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fix(performance): Implemented performance improvements including improvements suggested by @briochh (#1092) (#1097) 

* fix(performance): Implemented performance improvements including improvements suggested by @briochh (#1092)

* fix(performance): Implemented additional performance improvements
develop
spaulins-usgs 2021-04-12 12:54:46 -07:00 committed by GitHub
parent 801a41705d
commit 4104cf5e6a
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GPG Key ID: 4AEE18F83AFDEB23
8 changed files with 100 additions and 29 deletions
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9
flopy/mf6/coordinates/modelgrid.py
View File

@ -594,13 +594,14 @@ class ModelGrid:
return ["node"]
def get_num_spatial_coordinates(self):
if self.grid_type() == DiscretizationType.DIS:
grid_type = self.grid_type()
if grid_type == DiscretizationType.DIS:
return 3
elif self.grid_type() == DiscretizationType.DISV:
elif grid_type == DiscretizationType.DISV:
return 2
elif (
self.grid_type() == DiscretizationType.DISU
or self.grid_type() == DiscretizationType.DISL
grid_type == DiscretizationType.DISU
or grid_type == DiscretizationType.DISL
):
return 1

50
flopy/mf6/data/mfdata.py
View File

@ -12,6 +12,7 @@ from ..coordinates.modeldimensions import DataDimensions, DiscretizationType
from ...datbase import DataInterface, DataType
from .mfdatastorage import DataStructureType
from .mfdatautil import to_string
from ...mbase import ModelInterface
class MFTransient:
@ -256,6 +257,10 @@ class MFData(DataInterface):
self._structure_init()
# tie this to the simulation dictionary
sim_data.mfdata[self._path] = self
# set up model grid caching
self._cache_next_grid = False
self._grid_cached = False
self._cached_model_grid = None
def __repr__(self):
return repr(self._get_storage_obj())
@ -300,6 +305,20 @@ class MFData(DataInterface):
"must define plottable in child " "class to use this base class"
)
@property
def _cache_model_grid(self):
return self._cache_next_grid
@_cache_model_grid.setter
def _cache_model_grid(self, cache_model_grid):
if cache_model_grid:
self._cache_next_grid = True
self._grid_cached = False
else:
self._cache_next_grid = False
self._grid_cached = False
self._cached_model_grid = None
def _resync(self):
model = self.model
if model is not None:
@ -440,6 +459,31 @@ class MFData(DataInterface):
# TODO: Implement for each data type
return self._valid
def _get_model_grid(self):
mg = None
if (
self._cache_next_grid
or not self._grid_cached
or self._cached_model_grid is None
):
# construct a new model grid
if isinstance(self._model_or_sim, ModelInterface) and hasattr(
self._model_or_sim, "modelgrid"
):
# get model grid info
mg = self._model_or_sim.modelgrid
else:
mg = None
if self._grid_cached and self._cached_model_grid is not None:
# get the model grid from cache
mg = self._cached_model_grid
elif self._cache_next_grid:
# cache the existing model grid
self._cached_model_grid = mg
self._grid_cached = mg is not None
self._cache_next_grid = False
return mg
def _structure_init(self, data_set=None):
if data_set is None:
# Initialize variables
@ -466,7 +510,11 @@ class MFData(DataInterface):
sim_data = self._simulation_data
const_format = list(sim_data.constant_formatting)
const_format[1] = to_string(
const_val, data_type, self._simulation_data, self._data_dimensions
const_val,
data_type,
self._simulation_data,
self._data_dimensions,
verify_data=self._simulation_data.verify_data,
)
return "{}{}".format(sim_data.indent_string.join(const_format), suffix)

2
flopy/mf6/data/mfdataarray.py
View File

@ -1265,7 +1265,7 @@ class MFArray(MFMultiDimVar):
"not available."
)
modelgrid = self.model.modelgrid
modelgrid = self._get_model_grid()
a = self.array
num_plottable_layers = modelgrid.get_number_plottable_layers(a)

30
flopy/mf6/data/mfdatalist.py
View File

@ -389,8 +389,10 @@ class MFList(mfdata.MFMultiDimVar, DataListInterface):
data_check = None
else:
data_check = data
if data_check is None or (
isinstance(data_check, list) and len(data_check) == 0
if (
data_check is None
or not self._simulation_data.verify_data
or (isinstance(data_check, list) and len(data_check) == 0)
):
check_data = False
if iterable(data_check) and check_data:
@ -428,7 +430,7 @@ class MFList(mfdata.MFMultiDimVar, DataListInterface):
self._simulation_data.debug,
ex,
)
if check_data:
if check_data and self._simulation_data.verify_data:
# verify cellids
self._check_valid_cellids()
@ -438,7 +440,7 @@ class MFList(mfdata.MFMultiDimVar, DataListInterface):
self._model_or_sim, "modelgrid"
):
# get model grid info
mg = self._model_or_sim.modelgrid
mg = self._get_model_grid()
if not mg.is_complete:
return
idomain = mg.idomain
@ -530,8 +532,8 @@ class MFList(mfdata.MFMultiDimVar, DataListInterface):
self._simulation_data.debug,
)
def set_data(self, data, autofill=False):
self._set_data(data, autofill)
def set_data(self, data, autofill=False, check_data=True):
self._set_data(data, autofill, check_data=check_data)
def append_data(self, data):
try:
@ -811,6 +813,7 @@ class MFList(mfdata.MFMultiDimVar, DataListInterface):
data_item.is_cellid,
data_item.possible_cellid,
data_item,
self._simulation_data.verify_data,
)
)
index += 1
@ -988,6 +991,7 @@ class MFList(mfdata.MFMultiDimVar, DataListInterface):
k_data_item.is_cellid,
k_data_item.possible_cellid,
k_data_item,
self._simulation_data.verify_data,
)
)
except Exception as ex:
@ -1047,6 +1051,7 @@ class MFList(mfdata.MFMultiDimVar, DataListInterface):
self._data_dimensions,
False,
data_item=data_item,
verify_data=self._simulation_data.verify_data,
)
)
index += 1
@ -1060,6 +1065,7 @@ class MFList(mfdata.MFMultiDimVar, DataListInterface):
data_item.is_cellid,
data_item.possible_cellid,
data_item,
self._simulation_data.verify_data,
)
)
except Exception as ex:
@ -1455,6 +1461,7 @@ class MFTransientList(MFList, mfdata.MFTransient, DataListInterface):
replace_existing_external=True,
check_data=True,
):
self._cache_model_grid = True
sim_time = self._data_dimensions.package_dim.model_dim[
0
].simulation_time
@ -1478,6 +1485,7 @@ class MFTransientList(MFList, mfdata.MFTransient, DataListInterface):
replace_existing_external,
check_data,
)
self._cache_model_grid = False
def get_data(self, key=None, apply_mult=False, **kwargs):
if self._data_storage is not None and len(self._data_storage) > 0:
@ -1509,6 +1517,7 @@ class MFTransientList(MFList, mfdata.MFTransient, DataListInterface):
return None
def set_data(self, data, key=None, autofill=False):
self._cache_model_grid = True
if isinstance(data, dict) or isinstance(data, OrderedDict):
if "filename" not in data:
# each item in the dictionary is a list for one stress period
@ -1523,8 +1532,14 @@ class MFTransientList(MFList, mfdata.MFTransient, DataListInterface):
self.empty_keys[key] = True
else:
self.empty_keys[key] = False
if "check" in list_item:
check = list_item["check"]
else:
check = True
self._set_data_prep(list_item, key)
super().set_data(list_item, autofill=autofill)
super().set_data(
list_item, autofill=autofill, check_data=check
)
for key in del_keys:
del data[key]
else:
@ -1548,6 +1563,7 @@ class MFTransientList(MFList, mfdata.MFTransient, DataListInterface):
else:
self._set_data_prep(data, key)
super().set_data(data, autofill)
self._cache_model_grid = False
def get_file_entry(
self, key=0, ext_file_action=ExtFileAction.copy_relative_paths

2
flopy/mf6/data/mfdatascalar.py
View File

@ -453,6 +453,7 @@ class MFScalar(mfdata.MFData):
self._simulation_data,
self._data_dimensions,
data_item=data_item,
verify_data=self._simulation_data.verify_data,
)
)
except Exception as ex:
@ -529,6 +530,7 @@ class MFScalar(mfdata.MFData):
self._simulation_data,
self._data_dimensions,
data_item=data_item,
verify_data=self._simulation_data.verify_data,
)
except Exception as ex:
message = (

14
flopy/mf6/data/mfdatautil.py
View File

@ -126,6 +126,7 @@ def to_string(
is_cellid=False,
possible_cellid=False,
data_item=None,
verify_data=True,
):
if data_type == DatumType.double_precision:
if data_item is not None and data_item.support_negative_index:
@ -158,10 +159,14 @@ def to_string(
elif is_cellid or (possible_cellid and isinstance(val, tuple)):
if DatumUtil.is_int(val):
return str(val + 1)
if len(val) > 0 and isinstance(val, str) and val.lower() == "none":
if len(val) == 4 and isinstance(val, str) and val.lower() == "none":
# handle case that cellid is 'none'
return val
if is_cellid and data_dim.get_model_dim(None).model_name is not None:
if (
verify_data
and is_cellid
and data_dim.get_model_dim(None).model_name is not None
):
model_grid = data_dim.get_model_grid()
cellid_size = model_grid.get_num_spatial_coordinates()
if len(val) != cellid_size:
@ -199,10 +204,7 @@ def to_string(
return " ".join(string_val)
elif data_type == DatumType.integer:
if data_item is not None and data_item.numeric_index:
if isinstance(val, str):
return str(int(val) + 1)
else:
return str(int(val) + 1)
return str(int(val) + 1)
return str(int(val))
elif data_type == DatumType.string:
try:

1
flopy/mf6/data/mffileaccess.py
View File

@ -460,6 +460,7 @@ class MFFileAccessArray(MFFileAccess):
self._simulation_data,
self._data_dimensions,
is_cellid,
verify_data=self._simulation_data.verify_data,
)
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()

21
flopy/utils/datautil.py
View File

@ -265,34 +265,34 @@ class PyListUtil:
# consistent delimiter has been found. continue using that
# delimiter without doing further checks
if PyListUtil.delimiter_used is None:
comment_split = line.strip().split("#", 1)
comment_split = line.split("#", 1)
clean_line = comment_split[0].strip().split()
else:
comment_split = line.strip().split("#", 1)
comment_split = line.split("#", 1)
clean_line = (
comment_split[0].strip().split(PyListUtil.delimiter_used)
)
if len(comment_split) > 1:
clean_line.append("#")
clean_line.append(comment_split[1])
clean_line.append(comment_split[1].strip())
else:
# compare against the default split option without comments split
comment_split = line.strip().split("#", 1)
comment_split = line.split("#", 1)
clean_line = comment_split[0].strip().split()
if len(comment_split) > 1:
clean_line.append("#")
clean_line.append(comment_split[1])
clean_line.append(comment_split[1].strip())
# try different delimiters and use the one the breaks the data
# apart the most
max_split_size = len(clean_line)
max_split_type = None
max_split_list = clean_line
for delimiter in PyListUtil.delimiter_list:
comment_split = line.strip().split("#")
comment_split = line.split("#")
alt_split = comment_split[0].strip().split(delimiter)
if len(comment_split) > 1:
alt_split.append("#")
alt_split.append(comment_split[1])
alt_split.append(comment_split[1].strip())
alt_split_len = len(alt_split)
if alt_split_len > max_split_size:
max_split_size = len(alt_split)
@ -318,7 +318,8 @@ class PyListUtil:
arr_fixed_line = []
index = 0
# loop through line to fix quotes and delimiters
while index < len(clean_line):
len_cl = len(clean_line)
while index < len_cl:
item = clean_line[index]
if item and item not in PyListUtil.delimiter_list:
if item and item[0] in PyListUtil.quote_list:
@ -328,9 +329,9 @@ class PyListUtil:
else:
arr_fixed_line.append(item[1:])
# loop until trailing quote found
while index < len(clean_line):
while index < len_cl:
index += 1
if index < len(clean_line):
if index < len_cl:
item = clean_line[index]
if item[-1] in PyListUtil.quote_list:
arr_fixed_line[-1] = "{} {}".format(