noe/pipeline
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Add map for Q

Browse Source
This commit is contained in:
Noe Brucy
2019-04-16 16:31:10 +02:00
parent 9f53414ab1
commit 48165cc006
2 changed files with 101 additions and 52 deletions
Download Patch File Download Diff File Expand all files Collapse all files
disk_postprocess.py
+72 -36
View File
@@ -19,8 +19,11 @@ from pymses.analysis import Camera, raytracing, slicing
from pymses.filters import CellsToPoints
from pymses.analysis import ScalarOperator, FractionOperator, MaxLevelOperator
# extension for out files
out_ext = ".jpeg"
P.rcParams["image.cmap"] = "plasma"
P.rcParams["savefig.dpi"] = 800
P.rcParams["savefig.dpi"] = 400
def make_image_disk(
@@ -52,7 +55,7 @@ def make_image_disk(
"""
ro = pymses.RamsesOutput(path, num, order=order)
amr = ro.amr_source(["rho", "vel", "P", "Bl", "Br"])
amr = ro.amr_source(["rho", "vel", "P"])
rad = 0.5
center = [0.5, 0.5, 0.5]
@@ -86,6 +89,7 @@ def make_image_aux(
vel_red=20,
tag="",
cpuamr=False,
pos_star=np.array([1.0, 1.0, 1.0]),
put_title=True,
):
"""
@@ -122,7 +126,7 @@ def make_image_aux(
else:
directory = path
name = directory + "/coldens_z" + "_" + tag + "_" + format(num, "05") + ".jpeg"
name = directory + "/coldens_z" + "_" + tag + "_" + format(num, "05") + out_ext
if len(glob.glob(name)) == 1 and not force:
return
@@ -181,7 +185,7 @@ def make_image_aux(
cbar = P.colorbar(im)
cbar.set_label(r"$log(N)$ (code)")
name = directory + "/coldens_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
name_im = name + out_ext
P.savefig(name_im)
# Rho slice
@@ -248,7 +252,7 @@ def make_image_aux(
cbar.set_label(r"$log(n)$ (code)")
name = directory + "/rho_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
name_im = name + out_ext
P.savefig(name_im)
P_op = ScalarOperator(lambda dset: dset["P"], ro.info["unit_pressure"])
@@ -279,18 +283,48 @@ def make_image_aux(
cbar.set_label(r"$log(T) \, (K)$")
name = directory + "/T_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
name_im = name + out_ext
P.savefig(name_im)
# Toomre parameter
if False and ax_los == "z":
map_Q = np.log10(np.sqrt(dmap_P.map.T / dmap_rho.map.T)) / (
np.pi * map_col * G
)
if ax_los == "z":
def omega_rho_func(dset):
pos = dset.get_cell_centers()
pos = pos - (pos_star / lbox)
xx = pos[:, :, 0]
yy = pos[:, :, 1]
rc = np.sqrt(xx ** 2 + yy ** 2) # cylindrical radius
vx = dset["vel"][:, :, 0]
vy = dset["vel"][:, :, 1]
omega_rho = 1.0 / rc ** 2
omega_rho = omega_rho * dset["rho"]
vyx = vy * xx
vxy = vx * yy
omega_rho = omega_rho * (vyx - vxy)
return omega_rho
omega_op = FractionOperator(
omega_rho_func, lambda dset: dset["rho"], 1.0 / ro.info["unit_time"]
)
cs_op = FractionOperator(
lambda dset: dset["P"],
lambda dset: dset["rho"],
ro.info["unit_velocity"],
)
rt_omega = raytracing.RayTracer(amr, ro.info, omega_op)
rt_cs = raytracing.RayTracer(amr, ro.info, cs_op)
dmap_omega = rt_omega.process(cam)
dmap_cs = rt_cs.process(cam)
dmap_Q = (lbox * dmap_cs.map.T) * dmap_omega.map.T / (np.pi * G * dmap_col)
map_Q = np.log10(dmap_Q)
P.close()
im = P.imshow(
map_T,
map_Q,
extent=[
(-radius + center[0]) * lbox_units,
(radius + center[0]) * lbox_units,
@@ -308,10 +342,10 @@ def make_image_aux(
P.xlabel(title_ax[ax_h])
P.ylabel(title_ax[ax_v])
cbar = P.colorbar(im)
cbar.set_label(r"$log(T) \, (K)$")
cbar.set_label(r"$log(Q)$")
name = directory + "/Q_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
name_im = name + out_ext
P.savefig(name_im)
if cpuamr:
@@ -344,7 +378,7 @@ def make_image_aux(
cbar.set_label(r"level")
name = directory + "/level_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
name_im = name + out_ext
P.savefig(name_im)
cpu_op = ScalarOperator(
@@ -378,7 +412,7 @@ def make_image_aux(
cbar.set_label(r"cpu")
name = directory + "/cpu_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
name_im = name + out_ext
P.savefig(name_im)
@@ -432,7 +466,7 @@ def disk_prop(
ro = pymses.RamsesOutput(path_in, num)
lbox = ro.info["boxlen"] # boxlen in codeunits (=>pc)
time = ro.info["time"] # * scale_t / Myr
time = ro.info["time"] # time in codeunits
# Get array of cell positions
amr = ro.amr_source(["rho", "vel", "Br", "Bl", "P"])
@@ -440,9 +474,9 @@ def disk_prop(
cells = cell_source.flatten()
dx = cells.get_sizes()
pos = cells.points * lbox
# Get positions in the frame of the protostar
pos = pos - pos_star
# Get cylindrical radius
rc = np.sqrt(pos[:, 0] ** 2 + pos[:, 1] ** 2)
# Get velocities
@@ -474,6 +508,8 @@ def disk_prop(
v_az_disk = v_az[mask]
v_kepl = np.sqrt(mass_star * G / rc_disk)
total_mass_disk = np.sum(rho_disk * dvol_disk)
# Initialize binned quantities
cs_rad = np.zeros(nb_bin - 1)
temp_rad = np.zeros(nb_bin - 1)
@@ -552,6 +588,7 @@ def disk_prop(
prop_disk = {
"time": time,
"tot_mass": total_mass_disk,
"rad": rad[0 : nb_bin - 1],
"center": pos_star,
"alpha_rey": alpha_rey_rad,
@@ -572,16 +609,13 @@ def disk_prop(
f.close()
def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
def plot_disk_prop(path, num, force=False, tag=""):
"""
Plot properties of a disk
num id of the ramses output
path path to the properties file
force if set, redo plots even if already done
pdf if set, do output in pdf as well
"""
# Load property file
@@ -595,16 +629,22 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
f.close()
# Check if the output file exists, and exit if it is the case
name_save = path + "/rho_disk_r_" + str(num).zfill(5) + ".jpeg"
name_save = path + "/rho_disk_r_" + str(num).zfill(5) + out_ext
if not force and len(glob.glob(name_save)) != 0:
return
time = prop_disk["time"]
mass = prop_disk["tot_mass"]
title = "t=" + str(time)[0:5] + " (code)"
P.close()
P.plot(
np.log10(prop_disk["rad"]), np.log10(prop_disk["rho"]), color="k", linewidth=2
)
P.ylabel(r"$\log(n) \, (cm^{-3})$")
P.ylabel(r"$\log(n) \, (code)$")
P.xlabel("disk radius")
P.title(title)
P.savefig(path + "/rho_disk_r_" + str(num).zfill(5) + out_ext)
if pdf:
P.savefig(path + "/rho_disk_r_" + str(num).zfill(5) + ".pdf")
@@ -616,6 +656,8 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
)
P.ylabel(r"$\log(T) \, (K)$")
P.xlabel("disk radius")
P.title(title)
P.savefig(path + "/T_disk_r_" + str(num).zfill(5) + out_ext)
if pdf:
P.savefig(path + "/T_disk_r_" + str(num).zfill(5) + ".pdf")
@@ -636,9 +678,7 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
P.ylabel(r"$V \, (km s^{-1})$")
P.xlabel("disk radius")
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.savefig(path + "/V_disk_r_" + str(num).zfill(5) + out_ext)
P.close()
P.plot(
@@ -649,10 +689,8 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
)
P.ylabel(r"$\log(N) \, (cm^{-2})$")
P.xlabel("disk radius ")
if pdf:
P.savefig(path + "/coldens_disk_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "/coldens_disk_r_" + str(num).zfill(5) + ".jpeg")
P.title(title)
P.savefig(path + "/coldens_disk_r_" + str(num).zfill(5) + out_ext)
# Alpha
P.close()
@@ -664,10 +702,8 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
P.ylabel(r"$\alpha$")
P.xlabel("disk radius ")
if pdf:
P.savefig(path + "/alpha_disk_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "/alpha_disk_r_" + str(num).zfill(5) + ".jpeg")
P.title(title)
P.savefig(path + "/alpha_disk_r_" + str(num).zfill(5) + out_ext)
# Q
@@ -675,10 +711,10 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
P.xscale("log")
P.yscale("log", linthreshy=0.001)
P.plot(prop_disk["rad"], abs(prop_disk["Q_kepl"]), color="b", linewidth=2)
P.ylabel(r"$Q$")
P.xlabel("disk radius ")
P.title(title + ", mass of disk = {} (code)".format(mass))
P.savefig(path + "/Q_r_" + str(num).zfill(5) + out_ext)
if pdf:
P.savefig(path + "/Q_r_" + str(num).zfill(5) + ".pdf")
pipeline_disk.py
+24 -11
View File
@@ -14,18 +14,21 @@ storage_out = "/dsm/anais/storageA/"
parser = argparse.ArgumentParser()
parser.add_argument("runs", help="name of runs", nargs="*", default=["015_iso"])
parser.add_argument(
"-f", "--first_output", help="id of first output", type=int, default=1
)
parser.add_argument(
"-l", "--last_output", help="id of last output", type=int, default=100
)
parser.add_argument("-b", "--begin", help="id of first output", type=int, default=1)
parser.add_argument("-e", "--end", 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(
"-d", "--disk", help="do specific disk radial analysis", action="store_true"
)
parser.add_argument("-p", "--project", help="specify project name", default="disk")
parser.add_argument(
"-fr",
"--force_redo",
help="redo plots even if the files already exist",
action="store_true",
)
parser.add_argument(
"-w", "--watch", help="wait and watch for missing outputs", action="store_true"
)
@@ -52,8 +55,8 @@ folder = "simus"
project = args.project
runs = args.runs
first = args.first_output
last = args.last_output
first = args.begin
last = args.end
step = args.step
@@ -74,13 +77,23 @@ for run in runs:
while not success:
try:
dp.make_image_disk(
path_in, i, path_out=path_out, tag=run, map_size=1024
path_in,
i,
path_out=path_out,
tag=run,
map_size=1024,
force=args.force_redo,
)
if args.disk:
dp.disk_prop(
path_in, i, path_out=path_out, rad_ext=1, nb_bin=50, force=False
path_in,
i,
path_out=path_out,
rad_ext=1,
nb_bin=50,
force=args.force_redo,
)
dp.plot_disk_prop(path_out, i, tag=run)
dp.plot_disk_prop(path_out, i, tag=run, force=args.force_redo)
success = True
except ValueError:
if args.watch and failures < args.allowed_failures: