[MITgcm-support] Sample pTracer using flt package
Martin Losch
Martin.Losch at awi.de
Thu Jun 14 09:39:01 EDT 2018
Hi Qian,
I think I said before that I never used the flt-package, so I have no experience, how it actually works, but I’ll give ti a shot to answer you questions, see below:
> On 14. Jun 2018, at 15:16, 钱钰坤 <qianyk at mail3.sysu.edu.cn> wrote:
>
> Hi Martin,
>
> Thanks for your help. I've compiled and run these codes successfully. However, I get all zeros after the run.
>
> 1) You have suggested to modify the Lagrangian sampling code as (see previous email below):
> CALL FLT_BILINEAR (ix,jy,ss, pTracer(1-Olx,1-Oly,1,1,1, iTracer), kp,0,bi,bj,myThid)
> I just wonder why this line is not like:
> CALL FLT_BILINEAR (ix,jy,ss, pTracer(1-Olx,1-Oly,1,bi,bj, iTracer), kp,0,bi,bj,myThid)
> The index of 1 rather than bi/bj seems to works fine for sampling the tracer field.
in s/r flt_bilinear, the input “var” is defined as
_RL var(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr,nSx,nSy)
so as a full 5D field, but you are passing ptracers which is 6D. In Fortran 77 you actually only pass the address of the first element of a field, and this is what I suggested by pTracer(1-Olx,1-Oly,1,1,1, iTracer), so s/r flt_bilinear “sees” the address of where to start and assumes a 5D field (the last index varies most slowly). I assume that your bi/bj = 1 anyway, so the other form should have worked (as long as you not using the multi-thread-code where bi/bj can be > 1), but better do it right the first time. Passing the indices bi,bj tell s/r flt_bilinear, where to operate on in the input file “var”. E.g. in pkg/gchem/gchem_calc_tendency.F, cfc11_forcing assumes 3D input fields and you have to pass the proper pTracer(1-Olx,1-Oly,1,bi,bj, iTracer) fields. In Fortran90 things would be more transparent.
>
> 2) the predefined subroutines GAD_GRAD_X/Y in GAD package return tracer gradient much
> larger than expected. I looked into the code and found that these subroutines calculate the
> product of gradient and face area of grid cell. So I may need to divide the face area to get
> the right values of gradient. Is this correct? If so, I cannot just modify the subroutines because
> they may be called in other places.
Correct, it calculates a flux through the cell face, with area xA/yA
>
> 3) Subroutines GAD_GRAD_X/Y return non-zero values at the end of ptracer_integrate.F (this is
> verified by outputting pTrGrdx/y after calling GAD_GRAD_X/Y subroutines), however,
> in flt_traj.F, pTrGrdx/y becomes all zeros (this is verified by outputting pTrGrdx/y before calling
> FLT_BILINEAR). Therefore, Lagrangian sampling gives all zero results. Does this related to any
> execution sequence? Or any other possible reasons I cannot tell.
how do you define your xA/yA in flt_traj? in ptracers_integrate they are computed in s/r calc_adv_flow. In your case, because you don’t want your gradients multiplied with the area you could just define local fields
_RS xA (1-OLx:sNx+OLx,1-OLy:sNy+OLy)
_RS yA (1-OLx:sNx+OLx,1-OLy:sNy+OLy)
and set them to one. That would also solve your question (2).
Martin
>
> Many thanks.
>
> ------------------
> Best regards
>
> Yu-Kun Qian (钱钰坤)
> Center for Monsoon and Environment Research
> Department of Atmospheric Sciences
> School of Environmental Science and Engineering
> Sun Yat-sen University
> No. 135 Xingang West Road, Haizhu District
> Guangzhou, 510275, P.R. China
> Tel; 020-84115227
> Email: qianyk at mail3.sysu.edu.cn
>
>
>
>
> ------------------ 原始邮件 ------------------
> 发件人: "Martin Losch"<Martin.Losch at awi.de>;
> 发送时间: 2018年6月14日(星期四) 晚上7:38
> 收件人: "MITgcm Support"<mitgcm-support at mitgcm.org>;
> 主题: Re: [MITgcm-support] Sample pTracer using flt package
>
> Looks good to me.
>
> M.
>
> > On 14. Jun 2018, at 05:23, 钱钰坤 <qianyk at mail3.sysu.edu.cn> wrote:
> >
> > Hi all,
> >
> > Still along this line, I want to sample pTracer along Lagrangian trajectory using flt
> > package. Now I'm able to sample pTracer itself and I want to sample its gradient
> > too.
> >
> > I add two arrays to store the gradient (vector) of pTracer in PTRACER_FIELDS.h:
> > _RL pTrGrdx (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr,nSx,nSy)
> > _RL pTrGrdy (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr,nSx,nSy)
> >
> > Then I add the following lines at the end of ptracer_integrate.F to calculate the
> > gradient of the ninth tracer, which makes use of the predefined subroutines of
> > GAD_GRAD_X and GAD_GRAD_Y in GAD package:
> > IF (iTracer .EQ. 9) THEN
> > CALL GAD_GRAD_X(
> > I bi,bj,k,xA,pTracer(1-Olx,1-Oly,1,bi,bj,9),
> > O pTrGrdx(1-Olx,1-Oly,1,bi,bj),
> > I myThid)
> > CALL GAD_GRAD_Y(
> > I bi,bj,k,yA,pTracer(1-Olx,1-Oly,1,bi,bj,9),
> > O pTrGrdy(1-Olx,1-Oly,1,bi,bj),
> > I myThid)
> > ENDIF
> >
> > Finally, I modify the Lagrangian sampling code in flt_traj.F as:
> > CALL FLT_BILINEAR (ix,jy,uu,pTrGrdx(1-Olx,1-Oly,1,1,1),
> > I kp,1,bi,bj,myThid)
> > CALL FLT_BILINEAR (ix,jy,vv,pTrGrdy(1-Olx,1-Oly,1,1,1),
> > I kp,2,bi,bj,myThid)
> > so that the gradients are stored in the u/v samples of particles.
> >
> > I just want to make sure that this is OK. I am aware of that gradX is defined
> > at u-point and gradY is defined at v-point. So I guess this should be the best
> > way to get online sampled tracer gradient.
> >
> >
> > ------------------
> > Best regards
> >
> > Yu-Kun Qian (钱钰坤)
> > Center for Monsoon and Environment Research
> > Department of Atmospheric Sciences
> > School of Environmental Science and Engineering
> > Sun Yat-sen University
> > No. 135 Xingang West Road, Haizhu District
> > Guangzhou, 510275, P.R. China
> > Tel; 020-84115227
> > Email: qianyk at mail3.sysu.edu.cn
> >
> >
> >
> >
> > ------------------ 原始邮件 ------------------
> > 发件人: "qianyk"<qianyk at mail3.sysu.edu.cn>;
> > 发送时间: 2018年6月2日(星期六) 晚上7:12
> > 收件人: "mitgcm-support"<mitgcm-support at mitgcm.org>;
> > 主题: 回复： [MITgcm-support] Sample pTracer using flt package
> >
> > Hi Martin,
> >
> > Thanks very much for your suggestions. I can sample the value of ptracer online now.
> >
> > However, there are considerable differences between online-sampled and offline-sampled
> > values. I've doubted about the results of my offline-sampling program and that is why I
> > insist to get the online results to verify that. Since I have to also sample the gradient of
> > the tracer, there are more questions follow this line.
> >
> > For a quick solution, I hope to compute the tracer gradient online and then sample the
> > gradient field exactly the same way as I sample the tracer field (just passing the pointer
> > of the gradient to the subroutine FLT_BILINEAR). However, I've no idea how and where
> > to do this. I've found many diagnostics in available_diagnostics.log related to the tracer
> > itself (UTRAC01, ADVrTr01, ...) which could be modified slightly to be the tracer gradient.
> > I just wonder if this is the best way to do get Lagrangian sampling of tracer gradient.
> >
> > From a fundamental way, I just want to figure out the differences in the programs. The
> > tracer field is output as MDSIO format. As MITgcm uses C-grid, should the position of the
> > lower-left-corner value of the tracer be exactly zero, or be DXC (DYC), or be DXC/2 (DYC/2)?
> > I think this tiny differences in position will cause considerable sampled tracer value if the
> > gradient is large.
> >
> > I also set north and east wall boundaries so the domain is closed (the eastmost Nx and
> > northmost Ny grid points are all set to the undefined value of 0). Could the Lagrangian
> > particle get into the cell of these grid points or they just stay within [1 Nx-1]*[1 Ny-1]
> > grid points? More specifically, what are the upper and lower bounds of position for a
> > Lagrangian particle?
> >
> > Thanks again.
> >
> >
> >
> > ------------------
> > Best regards
> >
> > Yu-Kun Qian (钱钰坤)
> > Center for Monsoon and Environment Research
> > Department of Atmospheric Sciences
> > School of Environmental Science and Engineering
> > Sun Yat-sen University
> > No. 135 Xingang West Road, Haizhu District
> > Guangzhou, 510275, P.R. China
> > Tel; 020-84115227
> > Email: qianyk at mail3.sysu.edu.cn
> >
> >
> >
> >
> > ------------------ 原始邮件 ------------------
> > 发件人: "Martin Losch"<Martin.Losch at awi.de>;
> > 发送时间: 2018年6月1日(星期五) 晚上7:25
> > 收件人: "MITgcm Support"<mitgcm-support at mitgcm.org>;
> > 主题: Re: [MITgcm-support] Sample pTracer using flt package
> >
> > Hi Qian,
> >
> > I think you can do it that way.
> > You need to include the ptracer variables at the beginning of the routine like this:
> > #ifdef ALLOW_PTRACERS
> > #include "PTRACERS_SIZE.h"
> > #include “PTRACERS_FIELDS.h"
> > #endif
> >
> > and it’s always a good idea to bracket pkg-specific code by CPP-flags:
> > #ifdef ALLOW_PTRACERS
> > … your code ...
> > #endif
> >
> > I think you need to say
> > CALL FLT_BILINEAR (ix,jy,ss, pTracer(1-Olx,1-Oly,1,1,1, iTracer), kp,0,bi,bj,myThid)
> > to pass the approriate pointer to FLT_BILINEAR
> >
> > Martin
> > > On 1. Jun 2018, at 12:19, 钱钰坤 <qianyk at mail3.sysu.edu.cn> wrote:
> > >
> > > Hi all,
> > >
> > > I've inserted an passive tracer (using ptracer package) and deployed
> > > Lagrangian particles (using flt package) simultaneously into a dynamic flow.
> > > I wanted to sample the tracer value along each Lagrangian float but I only
> > > found the following five lines of code in flt_traj.F:
> > >
> > > CALL FLT_BILINEAR (ix,jy,uu,uVel, kp,1,bi,bj,myThid)
> > > CALL FLT_BILINEAR (ix,jy,vv,vVel, kp,2,bi,bj,myThid)
> > > CALL FLT_BILINEAR2D(ix,jy,pp,etaN, 0,bi,bj,myThid)
> > > CALL FLT_BILINEAR (ix,jy,tt,theta, kp,0,bi,bj,myThid)
> > > CALL FLT_BILINEAR (ix,jy,ss,salt, kp,0,bi,bj,myThid)
> > >
> > > which means the flt can only sample the basic flow states (u, v, eta, theta, and salt).
> > >
> > > I wonder if there is an easy way to achieve this by modifying the code slightly as:
> > >
> > > CALL FLT_BILINEAR (ix,jy,ss, pTracer(, , , , , iTracer), kp,0,bi,bj,myThid)
> > >
> > > and using the result to replace the salt which I do not care about?
> > >
> > > If yes, how to modify the #include or variable declarations at the beginning of flt_traj.F?
> > >
> > > Many thanks.
> > >
> > >
> > > ------------------
> > > Best regards
> > >
> > > Yu-Kun Qian (钱钰坤)
> > > Center for Monsoon and Environment Research
> > > Department of Atmospheric Sciences
> > > School of Environmental Science and Engineering
> > > Sun Yat-sen University
> > > No. 135 Xingang West Road, Haizhu District
> > > Guangzhou, 510275, P.R. China
> > > Tel; 020-84115227
> > > Email: qianyk at mail3.sysu.edu.cn
> > >
> > >
> > > _______________________________________________
> > > MITgcm-support mailing list
> > > MITgcm-support at mitgcm.org
> > > http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support
> >
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>
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