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Merge branch 'development' into add_cubic_interp
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@zingale
zingale authored May 29, 2024
2 parents 1784113 + 7893b5c commit adc1770
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1 change: 1 addition & 0 deletions .codespell-ignore-words
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Expand Up @@ -12,3 +12,4 @@ nd
ue
bion
aas
checkin
2 changes: 1 addition & 1 deletion .github/workflows/check_params.py
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Expand Up @@ -48,7 +48,7 @@ def doit(castro_dir):
# remove comments
idx = line.find("#")
if idx > 0:
line = line[idx:]
line = line[:idx]

found_param = pattern.match(line)
if not found_param:
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23 changes: 19 additions & 4 deletions .github/workflows/dependencies_hip.sh
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Expand Up @@ -17,10 +17,23 @@ set -eu -o pipefail
# failed files the given number of times.
echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries

# Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu
# Ref.: https://rocm.docs.amd.com/projects/install-on-linux/en/latest/how-to/native-install/ubuntu.html

# Make the directory if it doesn't exist yet.
# This location is recommended by the distribution maintainers.
sudo mkdir --parents --mode=0755 /etc/apt/keyrings

# Download the key, convert the signing-key to a full
# keyring required by apt and store in the keyring directory
wget https://repo.radeon.com/rocm/rocm.gpg.key -O - | \
gpg --dearmor | sudo tee /etc/apt/keyrings/rocm.gpg > /dev/null

curl -O https://repo.radeon.com/rocm/rocm.gpg.key
sudo apt-key add rocm.gpg.key
echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-debian}/ ubuntu main" \

source /etc/os-release # set UBUNTU_CODENAME: focal or jammy or ...

echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-latest} ${UBUNTU_CODENAME} main" \
| sudo tee /etc/apt/sources.list.d/rocm.list
echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
| sudo tee -a /etc/profile.d/rocm.sh
Expand All @@ -43,8 +56,10 @@ sudo apt-get install -y --no-install-recommends \
roctracer-dev \
rocprofiler-dev \
rocrand-dev \
rocprim-dev \
hiprand-dev
rocprim-dev

# hiprand-dev is a new package that does not exist in old versions
sudo apt-get install -y --no-install-recommends hiprand-dev || true

# activate
#
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2 changes: 1 addition & 1 deletion Docs/source/Hydrodynamics.rst
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Expand Up @@ -609,7 +609,7 @@ behavior:
Compute Primitive Variables
---------------------------

We compute the primtive variables from the conserved variables.
We compute the primitive variables from the conserved variables.

- :math:`\rho, \rho e`: directly copy these from the conserved state
vector
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2 changes: 1 addition & 1 deletion Docs/source/Verification.rst
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Expand Up @@ -495,7 +495,7 @@ test problem. A hot sphere is centered at the origin in a spherical
geometry. The spectrum from this sphere follows a Planck
distribution. The ambient medium is at a much lower temperature. A
frequency-dependent opacity makes the domain optically thin for high
frequecies and optically thick for low frequency. At long times, the
frequencies and optically thick for low frequency. At long times, the
solution will be a combination of the blackbody radiation from the
ambient medium plus the radiation that propagated from the hot sphere.
An analytic solution exists :cite:`graziani:2008` which gives the
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6 changes: 6 additions & 0 deletions Docs/source/conf.py
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Expand Up @@ -218,6 +218,12 @@ def get_version():
]


# -- Options for linkcheck

linkcheck_retries = 3
linkcheck_timeout = 100


# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
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3 changes: 0 additions & 3 deletions Docs/source/refs.bib
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Expand Up @@ -775,7 +775,6 @@ @article{SHESTAKOV2005
year = "2005",
issn = "0022-4073",
doi = "https://doi.org/10.1016/j.jqsrt.2004.05.052",
url = "http://www.sciencedirect.com/science/article/pii/S0022407304002092",
author = "A.I. Shestakov and J.H. Bolstad",
keywords = "Linearized, Multigroup diffusion, Radiation, Transfer, Transport",
abstract = "An exact solution, based on Fourier and Laplace (FL) transforms, is developed for a linearization of the system modeling the multifrequency radiation diffusion and matter energy balance equations. The model uses an ideal gas equation of state. Opacities are proportional to the inverse of the cube of the frequency, thereby simulating free–free transitions. The solution is obtained in terms of integrals over the FL coefficients of the initial conditions and explicit sources. Results are presented for two special cases. (1) No sources, initially cold radiation field, and a localized matter energy profile. (2) Initially cold matter and radiation fields and a source of matter energy extending over finite space and time intervals."
Expand Down Expand Up @@ -830,7 +829,6 @@ @article{suolson:1996
year = "1996",
issn = "0022-4073",
doi = "https://doi.org/10.1016/0022-4073(96)84524-9",
url = "http://www.sciencedirect.com/science/article/pii/0022407396845249",
author = "Su Bingjing and Gordon L. Olson",
abstract = "As an extension of previous work in the literature, this paper considers a particular one-dimensional, halfspace, non-equilibrium Marshak wave problem. The radiative transfer model employed is a one-group diffusion approximation with Marshak boundary condition, where the radiation and material fields are out of equilibrium. An analytic solution for the distribution of radiative energy and material temperature as a function of space and time to this problem is given and tables of numerical results are generated. These benchmark results, together with the previously published results, are useful as a reference for validating time-dependent radiation diffusion computer codes. A comparison with a finite difference solution is presented which shows excellent agreement when a fine spatial mesh and small time steps are used."
}
Expand All @@ -844,7 +842,6 @@ @article{suolson:1999
year = "1999",
issn = "0022-4073",
doi = "https://doi.org/10.1016/S0022-4073(98)00105-8",
url = "http://www.sciencedirect.com/science/article/pii/S0022407398001058",
author = "Bingjing Su and Gordon L. Olson",
abstract = "Benchmark solutions to time-dependent radiative transfer problems involving non-equilibrium coupling to the material temperature field are crucial for validating time-dependent radiation transport codes. Previous efforts on generating analytical solutions to non-equilibrium radiative transfer problems were all restricted to the one-group grey model. In this paper, a non-grey model, namely the picket-fence model, is considered for a two temperature non-equilibrium radiative transfer problem in an infinite medium. The analytical solutions, as functions of space and time, are constructed in the form of infinite integrals for both the diffusion description and transport description. These expressions are evaluated numerically and the benchmark results are generated. The asymptotic solutions for large and small times are also derived in terms of elementary functions and are compared with the exact results. Comparisons are given between the transport and diffusion solutions and between the grey and non-grey solutions."
}
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2 changes: 1 addition & 1 deletion Exec/gravity_tests/StarGrav/_prob_params
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@@ -1,4 +1,4 @@
model_name character "" y
model_name string "" y

m_0 real 1.e30_rt y

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14 changes: 7 additions & 7 deletions Exec/gravity_tests/hse_convergence_general/_prob_params
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Expand Up @@ -14,19 +14,19 @@ H_star real 500.e0_rt y

atm_delta real 25.e0_rt y

fuel1_name character "helium-4" y
fuel1_name string "helium-4" y

fuel2_name character "" y
fuel2_name string "" y

fuel3_name character "" y
fuel3_name string "" y

fuel4_name character "" y
fuel4_name string "" y

ash1_name character "iron-56" y
ash1_name string "iron-56" y

ash2_name character "" y
ash2_name string "" y

ash3_name character "" y
ash3_name string "" y

fuel1_frac real 1.0_rt y

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2 changes: 1 addition & 1 deletion Exec/gravity_tests/hydrostatic_adjust/_prob_params
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@@ -1,6 +1,6 @@
prob_type integer 1 y

model_name character "" y
model_name string "" y

hse_rho_top real 0.0_rt

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2 changes: 1 addition & 1 deletion Exec/hydro_tests/test_convect/_prob_params
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@@ -1,4 +1,4 @@
model_name character "" y
model_name string "" y

apply_vel_field integer 0 y

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2 changes: 1 addition & 1 deletion Exec/hydro_tests/toy_convect/_prob_params
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Expand Up @@ -2,7 +2,7 @@ H_min real 1.e-4_rt y

cutoff_density real 50.0_rt y

model_name character "" y
model_name string "" y

apply_vel_field integer 0 y

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2 changes: 1 addition & 1 deletion Exec/radiation_tests/RadBreakout/_prob_params
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Expand Up @@ -7,7 +7,7 @@ rbasefac real 0.99e0_rt y
filter_rhomax real -1.e20_rt y
filter_timemax real -1.e20_rt y

model_file character "model.input" y
model_file string "model.input" y

iye int -1 n
iinvmu int -1 n
2 changes: 1 addition & 1 deletion Exec/reacting_tests/reacting_bubble/_prob_params
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@@ -1,5 +1,5 @@

model_name character "" y
model_name string "" y

pert_temp_factor real 1.0_rt y

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12 changes: 6 additions & 6 deletions Exec/reacting_tests/reacting_convergence/_prob_params
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Expand Up @@ -13,17 +13,17 @@ p0 real 1.0_rt n

xn_zone real 0.0_rt n nspec

spec1_name character "helium-4" y
spec1_name string "helium-4" y

spec2_name character "" y
spec2_name string "" y

spec3_name character "" y
spec3_name string "" y

spec4_name character "" y
spec4_name string "" y

spec5_name character "" y
spec5_name string "" y

spec6_name character "" y
spec6_name string "" y

spec1_frac real 1.0_rt y

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26 changes: 21 additions & 5 deletions Exec/science/Detonation/README.md
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@@ -1,7 +1,7 @@
# detonation
# `Detonation`

A simple carbon detonation. The reaction network should be set
through the GNUmakefile.
A simple (carbon or helium) detonation. The reaction network should
be set through the GNUmakefile.

This sets up a domain with a uniform density (dens). A large
temperature (T_l) is placed in the left side of the domain, and an
Expand All @@ -24,9 +24,25 @@ shockwave (as seen in the pressure field).
Note: if the domain is too small, then the burning will decouple from
the shock wave, and you will not get a detonation.

Some important inputs files:
## Inputs files

Some important inputs files

* `inputs-det-x.nse` : this produces a nice detonation that gets hot
enough for the ash to be in NSE.

* `inputs-det-x.subch_base`: this produces a He4 detonation using the
same initial condition in the shell burning stage of the subchandra problem.
same initial condition in the shell burning stage of the subchandra
problem.


## Publications

This problem setup has been used in the following papers:

* *A Framework for Exploring Nuclear Physics Sensitivity in Numerical Simulations*

Zhi Chen, Eric T. Johnson, Max Katz, Alexander Smith Clark, Brendan
Boyd, & Michael Zingale, 2024, Journal of Physics: Conference Series,
2742, 1, 012021 (DOI: 10.1088/1742-6596/2742/1/012021)

2 changes: 1 addition & 1 deletion Exec/science/bwp-rad/_prob_params
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@@ -1 +1 @@
model_name character "" y
model_name string "" y
15 changes: 7 additions & 8 deletions Exec/science/convective_flame/_prob_params
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Expand Up @@ -10,7 +10,7 @@ cutoff_density real 1.e-8_rt y

refine_cutoff_frac real 0.5_rt y

refine_cutoff_height real 0.0_rt
refine_cutoff_height real 0.0_rt

T_hi real 5.e8_rt y

Expand All @@ -24,17 +24,17 @@ H_star real 500e0_rt y

atm_delta real 25.0e0_rt y

fuel1_name character "fuel" y
fuel1_name string "fuel" y

fuel2_name character "" y
fuel2_name string "" y

fuel3_name character "" y
fuel3_name string "" y

ash1_name character "inert" y
ash1_name string "inert" y

ash2_name character "" y
ash2_name string "" y

ash3_name character "" y
ash3_name string "" y

fuel1_frac real 1.0_rt y

Expand All @@ -51,4 +51,3 @@ ash3_frac real 0.0_rt y
low_density_cutoff real 1.e-4_rt y

smallx real 1.e-10_rt y

17 changes: 8 additions & 9 deletions Exec/science/flame/_prob_params
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Expand Up @@ -20,13 +20,13 @@ e_ash real 0.0_rt

xn_ash real 0.0_rt n nspec

fuel1_name character "helium-4" y
fuel1_name string "helium-4" y

fuel2_name character "" y
fuel2_name string "" y

fuel3_name character "" y
fuel3_name string "" y

fuel4_name character "" y
fuel4_name string "" y

X_fuel1 real 1.0_rt y

Expand All @@ -36,13 +36,13 @@ X_fuel3 real 0.0_rt y

X_fuel4 real 0.0_rt y

ash1_name character "oxygen-16" y
ash1_name string "oxygen-16" y

ash2_name character "" y
ash2_name string "" y

ash3_name character "" y
ash3_name string "" y

ash4_name character "" y
ash4_name string "" y

X_ash1 real 1.0_rt y

Expand All @@ -57,4 +57,3 @@ v_inflow real 0.0_rt y
mass_flux real 0.0_rt

smallx_init real 0.0_rt y

14 changes: 7 additions & 7 deletions Exec/science/flame_tube/_prob_params
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Expand Up @@ -29,19 +29,19 @@ H_star real 500.e0_rt y

atm_delta real 25.e0_rt y

fuel1_name character "helium-4" y
fuel1_name string "helium-4" y

fuel2_name character "" y
fuel2_name string "" y

fuel3_name character "" y
fuel3_name string "" y

fuel4_name character "" y
fuel4_name string "" y

ash1_name character "iron-56" y
ash1_name string "iron-56" y

ash2_name character "" y
ash2_name string "" y

ash3_name character "" y
ash3_name string "" y

fuel1_frac real 1.0_rt y

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14 changes: 7 additions & 7 deletions Exec/science/flame_wave/_prob_params
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Expand Up @@ -29,19 +29,19 @@ H_star real 500.e0_rt y

atm_delta real 25.e0_rt y

fuel1_name character "helium-4" y
fuel1_name string "helium-4" y

fuel2_name character "" y
fuel2_name string "" y

fuel3_name character "" y
fuel3_name string "" y

fuel4_name character "" y
fuel4_name string "" y

ash1_name character "iron-56" y
ash1_name string "iron-56" y

ash2_name character "" y
ash2_name string "" y

ash3_name character "" y
ash3_name string "" y

fuel1_frac real 1.0_rt y

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2 changes: 1 addition & 1 deletion Exec/science/massive_star/_prob_params
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@@ -1,4 +1,4 @@
model_name character "" y
model_name string "" y

interpolate_pres int 0 y

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