From 47fb8a9e279e3d5a62ea90357c367205aaf12e7b Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun, 15 Sep 2024 14:40:37 -0400
Subject: [PATCH] remove gresho from lm_atm + add docstring for bubble (#280)

it is not clear where the gresho initial conditions for low
Mach stratified flow came from.
---
 pyro/lm_atm/problems/__init__.py   |  2 +-
 pyro/lm_atm/problems/bubble.py     |  5 ++
 pyro/lm_atm/problems/gresho.py     | 89 ------------------------------
 pyro/lm_atm/problems/inputs.gresho | 33 -----------
 4 files changed, 6 insertions(+), 123 deletions(-)
 delete mode 100644 pyro/lm_atm/problems/gresho.py
 delete mode 100644 pyro/lm_atm/problems/inputs.gresho

diff --git a/pyro/lm_atm/problems/__init__.py b/pyro/lm_atm/problems/__init__.py
index 6496898d8..48e709910 100644
--- a/pyro/lm_atm/problems/__init__.py
+++ b/pyro/lm_atm/problems/__init__.py
@@ -1 +1 @@
-__all__ = ['bubble', 'gresho']
+__all__ = ['bubble']
diff --git a/pyro/lm_atm/problems/bubble.py b/pyro/lm_atm/problems/bubble.py
index abdb2b0b4..025f496f3 100644
--- a/pyro/lm_atm/problems/bubble.py
+++ b/pyro/lm_atm/problems/bubble.py
@@ -1,3 +1,8 @@
+"""Initialize a buoyant bubble in a hydrostatic atmosphere.  This is
+meant to be used to compare with the compressible solver bubble
+problem.
+"""
+
 import numpy
 
 from pyro.util import msg
diff --git a/pyro/lm_atm/problems/gresho.py b/pyro/lm_atm/problems/gresho.py
deleted file mode 100644
index 430461087..000000000
--- a/pyro/lm_atm/problems/gresho.py
+++ /dev/null
@@ -1,89 +0,0 @@
-import numpy
-
-from pyro.util import msg
-
-DEFAULT_INPUTS = "inputs.gresho"
-
-PROBLEM_PARAMS = {"gresho.dens_base": 10.0,  # density at the base of the atmosphere
-                  "gresho.scale_height": 2.0,  # scale height of the isothermal atmosphere
-                  "gresho.r": 1.0,
-                  "gresho.u0": 1.0,
-                  "gresho.p0": 1.0,
-                  "gresho.dens_cutoff": 0.01}
-
-
-def init_data(my_data, base, rp):
-    """ initialize the Gresho vortex problem """
-
-    if rp.get_param("driver.verbose"):
-        msg.bold("initializing the Gresho vortex problem...")
-
-    # get the density and velocities
-    dens = my_data.get_var("density")
-    xvel = my_data.get_var("x-velocity")
-    yvel = my_data.get_var("y-velocity")
-    eint = my_data.get_var("eint")
-
-    grav = rp.get_param("lm-atmosphere.grav")
-
-    gamma = rp.get_param("eos.gamma")
-
-    scale_height = rp.get_param("gresho.scale_height")
-    dens_base = rp.get_param("gresho.dens_base")
-    dens_cutoff = rp.get_param("gresho.dens_cutoff")
-
-    R = rp.get_param("gresho.r")
-    u0 = rp.get_param("gresho.u0")
-
-    # initialize the components -- we'll get a pressure too
-    # but that is used only to initialize the base state
-    xvel[:, :] = 0.0
-    yvel[:, :] = 0.0
-    dens[:, :] = dens_cutoff
-
-    # set the density to be stratified in the y-direction
-    myg = my_data.grid
-    pres = myg.scratch_array()
-
-    for j in range(myg.jlo, myg.jhi+1):
-        dens[:, j] = max(dens_base*numpy.exp(-myg.y[j]/scale_height),
-                         dens_cutoff)
-
-    cs2 = scale_height*abs(grav)
-
-    # set the pressure (P = cs2*dens)
-    pres = cs2*dens
-    eint[:, :] = pres/(gamma - 1.0)/dens
-
-    x_centre = 0.5 * (myg.x[0] + myg.x[-1])
-    y_centre = 0.5 * (myg.y[0] + myg.y[-1])
-
-    r = numpy.sqrt((myg.x2d - x_centre)**2 + (myg.y2d - y_centre)**2)
-
-    pres[r <= R] += 0.5 * (u0 * r[r <= R]/R)**2
-    pres[(r > R) & (r <= 2*R)] += u0**2 * \
-        (0.5 * (r[(r > R) & (r <= 2*R)]/R)**2 +
-        4 * (1 - r[(r > R) & (r <= 2*R)]/R +
-        numpy.log(r[(r > R) & (r <= 2*R)]/R)))
-    pres[r > 2*R] += u0**2 * (4 * numpy.log(2) - 2)
-    #
-    uphi = numpy.zeros_like(pres)
-    uphi[r <= R] = u0 * r[r <= R]/R
-    uphi[(r > R) & (r <= 2*R)] = u0 * (2 - r[(r > R) & (r <= 2*R)]/R)
-
-    xvel[:, :] = -uphi[:, :] * (myg.y2d - y_centre) / r[:, :]
-    yvel[:, :] = uphi[:, :] * (myg.x2d - x_centre) / r[:, :]
-
-    dens[:, :] = pres[:, :]/(eint[:, :]*(gamma - 1.0))
-
-    # do the base state
-    base["rho0"].d[:] = numpy.mean(dens, axis=0)
-    base["p0"].d[:] = numpy.mean(pres, axis=0)
-
-    # redo the pressure via HSE
-    for j in range(myg.jlo+1, myg.jhi):
-        base["p0"].d[j] = base["p0"].d[j-1] + 0.5*myg.dy*(base["rho0"].d[j] + base["rho0"].d[j-1])*grav
-
-
-def finalize():
-    """ print out any information to the user at the end of the run """
diff --git a/pyro/lm_atm/problems/inputs.gresho b/pyro/lm_atm/problems/inputs.gresho
deleted file mode 100644
index 49863f6d3..000000000
--- a/pyro/lm_atm/problems/inputs.gresho
+++ /dev/null
@@ -1,33 +0,0 @@
-# simple inputs files for the unsplit CTU hydro scheme
-
-[driver]
-max_steps = 2000
-tmax = 10000.0
-cfl = 0.8
-
-
-[LM-atmosphere]
-
-
-[io]
-basename = lm_gresho_128_
-n_out = 1
-
-
-[mesh]
-nx = 128
-ny = 128
-xmax = 1.0
-ymax = 1.0
-
-xlboundary = periodic
-xrboundary = periodic
-
-ylboundary = reflect
-yrboundary = outflow
-
-
-[gresho]
-r = 0.2
-u0 = 0.1
-p0 = 1