Corrected error (lbox) in mass determination

disk_postprocess.py

@@ -15,7 +15,7 @@ import glob as glob
 import pickle as pickle
 
 from pymses.sources.ramses import output
-from pymses.analysis import Camera, raytracing, slicing
+from pymses.analysis import Camera, raytracing, slicing, splatting
 from pymses.filters import CellsToPoints
 from pymses.analysis import ScalarOperator, FractionOperator, MaxLevelOperator
 
@@ -39,6 +39,7 @@ def make_image_disk(
     cpuamr=False,
     pos_star=np.array([1.0, 1.0, 1.0]),
     interactive=False,
+    fft=False,
 ):
     """
     Make several useful image of an output of a simulation
@@ -77,6 +78,7 @@ def make_image_disk(
         put_title=put_title,
         pos_star=pos_star,
         interactive=interactive,
+        fft=fft,
     )
 
 
@@ -96,6 +98,7 @@ def make_image_aux(
     pos_star=np.array([1.0, 1.0, 1.0]),
     put_title=True,
     interactive=False,
+    fft=False,
 ):
     """
     Make several useful image of an output of a simulation, auxillary function
@@ -136,6 +139,11 @@ def make_image_aux(
         return
 
     rho_op = ScalarOperator(lambda dset: dset["rho"], ro.info["unit_density"])
+
+    rt = None
+    if fft:
+        rt = splatting.SplatterProcessor(amr, ro.info, rho_op)
+    else:
         rt = raytracing.RayTracer(amr, ro.info, rho_op)
 
     axes_los = ["x", "y", "z"]  # Line of sight axes
@@ -336,6 +344,10 @@ def make_image_aux(
                 ro.info["unit_velocity"],
             )
             rt_omega = raytracing.RayTracer(amr, ro.info, omega_op)
+
+            if fft:
+                rt_cs = splatting.SplatterProcessor(amr, ro.info, cs_op, surf_qty=False)
+            else:
                 rt_cs = raytracing.RayTracer(amr, ro.info, cs_op)
 
             dmap_omega = rt_omega.process(cam)
@@ -505,7 +517,7 @@ def disk_prop(
     amr = ro.amr_source(["rho", "vel", "Br", "Bl", "P"])
     cell_source = CellsToPoints(amr)
     cells = cell_source.flatten()
-    dx = cells.get_sizes()
+    dx = cells.get_sizes() * lbox
     pos = cells.points * lbox
     # Get positions in the frame of the protostar
     pos = pos - pos_star
@@ -540,8 +552,13 @@ def disk_prop(
     v_rad_disk = v_rad[mask]
     v_az_disk = v_az[mask]
     v_kepl = np.sqrt(mass_star * G / rc_disk)
+    height_disk = height[mask]
 
     total_mass_disk = np.sum(rho_disk * dvol_disk)
+    total_mass = np.sum(cells["rho"] * dx ** 3)
+
+    print("Mass disk", total_mass_disk)
+    print("Mass box", total_mass)
 
     # Initialize binned quantities
     cs_rad = np.zeros(nb_bin - 1)
@@ -554,15 +571,12 @@ def disk_prop(
     v_rad_rad = np.zeros(nb_bin - 1)
     alpha_rey_rad = np.zeros(nb_bin - 1)
     Q_kepl_rad = np.zeros(nb_bin - 1)
+    height_rad = np.zeros(nb_bin - 1)
 
     for i in range(nb_bin - 1):
         mask_bin = (rc_disk > rad[i]) & (rc_disk < rad[i + 1])
 
-        print(
+        # print("Bin #{} : {} cells between {} and {}".format(i, np.sum(mask_bin), rad[i], rad[i + 1]))
-            "Bin #{} : {} cells between {} and {}".format(
-                i, np.sum(mask_bin), rad[i], rad[i + 1]
-            )
-        )
 
         press_rad[i] = np.sum(press_disk[mask_bin] * dvol_disk[mask_bin]) / np.sum(
             dvol_disk[mask_bin]
@@ -577,10 +591,8 @@ def disk_prop(
         # TODO verifier unites
         # Surface of a bin :  S = dr * 2 * pi * r with
         #  dr = rad[i + 1] - rad[i] and r = (rad[i + 1] + rad[i]) / 2.
-        coldens_rad[i] = (
+        coldens_rad[i] = np.sum(rho_disk[mask_bin] * dvol_disk[mask_bin]) / (
-            np.sum(rho_disk[mask_bin] * dvol_disk[mask_bin])
+            (rad[i + 1] - rad[i]) * (rad[i + 1] + rad[i]) * np.pi
-            * (lbox) ** 3
-            / ((rad[i + 1] - rad[i]) * (rad[i + 1] + rad[i]) * np.pi)
         )
 
         v_az_rad[i] = np.sum(
@@ -590,6 +602,9 @@ def disk_prop(
         v_rad_rad[i] = np.sum(
             v_rad_disk[mask_bin] * rho_disk[mask_bin] * dvol_disk[mask_bin]
         ) / np.sum(rho_disk[mask_bin] * dvol_disk[mask_bin])
+        height_rad[i] = np.sum(
+            height_disk[mask_bin] * rho_disk[mask_bin] * dvol_disk[mask_bin]
+        ) / np.sum(rho_disk[mask_bin] * dvol_disk[mask_bin])
 
         alpha_rey_rad[i] = (
             (
@@ -624,6 +639,7 @@ def disk_prop(
     prop_disk = {
         "time": time,
         "tot_mass": total_mass_disk,
+        "mass_box": total_mass,
         "rad": rad[0 : nb_bin - 1],
         "center": pos_star,
         "alpha_rey": alpha_rey_rad,
@@ -636,6 +652,7 @@ def disk_prop(
         "temp": temp_rad,
         "cs": cs_rad,
         "Q_kepl": Q_kepl_rad,
+        "height": height_rad,
     }
 
     # store the results
@@ -678,8 +695,10 @@ def plot_disk_prop(path, num, force=False, tag="", interactive=False):
         P.close()
 
     P.xscale("log")
-    P.plot(prop_disk["rad"], np.log10(prop_disk["rho"]), color="k", linewidth=2)
+    P.yscale("log")
-    P.ylabel(r"$\log(n) \, (code)$")
+    P.grid()
+    P.plot(prop_disk["rad"], prop_disk["rho"], color="k", linewidth=2)
+    P.ylabel(r"$n \, (code)$")
     P.xlabel("disk radius")
     P.title(title)
     if interactive:
@@ -689,8 +708,10 @@ def plot_disk_prop(path, num, force=False, tag="", interactive=False):
         P.close()
 
     P.xscale("log")
-    P.plot(prop_disk["rad"], np.log10(prop_disk["temp"]), color="k", linewidth=2)
+    P.yscale("log")
-    P.ylabel(r"$\log(T) \, (K)$")
+    P.grid()
+    P.plot(prop_disk["rad"], prop_disk["temp"], color="k", linewidth=2)
+    P.ylabel(r"$T \, (K)$")
     P.xlabel("disk radius")
     P.title(title)
     if interactive:
@@ -718,8 +739,10 @@ def plot_disk_prop(path, num, force=False, tag="", interactive=False):
         P.close()
 
     P.xscale("log")
-    P.plot(prop_disk["rad"], np.log10(prop_disk["coldens"]), color="k", linewidth=2)
+    P.yscale("log")
-    P.ylabel(r"$\log(N) \, (cm^{-2})$")
+    P.grid()
+    P.plot(prop_disk["rad"], prop_disk["coldens"], color="k", linewidth=2)
+    P.ylabel(r"$N\, (cm^{-2})$")
     P.xlabel("disk radius ")
     P.title(title)
     if interactive:
@@ -763,6 +786,20 @@ def plot_disk_prop(path, num, force=False, tag="", interactive=False):
         P.savefig(path + "/Q_r_" + str(num).zfill(5) + out_ext)
         P.close()
 
-    if pdf:
+    # height ration
-        P.savefig(path + "/Q_r_" + str(num).zfill(5) + ".pdf")
+    P.grid()
-    P.savefig(path + "/Q_r_" + str(num).zfill(5) + ".jpeg")
+    P.plot(
+        prop_disk["rad"],
+        abs(prop_disk["height"] / prop_disk["rad"]),
+        color="b",
+        linewidth=2,
+    )
+    P.ylabel(r"H ratio")
+    P.xlabel("disk radius ")
+    P.title(title + ", mass of box = {} (code)".format(prop_disk["mass_box"]))
+
+    if interactive:
+        pass
+    else:
+        P.savefig(path + "/H_r_" + str(num).zfill(5) + out_ext)
+        P.close()