Noe Brucy
659 lines
19 KiB
Python
659 lines
19 KiB
Python
# coding: utf-8
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import sys
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import numpy as np
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import os
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import pymses
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import pylab as P
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import glob as glob
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import pickle as pickle
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import module_extract as me
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from pymses.filters import CellsToPoints
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from pymses.sources.ramses import output
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from pymses.analysis import Camera, raytracing, slicing
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def make_image_temp(
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amr,
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ro,
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center,
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radius,
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num,
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path,
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i_im=0,
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force=False,
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path_out=None,
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col_dens_only=False,
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map_size=512,
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vel_red=20,
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im_pos=0.0,
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tag="",
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cpuamr=False,
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put_title=True,
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mass_norm=1.0,
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AU_units=False,
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):
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"""
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Make several useful image of an output of a simulation
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Parameters
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----------
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amr
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ro pymses.RamsesOutput object
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center 3D array for coordinates center
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num output number
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"""
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lbox = ro.info["boxlen"] # boxlen in codeunits (=>pc)
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(
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AU,
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pc,
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Ms,
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Myr,
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scale_n,
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scale_d,
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scale_t,
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scale_l,
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scale_v,
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scale_T2,
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scale_ener,
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scale_mag,
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microG,
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km_s,
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Cwnm,
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scale_mass,
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unit_col,
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lbox_pc,
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) = normalisation(ro)
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ntick = 6
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if AU_units:
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units = pc / AU
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lbox_units = lbox * units
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titre_x = "x (AU)"
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titre_y = "y (AU)"
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titre_z = "z (AU)"
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else:
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units = 1.0
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lbox_units = lbox
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titre_x = "x (pc)"
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titre_y = "y (pc)"
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titre_z = "z (pc)"
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lbox_cm = lbox * pc # lbox in cm
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time = ro.info["time"] # time in codeunits
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time = time * scale_t / Myr
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titre = "t=" + str(time)[0:5] + " (Myr)"
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if path_out is not None:
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directory = path_out
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else:
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directory = path
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rt = raytracing.RayTracer(amr, ro.info, rho_op)
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rho_op = ScalarOperator(lambda dset: dset["rho"], ro.info["unit_density"])
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ax_names = ["x", "y", "z"]
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up_axes = ["z", "z", "x"]
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other_axes = ["z", "x", "y"]
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image_names = ["coldens", "rho", "T"]
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for i, ax_name in enumerate(ax_names):
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cam = Camera(
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center=center,
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line_of_sight_axis=ax_name,
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region_size=[2.0 * radius, 2.0 * radius],
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distance=radius,
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far_cut_depth=radius,
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up_vector=up_axes[i],
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map_max_size=map_size,
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)
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datamap = rt.process(cam, surf_qty=True)
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map_col = np.log10(datamap.map.T * lbox_cm)
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P.clf()
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im = P.imshow(
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map_col,
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extent=[
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(-radius + center[0]) * lbox_units,
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(radius + center[0]) * lbox_units,
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(-radius + center[1]) * lbox_units,
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(radius + center[1]) * lbox_units,
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],
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origin="lower",
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)
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P.locator_params(axis=other_axes[i], nbins=ntick)
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P.locator_params(axis=up_axes[i], nbins=ntick)
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if put_title:
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P.title(titre)
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P.xlabel(titre_x)
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P.ylabel(titre_y)
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cbar = P.colorbar(im)
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cbar.set_label(r"$log(N) \, cm^{-2}$")
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name = directory + "/coldens_" + ax_name + "_" + tag + +"_" + format(num, "05")
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name_im = name + ".jpeg"
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P.savefig(name_im)
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dmap_rho = slicing.SliceMap(amr, cam, rho_op, z=0.0)
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map_rho = np.log10(dmap_rho.map)
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map_rho = map_rho.T
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vx_op = ScalarOperator(lambda dset: dset["vel"][:, 0], ro.info["unit_velocity"])
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dmap_vx = slicing.SliceMap(amr, cam_z, vx_op, z=0.0)
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map_vx_red = dmap_vx.map[::vel_red, ::vel_red]
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map_vx_red = map_vx_red.T
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vy_op = ScalarOperator(lambda dset: dset["vel"][:, 1], ro.info["unit_velocity"])
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dmap_vy = slicing.SliceMap(amr, cam, vy_op, z=0.0)
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map_vy_red = dmap_vy.map[::vel_red, ::vel_red]
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map_vy_red = map_vy_red.T
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P.clf()
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im = P.imshow(
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map_rho,
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extent=[
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(-radius + center[0]) * lbox_units,
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(radius + center[0]) * lbox_units,
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(-radius + center[1]) * lbox_units,
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(radius + center[1]) * lbox_units,
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],
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origin="lower",
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)
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P.locator_params(axis=other_axes[i], nbins=ntick)
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P.locator_params(axis=up_axes[i], nbins=ntick)
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nx = map_vx_red.shape[0]
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ny = map_vx_red.shape[1]
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vec_x = (
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np.arange(nx) * 2.0 / nx * radius - radius + center[0] + radius / nx
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) * lbox_units
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vec_y = (
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np.arange(ny) * 2.0 / ny * radius - radius + center[1] + radius / nx
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) * lbox_units
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xx, yy = np.meshgrid(vec_x, vec_y)
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map_vx_red = map_vx_red * scale_v / km_s
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map_vy_red = map_vy_red * scale_v / km_s
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max_v = np.max(np.sqrt(map_vx_red ** 2 + map_vy_red ** 2))
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Q = P.quiver(xx, yy, map_vx_red, map_vy_red, units="width")
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P.quiverkey(
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Q,
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0.7,
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0.95,
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max_v,
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r"$" + str(max_v)[0:4] + "\, km \, s^{-1}$",
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labelpos="E",
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coordinates="figure",
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)
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if put_title:
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P.title(titre)
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P.xlabel(titre_x)
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P.ylabel(titre_y)
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cbar = P.colorbar(im)
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cbar.set_label(r"$log(n) \, (cm^{-3})$")
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name = directory + "/rho_z" + "_" + tag + str(i_im) + "_" + format(num, "05")
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name_im = name + ".jpeg"
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P.savefig(name_im)
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P_op = ScalarOperator(lambda dset: dset["P"], ro.info["unit_pressure"])
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dmap_P = slicing.SliceMap(amr, cam_z, P_op, z=0.0)
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P.clf()
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map_T = np.log10(dmap_P.map.T / dmap_rho.map.T * scale_T2)
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im = P.imshow(
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map_T,
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extent=[
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(-radius + center[0]) * lbox_units,
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(radius + center[0]) * lbox_units,
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(-radius + center[1]) * lbox_units,
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(radius + center[1]) * lbox_units,
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],
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origin="lower",
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)
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P.locator_params(axis="x", nbins=ntick)
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P.locator_params(axis="y", nbins=ntick)
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if put_title:
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P.title(titre)
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P.xlabel(titre_x)
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P.ylabel(titre_y)
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cbar = P.colorbar(im)
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cbar.set_label(r"$log(T) \, (K)$")
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name = directory + "/T_z" + "_" + tag + str(i_im) + "_" + format(num, "05")
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name_im = name + ".jpeg"
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P.savefig(name_im)
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if cpuamr:
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level_op = MaxLevelOperator()
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amr.set_read_levelmax(20)
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rt = raytracing.RayTracer(amr, ro.info, level_op)
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datamap = rt.process(cam_z, surf_qty=True)
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map_level = datamap.map.T
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P.clf()
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im = P.imshow(
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map_level,
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extent=[
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(-radius + center[0]) * lbox_units,
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(radius + center[0]) * lbox_units,
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(-radius + center[1]) * lbox_units,
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(radius + center[1]) * lbox_units,
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],
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origin="lower",
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)
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P.locator_params(axis="x", nbins=ntick)
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P.locator_params(axis="y", nbins=ntick)
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if put_title:
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P.title(titre)
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P.xlabel(titre_x)
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P.ylabel(titre_y)
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cbar = P.colorbar(im)
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cbar.set_label(r"level")
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name = (
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directory + "/level_z" + "_" + tag + str(i_im) + "_" + format(num, "05")
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)
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name_im = name + ".jpeg"
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P.savefig(name_im)
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if ps:
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P.savefig(name + ".ps")
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if descrip is not None:
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dd = {}
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dd.update(
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{
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"name": "mean AMR level in the z-direction"
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+ " ("
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+ tag
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+ str(i_im)
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+ ")"
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}
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)
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dd.update({"type": "image"})
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dd.update({"description": "Mean AMR level in the z-direction."})
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dd.update({"display": 0})
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dd.update({"item": i_im})
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dd.update({"tag": tag})
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data = {"jpeg": name_im}
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dd.update({"data": data})
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list_im.append(dd)
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cpu_op = ScalarOperator(
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lambda dset: dset.icpu * (np.ones(dset["P"].shape)),
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ro.info["unit_pressure"],
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)
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rt = raytracing.RayTracer(amr, ro.info, cpu_op)
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datamap = rt.process(cam_z, surf_qty=True)
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map_cpu = datamap.map.T
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P.clf()
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im = P.imshow(
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map_cpu,
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extent=[
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(-radius + center[0]) * lbox_units,
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(radius + center[0]) * lbox_units,
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(-radius + center[1]) * lbox_units,
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(radius + center[1]) * lbox_units,
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],
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origin="lower",
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)
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P.locator_params(axis="x", nbins=ntick)
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P.locator_params(axis="y", nbins=ntick)
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if put_title:
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P.title(titre)
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P.xlabel(titre_x)
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P.ylabel(titre_y)
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cbar = P.colorbar(im)
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cbar.set_label(r"level")
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name = (
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directory + "/cpu_z" + "_" + tag + str(i_im) + "_" + format(num, "05")
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)
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name_im = name + ".jpeg"
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P.savefig(name_im)
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def disk_prop(
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path_in,
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num,
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path_out=None,
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force=False,
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nb_bin=20,
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rad_ext=100.0,
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mass_star=1.0,
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pos_star=np.array([1.0, 1.0, 1.0]),
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):
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"""
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Compute properties of a disk in the plane (0,x,y)
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with a protostar at the center of the box
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The region of the disk is defined by its scale height
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Parameters
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----------
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path_in path of the input data files (output of ramses)
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num id of the output
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path_out optional path to the output files
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force if set, redo ouptut even if already done
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nb_bin Number of radial bins
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rad_ext Outer radius of the disk
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pos_star position of the central protostar
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mass_star mass of the central protostar
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"""
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# Set th output directory
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if path_out is not None:
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directory_out = path_out
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else:
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directory_out = path_in
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# Check if the output file exists, and exit if it is the case
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name_save = directory_out + "/prop_disk_" + str(num).zfill(5) + ".save"
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if not force and len(glob.glob(name_save)) != 0:
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return
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# Compute the bins array
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lrad = np.log10(rad_ext)
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rad = np.logspace(lrad - 2.0, lrad, num=nb_bin)
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# Get Ramses data
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ro = pymses.RamsesOutput(path_in, num)
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lbox = ro.info["boxlen"] # boxlen in codeunits (=>pc)
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(
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AU,
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pc,
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Ms,
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Myr,
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scale_n,
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scale_d,
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scale_t,
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scale_l,
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scale_v,
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scale_T2,
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scale_ener,
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scale_mag,
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microG,
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km_s,
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Cwnm,
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scale_mass,
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unit_col,
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lbox_pc,
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) = me.normalisation(ro)
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time = ro.info["time"] * scale_t / Myr
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# Get array of cell positions
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amr = ro.amr_source(["rho", "vel", "Br", "Bl", "P"])
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cell_source = CellsToPoints(amr)
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cells = cell_source.flatten()
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dx = cells.get_sizes()
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pos = cells.points
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# Get positions in the frame of the protostar
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pos = pos - pos_star
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# Get cylindrical radius
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rc = np.sqrt(pos[:, 0] ** 2 + pos[:, 1] ** 2)
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# Get velocities
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vel = cells["vel"]
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# Get radial component of velocity
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norm_pos = rc
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norm_pos[rc == 0] = 1.0e-10 # Avoid division per 0
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v_rad = (pos[:, 0] * vel[:, 0] + pos[:, 1] * vel[:, 1]) / norm_pos
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# Get azimuthal component of velocity
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v_az = (pos[:, 0] * vel[:, 1] - pos[:, 1] * vel[:, 0]) / norm_pos
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# Select cells that are actually in the disk, ie within the scale height
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# TODO Check units
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G = 6.8e-8
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cs = np.sqrt(cells["P"] / cells["rho"]) * scale_v # sound velocity
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height = cs * np.sqrt(rc ** 3 / (G * mass_star))
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mask_pos = np.abs(pos[:, 2]) < height # condition on position
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mask_dens = cells["rho"] > 1.0e6 # condition on density
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mask = mask_pos | mask_dens
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print("Number of selected cells ", np.sum(mask))
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pos_disk = pos[mask]
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rc_disk = rc[mask]
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vel_disk = vel[mask]
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rho_disk = cells["rho"][mask] # density
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press_disk = cells["P"][mask] # pressure
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dx_disk = dx[mask]
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dvol_disk = dx_disk ** 3
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v_rad_disk = v_rad[mask]
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v_az_disk = v_az[mask]
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# TODO Check what do that does
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nzoom = 9
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eps = 0.5 ** nzoom
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# 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))
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# 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))
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# Initialize binned quantities
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norm_rad = lbox * scale_l / AU # radius in AU
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rdisk_AU = rc_disk * norm_rad
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cs_rad = np.zeros(nb_bin - 1)
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temp_rad = np.zeros(nb_bin - 1)
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press_rad = np.zeros(nb_bin - 1)
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rho_rad = np.zeros(nb_bin - 1)
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coldens_rad = np.zeros(nb_bin - 1)
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v_az_rad = np.zeros(nb_bin - 1)
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v_rad_rad = np.zeros(nb_bin - 1)
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alpha_rey_rad = np.zeros(nb_bin - 1)
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for i in range(nb_bin - 1):
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mask_bin = (rdisk_AU > rad[i]) & (rdisk_AU < rad[i + 1])
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print(
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"Bin {} cells between {} and {} AU".format(
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np.sum(mask_bin), rad[i], rad[i + 1]
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)
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)
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press_rad[i] = np.sum(press_disk[mask_bin] * dvol_disk[mask_bin]) / np.sum(
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dvol_disk[mask_bin]
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)
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rho_rad[i] = np.sum(rho_disk[mask_bin] * dvol_disk[mask_bin]) / np.sum(
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dvol_disk[mask_bin]
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)
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temp_rad[i] = press_rad[i] / rho_rad[i]
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# TODO verifier unites
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# Surface of a bin : S = dr * 2 * pi * r with
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# dr = rad[i + 1] - rad[i] and r = (rad[i + 1] + rad[i]) / 2.
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coldens_rad[i] = (
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np.sum(rho_disk[mask_bin] * dvol_disk[mask_bin])
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* (lbox * pc) ** 3
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/ ((rad[i + 1] - rad[i]) * (rad[i + 1] + rad[i]) * np.pi * AU ** 2)
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)
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v_az_rad[i] = np.sum(
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v_az_disk[mask_bin] * rho_disk[mask_bin] * dvol_disk[mask_bin]
|
|
) / np.sum(rho_disk[mask_bin] * dvol_disk[mask_bin])
|
|
|
|
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])
|
|
|
|
alpha_rey_rad[i] = (
|
|
(
|
|
np.sum(
|
|
v_az_disk[mask_bin]
|
|
* v_rad_disk[mask_bin]
|
|
* rho_disk[mask_bin]
|
|
* dvol_disk[mask_bin]
|
|
)
|
|
/ np.sum(dvol_disk[mask_bin] * press_disk[mask_bin])
|
|
- v_az_rad[i] * v_rad_rad[i] * rho_rad[i] / press_rad[i]
|
|
)
|
|
* v_az_rad[i]
|
|
/ abs(v_az_rad[i])
|
|
)
|
|
|
|
# Convert to good units (TODO check)
|
|
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
|
|
|
|
prop_disk = {
|
|
"time": time,
|
|
"rad_AU": rad[0 : nb_bin - 1],
|
|
"center": pos_star,
|
|
"alpha_rey": alpha_rey_rad,
|
|
"v_rad": v_rad_rad,
|
|
"v_az": v_az_rad,
|
|
"coldens": coldens_rad,
|
|
"rho": rho_rad,
|
|
"press": press_rad,
|
|
"temp": temp_rad,
|
|
"cs": cs_rad,
|
|
}
|
|
|
|
# store the results
|
|
f = open(name_save, "w")
|
|
pickle.dump(prop_disk, f)
|
|
f.close()
|
|
|
|
|
|
def plot_disk_prop(path, num, force=False, pdf=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
|
|
name_save = path + "/prop_disk_" + str(num).zfill(5) + ".save"
|
|
|
|
# Check if the properties file exists
|
|
if len(glob.glob(name_save)) == 0:
|
|
throw("no pickle file for disk properties. Run single_z_disk_prop")
|
|
f = open(name_save, "r")
|
|
prop_disk = pickle.load(f)
|
|
f.close()
|
|
|
|
P.clf()
|
|
P.plot(
|
|
np.log10(prop_disk["rad_AU"]),
|
|
np.log10(prop_disk["rho"]),
|
|
color="k",
|
|
linewidth=2,
|
|
)
|
|
P.ylabel(r"$\log(n) \, (cm^{-3})$")
|
|
P.xlabel("disk radius (AU)")
|
|
|
|
if pdf:
|
|
P.savefig(path + "/rho_disk_r_" + str(num).zfill(5) + ".pdf")
|
|
P.savefig(path + "/rho_disk_r_" + str(num).zfill(5) + ".jpeg")
|
|
|
|
P.clf()
|
|
P.plot(
|
|
np.log10(prop_disk["rad_AU"]),
|
|
np.log10(prop_disk["temp"]),
|
|
color="k",
|
|
linewidth=2,
|
|
)
|
|
P.ylabel(r"$\log(T) \, (K)$")
|
|
P.xlabel("disk radius (AU)")
|
|
|
|
if pdf:
|
|
P.savefig(path + "/T_disk_r_" + str(num).zfill(5) + ".pdf")
|
|
P.savefig(path + "/T_disk_r_" + str(num).zfill(5) + ".jpeg")
|
|
|
|
P.clf()
|
|
|
|
P.xscale("log")
|
|
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"]), (abs(prop_disk["v_az"])), color="r", 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.ylabel(r"$V \, (km s^{-1})$")
|
|
P.xlabel("disk 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.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.plot(
|
|
np.log10(prop_disk["rad_AU"]),
|
|
np.log10(prop_disk["coldens"]),
|
|
color="k",
|
|
linewidth=2,
|
|
)
|
|
P.ylabel(r"$\log(N) \, (cm^{-2})$")
|
|
P.xlabel("disk radius (AU)")
|
|
|
|
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.clf()
|
|
P.xscale("log")
|
|
P.yscale("symlog", linthreshy=0.001)
|
|
|
|
P.plot(prop_disk["rad_AU"], prop_disk["alpha_rey"], color="b", linewidth=2)
|
|
|
|
P.plot(prop_disc["rad_AU"], prop_disc["alpha_rey"], color="b", linewidth=2)
|
|
|
|
P.ylabel(r"$\alpha}$")
|
|
P.xlabel("disk radius (AU)")
|
|
|
|
if pdf:
|
|
P.savefig(path + "/alpha_disk_r_" + str(num).zfill(5) + ".pdf")
|
|
P.savefig(path + "/alpha_disk_r_" + str(num).zfill(5) + ".jpeg")
|
|
|
|
if pdf:
|
|
P.savefig(path + "alpha_disk_r_" + str(num).zfill(5) + ".pdf")
|
|
P.savefig(path + "alpha_disk_r_" + str(num).zfill(5) + ".jpeg")
|