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setrun.py.html |
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Source file: setrun.py
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Directory: /Users/rjl/clawpack_src/clawpack_master/geoclaw/examples/multi-layer/plane_wave
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Converted: Mon Feb 19 2024 at 14:29:46
using clawcode2html
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This documentation file will
not reflect any later changes in the source file.
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"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
from __future__ import absolute_import
from __future__ import print_function
import numpy
import clawpack.geoclaw.data
import clawpack.geoclaw.topotools as tt
# Rotation transformations
def transform_c2p(x,y,x0,y0,theta):
return ((x+x0)*numpy.cos(theta) - (y+y0)*numpy.sin(theta),
(x+x0)*numpy.sin(theta) + (y+y0)*numpy.cos(theta))
def transform_p2c(x,y,x0,y0,theta):
return ( x*numpy.cos(theta) + y*numpy.sin(theta) - x0,
-x*numpy.sin(theta) + y*numpy.cos(theta) - y0)
# Class containing some setup for the qinit especially for multilayer tests
class QinitMultilayerData(clawpack.geoclaw.data.QinitData):
r"""
Modified Qinit data object for multiple layers
"""
def __init__(self):
super(QinitMultilayerData, self).__init__()
# Test qinit data > 4
self.add_attribute("init_location", [0.0, 0.0])
self.add_attribute("wave_family", 1)
self.add_attribute("epsilon", 0.02)
self.add_attribute("angle", 0.0)
self.add_attribute("sigma", 0.02)
def write(self, out_file='qinit.data', data_source='setrun.py'):
# Initial perturbation
self.open_data_file('qinit.data',data_source)
self.data_write('qinit_type')
# Perturbation requested
if self.qinit_type == 0:
pass
elif 0 < self.qinit_type < 5:
# Check to see if each qinit file is present and then write the data
for tfile in self.qinitfiles:
try:
fname = "'%s'" % os.path.abspath(tfile[-1])
except:
raise Warning("File %s was not found." % fname)
# raise MissingFile("file not found")
self._out_file.write("\n%s \n" % fname)
self._out_file.write("%3i %3i \n" % tuple(tfile[:-1]))
elif self.qinit_type >= 5 and self.qinit_type <= 9:
self.data_write('epsilon')
self.data_write("init_location")
self.data_write("wave_family")
self.data_write("angle")
self.data_write("sigma")
else:
raise ValueError("Invalid qinit_type parameter %s." % self.qinit_type)
self.close_data_file()
#------------------------------
def setrun(claw_pkg='geoclaw'):
#------------------------------
"""
Define the parameters used for running Clawpack.
INPUT:
claw_pkg expected to be "geoclaw" for this setrun.
OUTPUT:
rundata - object of class ClawRunData
"""
from clawpack.clawutil import data
assert claw_pkg.lower() == 'geoclaw', "Expected claw_pkg = 'geoclaw'"
num_dim = 2
rundata = data.ClawRunData(claw_pkg, num_dim)
#------------------------------------------------------------------
# GeoClaw specific parameters:
#------------------------------------------------------------------
rundata = setgeo(rundata)
rundata = set_multilayer(rundata)
#------------------------------------------------------------------
# Standard Clawpack parameters to be written to claw.data:
# (or to amr2ez.data for AMR)
#------------------------------------------------------------------
clawdata = rundata.clawdata # initialized when rundata instantiated
# Set single grid parameters first.
# See below for AMR parameters.
# ---------------
# Spatial domain:
# ---------------
# Number of space dimensions:
clawdata.num_dim = num_dim
# Lower and upper edge of computational domain:
clawdata.lower[0] = -2 # west longitude
clawdata.upper[0] = 4.0 # east longitude
clawdata.lower[1] = -2.0 # south latitude
clawdata.upper[1] = 4.0 # north latitude
# Number of grid cells: Coarsest grid
clawdata.num_cells[0] = 80
clawdata.num_cells[1] = 80
# ---------------
# Size of system:
# ---------------
# Number of equations in the system:
clawdata.num_eqn = 6
# Number of auxiliary variables in the aux array (initialized in setaux)
# bathy == 1
# layer-depths = 2:3
clawdata.num_aux = 1 + rundata.multilayer_data.num_layers
# Index of aux array corresponding to capacity function, if there is one:
clawdata.capa_index = 0
# -------------
# Initial time:
# -------------
clawdata.t0 = 0.0
# Restart from checkpoint file of a previous run?
# If restarting, t0 above should be from original run, and the
# restart_file 'fort.chkNNNNN' specified below should be in
# the OUTDIR indicated in Makefile.
clawdata.restart = False # True to restart from prior results
clawdata.restart_file = 'fort.chk00036' # File to use for restart data
# -------------
# Output times:
#--------------
# Specify at what times the results should be written to fort.q files.
# Note that the time integration stops after the final output time.
# The solution at initial time t0 is always written in addition.
clawdata.output_style = 1
if clawdata.output_style==1:
# Output nout frames at equally spaced times up to tfinal:
clawdata.num_output_times = 10
clawdata.tfinal = 0.3
clawdata.output_t0 = True # output at initial (or restart) time?
elif clawdata.output_style == 2:
# Specify a list of output times.
clawdata.output_times = [0.5, 1.0]
elif clawdata.output_style == 3:
# Output every iout timesteps with a total of ntot time steps:
clawdata.output_step_interval = 1
clawdata.total_steps = 10
clawdata.output_t0 = True
clawdata.output_format = 'ascii' # 'ascii', 'binary32' or 'binary64'
clawdata.output_q_components = 'all' # need all
clawdata.output_aux_components = 'all' # eta=h+B is in q
clawdata.output_aux_onlyonce = False # output aux arrays each frame
# ---------------------------------------------------
# Verbosity of messages to screen during integration:
# ---------------------------------------------------
# The current t, dt, and cfl will be printed every time step
# at AMR levels <= verbosity. Set verbosity = 0 for no printing.
# (E.g. verbosity == 2 means print only on levels 1 and 2.)
clawdata.verbosity = 1
# --------------
# Time stepping:
# --------------
# if dt_variable==1: variable time steps used based on cfl_desired,
# if dt_variable==0: fixed time steps dt = dt_initial will always be used.
clawdata.dt_variable = True
# Initial time step for variable dt.
# If dt_variable==0 then dt=dt_initial for all steps:
clawdata.dt_initial = 0.00225
# Max time step to be allowed if variable dt used:
clawdata.dt_max = 1e+99
# Desired Courant number if variable dt used, and max to allow without
# retaking step with a smaller dt:
clawdata.cfl_desired = 0.75
clawdata.cfl_max = 1.0
# clawdata.cfl_desired = 0.45
# clawdata.cfl_max = 0.5
# Maximum number of time steps to allow between output times:
clawdata.steps_max = 5000
# ------------------
# Method to be used:
# ------------------
# Order of accuracy: 1 => Godunov, 2 => Lax-Wendroff plus limiters
clawdata.order = 2
# Use dimensional splitting? (not yet available for AMR)
# 0 or 'unsplit' or none' ==> Unsplit
# 1 or 'increment' ==> corner transport of waves
# 2 or 'all' ==> corner transport of 2nd order corrections too
clawdata.dimensional_split = "unsplit"
# For unsplit method, transverse_waves can be
# 0 or 'none' ==> donor cell (only normal solver used)
# 1 or 'increment' ==> corner transport of waves
# 2 or 'all' ==> corner transport of 2nd order corrections too
clawdata.transverse_waves = 2
# Number of waves in the Riemann solution:
clawdata.num_waves = 6
# List of limiters to use for each wave family:
# Required: len(limiter) == num_waves
# Some options:
# 0 or 'none' ==> no limiter (Lax-Wendroff)
# 1 or 'minmod' ==> minmod
# 2 or 'superbee' ==> superbee
# 3 or 'mc' ==> MC limiter
# 4 or 'vanleer' ==> van Leer
clawdata.limiter = ['mc', 'mc', 'mc', 'mc', 'mc', 'mc']
clawdata.use_fwaves = True # True ==> use f-wave version of algorithms
# Source terms splitting:
# src_split == 0 or 'none' ==> no source term (src routine never called)
# src_split == 1 or 'godunov' ==> Godunov (1st order) splitting used,
# src_split == 2 or 'strang' ==> Strang (2nd order) splitting used, not recommended.
clawdata.source_split = 'godunov'
# --------------------
# Boundary conditions:
# --------------------
# Number of ghost cells (usually 2)
clawdata.num_ghost = 2
# Choice of BCs at xlower and xupper:
# 0 => user specified (must modify bcN.f to use this option)
# 1 => extrapolation (non-reflecting outflow)
# 2 => periodic (must specify this at both boundaries)
# 3 => solid wall for systems where q(2) is normal velocity
clawdata.bc_lower[0] = 'extrap'
clawdata.bc_upper[0] = 'extrap'
clawdata.bc_lower[1] = 'extrap'
clawdata.bc_upper[1] = 'extrap'
# --------------
# Checkpointing:
# --------------
# Specify when checkpoint files should be created that can be
# used to restart a computation.
clawdata.checkpt_style = 0
if clawdata.checkpt_style == 0:
# Do not checkpoint at all
pass
elif numpy.abs(clawdata.checkpt_style) == 1:
# Checkpoint only at tfinal.
pass
elif numpy.abs(clawdata.checkpt_style) == 2:
# Specify a list of checkpoint times.
clawdata.checkpt_times = [0.1,0.15]
elif numpy.abs(clawdata.checkpt_style) == 3:
# Checkpoint every checkpt_interval timesteps (on Level 1)
# and at the final time.
clawdata.checkpt_interval = 5
# ---------------
# AMR parameters:
# ---------------
amrdata = rundata.amrdata
# max number of refinement levels:
amrdata.amr_levels_max = 3
# List of refinement ratios at each level (length at least mxnest-1)
amrdata.refinement_ratios_x = [2,2]
amrdata.refinement_ratios_y = [2,2]
amrdata.refinement_ratios_t = [2,2]
# Specify type of each aux variable in amrdata.auxtype.
# This must be a list of length maux, each element of which is one of:
# 'center', 'capacity', 'xleft', or 'yleft' (see documentation).
amrdata.aux_type = ['center','center','yleft','center','center','center']
# Flag using refinement routine flag2refine rather than richardson error
amrdata.flag_richardson = False # use Richardson?
amrdata.flag2refine = True
# steps to take on each level L between regriddings of level L+1:
amrdata.regrid_interval = 3
# width of buffer zone around flagged points:
# (typically the same as regrid_interval so waves don't escape):
amrdata.regrid_buffer_width = 2
# clustering alg. cutoff for (# flagged pts) / (total # of cells refined)
# (closer to 1.0 => more small grids may be needed to cover flagged cells)
amrdata.clustering_cutoff = 0.700000
# print info about each regridding up to this level:
amrdata.verbosity_regrid = 0
# ----- For developers -----
# Toggle debugging print statements:
amrdata.dprint = False # print domain flags
amrdata.eprint = False # print err est flags
amrdata.edebug = False # even more err est flags
amrdata.gprint = False # grid bisection/clustering
amrdata.nprint = False # proper nesting output
amrdata.pprint = False # proj. of tagged points
amrdata.rprint = False # print regridding summary
amrdata.sprint = False # space/memory output
amrdata.tprint = True # time step reporting each level
amrdata.uprint = False # update/upbnd reporting
# More AMR parameters can be set -- see the defaults in pyclaw/data.py
# ---------------
# Regions:
# ---------------
rundata.regiondata.regions = []
# to specify regions of refinement append lines of the form
# [minlevel,maxlevel,t1,t2,x1,x2,y1,y2]
# ---------------
# Gauges:
# ---------------
rundata.gaugedata.gauges = []
# for gauges append lines of the form [gaugeno, x, y, t1, t2]
gauge_locations = [-0.1,0.0,0.1,0.2,0.3]
for (i,x_c) in enumerate(gauge_locations):
# y0 = (self.run_data.clawdata.yupper - self.run_data.clawdata.ylower) / 2.0
# x_p,y_p = transform_c2p(x_c,0.0,location[0],location[1],angle)
x_p = x_c * numpy.cos(0.0)
y_p = x_c * numpy.sin(0.0)
# print "+=====+"
# print x_c,0.0
# print x_p,y_p
if (rundata.clawdata.lower[0] < x_p < rundata.clawdata.upper[0] and
rundata.clawdata.lower[1] < y_p < rundata.clawdata.upper[1]):
rundata.gaugedata.gauges.append([i, x_p, y_p, 0.0, 1e10])
# print "Gauge %s: (%s,%s)" % (i,x_p,y_p)
# print "+=====+"
return rundata
# end of function setrun
# ----------------------
#-------------------
def setgeo(rundata):
#-------------------
"""
Set GeoClaw specific runtime parameters.
For documentation see ....
"""
try:
geo_data = rundata.geo_data
except:
print("*** Error, this rundata has no geo_data attribute")
raise AttributeError("Missing geo_data attribute")
# == Physics ==
geo_data.gravity = 9.81
geo_data.coordinate_system = 1
geo_data.earth_radius = 6367.5e3
geo_data.rho = [922.5, 1025.0]
# == Forcing Options
geo_data.coriolis_forcing = False
# == Algorithm and Initial Conditions ==
geo_data.dry_tolerance = 1.e-3
geo_data.friction_forcing = True
geo_data.manning_coefficient = 0.025
geo_data.friction_depth = 1e6
# Refinement settings
refinement_data = rundata.refinement_data
refinement_data.variable_dt_refinement_ratios = True
refinement_data.wave_tolerance = 1.e-1
# == settopo.data values ==
topo_data = rundata.topo_data
# for topography, append lines of the form
# [topotype, fname]
topo_data.topofiles.append([2, 'topo.tt2'])
# == setdtopo.data values ==
dtopo_data = rundata.dtopo_data
# for moving topography, append lines of the form : (<= 1 allowed for now!)
# [topotype, fname]
return rundata
# end of function setgeo
# ----------------------
def set_multilayer(rundata):
data = rundata.multilayer_data
# Physics parameters
data.num_layers = 2
data.eta = [0.0, -0.6]
data.rho = [922.5, 1025.0]
# Algorithm parameters
data.eigen_method = 2
data.inundation_method = 2
data.richardson_tolerance = 0.95
data.wave_tolerance = [1e-3, 1e-2]
data.layer_index = 1
rundata.replace_data('qinit_data', QinitMultilayerData())
rundata.qinit_data.qinit_type = 6
rundata.qinit_data.epsilon = 0.02
rundata.qinit_data.angle = 0.0
rundata.qinit_data.sigma = 0.02
rundata.qinit_data.wave_family = 4
rundata.qinit_data.init_location = [-0.1, 0.0]
return rundata
def bathy_step(x, y, location=0.15, angle=0.0, left=-1.0, right=-0.2):
x_c, y_c = transform_p2c(x, y, location, 0.0, angle)
return ((x_c <= 0.0) * left +
(x_c > 0.0) * right)
def write_topo_file(run_data, out_file, **kwargs):
# Make topography
topo_func = lambda x, y: bathy_step(x, y, **kwargs)
topo = tt.Topography(topo_func=topo_func)
topo.x = numpy.linspace(run_data.clawdata.lower[0],
run_data.clawdata.upper[0],
run_data.clawdata.num_cells[0] + 8)
topo.y = numpy.linspace(run_data.clawdata.lower[1],
run_data.clawdata.upper[1],
run_data.clawdata.num_cells[1] + 8)
topo.write(out_file)
# Write out simple bathy geometry file for communication to the plotting
with open("./bathy_geometry.data", 'w') as bathy_geometry_file:
if "location" in kwargs:
location = kwargs['location']
else:
location = 0.15
if "angle" in kwargs:
angle = kwargs['angle']
else:
angle = 0.0
bathy_geometry_file.write("%s\n%s" % (location, angle))
if __name__ == '__main__':
# Set up run-time parameters and write all data files.
import sys
if len(sys.argv) == 2:
rundata = setrun(sys.argv[1])
else:
rundata = setrun()
rundata.write()
write_topo_file(rundata, 'topo.tt2')