FargoCPT Simulation movies¶
This notebook shows how to make movies from output data using matplotlib and ffmpeg
First we create a new directory and change to it.
example_name = "500_Movie"
example_dir = f"example_dirs/{example_name}"
import os
repo_root = os.path.abspath(os.path.join(os.getcwd(), "../"))
if not os.path.basename(os.getcwd()) == example_name:
!mkdir -p $example_dir
os.chdir(example_dir)
print(f"Current working directory: {os.getcwd()}")
print(f"Repository root directory: {repo_root}")
Current working directory: /home/rometsch/repo/fargocpt/examples/example_dirs/500_Movie
Repository root directory: /home/rometsch/repo/fargocpt
Preparing a setup file¶
We’ll take the example setup file from the examples directory and modify it in python. If you want to create setup files for a parameter study, just copy the code and make your own setup creator script.
configfile = "setup.yml"
!cp $repo_root/examples/config.yml $configfile
We’ll use the ruamel.yaml package to read and write the setup file. This can be set up to preserve comments which is very useful if you want to trace your decisions later on.
import ruamel.yaml
yaml = ruamel.yaml.YAML()
with open(configfile, "r") as infile:
config = yaml.load(infile)
config["nbody"][1]["accretion efficiency"] = "2"
config["MonitorTimestep"] = 0.0314 # monitor scalar files around every half orbit
config["Nmonitor"] = 5 # write a snapshot after every 20 monitor timesteps = every orbit
config["Nsnapshots"] = 100
config["cps"] = 4 # use medium resolution, this is only for show, but it should still look nice
config["Frame"] = "F"
config["OmegaFrame"] = 0
config["nbody"][1]["ramp-up time"] = 10
config["nbody"][1]["accretion efficiency"] = 10
config["DiskFeedback"] = "yes"
with open(configfile, "w") as outfile:
yaml.dump(config, outfile)
Running the code¶
from fargocpt import run
np = 2 # Number of mpi processes. Should be equal to the number of numa nodes on your machine, check your cluster docu or run `lscpu` or `./run_fargo --print-numa` if you're on linux.
nt = 8 # Number of threads per mpi process, set it to the number of cores you want to use / number of MPI processes
run(["start", configfile], np=np, nt=nt, exe=repo_root+"/bin/fargocpt_exe", detach=False)
Running command: mpirun -np 2 --report-pid /tmp/tmpu58irt78 --map-by ppr:1:numa --bind-to numa -x OMP_WAIT_POLICY=active -x OMP_PROC_BIND=close -x OMP_PLACES=cores -x OMP_NUM_THREADS=8 /home/rometsch/repo/fargocpt/bin/fargocpt_exe start setup.yml
fargo process pid 179663
[0] MPI rank # 0 runs as process 179666
[1] MPI rank # 1 runs as process 179667
[0] MPI rank # 0 OpenMP thread # 0 of 8 on cpt-kamino
[1] MPI rank # 1 OpenMP thread # 0 of 8 on cpt-kamino
[0] MPI rank # 0 OpenMP thread # 2 of 8 on cpt-kamino
[1] MPI rank # 1 OpenMP thread # 3 of 8 on cpt-kamino
[1] MPI rank # 1 OpenMP thread # 2 of 8 on cpt-kamino
[1] MPI rank # 1 OpenMP thread # 1 of 8 on cpt-kamino
[1] MPI rank # 1 OpenMP thread # 7 of 8 on cpt-kamino
[1] MPI rank # 1 OpenMP thread # 5 of 8 on cpt-kamino
[1] MPI rank # 1 OpenMP thread # 4 of 8 on cpt-kamino
[0] MPI rank # 0 OpenMP thread # 5 of 8 on cpt-kamino
[0] MPI rank # 0 OpenMP thread # 7 of 8 on cpt-kamino
[0] MPI rank # 0 OpenMP thread # 1 of 8 on cpt-kamino
[1] MPI rank # 1 OpenMP thread # 6 of 8 on cpt-kamino
[0] MPI rank # 0 OpenMP thread # 6 of 8 on cpt-kamino
[0] MPI rank # 0 OpenMP thread # 4 of 8 on cpt-kamino
[0] MPI rank # 0 OpenMP thread # 3 of 8 on cpt-kamino
[0] fargo: This file was compiled on Nov 14 2023, 20:52:20.
[0] fargo: This version of FARGO used _GNU_SOURCE
[0] fargo: This version of FARGO used NDEBUG. So no assertion checks!
[0] Using parameter file setup.yml
[0] Computing disk quantities within 5.00000e+00 L0 from coordinate center
[0] BC: Inner composite = reflecting
[0] BC: Outer composite = reflecting
[0] BC: Sigma inner = zerogradient
[0] BC: Sigma outer = zerogradient
[0] BC: Energy inner = zerogradient
[0] BC: Energy outer = zerogradient
[0] BC: Vrad inner = reflecting
[0] BC: Vrad outer = reflecting
[0] BC: Vaz inner = keplerian
[0] BC: Vaz outer = keplerian
[0] DampingTimeFactor: 1.00000e-01 Outer damping time is computed at radius of 2.50000e+00
[0] Damping VRadial to reference value at inner boundary.
[0] Damping VRadial to reference value at outer boundary.
[0] Damping VAzimuthal to reference value at inner boundary.
[0] Damping VAzimuthal to reference value at outer boundary.
[0] Damping SurfaceDensity to reference value at inner boundary.
[0] Damping SurfaceDensity to reference value at outer boundary.
[0] Damping Energy to reference value at inner boundary.
[0] Damping Energy to reference value at outer boundary.
[0] Radiative diffusion is disabled. Using fixed omega = 1.500000 with a maximum 50000 interations.
[0] Indirect Term computed as effective Hydro center acceleratrion with shifting the Nbody system to the center.
[0] Body force on gas computed via potential.
[0] Using FARGO algorithm for azimuthal advection.
[0] Using standard forward euler scheme for source terms.
[0] Cps is set, overwriting Nrad and Naz!
[0] Grid resolution set using cps = 4.000000
[0] The grid has (Nrad, Naz) = (148, 504) cells with (4.013071, 4.010705) cps.
[0] Computing scale height with respect to primary object.
[0] Using isothermal equation of state. AdiabaticIndex = 1.400.
[0] Viscosity is of alpha type with alpha = 1.000e-03
[0] Defaulting to VanLeer flux limiter
[0] Output information:
[0] Output directory: output/out/
[0] Number of files: 800
[0] Total output size: 0.00 GB
[0] Space Available: 38.76 GB
[0] Initializing 8 RNGs per MPI process.
[0] Warning : no `radii.dat' file found. Using default.
[0] The first 1 planets are used to calculate the hydro frame center.
[0] The mass of the planets used as hydro frame center is 1.000000e+00.
[0] 2 planet(s) initialized.
[0] Planet overview:
[0]
[0] # | name | mass [m0] | x [l0] | y [l0] | vx | vy |
[0] -----+-------------------------+------------+------------+------------+------------+------------+
[0] 0 | Star | 1 | 0 | -0 | 0 | 0 |
[0] 1 | Jupiter | 0.0009546033 | 1 | 0 | -0 | 1.000477 |
[0]
[0] # | e | a | T [t0] | T [a] | accreting | Accretion Type |
[0] -----+------------+------------+------------+------------+------------+----------------+
[0] 0 | 6.368246e-17 | 1 | 6.280188 | 0.999548 | 0 | No Accretion |
[0] 1 | 6.368246e-17 | 1 | 6.280188 | 0.999548 | 10 | Kley Accret. |
[0]
[0] # | Temp [K] | R [l0] | irradiates | rampuptime |
[0] -----+------------+------------+------------+------------+
[0] 0 | 5778 | 0.0046505 | yes | 0 |
[0] 1 | 0 | 4.6505e-05 | no | 10 |
[0]
[0] Using Tscharnuter-Winkler (1979) artificial viscosity with C = 1.410000.
[0] Artificial viscosity is used for dissipation.
[0] Surface density factor: 2.50663
[0] Tau factor: 0.5
[0] Tau min: 0.01
[0] Kappa factor: 1
[0] Minimum temperature: 2.81162e-05 K = 3.00000e+00
[0] Maximum temperature: 9.37206e+94 K = 1.00000e+100
[0] Heating from viscous dissipation is enabled. Using a total factor of 1.
[0] Cooling (beta) is disabled and reference temperature is floor. Using beta = 10.
[0] Cooling (radiative) is enabled. Using a total factor of 1.
[0] S-curve cooling is disabled.
[0] CFL parameter: 0.5
[0] Opacity uses tables from Lin & Papaloizou, 1985
[0] Particles are disabled.
[0] Initializing Sigma(r) = 2.25093e-05 = 200 g cm^-2 * [r/(1 AU)]^(-0.5)
[0] Total disk is mass is 0.000348846 = 6.9367e+29 g.
[0] Writing output output/out/snapshots/0, Snapshot Number 0, Time 0.000000.
[0] Writing output output/out/snapshots/reference, Snapshot Number 0, Time 0.000000.
[0] Writing output output/out/snapshots/1, Snapshot Number 1, Time 0.157000.
[0] Writing output output/out/snapshots/2, Snapshot Number 2, Time 0.314000.
[0] Writing output output/out/snapshots/3, Snapshot Number 3, Time 0.471000.
[0] Writing output output/out/snapshots/4, Snapshot Number 4, Time 0.628000.
[0] Writing output output/out/snapshots/5, Snapshot Number 5, Time 0.785000.
[0] Writing output output/out/snapshots/6, Snapshot Number 6, Time 0.942000.
[0] Writing output output/out/snapshots/7, Snapshot Number 7, Time 1.099000.
[0] Writing output output/out/snapshots/8, Snapshot Number 8, Time 1.256000.
[0] Writing output output/out/snapshots/9, Snapshot Number 9, Time 1.413000.
[0] Writing output output/out/snapshots/10, Snapshot Number 10, Time 1.570000.
[0] Writing output output/out/snapshots/11, Snapshot Number 11, Time 1.727000.
[0] Writing output output/out/snapshots/12, Snapshot Number 12, Time 1.884000.
[0] Writing output output/out/snapshots/13, Snapshot Number 13, Time 2.041000.
[0] Writing output output/out/snapshots/14, Snapshot Number 14, Time 2.198000.
[0] Writing output output/out/snapshots/15, Snapshot Number 15, Time 2.355000.
[0] Writing output output/out/snapshots/16, Snapshot Number 16, Time 2.512000.
[0] Writing output output/out/snapshots/17, Snapshot Number 17, Time 2.669000.
[0] Writing output output/out/snapshots/18, Snapshot Number 18, Time 2.826000.
[0] Writing output output/out/snapshots/19, Snapshot Number 19, Time 2.983000.
[0] Writing output output/out/snapshots/20, Snapshot Number 20, Time 3.140000.
[0] Writing output output/out/snapshots/21, Snapshot Number 21, Time 3.297000.
[0] Writing output output/out/snapshots/22, Snapshot Number 22, Time 3.454000.
[0] Writing output output/out/snapshots/23, Snapshot Number 23, Time 3.611000.
[0] Writing output output/out/snapshots/24, Snapshot Number 24, Time 3.768000.
[0] Writing output output/out/snapshots/25, Snapshot Number 25, Time 3.925000.
[0] Writing output output/out/snapshots/26, Snapshot Number 26, Time 4.082000.
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[0] Writing output output/out/snapshots/28, Snapshot Number 28, Time 4.396000.
[0] Writing output output/out/snapshots/29, Snapshot Number 29, Time 4.553000.
[0] Writing output output/out/snapshots/30, Snapshot Number 30, Time 4.710000.
[0] Writing output output/out/snapshots/31, Snapshot Number 31, Time 4.867000.
[0] Writing output output/out/snapshots/32, Snapshot Number 32, Time 5.024000.
[0] Writing output output/out/snapshots/33, Snapshot Number 33, Time 5.181000.
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[0] Writing output output/out/snapshots/39, Snapshot Number 39, Time 6.123000.
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[0] Writing output output/out/snapshots/44, Snapshot Number 44, Time 6.908000.
[0] Writing output output/out/snapshots/45, Snapshot Number 45, Time 7.065000.
[0] Writing output output/out/snapshots/46, Snapshot Number 46, Time 7.222000.
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[0] Writing output output/out/snapshots/90, Snapshot Number 90, Time 14.130000.
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[0] Writing output output/out/snapshots/92, Snapshot Number 92, Time 14.444000.
[0] Writing output output/out/snapshots/93, Snapshot Number 93, Time 14.601000.
[0] Writing output output/out/snapshots/94, Snapshot Number 94, Time 14.758000.
[0] Writing output output/out/snapshots/95, Snapshot Number 95, Time 14.915000.
[0] Writing output output/out/snapshots/96, Snapshot Number 96, Time 15.072000.
[0] Writing output output/out/snapshots/97, Snapshot Number 97, Time 15.229000.
[0] Writing output output/out/snapshots/98, Snapshot Number 98, Time 15.386000.
[0] Writing output output/out/snapshots/99, Snapshot Number 99, Time 15.543000.
[0] Writing output output/out/snapshots/100, Snapshot Number 100, Time 15.700000.
[0] -- Final: Total Hydrosteps 500, Time 15.70, Walltime 2.34 seconds, Time per Step: 4.69 milliseconds
0
Plotting¶
First, we define a function to plot the top down view on the disk.
Then, we plot all images seperately and store them in a directory.
Finally, we combine the single images into a movie by leveraging ffmpeg.
import numpy as np
import matplotlib.colors as mplcolors
import matplotlib.pyplot as plt
def plot_field(loader, name, N, ax=None, dataunit=None, vmin=None, vmax=None, cmap="viridis", title=None):
R, PHI, vals = loader.gas.vars2D.get(name, N, grid_for_plot=True)
if dataunit is None:
dataunit = vals.unit
C = vals.to_value(dataunit)
X = R*np.cos(PHI)
Y = R*np.sin(PHI)
if ax is None:
fig, ax = plt.subplots(dpi=150)
else:
fig = ax.get_figure()
norm = mplcolors.Normalize(vmin=vmin, vmax=vmax)
# Hacky way to support arrays that are defined on the radial interfaces
if C.shape[0] == X.shape[0]:
C = C[:-1,:]
pcm = ax.pcolormesh(X,Y,C, norm=norm, cmap=cmap)
ax.set_aspect("equal")
t = loader.snapshot_time[N].to_value("kyr")
if title is None:
title = ""
else:
title += "\n"
title += f" t={t:.2e}kyr, N={N}"
ax.set_title(title)
cbar = fig.colorbar(pcm, ax=ax)
cbar.set_label(f"{name} [{dataunit}]")
return fig
from fargocpt import Loader
l = Loader("output/out/")
folder = "imgs"
!mkdir -p $folder
# have a progress bar
!pip install tqdm
Requirement already satisfied: tqdm in /home/rometsch/repo/fargocpt/python-venv/lib/python3.10/site-packages (4.66.1)
We plot all snapshots, this might take a while.
from tqdm import tqdm
for n in tqdm(l.snapshots):
fig = plot_field(l, "Sigma", n, dataunit="g/cm2", vmin=0, vmax=600, cmap="magma", title="Sigma");
fig.savefig(f"imgs/Sigma{n}.jpg", dpi=300)
plt.close(fig)
0%| | 0/101 [00:00<?, ?it/s]100%|██████████| 101/101 [00:15<00:00, 6.61it/s]
Finally, we make the movie.
To change the file size, you can adjust framerate and the quality parameter. Try a few settings with a small number of frames to find your sweet stop.
framerate = 60
quality = 20
!ffmpeg -y -framerate $framerate -i $folder/Sigma%d.jpg -c:v libx264 -crf $quality output.mp4
ffmpeg version 4.4.2-0ubuntu0.22.04.1 Copyright (c) 2000-2021 the FFmpeg developers
built with gcc 11 (Ubuntu 11.2.0-19ubuntu1)
configuration: --prefix=/usr --extra-version=0ubuntu0.22.04.1 --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu --arch=amd64 --enable-gpl --disable-stripping --enable-gnutls --enable-ladspa --enable-libaom --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libcdio --enable-libcodec2 --enable-libdav1d --enable-libflite --enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libgme --enable-libgsm --enable-libjack --enable-libmp3lame --enable-libmysofa --enable-libopenjpeg --enable-libopenmpt --enable-libopus --enable-libpulse --enable-librabbitmq --enable-librubberband --enable-libshine --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libsrt --enable-libssh --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvorbis --enable-libvpx --enable-libwebp --enable-libx265 --enable-libxml2 --enable-libxvid --enable-libzimg --enable-libzmq --enable-libzvbi --enable-lv2 --enable-omx --enable-openal --enable-opencl --enable-opengl --enable-sdl2 --enable-pocketsphinx --enable-librsvg --enable-libmfx --enable-libdc1394 --enable-libdrm --enable-libiec61883 --enable-chromaprint --enable-frei0r --enable-libx264 --enable-shared
libavutil 56. 70.100 / 56. 70.100
libavcodec 58.134.100 / 58.134.100
libavformat 58. 76.100 / 58. 76.100
libavdevice 58. 13.100 / 58. 13.100
libavfilter 7.110.100 / 7.110.100
libswscale 5. 9.100 / 5. 9.100
libswresample 3. 9.100 / 3. 9.100
libpostproc 55. 9.100 / 55. 9.100
Input #0, image2, from 'imgs/Sigma%d.jpg':
Duration: 00:00:01.68, start: 0.000000, bitrate: N/A
Stream #0:0: Video: mjpeg (Baseline), yuvj420p(pc, bt470bg/unknown/unknown), 1920x1440 [SAR 300:300 DAR 4:3], 60 fps, 60 tbr, 60 tbn, 60 tbc
Stream mapping:
Stream #0:0 -> #0:0 (mjpeg (native) -> h264 (libx264))
Press [q] to stop, [?] for help
[1;36m[libx264 @ 0x557fecd5efc0] [0musing SAR=1/1
[1;36m[libx264 @ 0x557fecd5efc0] [0musing cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX FMA3 BMI2 AVX2
[1;36m[libx264 @ 0x557fecd5efc0] [0mprofile High, level 5.1, 4:2:0, 8-bit
[1;36m[libx264 @ 0x557fecd5efc0] [0m264 - core 163 r3060 5db6aa6 - H.264/MPEG-4 AVC codec - Copyleft 2003-2021 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=24 lookahead_threads=4 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'output.mp4':
Metadata:
encoder : Lavf58.76.100
Stream #0:0: Video: h264 (avc1 / 0x31637661), yuvj420p(pc, bt470bg/unknown/unknown, progressive), 1920x1440 [SAR 300:300 DAR 4:3], q=2-31, 60 fps, 15360 tbn
Metadata:
encoder : Lavc58.134.100 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: N/A
frame= 101 fps=0.0 q=-1.0 Lsize= 436kB time=00:00:01.63 bitrate=2187.8kbits/s speed=1.75x
video:434kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.470529%
[1;36m[libx264 @ 0x557fecd5efc0] [0mframe I:1 Avg QP:17.13 size: 47798
[1;36m[libx264 @ 0x557fecd5efc0] [0mframe P:25 Avg QP:18.13 size: 7060
[1;36m[libx264 @ 0x557fecd5efc0] [0mframe B:75 Avg QP:18.98 size: 2928
[1;36m[libx264 @ 0x557fecd5efc0] [0mconsecutive B-frames: 1.0% 0.0% 0.0% 99.0%
[1;36m[libx264 @ 0x557fecd5efc0] [0mmb I I16..4: 20.8% 72.9% 6.4%
[1;36m[libx264 @ 0x557fecd5efc0] [0mmb P I16..4: 0.7% 12.8% 0.1% P16..4: 4.6% 1.0% 0.6% 0.0% 0.0% skip:80.3%
[1;36m[libx264 @ 0x557fecd5efc0] [0mmb B I16..4: 0.4% 1.3% 0.0% B16..8: 8.4% 1.2% 0.1% direct: 1.1% skip:87.6% L0:50.6% L1:47.7% BI: 1.7%
[1;36m[libx264 @ 0x557fecd5efc0] [0m8x8 transform intra:86.4% inter:93.8%
[1;36m[libx264 @ 0x557fecd5efc0] [0mcoded y,uvDC,uvAC intra: 20.9% 29.4% 2.5% inter: 0.7% 2.8% 0.0%
[1;36m[libx264 @ 0x557fecd5efc0] [0mi16 v,h,dc,p: 48% 30% 12% 10%
[1;36m[libx264 @ 0x557fecd5efc0] [0mi8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 41% 23% 33% 1% 0% 0% 0% 0% 0%
[1;36m[libx264 @ 0x557fecd5efc0] [0mi4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 40% 23% 15% 4% 3% 4% 3% 4% 3%
[1;36m[libx264 @ 0x557fecd5efc0] [0mi8c dc,h,v,p: 46% 25% 26% 3%
[1;36m[libx264 @ 0x557fecd5efc0] [0mWeighted P-Frames: Y:0.0% UV:0.0%
[1;36m[libx264 @ 0x557fecd5efc0] [0mref P L0: 60.4% 3.6% 20.1% 15.9%
[1;36m[libx264 @ 0x557fecd5efc0] [0mref B L0: 82.4% 14.6% 3.0%
[1;36m[libx264 @ 0x557fecd5efc0] [0mref B L1: 96.1% 3.9%
[1;36m[libx264 @ 0x557fecd5efc0] [0mkb/s:2109.70
The result¶
If you have the IPython package installed, the following should show you the video.
from IPython.display import Video
# Display the video
Video(os.getcwd() + "/output.mp4")