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[WIP] xrb layered #396

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May 14, 2024
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ab06bbc
initial commit
simonguichandut Mar 7, 2023
96e29a3
describe initial model construction, slightly modify perturbation par…
simonguichandut Mar 8, 2023
071edbe
Merge branch 'development' into working_xrb_layered
zingale Apr 13, 2023
8f03bda
update initial model, smaller fe56 layer
simonguichandut Apr 24, 2023
b97fffd
py_mesa_reader as file
simonguichandut Apr 24, 2023
46a6995
Merge branch 'main' into working_xrb_layered
simonguichandut Apr 24, 2023
aba19b5
py_mesa_reader as file, update velpert height
simonguichandut Apr 24, 2023
463bf06
Merge branch 'working_xrb_layered' of https://github.com/simonguichan…
simonguichandut Apr 24, 2023
88e08a7
analysis files
simonguichandut Apr 29, 2023
ba63567
Merge branch 'main' into working_xrb_layered
simonguichandut Apr 29, 2023
137c3ca
Merge branch 'development' into working_xrb_layered
simonguichandut Apr 29, 2023
bcf4c99
remove fortran
simonguichandut Apr 29, 2023
d68cb54
Merge branch 'development' into working_xrb_layered
zingale Apr 29, 2023
5f258d6
Merge branch 'development' into working_xrb_layered
zingale May 8, 2023
43d095e
analysis notebooks, scripts, inputs and things
simonguichandut May 11, 2023
8a8ea32
new inputs for toy model
simonguichandut May 12, 2023
3327f90
some changes
simonguichandut Jun 1, 2023
5a85d3a
create initial toy model with constant flux radiative layer above adi…
simonguichandut Jun 2, 2023
88311cf
new inputs
simonguichandut Jun 5, 2023
723e9c9
add all hse models for construct_toy_model notebook
simonguichandut Jun 26, 2023
75539c7
clean up analysis and scripts dirs
simonguichandut Aug 30, 2023
fc4e61e
clean up initial model directory
simonguichandut Aug 30, 2023
17b86f1
clean up main dir
simonguichandut Aug 30, 2023
4a76666
merge from main and fix conflicts
simonguichandut Aug 30, 2023
bae89bf
correctly read input params
simonguichandut Aug 31, 2023
73ddb0b
clean up initial model directory
simonguichandut Aug 31, 2023
3c0744a
more cleanup
simonguichandut Aug 31, 2023
cb36b7a
update initial model again
simonguichandut Aug 31, 2023
23ef107
Merge branch 'development' into working_xrb_layered
zingale Aug 31, 2023
8b68656
remove many files
simonguichandut Aug 31, 2023
38315a1
Merge branch 'working_xrb_layered' of https://github.com/simonguichan…
simonguichandut Aug 31, 2023
15a74a8
analysis and custom scripts dont really need to be included in the re…
simonguichandut Aug 31, 2023
c7e7c08
fix typo
simonguichandut Sep 1, 2023
6e9cd2c
new initial model, with dF/dy=-eps, and X=X(y)
simonguichandut Sep 11, 2023
db938e3
new link
simonguichandut Sep 12, 2023
3d7b11e
lower T in castro model
simonguichandut Sep 14, 2023
a415f3e
Merge branch 'main' of https://github.com/AMReX-Astro/MAESTROeX into …
simonguichandut Sep 26, 2023
9bfc101
update gitignore
simonguichandut Sep 26, 2023
d95059d
Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROe…
simonguichandut Sep 26, 2023
4d361cb
new option use pres of initial model
simonguichandut Sep 26, 2023
df75c32
new initial model, just three power-laws. New notebook to explain
simonguichandut Oct 31, 2023
20e033c
remove old image files
simonguichandut Jan 9, 2024
6ea117f
merge development
simonguichandut Jan 9, 2024
414f766
do refinement based on height
simonguichandut Jan 11, 2024
717da25
cleanup
simonguichandut Jan 11, 2024
8a37d80
update initial model construction, ybase (y1) instead of rho_base
simonguichandut Feb 5, 2024
39ef7e1
rerun initial model once more
simonguichandut Feb 6, 2024
f94b9c5
Merge branch 'development' into working_xrb_layered
zingale Apr 17, 2024
cb4e4b4
updated inputs and scripts
simonguichandut Apr 18, 2024
f8c39df
Merge branch 'working_xrb_layered' of https://github.com/simonguichan…
simonguichandut Apr 18, 2024
8ded0f6
clean up typos and ifdefs
simonguichandut May 13, 2024
a045659
update initial model info
simonguichandut May 14, 2024
dcc780f
Merge branch 'development' into working_xrb_layered
zingale May 14, 2024
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new inputs for toy model
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simonguichandut committed May 12, 2023
commit 8a8ea32d7a5998585a6631e1b3b4005db39e0c81
1,050 changes: 1,050 additions & 0 deletions Exec/science/xrb_layered/create_initial_model/toy_xrb_layered_3cm.hse

Large diffs are not rendered by default.

139 changes: 139 additions & 0 deletions Exec/science/xrb_layered/inputs/inputs_2d_mesa_high_square_12cm
Original file line number Diff line number Diff line change
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# INITIAL MODEL
maestro.model_file = "xrb_layered_3cm.hse"
maestro.perturb_model = true

# PROBLEM SIZE
geometry.prob_lo = 0.0 0.0
geometry.prob_hi = 3840.0 3840.0

# BOUNDARY CONDITIONS
# 0 = Interior 3 = Symmetry
# 1 = Inflow 4 = Slipwall
# 2 = Outflow 5 = NoSlipWall
maestro.lo_bc = 0 4 2
maestro.hi_bc = 0 2 2
geometry.is_periodic = 1 0 0

# VERBOSITY
maestro.v = 1 # verbosity

# DEBUG FOR NAN
amrex.fpe_trap_invalid = 1 # floating point exception

# GRIDDING AND REFINEMENT
amr.n_cell = 320 320
amr.max_grid_size = 64
amr.max_level = 0 # maximum level number allowed
maestro.regrid_int = 2 # how often to regrid
amr.ref_ratio = 2 2 2 2 2 2 # refinement ratio
amr.blocking_factor = 8 # block factor in grid generation
amr.refine_grid_layout = 0 # chop grids up into smaller grids if nprocs > ngrids

amr.v = 1 # AMR verbosity

# TAGGING
maestro.temperr = 6.5e8 6.5e8 6.5e8

# TIME STEPPING
maestro.max_step = 30000000
maestro.stop_time = 1.0
maestro.cfl = 0.7 # cfl number for hyperbolic system
# In this test problem, the velocity is
# time-dependent. We could use 0.9 in
# the 3D test, but need to use 0.7 in 2D
# to satisfy CFL condition.

# ALGORITHMIC OPTIONS
maestro.spherical = 0
maestro.do_initial_projection = true
maestro.init_divu_iter = 1
maestro.init_iter = 1

maestro.grav_const = -1.29e14

maestro.init_shrink = 0.1e0
maestro.max_dt_growth = 1.1e0

maestro.use_tfromp = false
maestro.dpdt_factor = 0.0e0

maestro.species_pred_type = 3

maestro.limit_conductivity = true

maestro.anelastic_cutoff_density = 1.e2
maestro.base_cutoff_density = 1.e2

maestro.do_sponge = true
maestro.sponge_start_factor = 25.e0

maestro.ppm_type = 1

# PLOTFILES
maestro.plot_base_name = PLOTS/xrb_ # root name of plot file
maestro.plot_int = -1 # number of timesteps between plot files
maestro.plot_deltat = 1.e-4
maestro.small_plot_base_name = PLOTS/smallxrb_
maestro.small_plot_deltat = 1.e-5
maestro.small_plot_vars = Hnuc X(h1) X(he4) X(c12) magvel vort
maestro.plot_ad_excess = true

# CHECKPOINT
maestro.check_base_name = CHECKS/chk
maestro.chk_int = 1000

# tolerances for the initial projection
maestro.eps_init_proj_cart = 1.e-10
maestro.eps_init_proj_sph = 1.e-10
# tolerances for the divu iterations
maestro.eps_divu_cart = 5.e-11
maestro.eps_divu_sph = 1.e-10
maestro.divu_iter_factor = 100.
maestro.divu_level_factor = 10.
# tolerances for the MAC projection
maestro.eps_mac = 1.e-10
maestro.eps_mac_max = 1.e-8
maestro.mac_level_factor = 10.
maestro.eps_mac_bottom = 1.e-3
# tolerances for the nodal projection
maestro.eps_hg = 1.e-11
maestro.eps_hg_max = 1.e-10
maestro.hg_level_factor = 10.
maestro.eps_hg_bottom = 1.e-4

# BURNING
#maestro.burner_threshold_species = "H1"

# LINEAR SOLVERS
maestro.mg_bottom_solver = 4
maestro.hg_bottom_solver = 4
maestro.max_mg_bottom_nlevels = 4

# override the default values of the probin namelist values here
# temperature perturbation
problem.xrb_pert_size = 15
problem.xrb_pert_factor = 5.0e-2
problem.xrb_pert_type = 1
problem.xrb_pert_height = 1100.0

# velocity perturbation
problem.apply_vel_field = 1
problem.velpert_scale = 0.5e2
problem.velpert_amplitude = 1.0e5
problem.velpert_height_loc = 1200.0
problem.velpert_steep = 12.0e0 # not used
problem.num_vortices = 8

# Note that some of the parameters in this
# namelist are specific to the default EOS,
# network, and/or integrator used in the
# makefile. If you try a different set of
# microphysics routines be sure to check that
# the parameters in here are consistent.

eos.use_eos_coulomb = 1

integrator.jacobian = 1
integrator.atol_spec = 1.e-6
integrator.rtol_spec = 1.e-6

139 changes: 139 additions & 0 deletions Exec/science/xrb_layered/inputs/inputs_2d_mesa_high_square_3cm
Original file line number Diff line number Diff line change
@@ -0,0 +1,139 @@
# INITIAL MODEL
maestro.model_file = "xrb_layered_3cm.hse"
maestro.perturb_model = true

# PROBLEM SIZE
geometry.prob_lo = 0.0 0.0
geometry.prob_hi = 3840.0 3840.0

# BOUNDARY CONDITIONS
# 0 = Interior 3 = Symmetry
# 1 = Inflow 4 = Slipwall
# 2 = Outflow 5 = NoSlipWall
maestro.lo_bc = 0 4 2
maestro.hi_bc = 0 2 2
geometry.is_periodic = 1 0 0

# VERBOSITY
maestro.v = 1 # verbosity

# DEBUG FOR NAN
amrex.fpe_trap_invalid = 1 # floating point exception

# GRIDDING AND REFINEMENT
amr.n_cell = 1280 1280
amr.max_grid_size = 64
amr.max_level = 0 # maximum level number allowed
maestro.regrid_int = 2 # how often to regrid
amr.ref_ratio = 2 2 2 2 2 2 # refinement ratio
amr.blocking_factor = 8 # block factor in grid generation
amr.refine_grid_layout = 0 # chop grids up into smaller grids if nprocs > ngrids

amr.v = 1 # AMR verbosity

# TAGGING
maestro.temperr = 6.5e8 6.5e8 6.5e8

# TIME STEPPING
maestro.max_step = 30000000
maestro.stop_time = 1.0
maestro.cfl = 0.7 # cfl number for hyperbolic system
# In this test problem, the velocity is
# time-dependent. We could use 0.9 in
# the 3D test, but need to use 0.7 in 2D
# to satisfy CFL condition.

# ALGORITHMIC OPTIONS
maestro.spherical = 0
maestro.do_initial_projection = true
maestro.init_divu_iter = 1
maestro.init_iter = 1

maestro.grav_const = -1.29e14

maestro.init_shrink = 0.1e0
maestro.max_dt_growth = 1.1e0

maestro.use_tfromp = false
maestro.dpdt_factor = 0.0e0

maestro.species_pred_type = 3

maestro.limit_conductivity = true

maestro.anelastic_cutoff_density = 1.e2
maestro.base_cutoff_density = 1.e2

maestro.do_sponge = true
maestro.sponge_start_factor = 25.e0

maestro.ppm_type = 1

# PLOTFILES
maestro.plot_base_name = PLOTS/xrb_ # root name of plot file
maestro.plot_int = -1 # number of timesteps between plot files
maestro.plot_deltat = 1.e-4
maestro.small_plot_base_name = PLOTS/smallxrb_
maestro.small_plot_deltat = 1.e-5
maestro.small_plot_vars = Hnuc X(h1) X(he4) X(c12) magvel vort
maestro.plot_ad_excess = true

# CHECKPOINT
maestro.check_base_name = CHECKS/chk
maestro.chk_int = 1000

# tolerances for the initial projection
maestro.eps_init_proj_cart = 1.e-10
maestro.eps_init_proj_sph = 1.e-10
# tolerances for the divu iterations
maestro.eps_divu_cart = 5.e-11
maestro.eps_divu_sph = 1.e-10
maestro.divu_iter_factor = 100.
maestro.divu_level_factor = 10.
# tolerances for the MAC projection
maestro.eps_mac = 1.e-10
maestro.eps_mac_max = 1.e-8
maestro.mac_level_factor = 10.
maestro.eps_mac_bottom = 1.e-3
# tolerances for the nodal projection
maestro.eps_hg = 1.e-11
maestro.eps_hg_max = 1.e-10
maestro.hg_level_factor = 10.
maestro.eps_hg_bottom = 1.e-4

# BURNING
#maestro.burner_threshold_species = "H1"

# LINEAR SOLVERS
maestro.mg_bottom_solver = 4
maestro.hg_bottom_solver = 4
maestro.max_mg_bottom_nlevels = 4

# override the default values of the probin namelist values here
# temperature perturbation
problem.xrb_pert_size = 15
problem.xrb_pert_factor = 5.0e-2
problem.xrb_pert_type = 1
problem.xrb_pert_height = 1100.0

# velocity perturbation
problem.apply_vel_field = 1
problem.velpert_scale = 0.5e2
problem.velpert_amplitude = 1.0e5
problem.velpert_height_loc = 1200.0
problem.velpert_steep = 12.0e0 # not used
problem.num_vortices = 8

# Note that some of the parameters in this
# namelist are specific to the default EOS,
# network, and/or integrator used in the
# makefile. If you try a different set of
# microphysics routines be sure to check that
# the parameters in here are consistent.

eos.use_eos_coulomb = 1

integrator.jacobian = 1
integrator.atol_spec = 1.e-6
integrator.rtol_spec = 1.e-6

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