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Dust coagulation #25

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Dust coagulation #25

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e061712
merge with the develop branch
shengtai Dec 4, 2024
b191975
add files from gitlab/sli/coagulation branch and merge with develop
shengtai Dec 4, 2024
63e37b9
format fixed in pgen/dust_coagulation.hpp
shengtai Dec 4, 2024
d82919a
Merge branch 'develop' of github.com:lanl/artemis into sli/dust
shengtai Dec 4, 2024
6ba72b0
fixed omega_k calculation in dust.cpp
shengtai Dec 5, 2024
1beaf24
remove dust_drag
shengtai Dec 5, 2024
a26caad
modification based on merge comments
shengtai Dec 11, 2024
05da651
Merge branch 'develop' of github.com:lanl/artemis into sli/dust
shengtai Dec 11, 2024
548a9d1
Merge branch 'develop' into sli/dust
shengtai Dec 11, 2024
347ea01
merge with the head version and modify c2p to p2c in dust.cpp
shengtai Dec 11, 2024
11afd99
Merge branch 'sli/dust' of github.com:lanl/artemis into sli/dust
shengtai Dec 11, 2024
9061f6a
Merge branch 'develop' of github.com:lanl/artemis into sli/dust
shengtai Dec 23, 2024
ecf6de0
Merge branch 'develop' of github.com:lanl/artemis into sli/dust
shengtai Jan 2, 2025
053f77b
new modification based on units
shengtai Jan 3, 2025
0198b3b
new output file name based on problem_id
shengtai Jan 3, 2025
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146 changes: 146 additions & 0 deletions inputs/dust/SI_strat1_amr_BA.in
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# ========================================================================================
# (C) (or copyright) 2023-2024. 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.
# ========================================================================================

<artemis>
problem = SI_strat # name of the pgen
coordinates = cartesian

<parthenon/job>
problem_id = runBA # problem ID: basename of output filenames

<parthenon/output0>
file_type = hst
dt = 0.01

<parthenon/output1>
variables = gas.prim.density, &
gas.prim.velocity, &
dust.prim.density, &
dust.prim.velocity

file_type = hdf5 # HDF5 data dump
dt = 2.0 # time increment between outputs
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align comments here and elsewhere.


<parthenon/output2>
file_type = rst
dt = 100.0

<parthenon/time>
nlim = -1 # cycle limit
tlim = 400.0 # time limit
integrator = rk2 # time integration algorithm
ncycle_out = 100 # interval for stdout summary info

<parthenon/mesh>
nx1 = 1024 # Number of zones in X1-direction
x1min = -0.4 # minimum value of X1
x1max = 0.4 # maximum value of X1
ix1_bc = extrapolate # Inner-X1 boundary condition flag
ox1_bc = extrapolate # Outer-X1 boundary condition flag

nx2 = 512 # Number of zones in X2-direction
x2min = -0.2 # minimum value of X2
x2max = 0.2 # maximum value of X2
ix2_bc = extrapolate # Inner-X2 boundary condition flag
ox2_bc = extrapolate # Outer-X2 boundary condition flag

nx3 = 1 # Number of zones in X3-direction
x3min = -0.5 # minimum value of X3
x3max = 0.5 # maximum value of X3
ix3_bc = periodic # Inner-X3 boundary condition flag
ox3_bc = periodic # Outer-X3 boundary condition flag

# nghost = 2
refinement = static
numlevel = 2 #3

<parthenon/static_refinement1>
x1min = -0.3
x1max = 0.3
x2min = -0.02
x2max = 0.02
level = 1


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remove extraneous whitespace here and elsewhere.

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this input is removed in the new code


<parthenon/meshblock>
nx1 = 16 # Number of cells in each MeshBlock, X1-dir
nx2 = 16 # Number of cells in each MeshBlock, X2-dir
nx3 = 16 # Number of cells in each MeshBlock, X3-dir

<physics>
gas = true
gravity = false
rotating_frame = true
dust = true

<gas>
cfl = 0.6
gamma = 1.000001
reconstruct = plm
riemann = hlle
dfloor = 1.0e-10
siefloor = 1.0e-10
refine_field = density
refine_type = magnitude
refine_thr = 3.0
deref_thr = 0.8

<dust>
reconstruct = plm
riemann = hlle
nspecies = 1
const_stopping_time = true
size_input = none
stopping_time = 0.3
Hratio = 0.1

hst_out_d2g = true
Kai0 = 0.1 #2*etaVk*iso_cs

enable_dust_drag = true
enable_dust_feedback = true
drag_method = implicit
#rho_p = 1.25
#rho_g0 = 0.3555 #g/cm^2, code-to-physical convert
#user_input_size = true
#Size_1 = 10.0 # dust size


<gravity>
#type = uniform
#gx1 = 0.1 # 2*etaVk*Ome0
#gx2 = 0.0
#gx3 = 0.0

#type = point
#gm = 1e-5
#soft = .03
#x = 0
#y = 0
#z = 0

<rotating_frame>
omega = 1.0
qshear = 1.5
shboxcoord = 2 # 1=xy; 2=xz
stratified_flag = true

<problem>
rho0 = 0.3989422804 #1.0/sqrt(2*pi)
dens_min = 1.0e-10
pres_min = 1.0e-13
h = 1.0
etaVk = 0.05
amp = 0.1
dust_to_gas = 0.04
135 changes: 135 additions & 0 deletions inputs/dust/SI_strat_AB.in
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# ========================================================================================
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Only the two dust coagulation input files show be a part of this PR

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this input file is deleted in the new code

# (C) (or copyright) 2023-2024. 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.
# ========================================================================================

<artemis>
problem = SI_strat # name of the pgen
coordinates = cartesian

<parthenon/job>
problem_id = runAB # problem ID: basename of output filenames

<parthenon/output0>
file_type = hst
dt = 0.01

<parthenon/output1>
variables = gas.prim.density, &
gas.prim.velocity, &
dust.prim.density, &
dust.prim.velocity

file_type = hdf5 # HDF5 data dump
dt = 0.5 # time increment between outputs

<parthenon/output2>
file_type = rst
dt = 20.0

<parthenon/time>
nlim = -1 # cycle limit
tlim = 40.0 # time limit
integrator = rk2 # time integration algorithm
ncycle_out = 20 # interval for stdout summary info

<parthenon/mesh>
nx1 = 512 # Number of zones in X1-direction
x1min = -0.05 # minimum value of X1
x1max = 0.05 # maximum value of X1
ix1_bc = extrapolate # Inner-X1 boundary condition flag
ox1_bc = extrapolate # Outer-X1 boundary condition flag

nx2 = 512 # Number of zones in X2-direction
x2min = -0.05 # minimum value of X2
x2max = 0.05 # maximum value of X2
ix2_bc = periodic # Inner-X2 boundary condition flag
ox2_bc = periodic # Outer-X2 boundary condition flag

nx3 = 1 # Number of zones in X3-direction
x3min = -0.5 # minimum value of X3
x3max = 0.5 # maximum value of X3
ix3_bc = periodic # Inner-X3 boundary condition flag
ox3_bc = periodic # Outer-X3 boundary condition flag

# nghost = 2
# refinement = adaptive
# numlevel = 4

<parthenon/meshblock>
nx1 = 16 # Number of cells in each MeshBlock, X1-dir
nx2 = 16 # Number of cells in each MeshBlock, X2-dir
nx3 = 1 # Number of cells in each MeshBlock, X3-dir

<physics>
gas = true
gravity = false
rotating_frame = true
dust = true

<gas>
cfl = 0.6
gamma = 1.000001
reconstruct = plm
riemann = hlle
dfloor = 1.0e-10
siefloor = 1.0e-10
refine_field = density
refine_type = magnitude
refine_thr = 3.0
deref_thr = 0.8

<dust>
reconstruct = plm
riemann = hlle
nspecies = 1
const_stopping_time = true
size_input = none
stopping_time = 0.1
hst_out_d2g = true
Kai0 = 0.1 #2*etaVk*iso_cs

enable_dust_drag = true
enable_dust_feedback = true
drag_method = explicit
#rho_p = 1.25
#rho_g0 = 0.3555 #g/cm^2, code-to-physical convert
#user_input_size = true
#Size_1 = 10.0 # dust size


<gravity>
#type = uniform
#gx1 = 0.1 # 2*etaVk*Ome0
#gx2 = 0.0
#gx3 = 0.0

#type = point
#gm = 1e-5
#soft = .03
#x = 0
#y = 0
#z = 0

<rotating_frame>
omega = 1.0
qshear = 1.5
shboxcoord = 2 # 1=xy; 2=xz
stratified_flag = false

<problem>
rho0 = 1.0
dens_min = 1.0e-10
pres_min = 1.0e-13
h = 1.0
etaVk = 0.05
amp = 0.25
dust_to_gas = 1.0
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