update the xrb_layered analysis scripts

these are what I am using for the 3D simulation

Exec/science/xrb_layered/analysis/slice_vertical.py

@@ -14,10 +14,9 @@
 
 matplotlib.use('agg')
 
-def doit(plotfiles):
+def doit(pf, size=(19.2, 10.8)):
 
-    plotfile = sys.argv[1]
-    ds = CastroDataset(plotfile)
+    ds = CastroDataset(pf)
 
     xmin = ds.domain_left_edge[0]
     xmax = ds.domain_right_edge[0]
@@ -30,34 +29,23 @@ def doit(plotfiles):
 
     zmin = ds.domain_left_edge[2]
     zmax = ds.domain_right_edge[2]
-    zctr = 0.5*(zmin + zmax)
-
-
     zctr = 0.5*(zmin + zmax)
     L_z = zmax - zmin
 
-    fig = plt.figure()
-
-    grid = ImageGrid(fig, 111, nrows_ncols=(len(plotfiles), 1),
-                     axes_pad=0.25, label_mode="L",
-                     cbar_mode="single", cbar_size="3%")
-
-    for i, pf in enumerate(plotfiles):
-
-        ds = CastroDataset(pf)
+    fields = ["magvort", "enuc"]
 
-        f = "magvort"
-
-        sp = yt.SlicePlot(ds, "y", f, origin="native", center=[xctr, yctr, zctr],
-                          width=[L_z, L_x], fontsize="11")
-        sp.set_buff_size((4800,4800))
-        sp.swap_axes()
+    sp = yt.SlicePlot(ds, "y", fields,
+                      origin="native", center=[xctr, yctr, zctr],
+                      width=[L_z, L_x], fontsize="20")
+    sp.set_buff_size((4800,4800))
+    sp.swap_axes()
 
+    for f in fields:
         if f == "Temp":
             sp.set_zlim(f, 5.e5, 5.e8)
             sp.set_cmap(f, "magma_r")
         elif f == "enuc":
-            sp.set_zlim(f, 1.e14, 1.e17)
+            sp.set_zlim(f, 1.e16, 1.e21)
             sp.set_log(f, True)
             sp.set_cmap(f, "plasma_r")
         elif f == "density":
@@ -73,41 +61,28 @@ def doit(plotfiles):
             sp.set_zlim(f, 1.e-5, 1.0)
             sp.set_log(f, True)
 
-        sp.set_axes_unit("cm")
-
-        sp.annotate_text((0.05, 0.05), "{:5.2f} ms".format(1000.0*float(ds.current_time.in_cgs())),
-                         coord_system="figure", text_args={"color": "black", "size": 11})
+    sp.set_axes_unit("cm")
 
-        plot = sp.plots[f]
-        plot.figure = fig
-        plot.axes = grid[i].axes
-        plot.cax = grid.cbar_axes[i]
-        if i < len(plotfiles)-1:
-            grid[i].axes.xaxis.offsetText.set_visible(False)
+    layout = (1, len(fields))
 
-        sp._setup_plots()
+    fig = sp.export_to_mpl_figure((layout[0], layout[1]), axes_pad=(1.0, 0.4),
+                                  cbar_location="right", cbar_pad="2%")
 
-    fig.set_size_inches(8, 6.5)
-    fig.subplots_adjust(left=0.05, right=0.95, top=0.95, bottom=0.05)
+    fig.subplots_adjust(left=0.05, right=0.95, bottom=0.025, top=0.975)
+    fig.text(0.05, 0.01, f"t = {float(ds.current_time) * 1000:6.2f} ms",
+             fontsize="20",
+             transform=fig.transFigure)
+    fig.set_size_inches(size)
     fig.tight_layout()
-    fig.savefig(f"xrb_{f}.png")
+
+    fig.savefig(f"slice_{pf}.png")
 
 if __name__ == "__main__":
 
     p = argparse.ArgumentParser()
-
-    p.add_argument("--skip", type=int, default=1,
-                   help="interval between plotfiles")
-    p.add_argument("plotfiles", type=str, nargs="+",
-                   help="list of plotfiles to plot")
+    p.add_argument("plotfile", type=str, nargs=1,
+                   help="plotfiles to plot")
 
     args = p.parse_args()
 
-    plot_prefix = args.plotfiles[0].split("plt")[0] + "plt"
-    plot_nums = sorted([p.split("plt")[1] for p in args.plotfiles], key=int)
-
-    plotfiles = []
-    for n in range(0, len(plot_nums), args.skip):
-        plotfiles.append("{}{}".format(plot_prefix, plot_nums[n]))
-
-    doit(plotfiles)
+    doit(args.plotfile[0])

Exec/science/xrb_layered/analysis/vol-zvel.py

@@ -39,7 +39,7 @@ def doit(plotfile):
 
 
     # transfer function
-    vals = [-1.e7, -5.e6, -2.5e6, 2.5e6, 5.e6, 1.e7]
+    vals = [-2.e7, -1.e7, -5.e6, -2.5e6, 2.5e6, 5.e6, 1.e7, 2.e7]
     sigma = 5.e5
 
     tf =  yt.ColorTransferFunction((min(vals), max(vals)))
@@ -60,26 +60,26 @@ def doit(plotfile):
 
     center = 0.5*(ds.domain_left_edge + ds.domain_right_edge)
 
-    cam.position = [2.5*ds.domain_right_edge[0],
-                    2.5*ds.domain_right_edge[1],
-                    center[2]+0.5*ds.domain_right_edge[2]]
+    cam.position = [4*ds.domain_right_edge[0],
+                    4*ds.domain_right_edge[1],
+                    center[2]+ds.domain_right_edge[2]]
 
     # look toward the center -- we are dealing with an octant
     normal = (center - cam.position)
     normal /= np.sqrt(normal.dot(normal))
 
     cam.switch_orientation(normal_vector=normal,
                            north_vector=[0., 0., 1.])
-    cam.set_width(ds.domain_width)
-    cam.zoom(1.3)
+    cam.set_width(2*ds.domain_width)
+    #cam.zoom(0.5)
 
     sc.camera = cam
 
     sc.save(f"{plotfile}_zvel.png", sigma_clip=4.0)
 
     sc.annotate_axes(alpha=0.005, thickness=6)
     sc.annotate_domain(ds, color=np.array([0.05, 0.05, 0.05, 0.05]))
-    sc.save(f"{plotfile}_zvel_axes.png", sigma_clip=3.0)
+    #sc.save(f"{plotfile}_zvel_axes.png", sigma_clip=3.0)
 
     sc.save_annotated(f"{plotfile}_zvel_annotated.png",
                       sigma_clip=4.0, #label_fmt="%6.2g",