Merge pull request #33 from JosueBock/master

minor adjustments before publication

CREDITS

@@ -6,74 +6,74 @@ The main developers are:
 
 Below are listed all co-authors of papers dealing with previous versions of MISTRA that were published until 2015.
 
-- Aiuppa, A.
-- Allen, A. G.
-- Arellano, S.
+- Aiuppa, Alessandro
+- Allen, Andrew G.
+- Arellano, Santiago R.
 - Bleicher, Sergej
-- Bobrowski, N.
+- Bobrowski, Nicole
 - Bock, Josué
 - Bott, Andreas
 - Bräuer, Peter
-- Brought, N.
-- Burkholder, J. B.
+- Brough, Neil
+- Burkholder, James B.
 - Buxmann, Joelle
-- Buys, Z.
+- Buys, Zak
 - Carpenter, Lucy J.
 - Crutzen, Paul J.
-- D'Alessandro, W.
+- D'Alessandro, Walter
 - Dibb, Jack E.
 - Dunk, Rachel M.
-- Finley, B. D.
-- Franco, A.
-- Galle, B.
-- Giuffrida, G. B.
+- Finley, Brandon D.
+- Franco, Angela
+- Galle, Bo
+- Giuffrida, Giovanni B.
 - Held, Andreas
 - Hornsby, Karen E.
 - Huey, L. Gregory
-- Ibrahim, O. W.
-- Inguaggiato, S.
-- Johansson, M.
-- Jones, A. E.
+- Ibrahim, Ossama W.
+- Inguaggiato, Salvatore
+- Johansson, Mattias
+- Jones, Anna E.
 - Jones, Charlotte E.
 - Joyce, Patrick L.
-- Keene, W. C.
+- Keene, William C.
 - Kerkweg, Astrid
 - Landgraf, Jochen
-- Lawler, M. J.
-- Lefer, Barry
-- Liao, J.
-- Louban, I.
-- Loughlin, P. E.
-- Lovejoy, E. R.
+- Lawler, Michael J.
+- Lefer, Barry L.
+- Liao, Jin
+- Louban, Ilia
+- Loughlin, Peter E.
+- Lovejoy, Edward R.
 - Luo, Beiping
-- Mather, T. A.
+- Mather, Tamsin A.
 - McFiggans, Gordon
 - Ofner, Johannes
 - Panhans, Walter-Georg
 - Pechtl, Susanne
 - Piot, Matthias
 - Platt, Ulrich
-- Pszenny, A. A. P.
-- Pyle, D. M.
-- Read, K. A.
-- Saltzman, E. S.
+- Pszenny, Alexander A. P.
+- Pyle, David M.
+- Read, Katie A.
+- Saltzman, Eric S.
 - Sander, Rolf
-- Schmitz, G.
+- Schmitz, Guy
 - Schneider, Werner
-- Sievers, U.
-- Simpson, W. R.
+- Sievers, Uwe
+- Simpson, William R.
 - Smoydzin, Linda
 - Sommariva, Roberto
 - Stutz, Jochen
-- Tanner, D. J.
-- Tedesco, D.
+- Tanner, David J.
+- Tedesco, Dario
 - Thomas, Jennie L.
 - Toyota, Kenjiro
 - Trautmann, Thomas
-- Valenza, M.
+- Valenza, Mariano
 - von Glasow, Roland
 - Winterrath, Tanja
-- Yalire, M.
+- Yalire, Mathieu
 - Zdunkowski, Wilford G.
 - Zetzsch, Cornelius
 

plots/Buxmann_2015_Fig5_alpha.ncl

@@ -13,24 +13,9 @@ begin
 ; read in netCDF file
 ;************************************************
 
-; Buys et al file  
-  if (True) then
-    outd = "/media/josue/BACKUP2/mafalda-backup/data/Joelle/"
-    outdir = outd+"alpha/" ; NOK
-    outdir = outd+"alphwlHOBr/" ; panel 1 roughly ok
-    ;;outdir = outd+"alphwl1HCHO20"
-    ;outdir = outd+"alphwlBr/"
-    ;outdir = outd+"alphwl1/"
-    ;outdir = outd+"alphaloss/"
-    ;outdir = outd+"alphwl1HCHO20_nA/"
-    ;outdir = outd+"alphaloss2/"
-    ;outdir = outd+"alphaloss1/"
-    ;outdir = outd+"alphaloss1HCHO/"
-    ;outdir = outd+"alphwl10HCHO20/"
-    ;outdir = outd+"alphaloss10/"
-  end if
-
-  ;GridFile = addfile(outdir+"grid.nc","r")
+; Buys et al file
+  outdir = "~/Mistra_2019/out/Buxmann15_alpha/"
+
   MeteoFile = addfile(outdir+"meteo.nc","r")
   GasFile = addfile(outdir+"gas.nc","r")
 
@@ -145,10 +130,12 @@ begin
   res@vpWidthF            = 0.75
 
   ; Axis settings
-  ;res@trYMinF              = 0.
-  ;res@trYMaxF              = 600.
+  res@tiXAxisOn         = False
   res@tiXAxisString     = "Time (min)"
-  res@tiYAxisString     = "Mixing ratio (ppt)"
+  res@tiYAxisString     = "l"   ; string of limited width, that will not overlap the gsn_text (see below)
+  res@tiYAxisFontColor  = 0     ; use white fonts for Y-axix titles (use gsn_text_ndc later)
+  ;res@tiYAxisOn        = False ; this option did not work well, since the alignment with/without Y-axis
+                                ; is very different once panelled.
   ; Informations displayed on top
   res@gsnLeftString = ""
   res@gsnRightString = ""
@@ -162,8 +149,14 @@ begin
   res@tmXBTickStartF = -20.
   res@tmXBTickEndF = 140.
   res@tmXBTickSpacingF = 20.
+  res@tmXMajorGrid = True
+  res@tmXBMinorOn = False
+  res@tmXMajorGridLineColor = "Grey70"
+  res@tmXMajorGridLineDashPattern = 2
   res@xyLineThicknessF = 3
 
+  res@tiYAxisOffsetXF = 0.012 ; even if not displayed directly, offset the Y-axis to the right to account
+                              ; for the wider labels (4 digits here, only 3 in the next two plots)
   res@trYMaxF     = 2200.
   res@tmYLMode = "Manual"
   res@tmYLTickStartF = 0.
@@ -173,27 +166,64 @@ begin
   res@xyDashPatterns = (/1,8,0/)
   plot(0) = gsn_csm_xy(wks,time,data1,res)
 
-  res@trYMaxF     = 900.
-  res@tmYLTickStartF = 0.
-  res@tmYLTickEndF = 800.
+  res@tiYAxisOffsetXF = 0. ; back to default value (see explanation above)
+  res@trYMaxF = 900.
+  res@tmYLTickStartF   = 0.
+  res@tmYLTickEndF     = 800.
   res@tmYLTickSpacingF = 200.
-  res@xyLineColors := (/"royalblue4","royalblue4"/)
+  res@xyLineColors   := (/"royalblue4","royalblue4"/)
   res@xyDashPatterns := (/1,2/)
   plot(1) = gsn_csm_xy(wks,time,data2,res)
 
-  res@tiYAxisString     = "Mixing ratio (ppb)"
-  res@trYMaxF     = 300.
-  res@tmYLTickStartF = 0.
-  res@tmYLTickEndF = 300.
+  res@tiXAxisOn = True
+  res@trYMinF = -20.
+  res@trYMaxF = 300.
+  res@tmYLTickStartF   = 0.
+  res@tmYLTickEndF     = 300.
   res@tmYLTickSpacingF = 50.
-  res@xyLineColors = (/"red2","black"/)
-  res@xyDashPatterns = (/2,0/)
+  res@xyLineColors   := (/"red2","black"/)
+  res@xyDashPatterns := (/2,0/)
   plot(2) = gsn_csm_xy(wks,time,data3,res)
 
+;************************************************
+; add shading for dark time
+;************************************************
+  xpt1 = (/-20,0,0,-20,-20/)
+  ypt1 = (/-20,-20,2500,2500,-20/)
+  xpt2 = (/110,150,150,110,110/)
+  ypt2 = ypt1
+  plgres = True
+  plgres@tfPolyDrawOrder = "PreDraw"
+  plgres@gsFillColor = "Grey90"
+  plg0a = gsn_add_polygon(wks,plot(0),xpt1,ypt1,plgres)
+  plg0b = gsn_add_polygon(wks,plot(0),xpt2,ypt2,plgres)
+  plg1a = gsn_add_polygon(wks,plot(1),xpt1,ypt1,plgres)
+  plg1b = gsn_add_polygon(wks,plot(1),xpt2,ypt2,plgres)
+  plg2a = gsn_add_polygon(wks,plot(2),xpt1,ypt1,plgres)
+  plg2b = gsn_add_polygon(wks,plot(2),xpt2,ypt2,plgres)
 
 ;************************************************
-; create panel
+; add bommon y-axis title
 ;************************************************
-  gsn_panel(wks,plot,(/3,1/),False)             ; now draw as one plot
+  ; since these text are drawn before the panel, the individual titles of the three plots overlap these.
+  ; The solution found (see also the comments above) is to use a "l" (limited width) title, and white colour.
+  ; Last, the overlap is checked (by temporarily setting a visible colour) and the x/y positions are adjusted in the panel.
+  ; The y-axis of the third plot could have been kept, however using the same process allows perfect alignment of both titles.
+  txres = True
+  txres@txAngleF = 90
+  txres@txFontHeightF = 0.0214
+  gsn_text_ndc(wks,"Mixing ratio (pmol mol~S~-1~N~)",0.02,.70,txres)
+  gsn_text_ndc(wks,"Mixing ratio (nmol mol~S~-1~N~)",0.02,.222,txres)
 
-end
+;************************************************
+; create panel
+;************************************************
+  ;drawNDCGrid(wks) ; used for adjustments
+  resP = True
+  ;resP@gsnPanelDebug = True ; used for adjustments
+  resP@gsnPanelBottom = 0.04 ; keep space for tiXAxis
+  resP@gsnPanelXF = (/0.128225,0.128225,0.128225/)
+  resP@gsnPanelYF = (/0.970522,0.650522,0.330522/)
+  gsn_panel(wks,plot,(/3,1/),resP)             ; now draw as one plot
+
+end

plots/Buys_2013_Fig3.ncl

@@ -63,36 +63,43 @@ begin
   res@gsnMaximize                  = True            ; use full page
   res@gsnPaperOrientation          = "portrait"      ; prevent automatic rotation
   ; adjust plot to get same height and width
-  res@vpHeightF           = 0.4
-  res@vpWidthF            = 0.6
+  res@vpHeightF           = 0.44
+  res@vpWidthF            = 0.7
 
   ; X-Axis settings
-  ;res@trXMinF           = -3.
-  ;res@trXMaxF           = 26.
+  res@trXMinF           = -1.5
+  res@trXMaxF           = 27.
   res@tmXBMode          = "Manual"
   res@tmXBTickStartF    = 0.
   res@tmXBTickEndF      = 24.
   res@tmXBTickSpacingF  = 6.
   res@tmXBMinorPerMajor = 5
+  res@tmXTOn            = False
   res@tiYAxisString     = "Time (h)"
+  res@tiXAxisFontHeightF = 0.02
   ; Y-Axis settings
   ;res@trYMinF           = 0.
-  ;res@trYMaxF           = 15.
+  res@trYMaxF           = 15.
   res@tmYLMode          = "Manual"
   res@tmYLTickStartF    = 0.
   res@tmYLTickEndF      = 14.
   res@tmYLTickSpacingF  = 2.
   res@tmYLMinorPerMajor = 1
+  res@tmYROn            = False
   res@tiYAxisString     = "Br~B~2~N~ (pmol mol~S~-1~N~)"
+  res@tiYAxisFontHeightF = 0.02
   ; Informations displayed on top
   res@gsnLeftString = ""
   res@gsnRightString = ""
 
   plot(0) = gsn_csm_xy(wks,time,Br2,res)
 
   ; Adjust plot settings for BrCl
+  ; X-Axis settings
+  res@trXMinF           = -2.5
+  res@trXMaxF           = 26.5
   ; Y-Axis settings
-  res@trYMinF           = 0.
+  res@trYMinF           = -0.05
   res@trYMaxF           = 3.
   res@tmYLMode          = "Manual"
   res@tmYLTickStartF    = 0.
@@ -107,4 +114,4 @@ begin
 ;************************************************
   gsn_panel(wks,plot,(/1,2/),False)             ; now draw as one plot
 
-end
+end

plots/Joyce_2014_Fig2.ncl

@@ -94,10 +94,16 @@ begin
   res@lbOrientation        = "Vertical"  ; Default is horizontal
 
   ; Axis settings
-  res@trYMinF              = 0.
+  res@trYMinF              = 5.
   res@trYMaxF              = 600.
-  res@tiXAxisString     = "Time (h)"
-  res@tiYAxisString     = "Height (m)"
+  res@tiXAxisString = "Time (h)"
+  res@tiYAxisString = "Height (m)"
+  res@tiXAxisFontHeightF = 0.02
+  res@tmXBMinorOn = False
+  res@tmXTOn      = False
+  res@tmYLMode    = "Explicit"
+  res@tmYLValues  = (/5,50,100,150,200,250,300,350,400,450,500,550/)
+  res@tmYLLabels  = "" + res@tmYLValues
   ; Informations displayed on top: nothing in this plot
   res@gsnLeftString = ""
   res@gsnRightString = ""

plots/Joyce_2014_Fig3.ncl

@@ -20,8 +20,6 @@ begin
   GasFile = addfile(outdir+"gas.nc","r")
   AqFile = addfile(outdir+"aq.nc","r")
 
-  ntim=201 ; timesteps
-
 ; define bounds
 ; -------------
 ; plot up to ~600m: end at grid index 62 (remember index 1 is skipped (zero-height layer), index 2 middle of layer = 5m, index 62 = 605m)
@@ -41,6 +39,7 @@ begin
   nmin = GasFile->lmin(tidx:,0,0,0) ; file is (rec=, noz=1, y=1, x=1) ; units min
   time = nday*24. + nhour + nmin/60.
 
+  ntim=dimsizes(time) ; timesteps
 
 ; import data
 ; -----------
@@ -99,6 +98,8 @@ begin
   res@gsnFrame                     = False
   res@gsnMaximize                  = True            ; use full page
   res@gsnPaperOrientation          = "portrait"      ; prevent automatic rotation
+  res@gsnLeftStringFontHeightF     = 0.03
+  res@gsnRightStringFontHeightF    = 0.03
 
   ; adjust plot to get same height and width
   res@vpHeightF           = 0.6
@@ -110,15 +111,24 @@ begin
   res@cnLinesOn            = False
   res@cnLevelSelectionMode =  "ManualLevels"
   res@cnMinLevelValF       =  1.
-  res@cnMaxLevelValF       =  60.
+  res@cnMaxLevelValF       =  59.
   res@cnLevelSpacingF      =  4.
   res@lbOrientation        = "Vertical"  ; Default is horizontal
 
   ; Axis settings
-  res@trYMinF              = 0.
-  res@trYMaxF              = 600.
-  res@tiXAxisString     = "Time (h)"
-  res@tiYAxisString     = "Height (m)"
+  res@trYMinF = 5.
+  res@trYMaxF = 600.
+  res@tmXTOn               = False
+  res@tmXBLabelFontHeightF = 0.03
+  res@tmXBMinorOn          = False
+  res@tmYLMode             = "Explicit"
+  res@tmYLValues           = (/5,50,100,150,200,250,300,350,400,450,500,550/)
+  res@tmYLLabels           = "" + res@tmYLValues
+  res@tmYLLabelFontHeightF = 0.03
+  res@tiXAxisString      = "Time (h)"
+  res@tiYAxisString      = "Height (m)"
+  res@tiXAxisFontHeightF = 0.03
+  res@tiYAxisFontHeightF = 0.03
   ; Informations displayed on top
   res@gsnLeftString = "NO~B~x~N~ (nmol mol~S~-1~N~)"
   res@gsnRightString = "max = "+sprintf("%5.1f",max(NOx))
@@ -137,6 +147,8 @@ begin
 ;************************************************
 ; create panel
 ;************************************************
-  gsn_panel(wks,plot,(/2,1/),False)             ; now draw as one plot
+  resP = True
+  resP@gsnPanelYWhiteSpacePercent = 2
+  gsn_panel(wks,plot,(/2,1/),resP)             ; now draw as one plot
 
-end
+end