface boundary conditions (see ptracers_forcing_surf.F): you might find the situation (per “convertFW2Salt” value or “useRealFreshWaterFlux” flag) where the dilution/concentration effect is the difference between PTRACERS_ref at the surface and PTRACERS_EvPrRn i.e. if they’re both zero, then there’s no FW induced effect, where you might want one.</div><div class=""><br class=""></div><div class="">If you’re still getting weird pH values, then you might want to consider using the Munhoven (2013) carbonate system solver (#define CARBONCHEM_SOLVESAPHE in DIC_OPTIONS.h and selectPHsolver>0 in data.dic)…it’s probably more complicated and less efficient that the Follows et al (2006) scheme, but it may be a bit more robust to initialization shocks and varied paleoclimate conditions. </div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Jonathan</div><div class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">___________________________________________________________________________<br class="">Dr. Jonathan M. Lauderdale<br class="">Research Scientist<br class="">Department of Earth, Atmosphere and Planetary Sciences <br class="">Massachusetts Institute of Technology <br class="">77 Massachusetts Avenue (54-1518)<br class="">Cambridge, MA 02139, USA <br class="">Office: +1 617 324 1568 </div><div class="">Cell : +1 617 304 5661<br class="">Email:<span class="Apple-converted-space"> </span><a href="mailto:jml1@mit.edu" class="">mailto:jml1@mit.edu</a></div><div class=""><span style="text-align: -webkit-auto;" class="">Web: </span><span class=""></span><a href="http://paocweb.mit.edu/people/jml1" style="text-align: -webkit-auto;" class="">http://paocweb.mit.edu/people/jml1</a></div><span class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span class="">Twitter: </span><a href="https://twitter.com/jon_lauderdale" style="text-align: -webkit-auto;" class="">https://twitter.com/jon_lauderdale<br class=""></a><span style="text-align: -webkit-auto;" class="">Blog: </span><a href="https://seamanticscience.wordpress.com/" style="text-align: -webkit-auto;" class="">https://seamanticscience.wordpress.com/</a></div></span></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span class="">Git: </span><a href="https://github.com/seamanticscience" class="">https://github.com/seamanticscience</a><span class=""><br class=""></span><div class="">___________________________________________________________________________</div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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<div><br class=""><blockquote type="cite" class=""><div class="">On Nov 5, 2020, at 12:45 PM, Charline Ragon <<a href="mailto:Charline.Ragon@unige.ch" class="">Charline.Ragon@unige.ch</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div class="">
<font face="Times New Roman, Times, serif" class="">Dear all,<br class="">
<br class="">
I would like to restart a simulation originally performed without
the biogeochemical packages by activating them (thus including
PTRACERS, GCHEM and DIC). Since there are no some of the needed
pickups (namely, pickup_cpl and pickup_aimCo2), I have created
them by performing a simulation that starts from nIter0=0. My idea
is to use such pickups to restart my simulation, is this the right
procedure?<br class="">
<br class="">
Doing like this, I obtain reasonable values for the tracers if I
activate DIC_BOUNDS in order to avoid out-of-range pH values.<br class="">
<br class="">
Since I am performing paleo-climate simulations with huge
uncertainties on the concentrations of the different tracers, I am
wondering: <br class="">
<br class="">
1. Is it correct to set PTRACERS_ref to zero values and start from
PTRACERS_Iter0=nIter0 without any initial file? (if I understand
well, all fields would be initialised to 0 in this case)<br class="">
2. Is the model very sensitive to PTRACERS_EvPrRn? Or is it only
necessary to give a certain value for allowing
dilution/concentration? Which value?<br class="">
3. Which is the role of the input files in data.dic (ice, wind,
silica, atmospheric pressure)? Should they replace pickup files?<br class="">
<br class="">
Thanks in advance for any suggestion!<br class="">
<br class="">
Best,<br class="">
Charline<br class="">
<br class="">
<br class="">
</font>--<br class="">
<font face="Times New Roman, Times, serif" class=""><font face="Times New
Roman, Times, serif" class="">Charline RAGON<br class="">
PhD Student<br class="">
Group of Applied Physics & Institute for Environmental
Sciences<br class="">
University of Geneva, Switzerland</font></font>
</div>
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