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Merge branch 'main' into fill_boundaries_preadvance
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mbkuhn authored Oct 16, 2024
2 parents c856a3a + ca437af commit 4ac3e4a
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Showing 49 changed files with 338 additions and 187 deletions.
33 changes: 32 additions & 1 deletion amr-wind/utilities/index_operations.H
Original file line number Diff line number Diff line change
Expand Up @@ -36,12 +36,43 @@ AMREX_FORCE_INLINE T perpendicular_idx(const int normal)
return T{-1, -1};
}

/** Get the intersection with a boundary box while considering if on face or
* cell. Intended for auxiliary boundary fill calls.
*
* \param grown_interior_box box grown from domain interior to overlap with
* boundary
* \param domain_boundary_box box representing domain boundary containing data
* \param ori orientation of current boundary condition being evaluated
* \return The Box instance representing the intersection of the two inputs
* with shifts added to consider the location of the field associated with the
* grown_interior_box
*/
inline amrex::Box face_aware_boundary_box_intersection(
amrex::Box grown_interior_box,
const amrex::Box& domain_boundary_box,
const amrex::Orientation& ori)
{
const auto& field_location_vector = grown_interior_box.type();
if (!grown_interior_box.cellCentered()) {
grown_interior_box.enclosedCells();
}
auto bx = grown_interior_box & domain_boundary_box;
if (bx.isEmpty()) {
return bx;
}

if (ori.isHigh() && field_location_vector[ori.coordDir()] == 1) {
bx.shift(field_location_vector);
}
return bx;
}

/** Convert a bounding box into amrex::Box index space at a given level
*
* \param rbx Bounding box as defined in global domain coordinates
* \param geom AMReX geometry information for a given level
* \return The Box instance that defines the index space equivalent to bounding
* boxt
* box
*/
amrex::Box
realbox_to_box(const amrex::RealBox& rbx, const amrex::Geometry& geom);
Expand Down
6 changes: 2 additions & 4 deletions amr-wind/wind_energy/ABLBoundaryPlane.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -922,11 +922,9 @@ void ABLBoundaryPlane::populate_data(
++mfi) {

auto sbx = mfi.growntilebox(1);
if (!sbx.cellCentered()) {
sbx.enclosedCells();
}
const auto& src = m_in_data.interpolate_data(ori, lev);
const auto& bx = sbx & src.box();
const auto& bx = utils::face_aware_boundary_box_intersection(
sbx, src.box(), ori);
if (bx.isEmpty()) {
continue;
}
Expand Down
13 changes: 5 additions & 8 deletions amr-wind/wind_energy/ABLModulatedPowerLaw.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
#include "AMReX_Gpu.H"
#include "AMReX_ParmParse.H"
#include "amr-wind/utilities/ncutils/nc_interface.H"
#include "amr-wind/utilities/index_operations.H"
#include <AMReX_PlotFileUtil.H>

#include <sstream>
Expand Down Expand Up @@ -174,10 +175,8 @@ void ABLModulatedPowerLaw::set_velocity(

for (amrex::MFIter mfi(mfab); mfi.isValid(); ++mfi) {
auto gbx = amrex::grow(mfi.validbox(), nghost);
if (!gbx.cellCentered()) {
gbx.enclosedCells();
}
const auto& bx = gbx & dbx;
const auto& bx =
utils::face_aware_boundary_box_intersection(gbx, dbx, ori);
if (!bx.ok()) {
continue;
}
Expand Down Expand Up @@ -251,10 +250,8 @@ void ABLModulatedPowerLaw::set_temperature(

for (amrex::MFIter mfi(mfab); mfi.isValid(); ++mfi) {
auto gbx = amrex::grow(mfi.validbox(), nghost);
if (!gbx.cellCentered()) {
gbx.enclosedCells();
}
const auto& bx = gbx & dbx;
const auto& bx =
utils::face_aware_boundary_box_intersection(gbx, dbx, ori);
if (!bx.ok()) {
continue;
}
Expand Down
1 change: 0 additions & 1 deletion docs/sphinx/user/amr_wind_inputs.txt
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@ time.checkpoint_interval = 10000
time.use_force_cfl = false

# input/output settings
io.KE_int = -1
io.check_file = "chk"
io.plot_file = "plt"
io.restart_file = ""
Expand Down
10 changes: 5 additions & 5 deletions test/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ macro(setup_test)
file(MAKE_DIRECTORY ${CURRENT_TEST_BINARY_DIR})
file(GLOB TEST_FILES "${CURRENT_TEST_SOURCE_DIR}/*")
file(COPY ${TEST_FILES} DESTINATION "${CURRENT_TEST_BINARY_DIR}/")
set(RUNTIME_OPTIONS "time.max_step=10 io.plot_file=plt time.plot_interval=10 amrex.the_arena_is_managed=0 amrex.abort_on_out_of_gpu_memory=1")
set(RUNTIME_OPTIONS "time.max_step=10 io.plot_file=plt time.plot_interval=10 amrex.the_arena_is_managed=0 amrex.abort_on_out_of_gpu_memory=1 amrex.abort_on_unused_inputs=1")
if(AMR_WIND_ENABLE_FPE_TRAP_FOR_TESTS)
set(RUNTIME_OPTIONS "${RUNTIME_OPTIONS} amrex.signal_handling=1 amrex.fpe_trap_invalid=1 amrex.fpe_trap_zero=1 amrex.fpe_trap_overflow=1")
else()
Expand Down Expand Up @@ -81,7 +81,7 @@ endmacro(setup_test)
# Standard regression test
function(add_test_r TEST_NAME)
setup_test()
add_test(${TEST_NAME} sh -c "${MPI_COMMANDS} ${CMAKE_BINARY_DIR}/${amr_wind_exe_name} ${MPIEXEC_POSTFLAGS} ${CURRENT_TEST_BINARY_DIR}/${TEST_NAME}.inp ${RUNTIME_OPTIONS} 2>&1 | tee ${TEST_NAME}.log ${SAVE_GOLDS_COMMAND} ${FCOMPARE_COMMAND}")
add_test(${TEST_NAME} bash -c "set -o pipefail && ${MPI_COMMANDS} ${CMAKE_BINARY_DIR}/${amr_wind_exe_name} ${MPIEXEC_POSTFLAGS} ${CURRENT_TEST_BINARY_DIR}/${TEST_NAME}.inp ${RUNTIME_OPTIONS} 2>&1 | tee ${TEST_NAME}.log ${SAVE_GOLDS_COMMAND} ${FCOMPARE_COMMAND}")
# Set properties for test
set_tests_properties(${TEST_NAME} PROPERTIES
TIMEOUT 5400
Expand Down Expand Up @@ -126,7 +126,7 @@ function(add_test_v TEST_NAME LIST_OF_GRID_SIZES)
endif()
endforeach()
list(JOIN LIST_OF_GRID_SIZES " " STRING_OF_GRID_SIZES)
add_test(${TEST_NAME} sh -c "${MASTER_RUN_COMMAND} && cd ${CURRENT_TEST_BINARY_DIR} && ${PYTHON_EXECUTABLE} ${CURRENT_TEST_SOURCE_DIR}/plotter.py -f ${STRING_OF_GRID_SIZES}")
add_test(${TEST_NAME} bash -c "set -o pipefail && ${MASTER_RUN_COMMAND} && cd ${CURRENT_TEST_BINARY_DIR} && ${PYTHON_EXECUTABLE} ${CURRENT_TEST_SOURCE_DIR}/plotter.py -f ${STRING_OF_GRID_SIZES}")
set_tests_properties(${TEST_NAME} PROPERTIES TIMEOUT 14400 PROCESSORS ${TEST_NP} WORKING_DIRECTORY "${CURRENT_TEST_BINARY_DIR}" LABELS "verification;no_ci" ATTACHED_FILES "${CURRENT_TEST_BINARY_DIR}/plots.pdf")
endfunction(add_test_v)

Expand All @@ -139,7 +139,7 @@ function(add_test_u TEST_NAME)
else()
unset(MPI_COMMANDS)
endif()
add_test(${TEST_NAME} sh -c "${MPI_COMMANDS} ${CMAKE_BINARY_DIR}/${amr_wind_unit_test_exe_name}")
add_test(${TEST_NAME} bash -c "${MPI_COMMANDS} ${CMAKE_BINARY_DIR}/${amr_wind_unit_test_exe_name}")
set_tests_properties(${TEST_NAME} PROPERTIES
TIMEOUT 500
PROCESSORS ${TEST_NP}
Expand All @@ -151,7 +151,7 @@ endfunction(add_test_u)
function(add_test_pps TEST_NAME FORMAT NINT NSTEPS)
setup_test()
set(ADDL_RUNTIME_OPTIONS "sampling.output_format=${FORMAT} sampling.output_frequency=${NINT} time.plot_interval=-1 time.checkpoint_interval=-1 time.max_step=${NSTEPS}")
add_test("${TEST_NAME}_sampling_${FORMAT}" sh -c "${MPI_COMMANDS} ${CMAKE_BINARY_DIR}/${amr_wind_exe_name} ${MPIEXEC_POSTFLAGS} ${CURRENT_TEST_BINARY_DIR}/${TEST_NAME}.inp ${RUNTIME_OPTIONS} ${ADDL_RUNTIME_OPTIONS} 2>&1 | tee ${TEST_NAME}_sampling_${FORMAT}.log && ${Python3_EXECUTABLE} ${PROJECT_SOURCE_DIR}/tools/sampling_${TEST_NAME}_${FORMAT}.py")
add_test("${TEST_NAME}_sampling_${FORMAT}" bash -c "set -o pipefail && ${MPI_COMMANDS} ${CMAKE_BINARY_DIR}/${amr_wind_exe_name} ${MPIEXEC_POSTFLAGS} ${CURRENT_TEST_BINARY_DIR}/${TEST_NAME}.inp ${RUNTIME_OPTIONS} ${ADDL_RUNTIME_OPTIONS} 2>&1 | tee ${TEST_NAME}_sampling_${FORMAT}.log && ${Python3_EXECUTABLE} ${PROJECT_SOURCE_DIR}/tools/sampling_${TEST_NAME}_${FORMAT}.py")
# Set properties for test
set_tests_properties("${TEST_NAME}_sampling_${FORMAT}" PROPERTIES
TIMEOUT 5400
Expand Down
1 change: 0 additions & 1 deletion test/test_files/abl_bds/abl_bds.inp
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,6 @@ zhi.temperature = 0.003 # tracer is used to specify potential temperature gradie
#.......................................#
incflo.verbose = 0 # incflo_level

amrex.abort_on_out_of_memory=1
amrex.the_arena_is_managed=1
amrex.async_out=0
# needed because a debug build using BDS + amrex.the_arena_is_managed=0 OOMs the GPU (problem is in incflo as well)
Expand Down
2 changes: 0 additions & 2 deletions test/test_files/abl_bndry_input/abl_bndry_input.inp
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -63,7 +62,6 @@ amr.max_level = 0 # Max AMR level in hierarchy
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 0 0 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
xlo.type = "mass_inflow"
xlo.density = 1.0
Expand Down
2 changes: 0 additions & 2 deletions test/test_files/abl_bndry_input_amr/abl_bndry_input_amr.inp
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -66,7 +65,6 @@ tagging.static.static_refinement_def = "static_box.txt"
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 0 0 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
xlo.type = "mass_inflow"
xlo.density = 1.0
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -68,7 +67,6 @@ tagging.static.static_refinement_def = "static_box.txt"
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 0 0 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
xlo.type = "mass_inflow"
xlo.density = 1.0
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -66,7 +65,6 @@ tagging.static.static_refinement_def = "static_box.txt"
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 0 0 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
xlo.type = "mass_inflow"
xlo.density = 1.0
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -68,7 +67,6 @@ tagging.static.static_refinement_def = "static_box.txt"
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 0 0 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
xlo.type = "mass_inflow"
xlo.density = 1.0
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -66,7 +65,6 @@ tagging.static.static_refinement_def = "static_box.txt"
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 0 0 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
xlo.type = "pressure_outflow"
xhi.type = "mass_inflow"
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -63,7 +62,6 @@ amr.max_level = 0 # Max AMR level in hierarchy
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 0 0 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
xlo.type = "mass_inflow"
xlo.density = 1.0
Expand Down
2 changes: 0 additions & 2 deletions test/test_files/abl_bndry_output/abl_bndry_output.inp
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -64,7 +63,6 @@ amr.max_level = 0 # Max AMR level in hierarchy
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 1 1 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
zlo.type = "wall_model"

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -69,7 +68,6 @@ tagging.static.static_refinement_def = "static_box.txt"
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 1 1 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
zlo.type = "wall_model"

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -69,7 +68,6 @@ tagging.static.static_refinement_def = "static_box.txt"
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 1 1 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
zlo.type = "wall_model"

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,6 @@ turbulence.model = Smagorinsky
Smagorinsky_coeffs.Cs = 0.135
incflo.physics = ABL
ICNS.source_terms = CoriolisForcing GeostrophicForcing
BoussinesqBuoyancy.reference_temperature = 290.0
ABL.reference_temperature = 290.0
CoriolisForcing.east_vector = 1.0 0.0 0.0
CoriolisForcing.north_vector = 0.0 1.0 0.0
Expand Down Expand Up @@ -64,7 +63,6 @@ amr.max_level = 0 # Max AMR level in hierarchy
geometry.prob_lo = 0. 0. 0. # Lo corner coordinates
geometry.prob_hi = 1000. 1000. 1000. # Hi corner coordinates
geometry.is_periodic = 1 1 0 # Periodicity x y z (0/1)
incflo.delp = 0. 0. 0. # Prescribed (cyclic) pressure gradient
# Boundary conditions
zlo.type = "wall_model"

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,6 @@ transport.turbulent_prandtl = 0.333
# turbulence equation parameters
turbulence.model = Kosovic
Kosovic.surfaceRANS = false
Kosovic.surfaceRANSExp = 2
Kosovic.writeTerms = false
Kosovic.refMOL = -1e30
# Atmospheric boundary layer
Expand Down
23 changes: 2 additions & 21 deletions test/test_files/channel_mol_mesh_map_x/channel_mol_mesh_map_x.inp
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
#include <type_traits>
#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
# SIMULATION STOP #
#.......................................#
Expand Down Expand Up @@ -60,25 +59,7 @@ yhi.type = "no_slip_wall"
diffusion.max_coarsening_level = 0

incflo.verbose = 0
nodal_proj.mg_atol = 1.0e-12
nodal_proj.verbose = 0
nodal_proj.bottom_solver = hypre
nodal_proj.max_coarsening_level = 0
#
mac_proj.mg_rtol = 1.0e-11
mac_proj.mg_atol = 1.0e-12
mac_proj.mg_atol = 1.0e-11
mac_proj.do_semicoarsening = true
mac_proj.bottom_solver = hypre
mac_proj.bottom_verbose = 0
mac_proj.max_coarsening_level = 0
mac_proj.bottom_rtol = 1.0e-12
mac_proj.bottom_atol = 1.0e-16
#
hypre.hypre_solver = GMRES
hypre.hypre_preconditioner = BoomerAMG
hypre.verbose = 0
hypre.bamg_verbose = 0
hypre.num_krylov = 20
hypre.bamg_max_levels = 4
hypre.bamg_num_sweeps = 1
#
nodal_proj.mg_atol = 1.0e-11
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