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Allow keeping y boundary cells at second divertor #40

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merged 6 commits into from
Aug 7, 2019
Merged

Allow keeping y boundary cells at second divertor #40

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0d95372
Check for position of second divertor when keeping y-boundary cells
johnomotani Jul 22, 2019
3b428dc
Fix PEP8 warnings
johnomotani Jul 23, 2019
d182611
Refactored upper/lower limit logic out into a helper function
TomNicholas Jul 25, 2019
1fa5a6f
pep8 fix
TomNicholas Jul 25, 2019
6f1c6f4
Merged in changes to keep_guard_cells branch
TomNicholas Jul 29, 2019
94b16e7
Merge remote-tracking branch 'origin/master' into y-boundaries-second…
johnomotani Aug 6, 2019
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2 changes: 2 additions & 0 deletions xbout/boutdataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,8 @@ def open_boutdataset(datapath='./BOUT.dmp.*.nc',
If true, keep y-direction boundary cells (the cells past the physical edges of the
grid, where boundary conditions are set); increases the size of the y dimension in
the returned data-set. If false, trim these cells.
Note: in double-null topology, setting this argument to True loads the boundary
cells at the second divertor, so the length of the y-dimension would be ny+4*MYG.
run_name : str, optional
info : bool, optional

Expand Down
24 changes: 20 additions & 4 deletions xbout/load.py
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Expand Up @@ -12,6 +12,7 @@
'wtime_comms', 'wtime_io', 'wtime_per_rhs', 'wtime_per_rhs_e',
'wtime_per_rhs_i']


def _auto_open_mfboutdataset(datapath, chunks={}, info=True,
keep_xboundaries=False, keep_yboundaries=False):
filepaths, filetype = _expand_filepaths(datapath)
Expand Down Expand Up @@ -177,7 +178,7 @@ def _trim(ds, *, guards, keep_boundaries, nxpe, nype):
# Relies on a change to xarray so datasets always have source encoding
# See xarray GH issue #2550
lower_boundaries, upper_boundaries = _infer_contains_boundaries(
ds.encoding['source'], nxpe, nype)
ds, nxpe, nype)
else:
lower_boundaries, upper_boundaries = {}, {}

Expand Down Expand Up @@ -211,16 +212,19 @@ def _trim(ds, *, guards, keep_boundaries, nxpe, nype):
return trimmed_ds


def _infer_contains_boundaries(filename, nxpe, nype):
def _infer_contains_boundaries(ds, nxpe, nype):
"""
Uses the name of the output file and the domain decomposition to work out
whether this dataset contains boundary cells, and on which side.
Uses the name of the output file, BOUT++'s topology indices, and the domain
decomposition to work out whether this dataset contains boundary cells, and on which
side.

Uses knowledge that BOUT names its output files as /folder/prefix.num.nc,
with a numbering scheme
num = nxpe*i + j, where i={0, ..., nype}, j={0, ..., nxpe}
"""

filename = ds.encoding['source']

*prefix, filenum, extension = Path(filename).suffixes
filenum = int(filenum.replace('.', ''))

Expand All @@ -232,6 +236,18 @@ def _infer_contains_boundaries(filename, nxpe, nype):
lower_boundaries['y'] = filenum < nxpe
upper_boundaries['y'] = filenum >= (nype-1)*nxpe

jyseps2_1 = int(ds['jyseps2_1'])
jyseps1_2 = int(ds['jyseps1_2'])
if jyseps1_2 > jyseps2_1:
# second divertor present
yproc = filenum // nxpe
ny_inner = int(ds['ny_inner'])
mysub = int(ds['MYSUB'])
if mysub*(yproc + 1) == ny_inner:
upper_boundaries['y'] = True
elif mysub*yproc == ny_inner:
lower_boundaries['y'] = True

return lower_boundaries, upper_boundaries


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118 changes: 116 additions & 2 deletions xbout/tests/test_load.py
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Expand Up @@ -429,9 +429,81 @@ def test_infer_boundaries_2d_parallelization(self, filenum, nxpe, nype,
-----> x
"""

filename = "folder0/BOUT.dmp." + str(filenum) + ".nc"
ds = create_test_data(0)
ds['jyseps2_1'] = 0
ds['jyseps1_2'] = 0
ds.encoding['source'] = "folder0/BOUT.dmp." + str(filenum) + ".nc"
actual_lower_boundaries, actual_upper_boundaries = _infer_contains_boundaries(
filename, nxpe, nype)
ds, nxpe, nype)

assert actual_lower_boundaries == lower_boundaries
assert actual_upper_boundaries == upper_boundaries

@pytest.mark.parametrize("filenum, nxpe, nype, lower_boundaries, upper_boundaries",
# 1d parallelization along y:
# Bottom
[(0, 1, 4, {'x': True, 'y': True},
{'x': True, 'y': False}),
# Lower Middle
(1, 1, 4, {'x': True, 'y': False},
{'x': True, 'y': True}),
# Upper Middle
(2, 1, 4, {'x': True, 'y': True},
{'x': True, 'y': False}),
# Top
(3, 1, 4, {'x': True, 'y': False},
{'x': True, 'y': True}),

# 2d parallelization:
# Bottom left corner
(0, 3, 4, {'x': True, 'y': True},
{'x': False, 'y': False}),
(1, 3, 4, {'x': False, 'y': True},
{'x': False, 'y': False}),
# Bottom right corner
(2, 3, 4, {'x': False, 'y': True},
{'x': True, 'y': False}),
(3, 3, 4, {'x': True, 'y': False},
{'x': False, 'y': True}),
(4, 3, 4, {'x': False, 'y': False},
{'x': False, 'y': True}),
(5, 3, 4, {'x': False, 'y': False},
{'x': True, 'y': True}),
(6, 3, 4, {'x': True, 'y': True},
{'x': False, 'y': False}),
(7, 3, 4, {'x': False, 'y': True},
{'x': False, 'y': False}),
(8, 3, 4, {'x': False, 'y': True},
{'x': True, 'y': False}),
# Top left corner
(9, 3, 4, {'x': True, 'y': False},
{'x': False, 'y': True}),
(10, 3, 4, {'x': False, 'y': False},
{'x': False, 'y': True}),
# Top right corner
(11, 3, 4, {'x': False, 'y': False},
{'x': True, 'y': True}),
])
def test_infer_boundaries_2d_parallelization_doublenull(
self, filenum, nxpe, nype, lower_boundaries, upper_boundaries):
"""
Numbering scheme for nxpe=3, nype=4

y 9 10 11
^ 6 7 8
| 3 4 5
| 0 1 2
-----> x
"""

ds = create_test_data(0)
ds['jyseps2_1'] = 3
ds['jyseps1_2'] = 11
ds['ny_inner'] = 8
ds['MYSUB'] = 4
ds.encoding['source'] = "folder0/BOUT.dmp." + str(filenum) + ".nc"
actual_lower_boundaries, actual_upper_boundaries = _infer_contains_boundaries(
ds, nxpe, nype)

assert actual_lower_boundaries == lower_boundaries
assert actual_upper_boundaries == upper_boundaries
Expand All @@ -443,10 +515,52 @@ def test_keep_xboundaries(self):
# Manually add filename - encoding normally added by xr.open_dataset
ds.encoding['source'] = 'folder0/BOUT.dmp.0.nc'

ds['jyseps2_1'] = 8
ds['jyseps1_2'] = 8

actual = _trim(ds, guards={'x': 2}, keep_boundaries={'x': True}, nxpe=1, nype=1)
expected = ds # Should be unchanged
xrt.assert_equal(expected, actual)

def test_keep_yboundaries(self):
ds = create_test_data(0)
ds = ds.rename({'dim2': 'y'})

# Manually add filename - encoding normally added by xr.open_dataset
ds.encoding['source'] = 'folder0/BOUT.dmp.0.nc'

ds['jyseps2_1'] = 8
ds['jyseps1_2'] = 8

actual = _trim(ds, guards={'y': 2}, keep_boundaries={'y': True}, nxpe=1, nype=1)
expected = ds # Should be unchanged
xrt.assert_equal(expected, actual)

@pytest.mark.parametrize("filenum, lower, upper",
[(0, True, False),
(1, False, True),
(2, True, False),
(3, False, True)])
def test_keep_yboundaries_doublenull(self, filenum, lower, upper):
ds = create_test_data(0)
ds = ds.rename({'dim2': 'y'})

# Manually add filename - encoding normally added by xr.open_dataset
ds.encoding['source'] = 'folder0/BOUT.dmp.'+str(filenum)+'.nc'

ds['jyseps2_1'] = 3
ds['jyseps1_2'] = 11
ds['ny_inner'] = 8
ds['MYSUB'] = 4

actual = _trim(ds, guards={'y': 2}, keep_boundaries={'y': True}, nxpe=1, nype=4)
expected = ds # Should be unchanged
if not lower:
expected = expected.isel(y=slice(2, None, None))
if not upper:
expected = expected.isel(y=slice(None, -2, None))
xrt.assert_equal(expected, actual)

def test_trim_timing_info(self):
ds = create_test_data(0)
from xbout.load import _BOUT_TIMING_VARIABLES
Expand Down