checking on runs from 140604 showed that topography is probably not working because they all look the same, but I will look further into this once i have full results. I want to try a few runs with higher resolution. also, steve brought to my attentionthis morning that q should include vertical part, too, so i don't think i have to add it in the end, will plot qfull without it.
correcting runs from 140604 and 140605 on 140606. high res runs were badly scaled, corrected. narrowdw actually widened dw, tried something else. transport may be kept constant by jet eq, look into this. tried moving dw even closer to wall. corrected topography runs, paralleled the tests that were attempted in topo1-topo4 in topo12-topo42. main problem was that hb was not a common variable. also changed some int/float stuff that might have been problematic.
still waiting on the high resolution runs from 140606. reran topo12-42 with a parabolic taper down to zero under toposmooth1-4, strengthened the jet in movedwcloser4 to get more appropriate transport (?), varied height of topography in topoh1-2, varied zonal and meridional extent of curve in topom/z1-2 and broadened outflow in out1-2. varying runs are based on topo42 as the base case since it was most exciting. also found, using modelpsi.m (which i should probably adapt for python if i keep using it substantially), that jsi/jso are west/east respectively, not necessarily in/out.
140609 didn't change results too qualitatively, new host of runs post meeting with glenn explore 1) looking at the spinup, 2) changing the domain size (was superfluously large), 3) changing slope size and 4) current shape and width
also testing how much the outflow position matters and noting here that i messed ydim up initially as i didn't repos the dwbc
also note that the last commit was not done from top dir, this one was though, so will include whatever is missing in prev
results from 140613 are not earth shattering, but provide good diversity. confusing that ydim (efforts to make y range smaller) diverged, not sure why, not currently a priority, can look at spinup period to see. am now looking into whether q includes vertical or not by plotting zeta from u. this is for the purposes of looking into the stability criterion, relationship between q and psi, etc. also am restructuring quickplot.py
post-committee meeting: there was a mad rush to make plots, pdfs in particular for the resolution, so its a bit of a mess. focus now on science questions and on reproducing things appropriately (scales, etc.)
ran a few test cases in light of comm.meeting comments. messed up by running ydim_baro twice and not running ydim_barotopo at all. no matter, i am basically going to run the same scenarios over again, but with a stronger gs and move the currents further north.
added a psibaro to quickplot, which plots barotropic and baroclinic streamfunctions. noticed that baro_nt is not barotropic, there is a mistake in jet2.h. many interesting questions coming out of barotopo, difficult to tease out dwbc role, but gs distance to topo matters a lot for its interaction with topography.
rtest and agebot from 140711 finished and concluded that adding the extra viscous r tests does not affect results really, i can keep them in though... age tracer didn't work out, looking into why now.
found one problem with agebot, which is that it was not being stepped forward in time... this has been fixed in 140714, but still does not seem to be working quite right. Am letting longer run go and will address this issue further tomorrow. Have also updated quickplot.py to make 2d plots of stability criterion, not sure how useful this will be, but it is on hand. Things to work on are: 1) checking that my GS parameters are similar to Waterman and Jayne (where it is relevant, maybe also think about NAC) and 2) changing topographic size to look into the size of periodic NAC disturbances.
have been mostly battling age tracer in bottom layer. 140714 became a testing ground for what was going wrong. thought it was all fixed and started a bunch of longer runs in 140716. however, didn't come out right and email from steve pointed to fact that i was accumulating age wrong (was doing it in rhsage instead of in age directly). 140717 is a redo of 140716 but with the correction enforced
corrected 140717 results are more promising than 140716, quite a bit of noise and negative values coming from the edges, though. the bnd1-3 series is an attempt to address this. bnd1: limit the rhsage calculation to 2-m-1, etc, do not include boundary points as was done previously. bnd2: set western boundary to be non-zero (same value as interior). bnd3: elaborates on bnd2, also includes south and north boundaries in non-zero-ing. moving forward: once i hammer this down, and it seems like adding the upper layer will not be too tricky, take a step back and think about big picture/ relation to observations in heading new run efforts.
added a few more runs. did a longer bnd3 case in which i introduced a saving scheme that should save every 100 nondimensional time units, so that i can get a spread out view of how things are evolving. i did the same for bnd4, in which bnd3 and bnd1 conditions were simultaneously implemented. will have to do some script cleanup as well moving forward.