Adding amr inputs for testing

Docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'sphinx_doc'
+copyright = '2023, Mahesh Natarajan'
+author = 'Mahesh Natarajan'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']

Docs/source/index.rst

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+.. sphinx_doc documentation master file, created by
+ sphinx-quickstart on Fri Jul 21 10:29:31 2023.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to sphinx_doc's documentation!
+======================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

Exec/RegTests/Terrain2d_Cylinder/inputs.amr

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+# ------------------ INPUTS TO MAIN PROGRAM -------------------
+max_step = 6000
+
+amrex.fpe_trap_invalid = 1
+
+fabarray.mfiter_tile_size = 1024 1024 1024
+
+# PROBLEM SIZE & GEOMETRY
+geometry.prob_lo = 0 0. 0. 
+geometry.prob_hi = 30.0 1. 10.0
+
+amr.n_cell = 128 4 64 # dx=dy=dz=100 m, Straka et al 1993 / Xue et al 2000
+
+geometry.is_periodic = 0 1 0
+
+xlo.type = "Outflow"
+xhi.type = "Outflow"
+xlo.velocity = 1. 0. 0.
+xlo.density = 1.16
+xlo.theta = 300.
+xlo.scalar = 0.
+
+zlo.type = "SlipWall"
+zhi.type = "Outflow"
+
+# SPONGE ZONE BCS
+
+erf.sponge_strength = 10000.0
+erf.use_xlo_sponge_damping = true
+erf.xlo_sponge_end = 4.0
+erf.use_xhi_sponge_damping = true
+erf.xhi_sponge_start = 26.0
+erf.use_zhi_sponge_damping = true
+erf.zhi_sponge_start = 8.0 
+
+erf.sponge_density = 1.2
+erf.sponge_x_velocity = 10.0
+erf.sponge_y_velocity = 0.0
+erf.sponge_z_velocity = 0.0
+
+# TIME STEP CONTROL
+erf.no_substepping = 1
+#erf.fixed_dt = 1E-5
+erf.cfl = 0.3 
+
+# DIAGNOSTICS & VERBOSITY
+erf.sum_interval = 1 # timesteps between computing mass
+erf.v = 1 # verbosity in ERF.cpp
+amr.v = 1 # verbosity in Amr.cpp
+
+# REFINEMENT / REGRIDDING
+amr.max_level = 1 # maximum level number allowed
+
+
+# CHECKPOINT FILES
+erf.check_file = chk # root name of checkpoint file
+erf.check_int = 100 # number of timesteps between checkpoint
+#erf.restart = chk06000
+
+# PLOTFILES
+erf.plot_file_1 = plt # prefix of plotfile name
+erf.plot_int_1 = 100 # number of timesteps between plotfiles
+erf.plot_vars_1 = density x_velocity y_velocity z_velocity pressure theta pres_hse dens_hse pert_pres pert_dens z_phys detJ dpdx dpdy pres_hse_x pres_hse_y
+
+# SOLVER CHOICE
+erf.use_gravity = true
+erf.use_coriolis = false
+erf.use_rayleigh_damping = false
+erf.les_type = "None"
+
+# MULTILEVEL
+amr.max_level = 1
+amr.ref_ratio_vect = 2 2 1
+
+erf.refinement_indicators = box1
+erf.box1.max_level = 1
+erf.box1.in_box_lo = 2.2 0.25
+erf.box1.in_box_hi = 3.3 0.75
+
+# TERRRAIN GRID TYPE
+erf.use_terrain = true
+erf.terrain_smoothing = 0
+
+#erf.terrain_z_levels = 0 0.0236057 0.0486738 0.0752909 0.103548 0.133541 0.165372 0.199145 0.234973 0.272972 0.313264 0.355978 0.401247 0.449212 0.500017 0.553815 0.610764 0.671027 0.734774 0.802181 0.873428 0.948703 1.0282 1.1121 1.20063 1.29397 1.39234 1.49595 1.605 1.71971 1.84029 1.96694 2.09987 2.23928 2.38537 2.53831 2.69828 2.86545 3.03996 3.22194 3.41151 3.60875 3.81373 4.02649 4.24706 4.47539 4.71146 4.95516 5.20639 5.46498 5.73072 6.00339 6.28271 6.56834 6.85995 7.15712 7.45942 7.76639 8.07751 8.39226 8.71007 9.03036 9.35252 9.67594 10
+
+# USE WENO FOR ADVECTION
+#erf.all_use_WENO = true
+#erf.spatial_order_WENO = 5
+
+# Diffusion coefficient from Straka, K = 75 m^2/s
+erf.molec_diff_type = "ConstantAlpha"
+erf.rho0_trans = 1.0 # [kg/m^3], used to convert input diffusivities
+erf.dynamicViscosity = 0.0 # [kg/(m-s)] ==> nu = 75.0 m^2/s
+erf.alpha_T = 0.0 # [m^2/s]
+
+#erf.abl_driver_type = "PressureGradient"
+#erf.abl_pressure_grad = -0.2 0. 0.
+
+# PROBLEM PARAMETERS (optional)
+prob.T_0 = 300.0
+prob.U_0 = 0.0
+prob.rho_0 = 1.16