import xarray
import numpy as np
import time
import math
from mpas_tools.planar_hex import make_planar_hex_mesh
from mpas_tools.io import write_netcdf
from mpas_tools.mesh.conversion import convert, cull
from compass.ocean.vertical import init_vertical_coord
from compass.step import Step
[docs]
class InitialState(Step):
"""
A step for creating a mesh and initial condition for stratified
seiche test case
"""
[docs]
def __init__(self, test_case):
"""
Create the step
Parameters
----------
test_case : compass.TestCase
"""
super().__init__(test_case=test_case, name='initial_state')
for file in ['base_mesh.nc', 'culled_mesh.nc', 'culled_graph.info',
'initial_state.nc']:
self.add_output_file(file)
[docs]
def run(self):
"""
Run this step of the test case
"""
config = self.config
logger = self.logger
timeStart = time.time()
section = config['horizontal_grid']
nx = section.getint('nx')
ny = section.getint('ny')
dc = section.getfloat('dc')
dsMesh = make_planar_hex_mesh(nx=nx, ny=ny, dc=dc, nonperiodic_x=True,
nonperiodic_y=False)
write_netcdf(dsMesh, 'base_mesh.nc')
dsMesh = cull(dsMesh, logger=logger)
dsMesh = convert(dsMesh, graphInfoFileName='culled_graph.info',
logger=logger)
write_netcdf(dsMesh, 'culled_mesh.nc')
section = config['vertical_grid']
maxDepth = section.getfloat('bottom_depth')
nVertLevels = section.getint('vert_levels')
section = config['stratified_seiche']
config_eos_linear_alpha = section.getfloat('eos_linear_alpha')
config_eos_linear_Tref = section.getfloat('eos_linear_Tref')
config_eos_linear_Sref = section.getfloat('eos_linear_Sref')
config_eos_linear_densityref = section.getfloat(
'eos_linear_densityref')
deltaRho = section.getfloat('deltaRho')
interfaceThick = section.getfloat('interfaceThick')
amplitude = section.getfloat('amplitude')
wavenumber = section.getfloat('wavenumber')
# comment('obtain dimensions and mesh variables')
# vertical_coordinate = 'uniform'
ds = dsMesh.copy()
nCells = ds.nCells.size
nEdges = ds.nEdges.size
nVertices = ds.nVertices.size
xCell = ds.xCell
yCell = ds.yCell
xEdge = ds.xEdge
yEdge = ds.yEdge
angleEdge = ds.angleEdge
# Adjust coordinates so first edge is at zero in x and y
xOffset = xEdge.min()
xCell -= xOffset
xEdge -= xOffset
yOffset = np.min(yEdge)
yCell -= yOffset
yEdge -= yOffset
# initialize velocity field
u = np.zeros([1, nEdges, nVertLevels])
# comment('create and initialize variables')
time1 = time.time()
surfaceStress = np.nan * np.ones(nCells)
atmosphericPressure = np.nan * np.ones(nCells)
boundaryLayerDepth = np.nan * np.ones(nCells)
ds['bottomDepth'] = maxDepth * xarray.ones_like(xCell)
ds['ssh'] = xarray.zeros_like(xCell)
init_vertical_coord(config, ds)
# initial salinity, density, temperature
ds['salinity'] = (config_eos_linear_Sref *
xarray.ones_like(ds.zMid)).where(ds.cellMask)
ds['density'] = \
(config_eos_linear_densityref +
(deltaRho/2)*(1.0 - np.tanh(
(2/interfaceThick)*np.arctanh(0.99) *
(ds.zMid + 0.5*maxDepth -
amplitude*np.cos(wavenumber*ds.xCell)))))
# T = Tref - (rho - rhoRef)/alpha
ds['temperature'] = (config_eos_linear_Tref
- (ds.density - config_eos_linear_densityref) /
config_eos_linear_alpha)
# initial velocity on edges
ds['normalVelocity'] = (('Time', 'nEdges', 'nVertLevels',),
np.zeros([1, nEdges, nVertLevels]))
normalVelocity = ds['normalVelocity']
for iEdge in range(0, nEdges):
normalVelocity[0, iEdge, :] = u[0, iEdge, :] * math.cos(angleEdge[iEdge])
# Coriolis parameter
ds['fCell'] = (('nCells', 'nVertLevels',), np.zeros([nCells, nVertLevels]))
ds['fEdge'] = (('nEdges', 'nVertLevels',), np.zeros([nEdges, nVertLevels]))
ds['fVertex'] = (('nVertices', 'nVertLevels',),
np.zeros([nVertices, nVertLevels]))
# surface fields
surfaceStress[:] = 0.0
atmosphericPressure[:] = 0.0
boundaryLayerDepth[:] = 0.0
print(f' time: {time.time() - time1}')
# comment('finalize and write file')
time1 = time.time()
# If you prefer not to have NaN as the fill value, you should consider
# using mpas_tools.io.write_netcdf() instead
write_netcdf(ds, 'initial_state.nc')
print(f' time: {time.time() - time1}')
print(f'Total time: {time.time() - timeStart}')