From 43337de382b1188b1ad88e04a586e421b3c8ad02 Mon Sep 17 00:00:00 2001 From: Aaron Lattanzi Date: Wed, 17 Jul 2024 13:51:37 -0700 Subject: [PATCH 1/4] THis is a mess. --- Exec/ABL/Backtrace.0 | 54 +++ Exec/ABL/input_ReTau2000DNS_sounding.txt | 385 ++++++++++++++++++ Exec/ABL/input_ReTau2000DNS_sponge.txt | 384 +++++++++++++++++ Exec/ABL/input_ReTau2000DNS_xlo.txt | 384 +++++++++++++++++ Exec/ABL/input_ReTau2000DNS_xlo_w.txt | 385 ++++++++++++++++++ Exec/ABL/input_ReTau2000DNS_xlo_w.txt~ | 384 +++++++++++++++++ Exec/ABL/toc_inout_inputs | 100 +++++ Exec/ABL/toc_inout_inputs~ | 96 +++++ Exec/ABL/xlo_dirichlet_face | 384 +++++++++++++++++ .../BoundaryConditions_xvel.cpp | 13 +- .../BoundaryConditions_yvel.cpp | 8 +- .../BoundaryConditions_zvel.cpp | 8 +- Source/BoundaryConditions/ERF_FillPatch.cpp | 24 +- Source/BoundaryConditions/ERF_PhysBCFunct.H | 17 +- Source/BoundaryConditions/ERF_PhysBCFunct.cpp | 14 +- Source/ERF.H | 9 + Source/ERF.cpp | 7 +- Source/Initialization/ERF_init_bcs.cpp | 138 ++++++- Source/Utils/Interpolation_1D.H | 6 +- 19 files changed, 2755 insertions(+), 45 deletions(-) create mode 100644 Exec/ABL/Backtrace.0 create mode 100644 Exec/ABL/input_ReTau2000DNS_sounding.txt create mode 100644 Exec/ABL/input_ReTau2000DNS_sponge.txt create mode 100644 Exec/ABL/input_ReTau2000DNS_xlo.txt create mode 100644 Exec/ABL/input_ReTau2000DNS_xlo_w.txt create mode 100644 Exec/ABL/input_ReTau2000DNS_xlo_w.txt~ create mode 100644 Exec/ABL/toc_inout_inputs create mode 100644 Exec/ABL/toc_inout_inputs~ create mode 100644 Exec/ABL/xlo_dirichlet_face diff --git a/Exec/ABL/Backtrace.0 b/Exec/ABL/Backtrace.0 new file mode 100644 index 000000000..ddfc474b9 --- /dev/null +++ b/Exec/ABL/Backtrace.0 @@ -0,0 +1,54 @@ +Host Name: ghidorah +=== If no file names and line numbers are shown below, one can run + addr2line -Cpfie my_exefile my_line_address + to convert `my_line_address` (e.g., 0x4a6b) into file name and line number. + Or one can use amrex/Tools/Backtrace/parse_bt.py. + +=== Please note that the line number reported by addr2line may not be accurate. + One can use + readelf -wl my_exefile | grep my_line_address' + to find out the offset for that line. + + 0: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0xc73b4a) [0x567beb158b4a] + amrex::BLBackTrace::print_backtrace_info(_IO_FILE*) at /home/amlattanzi/git/amrex/Src/Base/AMReX_BLBackTrace.cpp:190 + + 1: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0xc7354a) [0x567beb15854a] + amrex::BLBackTrace::handler(int) at /home/amlattanzi/git/amrex/Src/Base/AMReX_BLBackTrace.cpp:100 + + 2: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0xa5f860) [0x567beaf44860] + amrex::ParallelDescriptor::Abort(int, bool) at /home/amlattanzi/git/amrex/Src/Base/AMReX_ParallelDescriptor.cpp:219 + + 3: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x9e0070) [0x567beaec5070] + amrex::Assert_host(char const*, char const*, int, char const*) at /home/amlattanzi/git/amrex/Src/Base/AMReX.cpp:292 + + 4: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x4e19c) [0x567bea53319c] + amrex::Assert(char const*, char const*, int, char const*) at /home/amlattanzi/git/amrex/Src/Base/AMReX.H:183 (discriminator 1) + (inlined by) amrex::Vector >::operator[](unsigned long) at /home/amlattanzi/git/amrex/Src/Base/AMReX_Vector.H:35 (discriminator 1) + + 5: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x7c54b4) [0x567beacaa4b4] + ERF::init_Dirichlet_bc_data(amrex::Orientation, std::__cxx11::basic_string, std::allocator >) at /home/amlattanzi/git/ERF/Exec/ABL/../../Source/Initialization/ERF_init_bcs.cpp:677 + + 6: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x7bcead) [0x567beaca1ead] + ERF::init_bcs()::{lambda(std::__cxx11::basic_string, std::allocator > const&, amrex::Orientation)#1}::operator()(std::__cxx11::basic_string, std::allocator > const&, amrex::Orientation) const at /home/amlattanzi/git/ERF/Exec/ABL/../../Source/Initialization/ERF_init_bcs.cpp:105 (discriminator 3) + + 7: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x7be4d1) [0x567beaca34d1] + ERF::init_bcs() at /home/amlattanzi/git/ERF/Exec/ABL/../../Source/Initialization/ERF_init_bcs.cpp:263 (discriminator 4) + + 8: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x2466a) [0x567bea50966a] + ERF::InitData() at /home/amlattanzi/git/ERF/Exec/ABL/../../Source/ERF.cpp:575 + + 9: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x1a6d3) [0x567bea4ff6d3] + main at /home/amlattanzi/git/ERF/Exec/ABL/../../Source/main.cpp:227 + +10: /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7bfcdd029d90] + +11: /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7bfcdd029e40] + +12: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x19eb5) [0x567bea4feeb5] + ?? ??:0 + + +===== TinyProfilers ====== +main() +ERF::InitData() + diff --git a/Exec/ABL/input_ReTau2000DNS_sounding.txt b/Exec/ABL/input_ReTau2000DNS_sounding.txt new file mode 100644 index 000000000..6585d799e --- /dev/null +++ b/Exec/ABL/input_ReTau2000DNS_sounding.txt @@ -0,0 +1,385 @@ +0.0 300.0 0.0 0.0 0.0 +1.217311652923492e-06 300.0 0.0 0.00011140613491415374 0.0 +6.086537518545931e-06 300.0 0.0 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1.1190000308462351 0.0 0.0 +0.9772973901174332 1.119075791838296 0.0 0.0 +0.9814246097461727 1.1191387316178165 0.0 0.0 +0.9855521459434584 1.1191889672245374 0.0 0.0 +0.9896799283663196 1.1192266886822442 0.0 0.0 +0.9938078866675891 1.119251954837764 0.0 0.0 +0.9979359504971027 1.1192646414784726 0.0 0.0 diff --git a/Exec/ABL/toc_inout_inputs b/Exec/ABL/toc_inout_inputs new file mode 100644 index 000000000..c6969b7f9 --- /dev/null +++ b/Exec/ABL/toc_inout_inputs @@ -0,0 +1,100 @@ +# ------------------ INPUTS TO MAIN PROGRAM ------------------- +start_time = 0. +stop_time = 0.5 +#stop_time = 35.0 + +#stop_time = 10.0 + +#max_step = 1000 + +#erf.incompressible = 1 + +amrex.fpe_trap_invalid = 1 + +fabarray.mfiter_tile_size = 1024 1024 1024 + +# PROBLEM SIZE & GEOMETRY +geometry.prob_extent = 20. 1. 1. +amr.n_cell = 512 32 64 + +geometry.is_periodic = 0 1 0 + +xlo.type = "Inflow" +xhi.type = "Outflow" +zlo.type = "NoSlipWall" +zhi.type = "SlipWall" + +xlo.dirichlet_file = "input_ReTau2000DNS_xlo_w.txt" + +# TIME STEP CONTROL +erf.no_substepping = 1 +erf.cfl = 0.5 + +erf.dynamicViscosity = 0.0001 # H = 1, therefore utau = 0.2 + +# DIAGNOSTICS & VERBOSITY +erf.sum_interval = 100 # timesteps between computing mass +erf.pert_interval = 100 # timesteps between perturbation output message +erf.v = 0 # verbosity in ERF.cpp +amr.v = 0 # verbosity in Amr.cpp + +# REFINEMENT / REGRIDDING +amr.max_level = 0 # maximum level number allowed + +# PLOTFILES +erf.plot_file_1 = plt # prefix of plotfile name +#erf.plot_per_1 = 0.1 +erf.plot_int_1 = 100 +erf.plot_vars_1 = density rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta + +# CHECKPOINT FILES +erf.check_file = chk # root name of checkpoint file +erf.check_per = 1.0 + +# SOLVER CHOICE +erf.alpha_T = 0.0 +erf.alpha_C = 1.0 +erf.use_gravity = false + +erf.molec_diff_type = "None" +erf.les_type = "Smagorinsky" +erf.Cs = 0.1 + +# Buoyancy type +erf.buoyancy_type = 1 + +# Initial condition for the entire field +erf.init_type = "input_sounding" +erf.input_sounding_file = "input_ReTau2000DNS_sounding.txt" + +# Inflow boundary condition +erf.sponge_type = "input_sponge" +erf.input_sponge_file = "input_ReTau2000DNS_sponge.txt" +erf.sponge_strength = 25000.0 +#erf.use_xlo_sponge_damping = true +#erf.xlo_sponge_end = 2.0 + + + +erf.use_xhi_sponge_damping = true +erf.xhi_sponge_start = 18.0 + +# Turbulent inflow generation +#erf.perturbation_type = "source" +#erf.perturbation_direction = 1 0 0 +#erf.perturbation_layers = 3 +#erf.perturbation_offset = 32 + +#erf.perturbation_box_dims = 6 4 8 # 0.25 0.25 0.125 +#erf.perturbation_nondimensional = 0.042 # Ri +#erf.perturbation_nondimensional = 0.1 # Ri +#erf.perturbation_T_infinity = 300.0 +#erf.perturbation_T_intensity = 0.1 + +# PROBLEM PARAMETERS +prob.rho_0 = 1.0 +prob.A_0 = 1.0 +prob.U_0 = 0.0 +prob.V_0 = 0.0 +prob.W_0 = 0.0 +prob.T_0 = 300.0 diff --git a/Exec/ABL/toc_inout_inputs~ b/Exec/ABL/toc_inout_inputs~ new file mode 100644 index 000000000..8c89121eb --- /dev/null +++ b/Exec/ABL/toc_inout_inputs~ @@ -0,0 +1,96 @@ +# ------------------ INPUTS TO MAIN PROGRAM ------------------- +start_time = 0. +stop_time = 0.5 +#stop_time = 35.0 + +#stop_time = 10.0 + +#max_step = 1000 + +#erf.incompressible = 1 + +amrex.fpe_trap_invalid = 1 + +fabarray.mfiter_tile_size = 1024 1024 1024 + +# PROBLEM SIZE & GEOMETRY +geometry.prob_extent = 20. 1. 1. +amr.n_cell = 512 32 64 + +geometry.is_periodic = 0 1 0 + +xlo.type = "Outflow" +xhi.type = "Outflow" +zlo.type = "NoSlipWall" +zhi.type = "SlipWall" + +# TIME STEP CONTROL +erf.no_substepping = 1 +erf.cfl = 0.5 + +erf.dynamicViscosity = 0.0001 # H = 1, therefore utau = 0.2 + +# DIAGNOSTICS & VERBOSITY +erf.sum_interval = 100 # timesteps between computing mass +erf.pert_interval = 100 # timesteps between perturbation output message +erf.v = 0 # verbosity in ERF.cpp +amr.v = 0 # verbosity in Amr.cpp + +# REFINEMENT / REGRIDDING +amr.max_level = 0 # maximum level number allowed + +# PLOTFILES +erf.plot_file_1 = plt # prefix of plotfile name +#erf.plot_per_1 = 0.1 +erf.plot_int_1 = 100 +erf.plot_vars_1 = density rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta + +# CHECKPOINT FILES +erf.check_file = chk # root name of checkpoint file +erf.check_per = 1.0 + +# SOLVER CHOICE +erf.alpha_T = 0.0 +erf.alpha_C = 1.0 +erf.use_gravity = false + +erf.molec_diff_type = "None" +erf.les_type = "Smagorinsky" +erf.Cs = 0.1 + +# Buoyancy type +erf.buoyancy_type = 1 + +# Initial condition for the entire field +erf.init_type = "input_sounding" +erf.input_sounding_file = "input_ReTau2000DNS_sounding.txt" + +# Inflow boundary condition +erf.sponge_type = "input_sponge" +erf.input_sponge_file = "input_ReTau2000DNS_sponge.txt" +erf.sponge_strength = 25000.0 +erf.use_xlo_sponge_damping = true +erf.xlo_sponge_end = 2.0 + +erf.use_xhi_sponge_damping = true +erf.xhi_sponge_start = 18.0 + +# Turbulent inflow generation +erf.perturbation_type = "source" +erf.perturbation_direction = 1 0 0 +erf.perturbation_layers = 3 +erf.perturbation_offset = 32 + +erf.perturbation_box_dims = 6 4 8 # 0.25 0.25 0.125 +#erf.perturbation_nondimensional = 0.042 # Ri +erf.perturbation_nondimensional = 0.1 # Ri +erf.perturbation_T_infinity = 300.0 +erf.perturbation_T_intensity = 0.1 + +# PROBLEM PARAMETERS +prob.rho_0 = 1.0 +prob.A_0 = 1.0 +prob.U_0 = 0.0 +prob.V_0 = 0.0 +prob.W_0 = 0.0 +prob.T_0 = 300.0 diff --git a/Exec/ABL/xlo_dirichlet_face b/Exec/ABL/xlo_dirichlet_face new file mode 100644 index 000000000..737895f86 --- /dev/null +++ b/Exec/ABL/xlo_dirichlet_face @@ -0,0 +1,384 @@ +0.0 0.0 0.0 +1.217311652923492e-06 0.00011140613491415374 0.0 +6.086537518545931e-06 0.0005570274195276387 0.0 +1.704221791976046e-05 0.001559660241516003 0.0 +3.651878945154508e-05 0.0033420734502807845 0.0 +6.69505434929274e-05 0.0061269859333703105 0.0 +0.0001107715847206148 0.010137027830325164 0.0 +0.0001704157896263991 0.015594654328461917 0.0 +0.0002470994533848581 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+0.9690441819093016 1.118911351122682 0.0 +0.9731705573948156 1.1190000308462351 0.0 +0.9772973901174332 1.119075791838296 0.0 +0.9814246097461727 1.1191387316178165 0.0 +0.9855521459434584 1.1191889672245374 0.0 +0.9896799283663196 1.1192266886822442 0.0 +0.9938078866675891 1.119251954837764 0.0 +0.9979359504971027 1.1192646414784726 0.0 diff --git a/Source/BoundaryConditions/BoundaryConditions_xvel.cpp b/Source/BoundaryConditions/BoundaryConditions_xvel.cpp index bd60b9775..2a974fd52 100644 --- a/Source/BoundaryConditions/BoundaryConditions_xvel.cpp +++ b/Source/BoundaryConditions/BoundaryConditions_xvel.cpp @@ -15,7 +15,8 @@ using namespace amrex; */ void ERFPhysBCFunct_u::impose_lateral_xvel_bcs (const Array4& dest_arr, - const Box& bx, const Box& domain, int bccomp) + const Box& bx, const Box& domain, int bccomp, + Vector>& xvel_bc_data) { BL_PROFILE_VAR("impose_lateral_xvel_bcs()",impose_lateral_xvel_bcs); const auto& dom_lo = lbound(domain); @@ -52,6 +53,8 @@ void ERFPhysBCFunct_u::impose_lateral_xvel_bcs (const Array4& dest_arr, // First do all ext_dir bcs if (!is_periodic_in_x) { + Real* xvel_xlo_ptr = xvel_bc_data[0].data(); + Real* xvel_xhi_ptr = xvel_bc_data[3].data(); Box bx_xlo(bx); bx_xlo.setBig (0,dom_lo.x-1); Box bx_xhi(bx); bx_xhi.setSmall(0,dom_hi.x+2); Box bx_xlo_face(bx); bx_xlo_face.setSmall(0,dom_lo.x ); bx_xlo_face.setBig(0,dom_lo.x ); @@ -61,7 +64,7 @@ void ERFPhysBCFunct_u::impose_lateral_xvel_bcs (const Array4& dest_arr, { int iflip = dom_lo.x - i; if (bc_ptr[n].lo(0) == ERFBCType::ext_dir) { - dest_arr(i,j,k) = l_bc_extdir_vals_d[n][0]; + dest_arr(i,j,k) = (xvel_xlo_ptr) ? xvel_xlo_ptr[k] : l_bc_extdir_vals_d[n][0]; } else if (bc_ptr[n].lo(0) == ERFBCType::foextrap) { dest_arr(i,j,k) = dest_arr(dom_lo.x,j,k); } else if (bc_ptr[n].lo(0) == ERFBCType::open) { @@ -78,7 +81,7 @@ void ERFPhysBCFunct_u::impose_lateral_xvel_bcs (const Array4& dest_arr, bx_xlo_face, ncomp, [=] AMREX_GPU_DEVICE (int i, int j, int k, int n) { if (bc_ptr[n].lo(0) == ERFBCType::ext_dir) { - dest_arr(i,j,k) = l_bc_extdir_vals_d[n][0]; + dest_arr(i,j,k) = (xvel_xlo_ptr) ? xvel_xlo_ptr[k] : l_bc_extdir_vals_d[n][0]; } else if (bc_ptr[n].lo(0) == ERFBCType::neumann_int) { dest_arr(i,j,k) = (4.0*dest_arr(dom_lo.x+1,j,k) - dest_arr(dom_lo.x+2,j,k))/3.0; } @@ -89,7 +92,7 @@ void ERFPhysBCFunct_u::impose_lateral_xvel_bcs (const Array4& dest_arr, { int iflip = 2*(dom_hi.x + 1) - i; if (bc_ptr[n].hi(0) == ERFBCType::ext_dir) { - dest_arr(i,j,k) = l_bc_extdir_vals_d[n][3]; + dest_arr(i,j,k) = (xvel_xhi_ptr) ? xvel_xhi_ptr[k] : l_bc_extdir_vals_d[n][3]; } else if (bc_ptr[n].hi(0) == ERFBCType::foextrap) { dest_arr(i,j,k) = dest_arr(dom_hi.x+1,j,k); } else if (bc_ptr[n].hi(0) == ERFBCType::open) { @@ -106,7 +109,7 @@ void ERFPhysBCFunct_u::impose_lateral_xvel_bcs (const Array4& dest_arr, bx_xhi_face, ncomp, [=] AMREX_GPU_DEVICE (int i, int j, int k, int n) { if (bc_ptr[n].hi(0) == ERFBCType::ext_dir) { - dest_arr(i,j,k) = l_bc_extdir_vals_d[n][3]; + dest_arr(i,j,k) = (xvel_xhi_ptr) ? xvel_xhi_ptr[k] : l_bc_extdir_vals_d[n][3]; } else if (bc_ptr[n].hi(0) == ERFBCType::neumann_int) { dest_arr(i,j,k) = (4.0*dest_arr(dom_hi.x,j,k) - dest_arr(dom_hi.x-1,j,k))/3.0; } diff --git a/Source/BoundaryConditions/BoundaryConditions_yvel.cpp b/Source/BoundaryConditions/BoundaryConditions_yvel.cpp index 886b17654..7c333f871 100644 --- a/Source/BoundaryConditions/BoundaryConditions_yvel.cpp +++ b/Source/BoundaryConditions/BoundaryConditions_yvel.cpp @@ -13,7 +13,7 @@ using namespace amrex; */ void ERFPhysBCFunct_v::impose_lateral_yvel_bcs (const Array4& dest_arr, const Box& bx, const Box& domain, - int bccomp) + int bccomp, Vector>& yvel_bc_data) { BL_PROFILE_VAR("impose_lateral_yvel_bcs()",impose_lateral_yvel_bcs); const auto& dom_lo = lbound(domain); @@ -51,13 +51,15 @@ void ERFPhysBCFunct_v::impose_lateral_yvel_bcs (const Array4& dest_arr, if (!is_periodic_in_x) { // Populate ghost cells on lo-x and hi-x domain boundaries + Real* yvel_xlo_ptr = yvel_bc_data[0].data(); + Real* yvel_xhi_ptr = yvel_bc_data[3].data(); Box bx_xlo(bx); bx_xlo.setBig (0,dom_lo.x-1); Box bx_xhi(bx); bx_xhi.setSmall(0,dom_hi.x+1); ParallelFor( bx_xlo, ncomp, [=] AMREX_GPU_DEVICE (int i, int j, int k, int n) { int iflip = dom_lo.x - 1- i; if (bc_ptr[n].lo(0) == ERFBCType::ext_dir) { - dest_arr(i,j,k) = l_bc_extdir_vals_d[n][0]; + dest_arr(i,j,k) = (yvel_xlo_ptr) ? yvel_xlo_ptr[k] : l_bc_extdir_vals_d[n][0]; } else if (bc_ptr[n].lo(0) == ERFBCType::foextrap) { dest_arr(i,j,k) = dest_arr(dom_lo.x,j,k); } else if (bc_ptr[n].lo(0) == ERFBCType::open) { @@ -71,7 +73,7 @@ void ERFPhysBCFunct_v::impose_lateral_yvel_bcs (const Array4& dest_arr, bx_xhi, ncomp, [=] AMREX_GPU_DEVICE (int i, int j, int k, int n) { int iflip = 2*dom_hi.x + 1 - i; if (bc_ptr[n].hi(0) == ERFBCType::ext_dir) { - dest_arr(i,j,k) = l_bc_extdir_vals_d[n][3]; + dest_arr(i,j,k) = (yvel_xhi_ptr) ? yvel_xhi_ptr[k] : l_bc_extdir_vals_d[n][3]; } else if (bc_ptr[n].hi(0) == ERFBCType::foextrap) { dest_arr(i,j,k) = dest_arr(dom_hi.x,j,k); } else if (bc_ptr[n].hi(0) == ERFBCType::open) { diff --git a/Source/BoundaryConditions/BoundaryConditions_zvel.cpp b/Source/BoundaryConditions/BoundaryConditions_zvel.cpp index ef04f7ee5..e8f3ddeb1 100644 --- a/Source/BoundaryConditions/BoundaryConditions_zvel.cpp +++ b/Source/BoundaryConditions/BoundaryConditions_zvel.cpp @@ -19,7 +19,7 @@ void ERFPhysBCFunct_w::impose_lateral_zvel_bcs (const Array4& dest_a const Box& bx, const Box& domain, const Array4& z_phys_nd, const GpuArray dxInv, - int bccomp) + int bccomp, Vector>& zvel_bc_data) { BL_PROFILE_VAR("impose_lateral_zvel_bcs()",impose_lateral_zvel_bcs); const auto& dom_lo = lbound(domain); @@ -60,13 +60,15 @@ void ERFPhysBCFunct_w::impose_lateral_zvel_bcs (const Array4& dest_a // First do all ext_dir bcs if (!is_periodic_in_x) { + Real* zvel_xlo_ptr = zvel_bc_data[0].data(); + Real* zvel_xhi_ptr = zvel_bc_data[3].data(); Box bx_xlo(bx); bx_xlo.setBig (0,dom_lo.x-1); Box bx_xhi(bx); bx_xhi.setSmall(0,dom_hi.x+1); ParallelFor( bx_xlo, ncomp, [=] AMREX_GPU_DEVICE (int i, int j, int k, int n) { int iflip = dom_lo.x - 1 - i; if (bc_ptr_w[n].lo(0) == ERFBCType::ext_dir) { - dest_arr(i,j,k) = l_bc_extdir_vals_d[n][0]; + dest_arr(i,j,k) = (zvel_xlo_ptr) ? zvel_xlo_ptr[k] : l_bc_extdir_vals_d[n][0]; if (l_use_terrain) { dest_arr(i,j,k) = WFromOmega(i,j,k,dest_arr(i,j,k),xvel_arr,yvel_arr,z_phys_nd,dxInv); } @@ -83,7 +85,7 @@ void ERFPhysBCFunct_w::impose_lateral_zvel_bcs (const Array4& dest_a bx_xhi, ncomp, [=] AMREX_GPU_DEVICE (int i, int j, int k, int n) { int iflip = 2*dom_hi.x + 1 - i; if (bc_ptr_w[n].hi(0) == ERFBCType::ext_dir) { - dest_arr(i,j,k) = l_bc_extdir_vals_d[n][3]; + dest_arr(i,j,k) = (zvel_xhi_ptr) ? zvel_xhi_ptr[k] : l_bc_extdir_vals_d[n][3]; if (l_use_terrain) { dest_arr(i,j,k) = WFromOmega(i,j,k,dest_arr(i,j,k),xvel_arr,yvel_arr,z_phys_nd,dxInv); } diff --git a/Source/BoundaryConditions/ERF_FillPatch.cpp b/Source/BoundaryConditions/ERF_FillPatch.cpp index e6c7c7fc9..9cdf0c5e5 100644 --- a/Source/BoundaryConditions/ERF_FillPatch.cpp +++ b/Source/BoundaryConditions/ERF_FillPatch.cpp @@ -108,7 +108,7 @@ ERF::FillPatch (int lev, Real time, FillPatchSingleLevel(*mfs_vel[Vars::zvel], time, fmf, ftime, icomp, icomp, ncomp_w, geom[lev], *physbcs_w_no_terrain[lev], BCVars::zvel_bc); (*physbcs_w[lev])(*mfs_vel[Vars::zvel],*mfs_vel[Vars::xvel],*mfs_vel[Vars::yvel], - ngvect_vels,time,BCVars::zvel_bc); + ngvect_vels,time,BCVars::zvel_bc,zvel_bc_data); } // !cons_only } else { @@ -161,7 +161,7 @@ ERF::FillPatch (int lev, Real time, *physbcs_w_no_terrain[lev ], BCVars::zvel_bc, refRatio(lev-1), mapper, domain_bcs_type, BCVars::zvel_bc); (*physbcs_w[lev])(*mfs_vel[Vars::zvel],*mfs_vel[Vars::xvel],*mfs_vel[Vars::yvel], - ngvect_vels,time,BCVars::zvel_bc); + ngvect_vels,time,BCVars::zvel_bc,zvel_bc_data); } // !cons_only } // lev > 0 @@ -183,10 +183,10 @@ ERF::FillPatch (int lev, Real time, // We call these even if init_type == real because these will fill the vertical bcs (*physbcs_cons[lev])(*mfs_vel[Vars::cons],icomp_cons,ncomp_cons,ngvect_cons,time,BCVars::cons_bc); if (!cons_only) { - (*physbcs_u[lev])(*mfs_vel[Vars::xvel],0,1,ngvect_vels,time,BCVars::xvel_bc); - (*physbcs_v[lev])(*mfs_vel[Vars::yvel],0,1,ngvect_vels,time,BCVars::yvel_bc); + (*physbcs_u[lev])(*mfs_vel[Vars::xvel],0,1,ngvect_vels,time,BCVars::xvel_bc, xvel_bc_data); + (*physbcs_v[lev])(*mfs_vel[Vars::yvel],0,1,ngvect_vels,time,BCVars::yvel_bc, yvel_bc_data); (*physbcs_w[lev])(*mfs_vel[Vars::zvel],*mfs_vel[Vars::xvel],*mfs_vel[Vars::yvel], - ngvect_vels,time,BCVars::zvel_bc); + ngvect_vels,time,BCVars::zvel_bc, zvel_bc_data); } } @@ -384,7 +384,7 @@ ERF::FillIntermediatePatch (int lev, Real time, *physbcs_w_no_terrain[lev ], BCVars::zvel_bc, refRatio(lev-1), mapper, domain_bcs_type, bccomp); (*physbcs_w[lev])(*mfs_vel[Vars::zvel],*mfs_vel[Vars::xvel],*mfs_vel[Vars::yvel], - ngvect,time,BCVars::zvel_bc); + ngvect,time,BCVars::zvel_bc,zvel_bc_data); } } // lev > 0 } // var_idx @@ -407,10 +407,10 @@ ERF::FillIntermediatePatch (int lev, Real time, // We call this even if init_type == real because this routine will fill the vertical bcs (*physbcs_cons[lev])(*mfs_vel[Vars::cons],icomp_cons,ncomp_cons,ngvect_cons,time,BCVars::cons_bc); if (!cons_only) { - (*physbcs_u[lev])(*mfs_vel[Vars::xvel],0,1,ngvect_vels,time,BCVars::xvel_bc); - (*physbcs_v[lev])(*mfs_vel[Vars::yvel],0,1,ngvect_vels,time,BCVars::yvel_bc); + (*physbcs_u[lev])(*mfs_vel[Vars::xvel],0,1,ngvect_vels,time,BCVars::xvel_bc,xvel_bc_data); + (*physbcs_v[lev])(*mfs_vel[Vars::yvel],0,1,ngvect_vels,time,BCVars::yvel_bc,yvel_bc_data); (*physbcs_w[lev])(*mfs_vel[Vars::zvel],*mfs_vel[Vars::xvel],*mfs_vel[Vars::yvel], - ngvect_vels,time,BCVars::zvel_bc); + ngvect_vels,time,BCVars::zvel_bc,zvel_bc_data); } // *************************************************************************** @@ -564,10 +564,10 @@ ERF::FillCoarsePatch (int lev, Real time) int ncomp_cons = vars_new[lev][Vars::cons].nComp(); (*physbcs_cons[lev])(vars_new[lev][Vars::cons],0,ncomp_cons,ngvect_cons,time,BCVars::cons_bc); - ( *physbcs_u[lev])(vars_new[lev][Vars::xvel],0,1 ,ngvect_vels,time,BCVars::xvel_bc); - ( *physbcs_v[lev])(vars_new[lev][Vars::yvel],0,1 ,ngvect_vels,time,BCVars::yvel_bc); + ( *physbcs_u[lev])(vars_new[lev][Vars::xvel],0,1 ,ngvect_vels,time,BCVars::xvel_bc,xvel_bc_data); + ( *physbcs_v[lev])(vars_new[lev][Vars::yvel],0,1 ,ngvect_vels,time,BCVars::yvel_bc,yvel_bc_data); ( *physbcs_w[lev])(vars_new[lev][Vars::zvel],vars_new[lev][Vars::xvel],vars_new[lev][Vars::yvel], - ngvect_vels,time,BCVars::zvel_bc); + ngvect_vels,time,BCVars::zvel_bc,zvel_bc_data); // *************************************************************************** // Since lev > 0 here we don't worry about m_r2d or wrfbdy data diff --git a/Source/BoundaryConditions/ERF_PhysBCFunct.H b/Source/BoundaryConditions/ERF_PhysBCFunct.H index c0000105b..0119c3c99 100644 --- a/Source/BoundaryConditions/ERF_PhysBCFunct.H +++ b/Source/BoundaryConditions/ERF_PhysBCFunct.H @@ -104,11 +104,12 @@ public: * @param[in] use_real_bcs if true then we fill boundary conditions for interior locations */ void operator() (amrex::MultiFab& mf, int icomp, int ncomp, - amrex::IntVect const& nghost, const amrex::Real time, int bccomp); + amrex::IntVect const& nghost, const amrex::Real time, int bccomp, + amrex::Vector>& xvel_bc_data); void impose_lateral_xvel_bcs (const amrex::Array4& dest_arr, const amrex::Box& bx, const amrex::Box& domain, - int bccomp); + int bccomp, amrex::Vector>& xvel_bc_data); void impose_vertical_xvel_bcs (const amrex::Array4& dest_arr, const amrex::Box& bx, const amrex::Box& domain, const amrex::Array4& z_nd, @@ -159,11 +160,13 @@ public: * @param[in] use_real_bcs if true then we fill boundary conditions for interior locations */ void operator() (amrex::MultiFab& mf, int icomp, int ncomp, - amrex::IntVect const& nghost, const amrex::Real time, int bccomp); + amrex::IntVect const& nghost, const amrex::Real time, int bccomp, + amrex::Vector>& yvel_bc_data); void impose_lateral_yvel_bcs (const amrex::Array4& dest_arr, const amrex::Box& bx, const amrex::Box& domain, - int bccomp); + int bccomp, + amrex::Vector>& yvel_bc_data); void impose_vertical_yvel_bcs (const amrex::Array4& dest_arr, const amrex::Box& bx, const amrex::Box& domain, const amrex::Array4& z_nd, @@ -214,7 +217,8 @@ public: * @param[in] use_real_bcs if true then we fill boundary conditions for interior locations */ void operator() (amrex::MultiFab& mf, amrex::MultiFab& xvel, amrex::MultiFab& yvel, - amrex::IntVect const& nghost, const amrex::Real time, int bccomp); + amrex::IntVect const& nghost, const amrex::Real time, int bccomp, + amrex::Vector>& zvel_bc_data); void impose_lateral_zvel_bcs (const amrex::Array4& dest_arr, const amrex::Array4& xvel_arr, @@ -222,7 +226,8 @@ public: const amrex::Box& bx, const amrex::Box& domain, const amrex::Array4& z_nd, const amrex::GpuArray dxInv, - int bccomp); + int bccomp, + amrex::Vector>& zvel_bc_data); void impose_vertical_zvel_bcs (const amrex::Array4& dest_arr, const amrex::Array4& xvel_arr, const amrex::Array4& yvel_arr, diff --git a/Source/BoundaryConditions/ERF_PhysBCFunct.cpp b/Source/BoundaryConditions/ERF_PhysBCFunct.cpp index 5868dcddb..2cba3662c 100644 --- a/Source/BoundaryConditions/ERF_PhysBCFunct.cpp +++ b/Source/BoundaryConditions/ERF_PhysBCFunct.cpp @@ -91,7 +91,8 @@ void ERFPhysBCFunct_cons::operator() (MultiFab& mf, int icomp, int ncomp, } // operator() void ERFPhysBCFunct_u::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, - IntVect const& nghost, const Real time, int bccomp) + IntVect const& nghost, const Real time, int bccomp, + Vector>& xvel_bc_data) { BL_PROFILE("ERFPhysBCFunct_u::()"); @@ -158,7 +159,7 @@ void ERFPhysBCFunct_u::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, { if (!gdomainx.contains(xbx1)) { - impose_lateral_xvel_bcs(velx_arr,xbx1,domain,bccomp); + impose_lateral_xvel_bcs(velx_arr,xbx1,domain,bccomp, xvel_bc_data); } } @@ -170,7 +171,8 @@ void ERFPhysBCFunct_u::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, } // operator() void ERFPhysBCFunct_v::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, - IntVect const& nghost, const Real /*time*/, int bccomp) + IntVect const& nghost, const Real /*time*/, int bccomp, + Vector>& yvel_bc_data) { BL_PROFILE("ERFPhysBCFunct_v::()"); @@ -235,7 +237,7 @@ void ERFPhysBCFunct_v::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, if (!m_use_real_bcs) { - impose_lateral_yvel_bcs(vely_arr,ybx1,domain,bccomp); + impose_lateral_yvel_bcs(vely_arr,ybx1,domain,bccomp, yvel_bc_data); } impose_vertical_yvel_bcs(vely_arr,ybx2,domain,z_nd_arr,dxInv,bccomp); @@ -247,7 +249,7 @@ void ERFPhysBCFunct_v::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, void ERFPhysBCFunct_w::operator() (MultiFab& mf, MultiFab& xvel, MultiFab& yvel, IntVect const& nghost, const Real /*time*/, - const int bccomp_w) + const int bccomp_w, Vector>& zvel_bc_data) { BL_PROFILE("ERFPhysBCFunct_w::()"); @@ -317,7 +319,7 @@ void ERFPhysBCFunct_w::operator() (MultiFab& mf, MultiFab& xvel, MultiFab& yvel, { if (!gdomainz.contains(zbx)) { - impose_lateral_zvel_bcs(velz_arr,velx_arr,vely_arr,zbx,domain,z_nd_arr,dxInv,bccomp_w); + impose_lateral_zvel_bcs(velz_arr,velx_arr,vely_arr,zbx,domain,z_nd_arr,dxInv,bccomp_w,zvel_bc_data); } } // m_use_real_bcs diff --git a/Source/ERF.H b/Source/ERF.H index cee060a75..e1b61b683 100644 --- a/Source/ERF.H +++ b/Source/ERF.H @@ -580,6 +580,15 @@ private: // Struct for working with the sponge data we take as an input InputSpongeData input_sponge_data; + // Vector (6 planes) of DeviceVectors (ncell in plane) for Dirichlet BC data + amrex::Vector> xvel_bc_data; + amrex::Vector> yvel_bc_data; + amrex::Vector> zvel_bc_data; + + // Function to read and populate above vectors (if input file exists) + void init_Dirichlet_bc_data (amrex::Orientation ori, + const std::string input_file); + // write checkpoint file to disk void WriteCheckpointFile () const; diff --git a/Source/ERF.cpp b/Source/ERF.cpp index b9153139b..dcf520e85 100644 --- a/Source/ERF.cpp +++ b/Source/ERF.cpp @@ -190,7 +190,6 @@ ERF::ERF () pp_inc.resize(nlevs_max); #endif - rU_new.resize(nlevs_max); rV_new.resize(nlevs_max); rW_new.resize(nlevs_max); @@ -306,6 +305,12 @@ ERF::ERF () } #endif + // Dirichlet BC data + int nfaces = 6; + xvel_bc_data.resize(nfaces); + yvel_bc_data.resize(nfaces); + zvel_bc_data.resize(nfaces); + // Initialize tagging criteria for mesh refinement refinement_criteria_setup(); diff --git a/Source/Initialization/ERF_init_bcs.cpp b/Source/Initialization/ERF_init_bcs.cpp index 073cbec09..7410dfb5c 100644 --- a/Source/Initialization/ERF_init_bcs.cpp +++ b/Source/Initialization/ERF_init_bcs.cpp @@ -1,8 +1,8 @@ #include #include #include - #include +#include using namespace amrex; @@ -96,12 +96,19 @@ void ERF::init_bcs () if (input_bndry_planes && m_r2d->ingested_velocity()) { m_bc_extdir_vals[BCVars::xvel_bc][ori] = 0.; m_bc_extdir_vals[BCVars::yvel_bc][ori] = 0.; - m_bc_extdir_vals[BCVars::zvel_bc][ori] = 0.; + m_bc_extdir_vals[BCVars::zvel_bc][ori] = 0.; } else { - pp.getarr("velocity", v, 0, AMREX_SPACEDIM); - m_bc_extdir_vals[BCVars::xvel_bc][ori] = v[0]; - m_bc_extdir_vals[BCVars::yvel_bc][ori] = v[1]; - m_bc_extdir_vals[BCVars::zvel_bc][ori] = v[2]; + // Test for input data file if at xlo face + std::string dirichlet_file; + auto file_exists = pp.query("dirichlet_file", dirichlet_file); + if (ori.isLow() && (ori.coordDir() == 0) && file_exists) { + init_Dirichlet_bc_data(ori, dirichlet_file); + } else { + pp.getarr("velocity", v, 0, AMREX_SPACEDIM); + m_bc_extdir_vals[BCVars::xvel_bc][ori] = v[0]; + m_bc_extdir_vals[BCVars::yvel_bc][ori] = v[1]; + m_bc_extdir_vals[BCVars::zvel_bc][ori] = v[2]; + } } Real rho_in; @@ -553,3 +560,122 @@ void ERF::init_bcs () Gpu::copy(Gpu::hostToDevice, domain_bcs_type.begin(), domain_bcs_type.end(), domain_bcs_type_d.begin()); } +void ERF::init_Dirichlet_bc_data (Orientation ori, + const std::string input_file) +{ + Print() << "START\n"; + // Only on coarsest level! + int lev = 0; + + const int klo = 0; + const int khi = geom[lev].Domain().bigEnd()[2]; + const int Nz = geom[lev].Domain().size()[2]; + const Real dz = geom[lev].CellSize()[2]; + + const bool use_terrain = (zlevels_stag.size() > 0); + const Real zbot = (use_terrain) ? zlevels_stag[klo] : geom[lev].ProbLo(2); + const Real ztop = (use_terrain) ? zlevels_stag[khi+1] : geom[lev].ProbHi(2); + + Vector z_inp(Nz+2); + Vector u_inp(Nz+2); + Vector v_inp(Nz+2); + Vector w_inp(Nz+2); + + Vector z_inp_tmp, u_inp_tmp, v_inp_tmp, w_inp_tmp; + + // Read the dirichlet_input file + Print() << "dirichlet_input file location : " << input_file << std::endl; + std::ifstream input_reader(input_file); + if(!input_reader.is_open()) { + Error("Error opening the dirichlet_input file.\n"); + } else { + // Read the contents of the input file + Print() << "Successfully opened the dirichlet_input file. Now reading... " << std::endl; + std::string line; + + // First, read the input data into temp vectors; then, interpolate vectors to the + // domain lo/hi and cell centers (from level 0) + + // Add surface + z_inp_tmp.push_back(zbot); // height above sea level [m] + u_inp_tmp.push_back(0.); + v_inp_tmp.push_back(0.); + w_inp_tmp.push_back(0.); + + // Read the vertical profile at each given height + Real z, u, v, w; + while(std::getline(input_reader, line)) { + std::istringstream iss_z(line); + iss_z >> z >> u >> v >> w; + if (z == zbot) { + u_inp_tmp[0] = u; + v_inp_tmp[0] = v; + w_inp_tmp[0] = w; + } else { + AMREX_ALWAYS_ASSERT(z > z_inp_tmp[z_inp_tmp.size()-1]); // sounding is increasing in height + z_inp_tmp.push_back(z); + u_inp_tmp.push_back(u); + v_inp_tmp.push_back(v); + w_inp_tmp.push_back(w); + if (z >= ztop) break; + } + } + + // At this point, we have an input from zbot up to + // z_inp_tmp[N-1] >= ztop. Now, interpolate to grid level 0 heights + const int Ninp = z_inp_tmp.size(); + z_inp[0] = zbot; + u_inp[0] = u_inp_tmp[0]; + v_inp[0] = v_inp_tmp[0]; + w_inp[0] = w_inp_tmp[0]; + for (int k=0; k < Nz; ++k) { + z_inp[k+1] = (use_terrain) ? 0.5 * (zlevels_stag[k] + zlevels_stag[k+1]) + : zbot + (k + 0.5) * dz; + u_inp[k+1] = interpolate_1d(z_inp_tmp.dataPtr(), u_inp_tmp.dataPtr(), z_inp[k+1], Ninp); + v_inp[k+1] = interpolate_1d(z_inp_tmp.dataPtr(), v_inp_tmp.dataPtr(), z_inp[k+1], Ninp); + w_inp[k+1] = interpolate_1d(z_inp_tmp.dataPtr(), w_inp_tmp.dataPtr(), z_inp[k+1], Ninp); + } + z_inp[Nz+1] = ztop; + u_inp[Nz+1] = interpolate_1d(z_inp_tmp.dataPtr(), u_inp_tmp.dataPtr(), ztop, Ninp); + v_inp[Nz+1] = interpolate_1d(z_inp_tmp.dataPtr(), v_inp_tmp.dataPtr(), ztop, Ninp); + w_inp[Nz+1] = interpolate_1d(z_inp_tmp.dataPtr(), w_inp_tmp.dataPtr(), ztop, Ninp); + } + + amrex::Print() << "Successfully read the dirichlet_input file..." << std::endl; + input_reader.close(); + + // Populate host vectors at their respective positions (only on lev==0) + Vector zcc(khi+1); + Vector znd(khi+2); + + if (z_phys_cc[lev]) { + // use_terrain=1 + // calculate the damping strength based on the max height at each k + reduce_to_max_per_level(zcc, z_phys_cc[lev]); + reduce_to_max_per_level(znd, z_phys_nd[lev]); + } else { + const auto *const prob_lo = geom[lev].ProbLo(); + const auto *const dx = geom[lev].CellSize(); + for (int k = 0; k <= khi; k++) { + zcc[k] = prob_lo[2] + (k+0.5) * dx[2]; + znd[k] = prob_lo[2] + (k ) * dx[2]; + } + znd[khi+1] = prob_lo[2] + (khi+1) * dx[2]; + } + + Vector u_dir_h(Nz ,0.); xvel_bc_data[ori].resize(Nz ,0.0); + Vector v_dir_h(Nz ,0.); yvel_bc_data[ori].resize(Nz ,0.0); + Vector w_dir_h(Nz+1,0.); zvel_bc_data[ori].resize(Nz+1,0.0); + for (int k = 0; k <= khi; k++) { + u_dir_h[k] = interpolate_1d(z_inp.dataPtr(), u_inp.dataPtr(), zcc[k], Nz ); + v_dir_h[k] = interpolate_1d(z_inp.dataPtr(), v_inp.dataPtr(), zcc[k], Nz ); + w_dir_h[k] = interpolate_1d(z_inp.dataPtr(), w_inp.dataPtr(), znd[k], Nz+1); + } + w_dir_h[khi+1] = interpolate_1d(z_inp.dataPtr(), w_inp.dataPtr(), znd[khi+1], Nz+1); + + + // Copy from host version to device version + Gpu::copy(Gpu::hostToDevice, u_dir_h.begin(), u_dir_h.end(), xvel_bc_data[ori].begin()); + Gpu::copy(Gpu::hostToDevice, v_dir_h.begin(), v_dir_h.end(), yvel_bc_data[ori].begin()); + Gpu::copy(Gpu::hostToDevice, w_dir_h.begin(), w_dir_h.end(), zvel_bc_data[ori].begin()); +} diff --git a/Source/Utils/Interpolation_1D.H b/Source/Utils/Interpolation_1D.H index e89b94b6b..40e434203 100644 --- a/Source/Utils/Interpolation_1D.H +++ b/Source/Utils/Interpolation_1D.H @@ -12,9 +12,7 @@ AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE amrex::Real interpolate_1d (const amrex::Real* alpha, const amrex::Real* beta, const amrex::Real alpha_interp, const int alpha_size) { - using namespace amrex; - - amrex::Real beta_interp; + amrex::Real beta_interp = -1.0e34; // If the interpolation point already exists in the array, // just return it @@ -42,6 +40,7 @@ amrex::Real interpolate_1d (const amrex::Real* alpha, const amrex::Real* beta, amrex::Real x0 = alpha[i]; amrex::Real x1 = alpha[i + 1]; beta_interp = y0 + (y1 - y0)*(x - x0) / (x1 - x0); + return beta_interp; } } } @@ -64,6 +63,7 @@ amrex::Real interpolate_1d (const amrex::Real* alpha, const amrex::Real* beta, amrex::Real x0 = alpha[i]; amrex::Real x1 = alpha[i + 1]; beta_interp = y0 + ((x - x0) / (x1 - x0)) * (y1 - y0); + return beta_interp; } return beta_interp; From 0f9a43757c9fcb6bcc3e85689f07fe669ec70350 Mon Sep 17 00:00:00 2001 From: AMLattanzi Date: Thu, 18 Jul 2024 12:43:58 -0700 Subject: [PATCH 2/4] This ran a step in debug mode. --- Exec/ABL/Backtrace.0 | 54 --- Exec/ABL/input_ReTau2000DNS_sounding.txt | 385 ------------------ Exec/ABL/input_ReTau2000DNS_sponge.txt | 384 ----------------- Exec/ABL/input_ReTau2000DNS_xlo.txt | 384 ----------------- Exec/ABL/input_ReTau2000DNS_xlo_w.txt | 385 ------------------ Exec/ABL/input_ReTau2000DNS_xlo_w.txt~ | 384 ----------------- Exec/ABL/toc_inout_inputs | 100 ----- Exec/ABL/xlo_dirichlet_face | 384 ----------------- .../BoundaryConditions_xvel.cpp | 7 +- .../BoundaryConditions_yvel.cpp | 6 +- .../BoundaryConditions_zvel.cpp | 6 +- Source/BoundaryConditions/ERF_FillPatch.cpp | 24 +- Source/BoundaryConditions/ERF_PhysBCFunct.H | 65 ++- Source/BoundaryConditions/ERF_PhysBCFunct.cpp | 14 +- Source/ERF.H | 4 +- Source/ERF.cpp | 2 +- Source/ERF_make_new_arrays.cpp | 22 +- Source/Initialization/ERF_init_bcs.cpp | 84 ++-- 18 files changed, 120 insertions(+), 2574 deletions(-) delete mode 100644 Exec/ABL/Backtrace.0 delete mode 100644 Exec/ABL/input_ReTau2000DNS_sounding.txt delete mode 100644 Exec/ABL/input_ReTau2000DNS_sponge.txt delete mode 100644 Exec/ABL/input_ReTau2000DNS_xlo.txt delete mode 100644 Exec/ABL/input_ReTau2000DNS_xlo_w.txt delete mode 100644 Exec/ABL/input_ReTau2000DNS_xlo_w.txt~ delete mode 100644 Exec/ABL/toc_inout_inputs delete mode 100644 Exec/ABL/xlo_dirichlet_face diff --git a/Exec/ABL/Backtrace.0 b/Exec/ABL/Backtrace.0 deleted file mode 100644 index ddfc474b9..000000000 --- a/Exec/ABL/Backtrace.0 +++ /dev/null @@ -1,54 +0,0 @@ -Host Name: ghidorah -=== If no file names and line numbers are shown below, one can run - addr2line -Cpfie my_exefile my_line_address - to convert `my_line_address` (e.g., 0x4a6b) into file name and line number. - Or one can use amrex/Tools/Backtrace/parse_bt.py. - -=== Please note that the line number reported by addr2line may not be accurate. - One can use - readelf -wl my_exefile | grep my_line_address' - to find out the offset for that line. - - 0: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0xc73b4a) [0x567beb158b4a] - amrex::BLBackTrace::print_backtrace_info(_IO_FILE*) at /home/amlattanzi/git/amrex/Src/Base/AMReX_BLBackTrace.cpp:190 - - 1: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0xc7354a) [0x567beb15854a] - amrex::BLBackTrace::handler(int) at /home/amlattanzi/git/amrex/Src/Base/AMReX_BLBackTrace.cpp:100 - - 2: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0xa5f860) [0x567beaf44860] - amrex::ParallelDescriptor::Abort(int, bool) at /home/amlattanzi/git/amrex/Src/Base/AMReX_ParallelDescriptor.cpp:219 - - 3: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x9e0070) [0x567beaec5070] - amrex::Assert_host(char const*, char const*, int, char const*) at /home/amlattanzi/git/amrex/Src/Base/AMReX.cpp:292 - - 4: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x4e19c) [0x567bea53319c] - amrex::Assert(char const*, char const*, int, char const*) at /home/amlattanzi/git/amrex/Src/Base/AMReX.H:183 (discriminator 1) - (inlined by) amrex::Vector >::operator[](unsigned long) at /home/amlattanzi/git/amrex/Src/Base/AMReX_Vector.H:35 (discriminator 1) - - 5: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x7c54b4) [0x567beacaa4b4] - ERF::init_Dirichlet_bc_data(amrex::Orientation, std::__cxx11::basic_string, std::allocator >) at /home/amlattanzi/git/ERF/Exec/ABL/../../Source/Initialization/ERF_init_bcs.cpp:677 - - 6: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x7bcead) [0x567beaca1ead] - ERF::init_bcs()::{lambda(std::__cxx11::basic_string, std::allocator > const&, amrex::Orientation)#1}::operator()(std::__cxx11::basic_string, std::allocator > const&, amrex::Orientation) const at /home/amlattanzi/git/ERF/Exec/ABL/../../Source/Initialization/ERF_init_bcs.cpp:105 (discriminator 3) - - 7: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x7be4d1) [0x567beaca34d1] - ERF::init_bcs() at /home/amlattanzi/git/ERF/Exec/ABL/../../Source/Initialization/ERF_init_bcs.cpp:263 (discriminator 4) - - 8: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x2466a) [0x567bea50966a] - ERF::InitData() at /home/amlattanzi/git/ERF/Exec/ABL/../../Source/ERF.cpp:575 - - 9: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x1a6d3) [0x567bea4ff6d3] - main at /home/amlattanzi/git/ERF/Exec/ABL/../../Source/main.cpp:227 - -10: /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7bfcdd029d90] - -11: /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7bfcdd029e40] - -12: ./ERF3d.gnu.DEBUG.TPROF.MPI.ex(+0x19eb5) [0x567bea4feeb5] - ?? ??:0 - - -===== TinyProfilers ====== -main() -ERF::InitData() - diff --git a/Exec/ABL/input_ReTau2000DNS_sounding.txt b/Exec/ABL/input_ReTau2000DNS_sounding.txt deleted file mode 100644 index 6585d799e..000000000 --- a/Exec/ABL/input_ReTau2000DNS_sounding.txt +++ /dev/null @@ -1,385 +0,0 @@ -0.0 300.0 0.0 0.0 0.0 -1.217311652923492e-06 300.0 0.0 0.00011140613491415374 0.0 -6.086537518545931e-06 300.0 0.0 0.0005570274195276387 0.0 -1.704221791976046e-05 300.0 0.0 0.001559660241516003 0.0 -3.651878945154508e-05 300.0 0.0 0.0033420734502807845 0.0 -6.69505434929274e-05 300.0 0.0 0.0061269859333703105 0.0 -0.0001107715847206148 300.0 0.0 0.010137027830325164 0.0 -0.0001704157896263991 300.0 0.0 0.015594654328461917 0.0 -0.0002470994533848581 300.0 0.0 0.022610560551618166 0.0 -0.0003408212691252688 300.0 0.0 0.03118329599615294 0.0 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------------------ INPUTS TO MAIN PROGRAM ------------------- -start_time = 0. -stop_time = 0.5 -#stop_time = 35.0 - -#stop_time = 10.0 - -#max_step = 1000 - -#erf.incompressible = 1 - -amrex.fpe_trap_invalid = 1 - -fabarray.mfiter_tile_size = 1024 1024 1024 - -# PROBLEM SIZE & GEOMETRY -geometry.prob_extent = 20. 1. 1. -amr.n_cell = 512 32 64 - -geometry.is_periodic = 0 1 0 - -xlo.type = "Inflow" -xhi.type = "Outflow" -zlo.type = "NoSlipWall" -zhi.type = "SlipWall" - -xlo.dirichlet_file = "input_ReTau2000DNS_xlo_w.txt" - -# TIME STEP CONTROL -erf.no_substepping = 1 -erf.cfl = 0.5 - -erf.dynamicViscosity = 0.0001 # H = 1, therefore utau = 0.2 - -# DIAGNOSTICS & VERBOSITY -erf.sum_interval = 100 # timesteps between computing mass -erf.pert_interval = 100 # timesteps between perturbation output message -erf.v = 0 # verbosity in ERF.cpp -amr.v = 0 # verbosity in Amr.cpp - -# REFINEMENT / REGRIDDING -amr.max_level = 0 # maximum level number allowed - -# PLOTFILES -erf.plot_file_1 = plt # prefix of plotfile name -#erf.plot_per_1 = 0.1 -erf.plot_int_1 = 100 -erf.plot_vars_1 = density rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta - -# CHECKPOINT FILES -erf.check_file = chk # root name of checkpoint file -erf.check_per = 1.0 - -# SOLVER CHOICE -erf.alpha_T = 0.0 -erf.alpha_C = 1.0 -erf.use_gravity = false - -erf.molec_diff_type = "None" -erf.les_type = "Smagorinsky" -erf.Cs = 0.1 - -# Buoyancy type -erf.buoyancy_type = 1 - -# Initial condition for the entire field -erf.init_type = "input_sounding" -erf.input_sounding_file = "input_ReTau2000DNS_sounding.txt" - -# Inflow boundary condition -erf.sponge_type = "input_sponge" -erf.input_sponge_file = "input_ReTau2000DNS_sponge.txt" -erf.sponge_strength = 25000.0 -#erf.use_xlo_sponge_damping = true -#erf.xlo_sponge_end = 2.0 - - - -erf.use_xhi_sponge_damping = true -erf.xhi_sponge_start = 18.0 - -# Turbulent inflow generation -#erf.perturbation_type = "source" -#erf.perturbation_direction = 1 0 0 -#erf.perturbation_layers = 3 -#erf.perturbation_offset = 32 - -#erf.perturbation_box_dims = 6 4 8 # 0.25 0.25 0.125 -#erf.perturbation_nondimensional = 0.042 # Ri -#erf.perturbation_nondimensional = 0.1 # Ri -#erf.perturbation_T_infinity = 300.0 -#erf.perturbation_T_intensity = 0.1 - -# PROBLEM PARAMETERS -prob.rho_0 = 1.0 -prob.A_0 = 1.0 -prob.U_0 = 0.0 -prob.V_0 = 0.0 -prob.W_0 = 0.0 -prob.T_0 = 300.0 diff --git a/Exec/ABL/xlo_dirichlet_face b/Exec/ABL/xlo_dirichlet_face deleted file mode 100644 index 737895f86..000000000 --- a/Exec/ABL/xlo_dirichlet_face +++ /dev/null @@ -1,384 +0,0 @@ -0.0 0.0 0.0 -1.217311652923492e-06 0.00011140613491415374 0.0 -6.086537518545931e-06 0.0005570274195276387 0.0 -1.704221791976046e-05 0.001559660241516003 0.0 -3.651878945154508e-05 0.0033420734502807845 0.0 -6.69505434929274e-05 0.0061269859333703105 0.0 -0.0001107715847206148 0.010137027830325164 0.0 -0.0001704157896263991 0.015594654328461917 0.0 -0.0002470994533848581 0.022610560551618166 0.0 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-0.9690441819093016 1.118911351122682 0.0 -0.9731705573948156 1.1190000308462351 0.0 -0.9772973901174332 1.119075791838296 0.0 -0.9814246097461727 1.1191387316178165 0.0 -0.9855521459434584 1.1191889672245374 0.0 -0.9896799283663196 1.1192266886822442 0.0 -0.9938078866675891 1.119251954837764 0.0 -0.9979359504971027 1.1192646414784726 0.0 diff --git a/Source/BoundaryConditions/BoundaryConditions_xvel.cpp b/Source/BoundaryConditions/BoundaryConditions_xvel.cpp index 2a974fd52..a1a52f599 100644 --- a/Source/BoundaryConditions/BoundaryConditions_xvel.cpp +++ b/Source/BoundaryConditions/BoundaryConditions_xvel.cpp @@ -15,8 +15,7 @@ using namespace amrex; */ void ERFPhysBCFunct_u::impose_lateral_xvel_bcs (const Array4& dest_arr, - const Box& bx, const Box& domain, int bccomp, - Vector>& xvel_bc_data) + const Box& bx, const Box& domain, int bccomp) { BL_PROFILE_VAR("impose_lateral_xvel_bcs()",impose_lateral_xvel_bcs); const auto& dom_lo = lbound(domain); @@ -53,8 +52,8 @@ void ERFPhysBCFunct_u::impose_lateral_xvel_bcs (const Array4& dest_arr, // First do all ext_dir bcs if (!is_periodic_in_x) { - Real* xvel_xlo_ptr = xvel_bc_data[0].data(); - Real* xvel_xhi_ptr = xvel_bc_data[3].data(); + Real* xvel_xlo_ptr = m_u_bc_data[0]; + Real* xvel_xhi_ptr = m_u_bc_data[3]; Box bx_xlo(bx); bx_xlo.setBig (0,dom_lo.x-1); Box bx_xhi(bx); bx_xhi.setSmall(0,dom_hi.x+2); Box bx_xlo_face(bx); bx_xlo_face.setSmall(0,dom_lo.x ); bx_xlo_face.setBig(0,dom_lo.x ); diff --git a/Source/BoundaryConditions/BoundaryConditions_yvel.cpp b/Source/BoundaryConditions/BoundaryConditions_yvel.cpp index 7c333f871..8ccdc549b 100644 --- a/Source/BoundaryConditions/BoundaryConditions_yvel.cpp +++ b/Source/BoundaryConditions/BoundaryConditions_yvel.cpp @@ -13,7 +13,7 @@ using namespace amrex; */ void ERFPhysBCFunct_v::impose_lateral_yvel_bcs (const Array4& dest_arr, const Box& bx, const Box& domain, - int bccomp, Vector>& yvel_bc_data) + int bccomp) { BL_PROFILE_VAR("impose_lateral_yvel_bcs()",impose_lateral_yvel_bcs); const auto& dom_lo = lbound(domain); @@ -51,8 +51,8 @@ void ERFPhysBCFunct_v::impose_lateral_yvel_bcs (const Array4& dest_arr, if (!is_periodic_in_x) { // Populate ghost cells on lo-x and hi-x domain boundaries - Real* yvel_xlo_ptr = yvel_bc_data[0].data(); - Real* yvel_xhi_ptr = yvel_bc_data[3].data(); + Real* yvel_xlo_ptr = m_v_bc_data[0]; + Real* yvel_xhi_ptr = m_v_bc_data[3]; Box bx_xlo(bx); bx_xlo.setBig (0,dom_lo.x-1); Box bx_xhi(bx); bx_xhi.setSmall(0,dom_hi.x+1); ParallelFor( diff --git a/Source/BoundaryConditions/BoundaryConditions_zvel.cpp b/Source/BoundaryConditions/BoundaryConditions_zvel.cpp index e8f3ddeb1..14ea1564c 100644 --- a/Source/BoundaryConditions/BoundaryConditions_zvel.cpp +++ b/Source/BoundaryConditions/BoundaryConditions_zvel.cpp @@ -19,7 +19,7 @@ void ERFPhysBCFunct_w::impose_lateral_zvel_bcs (const Array4& dest_a const Box& bx, const Box& domain, const Array4& z_phys_nd, const GpuArray dxInv, - int bccomp, Vector>& zvel_bc_data) + int bccomp) { BL_PROFILE_VAR("impose_lateral_zvel_bcs()",impose_lateral_zvel_bcs); const auto& dom_lo = lbound(domain); @@ -60,8 +60,8 @@ void ERFPhysBCFunct_w::impose_lateral_zvel_bcs (const Array4& dest_a // First do all ext_dir bcs if (!is_periodic_in_x) { - Real* zvel_xlo_ptr = zvel_bc_data[0].data(); - Real* zvel_xhi_ptr = zvel_bc_data[3].data(); + Real* zvel_xlo_ptr = m_w_bc_data[0]; + Real* zvel_xhi_ptr = m_w_bc_data[3]; Box bx_xlo(bx); bx_xlo.setBig (0,dom_lo.x-1); Box bx_xhi(bx); bx_xhi.setSmall(0,dom_hi.x+1); ParallelFor( diff --git a/Source/BoundaryConditions/ERF_FillPatch.cpp b/Source/BoundaryConditions/ERF_FillPatch.cpp index 9cdf0c5e5..8154338e5 100644 --- a/Source/BoundaryConditions/ERF_FillPatch.cpp +++ b/Source/BoundaryConditions/ERF_FillPatch.cpp @@ -108,7 +108,7 @@ ERF::FillPatch (int lev, Real time, FillPatchSingleLevel(*mfs_vel[Vars::zvel], time, fmf, ftime, icomp, icomp, ncomp_w, geom[lev], *physbcs_w_no_terrain[lev], BCVars::zvel_bc); (*physbcs_w[lev])(*mfs_vel[Vars::zvel],*mfs_vel[Vars::xvel],*mfs_vel[Vars::yvel], - ngvect_vels,time,BCVars::zvel_bc,zvel_bc_data); + ngvect_vels,time,BCVars::zvel_bc); } // !cons_only } else { @@ -161,7 +161,7 @@ ERF::FillPatch (int lev, Real time, *physbcs_w_no_terrain[lev ], BCVars::zvel_bc, refRatio(lev-1), mapper, domain_bcs_type, BCVars::zvel_bc); (*physbcs_w[lev])(*mfs_vel[Vars::zvel],*mfs_vel[Vars::xvel],*mfs_vel[Vars::yvel], - ngvect_vels,time,BCVars::zvel_bc,zvel_bc_data); + ngvect_vels,time,BCVars::zvel_bc); } // !cons_only } // lev > 0 @@ -183,10 +183,10 @@ ERF::FillPatch (int lev, Real time, // We call these even if init_type == real because these will fill the vertical bcs (*physbcs_cons[lev])(*mfs_vel[Vars::cons],icomp_cons,ncomp_cons,ngvect_cons,time,BCVars::cons_bc); if (!cons_only) { - (*physbcs_u[lev])(*mfs_vel[Vars::xvel],0,1,ngvect_vels,time,BCVars::xvel_bc, xvel_bc_data); - (*physbcs_v[lev])(*mfs_vel[Vars::yvel],0,1,ngvect_vels,time,BCVars::yvel_bc, yvel_bc_data); + (*physbcs_u[lev])(*mfs_vel[Vars::xvel],0,1,ngvect_vels,time,BCVars::xvel_bc); + (*physbcs_v[lev])(*mfs_vel[Vars::yvel],0,1,ngvect_vels,time,BCVars::yvel_bc); (*physbcs_w[lev])(*mfs_vel[Vars::zvel],*mfs_vel[Vars::xvel],*mfs_vel[Vars::yvel], - ngvect_vels,time,BCVars::zvel_bc, zvel_bc_data); + ngvect_vels,time,BCVars::zvel_bc); } } @@ -384,7 +384,7 @@ ERF::FillIntermediatePatch (int lev, Real time, *physbcs_w_no_terrain[lev ], BCVars::zvel_bc, refRatio(lev-1), mapper, domain_bcs_type, bccomp); (*physbcs_w[lev])(*mfs_vel[Vars::zvel],*mfs_vel[Vars::xvel],*mfs_vel[Vars::yvel], - ngvect,time,BCVars::zvel_bc,zvel_bc_data); + ngvect,time,BCVars::zvel_bc); } } // lev > 0 } // var_idx @@ -407,10 +407,10 @@ ERF::FillIntermediatePatch (int lev, Real time, // We call this even if init_type == real because this routine will fill the vertical bcs (*physbcs_cons[lev])(*mfs_vel[Vars::cons],icomp_cons,ncomp_cons,ngvect_cons,time,BCVars::cons_bc); if (!cons_only) { - (*physbcs_u[lev])(*mfs_vel[Vars::xvel],0,1,ngvect_vels,time,BCVars::xvel_bc,xvel_bc_data); - (*physbcs_v[lev])(*mfs_vel[Vars::yvel],0,1,ngvect_vels,time,BCVars::yvel_bc,yvel_bc_data); + (*physbcs_u[lev])(*mfs_vel[Vars::xvel],0,1,ngvect_vels,time,BCVars::xvel_bc); + (*physbcs_v[lev])(*mfs_vel[Vars::yvel],0,1,ngvect_vels,time,BCVars::yvel_bc); (*physbcs_w[lev])(*mfs_vel[Vars::zvel],*mfs_vel[Vars::xvel],*mfs_vel[Vars::yvel], - ngvect_vels,time,BCVars::zvel_bc,zvel_bc_data); + ngvect_vels,time,BCVars::zvel_bc); } // *************************************************************************** @@ -564,10 +564,10 @@ ERF::FillCoarsePatch (int lev, Real time) int ncomp_cons = vars_new[lev][Vars::cons].nComp(); (*physbcs_cons[lev])(vars_new[lev][Vars::cons],0,ncomp_cons,ngvect_cons,time,BCVars::cons_bc); - ( *physbcs_u[lev])(vars_new[lev][Vars::xvel],0,1 ,ngvect_vels,time,BCVars::xvel_bc,xvel_bc_data); - ( *physbcs_v[lev])(vars_new[lev][Vars::yvel],0,1 ,ngvect_vels,time,BCVars::yvel_bc,yvel_bc_data); + ( *physbcs_u[lev])(vars_new[lev][Vars::xvel],0,1 ,ngvect_vels,time,BCVars::xvel_bc); + ( *physbcs_v[lev])(vars_new[lev][Vars::yvel],0,1 ,ngvect_vels,time,BCVars::yvel_bc); ( *physbcs_w[lev])(vars_new[lev][Vars::zvel],vars_new[lev][Vars::xvel],vars_new[lev][Vars::yvel], - ngvect_vels,time,BCVars::zvel_bc,zvel_bc_data); + ngvect_vels,time,BCVars::zvel_bc); // *************************************************************************** // Since lev > 0 here we don't worry about m_r2d or wrfbdy data diff --git a/Source/BoundaryConditions/ERF_PhysBCFunct.H b/Source/BoundaryConditions/ERF_PhysBCFunct.H index 0119c3c99..ad7e2bd70 100644 --- a/Source/BoundaryConditions/ERF_PhysBCFunct.H +++ b/Source/BoundaryConditions/ERF_PhysBCFunct.H @@ -83,7 +83,8 @@ public: amrex::Array,AMREX_SPACEDIM+NVAR_max> bc_extdir_vals, amrex::Array,AMREX_SPACEDIM+NVAR_max> bc_neumann_vals, std::unique_ptr& z_phys_nd, - const bool use_real_bcs) + const bool use_real_bcs, + amrex::Vector u_bc_data) : m_lev(lev), m_geom(geom), m_domain_bcs_type(domain_bcs_type), m_domain_bcs_type_d(domain_bcs_type_d), @@ -91,7 +92,13 @@ public: m_bc_neumann_vals(bc_neumann_vals), m_z_phys_nd(z_phys_nd.get()), m_use_real_bcs(use_real_bcs) - {} + { + int nval = u_bc_data.size(); + m_u_bc_data.resize(nval); + for (int ival(0); ival>& xvel_bc_data); + amrex::IntVect const& nghost, const amrex::Real time, int bccomp); void impose_lateral_xvel_bcs (const amrex::Array4& dest_arr, const amrex::Box& bx, const amrex::Box& domain, - int bccomp, amrex::Vector>& xvel_bc_data); + int bccomp); void impose_vertical_xvel_bcs (const amrex::Array4& dest_arr, const amrex::Box& bx, const amrex::Box& domain, const amrex::Array4& z_nd, @@ -126,6 +132,7 @@ private: amrex::Array,AMREX_SPACEDIM+NVAR_max> m_bc_neumann_vals; amrex::MultiFab* m_z_phys_nd; bool m_use_real_bcs; + amrex::Vector m_u_bc_data; }; class ERFPhysBCFunct_v @@ -137,7 +144,8 @@ public: amrex::Array,AMREX_SPACEDIM+NVAR_max> bc_extdir_vals, amrex::Array,AMREX_SPACEDIM+NVAR_max> bc_neumann_vals, std::unique_ptr& z_phys_nd, - const bool use_real_bcs) + const bool use_real_bcs, + amrex::Vector v_bc_data) : m_lev(lev), m_geom(geom), m_domain_bcs_type(domain_bcs_type), m_domain_bcs_type_d(domain_bcs_type_d), @@ -145,7 +153,13 @@ public: m_bc_neumann_vals(bc_neumann_vals), m_z_phys_nd(z_phys_nd.get()), m_use_real_bcs(use_real_bcs) - {} + { + int nval = v_bc_data.size(); + m_v_bc_data.resize(nval); + for (int ival(0); ival>& yvel_bc_data); + amrex::IntVect const& nghost, const amrex::Real time, int bccomp); void impose_lateral_yvel_bcs (const amrex::Array4& dest_arr, const amrex::Box& bx, const amrex::Box& domain, - int bccomp, - amrex::Vector>& yvel_bc_data); + int bccomp); void impose_vertical_yvel_bcs (const amrex::Array4& dest_arr, const amrex::Box& bx, const amrex::Box& domain, const amrex::Array4& z_nd, @@ -182,6 +194,7 @@ private: amrex::Array,AMREX_SPACEDIM+NVAR_max> m_bc_neumann_vals; amrex::MultiFab* m_z_phys_nd; bool m_use_real_bcs; + amrex::Vector m_v_bc_data; }; class ERFPhysBCFunct_w @@ -193,7 +206,8 @@ public: amrex::Array,AMREX_SPACEDIM+NVAR_max> bc_extdir_vals, amrex::Array,AMREX_SPACEDIM+NVAR_max> bc_neumann_vals, const TerrainType& terrain_type, std::unique_ptr& z_phys_nd, - const bool use_real_bcs) + const bool use_real_bcs, + amrex::Vector w_bc_data) : m_lev(lev), m_geom(geom), m_domain_bcs_type(domain_bcs_type), m_domain_bcs_type_d(domain_bcs_type_d), @@ -202,7 +216,13 @@ public: m_terrain_type(terrain_type), m_z_phys_nd(z_phys_nd.get()), m_use_real_bcs(use_real_bcs) - {} + { + int nval = w_bc_data.size(); + m_w_bc_data.resize(nval); + for (int ival(0); ival>& zvel_bc_data); + amrex::IntVect const& nghost, const amrex::Real time, int bccomp); void impose_lateral_zvel_bcs (const amrex::Array4& dest_arr, const amrex::Array4& xvel_arr, @@ -226,8 +245,7 @@ public: const amrex::Box& bx, const amrex::Box& domain, const amrex::Array4& z_nd, const amrex::GpuArray dxInv, - int bccomp, - amrex::Vector>& zvel_bc_data); + int bccomp); void impose_vertical_zvel_bcs (const amrex::Array4& dest_arr, const amrex::Array4& xvel_arr, const amrex::Array4& yvel_arr, @@ -247,6 +265,7 @@ private: TerrainType m_terrain_type; amrex::MultiFab* m_z_phys_nd; bool m_use_real_bcs; + amrex::Vector m_w_bc_data; }; class ERFPhysBCFunct_w_no_terrain @@ -258,14 +277,21 @@ public: const amrex::Gpu::DeviceVector& domain_bcs_type_d, amrex::Array,AMREX_SPACEDIM+NVAR_max> bc_extdir_vals, amrex::Array,AMREX_SPACEDIM+NVAR_max> bc_neumann_vals, - const bool use_real_bcs) + const bool use_real_bcs, + amrex::Vector w_bc_data) : m_lev(lev), m_geom(geom), m_domain_bcs_type(domain_bcs_type), m_domain_bcs_type_d(domain_bcs_type_d), m_bc_extdir_vals(bc_extdir_vals), m_bc_neumann_vals(bc_neumann_vals), m_use_real_bcs(use_real_bcs) - {} + { + int nval = w_bc_data.size(); + m_w_bc_data.resize(nval); + for (int ival(0); ival,AMREX_SPACEDIM+NVAR_max> m_bc_extdir_vals; amrex::Array,AMREX_SPACEDIM+NVAR_max> m_bc_neumann_vals; bool m_use_real_bcs; + amrex::Vector m_w_bc_data; }; #endif diff --git a/Source/BoundaryConditions/ERF_PhysBCFunct.cpp b/Source/BoundaryConditions/ERF_PhysBCFunct.cpp index 2cba3662c..614f00b10 100644 --- a/Source/BoundaryConditions/ERF_PhysBCFunct.cpp +++ b/Source/BoundaryConditions/ERF_PhysBCFunct.cpp @@ -91,8 +91,7 @@ void ERFPhysBCFunct_cons::operator() (MultiFab& mf, int icomp, int ncomp, } // operator() void ERFPhysBCFunct_u::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, - IntVect const& nghost, const Real time, int bccomp, - Vector>& xvel_bc_data) + IntVect const& nghost, const Real time, int bccomp) { BL_PROFILE("ERFPhysBCFunct_u::()"); @@ -159,7 +158,7 @@ void ERFPhysBCFunct_u::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, { if (!gdomainx.contains(xbx1)) { - impose_lateral_xvel_bcs(velx_arr,xbx1,domain,bccomp, xvel_bc_data); + impose_lateral_xvel_bcs(velx_arr,xbx1,domain,bccomp); } } @@ -171,8 +170,7 @@ void ERFPhysBCFunct_u::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, } // operator() void ERFPhysBCFunct_v::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, - IntVect const& nghost, const Real /*time*/, int bccomp, - Vector>& yvel_bc_data) + IntVect const& nghost, const Real /*time*/, int bccomp) { BL_PROFILE("ERFPhysBCFunct_v::()"); @@ -237,7 +235,7 @@ void ERFPhysBCFunct_v::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, if (!m_use_real_bcs) { - impose_lateral_yvel_bcs(vely_arr,ybx1,domain,bccomp, yvel_bc_data); + impose_lateral_yvel_bcs(vely_arr,ybx1,domain,bccomp); } impose_vertical_yvel_bcs(vely_arr,ybx2,domain,z_nd_arr,dxInv,bccomp); @@ -249,7 +247,7 @@ void ERFPhysBCFunct_v::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, void ERFPhysBCFunct_w::operator() (MultiFab& mf, MultiFab& xvel, MultiFab& yvel, IntVect const& nghost, const Real /*time*/, - const int bccomp_w, Vector>& zvel_bc_data) + const int bccomp_w) { BL_PROFILE("ERFPhysBCFunct_w::()"); @@ -319,7 +317,7 @@ void ERFPhysBCFunct_w::operator() (MultiFab& mf, MultiFab& xvel, MultiFab& yvel, { if (!gdomainz.contains(zbx)) { - impose_lateral_zvel_bcs(velz_arr,velx_arr,vely_arr,zbx,domain,z_nd_arr,dxInv,bccomp_w,zvel_bc_data); + impose_lateral_zvel_bcs(velz_arr,velx_arr,vely_arr,zbx,domain,z_nd_arr,dxInv,bccomp_w); } } // m_use_real_bcs diff --git a/Source/ERF.H b/Source/ERF.H index e1b61b683..9c31d6182 100644 --- a/Source/ERF.H +++ b/Source/ERF.H @@ -584,8 +584,8 @@ private: amrex::Vector> xvel_bc_data; amrex::Vector> yvel_bc_data; amrex::Vector> zvel_bc_data; - - // Function to read and populate above vectors (if input file exists) + + // Function to read and populate above vectors (if input file exists) void init_Dirichlet_bc_data (amrex::Orientation ori, const std::string input_file); diff --git a/Source/ERF.cpp b/Source/ERF.cpp index dcf520e85..7e072569e 100644 --- a/Source/ERF.cpp +++ b/Source/ERF.cpp @@ -310,7 +310,7 @@ ERF::ERF () xvel_bc_data.resize(nfaces); yvel_bc_data.resize(nfaces); zvel_bc_data.resize(nfaces); - + // Initialize tagging criteria for mesh refinement refinement_criteria_setup(); diff --git a/Source/ERF_make_new_arrays.cpp b/Source/ERF_make_new_arrays.cpp index 138f69499..4cab94eca 100644 --- a/Source/ERF_make_new_arrays.cpp +++ b/Source/ERF_make_new_arrays.cpp @@ -473,19 +473,33 @@ ERF::initialize_integrator (int lev, MultiFab& cons_mf, MultiFab& vel_mf) void ERF::initialize_bcs (int lev) { + // Dirichlet BC data only lives on level 0 + int nface = 6; // 6 faces + Vector u_bc_tmp; u_bc_tmp.resize(nface,nullptr); + Vector v_bc_tmp; v_bc_tmp.resize(nface,nullptr); + Vector w_bc_tmp; w_bc_tmp.resize(nface,nullptr); + if (lev==0) { + for (int iface(0); iface (lev, geom[lev], domain_bcs_type, domain_bcs_type_d, m_bc_extdir_vals, m_bc_neumann_vals, z_phys_nd[lev], use_real_bcs); physbcs_u[lev] = std::make_unique (lev, geom[lev], domain_bcs_type, domain_bcs_type_d, m_bc_extdir_vals, m_bc_neumann_vals, - z_phys_nd[lev], use_real_bcs); + z_phys_nd[lev], use_real_bcs, u_bc_tmp); physbcs_v[lev] = std::make_unique (lev, geom[lev], domain_bcs_type, domain_bcs_type_d, m_bc_extdir_vals, m_bc_neumann_vals, - z_phys_nd[lev], use_real_bcs); + z_phys_nd[lev], use_real_bcs, v_bc_tmp); physbcs_w[lev] = std::make_unique (lev, geom[lev], domain_bcs_type, domain_bcs_type_d, m_bc_extdir_vals, m_bc_neumann_vals, - solverChoice.terrain_type, z_phys_nd[lev], use_real_bcs); + solverChoice.terrain_type, z_phys_nd[lev], + use_real_bcs, w_bc_tmp); physbcs_w_no_terrain[lev] = std::make_unique (lev, geom[lev], domain_bcs_type, domain_bcs_type_d, - m_bc_extdir_vals, m_bc_neumann_vals, use_real_bcs); + m_bc_extdir_vals, m_bc_neumann_vals, use_real_bcs, + w_bc_tmp); } diff --git a/Source/Initialization/ERF_init_bcs.cpp b/Source/Initialization/ERF_init_bcs.cpp index 7410dfb5c..c32799f29 100644 --- a/Source/Initialization/ERF_init_bcs.cpp +++ b/Source/Initialization/ERF_init_bcs.cpp @@ -96,7 +96,7 @@ void ERF::init_bcs () if (input_bndry_planes && m_r2d->ingested_velocity()) { m_bc_extdir_vals[BCVars::xvel_bc][ori] = 0.; m_bc_extdir_vals[BCVars::yvel_bc][ori] = 0.; - m_bc_extdir_vals[BCVars::zvel_bc][ori] = 0.; + m_bc_extdir_vals[BCVars::zvel_bc][ori] = 0.; } else { // Test for input data file if at xlo face std::string dirichlet_file; @@ -563,10 +563,9 @@ void ERF::init_bcs () void ERF::init_Dirichlet_bc_data (Orientation ori, const std::string input_file) { - Print() << "START\n"; // Only on coarsest level! int lev = 0; - + const int klo = 0; const int khi = geom[lev].Domain().bigEnd()[2]; const int Nz = geom[lev].Domain().size()[2]; @@ -576,11 +575,14 @@ void ERF::init_Dirichlet_bc_data (Orientation ori, const Real zbot = (use_terrain) ? zlevels_stag[klo] : geom[lev].ProbLo(2); const Real ztop = (use_terrain) ? zlevels_stag[khi+1] : geom[lev].ProbHi(2); - Vector z_inp(Nz+2); - Vector u_inp(Nz+2); - Vector v_inp(Nz+2); - Vector w_inp(Nz+2); + // Size of Nz (domain grid) + Vector zcc_inp(Nz ); + Vector znd_inp(Nz+1); + Vector u_inp(Nz ); xvel_bc_data[ori].resize(Nz ,0.0); + Vector v_inp(Nz ); yvel_bc_data[ori].resize(Nz ,0.0); + Vector w_inp(Nz+1); zvel_bc_data[ori].resize(Nz+1,0.0); + // Size of Ninp (number of z points in input file) Vector z_inp_tmp, u_inp_tmp, v_inp_tmp, w_inp_tmp; // Read the dirichlet_input file @@ -589,12 +591,10 @@ void ERF::init_Dirichlet_bc_data (Orientation ori, if(!input_reader.is_open()) { Error("Error opening the dirichlet_input file.\n"); } else { - // Read the contents of the input file Print() << "Successfully opened the dirichlet_input file. Now reading... " << std::endl; std::string line; - // First, read the input data into temp vectors; then, interpolate vectors to the - // domain lo/hi and cell centers (from level 0) + // First, read the input data into temp vectors; (Ninp from size of input file) // Add surface z_inp_tmp.push_back(zbot); // height above sea level [m] @@ -624,58 +624,26 @@ void ERF::init_Dirichlet_bc_data (Orientation ori, // At this point, we have an input from zbot up to // z_inp_tmp[N-1] >= ztop. Now, interpolate to grid level 0 heights const int Ninp = z_inp_tmp.size(); - z_inp[0] = zbot; - u_inp[0] = u_inp_tmp[0]; - v_inp[0] = v_inp_tmp[0]; - w_inp[0] = w_inp_tmp[0]; - for (int k=0; k < Nz; ++k) { - z_inp[k+1] = (use_terrain) ? 0.5 * (zlevels_stag[k] + zlevels_stag[k+1]) - : zbot + (k + 0.5) * dz; - u_inp[k+1] = interpolate_1d(z_inp_tmp.dataPtr(), u_inp_tmp.dataPtr(), z_inp[k+1], Ninp); - v_inp[k+1] = interpolate_1d(z_inp_tmp.dataPtr(), v_inp_tmp.dataPtr(), z_inp[k+1], Ninp); - w_inp[k+1] = interpolate_1d(z_inp_tmp.dataPtr(), w_inp_tmp.dataPtr(), z_inp[k+1], Ninp); + for (int k(0); k zcc(khi+1); - Vector znd(khi+2); - - if (z_phys_cc[lev]) { - // use_terrain=1 - // calculate the damping strength based on the max height at each k - reduce_to_max_per_level(zcc, z_phys_cc[lev]); - reduce_to_max_per_level(znd, z_phys_nd[lev]); - } else { - const auto *const prob_lo = geom[lev].ProbLo(); - const auto *const dx = geom[lev].CellSize(); - for (int k = 0; k <= khi; k++) { - zcc[k] = prob_lo[2] + (k+0.5) * dx[2]; - znd[k] = prob_lo[2] + (k ) * dx[2]; - } - znd[khi+1] = prob_lo[2] + (khi+1) * dx[2]; - } - Vector u_dir_h(Nz ,0.); xvel_bc_data[ori].resize(Nz ,0.0); - Vector v_dir_h(Nz ,0.); yvel_bc_data[ori].resize(Nz ,0.0); - Vector w_dir_h(Nz+1,0.); zvel_bc_data[ori].resize(Nz+1,0.0); - for (int k = 0; k <= khi; k++) { - u_dir_h[k] = interpolate_1d(z_inp.dataPtr(), u_inp.dataPtr(), zcc[k], Nz ); - v_dir_h[k] = interpolate_1d(z_inp.dataPtr(), v_inp.dataPtr(), zcc[k], Nz ); - w_dir_h[k] = interpolate_1d(z_inp.dataPtr(), w_inp.dataPtr(), znd[k], Nz+1); - } - w_dir_h[khi+1] = interpolate_1d(z_inp.dataPtr(), w_inp.dataPtr(), znd[khi+1], Nz+1); + // Copy host data to the device + Gpu::copy(Gpu::hostToDevice, u_inp.begin(), u_inp.end(), xvel_bc_data[ori].begin()); + Gpu::copy(Gpu::hostToDevice, v_inp.begin(), v_inp.end(), yvel_bc_data[ori].begin()); + Gpu::copy(Gpu::hostToDevice, w_inp.begin(), w_inp.end(), zvel_bc_data[ori].begin()); - - // Copy from host version to device version - Gpu::copy(Gpu::hostToDevice, u_dir_h.begin(), u_dir_h.end(), xvel_bc_data[ori].begin()); - Gpu::copy(Gpu::hostToDevice, v_dir_h.begin(), v_dir_h.end(), yvel_bc_data[ori].begin()); - Gpu::copy(Gpu::hostToDevice, w_dir_h.begin(), w_dir_h.end(), zvel_bc_data[ori].begin()); + // NOTE: These device vectors are passed to the PhysBC constructors when that + // class is instantiated in ERF_make_new_arrays.cpp. } From 24eded902e503c5502fd429a41afd4b06b165bb2 Mon Sep 17 00:00:00 2001 From: AMLattanzi Date: Thu, 18 Jul 2024 12:47:09 -0700 Subject: [PATCH 3/4] clean up. --- Exec/ABL/toc_inout_inputs~ | 96 -------------------------------------- 1 file changed, 96 deletions(-) delete mode 100644 Exec/ABL/toc_inout_inputs~ diff --git a/Exec/ABL/toc_inout_inputs~ b/Exec/ABL/toc_inout_inputs~ deleted file mode 100644 index 8c89121eb..000000000 --- a/Exec/ABL/toc_inout_inputs~ +++ /dev/null @@ -1,96 +0,0 @@ -# ------------------ INPUTS TO MAIN PROGRAM ------------------- -start_time = 0. -stop_time = 0.5 -#stop_time = 35.0 - -#stop_time = 10.0 - -#max_step = 1000 - -#erf.incompressible = 1 - -amrex.fpe_trap_invalid = 1 - -fabarray.mfiter_tile_size = 1024 1024 1024 - -# PROBLEM SIZE & GEOMETRY -geometry.prob_extent = 20. 1. 1. -amr.n_cell = 512 32 64 - -geometry.is_periodic = 0 1 0 - -xlo.type = "Outflow" -xhi.type = "Outflow" -zlo.type = "NoSlipWall" -zhi.type = "SlipWall" - -# TIME STEP CONTROL -erf.no_substepping = 1 -erf.cfl = 0.5 - -erf.dynamicViscosity = 0.0001 # H = 1, therefore utau = 0.2 - -# DIAGNOSTICS & VERBOSITY -erf.sum_interval = 100 # timesteps between computing mass -erf.pert_interval = 100 # timesteps between perturbation output message -erf.v = 0 # verbosity in ERF.cpp -amr.v = 0 # verbosity in Amr.cpp - -# REFINEMENT / REGRIDDING -amr.max_level = 0 # maximum level number allowed - -# PLOTFILES -erf.plot_file_1 = plt # prefix of plotfile name -#erf.plot_per_1 = 0.1 -erf.plot_int_1 = 100 -erf.plot_vars_1 = density rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta - -# CHECKPOINT FILES -erf.check_file = chk # root name of checkpoint file -erf.check_per = 1.0 - -# SOLVER CHOICE -erf.alpha_T = 0.0 -erf.alpha_C = 1.0 -erf.use_gravity = false - -erf.molec_diff_type = "None" -erf.les_type = "Smagorinsky" -erf.Cs = 0.1 - -# Buoyancy type -erf.buoyancy_type = 1 - -# Initial condition for the entire field -erf.init_type = "input_sounding" -erf.input_sounding_file = "input_ReTau2000DNS_sounding.txt" - -# Inflow boundary condition -erf.sponge_type = "input_sponge" -erf.input_sponge_file = "input_ReTau2000DNS_sponge.txt" -erf.sponge_strength = 25000.0 -erf.use_xlo_sponge_damping = true -erf.xlo_sponge_end = 2.0 - -erf.use_xhi_sponge_damping = true -erf.xhi_sponge_start = 18.0 - -# Turbulent inflow generation -erf.perturbation_type = "source" -erf.perturbation_direction = 1 0 0 -erf.perturbation_layers = 3 -erf.perturbation_offset = 32 - -erf.perturbation_box_dims = 6 4 8 # 0.25 0.25 0.125 -#erf.perturbation_nondimensional = 0.042 # Ri -erf.perturbation_nondimensional = 0.1 # Ri -erf.perturbation_T_infinity = 300.0 -erf.perturbation_T_intensity = 0.1 - -# PROBLEM PARAMETERS -prob.rho_0 = 1.0 -prob.A_0 = 1.0 -prob.U_0 = 0.0 -prob.V_0 = 0.0 -prob.W_0 = 0.0 -prob.T_0 = 300.0 From e003fbd806923a0766b6e9e72ba6d834e332e15f Mon Sep 17 00:00:00 2001 From: AMLattanzi Date: Thu, 18 Jul 2024 12:50:23 -0700 Subject: [PATCH 4/4] more clean up. --- Source/BoundaryConditions/ERF_PhysBCFunct.cpp | 6 +++--- Source/Initialization/ERF_init_bcs.cpp | 1 - 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/Source/BoundaryConditions/ERF_PhysBCFunct.cpp b/Source/BoundaryConditions/ERF_PhysBCFunct.cpp index 614f00b10..5868dcddb 100644 --- a/Source/BoundaryConditions/ERF_PhysBCFunct.cpp +++ b/Source/BoundaryConditions/ERF_PhysBCFunct.cpp @@ -158,7 +158,7 @@ void ERFPhysBCFunct_u::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, { if (!gdomainx.contains(xbx1)) { - impose_lateral_xvel_bcs(velx_arr,xbx1,domain,bccomp); + impose_lateral_xvel_bcs(velx_arr,xbx1,domain,bccomp); } } @@ -235,7 +235,7 @@ void ERFPhysBCFunct_v::operator() (MultiFab& mf, int /*icomp*/, int /*ncomp*/, if (!m_use_real_bcs) { - impose_lateral_yvel_bcs(vely_arr,ybx1,domain,bccomp); + impose_lateral_yvel_bcs(vely_arr,ybx1,domain,bccomp); } impose_vertical_yvel_bcs(vely_arr,ybx2,domain,z_nd_arr,dxInv,bccomp); @@ -317,7 +317,7 @@ void ERFPhysBCFunct_w::operator() (MultiFab& mf, MultiFab& xvel, MultiFab& yvel, { if (!gdomainz.contains(zbx)) { - impose_lateral_zvel_bcs(velz_arr,velx_arr,vely_arr,zbx,domain,z_nd_arr,dxInv,bccomp_w); + impose_lateral_zvel_bcs(velz_arr,velx_arr,vely_arr,zbx,domain,z_nd_arr,dxInv,bccomp_w); } } // m_use_real_bcs diff --git a/Source/Initialization/ERF_init_bcs.cpp b/Source/Initialization/ERF_init_bcs.cpp index c32799f29..e008606c4 100644 --- a/Source/Initialization/ERF_init_bcs.cpp +++ b/Source/Initialization/ERF_init_bcs.cpp @@ -2,7 +2,6 @@ #include #include #include -#include using namespace amrex;