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write runnable baseline gwf simulations (#43)
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* write runnable gwf base simulation

* remove temp path checks

* add gwf disu test

* add gwf disv test

* misc cleanup

---------

Co-authored-by: mjreno <[email protected]>
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@mjreno
mjreno and mjreno authored Nov 18, 2024
1 parent 76dee30 commit 59923f0
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Showing 79 changed files with 11,815 additions and 363 deletions.
19 changes: 13 additions & 6 deletions docs/examples/array_example.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,11 +62,12 @@
constant = data_path / "constant.txt"
external = data_path / "external.txt"
shape = (1000, 100)
dtype = "double"

# Open and load a NumPy array representation

fhandle = open(internal)
imfa = MFArray.load(fhandle, data_path, shape, header=False)
imfa = MFArray.load(fhandle, data_path, shape, type=dtype, header=False)

# Get values

Expand All @@ -87,7 +88,7 @@
plt.colorbar()

fhandle = open(constant)
cmfa = MFArray.load(fhandle, data_path, shape, header=False)
cmfa = MFArray.load(fhandle, data_path, shape, type=dtype, header=False)
cvals = cmfa.value
plt.imshow(cvals[0:100])
plt.colorbar()
Expand All @@ -110,7 +111,7 @@
# External

fhandle = open(external)
emfa = MFArray.load(fhandle, data_path, shape, header=False)
emfa = MFArray.load(fhandle, data_path, shape, type=dtype, header=False)
evals = emfa.value
evals

Expand All @@ -135,7 +136,9 @@

fhandle = open(ilayered)
shape = (3, 1000, 100)
ilmfa = MFArray.load(fhandle, data_path, shape, header=False, layered=True)
ilmfa = MFArray.load(
fhandle, data_path, shape, type=dtype, header=False, layered=True
)
vals = ilmfa.value

ilmfa._value # internal storage
Expand Down Expand Up @@ -182,7 +185,9 @@

fhandle = open(clayered)
shape = (3, 1000, 100)
clmfa = MFArray.load(fhandle, data_path, shape, header=False, layered=True)
clmfa = MFArray.load(
fhandle, data_path, shape, type=dtype, header=False, layered=True
)

clmfa._value

Expand Down Expand Up @@ -235,7 +240,9 @@

fhandle = open(mlayered)
shape = (3, 1000, 100)
mlmfa = MFArray.load(fhandle, data_path, shape, header=False, layered=True)
mlmfa = MFArray.load(
fhandle, data_path, shape, type=dtype, header=False, layered=True
)

mlmfa.how

Expand Down
62 changes: 47 additions & 15 deletions flopy4/array.py
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Original file line number Diff line number Diff line change
Expand Up @@ -434,6 +434,16 @@ def load(cls, f, cwd, shape, header=True, **kwargs):
model_shape = kwargs.pop("model_shape", None)
params = kwargs.pop("blk_params", {})
mempath = kwargs.pop("mempath", None)
atype = kwargs.get("type", None)

if atype is not None:
if atype == "integer":
dtype = np.int32
elif atype == "double":
dtype = np.float64
else:
raise ValueError("array spec type not defined")

if model_shape and isinstance(shape, str):
if shape == "(nodes)":
n = math.prod([x for x in model_shape])
Expand All @@ -446,20 +456,30 @@ def load(cls, f, cwd, shape, header=True, **kwargs):
nlay = params.get("dimensions").get("nlay")
nrow = params.get("dimensions").get("nrow")
ncol = params.get("dimensions").get("ncol")
shape = (nlay, nrow, ncol)
elif "disv" in mempath.split("/"):
nlay = params.get("dimensions").get("nlay")
ncpl = params.get("dimensions").get("ncpl")
nodes = params.get("dimensions").get("nodes")
if nrow and ncol:
shape = (nlay, nrow, ncol)
elif ncpl:
nvert = params.get("dimensions").get("nvert")
if shape == "(ncpl)":
shape = ncpl
elif shape == "(ncpl, nlay)":
shape = (nlay, ncpl)
elif nodes:
elif shape == "(nvert)":
shape = nvert
elif "disu" in mempath.split("/"):
nodes = params.get("dimensions").get("nodes")
nja = params.get("dimensions").get("nja")
if "nodes" in shape:
shape = nodes
elif "nja" in shape:
shape = nja
if layered:
nlay = shape[0]
lshp = shape[1:]
objs = []
for _ in range(nlay):
mfa = cls._load(f, cwd, lshp, name)
mfa = cls._load(f, cwd, lshp, dtype=dtype, name=name)
objs.append(mfa)

return MFArray(
Expand All @@ -474,11 +494,17 @@ def load(cls, f, cwd, shape, header=True, **kwargs):
else:
kwargs.pop("layered", None)
return cls._load(
f, cwd, shape, layered=layered, name=name, **kwargs
f,
cwd,
shape,
layered=layered,
dtype=dtype,
name=name,
**kwargs,
)

@classmethod
def _load(cls, f, cwd, shape, layered=False, **kwargs):
def _load(cls, f, cwd, shape, layered=False, dtype=None, **kwargs):
control_line = multi_line_strip(f).split()

if CommonNames.iprn.lower() in control_line:
Expand All @@ -491,25 +517,31 @@ def _load(cls, f, cwd, shape, layered=False, **kwargs):
clpos = 1

if how == MFArrayType.internal:
array = cls.read_array(f)
array = cls.read_array(f, dtype)

elif how == MFArrayType.constant:
array = float(control_line[clpos])
if dtype == np.float64:
array = float(control_line[clpos])
else:
array = int(control_line[clpos])
clpos += 1

elif how == MFArrayType.external:
extpath = Path(control_line[clpos])
fpath = cwd / extpath
with open(fpath) as foo:
array = cls.read_array(foo)
array = cls.read_array(foo, dtype)
clpos += 1

else:
raise NotImplementedError()

factor = None
if len(control_line) > 2:
factor = float(control_line[clpos + 1])
if dtype == np.float64:
factor = float(control_line[clpos + 1])
else:
factor = int(control_line[clpos + 1])

return cls(
shape,
Expand All @@ -521,7 +553,7 @@ def _load(cls, f, cwd, shape, layered=False, **kwargs):
)

@staticmethod
def read_array(f):
def read_array(f, dtype):
"""
Read a MODFLOW 6 array from an open file
into a flat NumPy array representation.
Expand All @@ -532,11 +564,11 @@ def read_array(f):
pos = f.tell()
line = f.readline()
line = line_strip(line)
if not re.match("^[0-9. ]+$", line):
if not re.match("^[-0-9. ]+$", line):
f.seek(pos, 0)
break
astr.append(line)

astr = StringIO(" ".join(astr))
array = np.genfromtxt(astr).ravel()
array = np.genfromtxt(astr, dtype=dtype).ravel()
return array
16 changes: 12 additions & 4 deletions flopy4/block.py
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Original file line number Diff line number Diff line change
Expand Up @@ -225,6 +225,7 @@ def load(cls, f, **kwargs):
name = None
index = None
found = False
period = False
params = dict()
members = cls.params

Expand All @@ -235,15 +236,20 @@ def load(cls, f, **kwargs):
line = f.readline()
if line == "":
raise ValueError("Early EOF, aborting")
if line == "\n":
if line == "\n" or line.lstrip().startswith("#"):
continue
words = strip(line).lower().split()
key = words[0]
if period:
key = "stress_period_data"
else:
key = words[0]
if key == "begin":
found = True
name = words[1]
if len(words) > 2 and str.isdigit(words[2]):
index = int(words[2])
if name == "period":
period = True
elif key == "end":
break
elif found:
Expand All @@ -268,20 +274,22 @@ def load(cls, f, **kwargs):
# TODO: inject from model somehow?
# and remove special handling here
kwrgs["cwd"] = ""
# kwrgs["type"] = param.type
kwrgs["mempath"] = f"{mempath}/{name}"
if ptype is not MFArray:
if ptype is not MFArray and ptype is not MFList:
kwrgs.pop("model_shape", None)
kwrgs.pop("blk_params", None)

params[param.name] = ptype.load(f, **kwrgs)
period = False

return cls(name=name, index=index, params=params)

def write(self, f):
"""Write the block to file."""
index = self.index if self.index is not None else ""
begin = f"BEGIN {self.name.upper()} {index}\n"
end = f"END {self.name.upper()}\n"
end = f"END {self.name.upper()}\n\n"

f.write(begin)
super().write(f)
Expand Down
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