From 1526b1a2c197d22a9bb591125552f2cd2b830f22 Mon Sep 17 00:00:00 2001
From: Ann Almgren <asalmgren@lbl.gov>
Date: Wed, 17 Jul 2024 17:47:22 -0700
Subject: [PATCH] update incompressible inputs and small fixes for refinement
 and WW3 stuff (#1692)

---
 .../incompressible_inputs                        | 11 ++---------
 Source/ERF_make_new_arrays.cpp                   | 13 ++++++++++---
 Source/TimeIntegration/ERF_make_tau_terms.cpp    | 16 +++++++++++++++-
 3 files changed, 27 insertions(+), 13 deletions(-)

diff --git a/Exec/DevTests/ABL_perturbation_inflow/incompressible_inputs b/Exec/DevTests/ABL_perturbation_inflow/incompressible_inputs
index 06d3306c8..8122dba68 100644
--- a/Exec/DevTests/ABL_perturbation_inflow/incompressible_inputs
+++ b/Exec/DevTests/ABL_perturbation_inflow/incompressible_inputs
@@ -12,8 +12,8 @@ amrex.fpe_trap_invalid = 1
 fabarray.mfiter_tile_size = 1024 1024 1024
 
 # PROBLEM SIZE & GEOMETRY
-geometry.prob_extent =  16.    2.    8.
-amr.n_cell           = 128     16    64
+geometry.prob_extent =   2.    0.25    1.
+amr.n_cell           = 128     16     64
 
 geometry.is_periodic = 0 1 0
 
@@ -67,13 +67,6 @@ erf.buoyancy_type = 1
 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 = 100000.0
-erf.use_xlo_sponge_damping = true
-erf.xlo_sponge_end = 1.0
-
 # Turbulent inflow generation
 erf.perturbation_type = "source"
 erf.perturbation_direction = 1 0 0
diff --git a/Source/ERF_make_new_arrays.cpp b/Source/ERF_make_new_arrays.cpp
index 138f69499..9bdb45f79 100644
--- a/Source/ERF_make_new_arrays.cpp
+++ b/Source/ERF_make_new_arrays.cpp
@@ -262,12 +262,19 @@ ERF::init_stuff (int lev, const BoxArray& ba, const DistributionMapping& dm,
 
     Hwave_onegrid[lev] = std::make_unique<MultiFab>(ba2d_onegrid,dm_onegrid,1,IntVect(1,1,0));
     Lwave_onegrid[lev] = std::make_unique<MultiFab>(ba2d_onegrid,dm_onegrid,1,IntVect(1,1,0));
-    Hwave[lev] = std::make_unique<MultiFab>(ba2d,dm,1,IntVect(3,3,0));
-    Lwave[lev] = std::make_unique<MultiFab>(ba2d,dm,1,IntVect(3,3,0));
+
+    BoxList bl2d_wave = ba.boxList();
+    for (auto& b : bl2d_wave) {
+        b.setRange(2,0);
+    }
+    BoxArray ba2d_wave(std::move(bl2d_wave));
+
+    Hwave[lev] = std::make_unique<MultiFab>(ba2d_wave,dm,1,IntVect(3,3,0));
+    Lwave[lev] = std::make_unique<MultiFab>(ba2d_wave,dm,1,IntVect(3,3,0));
+
     std::cout<<ba_onegrid<<std::endl;
     std::cout<<ba2d_onegrid<<std::endl;
     std::cout<<dm_onegrid<<std::endl;
-    std::cout<<dm_onegrid<<std::endl;
 #endif
 
 
diff --git a/Source/TimeIntegration/ERF_make_tau_terms.cpp b/Source/TimeIntegration/ERF_make_tau_terms.cpp
index 6d3300193..80c26207a 100644
--- a/Source/TimeIntegration/ERF_make_tau_terms.cpp
+++ b/Source/TimeIntegration/ERF_make_tau_terms.cpp
@@ -1,4 +1,4 @@
-#include <AMReX_MultiFab.H>
+
 #include <AMReX_ArrayLim.H>
 #include <AMReX_BCRec.H>
 #include <AMReX_GpuContainers.H>
@@ -140,6 +140,20 @@ void erf_make_tau_terms (int level, int nrk,
             tbxxz.grow(IntVect(1,1,0));
             tbxyz.grow(IntVect(1,1,0));
 
+            if (bxcc.smallEnd(2) != domain.smallEnd(2)) {
+                 bxcc.growLo(2,1);
+                tbxxy.growLo(2,1);
+                tbxxz.growLo(2,1);
+                tbxyz.growLo(2,1);
+            }
+
+            if (bxcc.bigEnd(2) != domain.bigEnd(2)) {
+                 bxcc.growHi(2,1);
+                tbxxy.growHi(2,1);
+                tbxxz.growHi(2,1);
+                tbxyz.growHi(2,1);
+            }
+
             // Expansion rate
             Array4<Real> er_arr = expr->array(mfi);