Merge branch 'development' into fix_moist_getT

Docs/sphinx_doc/BoundaryConditions.rst

@@ -226,3 +226,125 @@ The sponge data is input as a text file with 3 columns containing :math:`z, u, v
           erf.sponge_strength = 1000.0
           erf.use_xlo_sponge_damping = true
           erf.xlo_sponge_end = 4.0
+
+Inflow turbulence generation
+---------------------------
+
+ERF provides the capability to apply a perturbation zone at the inflow domain boundary to mechanically trip turbulence into the domain.
+
+.. |PBinflw| image:: figures/PBIllustration.png
+           :width: 600
+
+.. _fig:pb_fig:
+
+.. table:: Box perturbation method
+
+   +-----------------------------------------------------+
+   |                     |PBinflw|                       |
+   +-----------------------------------------------------+
+   |  Image taken from `DeLeon et al. (2018)`            |
+   +-----------------------------------------------------+
+
+Two different types of perturbation are currently available, ``source``, adopted from `DeLeon et al. (2018)`_
+
+..
+   _`DeLeon et al. (2018)`: https://doi.org/10.2514/1.J057245
+
+and ``direct``, adopted from `Munoz-Esparza et al. (2015)`_. The ``source`` option applies the perturbation amplitude range, `\pm \Phi_{PB}`, to each cell within the perturbation box as a source term. It's important to note that while this perturbation starts as white noise, it becomes colored noise due to the eddy viscosity turbulence closure. Conversely, the ``direct`` option applies the calculated temperature difference directly onto the `\rho \theta field`.
+
+The current implementation only supports West and South face perturbations, specified by ``erf.perturbation_direction``, where the 3 integer inputs represent the `x`, `y`, and `z` directions, respectively. The flow perturbation method requires the dimensions of an individual box input through ``erf.perturbation_box_dim``, with 3 integer inputs representing `nx_{pb}`, `ny_{pb}`, and `nz_{pb}`, respectively. Following the guidance of `Ma and Senocak (2023)`_,
+
+.. _`Ma and Senocak (2023)`: https://link.springer.com/article/10.1007/s10546-023-00786-1
+
+the general rule of thumb is to use `H_{PB} = 1/8 \delta` as the height of the perturbation box, where `\delta` is the boundary layer height. The length of the box in the x-direction should be `L_{PB} = 2H_{PB}`. Depending on the direction of the bulk flow, the width of the box in the y-direction should be defined as `W_{PB} = L_{PB} \tan{\theta_{inflow}}`. Note that the current implementation only accepts ``int`` entries. Therefore, considering the domain size and mesh resolution, the dimensions of a singular box can be determined.
+
+The specification of the number of layers and the offset into the domain of the perturbation boxes can be made through ``erf.perturbation_layers`` and ``erf.perturbation_offset``, respectively.
+
+::
+
+          erf.inlet_perturbation_type = "source"
+
+          erf.perturbation_direction = 1 0 0
+          erf.perturbation_box_dims = 8 8 4
+          erf.perturbation_layers = 3
+          erf.perturbation_offset = 1
+
+          erf.perturbation_nondimensional = 0.042
+          erf.perturbation_T_infinity = 300.0
+          erf.perturbation_T_intensity = 0.1
+
+Before delving into the details, it's important to note that the two methods are interchangeable. While we adhere to the guidelines from the referenced publications, the use of ``direct`` type forcing is not restricted to having unity cell height, nor is ``source`` type forcing limited to boxes. We have generalized the perturbation methods to allow for flexibility in mixing and matching different types of turbulence generation.
+
+Source type forcing
+-------------------
+
+The perturbation update interval is determined by the equation,
+
+.. math::
+
+   \frac{t_p \langle U(z) \rangle_{PB}}{D_{PB}} = 1,
+
+The change in the perturbation is defined as,
+
+.. math::
+
+   {Ri}_{PB} = \frac{g \beta \Delta \overline{\phi} H_{PB}}{{\langle U(z) \rangle}^2_{PB}}.
+
+The magnitude of the perturbation, ignoring the advection and diffusion effects in the transport equation can be made through a proportionality ratio between the update time and change in the box temperature,
+
+.. math::
+
+   \Phi_{PB} \propto \frac{\Delta \overliner{\phi}}{t_p}
+
+and the perturbation amplitude is determined by the equation,
+
+.. math::
+
+   \Phi_{PB} = \frac{Ri_{PB} {\langle U(z) \rangle}^3_{PB}}{g \beta D_{PB} H_{PB}}.
+
+The ``source`` type forcing can adopt the box perturbation method by having the following inputs list.
+
+::
+
+          erf.inlet_perturbation_type = "source"
+
+          erf.perturbation_direction = 1 0 0
+          erf.perturbation_box_dims = 8 8 4
+          erf.perturbation_layers = 3
+          erf.perturbation_offset = 1
+
+          erf.perturbation_nondimensional = 0.042 # Ri
+          erf.perturbation_T_infinity = 300.0
+          erf.perturbation_T_intensity = 0.1
+
+Direct type forcing
+-------------------
+
+The perturbation update interval is determined by the equation,
+.. math::
+
+   \frac{t_p U_{1}}{d_{c}}
+
+and the perturbation amplitude is determined by the equation,
+.. math::
+
+   Ec = \frac{{U_g}^2}{\rho c_p \theta_{pm}}.
+
+The ``direct`` type forcing can adopt the cell perturbation method by having the following inputs list.
+::
+
+          erf.inlet_perturbation_type = "direct"
+
+          erf.perturbation_direction = 1 0 0
+          erf.perturbation_box_dims = 8 8 1
+          erf.perturbation_layers = 3
+          erf.perturbation_offset = 1
+
+          erf.perturbation_nondimensional = 0.16 #Ec
+          erf.perturbation_rho_0 = 1.0
+          erf.perturbation_cp = 1250
+
+From `Munoz-Esparza et al. (2015)`_ the choice of the Eckert number is 0.16.
+
+..
+   _`Munoz-Esparza et al. (2015)`: https://doi.org/10.1063/1.4913572

Exec/DevTests/ABL_perturbation_inflow/CMakeLists.txt

@@ -0,0 +1,12 @@
+set(erf_exe_name erf_abl_perturbation_inflow)
+
+add_executable(${erf_exe_name} "")
+target_sources(${erf_exe_name}
+   PRIVATE
+     prob.cpp
+)
+
+target_include_directories(${erf_exe_name} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+
+include(${CMAKE_SOURCE_DIR}/CMake/BuildERFExe.cmake)
+build_erf_exe(${erf_exe_name})

Exec/DevTests/ABL_perturbation_inflow/GNUmakefile

@@ -0,0 +1,34 @@
+# AMReX
+COMP = gnu
+PRECISION = DOUBLE
+
+# Profiling
+PROFILE       = FALSE
+TINY_PROFILE  = TRUE
+COMM_PROFILE  = FALSE
+TRACE_PROFILE = FALSE
+MEM_PROFILE   = FALSE
+USE_GPROF     = FALSE
+
+# Performance
+USE_MPI  = TRUE
+USE_OMP  = FALSE
+
+USE_CUDA = FALSE
+USE_HIP  = FALSE
+USE_SYCL = FALSE
+
+# Debugging
+DEBUG = TRUE
+
+TEST = TRUE
+USE_ASSERTION = TRUE
+
+#USE_POISSON_SOLVE = TRUE
+
+# GNU Make
+Bpack := ./Make.package
+Blocs := .
+ERF_HOME := ../../..
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DevTests/ABL_perturbation_inflow
+include $(ERF_HOME)/Exec/Make.ERF

Exec/DevTests/ABL_perturbation_inflow/Make.package

@@ -0,0 +1,2 @@
+CEXE_headers += prob.H
+CEXE_sources += prob.cpp

Exec/DevTests/ABL_perturbation_inflow/README

@@ -0,0 +1,7 @@
+This problem setup is for simulation of the Atmospheric Boundary Layer (ABL)
+using one of two turbulence schemes (Smagorinsky or Deardorff) and the bottom
+boundary condition possibly specified by Monin Obukhov Similarity Theory (MOST).
+
+This version of the ABL problem initializes the data from an input sounding file,
+and initializes turbulence at the inflow. The target is to transition turbulence
+from coarse to fine grid interface.

Exec/DevTests/ABL_perturbation_inflow/input_ReTau2000Ana_sounding.txt

@@ -0,0 +1,34 @@
+0.0 300.0 0.0
+1.00000000e-02 3.00000000e+02 0.00000000e+00 1.25066641e+01 0.00000000e+00
+3.22187500e-01 3.00000000e+02 0.00000000e+00 2.09762948e+01 0.00000000e+00
+6.34375000e-01 3.00000000e+02 0.00000000e+00 2.26287499e+01 0.00000000e+00
+9.46562500e-01 3.00000000e+02 0.00000000e+00 2.36048395e+01 0.00000000e+00
+1.25875000e+00 3.00000000e+02 0.00000000e+00 2.43000527e+01 0.00000000e+00
+1.57093750e+00 3.00000000e+02 0.00000000e+00 2.48404269e+01 0.00000000e+00
+1.88312500e+00 3.00000000e+02 0.00000000e+00 2.52825246e+01 0.00000000e+00
+2.19531250e+00 3.00000000e+02 0.00000000e+00 2.56566509e+01 0.00000000e+00
+2.50750000e+00 3.00000000e+02 0.00000000e+00 2.59809480e+01 0.00000000e+00
+2.81968750e+00 3.00000000e+02 0.00000000e+00 2.62671427e+01 0.00000000e+00
+3.13187500e+00 3.00000000e+02 0.00000000e+00 2.65232545e+01 0.00000000e+00
+3.44406250e+00 3.00000000e+02 0.00000000e+00 2.67550102e+01 0.00000000e+00
+3.75625000e+00 3.00000000e+02 0.00000000e+00 2.69666429e+01 0.00000000e+00
+4.06843750e+00 3.00000000e+02 0.00000000e+00 2.71613695e+01 0.00000000e+00
+4.38062500e+00 3.00000000e+02 0.00000000e+00 2.73416924e+01 0.00000000e+00
+4.69281250e+00 3.00000000e+02 0.00000000e+00 2.75095964e+01 0.00000000e+00
+5.00500000e+00 3.00000000e+02 0.00000000e+00 2.76666826e+01 0.00000000e+00
+5.31718750e+00 3.00000000e+02 0.00000000e+00 2.78142609e+01 0.00000000e+00
+5.62937500e+00 3.00000000e+02 0.00000000e+00 2.79534168e+01 0.00000000e+00
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+6.25375000e+00 3.00000000e+02 0.00000000e+00 2.82099603e+01 0.00000000e+00
+6.56593750e+00 3.00000000e+02 0.00000000e+00 2.83287750e+01 0.00000000e+00
+6.87812500e+00 3.00000000e+02 0.00000000e+00 2.84420696e+01 0.00000000e+00
+7.19031250e+00 3.00000000e+02 0.00000000e+00 2.85503344e+01 0.00000000e+00
+7.50250000e+00 3.00000000e+02 0.00000000e+00 2.86539970e+01 0.00000000e+00
+7.81468750e+00 3.00000000e+02 0.00000000e+00 2.87534328e+01 0.00000000e+00
+8.12687500e+00 3.00000000e+02 0.00000000e+00 2.88489730e+01 0.00000000e+00
+8.43906250e+00 3.00000000e+02 0.00000000e+00 2.89409114e+01 0.00000000e+00
+8.75125000e+00 3.00000000e+02 0.00000000e+00 2.90295098e+01 0.00000000e+00
+9.06343750e+00 3.00000000e+02 0.00000000e+00 2.91150023e+01 0.00000000e+00
+9.37562500e+00 3.00000000e+02 0.00000000e+00 2.91975993e+01 0.00000000e+00
+9.68781250e+00 3.00000000e+02 0.00000000e+00 2.92774905e+01 0.00000000e+00
+1.00000000e+01 3.00000000e+02 0.00000000e+00 2.93548477e+01 0.00000000e+00

Exec/DevTests/ABL_perturbation_inflow/input_ReTau2000Ana_sponge.txt

@@ -0,0 +1,33 @@
+1.00000000e-02 1.25066641e+01 0.00000000e+00
+3.22187500e-01 2.09762948e+01 0.00000000e+00
+6.34375000e-01 2.26287499e+01 0.00000000e+00
+9.46562500e-01 2.36048395e+01 0.00000000e+00
+1.25875000e+00 2.43000527e+01 0.00000000e+00
+1.57093750e+00 2.48404269e+01 0.00000000e+00
+1.88312500e+00 2.52825246e+01 0.00000000e+00
+2.19531250e+00 2.56566509e+01 0.00000000e+00
+2.50750000e+00 2.59809480e+01 0.00000000e+00
+2.81968750e+00 2.62671427e+01 0.00000000e+00
+3.13187500e+00 2.65232545e+01 0.00000000e+00
+3.44406250e+00 2.67550102e+01 0.00000000e+00
+3.75625000e+00 2.69666429e+01 0.00000000e+00
+4.06843750e+00 2.71613695e+01 0.00000000e+00
+4.38062500e+00 2.73416924e+01 0.00000000e+00
+4.69281250e+00 2.75095964e+01 0.00000000e+00
+5.00500000e+00 2.76666826e+01 0.00000000e+00
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+5.94156250e+00 2.80850600e+01 0.00000000e+00
+6.25375000e+00 2.82099603e+01 0.00000000e+00
+6.56593750e+00 2.83287750e+01 0.00000000e+00
+6.87812500e+00 2.84420696e+01 0.00000000e+00
+7.19031250e+00 2.85503344e+01 0.00000000e+00
+7.50250000e+00 2.86539970e+01 0.00000000e+00
+7.81468750e+00 2.87534328e+01 0.00000000e+00
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