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Remove idomain from Dataset #250

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merged 5 commits into from
Aug 25, 2023
Merged

Remove idomain from Dataset #250

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4ddd093
Remove idomain from Dataset
rubencalje Aug 25, 2023
cec77d4
Add docstring to get_idomain
rubencalje Aug 25, 2023
a9002da
Fix tests and rename "active" to "active_domain"
rubencalje Aug 25, 2023
94198fc
set idomain above/below the first/last active layer to 0
rubencalje Aug 25, 2023
a525f7d
Change typo
rubencalje Aug 25, 2023
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40 changes: 13 additions & 27 deletions docs/examples/01_basic_model.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -76,7 +75,7 @@
"steady_state = True\n",
"start_time = \"2015-1-1\"\n",
"add_northsea = True\n",
"starting_head = 1.0\n"
"starting_head = 1.0"
]
},
{
Expand All @@ -103,7 +102,7 @@
")\n",
"\n",
"if add_northsea:\n",
" ds = nlmod.read.rws.add_northsea(ds, cachedir=cachedir)\n"
" ds = nlmod.read.rws.add_northsea(ds, cachedir=cachedir)"
]
},
{
Expand Down Expand Up @@ -134,7 +133,7 @@
"ic = nlmod.gwf.ic(ds, gwf, starting_head=starting_head)\n",
"\n",
"# Create the output control package\n",
"oc = nlmod.gwf.oc(ds, gwf)\n"
"oc = nlmod.gwf.oc(ds, gwf)"
]
},
{
Expand All @@ -152,7 +151,7 @@
"ds.update(rws_ds)\n",
"\n",
"# build ghb package\n",
"ghb = nlmod.gwf.ghb(ds, gwf, bhead=f\"{da_name}_stage\", cond=f\"{da_name}_cond\")\n"
"ghb = nlmod.gwf.ghb(ds, gwf, bhead=f\"{da_name}_stage\", cond=f\"{da_name}_cond\")"
]
},
{
Expand All @@ -167,7 +166,7 @@
"ds.update(ahn_ds)\n",
"\n",
"# build surface level drain package\n",
"drn = nlmod.gwf.surface_drain_from_ds(ds, gwf, resistance=10.0)\n"
"drn = nlmod.gwf.surface_drain_from_ds(ds, gwf, resistance=10.0)"
]
},
{
Expand All @@ -177,8 +176,8 @@
"outputs": [],
"source": [
"# add constant head cells at model boundaries\n",
"ds.update(nlmod.grid.mask_model_edge(ds, ds[\"idomain\"]))\n",
"chd = nlmod.gwf.chd(ds, gwf, mask=\"edge_mask\", head=\"starting_head\")\n"
"ds.update(nlmod.grid.mask_model_edge(ds))\n",
"chd = nlmod.gwf.chd(ds, gwf, mask=\"edge_mask\", head=\"starting_head\")"
]
},
{
Expand All @@ -193,7 +192,7 @@
"ds.update(knmi_ds)\n",
"\n",
"# create recharge package\n",
"rch = nlmod.gwf.rch(ds, gwf)\n"
"rch = nlmod.gwf.rch(ds, gwf)"
]
},
{
Expand All @@ -209,7 +208,7 @@
"metadata": {},
"outputs": [],
"source": [
"ds\n"
"ds"
]
},
{
Expand All @@ -228,7 +227,7 @@
"metadata": {},
"outputs": [],
"source": [
"nlmod.sim.write_and_run(sim, ds, write_ds=True, script_path=\"01_basic_model.ipynb\")\n"
"nlmod.sim.write_and_run(sim, ds, write_ds=True, script_path=\"01_basic_model.ipynb\")"
]
},
{
Expand All @@ -246,7 +245,7 @@
"outputs": [],
"source": [
"ax = nlmod.plot.modelgrid(ds)\n",
"nlmod.plot.surface_water(ds, ax=ax)\n"
"nlmod.plot.surface_water(ds, ax=ax)"
]
},
{
Expand All @@ -265,7 +264,7 @@
"fig, axes = nlmod.plot.get_map(ds.extent, nrows=2, ncols=2, figsize=14)\n",
"ds[\"ahn\"].plot(ax=axes[0][0])\n",
"ds[\"botm\"][0].plot(ax=axes[0][1])\n",
"ds[\"idomain\"][0].plot(ax=axes[1][0])\n",
"nlmod.layers.get_idomain(ds)[0].plot(ax=axes[1][0])\n",
"ds[\"edge_mask\"][0].plot(ax=axes[1][1])\n",
"\n",
"fig, axes = nlmod.plot.get_map(ds.extent, nrows=2, ncols=2, figsize=14)\n",
Expand All @@ -274,24 +273,11 @@
"ds[\"kh\"][1].plot(ax=axes[1][0])\n",
"ds[\"recharge\"].plot(ax=axes[1][1]);"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "artesia",
"language": "python",
"name": "python3"
},
"language_info": {
"name": "python",
"version": "3.10.12"
"name": "python"
}
},
"nbformat": 4,
Expand Down
12 changes: 2 additions & 10 deletions docs/examples/03_local_grid_refinement.ipynb
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -44,7 +43,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -116,7 +114,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -191,7 +188,7 @@
"drn = nlmod.gwf.surface_drain_from_ds(ds, gwf, resistance=10.0)\n",
"\n",
"# add constant head cells at model boundaries\n",
"ds.update(nlmod.grid.mask_model_edge(ds, ds[\"idomain\"]))\n",
"ds.update(nlmod.grid.mask_model_edge(ds))\n",
"chd = nlmod.gwf.chd(ds, gwf, mask=\"edge_mask\", head=\"starting_head\")"
]
},
Expand Down Expand Up @@ -219,7 +216,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -238,7 +234,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -272,7 +267,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -289,7 +283,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -308,7 +301,7 @@
"\n",
"nlmod.plot.data_array(ds[\"ahn\"], ds, ax=axes[0][0])\n",
"nlmod.plot.data_array(ds[\"botm\"][0], ds, ax=axes[0][1])\n",
"nlmod.plot.data_array(ds[\"idomain\"][0], ds, ax=axes[1][0])\n",
"nlmod.plot.data_array(nlmod.layers.get_idomain(ds)[0], ds, ax=axes[1][0])\n",
"nlmod.plot.data_array(ds[\"edge_mask\"][0], ds, ax=axes[1][1])\n",
"\n",
"fig, axes = nlmod.plot.get_map(extent, nrows=2, ncols=2, figsize=(14, 11))\n",
Expand All @@ -319,7 +312,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down
26 changes: 4 additions & 22 deletions docs/examples/06_gridding_vector_data.ipynb
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -33,7 +32,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -57,7 +55,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -116,15 +113,13 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"### Points"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -165,7 +160,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -208,7 +202,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -249,7 +242,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -290,7 +282,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -328,7 +319,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -374,7 +364,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -411,14 +400,11 @@
"# add a nodata value\n",
"ds.attrs[\"nodata\"] = -999\n",
"\n",
"# create an idomain of ones except for the first cell which is zero\n",
"idomain = np.ones((ds.dims[\"layer\"], ds.dims[\"y\"], ds.dims[\"x\"]))\n",
"idomain[0, 0, 0] = 0\n",
"ds[\"idomain\"] = (\"layer\", \"y\", \"x\"), idomain"
"# set the thickness of the first cell to 0, so this cell will become inactive\n",
"ds['top'][0,0] = ds['botm'][0,0,0]"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -441,7 +427,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -465,7 +450,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -501,7 +485,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -523,7 +506,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -540,14 +522,14 @@
"outputs": [],
"source": [
"# create a reclist with col1 (str), col2 (DataArray), col3 (int)\n",
"idomain = nlmod.layers.get_idomain(ds)\n",
"reclist5 = nlmod.grid.da_to_reclist(\n",
" ds, mask3d, col1=ds[\"idomain\"], col2=\"da1\", col3=9, layer=0, only_active_cells=False\n",
" ds, mask3d, col1=idomain, col2=\"da1\", col3=9, layer=0, only_active_cells=False\n",
")\n",
"reclist5"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down
6 changes: 2 additions & 4 deletions nlmod/dims/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
from .. import util
from ..epsg28992 import EPSG_28992
from . import resample
from .layers import fill_nan_top_botm_kh_kv, set_idomain
from .layers import fill_nan_top_botm_kh_kv

logger = logging.getLogger(__name__)

Expand Down Expand Up @@ -167,16 +167,14 @@ def to_model_ds(
ds = set_ds_attrs(ds, model_name, model_ws)
ds.attrs["transport"] = int(transport)

# fill nan's and add idomain
# fill nan's
if fill_nan:
ds = fill_nan_top_botm_kh_kv(
ds,
anisotropy=anisotropy,
fill_value_kh=fill_value_kh,
fill_value_kv=fill_value_kv,
)
else:
ds = set_idomain(ds, remove_nan_layers=False)

return ds

Expand Down
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