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The OIFS Scheme #1306

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The OIFS Scheme #1306

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0d8704c
Making the lint happier
Kamyarmvn Aug 27, 2024
bd5e7a1
Merge branch 'Resolving-conflict-in-advection_fctry' of https://githu…
Kamyarmvn Aug 27, 2024
8f6c71a
Making the lint happier
Kamyarmvn Aug 27, 2024
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21 changes: 13 additions & 8 deletions src/.depends
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Expand Up @@ -26,7 +26,7 @@ sem/dofmap.o : sem/dofmap.f90 mesh/hex.o mesh/quad.o mesh/element.o math/math.o
sem/coef.o : sem/coef.f90 device/device.o math/mxm_wrapper.o sem/bcknd/device/device_coef.o math/bcknd/device/device_math.o mesh/mesh.o math/math.o sem/space.o sem/dofmap.o config/num_types.o config/neko_config.o gs/gs_ops.o gs/gather_scatter.o
sem/cpr.o : sem/cpr.f90 sem/dofmap.o common/log.o math/mxm_wrapper.o math/tensor.o sem/coef.o mesh/mesh.o math/math.o sem/space.o field/field.o config/num_types.o config/neko_config.o gs/gather_scatter.o
sem/spectral_error_indicator.o : sem/spectral_error_indicator.f90 common/utils.o comm/comm.o device/device.o config/neko_config.o gs/gather_scatter.o math/bcknd/device/device_math.o math/tensor.o io/file.o math/math.o field/field_list.o sem/coef.o field/field.o config/num_types.o
common/time_interpolator.o : common/time_interpolator.f90 common/utils.o math/math.o math/bcknd/device/device_math.o config/neko_config.o field/field.o config/num_types.o
common/time_interpolator.o : common/time_interpolator.f90 math/fast3d.o common/utils.o math/math.o math/bcknd/device/device_math.o config/neko_config.o field/field.o config/num_types.o
sem/interpolation.o : sem/interpolation.f90 sem/space.o math/bcknd/cpu/tensor_cpu.o math/tensor.o math/fast3d.o device/device.o config/num_types.o config/neko_config.o
sem/point_interpolator.o : sem/point_interpolator.f90 config/neko_config.o math/bcknd/device/device_math.o device/device.o common/utils.o math/fast3d.o math/math.o mesh/point.o config/num_types.o sem/space.o math/tensor.o
sem/bcknd/device/device_coef.o : sem/bcknd/device/device_coef.F90 common/utils.o config/num_types.o
Expand Down Expand Up @@ -78,16 +78,20 @@ math/bcknd/cpu/cdtp.o : math/bcknd/cpu/cdtp.f90 config/num_types.o
math/bcknd/cpu/conv1.o : math/bcknd/cpu/conv1.f90 config/num_types.o
math/bcknd/cpu/dudxyz.o : math/bcknd/cpu/dudxyz.f90 config/num_types.o
math/bcknd/cpu/opgrad.o : math/bcknd/cpu/opgrad.f90 config/num_types.o
math/bcknd/cpu/convect_scalar.o : math/bcknd/cpu/convect_scalar.f90 gs/gather_scatter.o math/math.o sem/interpolation.o sem/space.o sem/coef.o config/num_types.o
math/bcknd/cpu/set_convect_rst.o : math/bcknd/cpu/set_convect_rst.f90 config/num_types.o
math/bcknd/sx/sx_cdtp.o : math/bcknd/sx/sx_cdtp.f90 math/math.o config/num_types.o
math/bcknd/sx/sx_conv1.o : math/bcknd/sx/sx_conv1.f90 config/num_types.o
math/bcknd/sx/sx_dudxyz.o : math/bcknd/sx/sx_dudxyz.f90 math/math.o config/num_types.o
math/bcknd/sx/sx_opgrad.o : math/bcknd/sx/sx_opgrad.f90 config/num_types.o
math/bcknd/sx/sx_cfl.o : math/bcknd/sx/sx_cfl.f90 config/num_types.o
math/bcknd/sx/sx_lambda2.o : math/bcknd/sx/sx_lambda2.f90 math/math.o config/num_types.o
math/operators.o : math/operators.f90 comm/comm.o field/scratch_registry.o math/bcknd/device/device_math.o device/device.o math/math.o field/field.o sem/coef.o sem/space.o math/bcknd/device/opr_device.o math/bcknd/xsmm/opr_xsmm.o math/bcknd/sx/opr_sx.o math/bcknd/cpu/opr_cpu.o config/num_types.o config/neko_config.o
math/bcknd/cpu/opr_cpu.o : math/bcknd/cpu/opr_cpu.f90 math/mathops.o gs/gather_scatter.o field/field.o math/math.o sem/coef.o sem/space.o config/num_types.o math/bcknd/cpu/conv1.o math/bcknd/cpu/cdtp.o math/bcknd/cpu/opgrad.o math/bcknd/cpu/dudxyz.o
math/bcknd/sx/opr_sx.o : math/bcknd/sx/opr_sx.f90 math/mathops.o field/field.o math/math.o sem/coef.o sem/space.o config/num_types.o gs/gather_scatter.o math/bcknd/sx/sx_lambda2.o math/bcknd/sx/sx_cfl.o math/bcknd/sx/sx_cdtp.o math/bcknd/sx/sx_conv1.o math/bcknd/sx/sx_opgrad.o math/bcknd/sx/sx_dudxyz.o
math/bcknd/xsmm/opr_xsmm.o : math/bcknd/xsmm/opr_xsmm.F90 math/mathops.o gs/gather_scatter.o field/field.o mesh/mesh.o math/math.o sem/coef.o sem/space.o math/mxm_wrapper.o config/num_types.o
math/bcknd/sx/sx_convect_scalar.o : math/bcknd/sx/sx_convect_scalar.f90 gs/gather_scatter.o math/math.o sem/interpolation.o sem/space.o sem/coef.o config/num_types.o
math/bcknd/sx/sx_set_convect_rst.o : math/bcknd/sx/sx_set_convect_rst.f90 config/num_types.o
math/operators.o : math/operators.f90 comm/comm.o sem/interpolation.o field/scratch_registry.o math/bcknd/device/device_math.o device/device.o math/math.o field/field.o sem/coef.o sem/space.o math/bcknd/device/opr_device.o math/bcknd/xsmm/opr_xsmm.o math/bcknd/sx/opr_sx.o math/bcknd/cpu/opr_cpu.o config/num_types.o config/neko_config.o
math/bcknd/cpu/opr_cpu.o : math/bcknd/cpu/opr_cpu.f90 math/mathops.o gs/gather_scatter.o sem/interpolation.o field/field.o math/math.o sem/coef.o sem/space.o config/num_types.o math/bcknd/cpu/set_convect_rst.o math/bcknd/cpu/convect_scalar.o math/bcknd/cpu/conv1.o math/bcknd/cpu/cdtp.o math/bcknd/cpu/opgrad.o math/bcknd/cpu/dudxyz.o
math/bcknd/sx/opr_sx.o : math/bcknd/sx/opr_sx.f90 math/mathops.o field/field.o math/math.o sem/coef.o sem/space.o config/num_types.o sem/interpolation.o gs/gather_scatter.o math/bcknd/sx/sx_set_convect_rst.o math/bcknd/sx/sx_convect_scalar.o math/bcknd/sx/sx_lambda2.o math/bcknd/sx/sx_cfl.o math/bcknd/sx/sx_cdtp.o math/bcknd/sx/sx_conv1.o math/bcknd/sx/sx_opgrad.o math/bcknd/sx/sx_dudxyz.o
math/bcknd/xsmm/opr_xsmm.o : math/bcknd/xsmm/opr_xsmm.F90 math/mathops.o gs/gather_scatter.o sem/interpolation.o field/field.o mesh/mesh.o math/math.o sem/coef.o sem/space.o math/mxm_wrapper.o config/num_types.o
math/bcknd/device/opr_device.o : math/bcknd/device/opr_device.F90 comm/comm.o common/utils.o field/field.o mesh/mesh.o sem/coef.o sem/space.o device/device.o math/bcknd/device/device_mathops.o math/bcknd/device/device_math.o config/num_types.o gs/gather_scatter.o
math/tensor.o : math/tensor.f90 device/device.o config/neko_config.o math/mxm_wrapper.o config/num_types.o math/bcknd/device/tensor_device.o math/bcknd/sx/tensor_sx.o math/bcknd/cpu/tensor_cpu.o math/bcknd/xsmm/tensor_xsmm.o
math/bcknd/cpu/tensor_cpu.o : math/bcknd/cpu/tensor_cpu.f90 math/mxm_wrapper.o config/num_types.o
Expand Down Expand Up @@ -192,7 +196,7 @@ fluid/stress_formulation/bcknd/cpu/pnpn_res_stress_cpu.o : fluid/stress_formulat
fluid/stress_formulation/bcknd/device/pnpn_res_stress_device.o : fluid/stress_formulation/bcknd/device/pnpn_res_stress_device.F90 math/bcknd/device/device_math.o math/bcknd/device/device_mathops.o sem/space.o config/num_types.o mesh/mesh.o field/scratch_registry.o fluid/pnpn_res.o bc/facet_normal.o sem/coef.o math/ax.o field/field.o math/operators.o common/utils.o gs/gather_scatter.o
fluid/fluid_scheme.o : fluid/fluid_scheme.f90 math/field_math.o common/time_step_controller.o field/field_series.o common/material_properties.o common/utils.o common/user_intf.o field/scratch_registry.o common/json_utils.o field/field_registry.o common/log.o math/operators.o time_schemes/time_scheme_controller.o math/bcknd/device/device_math.o math/math.o mesh/mesh.o bc/bc.o fluid/fluid_stats.o krylov/precon_fctry.o krylov/krylov_fctry.o krylov/precon.o krylov/pc_hsmg.o krylov/bcknd/device/pc_jacobi_device.o krylov/bcknd/sx/pc_jacobi_sx.o krylov/bcknd/cpu/pc_jacobi.o bc/field_dirichlet_vector.o bc/field_dirichlet.o bc/symmetry.o bc/dong_outflow.o bc/dirichlet.o bc/blasius.o bc/usr_inflow.o bc/inflow.o bc/wall.o sem/coef.o krylov/krylov.o sem/dofmap.o sem/space.o field/field.o fluid/fluid_source_term.o comm/comm.o config/num_types.o fluid/mean_flow.o common/checkpoint.o config/neko_config.o fluid/mean_sqr_flow.o gs/gather_scatter.o
fluid/fluid_aux.o : fluid/fluid_aux.f90 krylov/krylov.o config/num_types.o common/log.o
fluid/fluid_pnpn.o : fluid/fluid_pnpn.f90 math/field_math.o common/utils.o bc/bc.o math/mathops.o math/math.o config/neko_config.o gs/gather_scatter.o common/time_step_controller.o common/user_intf.o mesh/mesh.o bc/non_normal.o bc/facet_normal.o bc/dirichlet.o field/field.o math/ax.o fluid/advection_fctry.o common/material_properties.o common/profiler.o fluid/advection.o device/device.o common/projection.o time_schemes/time_scheme_controller.o fluid/fluid_aux.o math/bcknd/device/device_mathops.o fluid/fluid_scheme.o fluid/fluid_volflow.o common/rhs_maker.o common/rhs_maker_fctry.o math/ax_helm_fctry.o fluid/pnpn_res.o fluid/stress_formulation/pnpn_res_stress_fctry.o fluid/pnpn_res_fctry.o krylov/krylov.o config/num_types.o
fluid/fluid_pnpn.o : fluid/fluid_pnpn.f90 math/field_math.o common/utils.o bc/bc.o math/mathops.o math/math.o config/neko_config.o gs/gather_scatter.o common/time_step_controller.o common/user_intf.o mesh/mesh.o bc/non_normal.o bc/facet_normal.o bc/dirichlet.o field/field.o math/ax.o fluid/advection_fctry.o common/material_properties.o common/json_utils.o common/profiler.o fluid/advection.o device/device.o common/projection.o time_schemes/time_scheme_controller.o fluid/fluid_aux.o math/bcknd/device/device_mathops.o fluid/fluid_scheme.o fluid/fluid_volflow.o common/rhs_maker.o common/rhs_maker_fctry.o math/ax_helm_fctry.o fluid/pnpn_res.o fluid/stress_formulation/pnpn_res_stress_fctry.o fluid/pnpn_res_fctry.o krylov/krylov.o config/num_types.o
fluid/fluid_fctry.o : fluid/fluid_fctry.f90 common/utils.o fluid/fluid_pnpn.o fluid/fluid_scheme.o
fluid/fluid_volflow.o : fluid/fluid_volflow.f90 math/ax.o bc/bc.o field/scratch_registry.o common/json_utils.o gs/gather_scatter.o math/bcknd/device/device_mathops.o math/bcknd/device/device_math.o config/neko_config.o comm/comm.o math/math.o time_schemes/time_scheme_controller.o sem/coef.o field/field.o sem/dofmap.o krylov/precon.o krylov/krylov.o math/mathops.o config/num_types.o math/operators.o
fluid/pnpn_res.o : fluid/pnpn_res.f90 config/num_types.o mesh/mesh.o sem/space.o bc/facet_normal.o sem/coef.o field/field.o math/ax.o gs/gather_scatter.o
Expand All @@ -203,16 +207,17 @@ fluid/mean_sqr_flow.o : fluid/mean_sqr_flow.f90 field/field.o field/mean_sqr_fie
fluid/flow_profile.o : fluid/flow_profile.f90 config/num_types.o
fluid/flow_ic.o : fluid/flow_ic.f90 mesh/point_zone_registry.o mesh/point_zone.o common/json_utils.o common/user_intf.o math/bcknd/device/device_math.o math/math.o sem/coef.o common/utils.o field/field.o device/device.o fluid/flow_profile.o config/neko_config.o gs/gather_scatter.o config/num_types.o
fluid/advection.o : fluid/advection.f90 sem/coef.o field/field.o sem/space.o config/num_types.o
fluid/advection_fctry.o : fluid/advection_fctry.f90 fluid/bcknd/advection/adv_no_dealias.o fluid/bcknd/advection/adv_dealias.o fluid/advection.o common/json_utils.o sem/coef.o
fluid/advection_fctry.o : fluid/advection_fctry.f90 fluid/bcknd/advection/adv_oifs.o fluid/bcknd/advection/adv_no_dealias.o fluid/bcknd/advection/adv_dealias.o fluid/advection.o config/num_types.o common/time_interpolator.o time_schemes/time_scheme_controller.o field/field_series.o common/json_utils.o sem/coef.o
fluid/bcknd/advection/adv_dealias.o : fluid/bcknd/advection/adv_dealias.f90 device/device.o sem/interpolation.o math/operators.o config/neko_config.o math/bcknd/device/device_math.o sem/coef.o field/field.o sem/space.o math/math.o config/num_types.o fluid/advection.o
fluid/bcknd/advection/adv_no_dealias.o : fluid/bcknd/advection/adv_no_dealias.f90 device/device.o math/operators.o config/neko_config.o math/bcknd/device/device_math.o sem/coef.o field/field.o sem/space.o math/math.o config/num_types.o fluid/advection.o
fluid/bcknd/advection/adv_oifs.o : fluid/bcknd/advection/adv_oifs.f90 device/device.o time_schemes/time_scheme_controller.o field/field_series.o common/time_interpolator.o sem/interpolation.o config/neko_config.o math/operators.o math/math.o sem/coef.o field/field.o sem/space.o config/num_types.o fluid/advection.o
fluid/bcknd/cpu/pnpn_res_cpu.o : fluid/bcknd/cpu/pnpn_res_cpu.f90 math/math.o sem/space.o config/num_types.o mesh/mesh.o field/scratch_registry.o fluid/pnpn_res.o bc/facet_normal.o sem/coef.o math/ax.o field/field.o math/operators.o gs/gather_scatter.o
fluid/bcknd/sx/pnpn_res_sx.o : fluid/bcknd/sx/pnpn_res_sx.f90 math/math.o sem/space.o config/num_types.o mesh/mesh.o field/scratch_registry.o fluid/pnpn_res.o bc/facet_normal.o sem/coef.o math/ax.o field/field.o math/operators.o gs/gather_scatter.o
fluid/bcknd/device/pnpn_res_device.o : fluid/bcknd/device/pnpn_res_device.F90 field/scratch_registry.o fluid/pnpn_res.o math/bcknd/device/device_mathops.o math/bcknd/device/device_math.o sem/space.o config/num_types.o mesh/mesh.o bc/facet_normal.o sem/coef.o math/ax.o field/field.o math/operators.o gs/gather_scatter.o
fluid/fluid_user_source_term.o : fluid/fluid_user_source_term.f90 sem/dofmap.o math/math.o math/bcknd/device/device_math.o device/device.o sem/coef.o field/field_list.o source_terms/source_term.o common/utils.o config/num_types.o config/neko_config.o
fluid/fluid_source_term.o : fluid/fluid_source_term.f90 common/utils.o common/user_intf.o sem/coef.o common/json_utils.o field/field_list.o field/field.o source_terms/source_term_fctry.o source_terms/source_term.o fluid/fluid_user_source_term.o config/num_types.o config/neko_config.o
common/time_step_controller.o : common/time_step_controller.f90 common/json_utils.o common/log.o config/num_types.o
simulation.o : simulation.f90 common/time_step_controller.o common/json_utils.o simulation_components/simcomp_executor.o common/profiler.o field/field.o common/jobctrl.o math/bcknd/device/device_math.o device/device.o common/log.o math/math.o io/file.o time_schemes/time_scheme_controller.o gs/gather_scatter.o case.o
simulation.o : simulation.f90 common/time_step_controller.o common/json_utils.o simulation_components/simcomp_executor.o common/profiler.o field/field.o common/jobctrl.o common/log.o io/file.o time_schemes/time_scheme_controller.o gs/gather_scatter.o case.o config/num_types.o
math/ax_helm_fctry.o : math/ax_helm_fctry.f90 common/utils.o math/ax.o math/bcknd/cpu/ax_helm_full_cpu.o math/bcknd/cpu/ax_helm_cpu.o math/ax_helm.o math/bcknd/sx/ax_helm_sx.o math/bcknd/xsmm/ax_helm_xsmm.o math/bcknd/device/ax_helm_device.o config/neko_config.o
math/ax_helm.o : math/ax_helm.f90 math/math.o mesh/mesh.o sem/space.o sem/coef.o config/num_types.o math/ax.o
math/ax_helm_full.o : math/ax_helm_full.f90 common/utils.o math/math.o mesh/mesh.o sem/space.o sem/coef.o config/num_types.o math/ax.o
Expand Down
5 changes: 5 additions & 0 deletions src/Makefile.am
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Expand Up @@ -81,12 +81,16 @@ neko_fortran_SOURCES = \
math/bcknd/cpu/conv1.f90\
math/bcknd/cpu/dudxyz.f90\
math/bcknd/cpu/opgrad.f90\
math/bcknd/cpu/convect_scalar.f90\
math/bcknd/cpu/set_convect_rst.f90\
math/bcknd/sx/sx_cdtp.f90\
math/bcknd/sx/sx_conv1.f90\
math/bcknd/sx/sx_dudxyz.f90\
math/bcknd/sx/sx_opgrad.f90\
math/bcknd/sx/sx_cfl.f90\
math/bcknd/sx/sx_lambda2.f90\
math/bcknd/sx/sx_convect_scalar.f90\
math/bcknd/sx/sx_set_convect_rst.f90\
math/operators.f90\
math/bcknd/cpu/opr_cpu.f90\
math/bcknd/sx/opr_sx.f90\
Expand Down Expand Up @@ -209,6 +213,7 @@ neko_fortran_SOURCES = \
fluid/advection_fctry.f90\
fluid/bcknd/advection/adv_dealias.f90\
fluid/bcknd/advection/adv_no_dealias.f90\
fluid/bcknd/advection/adv_oifs.f90\
fluid/bcknd/cpu/pnpn_res_cpu.f90\
fluid/bcknd/sx/pnpn_res_sx.f90\
fluid/bcknd/device/pnpn_res_device.F90\
Expand Down
34 changes: 20 additions & 14 deletions src/case.f90
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I get flinter error for: if (pe_rank .ne. 0) allocate(character(len = integer_val) :: json_buffer). It seems that it requires an space between the separators (: :) which is wrong. Is there any way this can be solved?

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Have you synced with a recent develop? There has been some fixes for the linter that addressed similar issues

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Yes, the branch is up to date.
Also, should I use submodules for opr_cpu subroutines?

Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
! Copyright (c) 2020-2023, The Neko Authors
! Copyright (c) 2020-2024, The Neko Authors
! All rights reserved.
!
! Redistribution and use in source and binary forms, with or without
Expand Down Expand Up @@ -41,7 +41,7 @@ module case
use mean_sqr_flow_output, only : mean_sqr_flow_output_t
use mean_flow_output, only : mean_flow_output_t
use fluid_stats_output, only : fluid_stats_output_t
use mpi_f08
use mpi_f08, only : MPI_Bcast, MPI_CHARACTER
use mesh_field, only : mesh_fld_t, mesh_field_init, mesh_field_free
use parmetis, only : parmetis_partmeshkway
use redist, only : redist_mesh
Expand All @@ -52,7 +52,7 @@ module case
use file, only : file_t
use utils, only : neko_error
use mesh, only : mesh_t
use comm
use comm, only: NEKO_COMM, MPI_INTEGER, pe_rank, pe_size
use time_scheme_controller, only : time_scheme_controller_t
use logger, only : neko_log, NEKO_LOG_QUIET, LOG_SIZE
use jobctrl, only : jobctrl_set_time_limit
Expand Down Expand Up @@ -112,11 +112,15 @@ subroutine case_init_from_file(C, case_file)
end if

call MPI_Bcast(integer_val, 1, MPI_INTEGER, 0, NEKO_COMM, ierr)
if (pe_rank .ne. 0) allocate(character(len=integer_val) :: json_buffer)
if (pe_rank .ne. 0) allocate(character(len = integer_val) :: json_buffer)


call MPI_Bcast(json_buffer, integer_val, MPI_CHARACTER, 0, NEKO_COMM, ierr)
call C%params%load_from_string(json_buffer)

deallocate(json_buffer)
if (allocated(json_buffer)) then
deallocate(json_buffer)
end if

call case_init_common(C)

Expand Down Expand Up @@ -201,6 +205,11 @@ subroutine case_init_common(C)
call C%usr%init()
call C%usr%user_mesh_setup(C%msh)

!
! Set order of timestepper
!
call json_get(C%params, 'case.numerics.time_order', integer_val)
call C%ext_bdf%init(integer_val)

!
! Material properties
Expand All @@ -215,9 +224,10 @@ subroutine case_init_common(C)

call json_get(C%params, 'case.numerics.polynomial_order', lx)
lx = lx + 1 ! add 1 to get number of gll points
call C%fluid%init(C%msh, lx, C%params, C%usr, C%material_properties)
C%fluid%chkp%tlag => C%tlag
C%fluid%chkp%dtlag => C%dtlag
call C%fluid%init(C%msh, lx, C%params, C%usr, C%material_properties, &
C%ext_bdf)
select type (f => C%fluid)
type is (fluid_pnpn_t)
f%chkp%abx1 => f%abx1
Expand All @@ -228,7 +238,6 @@ subroutine case_init_common(C)
f%chkp%abz2 => f%abz2
end select


!
! Setup scratch registry
!
Expand All @@ -245,8 +254,11 @@ subroutine case_init_common(C)

if (scalar) then
allocate(C%scalar)
C%scalar%chkp%tlag => C%tlag
C%scalar%chkp%dtlag => C%dtlag
call C%scalar%init(C%msh, C%fluid%c_Xh, C%fluid%gs_Xh, C%params, C%usr,&
C%material_properties)
C%material_properties, C%fluid%ulag, C%fluid%vlag, &
C%fluid%wlag, C%ext_bdf)
call C%fluid%chkp%add_scalar(C%scalar%s)
C%fluid%chkp%abs1 => C%scalar%abx1
C%fluid%chkp%abs2 => C%scalar%abx2
Expand Down Expand Up @@ -311,12 +323,6 @@ subroutine case_init_common(C)
call C%scalar%validate
end if

!
! Set order of timestepper
!
call json_get(C%params, 'case.numerics.time_order', integer_val)
call C%ext_bdf%init(integer_val)

!
! Get and process output directory
!
Expand Down
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