Merge branch 'master' into readthedocs

.gitignore

@@ -0,0 +1,7 @@
+docs/_build
+.ipynb_checkpoints
+octave-workspace
+release2_climatology
+GRID
+devel
+

gcmfaces_calc/calc_UEVNfromUXVY.m

@@ -3,25 +3,9 @@
 %inputs:    fldU/fldV are the X/Y vector fields at velocity points
 %outputs:   fldUe/fldVn are the Eastward/Northward vectors at tracer points
 
-global mygrid;
+gcmfaces_global;
 
 %fldU(mygrid.hFacW==0)=NaN; fldV(mygrid.hFacS==0)=NaN;
 nr=size(fldU.f1,3); fldU(mygrid.hFacW(:,:,1:nr)==0)=NaN; fldV(mygrid.hFacS(:,:,1:nr)==0)=NaN;
 
-[FLDU,FLDV]=exch_UV(fldU,fldV);
-
-fldUe=fldU; fldVn=fldV;
-for iF=1:fldU.nFaces; 
-tmp1=FLDU{iF}(1:end-1,:,:); tmp2=FLDU{iF}(2:end,:,:);
-fldUe{iF}=reshape(nanmean([tmp1(:) tmp2(:)],2),size(tmp1));
-tmp1=FLDV{iF}(:,1:end-1,:); tmp2=FLDV{iF}(:,2:end,:);
-fldVn{iF}=reshape(nanmean([tmp1(:) tmp2(:)],2),size(tmp1));
-end;
-
-FLDU=fldUe; FLDV=fldVn;
-cs=mk3D(mygrid.AngleCS,FLDU); sn=mk3D(mygrid.AngleSN,FLDU);
-
-fldUe=+FLDU.*cs-FLDV.*sn;
-fldVn=FLDU.*sn+FLDV.*cs;
-
-
+[fldUe,fldVn]=calc_UV_zonmer(fldU,fldV);

gcmfaces_calc/calc_UV_zonmer.m

@@ -0,0 +1,26 @@
+function [fldUe,fldVn]=calc_UV_zonmer(fldU,fldV);
+%object:    compute Eastward/Northward vectors form X/Y vectors
+%inputs:    fldU/fldV are the X/Y vector fields at velocity points
+%outputs:   fldUe/fldVn are the Eastward/Northward vectors at tracer points
+%
+%note: this routine does no apply any mask -- unlike the old calc_UEVNfromUXVY.m
+
+gcmfaces_global;
+
+[FLDU,FLDV]=exch_UV(fldU,fldV);
+
+fldUe=fldU; fldVn=fldV;
+for iF=1:fldU.nFaces; 
+tmp1=FLDU{iF}(1:end-1,:,:); tmp2=FLDU{iF}(2:end,:,:);
+fldUe{iF}=reshape(nanmean([tmp1(:) tmp2(:)],2),size(tmp1));
+tmp1=FLDV{iF}(:,1:end-1,:); tmp2=FLDV{iF}(:,2:end,:);
+fldVn{iF}=reshape(nanmean([tmp1(:) tmp2(:)],2),size(tmp1));
+end;
+
+FLDU=fldUe; FLDV=fldVn;
+cs=mk3D(mygrid.AngleCS,FLDU); sn=mk3D(mygrid.AngleSN,FLDU);
+
+fldUe=+FLDU.*cs-FLDV.*sn;
+fldVn=FLDU.*sn+FLDV.*cs;
+
+

gcmfaces_devel/calc_UV_geos.m

@@ -25,13 +25,15 @@
 %  kk=10; cc=[-1 1]*0.1;
 %  kk=30; cc=[-1 1]*0.05;
 %  kk=40; cc=[-1 1]*0.02;
-%  figure; orient tall; m=mygrid.mskC(:,:,kk);
-%  [tmpu,tmpv]=calc_UEVNfromUXVY(U(:,:,kk),V(:,:,kk));
-%  [tmpug,tmpvg]=calc_UEVNfromUXVY(Ug(:,:,kk),Vg(:,:,kk));
-%  subplot(3,1,1); qwckplot(m.*tmpu); caxis(cc); colorbar; title('zonal flow');
-%  subplot(3,1,2); qwckplot(m.*tmpug); caxis(cc); colorbar; title('geostrophic flow');
-%  subplot(3,1,3); qwckplot(m.*tmpu-tmpug); caxis(cc); colorbar; title('difference');
-%
+%  m=mygrid.mskC(:,:,kk); 
+%  tmpP=P(:,:,kk); tmpP=tmpP-nanmedian(tmpP);
+%  [tmpu,tmpv]=calc_UV_zonmer(U(:,:,kk),V(:,:,kk));
+%  [tmpug,tmpvg]=calc_UV_zonmer(Ug(:,:,kk),Vg(:,:,kk));
+%  figure; m_map_gcmfaces(m.*tmpu,1.2,{'myCaxis',cc}); title('zonal flow');
+%  figure; m_map_gcmfaces(m.*tmpug,1.2,{'myCaxis',cc}); title('geostrophic flow');
+%  figure; m_map_gcmfaces(m.*tmpu-tmpug,1.2,{'myCaxis',cc}); title('deviation from geostrophy');
+%  figure; m_map_gcmfaces(m.*tmpP,1.2,{'myCaxis',[-5:0.5:5]}); title('hydrostatic pressure');
+
 
 % development notes:
 %  is P assumed NaN-masked?

gcmfaces_diags/diags_driver.m

@@ -67,7 +67,7 @@
 
     nmDiag=setDiags{iDiag};
 
-    normalLoop=~strcmp(nmDiag,'B')&~strcmp(nmDiag,'D')&...
+    normalLoop=~strcmp(nmDiag,'B')&~strcmp(nmDiag,'D')&~strcmp(nmDiag,'drwn3')&...
                ~strcmp(nmDiag,'profiles')&~strcmp(nmDiag,'ecco')&~strcmp(nmDiag,'ctrl');
 
     if normalLoop;
@@ -82,6 +82,11 @@
       recInAve=[myparms.recInAve(1):myparms.recInAve(2)];
       diags_select(dirModel,dirMat,'B',1,recInAve);
 
+    elseif strcmp(nmDiag,'drwn3');
+      recs=(years(1)-1)*12+1:years(end)*12;
+      recs=recs(recs<=myparms.diagsNbRec);
+      diags_select(dirModel,dirMat,'drwn3',1,recs);
+
     elseif strcmp(nmDiag,'D');
       for kk=myparms.budgetList;
       for myYear=years;

gcmfaces_diags/diags_driver_tex.m

@@ -222,6 +222,9 @@
   elseif strcmp(setDiags{ii},'SEAICE');
       write2tex(fileTex,1,'seaice and snow fields',1);
       diags_display({dirMat,dirMatRef},'SEAICE',dirTex,nameTex);
+  elseif strcmp(setDiags{ii},'drwn3');
+      write2tex(fileTex,1,'Plankton and related fields',1);
+      diags_display({dirMat,dirMatRef},'drwn3',dirTex,nameTex);
   elseif strcmp(setDiags{ii},'controls');
         %controls
         write2tex(fileTex,1,'controls',1);

gcmfaces_diags/diags_grid_parms.m

@@ -27,7 +27,7 @@
 
 %issue warning if myparms.recInAve seems inconsistent compared with myparms.diagsNbRec~:
 if myparms.diagsNbRec~=(myparms.recInAve(2)-myparms.recInAve(1)+1); 
-  warning(['It appears that myparms.recInAve does not match myparms.recInAve']);
+  warning(['It appears that myparms.diagsNbRec does not match myparms.recInAve']);
   warning(['This may suggest that the oInteractive=1 option should be used.']); 
   pause(5);
 end;

gcmfaces_diags/diags_list_times.m

@@ -19,7 +19,7 @@
     if isempty(who('listSubdirs'));
         listSubdirs={[myenv.matdir 'BUDG/' ],[myenv.diagsdir '/BUDG/' ],[myenv.diagsdir '/OTHER/' ],...
             [myenv.diagsdir '/STATE/' ],[myenv.diagsdir '/TRSP/'],[myenv.diagsdir '/' ]};
-        listFiles={'state_2d_set1','trsp_3d_set1','budg2d_zflux_set1'};
+        listFiles={'state_2d_set1','trsp_3d_set1','budg2d_zflux_set1','gud_3d_set1'};
     end;
     %
     listTimes=[];

gcmfaces_maps/gcmfaces_cmap_cbar.m

@@ -52,13 +52,26 @@
     end;
 end;
 
+%white/black at colorbar edges/center?
 if strcmp(myCmap,'jetBW1'); myCmap='jet'; myBW=1; end;
 if strcmp(myCmap,'jetBW2'); myCmap='jet'; myBW=2; end;
 
+%flip colormap direction?
+flipCmap=0;
+if ~isempty(strfind(myCmap,'FLIP')); flipCmap=1; myCmap=myCmap(5:end); end;
+
+%need to revert to known colormap?
+test1=isempty(which(myCmap));
+if test1; 
+    warning(['Colormap ' myCmap ' not found => reverting to jet.']); 
+    myCmap='jet';
+end;
+
 %vecLimCol must be strickly increasing :
 tmp1=vecLimCol(2:end)-vecLimCol(1:end-1);
-if ~isempty(find(tmp1<=0)); fprintf('please use increasing values \n');
-    myColorbar=-1; return; end;
+if ~isempty(find(tmp1<=0)); 
+    error('Non-increasing sequence in vecLimCol');
+end;
 
 %original colormap precision :
 %nb_colors=64*3;
@@ -69,12 +82,8 @@
 %nb_colors=64*500*tmp3;
 
 %colormap and caxis :
-if ~isempty(strfind(myCmap,'FLIP'));
-    eval(['tmp_map=colormap(' myCmap(5:end)  '(nb_colors));']);
-    tmp_map=flipdim(tmp_map,1);
-else;
-    eval(['tmp_map=colormap(' myCmap  '(nb_colors));']);
-end;
+eval(['tmp_map=colormap(' myCmap  '(nb_colors));']);
+if flipCmap; tmp_map=flipdim(tmp_map,1); end;
 tmp_val=[vecLimCol(1) vecLimCol(end)];
 tmp_val=[tmp_val(1) : (tmp_val(2)-tmp_val(1))/(nb_colors-1) : tmp_val(2)];
 caxis([tmp_val(1) tmp_val(end)]);