"""
Support for MODPATH 7 particle release configurations. Contains the
ParticleData, CellDataType, FaceDataType, and NodeParticleData classes.
"""
from collections import namedtuple
from itertools import product
from typing import Iterator, Tuple
import numpy as np
import pandas as pd
from numpy.lib.recfunctions import unstructured_to_structured
from ..utils.recarray_utils import create_empty_recarray
[docs]def reversed_product(*iterables, repeat=1):
"""
Like `itertools.product()`, but left-most elements advance first.
Adapted from https://stackoverflow.com/a/32998481/6514033.
"""
for t in product(*reversed(iterables), repeat=repeat):
yield tuple(reversed(t))
[docs]class ParticleData:
"""
Class to create the most basic particle data type (starting location
input style 1). Input style 1 is the most general input style and
provides the most flexibility in customizing starting locations.
Parameters
----------
partlocs : list/tuple of int, list/tuple of list/tuple, or np.ndarray
Particle locations (zero-based) that are either layer, row, column
locations or nodes.
structured : bool
Boolean defining if a structured (True) or unstructured
particle recarray will be created (default is False).
particleids : list, tuple, or np.ndarray
Particle ids for the defined particle locations. If particleids
is None, MODPATH 7 will define the particle ids to each particle
location. If particleids is provided a particle
id must be provided for each partloc (default is None).
localx : float, list, tuple, or np.ndarray
Local x-location of the particle in the cell. If a single value is
provided all particles will have the same localx position. If
a list, tuple, or np.ndarray is provided a localx position must
be provided for each partloc. If localx is None, a value of
0.5 (center of the cell) will be used (default is None).
localy : float, list, tuple, or np.ndarray
Local y-location of the particle in the cell. If a single value is
provided all particles will have the same localy position. If
a list, tuple, or np.ndarray is provided a localy position must
be provided for each partloc. If localy is None, a value of
0.5 (center of the cell) will be used (default is None).
localz : float, list, tuple, or np.ndarray
Local z-location of the particle in the cell. If a single value is
provided all particles will have the same localz position. If
a list, tuple, or np.ndarray is provided a localz position must
be provided for each partloc. If localy is None, a value of
0.5 (center of the cell) will be used (default is None).
timeoffset : float, list, tuple, or np.ndarray
Timeoffset of the particle relative to the release time. If a
single value is provided all particles will have the same
timeoffset. If a list, tuple, or np.ndarray is provided a
timeoffset must be provided for each partloc. If timeoffset is
None, a value of 0. (equal to the release time) will be used
(default is None).
drape : int, list, tuple, or np.ndarray
Drape indicates how particles are treated when starting locations
are specified for cells that are dry. If drape is 0, Particles are
placed in the specified cell. If the cell is dry at the time of
release, the status of the particle is set to unreleased and
removed from the simulation. If drape is 1, particles are placed
in the upper most active grid cell directly beneath the specified
layer, row, column or node location. If a single value is provided
all particles will have the same drape value. If a list, tuple, or
np.ndarray is provided a drape value must be provided for each
partloc. If drape is None, a value of 0 will be used (default
is None).
Examples
--------
>>> import flopy
>>> locs = [(0, 0, 0), (1, 0, 0), (2, 0, 0)]
>>> pd = flopy.modpath.ParticleData(locs, structured=True, drape=0,
... localx=0.5, localy=0.5, localz=1)
"""
def __init__(
self,
partlocs=None,
structured=False,
particleids=None,
localx=None,
localy=None,
localz=None,
timeoffset=None,
drape=None,
):
"""
Class constructor
"""
self.name = "ParticleData"
if structured:
locationstyle = 1
else:
locationstyle = 2
if partlocs is None:
if structured:
partlocs = [(0, 0, 0)]
else:
partlocs = [(0,)]
# create dtype
dtype = []
if structured:
dtype.append(("k", np.int32))
dtype.append(("i", np.int32))
dtype.append(("j", np.int32))
else:
dtype.append(("node", np.int32))
dtype = np.dtype(dtype)
if isinstance(partlocs, (list, tuple)):
# determine if the list or tuple contains lists or tuples
alllsttup = all(isinstance(el, (list, tuple)) for el in partlocs)
if structured:
if alllsttup:
alllen3 = all(len(el) == 3 for el in partlocs)
if not alllen3:
raise ValueError(
"{}: all partlocs entries must have 3 items for "
"structured particle data".format(self.name)
)
else:
raise ValueError(
"{}: partlocs list or tuple "
"for structured particle data should "
"contain list or tuple entries".format(self.name)
)
else:
allint = all(
isinstance(el, (int, np.int32, np.int64))
for el in partlocs
)
# convert to a list of tuples
if allint:
t = []
for el in partlocs:
t.append((el,))
partlocs = t
alllsttup = all(
isinstance(el, (list, tuple)) for el in partlocs
)
if alllsttup:
alllen1 = all(len(el) == 1 for el in partlocs)
if not alllen1:
raise ValueError(
"{}: all entries of partlocs must have 1 items "
"for unstructured particle data".format(self.name)
)
else:
raise ValueError(
"{}: partlocs list or tuple for unstructured particle "
"data should contain integers or a list or tuple with "
"one entry".format(self.name)
)
# convert partlocs to numpy array with proper dtype
partlocs = np.array(partlocs)
if len(partlocs.shape) == 1:
partlocs = partlocs.reshape(len(partlocs), 1)
partlocs = unstructured_to_structured(
np.array(partlocs), dtype=dtype
)
elif isinstance(partlocs, np.ndarray):
# reshape and convert dtype if needed
if len(partlocs.shape) == 1:
partlocs = partlocs.reshape(len(partlocs), 1)
dtypein = partlocs.dtype
if dtypein != dtype:
partlocs = unstructured_to_structured(partlocs, dtype=dtype)
else:
raise ValueError(
f"{self.name}: partlocs must be a list or tuple with lists or tuples, or an ndarray"
)
# localx
if localx is None:
localx = 0.5
else:
if isinstance(localx, (float, int)):
localx = np.ones(partlocs.shape[0], dtype=np.float32) * localx
elif isinstance(localx, (list, tuple)):
localx = np.array(localx, dtype=np.float32)
if isinstance(localx, np.ndarray):
if localx.shape[0] != partlocs.shape[0]:
raise ValueError(
"{}:shape of localx ({}) is not equal to the shape "
"of partlocs ({}).".format(
self.name, localx.shape[0], partlocs.shape[0]
)
)
# localy
if localy is None:
localy = 0.5
else:
if isinstance(localy, (float, int)):
localy = np.ones(partlocs.shape[0], dtype=np.float32) * localy
elif isinstance(localy, (list, tuple)):
localy = np.array(localy, dtype=np.float32)
if isinstance(localy, np.ndarray):
if localy.shape[0] != partlocs.shape[0]:
raise ValueError(
"{}:shape of localy ({}) is not equal to the shape "
"of partlocs ({}).".format(
self.name, localy.shape[0], partlocs.shape[0]
)
)
# localz
if localz is None:
localz = 0.5
else:
if isinstance(localz, (float, int)):
localz = np.ones(partlocs.shape[0], dtype=np.float32) * localz
elif isinstance(localz, (list, tuple)):
localz = np.array(localz, dtype=np.float32)
if isinstance(localz, np.ndarray):
if localz.shape[0] != partlocs.shape[0]:
raise ValueError(
"{}:shape of localz ({}) is not equal to the shape "
"of partlocs ({}).".format(
self.name, localz.shape[0], partlocs.shape[0]
)
)
# timeoffset
if timeoffset is None:
timeoffset = 0.0
else:
if isinstance(timeoffset, (float, int)):
timeoffset = (
np.ones(partlocs.shape[0], dtype=np.float32) * timeoffset
)
elif isinstance(timeoffset, (list, tuple)):
timeoffset = np.array(timeoffset, dtype=np.float32)
if isinstance(timeoffset, np.ndarray):
if timeoffset.shape[0] != partlocs.shape[0]:
raise ValueError(
"{}:shape of timeoffset ({}) is not equal to the "
"shape of partlocs ({}).".format(
self.name, timeoffset.shape[0], partlocs.shape[0]
)
)
# drape
if drape is None:
drape = 0
else:
if isinstance(drape, (float, int)):
drape = np.ones(partlocs.shape[0], dtype=np.float32) * drape
elif isinstance(drape, (list, tuple)):
drape = np.array(drape, dtype=np.int32)
if isinstance(drape, np.ndarray):
if drape.shape[0] != partlocs.shape[0]:
raise ValueError(
"{}:shape of drape ({}) is not equal to the shape "
"of partlocs ({}).".format(
self.name, drape.shape[0], partlocs.shape[0]
)
)
# particleids
if particleids is None:
particleid = False
particleidoption = 0
else:
particleid = True
particleidoption = 1
if isinstance(particleids, (int, float)):
raise TypeError(
"{}:A particleid must be provided for each partloc "
"as a list/tuple/np.ndarray of size {}. "
"A single particleid has been provided.".format(
self.name, partlocs.shape[0]
)
)
elif isinstance(particleids, (list, tuple)):
particleids = np.array(particleids, dtype=np.int32)
if isinstance(particleids, np.ndarray):
if particleids.shape[0] != partlocs.shape[0]:
raise ValueError(
"{}:shape of particleids ({}) is not equal to the "
"shape of partlocs ({}).".format(
self.name, particleids.shape[0], partlocs.shape[0]
)
)
# create empty particle
ncells = partlocs.shape[0]
self.dtype = self._get_dtype(structured, particleid)
particledata = create_empty_recarray(
ncells, self.dtype, default_value=0
)
# fill particle
if structured:
particledata["k"] = partlocs["k"]
particledata["i"] = partlocs["i"]
particledata["j"] = partlocs["j"]
else:
particledata["node"] = partlocs["node"]
particledata["localx"] = localx
particledata["localy"] = localy
particledata["localz"] = localz
particledata["timeoffset"] = timeoffset
particledata["drape"] = drape
if particleid:
particledata["id"] = particleids
self.particlecount = particledata.shape[0]
self.particleidoption = particleidoption
self.locationstyle = locationstyle
self.dtype = particledata.dtype
self.particledata = pd.DataFrame.from_records(particledata)
[docs] def write(self, f=None):
"""
Write the particle data template to a file.
Parameters
----------
f : fileobject
Fileobject that is open with write access
"""
# validate that a valid file object was passed
if not hasattr(f, "write"):
raise ValueError(
"{}: cannot write data for template without passing a valid "
"file object ({}) open for writing".format(self.name, f)
)
# particle data item 4 and 5
d = np.recarray.copy(self.particledata.to_records(index=False))
lnames = [name.lower() for name in d.dtype.names]
# Add one to the kij and node indices
for idx in (
"k",
"i",
"j",
"node",
):
if idx in lnames:
d[idx] += 1
# Add one to the particle id if required
if self.particleidoption == 0 and "id" in lnames:
d["id"] += 1
# write the particle data
fmt = self._fmt_string + "\n"
for v in d:
f.write(fmt.format(*v))
[docs] def to_coords(self, grid, localz=False) -> Iterator[tuple]:
"""
Compute particle coordinates on the given grid.
Parameters
----------
grid : flopy.discretization.grid.Grid
The grid on which to locate particle release points.
localz : bool, optional
Whether to return local z coordinates.
Returns
-------
Generates coordinate tuples (x, y, z)
"""
def cvt_xy(p, vs):
mn, mx = min(vs), max(vs)
span = mx - mn
return mn + span * p
if grid.grid_type == "structured":
if not hasattr(self.particledata, "k"):
raise ValueError(
"Particle representation is not structured but grid is"
)
def cvt_z(p, k, i, j):
mn, mx = (
grid.botm[k, i, j],
grid.top[i, j] if k == 0 else grid.botm[k - 1, i, j],
)
span = mx - mn
return mn + span * p
def convert(row) -> Tuple[float, float, float]:
verts = grid.get_cell_vertices(row.i, row.j)
xs, ys = list(zip(*verts))
return [
cvt_xy(row.localx, xs),
cvt_xy(row.localy, ys),
row.localz
if localz
else cvt_z(row.localz, row.k, row.i, row.j),
]
else:
if hasattr(self.particledata, "k"):
raise ValueError(
"Particle representation is structured but grid is not"
)
def cvt_z(p, nn):
k, j = grid.get_lni([nn])[0]
mn, mx = (
grid.botm[k, j],
grid.top[j] if k == 0 else grid.botm[k - 1, j],
)
span = mx - mn
return mn + span * p
def convert(row) -> Tuple[float, float, float]:
verts = grid.get_cell_vertices(row.node)
xs, ys = list(zip(*verts))
return [
cvt_xy(row.localx, xs),
cvt_xy(row.localy, ys),
row.localz if localz else cvt_z(row.localz, row.node),
]
for t in self.particledata.itertuples():
yield convert(t)
[docs] def to_prp(self, grid, localz=False) -> Iterator[tuple]:
"""
Convert particle data to PRT particle release point (PRP)
package data entries for the given grid. A model grid is
required because MODPATH supports several ways to specify
particle release locations by cell ID and subdivision info
or local coordinates, but PRT expects global coordinates.
Parameters
----------
grid : flopy.discretization.grid.Grid
The grid on which to locate particle release points.
localz : bool, optional
Whether to return local z coordinates.
Returns
-------
Generates PRT particle release point (PRP) package
data tuples: release point index, k, [i,] j, x, y, z.
If the grid is not structured, i is omitted and j is
the within-layer cell index for vertex grids.
"""
for i, (t, c) in enumerate(
zip(
self.particledata.itertuples(index=False),
self.to_coords(grid, localz),
)
):
row = [i] # release point index (irpt)
if "node" in self.particledata:
k, j = grid.get_lni([t.node])[0]
row.extend([(k, j)])
else:
row.extend([t.k, t.i, t.j])
row.extend(c)
yield tuple(row)
def _get_dtype(self, structured, particleid):
"""
define the dtype for a structured or unstructured
particledata recarray. Optionally, include a particleid column in
the dtype.
Parameters
----------
structured : bool
Boolean defining if a structured (True) or unstructured
particle dtype will be created.
particleid : bool
Boolean defining if the dtype will include a particle id
column.
Returns
-------
dtype : numpy dtype
Examples
--------
>>> import flopy.modpath as fmp
>>> dtype = fmp.ParticleGroup.get_particledata_dtype(structured=True,
... particleid=True)
"""
dtype = []
if particleid:
dtype.append(("id", np.int32))
if structured:
dtype.append(("k", np.int32))
dtype.append(("i", np.int32))
dtype.append(("j", np.int32))
else:
dtype.append(("node", np.int32))
dtype.append(("localx", np.float32))
dtype.append(("localy", np.float32))
dtype.append(("localz", np.float32))
dtype.append(("timeoffset", np.float32))
dtype.append(("drape", np.int32))
return np.dtype(dtype)
@property
def _fmt_string(self):
"""
Returns a python-style fmt string to write particle data
that corresponds to the dtype
Parameters
----------
Returns
-------
fmt : str
python format string with space delimited entries
"""
fmts = []
for field in self.dtype.descr:
vtype = field[1][1].lower()
if vtype == "i" or vtype == "b":
fmts.append("{:9d}")
elif vtype == "f":
if field[1][2] == 8:
fmts.append("{:23.16g}")
else:
fmts.append("{:15.7g}")
elif vtype == "o":
fmts.append("{:9s}")
elif vtype == "s":
raise TypeError(
"Particles.fmt_string error: 'str' type found in dtype. "
"This gives unpredictable results when recarray to file - "
"change to 'object' type"
)
else:
raise TypeError(
f"MfList.fmt_string error: unknown vtype in field: {field}"
)
return " " + " ".join(fmts)
[docs]class FaceDataType:
"""
Face data type class to create a MODPATH 7 particle location template for
input style 2, 3, and 4 on cell faces (templatesubdivisiontype = 2).
Parameters
----------
drape : int
Drape indicates how particles are treated when starting locations
are specified for cells that are dry. If drape is 0, Particles are
placed in the specified cell. If the cell is dry at the time of
release, the status of the particle is set to unreleased and
removed from the simulation. If drape is 1, particles are placed
in the upper most active grid cell directly beneath the specified
layer, row, column or node location (default is 0).
verticaldivisions1 : int
The number of vertical subdivisions that define the two-dimensional
array of particles on cell face 1 (default is 3).
horizontaldivisions1 : int
The number of horizontal subdivisions that define the two-dimensional
array of particles on cell face 1 (default is 3).
verticaldivisions2 : int
The number of vertical subdivisions that define the two-dimensional
array of particles on cell face 2 (default is 3).
horizontaldivisions2 : int
The number of horizontal subdivisions that define the two-dimensional
array of particles on cell face 2 (default is 3).
verticaldivisions3 : int
The number of vertical subdivisions that define the two-dimensional
array of particles on cell face 3 (default is 3).
horizontaldivisions3 : int
The number of horizontal subdivisions that define the two-dimensional
array of particles on cell face 3 (default is 3).
verticaldivisions4 : int
The number of vertical subdivisions that define the two-dimensional
array of particles on cell face 4 (default is 3).
horizontaldivisions4 : int
The number of horizontal subdivisions that define the two-dimensional
array of particles on cell face 4 (default is 3).
rowdivisions5 : int
The number of row subdivisions that define the two-dimensional array
of particles on the bottom cell face (face 5) (default is 3).
columndivisions5 : int
The number of column subdivisions that define the two-dimensional array
of particles on the bottom cell face (face 5) (default is 3).
rowdivisions6 : int
The number of row subdivisions that define the two-dimensional array
of particles on the top cell face (face 6) (default is 3).
columndivisions6 : int
The number of column subdivisions that define the two-dimensional array
of particles on the top cell face (face 6) (default is 3).
Examples
--------
>>> import flopy
>>> fd = flopy.modpath.FaceDataType()
"""
def __init__(
self,
drape=0,
verticaldivisions1=3,
horizontaldivisions1=3,
verticaldivisions2=3,
horizontaldivisions2=3,
verticaldivisions3=3,
horizontaldivisions3=3,
verticaldivisions4=3,
horizontaldivisions4=3,
rowdivisions5=3,
columndivisions5=3,
rowdivisions6=3,
columndivisions6=3,
):
"""
Class constructor
"""
self.name = "FaceDataType"
# assign attributes
self.templatesubdivisiontype = 1
self.drape = drape
self.verticaldivisions1 = verticaldivisions1
self.horizontaldivisions1 = horizontaldivisions1
self.verticaldivisions2 = verticaldivisions2
self.horizontaldivisions2 = horizontaldivisions2
self.verticaldivisions3 = verticaldivisions3
self.horizontaldivisions3 = horizontaldivisions3
self.verticaldivisions4 = verticaldivisions4
self.horizontaldivisions4 = horizontaldivisions4
self.rowdivisions5 = rowdivisions5
self.columndivisions5 = columndivisions5
self.rowdivisions6 = rowdivisions6
self.columndivisions6 = columndivisions6
[docs] def write(self, f=None):
"""
Parameters
----------
f : fileobject
Fileobject that is open with write access
Returns
-------
"""
# validate that a valid file object was passed
if not hasattr(f, "write"):
raise ValueError(
"{}: cannot write data for template "
"without passing a valid file object ({}) "
"open for writing".format(self.name, f)
)
# item 4
fmt = 12 * " {}" + "\n"
line = fmt.format(
self.verticaldivisions1,
self.horizontaldivisions1,
self.verticaldivisions2,
self.horizontaldivisions2,
self.verticaldivisions3,
self.horizontaldivisions3,
self.verticaldivisions4,
self.horizontaldivisions4,
self.rowdivisions5,
self.columndivisions5,
self.rowdivisions6,
self.columndivisions6,
)
f.write(line)
[docs]class CellDataType:
"""
Cell data type class to create a MODPATH 7 particle location template for
input style 2, 3, and 4 in cells (templatesubdivisiontype = 2).
Parameters
----------
drape : int
Drape indicates how particles are treated when starting locations
are specified for cells that are dry. If drape is 0, Particles are
placed in the specified cell. If the cell is dry at the time of
release, the status of the particle is set to unreleased and
removed from the simulation. If drape is 1, particles are placed
in the upper most active grid cell directly beneath the specified
layer, row, column or node location (default is 0).
columncelldivisions : int
Number of particles in a cell in the column (x-coordinate)
direction (default is 3).
rowcelldivisions : int
Number of particles in a cell in the row (y-coordinate)
direction (default is 3).
layercelldivisions : int
Number of particles in a cell in the layer (z-coordinate)
direction (default is 3).
Examples
--------
>>> import flopy
>>> cd = flopy.modpath.CellDataType()
"""
def __init__(
self,
drape=0,
columncelldivisions=3,
rowcelldivisions=3,
layercelldivisions=3,
):
"""
Class constructor
"""
self.name = "CellDataType"
# assign attributes
self.templatesubdivisiontype = 2
self.drape = drape
self.columncelldivisions = columncelldivisions
self.rowcelldivisions = rowcelldivisions
self.layercelldivisions = layercelldivisions
[docs] def write(self, f=None):
"""
Write the cell data template to a file.
Parameters
----------
f : fileobject
Fileobject that is open with write access
"""
# validate that a valid file object was passed
if not hasattr(f, "write"):
raise ValueError(
"{}: cannot write data for template "
"without passing a valid file object ({}) "
"open for writing".format(self.name, f)
)
# item 5
fmt = " {} {} {}\n"
line = fmt.format(
self.columncelldivisions,
self.rowcelldivisions,
self.layercelldivisions,
)
f.write(line)
Extent = namedtuple(
"Extent",
[
"minx",
"maxx",
"miny",
"maxy",
"minz",
"maxz",
"xspan",
"yspan",
"zspan",
],
)
[docs]def get_extent(grid, k=None, i=None, j=None, nn=None, localz=False) -> Extent:
# get cell coords and span in each dimension
if not (k is None or i is None or j is None):
verts = grid.get_cell_vertices(i, j)
minz, maxz = (
(0, 1)
if localz
else (
grid.botm[k, i, j],
grid.top[i, j] if k == 0 else grid.botm[k - 1, i, j],
)
)
elif nn is not None:
verts = grid.get_cell_vertices(nn)
if grid.grid_type == "structured":
k, i, j = grid.get_lrc([nn])[0]
minz, maxz = (
grid.botm[k, i, j],
grid.top[i, j] if k == 0 else grid.botm[k - 1, i, j],
)
else:
k, j = grid.get_lni([nn])[0]
minz, maxz = (
(0, 1)
if localz
else (
grid.botm[k, j],
grid.top[j] if k == 0 else grid.botm[k - 1, j],
)
)
else:
raise ValueError(
"A cell (node) must be specified by indices (for structured grids) or node number (for vertex/unstructured)"
)
xs, ys = list(zip(*verts))
minx, maxx = min(xs), max(xs)
miny, maxy = min(ys), max(ys)
xspan = maxx - minx
yspan = maxy - miny
zspan = maxz - minz
return Extent(minx, maxx, miny, maxy, minz, maxz, xspan, yspan, zspan)
[docs]def get_face_release_points(
subdivisiondata, cellid, extent
) -> Iterator[tuple]:
"""
Get release points for MODPATH 7 input style 2, template
subdivision style 1, i.e. face (2D) subdivision, for the
given cell with the given extent.
"""
# Product incrementing left elements first, to
# match the release point ordering used by MP7
product = reversed_product
# x1 (west)
if (
subdivisiondata.verticaldivisions1 > 0
and subdivisiondata.horizontaldivisions1 > 0
):
yincr = extent.yspan / subdivisiondata.horizontaldivisions1
ylocs = [
(extent.miny + (yincr * 0.5) + (yincr * d))
for d in range(subdivisiondata.horizontaldivisions1)
]
zincr = extent.zspan / subdivisiondata.verticaldivisions1
zlocs = [
(extent.minz + (zincr * 0.5) + (zincr * d))
for d in range(subdivisiondata.verticaldivisions1)
]
for p in product(*[ylocs, zlocs]):
yield cellid + [extent.minx, p[0], p[1]]
# x2 (east)
if (
subdivisiondata.verticaldivisions2 > 0
and subdivisiondata.horizontaldivisions2 > 0
):
yincr = extent.yspan / subdivisiondata.horizontaldivisions2
ylocs = [
(extent.miny + (yincr * 0.5) + (yincr * d))
for d in range(subdivisiondata.horizontaldivisions2)
]
zincr = extent.zspan / subdivisiondata.verticaldivisions2
zlocs = [
(extent.minz + (zincr * 0.5) + (zincr * d))
for d in range(subdivisiondata.verticaldivisions2)
]
for p in product(*[ylocs, zlocs]):
yield cellid + [extent.maxx, p[0], p[1]]
# y1 (south)
if (
subdivisiondata.verticaldivisions3 > 0
and subdivisiondata.horizontaldivisions3 > 0
):
xincr = extent.xspan / subdivisiondata.horizontaldivisions3
xlocs = [
(extent.minx + (xincr * 0.5) + (xincr * rd))
for rd in range(subdivisiondata.horizontaldivisions3)
]
zincr = extent.zspan / subdivisiondata.verticaldivisions3
zlocs = [
(extent.minz + (zincr * 0.5) + (zincr * d))
for d in range(subdivisiondata.verticaldivisions3)
]
for p in product(*[xlocs, zlocs]):
yield cellid + [p[0], extent.miny, p[1]]
# y2 (north)
if (
subdivisiondata.verticaldivisions4 > 0
and subdivisiondata.horizontaldivisions4 > 0
):
xincr = extent.xspan / subdivisiondata.horizontaldivisions4
xlocs = [
(extent.minx + (xincr * 0.5) + (xincr * rd))
for rd in range(subdivisiondata.horizontaldivisions4)
]
zincr = extent.zspan / subdivisiondata.verticaldivisions4
zlocs = [
(extent.minz + (zincr * 0.5) + (zincr * d))
for d in range(subdivisiondata.verticaldivisions4)
]
for p in product(*[xlocs, zlocs]):
yield cellid + [p[0], extent.maxy, p[1]]
# z1 (bottom)
if (
subdivisiondata.rowdivisions5 > 0
and subdivisiondata.columndivisions5 > 0
):
xincr = extent.xspan / subdivisiondata.columndivisions5
xlocs = [
(extent.minx + (xincr * 0.5) + (xincr * rd))
for rd in range(subdivisiondata.columndivisions5)
]
yincr = extent.yspan / subdivisiondata.rowdivisions5
ylocs = [
(extent.miny + (yincr * 0.5) + (yincr * rd))
for rd in range(subdivisiondata.rowdivisions5)
]
for p in product(*[xlocs, ylocs]):
yield cellid + [p[0], p[1], extent.minz]
# z2 (top)
if (
subdivisiondata.rowdivisions6 > 0
and subdivisiondata.columndivisions6 > 0
):
xincr = extent.xspan / subdivisiondata.columndivisions6
xlocs = [
(extent.minx + (xincr * 0.5) + (xincr * rd))
for rd in range(subdivisiondata.columndivisions6)
]
yincr = extent.yspan / subdivisiondata.rowdivisions6
ylocs = [
(extent.miny + (yincr * 0.5) + (yincr * rd))
for rd in range(subdivisiondata.rowdivisions6)
]
for p in product(*[xlocs, ylocs]):
yield cellid + [p[0], p[1], extent.maxz]
[docs]def get_cell_release_points(
subdivisiondata, cellid, extent
) -> Iterator[tuple]:
"""
Get release points for MODPATH 7 input style 2, template
subdivision type 2, i.e. cell (3D) subdivision, for the
given cell with the given extent.
"""
# Product incrementing left elements first, to
# match the release point ordering used by MP7
product = reversed_product
xincr = extent.xspan / subdivisiondata.columncelldivisions
xlocs = [
(extent.minx + (xincr * 0.5) + (xincr * rd))
for rd in range(subdivisiondata.columncelldivisions)
]
yincr = extent.yspan / subdivisiondata.rowcelldivisions
ylocs = [
(extent.miny + (yincr * 0.5) + (yincr * d))
for d in range(subdivisiondata.rowcelldivisions)
]
zincr = extent.zspan / subdivisiondata.layercelldivisions
zlocs = [
(extent.minz + (zincr * 0.5) + (zincr * d))
for d in range(subdivisiondata.layercelldivisions)
]
for p in product(*[xlocs, ylocs, zlocs]):
yield cellid + [p[0], p[1], p[2]]
[docs]def get_release_points(
subdivisiondata, grid, k=None, i=None, j=None, nn=None, localz=False
) -> Iterator[tuple]:
"""
Get MODPATH 7 release point tuples for the given cell.
"""
if nn is None and (k is None or i is None or j is None):
raise ValueError(
"A cell (node) must be specified by indices (for structured grids) or node number (for vertex/unstructured)"
)
cellid = [k, i, j] if nn is None else [nn]
extent = get_extent(grid, k, i, j, nn, localz)
if isinstance(subdivisiondata, FaceDataType):
return get_face_release_points(subdivisiondata, cellid, extent)
elif isinstance(subdivisiondata, CellDataType):
return get_cell_release_points(subdivisiondata, cellid, extent)
else:
raise ValueError(
f"Unsupported subdivision data type: {type(subdivisiondata)}"
)
[docs]class LRCParticleData:
"""
MODPATH 7 particle release location template class for particle input style 2.
Assigns particles to locations on cell faces (templatesubdivisiontype=1) and/or
in cells (templatesubdivisiontype=2) for cells specified by (layer, row, column).
Parameters
----------
subdivisiondata : FaceDataType, CellDataType or array-like of such, optional
Particle template(s) defining how particles are arranged within each cell.
If None, defaults to CellDataType with 27 particles per cell (default is None).
lrcregions : array-like of array-like, optional
0-based regions (minlayer, minrow, mincolumn, maxlayer, maxrow, maxcolumn).
If subdivisiondata is array-like, regions must be the same length.
If None, particles are placed in the first model cell (default is None).
Examples
--------
>>> import flopy
>>> pg = flopy.modpath.LRCParticleData(lrcregions=[[0, 0, 0, 3, 10, 10]])
"""
def __init__(self, subdivisiondata=None, lrcregions=None):
"""
Class constructor
"""
self.name = "LRCParticleData"
if subdivisiondata is None:
subdivisiondata = CellDataType()
if lrcregions is None:
lrcregions = [[[0, 0, 0, 0, 0, 0]]]
if isinstance(subdivisiondata, (CellDataType, FaceDataType)):
subdivisiondata = [subdivisiondata]
for idx, fd in enumerate(subdivisiondata):
if not isinstance(fd, (CellDataType, FaceDataType)):
raise TypeError(
"{}: facedata item {} is of type {} instead of an "
"instance of CellDataType or FaceDataType".format(
self.name, idx, type(fd)
)
)
# validate lrcregions data
if isinstance(lrcregions, (list, tuple, np.ndarray)):
# determine if the list or tuple contains lists or tuples
alllsttup = all(
isinstance(el, (list, tuple, np.ndarray)) for el in lrcregions
)
if not alllsttup:
raise TypeError(
"{}: lrcregions should be "
"a list with lists, tuples, or arrays".format(self.name)
)
t = []
for lrcregion in lrcregions:
t.append(np.array(lrcregion, dtype=np.int32))
lrcregions = t
else:
raise TypeError(
"{}: lrcregions should be a list of lists, tuples, or arrays "
"not a {}.".format(self.name, type(lrcregions))
)
# validate size of nodes relative to subdivisiondata
shape = len(subdivisiondata)
if len(lrcregions) != shape:
raise ValueError(
"{}: lrcregions data must have {} rows but a total of {} rows "
"were provided.".format(self.name, shape, lrcregions.shape[0])
)
# validate that there are 6 columns in each lrcregions entry
for idx, lrcregion in enumerate(lrcregions):
shapel = lrcregion.shape
if len(shapel) == 1:
lrcregions[idx] = lrcregion.reshape(1, shapel)
shapel = lrcregion[idx].shape
if shapel[1] != 6:
raise ValueError(
"{}: Each lrcregions entry must "
"have 6 columns passed lrcregions has "
"{} columns".format(self.name, shapel[1])
)
totalcellregioncount = 0
for lrcregion in lrcregions:
totalcellregioncount += lrcregion.shape[0]
# assign attributes
self.particletemplatecount = shape
self.totalcellregioncount = totalcellregioncount
self.subdivisiondata = subdivisiondata
self.lrcregions = lrcregions
[docs] def write(self, f=None):
"""
Write the layer-row-column particle data template to a file.
Parameters
----------
f : fileobject
Fileobject that is open with write access
"""
# validate that a valid file object was passed
if not hasattr(f, "write"):
raise ValueError(
"{}: cannot write data for template "
"without passing a valid file object ({}) "
"open for writing".format(self.name, f)
)
# item 2
f.write(f"{self.particletemplatecount} {self.totalcellregioncount}\n")
for sd, region in zip(self.subdivisiondata, self.lrcregions):
# item 3
f.write(
f"{sd.templatesubdivisiontype} {region.shape[0]} {sd.drape}\n"
)
# item 4 or 5
sd.write(f)
# item 6
for row in region:
line = ""
for lrc in row:
line += f"{lrc + 1} "
line += "\n"
f.write(line)
[docs] def to_coords(self, grid, localz=False) -> Iterator[tuple]:
"""
Compute global particle coordinates on the given grid.
Parameters
----------
grid : flopy.discretization.grid.Grid
The grid on which to locate particle release points.
localz : bool, optional
Whether to return local z coordinates.
Returns
-------
Generator of coordinate tuples (x, y, z)
"""
for region in self.lrcregions:
for row in region:
mink, mini, minj, maxk, maxi, maxj = row
for k in range(mink, maxk + 1):
for i in range(mini, maxi + 1):
for j in range(minj, maxj + 1):
for sd in self.subdivisiondata:
for rpt in get_release_points(
sd, grid, k, i, j, localz=localz
):
yield (*rpt[3:6],)
[docs] def to_prp(self, grid, localz=False) -> Iterator[tuple]:
"""
Convert particle data to PRT particle release point (PRP)
package data entries for the given grid. A model grid is
required because MODPATH supports several ways to specify
particle release locations by cell ID and subdivision info
or local coordinates, but PRT expects global coordinates.
Parameters
----------
grid : flopy.discretization.grid.Grid
The grid on which to locate particle release points.
localz : bool, optional
Whether to return local z coordinates.
Returns
-------
Generates PRT particle release point (PRP) package
data tuples: release point index, k, i, j, x, y, z
"""
if grid.grid_type != "structured":
raise ValueError(
"Particle representation is structured but grid is not"
)
irpt_offset = 0
for region in self.lrcregions:
for row in region:
mink, mini, minj, maxk, maxi, maxj = row
for k in range(mink, maxk + 1):
for i in range(mini, maxi + 1):
for j in range(minj, maxj + 1):
for sd in self.subdivisiondata:
for irpt, rpt in enumerate(
get_release_points(
sd, grid, k, i, j, localz=localz
)
):
assert rpt[0] == k
assert rpt[1] == i
assert rpt[2] == j
yield (
irpt_offset + irpt,
k,
i,
j,
rpt[3],
rpt[4],
rpt[5],
)
irpt_offset += irpt + 1
[docs]class NodeParticleData:
"""
MODPATH 7 particle release location template class for particle input style 3.
Assigns particles to locations on cell faces (templatesubdivisiontype=1) and/or
in cells (templatesubdivisiontype=2) for cells specified by node number
Parameters
----------
subdivisiondata : FaceDataType, CellDataType array-like of such, optional
Particle template(s) defining how particles are arranged within each cell.
If None, defaults to CellDataType with 27 particles per cell (default is None).
nodes : int or array-like of ints, optional
0-based node numbers. If subdivisiondata is array-like, nodes must be array-
like of the same length. If None, particles are placed in the first model cell
(default is None).
Examples
--------
>>> import flopy
>>> pg = flopy.modpath.NodeParticleData(nodes=[100, 101])
"""
def __init__(self, subdivisiondata=None, nodes=None):
"""
Class constructor
"""
self.name = "NodeParticleData"
if subdivisiondata is None:
subdivisiondata = CellDataType()
if nodes is None:
nodes = 0
if isinstance(subdivisiondata, (CellDataType, FaceDataType)):
subdivisiondata = [subdivisiondata]
if isinstance(nodes, (int, np.int32, np.int64)):
nodes = [(nodes,)]
elif isinstance(nodes, (float, np.float32, np.float64)):
raise TypeError(
"{}: nodes is of type {} but must be an int if a "
"single value is passed".format(self.name, type(nodes))
)
for idx, fd in enumerate(subdivisiondata):
if not isinstance(fd, (CellDataType, FaceDataType)):
raise TypeError(
"{}: facedata item {} is of type {} instead of an "
"instance of CellDataType or FaceDataType".format(
self.name, idx, type(fd)
)
)
# validate nodes data
if isinstance(nodes, np.ndarray):
if len(nodes.shape) == 1:
nodes = nodes.reshape(1, nodes.shape[0])
# convert to a list of numpy arrays
nodes = [
np.array(nodes[i, :], dtype=np.int32)
for i in range(nodes.shape[0])
]
elif isinstance(nodes, (list, tuple)):
# convert a single list/tuple to a list of tuples if only one
# entry in subdivisiondata
if len(subdivisiondata) == 1:
if len(nodes) > 1:
nodes = [tuple(nodes)]
# determine if the list or tuple contains lists or tuples
alllsttup = all(
isinstance(el, (list, tuple, np.ndarray)) for el in nodes
)
if not alllsttup:
raise TypeError(
"{}: nodes should be "
"a list or tuple with lists or tuple if a single "
"int or numpy array is not provided".format(self.name)
)
t = []
for idx in range(len(nodes)):
t.append(np.array(nodes[idx], dtype=np.int32))
nodes = t
else:
raise TypeError(
"{}: nodes should be a single integer, a numpy array, or a "
"list/tuple or lists/tuples.".format(self.name)
)
# validate size of nodes relative to subdivisiondata
shape = len(subdivisiondata)
if len(nodes) != shape:
raise ValueError(
"{}: node data must have {} rows but a total of {} rows were "
"provided.".format(self.name, shape, nodes.shape[0])
)
totalcellcount = 0
for t in nodes:
totalcellcount += t.shape[0]
# assign attributes
self.particletemplatecount = shape
self.totalcellcount = totalcellcount
self.subdivisiondata = subdivisiondata
self.nodedata = nodes
[docs] def write(self, f=None):
"""
Write the node particle data template to a file.
Parameters
----------
f : fileobject
Fileobject that is open with write access
"""
# validate that a valid file object was passed
if not hasattr(f, "write"):
raise ValueError(
"{}: cannot write data for template "
"without passing a valid file object ({}) "
"open for writing".format(self.name, f)
)
# item 2
f.write(f"{self.particletemplatecount} {self.totalcellcount}\n")
for sd, nodes in zip(self.subdivisiondata, self.nodedata):
# item 3
f.write(
f"{sd.templatesubdivisiontype} {nodes.shape[0]} {sd.drape}\n"
)
# item 4 or 5
sd.write(f)
# item 6
line = ""
for idx, node in enumerate(nodes):
line += f" {node + 1}"
lineend = False
if idx > 0:
if idx % 10 == 0 or idx == nodes.shape[0] - 1:
lineend = True
if lineend:
line += "\n"
f.write(line)
[docs] def to_coords(self, grid, localz=False) -> Iterator[tuple]:
"""
Compute global particle coordinates on the given grid.
Parameters
----------
grid : flopy.discretization.grid.Grid
The grid on which to locate particle release points.
localz : bool, optional
Whether to return local z coordinates.
Returns
-------
Generator of coordinate tuples (x, y, z)
"""
for sd in self.subdivisiondata:
for nd in self.nodedata:
for rpt in get_release_points(
sd, grid, nn=int(nd[0]), localz=localz
):
yield (*rpt[1:4],)
[docs] def to_prp(self, grid, localz=False) -> Iterator[tuple]:
"""
Convert particle data to PRT particle release point (PRP)
package data entries for the given grid. A model grid is
required because MODPATH supports several ways to specify
particle release locations by cell ID and subdivision info
or local coordinates, but PRT expects global coordinates.
Parameters
----------
grid : flopy.discretization.grid.Grid
The grid on which to locate particle release points.
localz : bool, optional
Whether to return local z coordinates.
Returns
-------
Generator of PRT particle release point (PRP) package
data tuples: release point index, k, j, x, y, z
"""
for sd in self.subdivisiondata:
for nd in self.nodedata:
for irpt, rpt in enumerate(
get_release_points(sd, grid, nn=int(nd[0]), localz=localz)
):
row = [irpt]
if grid.grid_type == "structured":
k, i, j = grid.get_lrc([rpt[0]])[0]
row.extend([k, i, j])
else:
k, j = grid.get_lni([rpt[0]])[0]
row.extend([(k, j)])
row.extend([rpt[1], rpt[2], rpt[3]])
yield tuple(row)