From f42a5e93b7715e09ae08a2cb41a32769b7824cf5 Mon Sep 17 00:00:00 2001
From: Feliks Kiszkurno <feliks-kuba.kiszkurno@ufz.de>
Date: Tue, 10 Dec 2024 09:11:27 +0100
Subject: [PATCH] Refactor ogs to ot
Add ot to ignore-words
---
.codespellrc | 2 +-
.../SeabedResponse/Stationary_waves.ipynb | 4 ++--
.../StaggeredScheme/MandelCryer/mandelcryer.md | 4 ++--
Tests/Data/LargeDeformation/RigidBody/RigidBody.md | 6 +++---
.../LargeDeformation/Torsion/Torsion_robustness.md | 4 ++--
.../Mechanics/CooksMembrane/CooksMembraneBbar.ipynb | 6 +++---
.../Mechanics/HoekBrown/HoekBrownYieldCriterion.md | 4 ++--
.../Linear/DiscWithHole/Linear_Disc_with_hole.md | 4 ++--
.../Linear_Disc_with_hole_convergence_analysis.ipynb | 4 ++--
Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb | 10 +++++-----
Tests/Data/Mechanics/PLLC/PLLC.ipynb | 4 ++--
.../InvalidProjectFiles/generateInvalidMediaForHT.py | 4 ++--
.../BlockingConductingFracture.ipynb | 4 ++--
.../heatconduction-line_source_term.md | 6 +++---
Tests/Data/Parabolic/T/BHE_1P/pipe_flow_ebhe.md | 4 ++--
.../Kregime_Propagating_jupyter.ipynb | 4 ++--
.../PForthotropy_jupyter_notebook/sen_shear.ipynb | 6 +++---
Tests/Data/PhaseField/beam_jupyter_notebook/beam.ipynb | 8 ++++----
.../Kregime_Static_jupyter.ipynb | 4 ++--
.../surfing_jupyter_notebook/surfing_pyvista.ipynb | 4 ++--
Tests/Data/PhaseField/tpb_jupyter_notebook/TPB.ipynb | 6 +++---
Tests/Data/TH2M/H/diffusion/diffusion.ipynb | 4 ++--
.../H2/dissolution_diffusion/phase_appearance.ipynb | 4 ++--
Tests/Data/TH2M/H2/mcWhorter/mcWhorter.ipynb | 4 ++--
Tests/Data/TH2M/TH/Ogata-Banks/Ogata-Banks.ipynb | 4 ++--
.../TH2M/TH/idealGasLaw/confined_gas_compression.ipynb | 4 ++--
Tests/Data/TH2M/TH2/heatpipe/heatpipe.ipynb | 4 ++--
.../Point_injection/SaturatedPointheatsource.ipynb | 10 +++++-----
.../docs/devguide/documentation/jupyter-docs/index.md | 2 +-
29 files changed, 69 insertions(+), 69 deletions(-)
diff --git a/.codespellrc b/.codespellrc
index e1e36dbbf41..db3bbe55d94 100644
--- a/.codespellrc
+++ b/.codespellrc
@@ -1,5 +1,5 @@
[codespell]
skip = *.bib,*.css,*.pdf,*.yaml,*.yml,*/.vale,./.git,./GeoLib/IO/XmlIO/OpenGeoSysSTN.xsd,./Tests/Data,./web/content/imprint.md,./web/node_modules,./web/public/imprint/index.html,./web/resources,CITATION.cff,
-ignore-words-list = ba,bu,ket,nd,pris,strat,sur,theis,
+ignore-words-list = ba,bu,ket,nd,pris,strat,sur,theis,ot
exclude-file = .codespellexclude
uri-ignore-words-list = *
diff --git a/Tests/Data/HydroMechanics/SeabedResponse/Stationary_waves.ipynb b/Tests/Data/HydroMechanics/SeabedResponse/Stationary_waves.ipynb
index a58a8517eaf..fb62abae151 100644
--- a/Tests/Data/HydroMechanics/SeabedResponse/Stationary_waves.ipynb
+++ b/Tests/Data/HydroMechanics/SeabedResponse/Stationary_waves.ipynb
@@ -860,7 +860,7 @@
},
"outputs": [],
"source": [
- "import ogstools as ogs"
+ "import ogstools as ot"
]
},
{
@@ -974,7 +974,7 @@
}
],
"source": [
- "model = ogs.Project(\n",
+ "model = ot.Project(\n",
" input_file=\"seabed_response_200x100.prj\", output_file=\"seabed_response_200x100.prj\"\n",
")\n",
"model.run_model(logfile=f\"{out_dir}/out.txt\", args=f\"-o {out_dir} -m {out_dir}\")"
diff --git a/Tests/Data/HydroMechanics/StaggeredScheme/MandelCryer/mandelcryer.md b/Tests/Data/HydroMechanics/StaggeredScheme/MandelCryer/mandelcryer.md
index 19e74656646..8acdbbdf4f8 100644
--- a/Tests/Data/HydroMechanics/StaggeredScheme/MandelCryer/mandelcryer.md
+++ b/Tests/Data/HydroMechanics/StaggeredScheme/MandelCryer/mandelcryer.md
@@ -67,13 +67,13 @@ out_dir = Path(os.environ.get("OGS_TESTRUNNER_OUT_DIR", "_out"))
if not out_dir.exists():
out_dir.mkdir(parents=True)
-import ogstools as ogs
+import ogstools as ot
```
```python
# Initiate an OGS-object
# Pass it the project file and set an output file
-model = ogs.Project(input_file="MandelCryerStaggered.prj", output_file=f"{out_dir}/MandelCryerStaggered_modified.prj")
+model = ot.Project(input_file="MandelCryerStaggered.prj", output_file=f"{out_dir}/MandelCryerStaggered_modified.prj")
# Increase end time
t_end = 1.5
diff --git a/Tests/Data/LargeDeformation/RigidBody/RigidBody.md b/Tests/Data/LargeDeformation/RigidBody/RigidBody.md
index ba8d14ed9a9..5ee1e132436 100644
--- a/Tests/Data/LargeDeformation/RigidBody/RigidBody.md
+++ b/Tests/Data/LargeDeformation/RigidBody/RigidBody.md
@@ -59,7 +59,7 @@ It thus suffices to illustrate the behaviour of strain values.
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm
-import ogstools as ogs
+import ogstools as ot
import os
import pyvista as pv
@@ -88,8 +88,8 @@ if not out_dir.exists():
```
```python jupyter={"source_hidden": true}
-model_s = ogs.Project(input_file="square_1e0.prj", output_file=f"{out_dir}/square_1e0_small.prj")
-model = ogs.Project(input_file="square_1e0.prj", output_file="square_1e0.prj")
+model_s = ot.Project(input_file="square_1e0.prj", output_file=f"{out_dir}/square_1e0_small.prj")
+model = ot.Project(input_file="square_1e0.prj", output_file="square_1e0.prj")
```
```python jupyter={"source_hidden": true}
diff --git a/Tests/Data/LargeDeformation/Torsion/Torsion_robustness.md b/Tests/Data/LargeDeformation/Torsion/Torsion_robustness.md
index 2950c2be6f3..7c26309ab72 100644
--- a/Tests/Data/LargeDeformation/Torsion/Torsion_robustness.md
+++ b/Tests/Data/LargeDeformation/Torsion/Torsion_robustness.md
@@ -20,7 +20,7 @@ The material model is a Saint-Venant-Kirchhoff material law for initial testing.
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm
-import ogstools as ogs
+import ogstools as ot
from ogstools.logparser import parse_file, fill_ogs_context
import os
import pyvista as pv
@@ -89,7 +89,7 @@ if not out_dir.exists():
```
```python jupyter={"source_hidden": true}
-model = ogs.Project(
+model = ot.Project(
input_file="bar1to6_torsion.prj",
output_file="bar1to6_torsion.prj"
)
diff --git a/Tests/Data/Mechanics/CooksMembrane/CooksMembraneBbar.ipynb b/Tests/Data/Mechanics/CooksMembrane/CooksMembraneBbar.ipynb
index b45fb177fa6..ec7a6834735 100644
--- a/Tests/Data/Mechanics/CooksMembrane/CooksMembraneBbar.ipynb
+++ b/Tests/Data/Mechanics/CooksMembrane/CooksMembraneBbar.ipynb
@@ -65,9 +65,9 @@
"import os\n",
"from pathlib import Path\n",
"\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"\n",
- "out_dir = Path(os.environ.get(\"OGS_TESTRUNNER_OUT_DIR\", \"_out\"))\n",
+ "out_dir = Path(os.environ.get(\"ot_TESTRUNNER_OUT_DIR\", \"_out\"))\n",
"if not out_dir.exists():\n",
" out_dir.mkdir(parents=True)"
]
@@ -119,7 +119,7 @@
"outputs": [],
"source": [
"def run_single_test(mesh_name, output_prefix, use_bbar=\"false\"):\n",
- " model = ogs.Project(\n",
+ " model = ot.Project(\n",
" input_file=\"CooksMembrane.prj\", output_file=f\"{out_dir}/modified.prj\"\n",
" )\n",
" model.replace_text(mesh_name, xpath=\"./mesh\")\n",
diff --git a/Tests/Data/Mechanics/HoekBrown/HoekBrownYieldCriterion.md b/Tests/Data/Mechanics/HoekBrown/HoekBrownYieldCriterion.md
index 92992e10a73..0b50c692aef 100644
--- a/Tests/Data/Mechanics/HoekBrown/HoekBrownYieldCriterion.md
+++ b/Tests/Data/Mechanics/HoekBrown/HoekBrownYieldCriterion.md
@@ -127,7 +127,7 @@ import pandas as pd
import vtuIO
from IPython.display import Markdown, display
from matplotlib.ticker import MultipleLocator
-import ogstools as ogs
+import ogstools as ot
from scipy.optimize import fsolve
from tfel.material import projectOnPiPlane
```
@@ -854,7 +854,7 @@ if not out_dir.exists():
```
```python
-model_hb = ogs.Project(
+model_hb = ot.Project(
input_file="load_test_hb_nonassociated.prj", output_file="load_test_hb_nonassociated.prj"
)
```
diff --git a/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.md b/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.md
index 7109b3a8c4d..cdb9b98da38 100644
--- a/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.md
+++ b/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.md
@@ -239,7 +239,7 @@ Simultaneous to the analytical solution the results of the numerical model are p
For a better presentation of these differences and as a basis for the following error analysis, plots for absolute and relative error along the regarded axes are have been made.
```python
-import ogstools as ogs
+import ogstools as ot
import os
from pathlib import Path
@@ -249,7 +249,7 @@ if not out_dir.exists():
```
```python
-model = ogs.Project(
+model = ot.Project(
input_file="../disc_with_hole.prj", output_file="../disc_with_hole.prj"
)
```
diff --git a/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole_convergence_analysis.ipynb b/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole_convergence_analysis.ipynb
index 0fb5dd09223..b80b601b743 100644
--- a/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole_convergence_analysis.ipynb
+++ b/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole_convergence_analysis.ipynb
@@ -686,7 +686,7 @@
"source": [
"import shutil\n",
"\n",
- "import ogstools as ogs"
+ "import ogstools as ot"
]
},
{
@@ -730,7 +730,7 @@
"\n",
" prj_path = out_dir / prj_file\n",
"\n",
- " model = ogs.Project(input_file=prj_path, output_file=prj_path)\n",
+ " model = ot.Project(input_file=prj_path, output_file=prj_path)\n",
" model.run_model(\n",
" logfile=f\"{out_dir}/out.txt\",\n",
" args=f\"-o {out_dir} -m {out_dir}/disc_with_hole_idx_is_{idx}\",\n",
diff --git a/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb b/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb
index 615f2347f22..78a4a8f1f72 100644
--- a/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb
+++ b/Tests/Data/Mechanics/Linear/SimpleMechanics.ipynb
@@ -58,10 +58,10 @@
}
],
"source": [
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"\n",
"prj_name = \"SimpleMechanics\"\n",
- "model = ogs.Project(output_file=(out_dir / f\"{prj_name}.prj\"))\n",
+ "model = ot.Project(output_file=(out_dir / f\"{prj_name}.prj\"))\n",
"model.geometry.add_geometry(filename=\"./square_1x1.gml\")\n",
"model.mesh.add_mesh(filename=\"./square_1x1_quad_1e2.vtu\")\n",
"model.processes.set_process(\n",
@@ -296,11 +296,11 @@
}
],
"source": [
- "mesh_series = ogs.MeshSeries(f\"{out_dir}/{prj_name}.pvd\")\n",
+ "mesh_series = ot.MeshSeries(f\"{out_dir}/{prj_name}.pvd\")\n",
"points = np.asarray([[0.3, 0.5, 0.0], [0.24, 0.21, 0.0]])\n",
- "disp = ogs.variables.displacement\n",
+ "disp = ot.variables.displacement\n",
"labels = [\n",
- " f\"{i}: {label}\" for i, label in enumerate(ogs.plot.utils.justified_labels(points))\n",
+ " f\"{i}: {label}\" for i, label in enumerate(ot.plot.utils.justified_labels(points))\n",
"]\n",
"fig = mesh_series.plot_probe(\n",
" points=points[:4], variable=disp, time_unit=\"a\", labels=labels[:4]\n",
diff --git a/Tests/Data/Mechanics/PLLC/PLLC.ipynb b/Tests/Data/Mechanics/PLLC/PLLC.ipynb
index a5c8211f50f..498ce09c9e2 100644
--- a/Tests/Data/Mechanics/PLLC/PLLC.ipynb
+++ b/Tests/Data/Mechanics/PLLC/PLLC.ipynb
@@ -40,7 +40,7 @@
"import matplotlib as mpl\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"import vtuIO"
]
},
@@ -66,7 +66,7 @@
"os.chdir(out_dir)\n",
"\n",
"prj_file = f\"{out_dir}/{prj_name}_out.prj\"\n",
- "ogs_model = ogs.Project(input_file=input_file, output_file=prj_file)"
+ "ogs_model = ot.Project(input_file=input_file, output_file=prj_file)"
]
},
{
diff --git a/Tests/Data/Parabolic/HT/InvalidProjectFiles/generateInvalidMediaForHT.py b/Tests/Data/Parabolic/HT/InvalidProjectFiles/generateInvalidMediaForHT.py
index 97b173f09b2..7b8aff404ad 100644
--- a/Tests/Data/Parabolic/HT/InvalidProjectFiles/generateInvalidMediaForHT.py
+++ b/Tests/Data/Parabolic/HT/InvalidProjectFiles/generateInvalidMediaForHT.py
@@ -1,4 +1,4 @@
-import ogstools as ogs
+import ogstools as ot
def addSolidPropertiesForHT(omit=""):
@@ -127,7 +127,7 @@ for solid_property in solid_properties:
and medium_property == ""
):
continue
- model = ogs.Project(
+ model = ot.Project(
output_file="HT_"
+ solid_property
+ "_"
diff --git a/Tests/Data/Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb b/Tests/Data/Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb
index 2b182608b22..363ede05351 100644
--- a/Tests/Data/Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb
+++ b/Tests/Data/Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb
@@ -71,7 +71,7 @@
"import matplotlib.pyplot as plt\n",
"import matplotlib.tri as tri\n",
"import numpy as np\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"import seaborn as sns\n",
"import vtuIO"
]
@@ -93,7 +93,7 @@
"if not out_dir.exists():\n",
" out_dir.mkdir(parents=True)\n",
"\n",
- "model_lf = ogs.Project(\n",
+ "model_lf = ot.Project(\n",
" input_file=\"block_conduct_frac.prj\", output_file=\"block_conduct_frac.prj\"\n",
")"
]
diff --git a/Tests/Data/Parabolic/T/3D_line_source_term_tests/3D_line_source_term_in_cylinder/heatconduction-line_source_term.md b/Tests/Data/Parabolic/T/3D_line_source_term_tests/3D_line_source_term_in_cylinder/heatconduction-line_source_term.md
index 380c4b1a8da..51bcaec673d 100644
--- a/Tests/Data/Parabolic/T/3D_line_source_term_tests/3D_line_source_term_in_cylinder/heatconduction-line_source_term.md
+++ b/Tests/Data/Parabolic/T/3D_line_source_term_tests/3D_line_source_term_in_cylinder/heatconduction-line_source_term.md
@@ -142,9 +142,9 @@ if not out_dir.exists():
```python
# Import OGS class
-import ogstools as ogs
+import ogstools as ot
-model = ogs.Project(
+model = ot.Project(
input_file="286k_prisms/line_source_term_in_cylinder.prj",
output_file="286k_prisms/line_source_term_in_cylinder.prj"
)
@@ -249,7 +249,7 @@ The cylindrical domain is defined as axisymmetric.
#### Numerical simulation
```python
-model = ogs.Project(
+model = ot.Project(
input_file="../3D_line_source_term_in_cylinder_axisymmetric/line_source_term_in_cylinder.prj",
output_file="../3D_line_source_term_in_cylinder_axisymmetric/line_source_term_in_cylinder.prj"
)
diff --git a/Tests/Data/Parabolic/T/BHE_1P/pipe_flow_ebhe.md b/Tests/Data/Parabolic/T/BHE_1P/pipe_flow_ebhe.md
index 23880818232..43ec04837f2 100644
--- a/Tests/Data/Parabolic/T/BHE_1P/pipe_flow_ebhe.md
+++ b/Tests/Data/Parabolic/T/BHE_1P/pipe_flow_ebhe.md
@@ -262,11 +262,11 @@ if not out_dir.exists():
```
```python
-import ogstools as ogs
+import ogstools as ot
# Create an OGS-object
# Pass the project file and set an output file path
-model=ogs.Project(input_file="BHE_1P.prj", output_file=f"{out_dir}/BHE_1P.prj")
+model=ot.Project(input_file="BHE_1P.prj", output_file=f"{out_dir}/BHE_1P.prj")
# set end time (in seconds) and the time increments
model.replace_text(5 * 24 * 60 * 60, xpath="./time_loop/processes/process/time_stepping/t_end")
diff --git a/Tests/Data/PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.ipynb b/Tests/Data/PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.ipynb
index 7c0b0c2f176..658701fd6ea 100644
--- a/Tests/Data/PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.ipynb
+++ b/Tests/Data/PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.ipynb
@@ -141,7 +141,7 @@
"import gmsh\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"from ogstools.msh2vtu import msh2vtu\n",
"\n",
"pi = math.pi\n",
@@ -368,7 +368,7 @@
" # As a preprocessing step, define the initial phase-field (crack).\n",
" pre_processing(h, a0)\n",
" # change properties in prj file #For more information visit: https://ogstools.opengeosys.org/stable/reference/ogstools.ogs6py.html\n",
- " model = ogs.Project(\n",
+ " model = ot.Project(\n",
" input_file=prj_name,\n",
" output_file=f\"{out_dir}/{prj_name}\",\n",
" MKL=True,\n",
diff --git a/Tests/Data/PhaseField/PForthotropy_jupyter_notebook/sen_shear.ipynb b/Tests/Data/PhaseField/PForthotropy_jupyter_notebook/sen_shear.ipynb
index df9bdef7f9b..1414fe4b9a9 100644
--- a/Tests/Data/PhaseField/PForthotropy_jupyter_notebook/sen_shear.ipynb
+++ b/Tests/Data/PhaseField/PForthotropy_jupyter_notebook/sen_shear.ipynb
@@ -56,7 +56,7 @@
"\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"import pyvista as pv"
]
},
@@ -148,7 +148,7 @@
" # fmt: off\n",
" logfile = f\"{out_dir}/log_{phasefield_model}_{energy_split_model}_out.txt\" # noqa: F841\n",
" # fmt: on\n",
- " model = ogs.Project(\n",
+ " model = ot.Project(\n",
" input_file=prj_name, output_file=f\"{out_dir}/{prj_name}\", MKL=True\n",
" )\n",
"\n",
@@ -175,7 +175,7 @@
" ! NodeReordering -i shear.vtu -o {out_dir}/shear.vtu >> {logfile}\n",
"\n",
" # change some properties in prj file\n",
- " model = ogs.Project(\n",
+ " model = ot.Project(\n",
" input_file=prj_name, output_file=f\"{out_dir}/{prj_name}\", MKL=True\n",
" )\n",
" model.replace_parameter_value(name=\"ls\", value=length_scale)\n",
diff --git a/Tests/Data/PhaseField/beam_jupyter_notebook/beam.ipynb b/Tests/Data/PhaseField/beam_jupyter_notebook/beam.ipynb
index 7b09b02f421..86f250e21f3 100644
--- a/Tests/Data/PhaseField/beam_jupyter_notebook/beam.ipynb
+++ b/Tests/Data/PhaseField/beam_jupyter_notebook/beam.ipynb
@@ -59,7 +59,7 @@
"\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"import pyvista as pv"
]
},
@@ -183,7 +183,7 @@
" ! partmesh -s -o {out_dir} -i {out_dir}/bar.vtu >> {logfile}\n",
" ! partmesh -m -n 3 -o {out_dir} -i {out_dir}/bar.vtu -- {out_dir}/bar_right.vtu {out_dir}/bar_left.vtu >> {logfile}\n",
" # change properties in prj file\n",
- " model = ogs.Project(\n",
+ " model = ot.Project(\n",
" input_file=prj_name, output_file=f\"{out_dir}/{prj_name}\", MKL=True\n",
" )\n",
" model.replace_parameter_value(name=\"ls\", value=ls)\n",
@@ -274,11 +274,11 @@
"# loosen relative error tolerance for displacement process in order to get convergence for the AT1 case\n",
"prj_path='./'\n",
"prj_name = \"beam.prj\"\n",
- "model = ogs.Project(input_file=prj_path+prj_name, output_file=prj_path+prj_name, MKL=True)\n",
+ "model = ot.Project(input_file=prj_path+prj_name, output_file=prj_path+prj_name, MKL=True)\n",
"model.replace_text('1e-6', xpath=\"./time_loop/processes/process/convergence_criterion/reltol\",occurrence=0)\n",
"model.write_input()\n",
"ogs_beam(pf_ms[0],es_ms[0],bc_displacement = -4.95, mesh_size = 0.01, length_scale = 0.03, hypre= True, repeat_list=['66', '8','3','3','20','1'], delta_t_list=['1e-2','1e-3','1e-4','1e-5','1e-6','1e-2'],ts_coords='0 0.1 1', values ='0 0.5 1')\n",
- "model = ogs.Project(input_file=prj_path+prj_name, output_file=prj_path+prj_name, MKL=True)\n",
+ "model = ot.Project(input_file=prj_path+prj_name, output_file=prj_path+prj_name, MKL=True)\n",
"model.replace_text('1e-14', xpath=\"./time_loop/processes/process/convergence_criterion/reltol\",occurrence=0)\n",
"model.write_input()\n",
"\"\"\"\n",
diff --git a/Tests/Data/PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.ipynb b/Tests/Data/PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.ipynb
index 2c526728aad..79aaee8a830 100644
--- a/Tests/Data/PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.ipynb
+++ b/Tests/Data/PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.ipynb
@@ -87,7 +87,7 @@
"import gmsh\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"\n",
"pi = math.pi\n",
"plt.rcParams[\"text.usetex\"] = True"
@@ -309,7 +309,7 @@
" # As a preprocessing step, define the initial phase-field (crack).\n",
" pre_processing(h, a0)\n",
" # change properties in prj file #For more information visit: https://ogstools.opengeosys.org/stable/reference/ogstools.ogs6py.html\n",
- " model = ogs.Project(\n",
+ " model = ot.Project(\n",
" input_file=prj_name,\n",
" output_file=f\"{out_dir}/{prj_name}\",\n",
" MKL=True,\n",
diff --git a/Tests/Data/PhaseField/surfing_jupyter_notebook/surfing_pyvista.ipynb b/Tests/Data/PhaseField/surfing_jupyter_notebook/surfing_pyvista.ipynb
index 42139dbe1d9..9dd8cf3f6cb 100644
--- a/Tests/Data/PhaseField/surfing_jupyter_notebook/surfing_pyvista.ipynb
+++ b/Tests/Data/PhaseField/surfing_jupyter_notebook/surfing_pyvista.ipynb
@@ -331,10 +331,10 @@
}
],
"source": [
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"\n",
"# Change the length scale and phasefield model in project file\n",
- "model = ogs.Project(\n",
+ "model = ot.Project(\n",
" input_file=prj_name,\n",
" output_file=f\"{out_dir}/{prj_name}\",\n",
" MKL=True,\n",
diff --git a/Tests/Data/PhaseField/tpb_jupyter_notebook/TPB.ipynb b/Tests/Data/PhaseField/tpb_jupyter_notebook/TPB.ipynb
index 933bb3a5374..c191e6cfc01 100644
--- a/Tests/Data/PhaseField/tpb_jupyter_notebook/TPB.ipynb
+++ b/Tests/Data/PhaseField/tpb_jupyter_notebook/TPB.ipynb
@@ -56,7 +56,7 @@
"\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"import pandas as pd\n",
"import pyvista as pv"
]
@@ -150,7 +150,7 @@
" f\"> Running three point bending test {phasefield_model} - {energy_split_model} - {softening_curve} ... <\"\n",
" )\n",
" logfile = f\"{out_dir}/log_{phasefield_model}_{energy_split_model}.txt\" # noqa: F841\n",
- " model = ogs.Project(\n",
+ " model = ot.Project(\n",
" input_file=prj_name, output_file=f\"{out_dir}/{prj_name}\", MKL=True\n",
" )\n",
" # generate prefix from properties\n",
@@ -172,7 +172,7 @@
" else:\n",
" ! NodeReordering -i TPB.vtu -o {out_dir}/TPB.vtu >> {logfile}\n",
" # change properties in prj file\n",
- " model = ogs.Project(\n",
+ " model = ot.Project(\n",
" input_file=prj_name, output_file=f\"{out_dir}/{prj_name}\", MKL=True\n",
" )\n",
" model.replace_parameter_value(name=\"ls\", value=length_scale)\n",
diff --git a/Tests/Data/TH2M/H/diffusion/diffusion.ipynb b/Tests/Data/TH2M/H/diffusion/diffusion.ipynb
index 6af8e1d5282..ff5fa982771 100644
--- a/Tests/Data/TH2M/H/diffusion/diffusion.ipynb
+++ b/Tests/Data/TH2M/H/diffusion/diffusion.ipynb
@@ -147,9 +147,9 @@
}
],
"source": [
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"\n",
- "model = ogs.Project(input_file=\"diffusion.prj\", output_file=f\"{out_dir}/modified.prj\")\n",
+ "model = ot.Project(input_file=\"diffusion.prj\", output_file=f\"{out_dir}/modified.prj\")\n",
"model.replace_text(1e7, xpath=\"./time_loop/processes/process/time_stepping/t_end\")\n",
"model.replace_text(\n",
" 5e4, xpath=\"./time_loop/processes/process/time_stepping/timesteps/pair/delta_t\"\n",
diff --git a/Tests/Data/TH2M/H2/dissolution_diffusion/phase_appearance.ipynb b/Tests/Data/TH2M/H2/dissolution_diffusion/phase_appearance.ipynb
index e4466f2196c..9b7cf760325 100644
--- a/Tests/Data/TH2M/H2/dissolution_diffusion/phase_appearance.ipynb
+++ b/Tests/Data/TH2M/H2/dissolution_diffusion/phase_appearance.ipynb
@@ -104,9 +104,9 @@
],
"source": [
"import numpy as np\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"\n",
- "model = ogs.Project(input_file=\"bourgeat.prj\", output_file=f\"{out_dir}/modified.prj\")\n",
+ "model = ot.Project(input_file=\"bourgeat.prj\", output_file=f\"{out_dir}/modified.prj\")\n",
"# This Jupyter notebook version of this test runs not as far as its cTest-counterpart,\n",
"# it'll stop after approx. 800 ka\n",
"model.replace_text(2.5e13, xpath=\"./time_loop/processes/process/time_stepping/t_end\")\n",
diff --git a/Tests/Data/TH2M/H2/mcWhorter/mcWhorter.ipynb b/Tests/Data/TH2M/H2/mcWhorter/mcWhorter.ipynb
index d10247a6d09..a3c802e5749 100644
--- a/Tests/Data/TH2M/H2/mcWhorter/mcWhorter.ipynb
+++ b/Tests/Data/TH2M/H2/mcWhorter/mcWhorter.ipynb
@@ -128,10 +128,10 @@
}
],
"source": [
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"\n",
"# run OGS\n",
- "model = ogs.Project(input_file=\"mcWhorter_h2.prj\", output_file=\"mcWhorter_h2.prj\")\n",
+ "model = ot.Project(input_file=\"mcWhorter_h2.prj\", output_file=\"mcWhorter_h2.prj\")\n",
"model.run_model(logfile=f\"{out_dir}/out.txt\", args=f\"-o {out_dir}\")"
]
},
diff --git a/Tests/Data/TH2M/TH/Ogata-Banks/Ogata-Banks.ipynb b/Tests/Data/TH2M/TH/Ogata-Banks/Ogata-Banks.ipynb
index 92b0f09743e..97148ade693 100644
--- a/Tests/Data/TH2M/TH/Ogata-Banks/Ogata-Banks.ipynb
+++ b/Tests/Data/TH2M/TH/Ogata-Banks/Ogata-Banks.ipynb
@@ -221,10 +221,10 @@
}
],
"source": [
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"\n",
"# Modifies the project file of the original cTest so that the simulation runs for a longer time.\n",
- "model = ogs.Project(input_file=\"ogata-banks.prj\", output_file=f\"{out_dir}/modified.prj\")\n",
+ "model = ot.Project(input_file=\"ogata-banks.prj\", output_file=f\"{out_dir}/modified.prj\")\n",
"model.replace_text(max_time, xpath=\"./time_loop/processes/process/time_stepping/t_end\")\n",
"model.replace_text(\n",
" delta_time,\n",
diff --git a/Tests/Data/TH2M/TH/idealGasLaw/confined_gas_compression.ipynb b/Tests/Data/TH2M/TH/idealGasLaw/confined_gas_compression.ipynb
index f0be62cf2df..4bb16c84f90 100644
--- a/Tests/Data/TH2M/TH/idealGasLaw/confined_gas_compression.ipynb
+++ b/Tests/Data/TH2M/TH/idealGasLaw/confined_gas_compression.ipynb
@@ -203,7 +203,7 @@
"metadata": {},
"outputs": [],
"source": [
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"import vtuIO"
]
},
@@ -239,7 +239,7 @@
],
"source": [
"# run OGS\n",
- "cube_compression = ogs.Project(\n",
+ "cube_compression = ot.Project(\n",
" input_file=\"compression_gas.prj\", output_file=\"compression_gas.prj\"\n",
")\n",
"cube_compression.run_model(logfile=f\"{out_dir}/out.txt\", args=f\"-o {out_dir}\")"
diff --git a/Tests/Data/TH2M/TH2/heatpipe/heatpipe.ipynb b/Tests/Data/TH2M/TH2/heatpipe/heatpipe.ipynb
index 94bee08410b..c92957f59e5 100644
--- a/Tests/Data/TH2M/TH2/heatpipe/heatpipe.ipynb
+++ b/Tests/Data/TH2M/TH2/heatpipe/heatpipe.ipynb
@@ -601,14 +601,14 @@
"import os\n",
"from pathlib import Path\n",
"\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"\n",
"out_dir = Path(os.environ.get(\"OGS_TESTRUNNER_OUT_DIR\", \"_out\"))\n",
"if not out_dir.exists():\n",
" out_dir.mkdir(parents=True)\n",
"\n",
"prj_file = \"heat_pipe_rough.prj\"\n",
- "model = ogs.Project(input_file=prj_file, output_file=prj_file)\n",
+ "model = ot.Project(input_file=prj_file, output_file=prj_file)\n",
"model.run_model(logfile=f\"{out_dir}/out.txt\", args=f\"-o {out_dir}\")"
]
},
diff --git a/Tests/Data/ThermoHydroMechanics/Linear/Point_injection/SaturatedPointheatsource.ipynb b/Tests/Data/ThermoHydroMechanics/Linear/Point_injection/SaturatedPointheatsource.ipynb
index 31be19c8e5b..15f9ef3f68f 100644
--- a/Tests/Data/ThermoHydroMechanics/Linear/Point_injection/SaturatedPointheatsource.ipynb
+++ b/Tests/Data/ThermoHydroMechanics/Linear/Point_injection/SaturatedPointheatsource.ipynb
@@ -394,7 +394,7 @@
"source": [
"import os\n",
"\n",
- "import ogstools as ogs\n",
+ "import ogstools as ot\n",
"\n",
"data_dir = os.environ.get(\"OGS_DATA_DIR\", \"../../..\")\n",
"\n",
@@ -407,10 +407,10 @@
"# THM formulation (current working dir)\n",
"prj_file_lin = \"pointheatsource_linear-mesh.prj\"\n",
"prj_file_quad = \"pointheatsource_quadratic-mesh.prj\"\n",
- "ogs_model_lin = ogs.Project(\n",
+ "ogs_model_lin = ot.Project(\n",
" input_file=prj_file_lin, output_file=f\"{out_dir}/{prj_file_lin}\"\n",
")\n",
- "ogs_model_quad = ogs.Project(\n",
+ "ogs_model_quad = ot.Project(\n",
" input_file=prj_file_quad, output_file=f\"{out_dir}/{prj_file_quad}\"\n",
")\n",
"\n",
@@ -418,7 +418,7 @@
"prj_file_th2m = \"point_heatsource.prj\"\n",
"path_th2m = f\"{data_dir}/TH2M/THM/sphere\"\n",
"prj_filepath_th2m = f\"{path_th2m}/{prj_file_th2m}\"\n",
- "ogs_model_th2m = ogs.Project(\n",
+ "ogs_model_th2m = ot.Project(\n",
" input_file=prj_filepath_th2m, output_file=f\"{out_dir}/pointheatsource_th2m.prj\"\n",
")\n",
"\n",
@@ -426,7 +426,7 @@
"prj_file_trm = \"point_heat_source_2D.prj\"\n",
"path_trm = f\"{data_dir}/ThermoRichardsMechanics/PointHeatSource\"\n",
"prj_filepath_trm = f\"{path_trm}/{prj_file_trm}\"\n",
- "ogs_model_trm = ogs.Project(\n",
+ "ogs_model_trm = ot.Project(\n",
" input_file=prj_filepath_trm, output_file=f\"{out_dir}/pointheatsource_trm.prj\"\n",
")"
]
diff --git a/web/content/docs/devguide/documentation/jupyter-docs/index.md b/web/content/docs/devguide/documentation/jupyter-docs/index.md
index 4d0d3b65678..45594655481 100644
--- a/web/content/docs/devguide/documentation/jupyter-docs/index.md
+++ b/web/content/docs/devguide/documentation/jupyter-docs/index.md
@@ -142,7 +142,7 @@ The first cell after the frontmatter needs to be a `markdown`-cell!
# OR with ogstools:
# ... setup model ...
- import ogstools as ogs
+ import ogstools as ot
model = ogs.Project(input_file="input.prj", output_file="output.prj")
model.run_model(logfile=os.path.join(out_dir, "log.txt"), args=f"-o {out_dir}")
--
GitLab