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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: bf5a0075b1317791b61b778ce8adbef7
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/index.rst.txt

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+.. artemis documentation master file, created by
+   sphinx-quickstart on Tue Aug 27 07:51:41 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+artemis documentation
+=====================
+
+|code| is a performance-portable, multi-fluid, AMR hydrodynamics code built on top of the `Parthenon`_ mesh refinement library.
+|code| solves the multi-fluid Navier-Stokes equations:
+
+.. math::
+
+   \frac{D \rho_i}{D t} & = -\rho \nabla \cdot \mathbf{v_i}   \\\\
+   \rho_i \frac{D \mathbf{v}_i }{D t} & = -\nabla P_i + \rho_i \mathbf{g}_i + \nabla \cdot \mathbf{\Pi}_i + \sum_j \mathbf{R}_{ij}  \\\\
+   \rho_i \frac{D e_i }{D t} & = - P_i \nabla \cdot \mathbf{v}_i + \mathbf{\Pi}_i : \nabla \mathbf{v}_i + \Gamma - \Lambda
+
+where :math:`(\rho_i, e_i, \mathbf{v}_i)` are the material density, specific internal energy, and velocitity. 
+The convective derivative is defined as :math:`D/Dt = \partial_t + \mathbf{v}_i \cdot \nabla`. 
+Material temperature and pressure are specified by an equation of state EOS written in terms of the density and specific internal energy, :math:`T_i(\rho_i,e_i)` and :math:`P_i(\rho_i, e_i)`. 
+Fluids interact via the collision operator, :math:`\mathbf{R}_{ij}`. 
+
+
+
+Key Features
+^^^^^^^^^^^^^
+* Adaptive and static mesh refinement.
+* Runs on CPUs or GPUs. 
+* First- to third-order time stepping. 
+* Full support for Cartesian or curvilinear coordinate systems, including axisymmetric, cylindrical, and spherical coordinates. 
+* Various microphysics processes such as viscosity, cooling, and conduction.
+* Dust coagulation models
+* Coupling to arbitrarily complicated N-Body systems. 
+* One executable design. No need to recompile. 
+
+A full listing of the available physics in |code| can be found in :ref:`physics`.
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+   :glob:
+
+   src/*
+
+
+.. _Parthenon: https://github.com/parthenon-hpc-lab/parthenon

_sources/src/bcs.rst.txt

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+.. =======================================================================================
+.. (C) (or copyright) 2024. Triad National Security, LLC. All rights reserved.
+..
+.. This program was produced under U.S. Government contract 89233218CNA000001 for Los
+.. Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC
+.. for the U.S. Department of Energy/National Nuclear Security Administration. All rights
+.. in the program are reserved by Triad National Security, LLC, and the U.S. Department
+.. of Energy/National Nuclear Security Administration. The Government is granted for
+.. itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide
+.. license in this material to reproduce, prepare derivative works, distribute copies to
+.. the public, perform publicly and display publicly, and to permit others to do so.
+.. =======================================================================================
+
+.. _bc:
+
+Boundary Conditions
+===================
+
+There are several types of boundary conditions available in |code|.
+Some of these are inherited from ``parthenon``.
+
+Choosing boundary conditions is done in the ``<parthenon/mesh>`` input block.
+Each boundary in the problem can be set separately.
+
+An example input block specify periodic boundaries in the ``x1``-direction and reflecting boundaries in the ``x2``-direction is:
+
+::
+
+  <parthenon/mesh>
+  ....
+  ix1_bc = periodic
+  ox1_bc = periodic
+
+  ...
+  ix2_bc = reflecting
+  ox2_bc = reflecting
+
+  ...
+
+Note that there are no ``user`` boundary conditions in |code|, as with some other Parthenon codes.
+All boundary conditions are specified directly in the ``<parthenon/mesh>`` node.
+Also note that some boundary conditions are only compatible with certain :ref:`pgen`.
+Below is a complete listing of available boundary conditions.
+
+
+periodic
+--------
+
+``periodic`` boundary conditions connect opposite ends of the domain.
+
+
+reflecting
+----------
+
+``reflecting`` boundary conditions act as walls that try to keep the fluid inside the domain
+by mirroring variables across the boundary, and negating the sign of the normal component of
+vector quantities.
+
+outflow
+-------
+
+``outflow`` boundary conditions attempt to let material freely leave the domain.
+This is not always perfect, however, and reflections can happen.
+
+ic
+--
+``ic`` boundaries keep the solution at the initial condition in the ghost zones.
+Only the ``disk`` problem generator works with ``ic`` boundaries.
+
+viscous
+-------
+
+``viscous`` boundary conditions are meant to provide continuous injection at the outer radial boundary and an outflow condition at the inner radial boundary of a disk calculation.
+They arise from the solution of the 1D steady-state accretion disk equations which read,
+
+.. math::
+  \dot{M}  & = {\rm const} \\\\
+  \partial_R ( F_\nu - \dot{M} \ell) & = 0
+
+where :math:`\dot{M}` is the radial mass flux, :math:`\ell = R^2 \Omega` is the specific angular momentum, and :math:`F_\nu = 3 \pi \nu \Sigma \ell` is the viscous flux of angular momentum.
+At the innner radial boundary we enforce:
+
+.. math::
+  F_\nu = \dot{M} \ell
+
+which corresponds to keeping :math:`\nu \Sigma = {\rm const}` across the boundary (since :math:`\dot{M} = 3\pi \nu \Sigma`).
+At the outer boundary, we set
+
+.. math::
+  \partial_R F_\nu = \dot{M} \partial_R \ell
+
+by linearly expanding :math:`\ell` and :math:`F_nu`. This is, therefore, and extrapolation boundary at fixed :math:`\dot{M}`.
+Once :math:`F_\nu` is set, the gas density is set, and from that and :math:`\dot{M}`, the radial velocity is set.
+
+The value of the injection :math:`\dot{M}` is set in the ``<problem>`` block:
+
+::
+
+  <problem>
+  ...
+  mdot0 = 1e-6
+
+Note that the derivation above was for 1D.
+2D cylindrical simulations with planets have been shown to behave well with ``viscous`` boundary conditions.
+3D simulations have been largely untested, however.
+
+The ``viscous`` boundary condition is only allowed in the  ``disk`` problem generator, and only when viscosity is active.
+
+
+extrapolate
+-----------
+
+``extrapolate`` boundaries are meant to provide an outflow boundary condition in situations where the fluid variables have non-trivial slopes.
+Examples include:
+
+ * maintaining vertical hydrostatic balance in the ``strat`` problem generator.
+ * maintaining the background shear profile at the :math:`x` boundaries in the ``strat`` problem generator.
+ * maintaining radial profiles of density, temperature, and velocity in the ``disk`` problem generator.
+
+The ``extrapolate`` boundary condition is only allowed in the ``strat`` and ``disk`` problem generators.
+
+conducting
+----------
+
+``conducting`` boundaries are meant to provide a constant thermal heat flux at one boundary, while fixing the temperature at the opposite boundary.
+This allows the domain to relax to a steady-state, hydrostatic, solution with constant heat flux.
+This is mainly used for internal testing.
+When ``conducting`` boundaries are active, the ``flux`` parameter should be set under the ``<problem>`` block.
+The ``conducting`` boundary condition is only allowed in the ``conduction`` problem generator.
+
+
+inflow
+------
+
+``inflow`` boundaries are needed for the shearing-box (See :ref:`pgen`) in the ``y``-direction.
+They are actually a combination of inflow and outflow depending on what side of :math:`x=0` the boundary is on.
+On the inflow side, :math:`v_y` is set to :math:`- q \Omega x`, and the other fluid variables are set to their initial values.
+On the outflow side, outflow conditions are set.
+At the lower :math:`y`-boundary, inflow occurs for :math:`x>0`, whereas for the upper :math:`y`-boundary, inflow occurs for :math:`x<0`.
+This boundary condition is only compatible with the ``strat`` problem generator.
+
+
+
+
+