-
Notifications
You must be signed in to change notification settings - Fork 2
Expand file tree
/
Copy pathmodel_options_3d.html
More file actions
677 lines (664 loc) · 33.6 KB
/
model_options_3d.html
File metadata and controls
677 lines (664 loc) · 33.6 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
<!DOCTYPE html>
<html lang="en" data-content_root="./">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
<title>3D model options — Thetis 2025.10.1+1.gf513865b documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
<link rel="stylesheet" type="text/css" href="_static/thetis.css?v=0f3339d6" />
<script src="_static/documentation_options.js?v=b0987aea"></script>
<script src="_static/doctools.js?v=9bcbadda"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<!--[if lte IE 6]>
<link rel="stylesheet" href="_static/ie6.css" type="text/css" media="screen" charset="utf-8" />
<![endif]-->
<!-- <link rel="stylesheet" href="_static/featured.css"> -->
<link rel="shortcut icon" href="_static/icon_thetis.ico" />
</head><body>
<div class="wrapper">
<a href="index.html"><img src="_static/banner.jpg" height="180px" alt="Thetis Project Banner" /></a>
<div id="access">
<div class="menu">
<ul>
<li class="page_item"><a href="documentation.html" title="Thetis documentation">Documentation</a></li>
<li class="page_item"><a href="download.html" title="Install Thetis">Download</a></li>
<li class="page_item"><a href="team.html" title="Development team">Team</a></li>
<li class="page_item"><a href="publications.html" title="Publications">Publications</a></li>
<li class="page_item"><a href="funding.html" title="Our financial supporters">Funding</a></li>
<li class="page_item"><a href="contact.html" title="Getting in touch">Contact</a></li>
<li class="page_item"><a href="https://github.com/thetisproject/thetis" title="Thetis source on GitHub">GitHub</a></li>
</ul>
</div><!-- .menu -->
</div><!-- #access -->
</div><!-- #wrapper -->
<div class="document">
<div class="model_options_3d">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<section id="d-model-options">
<span id="model-options-3d"></span><h1>3D model options<a class="headerlink" href="#d-model-options" title="Link to this heading">¶</a></h1>
<p>This page lists all available options for the 3D model.</p>
<p>See also <a class="reference internal" href="turbulence_options.html#turbulence-options"><span class="std std-ref">Turbulence model options</span></a> and <a class="reference internal" href="eos_options.html#eos-options"><span class="std std-ref">Equation of State options</span></a>.</p>
<dl>
<dt>CommonModelOptions.<strong>atmospheric_pressure</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Atmospheric pressure at free surface, in pascals</p>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>CommonModelOptions.<strong>cfl_2d</strong><span class="classifier">PositiveFloat</span></dt><dd><p>Factor to scale the 2d time step OBSOLETE</p>
<p>Default:</p>
<p>1.0</p>
</dd>
<dt>CommonModelOptions.<strong>cfl_3d</strong><span class="classifier">PositiveFloat</span></dt><dd><p>Factor to scale the 2d time step OBSOLETE</p>
<p>Default:</p>
<p>1.0</p>
</dd>
<dt>CommonModelOptions.<strong>check_volume_conservation_2d</strong><span class="classifier">Bool</span></dt><dd><p>Compute volume of the 2D mode at every export</p>
<blockquote>
<div><p>2D volume is defined as the integral of the water elevation field.
Prints deviation from the initial volume to stdout.</p>
</div></blockquote>
<p>Default:</p>
<p>False</p>
</dd>
<dt>CommonModelOptions.<strong>coriolis_frequency</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>2D Coriolis parameter</p>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>CommonModelOptions.<strong>element_family</strong><span class="classifier">‘dg-dg’|’rt-dg’|’bdm-dg’|’dg-cg’</span></dt><dd><p>Finite element family</p>
<blockquote>
<div><p>2D solver supports ‘dg-dg’, ‘rt-dg’, ‘bdm-dg’, or ‘dg-cg’ velocity-pressure pairs.
3D solver supports ‘dg-dg’, ‘rt-dg’, or ‘bdm-dg’ velocity-pressure pairs.</p>
</div></blockquote>
<p>Default:</p>
<p>‘dg-dg’</p>
</dd>
<dt>CommonModelOptions.<strong>export_diagnostics</strong><span class="classifier">Bool</span></dt><dd><p>Store diagnostic variables to disk in HDF5 format</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>CommonModelOptions.<strong>fields_to_export</strong><span class="classifier">List</span></dt><dd><p>Fields to export in VTK format</p>
<p>Default:</p>
<p>[‘elev_2d’, ‘uv_2d’, ‘uv_3d’, ‘w_3d’]</p>
</dd>
<dt>CommonModelOptions.<strong>fields_to_export_hdf5</strong><span class="classifier">List</span></dt><dd><p>Fields to export in HDF5 format</p>
<p>Default:</p>
<p>[]</p>
</dd>
<dt>CommonModelOptions.<strong>horizontal_diffusivity_scale</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><p>Maximum horizontal diffusivity</p>
<blockquote>
<div><p>Used to compute the mesh Peclet number in
the 2D tracer SUPG stabilization scheme.</p>
</div></blockquote>
<p>Default:</p>
<p>Constant(1.0)</p>
</dd>
<dt>CommonModelOptions.<strong>horizontal_velocity_scale</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><p>Maximum horizontal velocity magnitude</p>
<blockquote>
<div><p>Used to compute max stable advection time step.</p>
</div></blockquote>
<p>Default:</p>
<p>Constant(0.1)</p>
</dd>
<dt>CommonModelOptions.<strong>horizontal_viscosity</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Horizontal viscosity</p>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>CommonModelOptions.<strong>horizontal_viscosity_scale</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><p>Maximum horizontal viscosity</p>
<blockquote>
<div><p>Used to compute max stable diffusion time step.</p>
</div></blockquote>
<p>Default:</p>
<p>Constant(1.0)</p>
</dd>
<dt>CommonModelOptions.<strong>lax_friedrichs_tracer_scaling_factor</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><p>Scaling factor for tracer Lax Friedrichs stability term.</p>
<p>Default:</p>
<p>Constant(1.0)</p>
</dd>
<dt>CommonModelOptions.<strong>lax_friedrichs_velocity_scaling_factor</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><p>Scaling factor for Lax Friedrichs stabilisation term in horizontal momentum advection.</p>
<p>Default:</p>
<p>Constant(1.0)</p>
</dd>
<dt>CommonModelOptions.<strong>linear_drag_coefficient</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>2D linear drag parameter <span class="math notranslate nohighlight">\(L\)</span></p>
<blockquote>
<div><p>Bottom stress is <span class="math notranslate nohighlight">\(\tau_b/\rho_0 = -L \mathbf{u} H\)</span></p>
</div></blockquote>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>CommonModelOptions.<strong>log_output</strong><span class="classifier">Bool</span></dt><dd><p>Redirect all output to log file in output directory</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>CommonModelOptions.<strong>manning_drag_coefficient</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Manning-Strickler 2D quadratic drag parameter <span class="math notranslate nohighlight">\(\mu\)</span></p>
<blockquote>
<div><p>Bottom stress is <span class="math notranslate nohighlight">\(\tau_b/\rho_0 = -g \mu^2 |\mathbf{u}|\mathbf{u}/H^{1/3}\)</span></p>
</div></blockquote>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>CommonModelOptions.<strong>momentum_source_2d</strong><span class="classifier">FiredrakeVectorExpression</span></dt><dd><p>Source term for 2D momentum equation</p>
<p>Default:</p>
<p>UFL vector expression</p>
</dd>
<dt>CommonModelOptions.<strong>nh_model_options</strong><span class="classifier">Instance</span></dt><dd><p>No description</p>
<p>Default:</p>
<p><thetis.options.NonhydrostaticModelOptions object at 0x739c381adc40></p>
</dd>
<dt>CommonModelOptions.<strong>nikuradse_bed_roughness</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Nikuradse bed roughness length used to construct the 2D quadratic drag parameter <span class="math notranslate nohighlight">\(C_D\)</span>.</p>
<blockquote>
<div><p>In sediment transport this term is usually three times the average sediment diameter size.</p>
</div></blockquote>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>CommonModelOptions.<strong>no_exports</strong><span class="classifier">Bool</span></dt><dd><p>Do not store any outputs to disk</p>
<blockquote>
<div><p>Disables VTK and HDF5 field outputs. and HDF5 diagnostic outputs.
Used in CI test suite.</p>
</div></blockquote>
<p>Default:</p>
<p>False</p>
</dd>
<dt>CommonModelOptions.<strong>norm_smoother</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><dl class="simple">
<dt>Coefficient used to avoid non-differentiable functions in the continuous formulation of the velocity norm in</dt><dd><p>the quadratic bottom drag term in the momentum equation. This replaces the velocity norm in the quadratic
bottom drag term with <span class="math notranslate nohighlight">\(\|u\| \approx \sqrt{\|u\|^2 + \alpha^2}\)</span></p>
</dd>
</dl>
<p>Default:</p>
<p>Constant(0.0)</p>
</dd>
<dt>CommonModelOptions.<strong>output_directory</strong><span class="classifier">Unicode</span></dt><dd><p>Directory where model output files are stored</p>
<p>Default:</p>
<p>‘outputs’</p>
</dd>
<dt>CommonModelOptions.<strong>polynomial_degree</strong><span class="classifier">NonNegativeInteger</span></dt><dd><p>Polynomial degree of elements</p>
<p>Default:</p>
<p>1</p>
</dd>
<dt>CommonModelOptions.<strong>quadratic_drag_coefficient</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Dimensionless 2D quadratic drag parameter <span class="math notranslate nohighlight">\(C_D\)</span></p>
<blockquote>
<div><p>Bottom stress is <span class="math notranslate nohighlight">\(\tau_b/\rho_0 = -C_D |\mathbf{u}|\mathbf{u}\)</span></p>
</div></blockquote>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>CommonModelOptions.<strong>simulation_end_date</strong><span class="classifier">DatetimeTraitlet</span></dt><dd><p>Simulation end date</p>
<p>Default:</p>
<p>None</p>
</dd>
<dt>CommonModelOptions.<strong>simulation_end_time</strong><span class="classifier">PositiveFloat</span></dt><dd><p>Simulation duration in seconds</p>
<p>Default:</p>
<p>None</p>
</dd>
<dt>CommonModelOptions.<strong>simulation_export_time</strong><span class="classifier">PositiveFloat</span></dt><dd><p>Export interval in seconds</p>
<blockquote>
<div><p>All fields in fields_to_export list will be stored to disk and
diagnostics will be computed</p>
</div></blockquote>
<p>Default:</p>
<p>100.0</p>
</dd>
<dt>CommonModelOptions.<strong>simulation_initial_date</strong><span class="classifier">DatetimeTraitlet</span></dt><dd><p>Model initialization date. Corresponds to zero in simulation time.</p>
<p>Default:</p>
<p>None</p>
</dd>
<dt>CommonModelOptions.<strong>sipg_factor</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Penalty parameter scaling factor for horizontal viscosity terms.</p>
<p>Default:</p>
<p>Constant(1.0)</p>
</dd>
<dt>CommonModelOptions.<strong>sipg_factor_tracer</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Penalty parameter scaling factor for horizontal diffusivity terms.</p>
<p>Default:</p>
<p>Constant(1.0)</p>
</dd>
<dt>CommonModelOptions.<strong>timestep</strong><span class="classifier">PositiveFloat</span></dt><dd><p>Time step</p>
<p>Default:</p>
<p>10.0</p>
</dd>
<dt>CommonModelOptions.<strong>use_grad_depth_viscosity_term</strong><span class="classifier">Bool</span></dt><dd><p>Include <span class="math notranslate nohighlight">\(\nabla H\)</span> term in the depth-averaged viscosity</p>
<blockquote>
<div><p>See <a class="reference internal" href="thetis.html#thetis.shallowwater_eq.HorizontalViscosityTerm" title="thetis.shallowwater_eq.HorizontalViscosityTerm"><code class="xref py py-class docutils literal notranslate"><span class="pre">shallowwater_eq.HorizontalViscosityTerm</span></code></a> for details.</p>
</div></blockquote>
<p>Default:</p>
<p>True</p>
</dd>
<dt>CommonModelOptions.<strong>use_grad_div_viscosity_term</strong><span class="classifier">Bool</span></dt><dd><p>Include <span class="math notranslate nohighlight">\(\nabla (\nu_h \nabla \cdot \bar{\textbf{u}})\)</span> term in the depth-averaged viscosity</p>
<blockquote>
<div><p>See <a class="reference internal" href="thetis.html#thetis.shallowwater_eq.HorizontalViscosityTerm" title="thetis.shallowwater_eq.HorizontalViscosityTerm"><code class="xref py py-class docutils literal notranslate"><span class="pre">shallowwater_eq.HorizontalViscosityTerm</span></code></a> for details.</p>
</div></blockquote>
<p>Default:</p>
<p>False</p>
</dd>
<dt>CommonModelOptions.<strong>use_lax_friedrichs_tracer</strong><span class="classifier">Bool</span></dt><dd><p>Use Lax Friedrichs stabilisation in tracer advection.</p>
<p>Default:</p>
<p>False</p>
</dd>
<dt>CommonModelOptions.<strong>use_lax_friedrichs_velocity</strong><span class="classifier">Bool</span></dt><dd><p>use Lax Friedrichs stabilisation in horizontal momentum advection.</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>CommonModelOptions.<strong>use_limiter_for_tracers</strong><span class="classifier">Bool</span></dt><dd><p>Apply P1DG limiter for tracer fields</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>CommonModelOptions.<strong>use_nonlinear_equations</strong><span class="classifier">Bool</span></dt><dd><p>Use nonlinear shallow water equations</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>CommonModelOptions.<strong>verbose</strong><span class="classifier">Int</span></dt><dd><p>Verbosity level</p>
<p>Default:</p>
<p>0</p>
</dd>
<dt>CommonModelOptions.<strong>volume_source_2d</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Source term for 2D continuity equation</p>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>CommonModelOptions.<strong>wind_stress</strong><span class="classifier">FiredrakeVectorExpression</span></dt><dd><p>Stress at free surface (2D vector function)</p>
<p>Default:</p>
<p>UFL vector expression</p>
</dd>
<dt>ModelOptions3d.<strong>bottom_roughness</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Bottom roughness length in meters.</p>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>ModelOptions3d.<strong>check_salinity_conservation</strong><span class="classifier">Bool</span></dt><dd><p>Compute total salinity mass at every export</p>
<blockquote>
<div><p>Prints deviation from the initial mass to stdout.</p>
</div></blockquote>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>check_salinity_overshoot</strong><span class="classifier">Bool</span></dt><dd><p>Compute salinity overshoots at every export</p>
<blockquote>
<div><p>Prints overshoot values that exceed the initial range to stdout.</p>
</div></blockquote>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>check_temperature_conservation</strong><span class="classifier">Bool</span></dt><dd><p>Compute total temperature mass at every export</p>
<blockquote>
<div><p>Prints deviation from the initial mass to stdout.</p>
</div></blockquote>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>check_temperature_overshoot</strong><span class="classifier">Bool</span></dt><dd><p>Compute temperature overshoots at every export</p>
<blockquote>
<div><p>Prints overshoot values that exceed the initial range to stdout.</p>
</div></blockquote>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>check_volume_conservation_3d</strong><span class="classifier">Bool</span></dt><dd><p>Compute volume of the 3D domain at every export</p>
<blockquote>
<div><p>Prints deviation from the initial volume to stdout.</p>
</div></blockquote>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>constant_salinity</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><p>Constant salinity if salinity is not solved</p>
<p>Default:</p>
<p>Constant(0.0)</p>
</dd>
<dt>ModelOptions3d.<strong>constant_temperature</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><p>Constant temperature if temperature is not solved</p>
<p>Default:</p>
<p>Constant(10.0)</p>
</dd>
<dt>ModelOptions3d.<strong>equation_of_state_type</strong><span class="classifier">‘full’|’linear’</span></dt><dd><p>Type of equation of state</p>
<p>Default:</p>
<p>‘full’</p>
<p>Setting value implies configuration of sub-tree ModelOptions3d.equation_of_state_options:</p>
<p>‘full’:</p>
<p>‘linear’:</p>
<blockquote>
<div><dl>
<dt>ModelOptions3d.equation_of_state_options.<strong>alpha</strong><span class="classifier">Float</span></dt><dd><p>Thermal expansion coefficient of ocean water</p>
<p>Default:</p>
<p>0.2</p>
</dd>
<dt>ModelOptions3d.equation_of_state_options.<strong>beta</strong><span class="classifier">Float</span></dt><dd><p>Saline contraction coefficient of ocean water</p>
<p>Default:</p>
<p>0.77</p>
</dd>
<dt>ModelOptions3d.equation_of_state_options.<strong>rho_ref</strong><span class="classifier">NonNegativeFloat</span></dt><dd><p>Reference water density</p>
<p>Default:</p>
<p>1000.0</p>
</dd>
<dt>ModelOptions3d.equation_of_state_options.<strong>s_ref</strong><span class="classifier">NonNegativeFloat</span></dt><dd><p>Reference water salinity</p>
<p>Default:</p>
<p>35.0</p>
</dd>
<dt>ModelOptions3d.equation_of_state_options.<strong>th_ref</strong><span class="classifier">Float</span></dt><dd><p>Reference water temperature</p>
<p>Default:</p>
<p>15.0</p>
</dd>
</dl>
</div></blockquote>
</dd>
<dt>ModelOptions3d.<strong>horizontal_diffusivity</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Horizontal diffusivity for tracers</p>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>ModelOptions3d.<strong>internal_pg_scalar</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><p>A constant to scale the internal pressure gradient. Used to ramp up the model.</p>
<p>Default:</p>
<p>None</p>
</dd>
<dt>ModelOptions3d.<strong>momentum_source_3d</strong><span class="classifier">FiredrakeVectorExpression</span></dt><dd><p>Source term for 3D momentum equation</p>
<p>Default:</p>
<p>UFL vector expression</p>
</dd>
<dt>ModelOptions3d.<strong>salinity_source_3d</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Source term for salinity equation</p>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>ModelOptions3d.<strong>sipg_factor_turb</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Penalty parameter scaling factor for horizontal diffusivity terms of the turbulence model.</p>
<p>Default:</p>
<p>Constant(1.0)</p>
</dd>
<dt>ModelOptions3d.<strong>sipg_factor_vertical</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Penalty parameter scaling factor for vertical viscosity terms.</p>
<p>Default:</p>
<p>Constant(1.0)</p>
</dd>
<dt>ModelOptions3d.<strong>sipg_factor_vertical_tracer</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Penalty parameter scaling factor for vertical diffusivity terms.</p>
<p>Default:</p>
<p>Constant(1.0)</p>
</dd>
<dt>ModelOptions3d.<strong>sipg_factor_vertical_turb</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Penalty parameter scaling factor for vertical diffusivity terms of the turbulence model.</p>
<p>Default:</p>
<p>Constant(1.0)</p>
</dd>
<dt>ModelOptions3d.<strong>smagorinsky_coefficient</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><p>Smagorinsky viscosity coefficient <span class="math notranslate nohighlight">\(C_S\)</span></p>
<blockquote>
<div><p>See <a class="reference internal" href="thetis.html#thetis.utility3d.SmagorinskyViscosity" title="thetis.utility3d.SmagorinskyViscosity"><code class="xref py py-class docutils literal notranslate"><span class="pre">SmagorinskyViscosity</span></code></a>.</p>
</div></blockquote>
<p>Default:</p>
<p>Constant(0.1)</p>
</dd>
<dt>ModelOptions3d.<strong>solve_salinity</strong><span class="classifier">Bool</span></dt><dd><p>Solve salinity transport</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.<strong>solve_temperature</strong><span class="classifier">Bool</span></dt><dd><p>Solve temperature transport</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.<strong>temperature_source_3d</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Source term for temperature equation</p>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>ModelOptions3d.<strong>timestep_2d</strong><span class="classifier">PositiveFloat</span></dt><dd><p>Time step of the 2d mode</p>
<blockquote>
<div><p>This option is only used in the 3d solver, if 2d mode is solved
explicitly.</p>
</div></blockquote>
<p>Default:</p>
<p>10.0</p>
</dd>
<dt>ModelOptions3d.<strong>timestepper_type</strong><span class="classifier">‘LeapFrog’|’SSPRK22’</span></dt><dd><p>Name of the 3D time integrator</p>
<p>Default:</p>
<p>‘SSPRK22’</p>
<p>Setting value implies configuration of sub-tree ModelOptions3d.timestepper_options:</p>
<p>‘LeapFrog’:</p>
<p>‘SSPRK22’:</p>
<blockquote>
<div><dl>
<dt>ModelOptions3d.timestepper_options.<strong>use_automatic_timestep</strong><span class="classifier">Bool</span></dt><dd><p>Set time step automatically based on local CFL conditions.</p>
<p>Default:</p>
<p>True</p>
</dd>
</dl>
</div></blockquote>
</dd>
<dt>ModelOptions3d.<strong>turbulence_model_type</strong><span class="classifier">‘gls’|’pacanowski’</span></dt><dd><p>Type of vertical turbulence model</p>
<p>Default:</p>
<p>‘gls’</p>
<p>Setting value implies configuration of sub-tree ModelOptions3d.turbulence_model_options:</p>
<p>‘gls’:</p>
<blockquote>
<div><dl>
<dt>ModelOptions3d.turbulence_model_options.<strong>c1</strong><span class="classifier">Float</span></dt><dd><p>float: c1 parameter for Psi equations</p>
<p>Default:</p>
<p>1.44</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>c2</strong><span class="classifier">Float</span></dt><dd><p>float: c2 parameter for Psi equations</p>
<p>Default:</p>
<p>1.92</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>c3_minus</strong><span class="classifier">Float</span></dt><dd><p>float: c3 parameter for Psi equations, stable stratification</p>
<blockquote>
<div><p>If <code class="xref py py-attr docutils literal notranslate"><span class="pre">compute_c3_minus</span></code> is True this value will be overriden</p>
</div></blockquote>
<p>Default:</p>
<p>-0.52</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>c3_plus</strong><span class="classifier">Float</span></dt><dd><p>float: c3 parameter for Psi equations, unstable stratification</p>
<p>Default:</p>
<p>1.0</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>closure_name</strong><span class="classifier">‘k-epsilon’|’k-omega’|’Generic Length Scale’</span></dt><dd><p>Name of two-equation closure</p>
<p>Default:</p>
<p>‘k-epsilon’</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>cmu0</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: cmu0 parameter</p>
<p>Default:</p>
<p>0.5477</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>compute_c3_minus</strong><span class="classifier">Bool</span></dt><dd><p>bool: compute <code class="xref py py-attr docutils literal notranslate"><span class="pre">c3_minus</span></code> from <code class="xref py py-attr docutils literal notranslate"><span class="pre">ri_st</span></code></p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>compute_cmu0</strong><span class="classifier">Bool</span></dt><dd><p>bool: compute cmu0 from stability function parameters</p>
<blockquote>
<div><p>If <code class="xref py py-attr docutils literal notranslate"><span class="pre">compute_cmu0</span></code> is True, this value will be overriden</p>
</div></blockquote>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>compute_galperin_clim</strong><span class="classifier">Bool</span></dt><dd><p>bool: compute c_lim length scale limiting factor</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>compute_kappa</strong><span class="classifier">Bool</span></dt><dd><p>bool: compute von Karman constant from <code class="xref py py-attr docutils literal notranslate"><span class="pre">schmidt_nb_psi</span></code></p>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>compute_len_min</strong><span class="classifier">Bool</span></dt><dd><p>bool: compute min_len from k_min and psi_min</p>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>compute_psi_min</strong><span class="classifier">Bool</span></dt><dd><p>bool: compute psi_len from k_min and eps_min</p>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>compute_schmidt_nb_psi</strong><span class="classifier">Bool</span></dt><dd><p>bool: compute psi Schmidt number</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>diff_min</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: minimum value for eddy diffusivity</p>
<p>Default:</p>
<p>1e-08</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>eps_min</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: minimum value for epsilon</p>
<p>Default:</p>
<p>1e-14</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>f_wall</strong><span class="classifier">Float</span></dt><dd><p>float: wall function parameter</p>
<p>Default:</p>
<p>1.0</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>galperin_clim</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: Galperin length scale limitation parameter</p>
<p>Default:</p>
<p>0.3</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>k_min</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: minimum value for turbulent kinetic energy</p>
<p>Default:</p>
<p>1e-06</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>kappa</strong><span class="classifier">Float</span></dt><dd><p>float: von Karman constant</p>
<blockquote>
<div><p>If <code class="xref py py-attr docutils literal notranslate"><span class="pre">compute_kappa</span></code> is True this value will be overriden</p>
</div></blockquote>
<p>Default:</p>
<p>0.4</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>len_min</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: minimum value for turbulent length scale</p>
<p>Default:</p>
<p>1e-12</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>limit_eps</strong><span class="classifier">Bool</span></dt><dd><p>bool: apply Galperin length scale limit on epsilon</p>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>limit_len</strong><span class="classifier">Bool</span></dt><dd><p>bool: apply Galperin length scale limit</p>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>limit_len_min</strong><span class="classifier">Bool</span></dt><dd><p>bool: limit minimum turbulent length scale to len_min</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>limit_psi</strong><span class="classifier">Bool</span></dt><dd><p>bool: apply Galperin length scale limit on psi</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>m</strong><span class="classifier">Float</span></dt><dd><p>float: parameter m for the definition of psi</p>
<p>Default:</p>
<p>1.5</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>n</strong><span class="classifier">Float</span></dt><dd><p>float: parameter n for the definition of psi</p>
<p>Default:</p>
<p>-1.0</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>p</strong><span class="classifier">Float</span></dt><dd><p>float: parameter p for the definition of psi</p>
<p>Default:</p>
<p>3.0</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>psi_min</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: minimum value for psi</p>
<p>Default:</p>
<p>1e-14</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>ri_st</strong><span class="classifier">Float</span></dt><dd><p>steady state gradient Richardson number</p>
<p>Default:</p>
<p>0.25</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>schmidt_nb_psi</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: psi Schmidt number</p>
<p>Default:</p>
<p>1.3</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>schmidt_nb_tke</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: turbulent kinetic energy Schmidt number</p>
<p>Default:</p>
<p>1.0</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>stability_function_name</strong><span class="classifier">‘Canuto A’|’Canuto B’|’Kantha-Clayson’|’Cheng’</span></dt><dd><p>Name of stability function family</p>
<p>Default:</p>
<p>‘Canuto A’</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>visc_min</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: minimum value for eddy viscosity</p>
<p>Default:</p>
<p>1e-08</p>
</dd>
</dl>
</div></blockquote>
<p>‘pacanowski’:</p>
<blockquote>
<div><dl>
<dt>ModelOptions3d.turbulence_model_options.<strong>alpha</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: Richardson number multiplier</p>
<p>Default:</p>
<p>10.0</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>exponent</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: Exponent of viscosity numerator <span class="math notranslate nohighlight">\(n\)</span></p>
<p>Default:</p>
<p>2.0</p>
</dd>
<dt>ModelOptions3d.turbulence_model_options.<strong>max_viscosity</strong><span class="classifier">PositiveFloat</span></dt><dd><p>float: Constant maximum viscosity <span class="math notranslate nohighlight">\(\nu_{max}\)</span></p>
<p>Default:</p>
<p>0.05</p>
</dd>
</dl>
</div></blockquote>
</dd>
<dt>ModelOptions3d.<strong>use_ale_moving_mesh</strong><span class="classifier">Bool</span></dt><dd><p>Use ALE formulation where 3D mesh tracks free surface</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.<strong>use_baroclinic_formulation</strong><span class="classifier">Bool</span></dt><dd><p>Compute internal pressure gradient in momentum equation</p>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>use_bottom_friction</strong><span class="classifier">Bool</span></dt><dd><p>Apply log layer bottom stress in the 3D model</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.<strong>use_implicit_vertical_diffusion</strong><span class="classifier">Bool</span></dt><dd><p>Solve vertical diffusion and viscosity implicitly</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.<strong>use_limiter_for_velocity</strong><span class="classifier">Bool</span></dt><dd><p>Apply P1DG limiter for 3D horizontal velocity field</p>
<p>Default:</p>
<p>True</p>
</dd>
<dt>ModelOptions3d.<strong>use_quadratic_density</strong><span class="classifier">Bool</span></dt><dd><p>Water density is projected to P2DGxP2 space.</p>
<blockquote>
<div><p>This reduces pressure gradient errors associated with nonlinear
equation of state.
If False, density is computed point-wise in the tracer space.</p>
</div></blockquote>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>use_quadratic_pressure</strong><span class="classifier">Bool</span></dt><dd><p>Use P2DGxP2 space for baroclinic head.</p>
<blockquote>
<div><p>If element_family=’dg-dg’, P2DGxP1DG space is also used for the internal
pressure gradient.</p>
<p>This is useful to alleviate bathymetry-induced pressure gradient errors.
If False, the baroclinic head is in the tracer space, and internal
pressure gradient is in the velocity space.</p>
</div></blockquote>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>use_smagorinsky_viscosity</strong><span class="classifier">Bool</span></dt><dd><p>Use Smagorinsky horisontal viscosity parametrization</p>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>use_turbulence</strong><span class="classifier">Bool</span></dt><dd><p>Activate turbulence model in the 3D model</p>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>use_turbulence_advection</strong><span class="classifier">Bool</span></dt><dd><p>Advect TKE and Psi in the GLS turbulence model</p>
<p>Default:</p>
<p>False</p>
</dd>
<dt>ModelOptions3d.<strong>vertical_diffusivity</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Vertical diffusivity for tracers</p>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
<dt>ModelOptions3d.<strong>vertical_velocity_scale</strong><span class="classifier">FiredrakeConstantTraitlet</span></dt><dd><p>Maximum vertical velocity magnitude</p>
<blockquote>
<div><p>Used to compute max stable advection time step.</p>
</div></blockquote>
<p>Default:</p>
<p>Constant(0.0001)</p>
</dd>
<dt>ModelOptions3d.<strong>vertical_viscosity</strong><span class="classifier">FiredrakeScalarExpression</span></dt><dd><p>Vertical viscosity</p>
<p>Default:</p>
<p>UFL scalar expression</p>
</dd>
</dl>
</section>
<div class="clearer"></div>
</div>
</div>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer" role="contentinfo">
© Copyright 2016-2025, Tuomas Kärnä et al..
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.1.3.
</div>
</body>
</html>