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Author: Stéphane Michoulier
Email: [email protected]

Pamdeas: version 1.5

DESCRIPTION:

Pamdeas (Porous Aggregate Model and Dust Evolution in protoplAnetary discS) is a 1D code primarily wrote to study the evolution of grain porosity within protoplanetary discs considering different physical processes such as growth, fragmentation, drift, pressure bump, snowline (Vericel & Gonzalez 2020), rotational disruption (Tatsuuma et al. 2021), erosion (Rozner et al. 2020) etc.
This code allows you to follow the evolution of a given number of particles from a set of initial conditions chosen by the user in a stationary non self-gravitating gas disc and was mainly developed to understand the behavior of porous grains, but also to test the porosity algorithms for future implementation in 3D Hydrodynamics code.

FEW WORDS ON INPUT FILE OPTION (Respect the blank space, or expect unforeseen consequences).
2 models can be used to study the evolution of the porosity. One is based on the increase of mass (dm/dt) and use A. Garcia's reformulated algorithms (Garcia 2018),(Garcia & Gonzalez 2020), the other one is based on the increase of size (ds/dt) and use my algorithms.
The dmdt model (use this one by default) support the bounce process, but not the dsdt model.
The degeneracy due to the filling factor in the dsdt model is taken into account.
The dmdt model should be used by default.

You can smooth the inner disc following the usual prescription Sigma(r) = sigma0 * (1-sqrt(Rin/R)) * (R/R0)^-p You are also allowed to create artificially a pressure bump, by adding a gaussian profile to the gas surface density. To create the desired pressure bump, the easiest way is to set ngrains to 0, profile to 1 and plot Sigma vs R, Pg vs R and dustfrac vs R in order to visualise your bump. Then, proceed by iteration.

Be aware that using a pressure bump with radial drift and fragmentation is way slower than any other setup due to small time step.

For porous grains, physical properties of the material have to be changed if the intrinsic density is changed.

LAUNCHING THE PROGRAM

Set your SYSTEM environment to be able to build programs in C++: export SYSTEM=g++
To use all functionality of the program, be sure to have the latest C++ version installed.

If the program is not yet built, follow the instruction below:

• Open a new terminal
• Use the command cd to reach "pamdeas" directory: cd 'Yourdirectory'/pamdeas
• Once in the directory, build the code with: make
• Then, source file will be compiled in "source" folder and the program will be built
• The simulation can then be launch. To do this, go inside the "build" folder where the executable is: cd build
• First, the input file need to be created. In order to write it, write: ./pamdeas setup
• Then, modify the input file to make your own simulation. Don't forget to save your setup
• The input file is store in the input folder
• Run Pamdeas: ./pamdeas (if you have multiple setup files, use ./pamdeas mysetup.in )
• if your input is in a different folder, use ./pamdeas mysetup.in folder (if your input is stored in Pamdeas/myfoldermyinput.in)

Once the simulation is finished, multiple output files are written into the build folder depending on the option:

• Initials_Conditions_Rref.txt summarises your setup
• output_setup name.out: one output file for each particle. The file name depends on the model used (dmdt/dsdt and porous/compact grains)
• disc_profiles.out contains different profiles (surface density, pressure, etc).
• disrupt_param_model.out contains parameters of disrupted grains.

A test suite is also available to test different modules.

• ./pamdeas test runs all the tests
• ./pamdeas testdisc test the initialisation of the disc
• ./pamdeas tesgrowth test the growth rate of a grain
• ./pamdeas testdrift test the radial drift of a grain
• ./pamdeas testporosity test the porosity module of a grain
• ./pamdeas testdisrupt test the disruption of a grain

A Notebook is available to analyse your data easily. It is located in the python folder.

HOW THE PROGRAM IS BUILT ?

The program contains multiple files in the source folder "source" and in the header folder "header":

1. Source files (.CPP and .H)

• a. simulation.cpp & simulation.h

  Contains all variables declarations and time loop to run a simulation.

• b. constantandconversion.h

  Contains the declaration of physical constants and conversion functions between some useful units.

• c. readwrite.cpp & readwrite.h

  Contain reading and writing functions.

• d. disc.cpp & disc.h

  Contain general functions describing gas disks such as gas density, pressure, etc. The full list is given in the .h file

• e. dust.cpp & dust.h

  Contain general functions describing properties of dust grains as kinetic energy, relative velocity or Stokes number. The full list is given in the .h file.

• f. porosity.cpp & porosity.h

  Contain all the algorithms driving the evolution of the filling factor depending on the mass/size and the different processes: growth, frag, compression by collision/gravity etc.

• g. evol.cpp & evol.h

  Contain all the algorithms linked to time stepping: growth rate, drift velocity, adaptative time step etc.

• h. disruption.cpp & disruption.h

  Contain all the algorithms to compute disruption of grains.

• i. tests.cpp & tests.h

  Contains algorithm to test Pamdeas.

References

Arnaud Vericel and Jean-François Gonzalez. Self-induced dust traps around snow lines in protoplanetary discs. MNRAS, 492(1) :210–222, February 2020. doi : 10.1093/mnras/stz3444.

Anthony Garcia. Evolution of grain porosity during growth : a solution to planetary formation barriers? Phd thesis, Université de Lyon, September 2018. URL https://tel.archives-ouvertes.fr/tel-01977317.

Anthony J. L. Garcia and Jean-François Gonzalez. Evolution of porous dust grains in protoplanetary discs - I. Growing grains. MNRAS, 493(2) :1788–1800, April 2020. doi : 10.1093/mnras/staa382.

Tatsuuma M., Kataoka A., Tanaka H., Rotational Disruption of Porous Dust Aggregates due to Gas Flow in Protoplanetary Disks, 2019, The Astrophysical Journal, 874,159

Rozner, Mor, et al. « The aeolian-erosion barrier for the growth of metre-size objects in protoplanetary discs ». Monthly Notices of the Royal Astronomical Society, vol. 496, août 2020, p. 4827‑35.

J. D. Hunter. Matplotlib : A 2d graphics environment. Computing in Science & Engineering, 9(3) :90–95, 2007. doi : 10.1109/MCSE.2007.55.