Skip to content

Commit 7900998

Browse files
ThomasCeulemansThomasCeulemans
authored
Merge pull request #264 from Magritte-code/260-documentation-update-required
260 documentation update required
2 parents 3998362 + 1e404fb commit 7900998

29 files changed

+154
-154
lines changed

‎docs/src/1_examples/0_creating_models/0_create_analytic_disk.ipynb

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -510,11 +510,11 @@
510510
"model.geometry.rays.direction.set(direction) # Comment out to use all directions\n",
511511
"model.geometry.rays.weight .set(0.5 * np.ones(2)) # Comment out to use all directions\n",
512512
"\n",
513-
"# model = setup.set_uniform_rays (model) # Uncomment to use all directions\n",
514-
"model = setup.set_boundary_condition_CMB (model)\n",
515-
"model = setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
516-
"# model = setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
517-
"model = setup.set_quadrature (model)\n",
513+
"# setup.set_uniform_rays (model) # Uncomment to use all directions\n",
514+
"setup.set_boundary_condition_CMB (model)\n",
515+
"setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
516+
"# setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
517+
"setup.set_quadrature (model)\n",
518518
"\n",
519519
"model.write()"
520520
]
@@ -686,7 +686,7 @@
686686
"name": "python",
687687
"nbconvert_exporter": "python",
688688
"pygments_lexer": "ipython3",
689-
"version": "3.9.16"
689+
"version": "3.10.14"
690690
},
691691
"widgets": {
692692
"application/vnd.jupyter.widget-state+json": {

‎docs/src/1_examples/0_creating_models/1_create_analytic_spiral.ipynb

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -589,11 +589,11 @@
589589
"model.parameters.set_nboundary(nb_boundary)\n",
590590
"model.geometry.boundary.boundary2point.set(np.arange(nb_boundary))\n",
591591
"\n",
592-
"model = setup.set_boundary_condition_CMB (model)\n",
593-
"model = setup.set_uniform_rays (model)\n",
594-
"model = setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
595-
"# model = setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
596-
"model = setup.set_quadrature (model)\n",
592+
"setup.set_boundary_condition_CMB (model)\n",
593+
"setup.set_uniform_rays (model)\n",
594+
"setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
595+
"# setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
596+
"setup.set_quadrature (model)\n",
597597
"\n",
598598
"model.write()"
599599
]

‎docs/src/1_examples/1_post-processing/0_create_AMRVAC_1D.ipynb

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -315,12 +315,12 @@
315315
"model.thermodynamics.temperature.gas .set(tmp)\n",
316316
"model.thermodynamics.turbulence.vturb2.set(trb)\n",
317317
"\n",
318-
"model = setup.set_Delaunay_neighbor_lists (model)\n",
319-
"model = setup.set_Delaunay_boundary (model)\n",
320-
"model = setup.set_boundary_condition_CMB (model)\n",
321-
"model = setup.set_uniform_rays (model)\n",
322-
"model = setup.set_linedata_from_LAMDA_file (model, lamda_file)\n",
323-
"model = setup.set_quadrature (model)\n",
318+
"setup.set_Delaunay_neighbor_lists (model)\n",
319+
"setup.set_Delaunay_boundary (model)\n",
320+
"setup.set_boundary_condition_CMB (model)\n",
321+
"setup.set_uniform_rays (model)\n",
322+
"setup.set_linedata_from_LAMDA_file (model, lamda_file)\n",
323+
"setup.set_quadrature (model)\n",
324324
"\n",
325325
"model.write()"
326326
]

‎docs/src/1_examples/1_post-processing/1_create_AMRVAC_3D.ipynb

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -364,11 +364,11 @@
364364
"# model.geometry.boundary.boundary2point.set(np.arange(boundary.shape[0]))\n",
365365
"model.geometry.boundary.boundary2point.set(boundary)\n",
366366
"\n",
367-
"model = setup.set_boundary_condition_CMB (model)\n",
368-
"model = setup.set_uniform_rays (model)\n",
369-
"model = setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
370-
"# model = setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
371-
"model = setup.set_quadrature (model)\n",
367+
"setup.set_boundary_condition_CMB (model)\n",
368+
"setup.set_uniform_rays (model)\n",
369+
"setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
370+
"# setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
371+
"setup.set_quadrature (model)\n",
372372
"\n",
373373
"model.write()"
374374
]

‎docs/src/1_examples/1_post-processing/2_reduce_AMRVAC_3D.ipynb

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -350,11 +350,11 @@
350350
"model.parameters.set_nboundary(nb_boundary)\n",
351351
"model.geometry.boundary.boundary2point.set(range(nb_boundary))\n",
352352
"\n",
353-
"model = setup.set_boundary_condition_CMB (model)\n",
354-
"model = setup.set_uniform_rays (model)\n",
355-
"model = setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
356-
"# model = setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
357-
"model = setup.set_quadrature (model)\n",
353+
"setup.set_boundary_condition_CMB (model)\n",
354+
"setup.set_uniform_rays (model)\n",
355+
"setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
356+
"# setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
357+
"setup.set_quadrature (model)\n",
358358
"\n",
359359
"model.write()"
360360
]

‎docs/src/1_examples/1_post-processing/3_create_Phantom_3D.ipynb

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -332,11 +332,11 @@
332332
"model.geometry.rays.direction.set(direction) # Comment out to use all directions\n",
333333
"model.geometry.rays.weight .set(0.5 * np.ones(2)) # Comment out to use all directions\n",
334334
"\n",
335-
"# model = setup.set_uniform_rays (model) # Uncomment to use all directions\n",
336-
"model = setup.set_boundary_condition_CMB (model)\n",
337-
"model = setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
338-
"# model = setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
339-
"model = setup.set_quadrature (model)\n",
335+
"# setup.set_uniform_rays (model) # Uncomment to use all directions\n",
336+
"setup.set_boundary_condition_CMB (model)\n",
337+
"setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
338+
"# setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
339+
"setup.set_quadrature (model)\n",
340340
"\n",
341341
"model.write()"
342342
]
@@ -457,7 +457,7 @@
457457
"name": "python",
458458
"nbconvert_exporter": "python",
459459
"pygments_lexer": "ipython3",
460-
"version": "3.10.13"
460+
"version": "3.10.14"
461461
},
462462
"widgets": {
463463
"application/vnd.jupyter.widget-state+json": {

‎docs/src/1_examples/1_post-processing/3_create_Phantom_3D_column.ipynb

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -345,10 +345,10 @@
345345
"model.parameters.set_nboundary(boundary.shape[0])\n",
346346
"model.geometry.boundary.boundary2point.set(boundary)\n",
347347
"\n",
348-
"model = setup.set_uniform_rays (model) # Uncomment to use all directions\n",
349-
"model = setup.set_boundary_condition_CMB (model)\n",
350-
"model = setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
351-
"model = setup.set_quadrature (model)\n",
348+
"setup.set_uniform_rays (model) # Uncomment to use all directions\n",
349+
"setup.set_boundary_condition_CMB (model)\n",
350+
"setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
351+
"setup.set_quadrature (model)\n",
352352
"\n",
353353
"model.write()"
354354
]

‎docs/src/1_examples/1_post-processing/4_reduce_Phantom_3D.ipynb

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -378,11 +378,11 @@
378378
"model.geometry.rays.direction.set(direction) # Comment out to use all directions\n",
379379
"model.geometry.rays.weight .set(0.5 * np.ones(2)) # Comment out to use all directions\n",
380380
"\n",
381-
"# model = setup.set_uniform_rays (model) # Uncomment to use all directions\n",
382-
"model = setup.set_boundary_condition_CMB (model)\n",
383-
"model = setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
384-
"# model = setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
385-
"model = setup.set_quadrature (model)\n",
381+
"# setup.set_uniform_rays (model) # Uncomment to use all directions\n",
382+
"setup.set_boundary_condition_CMB (model)\n",
383+
"setup.set_linedata_from_LAMDA_file(model, lamda_file, {'considered transitions': [0]})\n",
384+
"# setup.set_linedata_from_LAMDA_file(model, lamda_file) # Consider all transitions\n",
385+
"setup.set_quadrature (model)\n",
386386
"\n",
387387
"model.write()"
388388
]
@@ -498,7 +498,7 @@
498498
"name": "python",
499499
"nbconvert_exporter": "python",
500500
"pygments_lexer": "ipython3",
501-
"version": "3.10.13"
501+
"version": "3.9.16"
502502
},
503503
"widgets": {
504504
"application/vnd.jupyter.widget-state+json": {

‎docs/src/4_extra_options/NLTE_in_low_density.rst

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ This means that the resulting line opacity (and optical depth) can become close
66
Unfortunately, our solvers cannot handle a rapid change in source function (emissivity/opacity) too well, and might produce unphysical results.
77

88
This is why we implement a workaround by setting the minimum allowed value for the line opacity (starting from version 0.7.0).
9-
This value is set to 1e-10 [W sr−1 m−3] by default, but can be changed by the user. Higher values might overestimate the impact of the less dense model regions on the intensity, while lower value can lead to numerical artifacts in the NLTE intensities.
9+
This value is set to 1e-10 [W sr−1 m−3] by default, but can be changed by the user. Higher values can overestimate the impact of the less dense model regions on the intensity, while lower value can lead to numerical artifacts in the NLTE intensities (ring-like structures in the channel maps).
1010

1111
.. code-block:: python
1212

‎tests/benchmarks/analytic/all_constant_single_ray.py

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -57,12 +57,12 @@ def create_model ():
5757
model.thermodynamics.temperature.gas .set( temp * np.ones(npoints))
5858
model.thermodynamics.turbulence.vturb2.set((turb/magritte.CC)**2 * np.ones(npoints))
5959

60-
model = setup.set_Delaunay_neighbor_lists (model)
61-
model = setup.set_Delaunay_boundary (model)
62-
model = setup.set_boundary_condition_CMB (model)
63-
model = setup.set_uniform_rays (model)
64-
model = setup.set_linedata_from_LAMDA_file(model, lamdaFile)
65-
model = setup.set_quadrature (model)
60+
setup.set_Delaunay_neighbor_lists (model)
61+
setup.set_Delaunay_boundary (model)
62+
setup.set_boundary_condition_CMB (model)
63+
setup.set_uniform_rays (model)
64+
setup.set_linedata_from_LAMDA_file(model, lamdaFile)
65+
setup.set_quadrature (model)
6666

6767
model.write()
6868

0 commit comments

Comments
 (0)