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adapt disk analysis

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This commit is contained in:
Noe Brucy
2019-04-08 10:54:31 +02:00
parent dca8ab5d41
commit 260dcfc7a5
2 changed files with 46 additions and 70 deletions
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disk_postprocess.py
+36 -68
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@@ -9,7 +9,6 @@ import pickle as pickle
import module_extract as me import module_extract as me
from pymses.filters import CellsToPoints from pymses.filters import CellsToPoints
from pymses.sources.ramses import output from pymses.sources.ramses import output
from pymses.analysis import Camera, raytracing, slicing from pymses.analysis import Camera, raytracing, slicing
@@ -343,7 +342,7 @@ def disk_prop(
path_out=None, path_out=None,
force=False, force=False,
nb_bin=20, nb_bin=20,
rad_ext=100.0, rad_ext=1.0,
mass_star=1.0, mass_star=1.0,
pos_star=np.array([1.0, 1.0, 1.0]), pos_star=np.array([1.0, 1.0, 1.0]),
): ):
@@ -387,42 +386,21 @@ def disk_prop(
ro = pymses.RamsesOutput(path_in, num) ro = pymses.RamsesOutput(path_in, num)
lbox = ro.info["boxlen"] # boxlen in codeunits (=>pc) lbox = ro.info["boxlen"] # boxlen in codeunits (=>pc)
( time = ro.info["time"] # * scale_t / Myr
AU,
pc,
Ms,
Myr,
scale_n,
scale_d,
scale_t,
scale_l,
scale_v,
scale_T2,
scale_ener,
scale_mag,
microG,
km_s,
Cwnm,
scale_mass,
unit_col,
lbox_pc,
) = me.normalisation(ro)
time = ro.info["time"] * scale_t / Myr
# Get array of cell positions # Get array of cell positions
amr = ro.amr_source(["rho", "vel", "Br", "Bl", "P"]) amr = ro.amr_source(["rho", "vel", "Br", "Bl", "P"])
cell_source = CellsToPoints(amr) cell_source = CellsToPoints(amr)
cells = cell_source.flatten() cells = cell_source.flatten()
dx = cells.get_sizes() dx = cells.get_sizes()
pos = cells.points pos = cells.points * lbox
# Get positions in the frame of the protostar # Get positions in the frame of the protostar
pos = pos - pos_star pos = pos - pos_star
# Get cylindrical radius # Get cylindrical radius
rc = np.sqrt(pos[:, 0] ** 2 + pos[:, 1] ** 2) rc = np.sqrt(pos[:, 0] ** 2 + pos[:, 1] ** 2)
# Get velocities # Get velocities
vel = cells["vel"] vel = cells["vel"] * lbox
# Get radial component of velocity # Get radial component of velocity
norm_pos = rc norm_pos = rc
norm_pos[rc == 0] = 1.0e-10 # Avoid division per 0 norm_pos[rc == 0] = 1.0e-10 # Avoid division per 0
@@ -432,12 +410,12 @@ def disk_prop(
# Select cells that are actually in the disk, ie within the scale height # Select cells that are actually in the disk, ie within the scale height
# TODO Check units # TODO Check units
G = 6.8e-8 G = 1.0 # G=6.8e-8
cs = np.sqrt(cells["P"] / cells["rho"]) * scale_v # sound velocity cs = np.sqrt(cells["P"] / cells["rho"]) # sound velocity
height = cs * np.sqrt(rc ** 3 / (G * mass_star)) height = cs * np.sqrt(rc ** 3 / (G * mass_star))
mask_pos = np.abs(pos[:, 2]) < height # condition on position mask_pos = np.abs(pos[:, 2]) < height # condition on position
mask_dens = cells["rho"] > 1.0e6 # condition on density mask_dens = cells["rho"] > 1.0e6 # condition on density
mask = mask_pos | mask_dens mask = mask_pos # & mask_dens
print("Number of selected cells ", np.sum(mask)) print("Number of selected cells ", np.sum(mask))
pos_disk = pos[mask] pos_disk = pos[mask]
@@ -449,33 +427,25 @@ def disk_prop(
dvol_disk = dx_disk ** 3 dvol_disk = dx_disk ** 3
v_rad_disk = v_rad[mask] v_rad_disk = v_rad[mask]
v_az_disk = v_az[mask] v_az_disk = v_az[mask]
v_kepl = np.sqrt(mass_star * G / rc_disk)
# TODO Check what do that does
nzoom = 9
eps = 0.5 ** nzoom
# map_coldens , map_w13, xedges, yedges = me.make_hierarch_map(pos_disk_x,pos_disk_y,pos_disk_z,dx_disk,rho_disk,rho_disk,eps,center=[0.,0.,0.],make_image=do_plot,path_out=directory_out,tag='xy_'+ str(num).zfill(5))
# map_coldens , map_w13, xedges, yedges = me.make_hierarch_map(pos_disk_z,pos_disk_x,pos_disk_y,dx_disk,rho_disk,rho_disk,eps,center=[0.,0.,0.],make_image=do_plot,path_out=directory_out,tag='xz_'+ str(num).zfill(5))
# Initialize binned quantities # Initialize binned quantities
norm_rad = lbox * scale_l / AU # radius in AU
rdisk_AU = rc_disk * norm_rad
cs_rad = np.zeros(nb_bin - 1) cs_rad = np.zeros(nb_bin - 1)
temp_rad = np.zeros(nb_bin - 1) temp_rad = np.zeros(nb_bin - 1)
press_rad = np.zeros(nb_bin - 1) press_rad = np.zeros(nb_bin - 1)
rho_rad = np.zeros(nb_bin - 1) rho_rad = np.zeros(nb_bin - 1)
coldens_rad = np.zeros(nb_bin - 1) coldens_rad = np.zeros(nb_bin - 1)
v_az_rad = np.zeros(nb_bin - 1) v_az_rad = np.zeros(nb_bin - 1)
v_kepl_rad = np.zeros(nb_bin - 1)
v_rad_rad = np.zeros(nb_bin - 1) v_rad_rad = np.zeros(nb_bin - 1)
alpha_rey_rad = np.zeros(nb_bin - 1) alpha_rey_rad = np.zeros(nb_bin - 1)
for i in range(nb_bin - 1): for i in range(nb_bin - 1):
mask_bin = (rdisk_AU > rad[i]) & (rdisk_AU < rad[i + 1]) mask_bin = (rc_disk > rad[i]) & (rc_disk < rad[i + 1])
print( print(
"Bin {} cells between {} and {} AU".format( "Bin #{} : {} cells between {} and {}".format(
np.sum(mask_bin), rad[i], rad[i + 1] i, np.sum(mask_bin), rad[i], rad[i + 1]
) )
) )
@@ -492,8 +462,8 @@ def disk_prop(
# dr = rad[i + 1] - rad[i] and r = (rad[i + 1] + rad[i]) / 2. # 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])
* (lbox * pc) ** 3 * (lbox) ** 3
/ ((rad[i + 1] - rad[i]) * (rad[i + 1] + rad[i]) * np.pi * AU ** 2) / ((rad[i + 1] - rad[i]) * (rad[i + 1] + rad[i]) * np.pi)
) )
v_az_rad[i] = np.sum( v_az_rad[i] = np.sum(
@@ -519,13 +489,18 @@ def disk_prop(
/ abs(v_az_rad[i]) / abs(v_az_rad[i])
) )
# Convert to good units (TODO check) v_kepl_rad[i] = np.sum(
cs_rad = np.sqrt(temp_rad) * scale_v / km_s v_kepl[mask_bin] * rho_disk[mask_bin] * dvol_disk[mask_bin]
temp_rad = temp_rad * scale_T2 ) / np.sum(rho_disk[mask_bin] * dvol_disk[mask_bin])
press_rad = press_rad * scale_v ** 2 * scale_d
v_az_rad = v_az_rad * scale_v / km_s # Convert to good units (TODO check)
v_rad_rad = v_rad_rad * scale_v / km_s cs_rad = np.sqrt(temp_rad) # *scale_v / km_s
temp_rad = temp_rad # * scale_T2
press_rad = press_rad # * scale_v**2 * scale_d
v_az_rad = v_az_rad # * scale_v / km_s
v_rad_rad = v_rad_rad # * scale_v / km_s
v_kepl_rad = v_kepl_rad
prop_disk = { prop_disk = {
"time": time, "time": time,
@@ -534,6 +509,7 @@ def disk_prop(
"alpha_rey": alpha_rey_rad, "alpha_rey": alpha_rey_rad,
"v_rad": v_rad_rad, "v_rad": v_rad_rad,
"v_az": v_az_rad, "v_az": v_az_rad,
"v_kepl": v_kepl_rad,
"coldens": coldens_rad, "coldens": coldens_rad,
"rho": rho_rad, "rho": rho_rad,
"press": press_rad, "press": press_rad,
@@ -577,7 +553,7 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
linewidth=2, linewidth=2,
) )
P.ylabel(r"$\log(n) \, (cm^{-3})$") P.ylabel(r"$\log(n) \, (cm^{-3})$")
P.xlabel("disk radius (AU)") P.xlabel("disk radius")
if pdf: if pdf:
P.savefig(path + "/rho_disk_r_" + str(num).zfill(5) + ".pdf") P.savefig(path + "/rho_disk_r_" + str(num).zfill(5) + ".pdf")
@@ -591,7 +567,7 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
linewidth=2, linewidth=2,
) )
P.ylabel(r"$\log(T) \, (K)$") P.ylabel(r"$\log(T) \, (K)$")
P.xlabel("disk radius (AU)") P.xlabel("disk radius")
if pdf: if pdf:
P.savefig(path + "/T_disk_r_" + str(num).zfill(5) + ".pdf") P.savefig(path + "/T_disk_r_" + str(num).zfill(5) + ".pdf")
@@ -603,27 +579,19 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
P.yscale("symlog", linthreshy=0.01) P.yscale("symlog", linthreshy=0.01)
P.plot((prop_disk["rad_AU"]), ((prop_disk["v_rad"])), color="k", linewidth=2) P.plot((prop_disk["rad_AU"]), ((prop_disk["v_rad"])), color="k", linewidth=2)
P.plot((prop_disk["rad_AU"]), ((prop_disk["v_kepl"])), color="b", linewidth=2)
P.plot((prop_disk["rad_AU"]), (abs(prop_disk["v_az"])), color="r", linewidth=2) P.plot((prop_disk["rad_AU"]), (abs(prop_disk["v_az"])), color="r", linewidth=2)
P.plot((prop_disk["rad_AU"]), ((prop_disk["cs"])), color="c", linewidth=2) P.plot((prop_disk["rad_AU"]), ((prop_disk["cs"])), color="c", linewidth=2)
P.legend((r"$v_r$", r"$v_\phi$", r"$c_s$"), loc="upper right") P.legend((r"$v_r$", r"$v_{kepl}$", r"$v_\phi$", r"$c_s$"), loc="upper right")
P.ylabel(r"$V \, (km s^{-1})$") P.ylabel(r"$V \, (km s^{-1})$")
P.xlabel("disk radius (AU)") P.xlabel("disk radius")
if pdf: if pdf:
P.savefig(path + "/V_disk_r_" + str(num).zfill(5) + ".pdf") P.savefig(path + "/V_disk_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "/V_disk_r_" + str(num).zfill(5) + ".jpeg") P.savefig(path + "/V_disk_r_" + str(num).zfill(5) + ".jpeg")
P.legend((r"$v_r$", r"$v_\phi$", r"$c_s$"), loc="upper right")
P.ylabel(r"$V \, (km s^{-1})$")
P.xlabel("disc radius (AU)")
if pdf:
P.savefig(path + "V_disk_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "V_disk_r_" + str(num).zfill(5) + ".jpeg")
P.clf() P.clf()
P.plot( P.plot(
np.log10(prop_disk["rad_AU"]), np.log10(prop_disk["rad_AU"]),
@@ -632,7 +600,7 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
linewidth=2, linewidth=2,
) )
P.ylabel(r"$\log(N) \, (cm^{-2})$") P.ylabel(r"$\log(N) \, (cm^{-2})$")
P.xlabel("disk radius (AU)") P.xlabel("disk radius ")
if pdf: if pdf:
P.savefig(path + "/coldens_disk_r_" + str(num).zfill(5) + ".pdf") P.savefig(path + "/coldens_disk_r_" + str(num).zfill(5) + ".pdf")
@@ -642,12 +610,12 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
P.xscale("log") P.xscale("log")
P.yscale("symlog", linthreshy=0.001) P.yscale("symlog", linthreshy=0.001)
P.plot(prop_disk["rad_AU"], prop_disk["alpha_rey"], color="b", linewidth=2) P.plot(prop_disk["rad_AU"], abs(prop_disk["alpha_rey"]), color="b", linewidth=2)
P.plot(prop_disc["rad_AU"], prop_disc["alpha_rey"], color="b", linewidth=2) # P.legend(r'$\alpha_{Rey}$', loc='upper right')
P.ylabel(r"$\alpha}$") P.ylabel(r"$\alpha$")
P.xlabel("disk radius (AU)") P.xlabel("disk radius ")
if pdf: if pdf:
P.savefig(path + "/alpha_disk_r_" + str(num).zfill(5) + ".pdf") P.savefig(path + "/alpha_disk_r_" + str(num).zfill(5) + ".pdf")
pipeline_disk.py
+10 -2
View File
@@ -21,6 +21,10 @@ parser.add_argument(
"-l", "--last_output", help="id of last output", type=int, default=100 "-l", "--last_output", help="id of last output", type=int, default=100
) )
parser.add_argument("-s", "--step", help="step between two output", type=int, default=1) parser.add_argument("-s", "--step", help="step between two output", type=int, default=1)
parser.add_argument(
"-d", "--disk", help="do specific disk radial analysis", action="store_true"
)
args = parser.parse_args() args = parser.parse_args()
@@ -54,5 +58,9 @@ for run in runs:
mag_im=False, mag_im=False,
AU_units=False, AU_units=False,
) )
dp.disk_prop(path_in, i, path_out=path_out, rad_ext=50000) # me.look(path_in, i)
dp.plot_disk_prop(path_out, i, tag=run + "_") if args.disk:
dp.disk_prop(
path_in, i, path_out=path_out, rad_ext=1, nb_bin=50, force=True
)
dp.plot_disk_prop(path_out, i, tag=run + "_")