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- Committer: tmb1
- Date: 2010-10-27 12:18:35 UTC
- Revision ID: svn-v4:5bf5533e-7014-46e3-b1bb-cce4b9d03719:trunk:2279
Adding a new schemas/ directory following discussion at the dev meeting and
moving all *.rn[c|g] files into it. I'm no schema expert so this may well
require various changes elsewhere to maintain consistency; please could those
who know what they're doing make these changes!
Patrick in particular - please update spud accordingly.
moving all *.rn[c|g] files into it. I'm no schema expert so this may well
require various changes elsewhere to maintain consistency; please could those
who know what they're doing make these changes!
Patrick in particular - please update spud accordingly.
- files added:
- schemas
added
removed
schemas/test_advection_diffusion_options.rnc
1
include "spud_base.rnc"
2
3
include "diagnostic_algorithms.rnc"
4
include "stabilisation.rnc"
5
6
start =
7
(
8
## The root node of the options dictionary.
9
element fluidity_options {
10
comment,
11
## Model output files are named according to the simulation
12
## name, e.g. [simulation_name]_0.vtu. Non-standard
13
## characters in the simulation name should be avoided.
14
element simulation_name {
15
anystring
16
},
17
## Options dealing with the specification of geometry
18
element geometry {
19
## Dimension of the problem.
20
## <b>This can only be set once</b>
21
element dimension {
22
attribute replaces {"NDIM"},
23
element integer_value {
24
attribute rank {"0"},
25
("3"|"2"|"1")
26
}
27
},
28
## The position mesh
29
element mesh {
30
attribute name { "CoordinateMesh" },
31
mesh_info
32
},
33
## The velocity mesh
34
element mesh {
35
attribute name { "VelocityMesh" },
36
mesh_info
37
},
38
element mesh {
39
attribute name { xsd:string },
40
mesh_info,
41
element exclude_from_mesh_adaptivity{empty}?
42
}*,
43
## Quadrature
44
element quadrature {
45
## Quadrature degree
46
##
47
## note: this specifies the degree of quadrature,
48
## not the number of gauss points
49
element degree {
50
attribute replaces {"NGI"},
51
integer
52
},
53
## Surface quadrature degree
54
##
55
## note: this specifies the degree of surface
56
## quadrature not the number of surface gauss points
57
element surface_degree {
58
attribute replaces {"SNGI"},
59
integer
60
}?,
61
## Select which family of quadrature rules to use.
62
## The default is family_cools.
63
## family_wandzura allows for degree up to 30
64
## on triangular meshes.
65
## family_grundmann_moeller allows for degree up to
66
## 29 on simplicial meshes in arbitrary dimension.
67
element quadrature_family {
68
( "family_cools" | "family_grundmann_moeller" | "family_wandzura" )
69
}?
70
}
71
},
72
## Input/output options
73
element io {
74
## Format for dump files. Only vtk for now.
75
element dump_format {
76
element string_value{
77
"vtk"
78
}
79
},
80
(
81
## Period between dumps in time units.
82
##
83
## Specifies the period between each dump of the solution to disk.
84
## A value of 0.0 indicates that there would be a dump at every timestep.
85
element dump_period {
86
(
87
element constant {
88
attribute replaces {"TIMDUM"},
89
real
90
}|
91
## Python function prescribing real input. Functions should be of the form:
92
##
93
## def val(t):
94
## # Function code
95
## return # Return value
96
##
97
##
98
element python {
99
attribute replaces {"TIMDUM"},
100
python_code
101
}
102
)
103
}|
104
## Dump period, in timesteps.
105
##
106
## Specifies the number of timesteps between each dump of the solution to disk.
107
## A value of 0 indicates a dump at every timestep.
108
element dump_period_in_timesteps {
109
(
110
element constant {
111
integer
112
}|
113
## Python function prescribing real input. Functions should be of the form:
114
##
115
## def val(t):
116
## # Function code
117
## return # Return value
118
##
119
##
120
element python {
121
python_code
122
}
123
)
124
}
125
),
126
# every CPUDUM seconds write results to disc.
127
## This is usually disabled.
128
element cpu_dump_period {
129
attribute replaces {"CPUDUM"},
130
real
131
}?,
132
## The period between dumps in walltime seconds. This is usually disabled.
133
element wall_time_dump_period {
134
attribute replaces {"WTIDUM"},
135
real
136
}?,
137
(
138
## The mesh on to which all the fields will be
139
## interpolated for VTK output.
140
element output_mesh {
141
attribute name { "VelocityMesh" }
142
}|
143
## The mesh on to which all the fields will be
144
## interpolated for VTK output.
145
element output_mesh {
146
attribute name { "PressureMesh" }
147
}|
148
## The mesh on to which all the fields will be
149
## interpolated for VTK output.
150
element output_mesh {
151
attribute name { "CoordinateMesh" }
152
}|
153
## The mesh on to which all the fields will be
154
## interpolated for VTK output.
155
element output_mesh {
156
attribute name { xsd:string }
157
}
158
)
159
},
160
## Options dealing with time discretisation
161
element timestepping {
162
## Current simulation time. At the start of the simulation this
163
## is the start time.
164
element current_time {
165
attribute replaces {"ACCTIM"},
166
real,
167
## The following excerpt from the Udunits
168
## documentation explains the time unit encoding by
169
## example:
170
##
171
## The specification:
172
##
173
## seconds since 1992-10-8 15:15:42.5 -6:00
174
##
175
## indicates seconds since October 8th, 1992 at 3
176
## hours, 15 minutes and 42.5 seconds in the afternoon
177
## in the time zone which is six hours to the west of
178
## Coordinated Universal Time (i.e. Mountain Daylight
179
## Time). The time zone specification can also be
180
## written without a colon using one or two-digits
181
## (indicating hours) or three or four digits
182
## (indicating hours and minutes).
183
##
184
## Time units are particularly required in situations
185
## where the problem (time-varying) boundary conditions
186
## and/ initial conditions are a function of time as
187
## defined by a calendar. Examples include atmospheric
188
## forcing and climatology. The current time, specified
189
## above, is zero at the reference data/time.
190
element time_units{attribute date { xsd:string }}?
191
},
192
## The time step size. If adaptive time stepping is used
193
## then this is the initial time step size.
194
element timestep {
195
attribute replaces {"DT"},
196
real
197
},
198
## Simulation time at which the simulation should end.
199
element finish_time {
200
attribute replaces {"LTIME"},
201
real
202
},
203
## Timestep after which the simulation should end.
204
element final_timestep {
205
integer
206
}?,
207
## Maximum CPU time (secs) taken up before
208
## simulation terminates writing results to disc.
209
##
210
## Manual suggests 1.E+20
211
element cpu_time_limit {
212
attribute replaces {"CPULIM"},
213
real
214
}?,
215
## Maximum wall time (secs) taken up before
216
## simulation terminates writing results to disc.
217
##
218
## This is usually disabled.
219
element wall_time_limit {
220
attribute replaces {"WATIME"},
221
real
222
}?
223
},
224
## The material or phase options
225
element material_phase {
226
attribute name { "Fluid" },
227
(
228
## Velocity vector and momentum options
229
element vector_field {
230
attribute rank { "1" },
231
attribute name { "Velocity" },
232
## Field type
233
element prescribed {
234
element mesh {
235
attribute name { "VelocityMesh" }
236
},
237
prescribed_vector_field
238
}
239
}?,
240
## Passive Tracer
241
element scalar_field {
242
attribute rank { "0" },
243
attribute name { "Tracer" },
244
attribute replaces { "IDENT = 666" },
245
element prognostic {
246
velocity_mesh_choice,
247
prognostic_scalar_field
248
}
249
},
250
## CFLNumber
251
##
252
## See http://amcg.ese.ic.ac.uk/index.php?title=Local:Diagnostics#CFL_Number
253
##
254
## Adapting to this field is not recommended
255
element scalar_field {
256
attribute rank { "0" },
257
attribute name { "CFLNumber" },
258
attribute replaces { "IDENT = -601" },
259
(
260
element diagnostic {
261
internal_algorithm,
262
velocity_mesh_choice,
263
diagnostic_scalar_field
264
}
265
)
266
}?
267
#scalar_field_choice*,
268
#vector_field_choice*,
269
#tensor_field_choice*
270
)
271
}
272
}
273
)
274
275
# Choice of input method, e.g. for boundary conditions
276
input_choice_real =
277
(
278
input_choice_real_contents
279
)
280
281
input_choice_real_plus_boundary_forcing =
282
(
283
input_choice_real_contents|
284
element from_file {
285
element tidal {
286
attribute file_name { string },
287
attribute variable_name_amplitude { string },
288
attribute variable_name_phase { string },
289
## See E.W. Schwiderski - Rev. Geophys. Space
290
## Phys. Vol. 18 No. 1 pp. 243--268, 1980
291
## for details of these constituent.
292
attribute name {"M2"|"S2"|"N2"|"K2"|"K1"|"O1"|"P1"|"Q1"|"Mf"|"Mm"|"Ssa"}
293
}+
294
}
295
)
296
297
input_choice_real_plus_file =
298
(
299
input_choice_real_contents|
300
## Initialise the field from an existing file (indended primarily for picking up prescribed fields from previously run prognostic simulations). The file mesh must match the mesh of this field (except for piecewise constant fields which will be remapped back from the discontinuous nodal values).
301
##
302
## THIS WILL NOT WORK FOR PRESCRIBED FIELDS NOT DIRECTLY UNDERNEATH /material_phase
303
element from_file {
304
attribute file_name { xsd:string },
305
## The format of the input file containing field data.
306
element format {
307
element string_value {
308
"vtu"
309
}
310
},
311
comment
312
}
313
)
314
315
input_choice_real_contents =
316
## Constant value
317
element constant {
318
real
319
}|
320
## Python function prescribing real input. Functions should be of the form:
321
##
322
## def val(X, t):
323
## # Function code
324
## return # Return value
325
##
326
## where X is a tuple of length geometry dimension.
327
element python {
328
python_code
329
}
330
331
# Choice of input method for initial conditions
332
# Note: combine = "choice" should be used here to combine with input_choice_real, but Diamond doesn't support it
333
input_choice_initial_condition_real =
334
(
335
## Constant value
336
element constant {
337
real
338
}|
339
## Python function prescribing real input. Functions should be of the form:
340
##
341
## def val(X, t):
342
## # Function code
343
## return # Return value
344
##
345
## where X is a tuple of length geometry dimension.
346
element python {
347
python_code
348
}|
349
## Initialise the field from an existing file (indended
350
## primarily for use in checkpointing). The file mesh must match
351
## the mesh of this field (except for piecewise constant fields
352
## which will be remapped back from the discontinuous nodal values).
353
## In parallel the process number is
354
## appended to the filename, e.g. if the file_name attribute is
355
## set to "input.vtu", process 0 reads from "input-0.vtu".
356
element from_file {
357
attribute file_name { xsd:string },
358
## The format of the input file containing field
359
## data. Supported formats include: NetCDF CF 1.4
360
## (http://cf-pcmdi.llnl.gov/)
361
element format {
362
element string_value {
363
"vtu"|"NetCDF - CF 1.x"
364
}
365
},
366
comment
367
}
368
)
369
370
# Choice of input method, e.g. for boundary conditions
371
input_choice_real_dim_vector =
372
(
373
input_choice_real_dim_vector_contents
374
)
375
376
# Choice of input method, e.g. for prescribed fields
377
input_choice_real_dim_vector_plus_file =
378
(
379
input_choice_real_dim_vector_contents|
380
## Initialise the field from an existing file (indended primarily for picking up prescribed fields from previously run prognostic simulations). The file mesh must match the mesh of this field (except for piecewise constant fields which will be remapped back from the discontinuous nodal values).
381
##
382
## THIS WILL NOT WORK FOR PRESCRIBED FIELDS NOT DIRECTLY UNDERNEATH /material_phase
383
element from_file {
384
attribute file_name { xsd:string },
385
## The format of the input file containing field data.
386
element format {
387
element string_value {
388
"vtu"
389
}
390
},
391
comment
392
}
393
)
394
395
input_choice_real_dim_vector_contents =
396
## Constant value
397
element constant {
398
real_dim_vector
399
}|
400
## Python function prescribing dimensional vector input. Functions should be of the form:
401
##
402
## def val(X, t):
403
## # Function code
404
## return # Return value
405
##
406
## where X and the return value are tuples of length geometry dimension.
407
element python {
408
python_code
409
}
410
411
# Choice of input method, e.g. for boundary conditions
412
# this one specifies a vector field of dim minus one
413
input_choice_real_dim_minus_one_vector =
414
(
415
## Constant value
416
element constant {
417
real_dim_minus_one_vector
418
}|
419
## Python function prescribing dimensional vector input. Functions should be of the form:
420
##
421
## def val(X, t):
422
## # Function code
423
## return # Return value
424
##
425
## where X and the return value are tuples of length geometry dimension.
426
element python {
427
python_code
428
}
429
)
430
431
## Import data from NetCDF CF-1.x file.
432
input_choice_netcdf =
433
(
434
element from_file {
435
## The format of this file should conform to NetCDF CF 1.x
436
## (http://cf-pcmdi.llnl.gov/)
437
attribute file_name { xsd:string },
438
comment
439
}
440
)
441
442
# Choice of input method for initial conditions
443
# Note: combine = "choice" should be used here to combine with input_choice_real, but Diamond doesn't support it
444
input_choice_initial_condition_vector =
445
(
446
## Constant value
447
element constant {
448
real_dim_vector
449
}|
450
## Python function prescribing dimensional vector input. Functions should be of the form:
451
##
452
## def val(X, t):
453
## # Function code
454
## return # Return value
455
##
456
## where X and the return value are tuples of length geometry dimension.
457
element python {
458
python_code
459
}|
460
## Initialise the field from an existing file (indended primarily for use in checkpointing). The file mesh must match the mesh of this field (except for piecewise constant fields which will be remapped back from the discontinuous nodal values).
461
element from_file {
462
attribute file_name { xsd:string },
463
## The format of the input file containing field data.
464
element format {
465
element string_value {
466
"vtu"
467
}
468
},
469
comment
470
}
471
)
472
473
# Choice of input method for initial/boundary conditions
474
# version for real symmetric tensor
475
input_choice_real_dim_symmetric_tensor =
476
(
477
## Constant symmetric tensor
478
element constant {
479
real_dim_symmetric_tensor
480
}|
481
## Python command prescribing symmetric tensor input.
482
##
483
## Note that it is for the python function to determine
484
## that the results it produces are, in fact, symmetric.
485
##
486
## An example that returns the three-dimensional identity:
487
##
488
## def val(X, t):
489
## return [[1, 0, 0],
490
## [0, 1, 0],
491
## [0, 0, 1]]
492
element python {
493
python_code
494
}
495
)
496
497
# Choice of input method for initial/boundary conditions
498
# version for real tensor
499
input_choice_real_dim_tensor =
500
(
501
## Constant tensor
502
element constant {
503
real_dim_tensor
504
}|
505
## Python command prescribing tensor input.
506
##
507
## An example that returns the three-dimensional identity:
508
##
509
## def val(X, t):
510
## return [[1, 0, 0],
511
## [0, 1, 0],
512
## [0, 0, 1]]
513
element python {
514
python_code
515
}
516
)
517
518
prognostic_velocity_field =
519
(
520
velocity_equation_choice,
521
## Spatial discretisation options
522
element spatial_discretisation {
523
(
524
## A new version of continuous galerkin assembly.
525
element continuous_galerkin {
526
## Stabilisation options for the galerkin discretisation
527
element stabilisation{
528
(
529
no_stabilisation|
530
su_stabilisation|
531
supg_stabilisation
532
)
533
},
534
## Discretisation options for the mass terms in the velocity equation.
535
element mass_terms{
536
## Lump the mass matrix - currently required if solving for pressure
537
element lump_mass_matrix {
538
## Lump on the submesh.
539
## This only works for simplex meshes and is only
540
## strictly valid on 2d meshes.
541
element use_submesh {
542
empty
543
}?
544
}?,
545
## Remove the mass terms from the equation.
546
element exclude_mass_terms {
547
empty
548
}?
549
},
550
## Discretisation options for the advection terms in the velocity equation.
551
element advection_terms {
552
## Integrate the advection terms of the momentum equation by parts.
553
## This allows for the imposition of weak boundary conditions.
554
## If activated the element advection matrix takes the form:
555
## / /
556
## - | (grad N_A dot nu) N_B rho dV - (1. - beta) | N_A ( div nu ) N_B rho dV
557
## / /
558
## otherwise it takes the standard form:
559
## / /
560
## | N_A (nu dot grad N_B) rho dV + beta | N_A ( div nu ) N_B rho dV
561
## / /
562
## where beta is set in conservative_advection, N is
563
## a shape function and nu is the relative nonlinear
564
## velocity.
565
element integrate_advection_by_parts {
566
empty
567
}?,
568
## Remove the advection terms (u.grad u rho + beta
569
## div u rho u) from the equation.
570
## This overrides any other advection term options
571
## (including conservative_advection below).
572
element exclude_advection_terms {
573
empty
574
}?
575
},
576
## Discretisation options for the stress terms in the velocity equation.
577
element stress_terms {
578
(
579
## Use tensor form of the stress terms.
580
##
581
## This is only valid for incompressible
582
## simulations as it is basically a simplication
583
## of full stress form when divergent elements can
584
## be cancelled out.
585
##
586
## ONLY DIAGONAL COMPONENTS OF VISCOSITY CAN BE
587
## SET (i.e. either isotropic or
588
## anistropic_symmetric with zero off diagonals
589
## tensors).
590
##
591
## If diagonal components differ from each other
592
## this must be for numerical reasons (i.e. not
593
## physical variations in viscosity otherwise
594
## simplification is not valid).
595
##
596
## If activated, the dim x dim (in this example
597
## 3d) stress matrix takes the form:
598
##
599
## / mu_xx*N_a,x*N_b,x + mu_yy*N_a,y*N_b,y + mu_zz*N_a,z*N_b,z
600
## | 0 ...
601
## \ 0
602
##
603
## 0
604
## ... mu_xx*N_a,x*N_b,x + mu_yy*N_a,y*N_b,y + mu_zz*N_a,z*N_b,z ...
605
## 0
606
##
607
## 0 \
608
## ... 0 |
609
## mu_xx*N_a,x*N_b,x + mu_yy*N_a,y*N_b,y + mu_zz*N_a,z*N_b,z /
610
##
611
## which is derived from b_a^T c b_b, where:
612
##
613
## b_a = / N_a,x \ c = / mu_xx 0 0 \
614
## | N_a,y | | 0 mu_yy 0 |
615
## \ N_a,z / \ 0 0 mu_zz /
616
##
617
## where N_a and N_b are shape functions of the
618
## ath and bth node respectively and mu are the
619
## components of the viscosity tensor.
620
element tensor_form {
621
empty
622
}|
623
## Use full stress form of the stress tensor.
624
##
625
## This is required if performing a compressible simulation.
626
##
627
## If using a viscosity ALL COMPONENTS OF
628
## VISCOSITY MUST BE SET (i.e. either
629
## anisotropic_symmetric or
630
## anisotropic_asymmetric tensors).
631
##
632
## If components differ form each other this must
633
## be for numerical reasons (i.e. not physical
634
## variations in viscosity).
635
##
636
## If activated, the dim x dim (in this example
637
## 3d) stress matrix takes the form:
638
##
639
## / 2*N_a,x*N_b,x*mu_xx + N_a,y*N_b,y*mu_yy + N_a,z*N_b,z*mu_zz - 2/3*N_a,x*N_b,x*mu_xx
640
## | N_a,x*N_b,y*mu_xy - 2/3*N_a,y*N_b,x*mu_yx ...
641
## \ N_a,x*N_b,z*mu_xz - 2/3*N_a,z*N_b,x*mu_zx
642
##
643
## N_a,y*N_b,x*mu_xy - 2/3*N_a,x*N_b,y*mu_xy
644
## ... N_a,x*N_b,x*mu_xx + 2*N_a,y*N_b,y*mu_yy + N_a,z*N_b,z*mu_zz - 2/3*N_a,y*N_b,y*mu_yy ...
645
## N_a,y*N_b,z*mu_yz - 2/3*N_a,z*N_b,y*mu_zy
646
##
647
## N_a,z*N_b,x*mu_xz - 2/3*N_a,x*N_b,z*mu_xz \
648
## ... N_a,z*N_b,y*mu_yz - 2/3*N_a,y*N_b,z*mu_yz |
649
## N_a,x*N_b,x*mu_xx + N_a,y*N_b,y*mu_yy + 2*N_a,z*N_b,z*mu_zz - 2/3*N_a,z*N_b,z*mu_zz /
650
##
651
## which is derived from b_a^T c b_b, where:
652
##
653
## b_a = / N_a,x 0 0 \ c = / 4/3*mu_xx -2/3*mu_xy -2/3*mu_xz 0 0 0 \
654
## | 0 N_a,y 0 | | -2/3*mu_yx 4/3*mu_yy -2/3*mu_yz 0 0 0 |
655
## | 0 0 N_a,z | | -2/3*mu_zx -2/3*mu_zy 4/3*mu_zz 0 0 0 |
656
## | N_a,y N_a,x 0 | | 0 0 0 mu_xy 0 0 |
657
## | N_a,z 0 N_a,x | | 0 0 0 0 mu_xz 0 |
658
## \ 0 N_a,z N_a,y / \ 0 0 0 0 0 mu_yz /
659
##
660
## where N_a and N_b are shape functions of the ath and bth node respectively and mu are the components of the viscosity tensor.
661
element stress_form {
662
## Use the legacy form of the stress tensor.
663
##
664
## If activated, the dim x dim (in this case
665
## 3d) stress matrix takes the form:
666
##
667
## / 2*N_a,x*N_b,x*mu_xx + N_a,y*N_b,y*mu_yy + N_a,z*N_b,z*mu_zz - 2/3*N_a,x*N_b,x*mu_xx
668
## | N_a,x*N_b,y*mu_yx - 2/3*N_a,y*N_b,x*mu_yy ...
669
## \ N_a,x*N_b,z*mu_zx - 2/3*N_a,z*N_b,x*mu_zz
670
##
671
## N_a,y*N_b,x*mu_xy - 2/3*N_a,x*N_b,y*mu_xx
672
## ... N_a,x*N_b,x*mu_xx + 2*N_a,y*N_b,y*mu_yy + N_a,z*N_b,z*mu_zz - 2/3*N_a,y*N_b,y*mu_yy ...
673
## N_a,y*N_b,z*mu_zy - 2/3*N_a,z*N_b,y*mu_zz
674
##
675
## N_a,z*N_b,x*mu_xz - 2/3*N_a,x*N_b,z*mu_xx \
676
## ... N_a,z*N_b,y*mu_yz - 2/3*N_a,y*N_b,z*mu_yy |
677
## N_a,x*N_b,x*mu_xx + N_a,y*N_b,y*mu_yy + 2*N_a,z*N_b,z*mu_zz - 2/3*N_a,z*N_b,z*mu_zz /
678
##
679
## where N_a and N_b are shape functions of
680
## the ath and bth node respectively and mu
681
## are the components of the viscosity tensor.
682
element legacy_stress_form {
683
empty
684
}?
685
}
686
)
687
},
688
element les_model {
689
## suggested value 0.1
690
element smagorinsky_coefficient {
691
real
692
},
693
element form {
694
element tensor_form{empty}
695
|
696
element stress_form{empty}
697
},
698
element order {
699
element second_order{empty}
700
|
701
element fourth_order{empty}
702
}
703
}?
704
}|
705
## Discontinuous galerkin formulation. This causes Momentum_DG to be
706
## called instead of diff3d. Confusingly it is not necessary to provide
707
## a discontinuous velocity field for this to work!
708
element discontinuous_galerkin {
709
attribute replaces { "DISOPT" },
710
## Discretisation options for the mass terms in the velocity equation.
711
element mass_terms{
712
## Lump the mass matrix
713
element lump_mass_matrix {
714
empty
715
}?
716
}?,
717
element viscosity_scheme {
718
(
719
## Classical scheme from Bassi and Rebay
720
## (JCP 131 267-179 1997)
721
element bassi_rebay {
722
empty
723
}|
724
## Scheme in which upwinding is applied in
725
## alternating directions. Devised by C.Pain.
726
element arbitrary_upwind {
727
empty
728
}|
729
## Classical interior penalty scheme
730
## see, e.g., SIAM Journal on Numerical Analysis
731
## Vol. 39, No. 5 (2002), pp. 1749-1779
732
element interior_penalty {
733
## Penalty_parameter
734
## The penalty term Int [u][v] dS on element boundaries
735
## is scaled by C = C_0 h**p
736
## This option specifies the C_0
737
## There is a theoretical lower bound for
738
## stability and hence convergence
739
element penalty_parameter {
740
real
741
},
742
## Penalty_parameter
743
## The penalty term Int [u][v] dS on element boundaries
744
## is scaled by C = C_0 h**p
745
## This option specifies p
746
## Theoretically p=-1 is required for linear elements
747
element edge_length_power {
748
real
749
},
750
## Switch on debugging output
751
element debug {
752
## Bound for testing element gradient matrix
753
element gradient_test_bound {
754
real
755
},
756
## Remove the elemental integral:
757
## Int grad u.kappa.grad v dV
758
element remove_element_integral {
759
empty
760
}?,
761
## Remove the primal fluxes
762
element remove_primal_fluxes {
763
empty
764
}?,
765
## Remove the penalty fluxes
766
element remove_penalty_fluxes {
767
empty
768
}?
769
}?
770
}
771
)
772
},
773
element advection_scheme {
774
(
775
## Straightforward upwinding of the nonlinear velocity.
776
element upwind {
777
empty
778
}|
779
## Disable advection
780
element none {
781
empty
782
}
783
),
784
## Integrate the advection terms of the momentum equation by parts.
785
##
786
## Integrating the advection term by parts is
787
## necessary for a discontinuous
788
## galerkin discretisation however it is possible to
789
## select how many times the
790
## integration by parts is performed.
791
## Twice is the norm.
792
element integrate_advection_by_parts {
793
(
794
## If activated the element advection matrix takes the form:
795
## / /
796
## | N_A (nu dot grad N_B) dV + beta | N_A ( div nu ) N_B dV
797
## / /
798
## / /
799
## + I | N_A_i (nu dot n) N_B_o ds + [(1-I) - 1] | N_A_i (nu dot n) N_B_i ds
800
## / /
801
## where beta is set in conservative_advection,
802
## N is a shape function (uppercase
803
## subscripts indicate nodes A or B while
804
## lowercase subscripts indicate inner or outer
805
## faces i and o respectively), nu is the
806
## nonlinear velocity and n is the outward
807
## pointing normal from the element.
808
element twice {
809
empty
810
}|
811
## If activated the element advection matrix takes the form:
812
## / /
813
## - | (grad N_A dot nu) N_B dV - (1. - beta) | N_A ( div nu ) N_B dV
814
## / /
815
## / /
816
## + I | N_A_i (nu dot n) N_B_o ds + (1-I) | N_A_i (nu dot n) N_B_i ds
817
## / /
818
## where beta is set in conservative_advection,
819
## N is a shape function (uppercase
820
## subscripts indicate nodes A or B while
821
## lowercase subscripts indicate inner or outer
822
## faces i and o respectively), nu is the
823
## nonlinear velocity and n is the outward
824
## pointing normal from the element.
825
element once {
826
empty
827
}
828
)
829
},
830
## If activated the conservation term:
831
## /
832
## | N_A ( div nu ) N_B dV
833
## /
834
## is integrated_by_parts such that the element
835
## advection matrix becomes:
836
## / /
837
## - beta | (grad N_A dot nu) N_B dV + (1. - beta) | N_A (nu dot grad N_B) dV
838
## / /
839
## / /
840
## + I | N_A_i (nu dot n) N_B_o ds + [(1-I) - (1-beta)] | N_A_i (nu dot n) N_B_i ds
841
## / /
842
## where beta is set in conservative_advection, N is
843
## a shape function (uppercase
844
## subscripts indicate nodes A or B while lowercase
845
## subscripts indicate inner or outer
846
## faces i and o respectively), nu is the nonlinear
847
## velocity and n is the outward pointing normal
848
## from the element.
849
## This is invariant regardless of whether the main
850
## advection term is integrated by parts once or
851
## twice.
852
element integrate_conservation_term_by_parts {
853
empty
854
}?
855
}
856
}|
857
## Use the legacy finite element discretisation
858
element legacy_continuous_galerkin {
859
attribute replaces { "DISOPT" },
860
(
861
## balancing diffusion based on (x,y) space.
862
element balancing_diffusion_x {
863
attribute replaces { "DISOPT = 1" },
864
empty
865
}|
866
## Laxwendrof balancing diffusion.
867
element laxwendroff_balancing_diffusion {
868
attribute replaces { "DISOPT = 2" },
869
empty
870
}|
871
## (x,y,t) -balancing diffusion.
872
element balancing_diffusion_xt {
873
attribute replaces { "DISOPT = 3" },
874
empty
875
}|
876
## No balancing diffusion.
877
element no_balancing_diffusion {
878
attribute replaces { "DISOPT = 4" },
879
empty
880
}|
881
## nonlinear streamline and cross stream diffusion.
882
element nonlinear_streamline_w_crossstream_diffusion {
883
attribute replaces { "DISOPT = 5" },
884
empty
885
}|
886
## nonlinear upwind in steapest direction.
887
element nonlinear_upwind_steepest {
888
attribute replaces { "DISOPT = 6" },
889
empty
890
}|
891
## nonlinear streamline+ cross stream diffusion(but restricted)
892
element nonlinear_streamline_w_restricted_crossstream_diffusion {
893
attribute replaces { "DISOPT = 7" },
894
empty
895
}|
896
## LES option using constant length scale.
897
element les_constant_length_scale {
898
attribute replaces { "DISOPT = 42" },
899
empty
900
}|
901
## LES option using isotropic length scale.
902
element les_isotropic_length_scale {
903
attribute replaces { "DISOPT = 43" },
904
empty
905
}|
906
## LES option which uses no balancing diffusion.
907
element les_no_balancing_diffusion {
908
attribute replaces { "DISOPT = 44" },
909
empty
910
}|
911
## LES option which uses no balancing diffusion.
912
element les_no_balancing_diffusion_2 {
913
attribute replaces { "DISOPT = 45" },
914
empty
915
}|
916
## same as 45 but with 4th order dissipation.
917
element les_no_balancing_diffusion_fourth_order_dissipation {
918
attribute replaces { "DISOPT = 46" },
919
empty
920
}|
921
## LES but in tensor form like hart3d
922
element les_tensor_form {
923
attribute replaces { "DISOPT = 47" },
924
empty
925
}|
926
## LES 4th order version of 47
927
element les_fourth_order {
928
attribute replaces { "DISOPT = 48" },
929
empty
930
}|
931
## NO balancing diffusion(DISOPT=4)and take out non-linear terms.
932
element no_balancing_diffusion_remove_nonlinear_terms {
933
attribute replaces { "DISOPT = 125" },
934
empty
935
}
936
),
937
## Lump the mass matrix in the momentum equation
938
element lump_mass_matrix {
939
attribute replaces {"MLUMP"},
940
empty
941
}?
942
}|
943
element legacy_discretisation {
944
## Legacy discretisation option (DISOPT)
945
##
946
## From diff3d comments (other possibilities are known to exist!):
947
## ==============================================================
948
## DISOPT=1 - balancing diffusion based on (x,y) space.
949
## DISOPT=2 - Laxwendrof balancing diffusion.
950
## DISOPT=3 - (x,y,t) -balancing diffusion.
951
## DISOPT=4 - No balancing diffusion.
952
## DISOPT=5 - nonlinear streamline and cross stream diffusion.
953
## DISOPT=6 - nonlinear upwind in steapest direction.
954
## DISOPT=7 - nonlinear streamline+ cross stream diffusion(but restricted)
955
##
956
## DISOPT=42- LES option using constant length scale.
957
## DISOPT=43- LES option using isotropic length scale.
958
## DISOPT=44- LES option which uses no balancing diffusion.
959
## DISOPT=45- LES option which uses no balancing diffusion.
960
## DISOPT=46- same as 45 but with 4th order dissipation.
961
## DISOPT=47 -LES but in tensor form like hart3d.
962
## DISOPT=48 -LES 4th order version of 47.
963
##
964
## DISOPT=125 - NO balancing diffusion(DISOPT=4)and take out non-linear terms.
965
element legacy_disopt {
966
attribute replaces {"DISOPT"},
967
integer
968
},
969
## Lump the mass matrix in the momentum equation
970
element legacy_mlump {
971
attribute replaces {"MLUMP"},
972
empty
973
}?,
974
## Legacy discretisation option for control volume advection of momentum (DISOPT)
975
## Set to 0 if not activated
976
## Method for face-value est. Time-stepping Limiting
977
## ------------------------------------------------------------------
978
## =0 1st order in space Theta=specified UNIVERSAL
979
## =1 1st order in space Theta=non-linear UNIVERSAL
980
## =2 Trapazoidal rule in space Theta=specified UNIVERSAL
981
## =3 Trapazoidal rule in space Theta=non-linear UNIVERSAL
982
## =4 Finite elements in space Theta=specified UNIVERSAL
983
## =5 Finite elements in space Theta=non-linear UNIVERSAL
984
## =6 Finite elements in space Theta=specified NONE
985
## =7 Finite elements in space Theta=non-linear NONE
986
## =8 Finite elements in space Theta=specified DOWNWIND+
987
## =9 Finite elements in space Theta=non-linear DOWNWIND+
988
element legacy_ndisop {
989
attribute replaces {"NDISOP"},
990
integer
991
}?
992
}
993
),
994
## Conservative discretisation of momentum equations
995
## BETA=1. -- conservative (divergence form)
996
## BETA=0. -- non-conservative
997
## 0. < BETA < 1.
998
element conservative_advection {
999
attribute replaces {"BETA"},
1000
real
1001
},
1002
inner_element_velocity?
1003
},
1004
## Temporal discretisation options
1005
element temporal_discretisation {
1006
## Implicit/explicit control (THETA)
1007
## =0. -- explicit
1008
## =0.5 -- Crank-Nicolson
1009
## =1. -- implicit
1010
element theta {
1011
attribute replaces {"THETA"},
1012
real
1013
},
1014
## Non-linear relaxation term
1015
## =0. -- previous timestep velocity solution used in non-linear terms of momentum equations
1016
## =1. -- previous iteration velocity solution used in non-linear terms of momentum equations
1017
## 0. < ITHETA < 1.
1018
element relaxation {
1019
attribute replaces {"ITHETA"},
1020
real
1021
},
1022
element discontinuous_galerkin {
1023
(
1024
## Use timestep subcycling to solve this equation.
1025
## Specify the number of subcycles.
1026
## This only works for pure control volume discretisations.
1027
element number_advection_subcycles {
1028
integer
1029
}
1030
)?
1031
}?
1032
},
1033
## Solver
1034
element solver {
1035
linear_solver_options_asym
1036
},
1037
constitutive_laws,
1038
(
1039
## Initial condition for WholeMesh
1040
##
1041
## Only specify one condition if not using mesh regions.
1042
## Otherwise select other initial_condition option, specify region_ids
1043
## and distinct names. Then add extra intial conditions for other regions.
1044
element initial_condition {
1045
attribute name { "WholeMesh" },
1046
input_choice_initial_condition_vector
1047
}|
1048
## Multiple initial_conditions are allowed if specifying
1049
## different values in different
1050
## regions of the mesh (defined by region_ids). In this case
1051
## each initial_condition
1052
## requires a distinct name for the options dictionary.
1053
element initial_condition {
1054
attribute name { string },
1055
region_ids,
1056
input_choice_initial_condition_vector
1057
}
1058
)+,
1059
## Boundary conditions
1060
element boundary_conditions {
1061
attribute replaces { "boundary, TMPER1 TMPER2 TMPERI" },
1062
attribute name { string },
1063
## Surface id:
1064
element surface_ids {
1065
integer_vector
1066
},
1067
velocity_boundary_conditions
1068
}*,
1069
## For a Newtonian fluid this is the shear viscosity.
1070
##
1071
## For continuous_galerkin see stress_terms to see how the
1072
## viscosity tensor is dealt with in the momentum equation.
1073
element tensor_field {
1074
attribute replaces {"MUPTXX MUPTYY MUPTZZ MUPTYZ MUPTXZ MUPTXY RMUPXX RMUPYY RMUPZZ RMUPYZ RMUPXZ RMUPXY CONMU ALLMU TWOMU ONEMU"},
1075
attribute name { "Viscosity" },
1076
attribute rank { "2" },
1077
(
1078
element prescribed {
1079
prescribed_values_tensor_field
1080
}|
1081
element diagnostic {
1082
internal_algorithm,
1083
diagnostic_tensor_field
1084
}
1085
)
1086
}?,
1087
## Source
1088
element vector_field {
1089
attribute name { "Source" },
1090
attribute rank { "1" },
1091
attribute replaces { "CONSOX CONSOY CONSOZ RONSOX RONSOY RONSOZ ZSOX ZSOY ZSOZ" },
1092
(
1093
element prescribed {
1094
mesh_choice?,
1095
prescribed_vector_field_no_adapt
1096
}|
1097
element diagnostic {
1098
internal_algorithm,
1099
diagnostic_vector_field
1100
}
1101
),
1102
element lump_source {
1103
attribute replaces { "SLUMP" },
1104
empty
1105
}?
1106
}?,
1107
## Absorption
1108
element vector_field {
1109
attribute name { "Absorption" },
1110
attribute rank { "1" },
1111
attribute replaces { "XABSZE YABSZE ZABSZE XABS YABS ZABS XABSOR YABSOR ZABSOR XABSCO YABSCO ZABSCO" },
1112
(
1113
element prescribed {
1114
prescribed_vector_field_no_adapt
1115
}|
1116
element diagnostic {
1117
internal_algorithm,
1118
diagnostic_vector_field
1119
}
1120
),
1121
(
1122
## Default absorption: no lumping, is fully evaluated before the
1123
## the pressure correction.
1124
element default_absorption {
1125
attribute replaces {"ABSLUM"},
1126
empty
1127
}|
1128
## Lump the inclusion of absorbtion terms.
1129
element lump_absorption {
1130
attribute replaces {"ABSLUM"},
1131
empty
1132
}|
1133
## Includes the pressure correction to the velocity in the
1134
## absorption term (for theta>0). This makes the absorption
1135
## term more implicit. The absorption term is lumped if and
1136
## only if the mass matrix is lumped (lump_mass_matrix).
1137
element include_pressure_correction {
1138
empty
1139
}
1140
)
1141
}?,
1142
## Elastic parameters for elastic and visco-elastic materials
1143
## For a linearly elastic solid
1144
## In legacy elastic solids were run with SOLIDS = 2 from solidity_options.inp.
1145
## In gem ONEMU and CONMU = .TRUE.
1146
## and RMUPZZ taken as the isotropic Young`s modulus
1147
## UNDER DEVELOPMENT
1148
## - currently only works for lagrangian meshes
1149
## - only single materials tested so far
1150
## - momentum equations assembled in solid3d so not all
1151
## discretisation options above are valid
1152
element tensor_field {
1153
attribute replaces { "SOLIDS = 1 from solidity_options.inp" },
1154
attribute name { "Elasticity" },
1155
attribute rank { "2" },
1156
(
1157
element prescribed {
1158
prescribed_values_tensor_field
1159
}|
1160
element diagnostic {
1161
internal_algorithm,
1162
diagnostic_tensor_field
1163
}
1164
)
1165
}?,
1166
## SurfaceTension
1167
element tensor_field {
1168
attribute name { "SurfaceTension" },
1169
attribute rank { "2" },
1170
(
1171
element diagnostic {
1172
internal_algorithm,
1173
attribute field_name { "MaterialVolumeFraction" },
1174
## Choose whether the mass matrix is lumped or not for the calculation of the gradient
1175
element lump_mass_matrix {
1176
empty
1177
}?,
1178
## Solver options are necessary if you're not lumping your mass or if you're field isn't dg
1179
element solver {
1180
linear_solver_options_sym
1181
}?,
1182
## Choose whether the surface tension term in the momentum equation is integrated by parts or not
1183
element integrate_by_parts {
1184
empty
1185
}?,
1186
diagnostic_tensor_field
1187
}
1188
)
1189
}?,
1190
## Cohesion for plastic materials
1191
## UNDER DEVELOPMENT
1192
## - currently only works for lagrangian meshes
1193
## - only single materials tested so far
1194
## - momentum equations assembled in solid3d so not all
1195
## discretisation options above are valid
1196
element scalar_field {
1197
attribute name { "Cohesion" },
1198
attribute rank { "0" },
1199
attribute replaces { "COHESI from solidity_options.inp" },
1200
(
1201
element prescribed {
1202
prescribed_scalar_field_no_adapt
1203
}|
1204
element diagnostic {
1205
internal_algorithm,
1206
diagnostic_scalar_field
1207
}
1208
)
1209
}?,
1210
## Friction Angle for plastic materials
1211
## UNDER DEVELOPMENT
1212
## - currently only works for lagrangian meshes
1213
## - only single materials tested so far
1214
## - momentum equations assembled in solid3d so not all
1215
## discretisation options above are valid
1216
element scalar_field {
1217
attribute name { "FrictionAngle" },
1218
attribute rank { "0" },
1219
attribute replaces { "FRCANG from solidity_options.inp" },
1220
(
1221
element prescribed {
1222
prescribed_scalar_field_no_adapt
1223
}|
1224
element diagnostic {
1225
internal_algorithm,
1226
diagnostic_scalar_field
1227
}
1228
)
1229
}?,
1230
prognostic_vector_output_options,
1231
prognostic_vector_stat_options,
1232
vector_convergence_options,
1233
prognostic_detector_options,
1234
vector_steady_state_options,
1235
adaptivity_options_prognostic_vector_field,
1236
interpolation_algorithm_vector,
1237
discrete_properties_algorithm_vector?
1238
)
1239
1240
prognostic_scalar_field =
1241
(
1242
## Solver
1243
element solver {
1244
linear_solver_options_sym
1245
},
1246
(
1247
## Initial condition for WholeMesh
1248
##
1249
## Only specify one condition if not using mesh regions.
1250
## Otherwise select other initial_condition option, specify region_ids
1251
## and distinct names. Then add extra intial conditions for other regions.
1252
element initial_condition {
1253
attribute name { "WholeMesh" },
1254
input_choice_initial_condition_real
1255
}|
1256
## Multiple initial_conditions are allowed if specifying
1257
## different values in different
1258
## regions of the mesh (defined by region_ids). In this case
1259
## each initial_condition
1260
## requires a distinct name for the options dictionary.
1261
element initial_condition {
1262
attribute name { string },
1263
region_ids,
1264
input_choice_initial_condition_real
1265
}
1266
),
1267
## Diffusivity for field
1268
element tensor_field {
1269
attribute name { "Diffusivity" },
1270
attribute rank { "2" },
1271
attribute replaces { "TMUXX TMUYY TMUZZ TMUYZ TMUXZ TMUXY TALLMU TCONMU" },
1272
element prescribed {
1273
mesh_choice?,
1274
prescribed_values_tensor_field
1275
}
1276
}?,
1277
prognostic_scalar_output_options,
1278
prognostic_scalar_stat_options
1279
)
1280
1281
# Default child of diagnostic scalar field
1282
diagnostic_scalar_field =
1283
(
1284
diagnostic_output_options,
1285
diagnostic_scalar_stat_options,
1286
scalar_convergence_options,
1287
diagnostic_detector_options,
1288
scalar_steady_state_options,
1289
adaptivity_options_scalar_field,
1290
recalculation_options?
1291
)
1292
1293
# Default child of diagnostic scalar field without adaptivity options
1294
diagnostic_scalar_field_no_adapt =
1295
(
1296
diagnostic_output_options,
1297
diagnostic_scalar_stat_options,
1298
diagnostic_detector_options
1299
)
1300
1301
# Default child of diagnostic scalar field
1302
diagnostic_scalar_field_tidal_range =
1303
(
1304
diagnostic_output_options,
1305
diagnostic_scalar_stat_options,
1306
diagnostic_detector_options,
1307
adaptivity_options_scalar_field,
1308
(
1309
element spin_up_time {
1310
real
1311
}
1312
)
1313
)
1314
1315
# Default child of prescribed scalar field
1316
# This is a choice of ways of inputing the prescribed field
1317
prescribed_scalar_field =
1318
(
1319
prescribed_scalar_field_no_adapt,
1320
adaptivity_options_scalar_field,
1321
interpolation_algorithm_scalar?,
1322
discrete_properties_algorithm_scalar?,
1323
recalculation_options?
1324
)
1325
1326
# Default child of prescribed scalar field without adaptivity options
1327
# This is a choice of ways of inputing the prescribed field
1328
prescribed_scalar_field_no_adapt =
1329
(
1330
prescribed_values_scalar_field,
1331
prescribed_output_options,
1332
prescribed_scalar_stat_options,
1333
prescribed_detector_options
1334
)
1335
1336
prescribed_values_scalar_field =
1337
(
1338
(
1339
## Value for WholeMesh
1340
## Only specify one value if not using mesh regions.
1341
## Otherwise select other value option, specify region_ids
1342
## and distinct names. Then add extra values for other regions.
1343
element value {
1344
attribute name { "WholeMesh" },
1345
input_choice_real_plus_file
1346
}|
1347
## Multiple values are now allowed if using different value assignments
1348
## in different regions of the mesh (specified by region_ids).
1349
## In this case each value requires a distinct name for the options dictionary.
1350
element value {
1351
attribute name { string },
1352
region_ids,
1353
input_choice_real_plus_file
1354
}
1355
)+
1356
)
1357
1358
# Default child of diagnostic vector field
1359
# Currently, this is empty, but in future this might include
1360
# options that are general to all diagnostic vector fields
1361
diagnostic_vector_field =
1362
(
1363
diagnostic_output_options,
1364
diagnostic_vector_stat_options,
1365
vector_convergence_options,
1366
diagnostic_detector_options,
1367
vector_steady_state_options,
1368
adaptivity_options_vector_field,
1369
recalculation_options?
1370
)
1371
1372
1373
diagnostic_vector_field_bed_shear_stress =
1374
(
1375
(
1376
element density {
1377
real
1378
}
1379
),
1380
(
1381
element drag_coefficient {
1382
real
1383
}
1384
),
1385
diagnostic_output_options,
1386
diagnostic_vector_stat_options,
1387
diagnostic_detector_options,
1388
adaptivity_options_vector_field
1389
)
1390
1391
1392
1393
# Default child of prescribed vector field
1394
# This is a choice of ways of inputing the prescribed field
1395
prescribed_vector_field =
1396
(
1397
prescribed_vector_field_no_adapt,
1398
adaptivity_options_vector_field,
1399
interpolation_algorithm_vector?,
1400
discrete_properties_algorithm_vector?,
1401
recalculation_options?
1402
)
1403
1404
# Default child of prescribed vector field without adaptivity options
1405
# This is a choice of ways of inputing the prescribed field
1406
prescribed_vector_field_no_adapt =
1407
(
1408
prescribed_values_vector_field,
1409
prescribed_output_options,
1410
prescribed_vector_stat_options,
1411
prescribed_detector_options
1412
)
1413
1414
prescribed_values_vector_field =
1415
(
1416
(
1417
## Value for WholeMesh
1418
##
1419
## Only specify one value if not using mesh regions.
1420
## Otherwise select other value option, specify region_ids
1421
## and distinct names. Then add extra values for other regions.
1422
element value {
1423
attribute name { "WholeMesh" },
1424
input_choice_real_dim_vector_plus_file
1425
}|
1426
## Multiple values are now allowed if using different value assignments
1427
## in different regions of the mesh (specified by region_ids).
1428
## In this case each value requires a distinct name for the options dictionary.
1429
element value {
1430
attribute name { string },
1431
region_ids,
1432
input_choice_real_dim_vector_plus_file
1433
}
1434
)+
1435
)
1436
1437
# Default child of diagnostic tensor field
1438
# Currently, this is empty, but in future this might include
1439
# options that are general to all diagnostic tensor fields
1440
diagnostic_tensor_field =
1441
(
1442
diagnostic_output_options,
1443
adaptivity_options_tensor_field
1444
)
1445
1446
# Default child of prescribed vector field
1447
# This is a choice of ways of inputing the prescribed tensor field
1448
# If the field is constant then a symmetric, or asymmetric tensor may be entered
1449
prescribed_tensor_field =
1450
(
1451
prescribed_values_tensor_field,
1452
adaptivity_options_tensor_field
1453
)
1454
1455
prescribed_values_tensor_field =
1456
(
1457
(
1458
## Value for WholeMesh
1459
##
1460
## Only specify one value if not using mesh regions.
1461
## Otherwise select other value option, specify region_ids
1462
## and distinct names. Then add extra values for other regions.
1463
element value {
1464
attribute name { "WholeMesh" },
1465
input_choice_tensor_field
1466
}|
1467
## Multiple values are now allowed if using different value assignments
1468
## in different regions of the mesh (specified by region_ids).
1469
## In this case each value requires a distinct name for the options dictionary.
1470
element value {
1471
attribute name { string },
1472
region_ids,
1473
input_choice_tensor_field
1474
}
1475
)+
1476
)
1477
1478
prognostic_pressure_field =
1479
(
1480
element spatial_discretisation {
1481
(
1482
element continuous_galerkin {
1483
## remove the fourth order pressure stabilisation term KCMC
1484
## must be removed for multimaterial and free surface calculations
1485
element remove_stabilisation_term {
1486
attribute replaces { "NOFILT" }
1487
}?,
1488
## Integrate the continuity equation by parts.
1489
##
1490
## This allows for the imposition of weak velocity boundary conditions with continuous_galerkin.
1491
## If activated this means that the pressure gradient operator is not integrated by parts.
1492
element integrate_continuity_by_parts {
1493
attribute replaces { "PREOPT" },
1494
empty
1495
}?
1496
}|
1497
element control_volumes {
1498
attribute replaces { "NCOLOP = X1XXXXX -> INTERF, NOFILT" }
1499
}
1500
)
1501
},
1502
## Reference node (Node at which pressure = 0.)
1503
##
1504
## Must be less than the total number of nodes.
1505
## If parallel must be less than the total number of nodes of the first processor.
1506
##
1507
## Note - it is also an option to remove the null-space of the residual vector. This
1508
## option is available under solvers.
1509
element reference_node {
1510
attribute replaces { "NDPSET" },
1511
integer
1512
}?,
1513
## **UNDER DEVELOPMENT**
1514
## This searches the CMC matrix diagonal looking for nodes that are less than the maximum value time epsilon(0.0) (i.e. nodes that are effectively zero).
1515
## It then zeros that row and column and places a one on the diagonal and a zero on the rhs.
1516
## At a debug level of 2 it also prints out the value and the sum of the row values.
1517
## This is useful as a debugging tool if PETSc complains about zeros on the diagonal (i.e. if you have a stiff node in your mesh) but doesn't necessary produce nice answers at the end.
1518
element repair_stiff_nodes {
1519
empty
1520
}?,
1521
## Atmospheric pressure
1522
##
1523
## Manual suggests 1.01325E+6
1524
element atmospheric_pressure {
1525
attribute replaces {"PATMOS"},
1526
real
1527
}?,
1528
## scheme
1529
element scheme {
1530
## Use a poisson pressure equation to calculate a first guess at pressure.
1531
## This does not necessarily satisfy continuity.
1532
## = 1 -- use a poisson guess at every timestep
1533
## = 0 -- never use a poisson guess
1534
## =-1 -- use a poisson guess at the first timestep only
1535
## Manual suggests -1
1536
element poisson_pressure_solution {
1537
attribute replaces {"POISON"},
1538
(
1539
element string_value{
1540
# Lines is a hint to the gui about the size of the text box.
1541
# It is not an enforced limit on string length.
1542
attribute lines { "1" },
1543
( "never" | "every timestep" | "only first timestep")
1544
},
1545
comment
1546
)
1547
},
1548
(
1549
## Use the incompressible projection method to determine
1550
## the pressure and satisfy continuity
1551
element use_projection_method {
1552
attribute replaces {"PROJEC"},
1553
## Assemble and use the full schur complement.
1554
## This allows you to not lump the mass matrix if you're using
1555
## cg and to use the full momentum matrix in the projection if
1556
## you so desire.
1557
element full_schur_complement {
1558
(
1559
## Specify the inner matrix (IM) to form the projection schur complement (C^T*IM^{-1}*C).
1560
## Use the full mass matrix.
1561
##
1562
## Make sure you've not lumped your mass in the velocity spatial_discretisation if you want to be consistent!
1563
element inner_matrix {
1564
attribute name { "FullMassMatrix" },
1565
element solver {
1566
linear_solver_options_sym
1567
}
1568
}|
1569
## Specify the inner matrix (IM) to form the projection schur complement (C^T*IM^{-1}*C).
1570
## Use the full momentum matrix.
1571
##
1572
## Doesn't really matter if you've lumped your mass or not but why would you if you're doing a full inner solve anyway?
1573
element inner_matrix {
1574
attribute name { "FullMomentumMatrix" },
1575
element solver {
1576
linear_solver_options_asym
1577
}
1578
}
1579
),
1580
(
1581
## Specify the preconditioner matrix to use on the schur complement.
1582
##
1583
## For DG, the LumpedSchurComplement is our best approximation to CMC.
1584
element preconditioner_matrix {
1585
attribute name { "LumpedSchurComplement" },
1586
element lump_on_submesh {
1587
empty
1588
}?
1589
}|
1590
## Specify the preconditioner matrix to use on the schur complement.
1591
##
1592
## DiagonalSchurComplement = C_P^T * [(Big_m)_diagonal]^-1 * C
1593
element preconditioner_matrix {
1594
attribute name { "DiagonalSchurComplement" },
1595
empty
1596
}|
1597
## Specify the preconditioner matrix to use on the schur complement.
1598
element preconditioner_matrix {
1599
attribute name { "NoPreconditionerMatrix" },
1600
empty
1601
}
1602
)
1603
}?
1604
}|
1605
## Use the compressible projection method to determine the
1606
## pressure and satisfy continuity and the eos.
1607
## This is only currently compatible with control volume
1608
## pressure spatial discretisations and requires a
1609
## multimaterial eos.
1610
element use_compressible_projection_method {
1611
attribute replaces {"MKCOMP from solidity_options.inp"},
1612
(
1613
## Variable (normally a density) used to normalise
1614
## each materials contribution
1615
## to the C_P^T matrix. Leave unselected for no normalisation.
1616
## Selects the MaterialDensity field.
1617
element normalisation {
1618
attribute name{ "MaterialDensity" },
1619
empty
1620
}|
1621
## Variable (normally a density) used to normalise
1622
## each materials contribution
1623
## to the C_P^T matrix. Leave unselected for no normalisation.
1624
## Selects the bulk Density field.
1625
element normalisation {
1626
attribute name{ "Density" },
1627
empty
1628
}|
1629
## Variable (normally a density) used to normalise
1630
## each materials contribution
1631
## to the C_P^T matrix. Leave unselected for no normalisation.
1632
## Allows the selection of an arbitrary field.
1633
element normalisation {
1634
attribute name{ string },
1635
empty
1636
}
1637
)?
1638
1639
}
1640
),
1641
## rediscretise the equations at every timestep and iteration
1642
## (for instance if using a compressible formulation
1643
## or if density varies a lot or if not using a Boussinesque approximation)
1644
element update_discretised_equation {
1645
attribute replaces {"CMCHAN"},
1646
empty
1647
}?
1648
},
1649
## Solver
1650
element solver {
1651
linear_solver_options_sym
1652
},
1653
(
1654
## Initial condition for WholeMesh
1655
##
1656
## Only specify one condition if not using mesh regions.
1657
## Otherwise select other initial_condition option, specify region_ids
1658
## and distinct names. Then add extra intial conditions for other regions.
1659
element initial_condition {
1660
attribute name { "WholeMesh" },
1661
input_choice_initial_condition_real
1662
}|
1663
## Multiple initial_conditions are allowed if specifying
1664
## different values in different
1665
## regions of the mesh (defined by region_ids). In this case
1666
## each initial_condition
1667
## requires a distinct name for the options dictionary.
1668
element initial_condition {
1669
attribute name { string },
1670
region_ids,
1671
input_choice_initial_condition_real
1672
}
1673
)*,
1674
element boundary_conditions {
1675
attribute name { string },
1676
## Surface id:
1677
element surface_ids {
1678
integer_vector
1679
},
1680
## Type
1681
element type {
1682
attribute name { "dirichlet" },
1683
## Apply the dirichlet bc weakly. Available
1684
## automatically with discontinuous_galerkin,
1685
## control_volume, and legacy_mixed_cv_cg
1686
## spatial_discretisations.
1687
## If not selected boundary conditions are applied strongly.
1688
element apply_weakly {
1689
## If the initial condition and boundary conditions
1690
## differ, setting this option will cause the initial
1691
## condition on the boundary to be overwritten with
1692
## the boundary condition. Since you are applying the
1693
## boundary condition weakly, you probably do *not*
1694
## want this.
1695
element boundary_overwrites_initial_condition {
1696
empty
1697
}?
1698
}?,
1699
input_choice_real_plus_boundary_forcing
1700
}
1701
}*,
1702
pressure_output_options,
1703
prognostic_scalar_stat_options,
1704
scalar_convergence_options,
1705
detector_options_disabled_default,
1706
scalar_steady_state_options,
1707
adaptivity_options_prognostic_scalar_field,
1708
interpolation_algorithm_scalar_full,
1709
discrete_properties_algorithm_scalar?
1710
)
1711
1712
prognostic_geostrophic_pressure_field =
1713
(
1714
element spatial_discretisation {
1715
## Select whether on not to include the buoyancy term "g" in the RHS:
1716
##
1717
## f = - grad p_gp + g
1718
element geostrophic_pressure_option {
1719
attribute replaces { "GEOBAL" },
1720
element string_value {
1721
"include_buoyancy" | "exclude_buoyancy"
1722
}
1723
}
1724
},
1725
(
1726
## Solver
1727
element solver {
1728
linear_solver_options_sym
1729
}
1730
),
1731
(
1732
## Initial condition for WholeMesh
1733
##
1734
## Only specify one condition if not using mesh regions.
1735
## Otherwise select other initial_condition option, specify region_ids
1736
## and distinct names. Then add extra intial conditions for other regions.
1737
element initial_condition {
1738
attribute name { "WholeMesh" },
1739
input_choice_initial_condition_real
1740
}|
1741
## Multiple initial_conditions are allowed if specifying
1742
## different values in different
1743
## regions of the mesh (defined by region_ids). In this case
1744
## each initial_condition
1745
## requires a distinct name for the options dictionary.
1746
element initial_condition {
1747
attribute name { string },
1748
region_ids,
1749
input_choice_initial_condition_real
1750
}
1751
)*,
1752
prognostic_scalar_output_options,
1753
prognostic_scalar_stat_options,
1754
prognostic_detector_options,
1755
scalar_steady_state_options,
1756
adaptivity_options_prognostic_scalar_field,
1757
interpolation_algorithm_scalar_full,
1758
discrete_properties_algorithm_scalar?
1759
)
1760
1761
# Balance pressure field, this is a copy of prognostic_scalar_field above
1762
# removing all options that don't apply (mainly advection related)
1763
prognostic_balance_pressure_field =
1764
(
1765
## Spatial discretisation options
1766
element spatial_discretisation {
1767
# note I removed disott here as it
1768
# will switch on free-surface options in geoeli1p
1769
# should be hard-coded to 0 in comsca therefore
1770
# tlump is irrelevant
1771
# suftem should be hard-coded to .false. if nlevel is set
1772
## Geostrophic pressure option
1773
element geostrophic_pressure_option {
1774
attribute replaces { "GEOBAL" },
1775
element string_value {
1776
"include_buoyancy"|"exclude_buoyancy"
1777
}
1778
}
1779
# unfortunately tbeta doesn`t make sense here
1780
# so we have to code an exception for not having it in comsca
1781
},
1782
# Temporal_discretisation doesn`t apply to balance pressure
1783
# (there`s no time derivative). Exception again
1784
# Solver block is the same as prognostic_scalar_field
1785
## Solver
1786
element solver {
1787
linear_solver_options_sym
1788
},
1789
# Alas, no initial_condition either, so we'd better not checkpointing it...
1790
## Disables checkpointing of this field
1791
element exclude_from_checkpointing {
1792
comment
1793
},
1794
# There are boundary conditions, but nothing you can set
1795
# (all derived from velocity b.c.s)
1796
# no Diffusivity tensor_field
1797
# no Source scalar_field
1798
# no Absorption scalar_field
1799
# no adaptive time-stepping
1800
prognostic_scalar_output_options,
1801
prognostic_scalar_stat_options,
1802
scalar_convergence_options,
1803
prognostic_detector_options,
1804
scalar_steady_state_options,
1805
adaptivity_options_prognostic_scalar_field,
1806
interpolation_algorithm_scalar_full,
1807
discrete_properties_algorithm_scalar?
1808
)
1809
1810
# Vertical balance pressure field, this is a copy of prognostic_scalar_field above
1811
# removing all options that don't apply (mainly advection related)
1812
prognostic_vertical_balance_pressure_field =
1813
(
1814
## Spatial discretisation options
1815
element spatial_discretisation {
1816
# we don't have any yet
1817
empty
1818
},
1819
# Temporal_discretisation doesn`t apply to balance pressure
1820
# (there`s no time derivative). Exception again
1821
# no solver block as we don't do a PETSc solve
1822
# Alas, no initial_condition either...
1823
# boundary conditions are fixed (p=0 on top)
1824
# no Diffusivity tensor_field
1825
# no Source scalar_field
1826
# no Absorption scalar_field
1827
# no adaptive time-stepping
1828
prognostic_scalar_output_options,
1829
prognostic_scalar_stat_options,
1830
scalar_convergence_options,
1831
prognostic_detector_options,
1832
scalar_steady_state_options,
1833
adaptivity_options_prognostic_scalar_field,
1834
interpolation_algorithm_scalar,
1835
discrete_properties_algorithm_scalar?
1836
)
1837
1838
# free surface field, this is a copy of prognostic_scalar_field above
1839
# removing all options that don't apply (mainly advection related)
1840
prognostic_free_surface_field =
1841
(
1842
(
1843
## Spatial discretisation options
1844
element spatial_discretisation {
1845
## Form a full 3D system for the free surface
1846
element free_surface_3D {
1847
attribute replaces { "DISOTT=2^0 (frees3d)" },
1848
empty
1849
}?,
1850
element fourth_order_dissipation {
1851
attribute replaces { "DISOTT=2^2 (fourthfrees_diss)" },
1852
empty
1853
}?,
1854
## low order (linear) free surface
1855
element low_order_free_surface {
1856
attribute replaces { "DISOTT=2^3 (geo_short)" },
1857
empty
1858
}?,
1859
(
1860
## Select free surface filter
1861
##
1862
## With PN-PN we need some filter to supress spurious modes.
1863
element default_free_surface_filter {
1864
empty
1865
}|
1866
## Select free surface filter
1867
##
1868
## With PN-PN we need some filter to supress spurious modes.
1869
element user_specified_free_surface_filter {
1870
## Default is to apply 0.01 and for wetting and drying cases 1.0
1871
element non_linear_filter_coefficient {
1872
real
1873
}
1874
}|
1875
## Switch off free surface filter, this is more efficient than setting the coefficient to 0.
1876
element switch_off_free_surface_filter {
1877
attribute replaces { "DISOTT=2^8 (nofsta)" },
1878
empty
1879
}
1880
),
1881
## Apply wetting and drying routines
1882
element wetting_drying {
1883
attribute replaces { "DISOTT=2^10 (wetdry)" },
1884
empty
1885
}?,
1886
## Tidal forcing options
1887
element tidal_forcing {
1888
## M2
1889
element M2 {
1890
attribute replaces {"DISOTT=2^11"},
1891
empty
1892
}?,
1893
## S2
1894
element S2 {
1895
empty
1896
}?,
1897
## N2
1898
element N2 {
1899
empty
1900
}?,
1901
## K2
1902
element K2 {
1903
empty
1904
}?,
1905
## K1
1906
element K1 {
1907
empty
1908
}?,
1909
## O1
1910
element O1 {
1911
empty
1912
}?,
1913
## P1
1914
element P1 {
1915
empty
1916
}?,
1917
## Q1
1918
element Q1 {
1919
empty
1920
}?,
1921
## Switch on all tidal components
1922
element all_tidal_components {
1923
attribute replaces { "DISOTT=2^5 (tidallcom)" },
1924
empty
1925
}?,
1926
## Switches on a Love number of 0.3
1927
element love_number {
1928
attribute replaces { "DISOTT=2^6 (tlove)" },
1929
empty
1930
}?,
1931
## Use static tidal force for testing
1932
element static_tidal_force {
1933
attribute replaces { "DISOTT=2^7 (statid)" },
1934
empty
1935
}?
1936
}?
1937
}|
1938
## Legacy Free Surface
1939
## Allows astronomical forcing for multiple tidal constituents.
1940
## Integer should be sum of desired components as follows:
1941
##
1942
## 3D Free Surface = 1
1943
##
1944
## Fourth Order Dissipation = 4
1945
##
1946
## Low Order Free Surface = 8
1947
##
1948
## Implicit absorption in the free surface (good for wetting/drying) = 16
1949
##
1950
## Turn on all tides = 32
1951
##
1952
## Love Number = 64
1953
##
1954
## Static Tidal Force = 128
1955
##
1956
## M2 constituent = 2048
1957
##
1958
## S2 constituent = 4096
1959
##
1960
## N2 constituent = 8192
1961
##
1962
## K2 constituent = 16384
1963
##
1964
## K1 constituent = 32768
1965
##
1966
## O1 constituent = 65536
1967
##
1968
## P1 constituent = 131072
1969
##
1970
## Q1 constituent = 262144
1971
element Legacy_Free_Surface {
1972
attribute replaces {"FREESDISOTT"},
1973
integer
1974
}
1975
),
1976
# atheta, ctheta and fstheta (absorption, coriolis and free surface)
1977
# need to go in temporal discretisation
1978
# they are currently hard-coded however
1979
element temporal_discretisation {
1980
## Implicit/explicitness for the free surface.
1981
##
1982
## Suggested value 1.0 (should be at least bigger than 0.5).
1983
## =0. -- explicit
1984
## =0.5 -- Crank-Nicolson
1985
## =1. -- implicit
1986
element theta {
1987
attribute replaces {"THETA"},
1988
real
1989
},
1990
# Maybe this should go under a proper absorption field under free surface?
1991
## Implicit/explicitness for absorption
1992
## =0. -- explicit (default)
1993
## =0.5 -- Crank-Nicolson
1994
## =1. -- implicit
1995
element absorption_theta {
1996
attribute replaces {"disott=2^4 (IMPABS)"},
1997
real
1998
}?
1999
},
2000
## Solver
2001
element solver {
2002
linear_solver_options_sym
2003
},
2004
(
2005
## Initial condition for WholeMesh
2006
##
2007
## Only specify one condition if not using mesh regions.
2008
## Otherwise select other initial_condition option, specify region_ids
2009
## and distinct names. Then add extra intial conditions for other regions.
2010
element initial_condition {
2011
attribute name { "WholeMesh" },
2012
input_choice_initial_condition_real
2013
}|
2014
## Multiple initial_conditions are allowed if specifying
2015
## different values in different
2016
## regions of the mesh (defined by region_ids). In this case
2017
## each initial_condition
2018
## requires a distinct name for the options dictionary.
2019
element initial_condition {
2020
attribute name { string },
2021
region_ids,
2022
input_choice_initial_condition_real
2023
}
2024
)+,
2025
## Boundary conditions
2026
element boundary_conditions {
2027
attribute replaces { "boundary, TTPER1 TTPER2 TTPERI" },
2028
attribute name { string },
2029
## Surface id:
2030
element surface_ids {
2031
integer_vector
2032
},
2033
## Type
2034
(
2035
element type {
2036
attribute name { "dirichlet" },
2037
(
2038
input_choice_real_contents|
2039
element from_file {
2040
element tidal {
2041
attribute file_name { string },
2042
attribute variable_name_amplitude { string },
2043
attribute variable_name_phase { string },
2044
## See E.W. Schwiderski - Rev. Geophys. Space
2045
## Phys. Vol. 18 No. 1 pp. 243--268, 1980
2046
## for details of these constituent.
2047
attribute name {"M2"|"S2"|"N2"|"K2"|"K1"|"O1"|"P1"|"Q1"|"Mf"|"Mm"|"Ssa"}
2048
}+
2049
}
2050
)
2051
}|
2052
element type {
2053
attribute name { "neumann" },
2054
input_choice_real
2055
}|
2056
element type {
2057
attribute name { "robin" },
2058
element order_zero_coefficient {
2059
input_choice_real
2060
},
2061
element order_one_coefficient {
2062
input_choice_real
2063
}
2064
}
2065
)
2066
}*,
2067
# no Diffusivity for field
2068
# no source term
2069
# no Absorption term
2070
# no Adaptive timestepping option
2071
prognostic_scalar_output_options,
2072
prognostic_scalar_stat_options,
2073
scalar_convergence_options,
2074
prognostic_detector_options,
2075
scalar_steady_state_options,
2076
adaptivity_options_prognostic_scalar_field,
2077
interpolation_algorithm_scalar,
2078
discrete_properties_algorithm_scalar?
2079
)
2080
2081
# stream function, this is a copy of prognostic_scalar_field above
2082
# removing all options that don't apply (mainly advection related)
2083
prognostic_stream_function_field =
2084
(
2085
## Solver
2086
element solver {
2087
linear_solver_options_asym
2088
},
2089
## Disables checkpointing of this field
2090
element exclude_from_checkpointing {
2091
comment
2092
},
2093
# no Diffusivity for field
2094
# no source term
2095
# no Absorption term
2096
# no Adaptive timestepping option
2097
prognostic_scalar_output_options,
2098
prognostic_scalar_stat_options,
2099
prognostic_detector_options,
2100
adaptivity_options_prognostic_scalar_field,
2101
interpolation_algorithm_scalar,
2102
discrete_properties_algorithm_scalar?
2103
)
2104
2105
# Richardson number field. This is a normal diagnostic scalar field, but with
2106
# Richardson number metric options added
2107
adaptivity_options_richardson_number_field.adaptivity_options =
2108
(
2109
## Do not use an interpolation error driven metric for this field
2110
element no_interpolation_measure {
2111
comment
2112
}
2113
)
2114
adaptivity_options_richardson_number_field.adaptivity_options |= adaptivity_options_scalar_field.adaptivity_options
2115
adaptivity_options_richardson_number_field =
2116
(
2117
element adaptivity_options {
2118
adaptivity_options_richardson_number_field.adaptivity_options,
2119
## An isotropic metric formulation based on the Richardson number. Uses
2120
## the logic that wherever the Richardson number is small, we expect
2121
## to need resolution. Generates edge lengths using:
2122
##
2123
## Edge length = min_edge_length if Ri <= min_ri
2124
## max_edge_length if Ri >= max_ri
2125
## a linear fit between min_edge_length and max_edge_length otherwise
2126
element richardson_number_metric {
2127
## Richardson number at which we have minimum edge length (default 0.0)
2128
element min_ri {
2129
real
2130
}?,
2131
## Richardson number at which we have maximum edge length
2132
element max_ri {
2133
real
2134
},
2135
## Minimum edge length that can be requested by the Richardson number
2136
## metric
2137
element min_edge_length {
2138
real
2139
},
2140
## Maximum edge length that can be requested by the Richardson number
2141
## metric
2142
element max_edge_length {
2143
real
2144
},
2145
## Enable to preserve anisotropy when merging with other metric
2146
## formulations
2147
element anisotropy_preserving_merge {
2148
comment
2149
}?,
2150
comment
2151
}?,
2152
adaptivity_preprocessing
2153
}?
2154
)
2155
diagnostic_richardson_number_field = diagnostic_scalar_field_no_adapt
2156
diagnostic_richardson_number_field &= adaptivity_options_richardson_number_field
2157
2158
diagnostic_cv_gradient_vector_field =
2159
(
2160
## Choose whether the mass matrix is lumped or not
2161
element lump_mass_matrix {
2162
empty
2163
}?,
2164
## Solver options are necessary if you're not lumping your mass or if you're field isn't dg
2165
element solver {
2166
linear_solver_options_sym
2167
}?,
2168
## Normalise the gradient by its magnitude
2169
element normalise {
2170
empty
2171
}?,
2172
diagnostic_output_options,
2173
diagnostic_vector_stat_options,
2174
vector_convergence_options,
2175
diagnostic_detector_options,
2176
vector_steady_state_options,
2177
adaptivity_options_vector_field,
2178
recalculation_options?
2179
)
2180
2181
diagnostic_gradient_vector_field =
2182
(
2183
## Solver
2184
element solver {
2185
linear_solver_options_sym
2186
},
2187
diagnostic_output_options,
2188
diagnostic_vector_stat_options,
2189
vector_convergence_options,
2190
diagnostic_detector_options,
2191
vector_steady_state_options,
2192
adaptivity_options_vector_field,
2193
recalculation_options?
2194
)
2195
2196
diagnostic_cv_divergence_scalar_field =
2197
(
2198
# No solver options because it can be solved directly!
2199
diagnostic_output_options,
2200
diagnostic_scalar_stat_options,
2201
scalar_convergence_options,
2202
diagnostic_detector_options,
2203
scalar_steady_state_options,
2204
adaptivity_options_scalar_field,
2205
recalculation_options?
2206
)
2207
2208
diagnostic_fe_divergence_scalar_field =
2209
(
2210
## Solver
2211
element solver {
2212
linear_solver_options_sym
2213
},
2214
diagnostic_output_options,
2215
diagnostic_scalar_stat_options,
2216
scalar_convergence_options,
2217
diagnostic_detector_options,
2218
scalar_steady_state_options,
2219
adaptivity_options_scalar_field,
2220
recalculation_options?
2221
)
2222
2223
# three optional input vectors for user-specified rotation matrix
2224
rotation_matrix_components =
2225
(
2226
## Select if you want to specify the normal direction
2227
## of the rotation matrix.
2228
## If off then fluidity computes the normal (replaces GETTAN = .TRUE.)
2229
## If on the tangents vectors must also be specified.
2230
element normal_direction {
2231
attribute replaces { "GETTAN=.FALSE." },
2232
input_choice_real_dim_vector
2233
}?,
2234
## specify first unit tangent vector to boundary
2235
element tangent_direction_1 {
2236
attribute replaces { "GETTAN=.FALSE." },
2237
input_choice_real_dim_vector
2238
}?,
2239
## specify second (if exists, i.e. if 3d) unit tangent vector to boundary
2240
element tangent_direction_2 {
2241
attribute replaces { "GETTAN=.FALSE." },
2242
input_choice_real_dim_vector
2243
}?
2244
)
2245
2246
velocity_components_choice =
2247
(
2248
(
2249
# rotated bcs are not implemented... this is where they should go when they are
2250
# element align_bc_with_surface {
2251
# element normal_component {
2252
# input_choice_real
2253
# }?,
2254
# element tangent_component_1 {
2255
# input_choice_real
2256
# }?,
2257
# element tangent_component_2 {
2258
# input_choice_real
2259
# }?,
2260
# rotation_matrix_components
2261
# }|
2262
element align_bc_with_cartesian {
2263
element x_component {
2264
input_choice_real_bc_component
2265
}?,
2266
element y_component {
2267
input_choice_real_bc_component
2268
}?,
2269
element z_component {
2270
input_choice_real_bc_component
2271
}?
2272
}
2273
)
2274
)
2275
2276
input_choice_real_bc_component =
2277
(
2278
input_choice_real|
2279
element synthetic_eddy_method {
2280
## use a large number to ensure Gaussian
2281
## behaviour of the fluctuating component
2282
element number_of_eddies {
2283
integer
2284
},
2285
element turbulence_lengthscale {
2286
input_choice_real
2287
},
2288
## mean profile
2289
##
2290
## usually a function of height,
2291
## for ABL simulations use a log profile
2292
element mean_profile {
2293
input_choice_real
2294
},
2295
## Reynolds stresses profile
2296
##
2297
## usually a function of height,
2298
## assumes that the remaining stresses are negligible
2299
element Re_stresses_profile {
2300
input_choice_real
2301
}
2302
}
2303
)
2304
2305
# and again for robin b.c.s
2306
robin_velocity_components_choice =
2307
(
2308
(
2309
# element align_bc_with_surface {
2310
# element normal_component {
2311
# element order_zero_coefficient {
2312
# input_choice_real
2313
# },
2314
# element order_one_coefficient {
2315
# input_choice_real
2316
# }
2317
# }?,
2318
# element tangent_component_1 {
2319
# element order_zero_coefficient {
2320
# input_choice_real
2321
# },
2322
# element order_one_coefficient {
2323
# input_choice_real
2324
# }
2325
# }?,
2326
# element tangent_component_2 {
2327
# element order_zero_coefficient {
2328
# input_choice_real
2329
# },
2330
# element order_one_coefficient {
2331
# input_choice_real
2332
# }
2333
# }?,
2334
# rotation_matrix_components
2335
# }|
2336
element align_bc_with_cartesian {
2337
element x_component {
2338
element order_zero_coefficient {
2339
input_choice_real
2340
},
2341
element order_one_coefficient {
2342
input_choice_real
2343
}
2344
}?,
2345
element y_component {
2346
element order_zero_coefficient {
2347
input_choice_real
2348
},
2349
element order_one_coefficient {
2350
input_choice_real
2351
}
2352
}?,
2353
element z_component {
2354
element order_zero_coefficient {
2355
input_choice_real
2356
},
2357
element order_one_coefficient {
2358
input_choice_real
2359
}
2360
}?
2361
}
2362
)
2363
)
2364
2365
velocity_boundary_conditions =
2366
(
2367
(
2368
element type {
2369
attribute name { "dirichlet" },
2370
## Apply the dirichlet bc weakly. Available automatically
2371
## with a discontinuous_galerkin Velocity
2372
## spatial_discretisation. Available if you
2373
## integrate_continuity_by_parts with a
2374
## continuous_galerkin Pressure or use a control_volume
2375
## Pressure spatial_discretisation and/or
2376
## integrate_advection_by_parts under Velocity
2377
## spatial_discretisation with continuous_galerkin.
2378
##
2379
## If not selected boundary conditions are applied strongly.
2380
element apply_weakly {
2381
## If the initial condition and boundary conditions
2382
## differ, setting this option will cause the initial
2383
## condition on the boundary to be overwritten with
2384
## the boundary condition. Since you are applying the
2385
## boundary condition weakly, you probably do *not*
2386
## want this.
2387
element boundary_overwrites_initial_condition {
2388
empty
2389
}?
2390
}?,
2391
velocity_components_choice
2392
}|
2393
element type {
2394
attribute name { "neumann" },
2395
velocity_components_choice
2396
}|
2397
element type {
2398
attribute name { "robin" },
2399
robin_velocity_components_choice
2400
}|
2401
element type {
2402
attribute name { "free_surface" }
2403
}|
2404
## Apply quadratic drag. Specify drag coefficient. If you
2405
## want to exactly replicate results from using the OCEDRA
2406
## option, set this to 0.003 and remember to apply to both
2407
## bottom and sides.
2408
element type {
2409
attribute name { "drag" },
2410
input_choice_real,
2411
(
2412
## Use a quadratic drag.
2413
##
2414
## This means that the drag coefficient is nondimensional.
2415
element quadratic_drag {
2416
empty
2417
}|
2418
## Use a linear drag (basically just a surface absorption term).
2419
##
2420
## This means that the drag coefficient has units of momentum.
2421
element linear_drag {
2422
empty
2423
}
2424
)
2425
}|
2426
2427
## Apply wind forcing specified by stress or wind velocity.
2428
## Replaces windy.dat and windy.py
2429
element type {
2430
attribute name { "wind_forcing" },
2431
(
2432
## Wind forcing with user specified wind stress
2433
##
2434
## <b> Note that the stress needs to be specified
2435
## using the same density units as the reference_density
2436
## under equation of state.</b>So if you use the recommended
2437
## non-dimensional value of 1.0 for reference_density and
2438
## your calculated stress is in kg m^-1s^-2 and the dimensional
2439
## reference_density is 1000.0 kg m^-3, you need to divide
2440
## the calculated stress in SI units by 1000.0.
2441
element wind_stress {
2442
input_choice_real_dim_minus_one_vector|
2443
element from_netcdf {
2444
## The format of this file should conform to NetCDF CF 1.x
2445
## (http://cf-pcmdi.llnl.gov/).
2446
attribute file_name { xsd:string },
2447
attribute east_west { xsd:string },
2448
attribute north_south { xsd:string },
2449
comment
2450
}
2451
}|
2452
## Wind forcing with user specified 10m wind velocity
2453
element wind_velocity {
2454
## Specify wind drag coefficient (dimensionless)
2455
## Suggested value: 4.0e-4
2456
element wind_drag_coefficient {
2457
input_choice_real
2458
},
2459
## Density of air.
2460
##
2461
## <b>Note that you have to specify
2462
## this density in the same units as the
2463
## reference_density under equation of state.</b>
2464
## So with a typicial value of rho_air=1.3 kgm^-3
2465
## and rho_water=1000 kgm^-3, if you fill in the
2466
## recommended (non-dimensional) value of 1.0 for
2467
## reference_density, this field needs to be 1.3e-3.
2468
element density_air {
2469
real
2470
},
2471
## Specify wind velocity
2472
element wind_velocity {
2473
input_choice_real_dim_minus_one_vector|
2474
element from_netcdf {
2475
## The format of this file should conform to NetCDF CF 1.x
2476
## (http://cf-pcmdi.llnl.gov/)
2477
attribute file_name { xsd:string },
2478
attribute east_west { xsd:string },
2479
attribute north_south { xsd:string },
2480
comment
2481
}
2482
}
2483
}
2484
)
2485
}|
2486
2487
## When using control_volumes under Pressure
2488
## spatial_discretisation or when using
2489
## integrate_continuity_by_parts with continuous_galerkin
2490
## Pressure and continuous_galerkin Velocity this
2491
## boundary condition type imposes a weak no normal flow
2492
## boundary condition on the surface_ids specified.
2493
element type {
2494
attribute name { "no_normal_flow" },
2495
empty
2496
}|
2497
2498
## Implements a penalty function for the near wall region.
2499
## Using this option coarse meshes can
2500
## be used in the near wall region.
2501
##
2502
## Should be used in combination with a no_normal_flow condition.
2503
##
2504
## See Bazilevs et al. 2007
2505
element type{
2506
attribute name { "near_wall_treatment" },
2507
element tolerance {real}
2508
}|
2509
## Log law of the wall
2510
##
2511
## Should be used in combination with a no_normal_flow condition.
2512
element type{
2513
attribute name { "log_law_of_wall" },
2514
element surface_roughness {real}
2515
}
2516
)
2517
)
2518
2519
# Output options for prognostic fields
2520
prognostic_scalar_output_options =
2521
(
2522
## Specify what is written to vtu dump files
2523
element output {
2524
## By default each field in the options file is written to vtu.
2525
## Select this option to exclude this field.
2526
element exclude_from_vtu {
2527
empty
2528
}?,
2529
## Select this option to also write the values of this field
2530
## on the previous timestep.
2531
## (included under the name: Old<field_name> )
2532
element include_previous_time_step {
2533
empty
2534
}?,
2535
## Select this option to also write the values of this field
2536
## used in the nonlinear iteration.
2537
## (included under the name: Nonlinear<field_name> )
2538
element include_nonlinear_field {
2539
empty
2540
}?,
2541
## Output a file details the convergence (or otherwise) of
2542
## this field with every advective nonlinear
2543
## iteration.
2544
## ONLY WORKS FOR PURE CONTROL VOLUME DISCRETISATIONS.
2545
element convergence_file {
2546
comment
2547
}?
2548
}
2549
)
2550
2551
# Output options for pressure (can't have a convergence file)
2552
pressure_output_options =
2553
(
2554
## Specify what is written to vtu dump files
2555
element output {
2556
## By default each field in the options file is written to vtu.
2557
## Select this option to exclude this field.
2558
element exclude_from_vtu {
2559
empty
2560
}?,
2561
## Select this option to also write the values of this field
2562
## on the previous timestep.
2563
## (included under the name: Old<field_name> )
2564
element include_previous_time_step {
2565
empty
2566
}?,
2567
## Select this option to also write the values of this field
2568
## used in the nonlinear iteration.
2569
## (included under the name: Nonlinear<field_name> )
2570
element include_nonlinear_field {
2571
empty
2572
}?,
2573
## Write out some extra debugging vtu files that can be used
2574
## to analyse what goes on in the pressure projection steps.
2575
## WARNING: this may create a huge amount of vtu files, as
2576
## multiple files are written per nonlinear iteration.
2577
element debugging_vtus {
2578
empty
2579
}?
2580
}
2581
)
2582
2583
# Output options for prognostic fields
2584
prognostic_vector_output_options =
2585
(
2586
## Specify what is written to vtu dump files
2587
element output {
2588
## By default each field in the options file is written to vtu.
2589
## Select this option to exclude this field.
2590
element exclude_from_vtu {
2591
empty
2592
}?,
2593
## Select this option to also write the values of this field
2594
## on the previous timestep.
2595
## (included under the name: Old<field_name> )
2596
element include_previous_time_step {
2597
empty
2598
}?,
2599
## Select this option to also write the values of this field
2600
## used in the nonlinear iteration.
2601
## (included under the name: Nonlinear<field_name> )
2602
element include_nonlinear_field {
2603
empty
2604
}?
2605
}
2606
)
2607
2608
# Output options for all other fields
2609
field_output_options =
2610
(
2611
## Specify what is written to vtu dump files
2612
element output {
2613
## By default each field in the options file is written to vtu.
2614
## Select this option to exclude this field.
2615
element exclude_from_vtu {
2616
empty
2617
}?
2618
}
2619
)
2620
2621
diagnostic_output_options = field_output_options
2622
prescribed_output_options = field_output_options
2623
2624
# Options for inclusion/exclusion of standard field statistics from the .stat
2625
# file
2626
include_stat =
2627
(
2628
## Include this field in the .stat file (magnitude and components)
2629
element include_in_stat {
2630
comment
2631
}
2632
)
2633
exclude_components_from_stat =
2634
(
2635
## Include just the magnitude of this field in the .stat file
2636
## (excluding the components)
2637
element exclude_components_from_stat {
2638
comment
2639
}
2640
)
2641
exclude_stat =
2642
(
2643
## Exclude this field from the .stat file.
2644
element exclude_from_stat {
2645
comment
2646
}
2647
)
2648
2649
# Diagnostic statistics options for prognostic scalar fields
2650
prognostic_scalar_stat_options =
2651
(
2652
## Specify what is added to .stat files
2653
element stat {
2654
prognostic_scalar_stat_options.stat
2655
}
2656
)
2657
2658
# Diagnostic statistics for all other scalar fields
2659
prognostic_scalar_stat_no_old_or_nonlinear_options =
2660
(
2661
## Specify what is added to .stat files
2662
element stat {
2663
prognostic_scalar_stat_no_old_or_nonlinear_options.stat
2664
2665
}
2666
)
2667
2668
diagnostic_scalar_stat_options = prognostic_scalar_stat_no_old_or_nonlinear_options
2669
prescribed_scalar_stat_options = prognostic_scalar_stat_no_old_or_nonlinear_options
2670
2671
# Combining of stat elements for scalar fields
2672
prognostic_scalar_stat_options.stat = prognostic_scalar_stat_no_old_or_nonlinear_options.stat
2673
prognostic_scalar_stat_options.stat &=
2674
(
2675
## Enable to include the previous timestep value of this field in the .stat file.
2676
element include_previous_time_step {
2677
comment
2678
}?,
2679
## Enable to include the values of this field in the nonlinear
2680
## iteration in the .stat file.
2681
element include_nonlinear_field {
2682
comment
2683
}?
2684
)
2685
prognostic_scalar_stat_no_old_or_nonlinear_options.stat =
2686
(
2687
exclude_stat?,
2688
cv_stats?,
2689
surface_integral_stats_scalar*,
2690
mixing_stats*
2691
)
2692
2693
# Diagnostic statistics options for vector fields, with enabled by default
2694
vector_field_stat_options_enabled_default = include_stat
2695
vector_field_stat_options_enabled_default |= exclude_components_from_stat
2696
vector_field_stat_options_enabled_default |= exclude_stat
2697
2698
# Diagnostic statistics options for vector fields, with enabled by default
2699
vector_field_stat_options_disabled_default = exclude_stat
2700
vector_field_stat_options_disabled_default |= exclude_components_from_stat
2701
vector_field_stat_options_disabled_default |= include_stat
2702
2703
# Diagnostic statistics for prognostic vector fields
2704
prognostic_vector_stat_options =
2705
(
2706
## Specify what is added to .stat files
2707
element stat {
2708
(
2709
prognostic_vector_stat_options.stat
2710
)
2711
}
2712
)
2713
2714
# Diagnostic statistics for all other vector fields
2715
prognostic_vector_stat_no_old_or_nonlinear_options =
2716
(
2717
## Specify what is added to .stat files
2718
element stat {
2719
prognostic_vector_stat_no_old_or_nonlinear_options.stat
2720
}
2721
)
2722
diagnostic_vector_stat_options = prognostic_vector_stat_no_old_or_nonlinear_options
2723
prescribed_vector_stat_options = prognostic_vector_stat_no_old_or_nonlinear_options
2724
2725
# Combining of stat elements for vector fields
2726
prognostic_vector_stat_options.stat = prognostic_vector_stat_no_old_or_nonlinear_options.stat
2727
prognostic_vector_stat_options.stat &=
2728
(
2729
## Specify how the previous timestep value of this field is added to the .stat file.
2730
element previous_time_step {
2731
vector_field_stat_options_disabled_default
2732
},
2733
## Specify how the values of this field used in the nonlinear iteration are added to the .stat file.
2734
element nonlinear_field {
2735
vector_field_stat_options_disabled_default
2736
},
2737
## What surface IDs do you want to do the calculation over?
2738
element compute_body_forces_on_surfaces {
2739
integer_vector
2740
}?
2741
)
2742
prognostic_vector_stat_no_old_or_nonlinear_options.stat =
2743
(
2744
vector_field_stat_options_enabled_default,
2745
surface_integral_stats_vector*
2746
)
2747
2748
# Convergence options for prognostic scalar fields
2749
scalar_convergence_options =
2750
(
2751
## Decide whether this field is tested for convergence
2752
## during nonlinear iterations
2753
## (if /timestepping/nonlinear_iterations and
2754
## /timestepping/nonlinear_iterations/tolerance are
2755
## enabled).
2756
## Also specifies whether the field is added to the
2757
## convergence file (if /io/convergence_file is enabled).
2758
element convergence {
2759
(
2760
## Include this field in convergence testing
2761
## (if /timestepping/nonlinear_iterations and
2762
## /timestepping/nonlinear_iterations/tolerance are
2763
## enabled) and file (if /io/convergence_file is enabled)
2764
element include_in_convergence {
2765
comment
2766
}|
2767
## Exclude this field from convergence testing and file
2768
element exclude_from_convergence {
2769
comment
2770
}
2771
)
2772
}
2773
)
2774
2775
# Convergence statistics options for prognostic vector fields (velocity)
2776
vector_convergence_options =
2777
(
2778
## Decide whether this field is tested for convergence
2779
## during nonlinear iterations
2780
## (if /timestepping/nonlinear_iterations and
2781
## /timestepping/nonlinear_iterations/tolerance are
2782
## enabled).
2783
## Also specifies whether the field is added to the
2784
## convergence file (if /io/convergence_file is enabled).
2785
element convergence {
2786
(
2787
## Include this field (magnitude and components)
2788
## in convergence testing
2789
## (if /timestepping/nonlinear_iterations and
2790
## /timestepping/nonlinear_iterations/tolerance are
2791
## enabled) and file (if /io/convergence_file is enabled)
2792
element include_in_convergence {
2793
comment
2794
}|
2795
## Include just the magnitude of this field
2796
## in convergence testing
2797
## (if /timestepping/nonlinear_iterations and
2798
## /timestepping/nonlinear_iterations/tolerance are
2799
## enabled) and file (if /io/convergence_file is enabled)
2800
## i.e. excluding the components
2801
element exclude_components_from_convergence {
2802
comment
2803
}|
2804
## Exclude this field entirely from convergence testing and file
2805
element exclude_from_convergence {
2806
comment
2807
}
2808
)
2809
}
2810
)
2811
2812
# Steady state options for prognostic scalar fields
2813
scalar_steady_state_options =
2814
(
2815
## Decide whether this field is tested for a steady state
2816
## between timesteps
2817
## (if /timestepping/steady_state is
2818
## enabled).
2819
element steady_state {
2820
(
2821
## Include this field in steady state testing
2822
## (if /timestepping/steady_state is
2823
## enabled)
2824
element include_in_steady_state {
2825
comment
2826
}|
2827
## Exclude this field from steady state testing
2828
element exclude_from_steady_state {
2829
comment
2830
}
2831
)
2832
}
2833
)
2834
2835
# Steady state statistics options for prognostic vector fields (velocity)
2836
vector_steady_state_options =
2837
(
2838
## Decide whether this field is tested for a steady state
2839
## between timesteps
2840
## (if /timestepping/steady_state is
2841
## enabled).
2842
element steady_state {
2843
(
2844
## Include this field (magnitude and components)
2845
## in steady state testing
2846
## (if /timestepping/steady_state is enabled)
2847
element include_in_steady_state {
2848
comment
2849
}|
2850
## Include just the magnitude of this field
2851
## in steady state testing
2852
## (if /timestepping/steady_state is
2853
## enabled)
2854
## i.e. excluding the components
2855
element exclude_components_from_steady_state {
2856
comment
2857
}|
2858
## Exclude this field entirely from convergence testing and file
2859
element exclude_from_steady_state {
2860
comment
2861
}
2862
)
2863
}
2864
)
2865
2866
# Options for whether a field is to be included in detector output.
2867
detector_options_enabled_default =
2868
(
2869
## Specify what is added to detector files
2870
element detectors {
2871
(
2872
## This field is output at each detector location.
2873
element include_in_detectors {
2874
comment
2875
}|
2876
## This field is not output at detector locations.
2877
element exclude_from_detectors {
2878
comment
2879
}
2880
)
2881
}
2882
)
2883
2884
# Options for whether a field is to be included in detector output.
2885
detector_options_disabled_default =
2886
(
2887
## Specify what is added to detector files
2888
element detectors {
2889
(
2890
## This field is not output at detector locations.
2891
element exclude_from_detectors {
2892
comment
2893
}|
2894
## This field is output at each detector location.
2895
element include_in_detectors {
2896
comment
2897
}
2898
)
2899
}
2900
)
2901
2902
# Detector output defaults on for prognostic and diagnostic fields,
2903
# off for prescribed.
2904
prognostic_detector_options = detector_options_enabled_default
2905
diagnostic_detector_options = detector_options_enabled_default
2906
prescribed_detector_options = detector_options_disabled_default
2907
2908
adaptivity_preprocessing =
2909
## Occasionally, it is desirable to apply operations or filters
2910
## to fields before using them for the purposes of adaptivity.
2911
element preprocessing {
2912
(
2913
## Invert a helmholtz operator to smooth out the field
2914
## before using it to adapt. This can help with noisy
2915
## fields.
2916
element helmholtz_smoother {
2917
element smoothing_length_scale {
2918
real_dim_symmetric_tensor
2919
},
2920
element solver {
2921
linear_solver_options_sym
2922
}
2923
}
2924
)
2925
}?
2926
2927
adaptivity_options_prognostic_scalar_field =
2928
(
2929
element adaptivity_options {
2930
(
2931
## When specifying absolute measure
2932
## one specifies the absolute interpolation
2933
## error in the units of the field that is
2934
## being adapted, e.g. you can specify
2935
## the error to be 1.3 units
2936
element absolute_measure {
2937
attribute replaces { "ADOPTT = 0" },
2938
element scalar_field {
2939
attribute rank { "0" },
2940
attribute name { "InterpolationErrorBound" },
2941
attribute replaces { "ADWEIT" },
2942
element prescribed {
2943
prescribed_scalar_field_no_adapt
2944
}
2945
}
2946
}|
2947
##When specifying relative measure
2948
##one specifies the interpolation error
2949
##relative to the field that is
2950
##being adapted, e.g. you can specify
2951
##the error to be 5% (i.e. 0.05)
2952
element relative_measure {
2953
attribute replaces { "ADOPTT = 1" },
2954
element scalar_field {
2955
attribute rank { "0" },
2956
attribute name { "InterpolationErrorBound" },
2957
attribute replaces { "ADADOT" },
2958
element prescribed {
2959
prescribed_scalar_field_no_adapt
2960
}
2961
},
2962
## The relative Hessian is calculated according to:
2963
##
2964
## Q = H / max{ |psi|, psi_min}
2965
##
2966
## where H is the Hessian, psi is the field value and
2967
## psi_min is the tolerance. The tolerance prevents
2968
## division by zero errors.
2969
##
2970
## Source: Fluidity/ICOM manual draft version 1.2
2971
element tolerance {
2972
attribute replaces { "ADATOT" },
2973
real
2974
}
2975
}|
2976
## Adapt using the anisotropic strategy of
2977
## Formaggia, Perotto, Micheletti.
2978
## Rather than taking two derivatives
2979
## and deriving the anisotropic information,
2980
## this approach computes an anisotropic Zienkiewicz-Zhu
2981
## error estimator for each element. The approach then
2982
## optimises the element orientation and length scales
2983
## to equidistribute the estimated error.
2984
element anisotropic_zienkiewicz_zhu {
2985
## Tau is an anisotropic estimate for the H1 seminorm of the
2986
## error. This estimator is efficient and reliable, under the
2987
## caveat that the initial mesh is sufficiently fine so as to
2988
## prevent data oscillation. (Micheletti & Perotto, 2006)
2989
## Typically, tau will be ~= 6-8 * |e|_H1.
2990
element tau {
2991
real
2992
}
2993
}
2994
),
2995
adaptivity_preprocessing
2996
}?
2997
)
2998
2999
adaptivity_options_scalar_field.adaptivity_options =
3000
(
3001
## When specifying absolute measure
3002
## one specifies the absolute interpolation
3003
## error in the units of the field that is
3004
## being adapted, e.g. you can specify
3005
## the error to be 1.3 units
3006
element absolute_measure {
3007
attribute replaces { "ADOPTT = 0" },
3008
element scalar_field {
3009
attribute rank { "0" },
3010
attribute name { "InterpolationErrorBound" },
3011
attribute replaces { "ADWEIT" },
3012
element prescribed {
3013
prescribed_scalar_field_no_adapt
3014
}
3015
}
3016
}|
3017
## When specifying relative measure
3018
## one specifies the interpolation error
3019
## relative to the field that is
3020
## being adapted, e.g. you can specify
3021
## the error to be 5% (i.e. 0.05)
3022
element relative_measure {
3023
attribute replaces { "ADOPTT = 1" },
3024
element scalar_field {
3025
attribute rank { "0" },
3026
attribute name { "InterpolationErrorBound" },
3027
attribute replaces { "ADADOT" },
3028
element prescribed {
3029
prescribed_scalar_field_no_adapt
3030
}
3031
},
3032
## The relative Hessian is calculated according to:
3033
##
3034
## Q = H / max{ |psi|, psi_min}
3035
##
3036
## where H is the Hessian, psi is the field value and
3037
## psi_min is the tolerance. The tolerance prevents
3038
## division by zero errors.
3039
##
3040
## Source: Fluidity/ICOM manual draft version 1.2
3041
element tolerance {
3042
attribute replaces { "ADATOT" },
3043
real
3044
}
3045
}|
3046
## Adapt using the anisotropic strategy of
3047
## Formaggia, Perotto, Micheletti.
3048
## Rather than taking two derivatives
3049
## and deriving the anisotropic information,
3050
## this approach computes an anisotropic Zienkiewicz-Zhu
3051
## error estimator for each element. The approach then
3052
## optimises the element orientation and length scales
3053
## to equidistribute the estimated error.
3054
element anisotropic_zienkiewicz_zhu {
3055
## Tau is an anisotropic estimate for the H1 seminorm of the
3056
## error. This estimator is efficient and reliable, under the
3057
## caveat that the initial mesh is sufficiently fine so as to
3058
## prevent data oscillation. (Micheletti & Perotto, 2006)
3059
## Typically, tau will be ~= 6-8 * |e|_H1.
3060
element tau {
3061
real
3062
}
3063
}
3064
)
3065
adaptivity_options_scalar_field =
3066
(
3067
element adaptivity_options {
3068
adaptivity_options_scalar_field.adaptivity_options,
3069
adaptivity_preprocessing
3070
}?
3071
)
3072
3073
adaptivity_options_prognostic_vector_field =
3074
(
3075
## Adaptivity weights
3076
element adaptivity_options {
3077
(
3078
## When specifying absolute measure
3079
## one specifies the absolute interpolation
3080
## error in the units of the field that is
3081
## being adapted, e.g. you can specify
3082
## the error to be 1.3 units
3083
element absolute_measure {
3084
element vector_field {
3085
attribute rank { "1" },
3086
attribute name { "InterpolationErrorBound" },
3087
attribute replaces { "ADWEIU ADWEIV ADWEIW" },
3088
element prescribed {
3089
prescribed_vector_field_no_adapt
3090
}
3091
}
3092
}|
3093
## When specifying relative measure
3094
## one specifies the interpolation error
3095
## relative to the field that is
3096
## being adapted, e.g. you can specify
3097
## the error to be 5% (i.e. 0.05)
3098
element relative_measure {
3099
element vector_field {
3100
attribute rank { "1" },
3101
attribute name { "InterpolationErrorBound" },
3102
attribute replaces { "ADATOU ADATOV ADATOW" },
3103
element prescribed {
3104
prescribed_vector_field_no_adapt
3105
}
3106
},
3107
## The relative Hessian is calculated according to:
3108
##
3109
## Q = H / max{ |psi|, psi_min}
3110
##
3111
## where H is the Hessian, psi is the field value and
3112
## psi_min is the tolerance. The tolerance prevents
3113
## division by zero errors.
3114
##
3115
## Source: Fluidity/ICOM manual draft version 1.2
3116
element tolerance {
3117
real_dim_vector
3118
}
3119
}
3120
),
3121
adaptivity_preprocessing
3122
}?
3123
)
3124
3125
adaptivity_options_vector_field =
3126
(
3127
## Adaptivity weights
3128
element adaptivity_options {
3129
(
3130
## When specifying absolute measure
3131
## one specifies the absolute interpolation
3132
## error in the units of the field that is
3133
## being adapted, e.g. you can specify
3134
## the error to be 1.3 units
3135
element absolute_measure {
3136
element vector_field {
3137
attribute rank { "1" },
3138
attribute name { "InterpolationErrorBound" },
3139
attribute replaces { "ADWEIU ADWEIV ADWEIW" },
3140
element prescribed {
3141
prescribed_vector_field_no_adapt
3142
}
3143
}
3144
}|
3145
## When specifying relative measure
3146
## one specifies the interpolation error
3147
## relative to the field that is
3148
## being adapted, e.g. you can specify
3149
## the error to be 5% (i.e. 0.05)
3150
element relative_measure {
3151
element vector_field {
3152
attribute rank { "1" },
3153
attribute name { "InterpolationErrorBound" },
3154
attribute replaces { "ADATOU ADATOV ADATOW" },
3155
element prescribed {
3156
prescribed_vector_field_no_adapt
3157
}
3158
},
3159
## The relative Hessian is calculated according to:
3160
##
3161
## Q = H / max{ |psi|, psi_min}
3162
##
3163
## where H is the Hessian, psi is the field value and
3164
## psi_min is the tolerance. The tolerance prevents
3165
## division by zero errors.
3166
##
3167
## Source: Fluidity/ICOM manual draft version 1.2
3168
element tolerance {
3169
real_dim_vector
3170
}
3171
}
3172
),
3173
adaptivity_preprocessing
3174
}?
3175
)
3176
3177
adaptivity_options_prognostic_tensor_field =
3178
(
3179
## Adaptivity weights
3180
element adaptivity_options {
3181
(
3182
## When specifying absolute measure
3183
## one specifies the absolute interpolation
3184
## error in the units of the field that is
3185
## being adapted, e.g. you can specify
3186
## the error to be 1.3 units
3187
element absolute_measure {
3188
element tensor_field {
3189
attribute rank { "2" },
3190
attribute name { "InterpolationErrorBound" },
3191
element prescribed {
3192
prescribed_values_tensor_field
3193
}
3194
}
3195
}|
3196
## When specifying relative measure
3197
## one specifies the interpolation error
3198
## relative to the field that is
3199
## being adapted, e.g. you can specify
3200
## the error to be 5% (i.e. 0.05)
3201
element relative_measure {
3202
element tensor_field {
3203
attribute rank { "2" },
3204
attribute name { "InterpolationErrorBound" },
3205
element prescribed {
3206
prescribed_values_tensor_field
3207
}
3208
},
3209
## The relative Hessian is calculated according to:
3210
##
3211
## Q = H / max{ |psi|, psi_min}
3212
##
3213
## where H is the Hessian, psi is the field value and
3214
## psi_min is the tolerance. The tolerance prevents
3215
## division by zero errors.
3216
##
3217
## Source: Fluidity/ICOM manual draft version 1.2
3218
element tolerance {
3219
real_dim_tensor
3220
}
3221
}
3222
),
3223
adaptivity_preprocessing
3224
}?
3225
)
3226
3227
adaptivity_options_tensor_field =
3228
(
3229
## Adaptivity weights
3230
element adaptivity_options {
3231
(
3232
## When specifying absolute measure
3233
## one specifies the absolute interpolation
3234
## error in the units of the field that is
3235
## being adapted, e.g. you can specify
3236
## the error to be 1.3 units
3237
element absolute_measure {
3238
element tensor_field {
3239
attribute rank { "2" },
3240
attribute name { "InterpolationErrorBound" },
3241
element prescribed {
3242
prescribed_values_tensor_field
3243
}
3244
}
3245
}|
3246
## When specifying relative measure
3247
## one specifies the interpolation error
3248
## relative to the field that is
3249
## being adapted, e.g. you can specify
3250
## the error to be 5% (i.e. 0.05)
3251
element relative_measure {
3252
element tensor_field {
3253
attribute rank { "2" },
3254
attribute name { "InterpolationErrorBound" },
3255
element prescribed {
3256
prescribed_values_tensor_field
3257
}
3258
},
3259
## The relative Hessian is calculated according to:
3260
##
3261
## Q = H / max{ |psi|, psi_min}
3262
##
3263
## where H is the Hessian, psi is the field value and
3264
## psi_min is the tolerance. The tolerance prevents
3265
## division by zero errors.
3266
##
3267
## Source: Fluidity/ICOM manual draft version 1.2
3268
element tolerance {
3269
real_dim_tensor
3270
}
3271
}
3272
),
3273
adaptivity_preprocessing
3274
}?
3275
)
3276
generic_aliased_field =
3277
(
3278
attribute material_phase_name { xsd:string },
3279
attribute field_name { xsd:string }
3280
)
3281
3282
# Most common mesh choices
3283
mesh_choice =
3284
(
3285
element mesh {
3286
attribute name { xsd:string }
3287
}|
3288
element mesh {
3289
attribute name { "CoordinateMesh" }
3290
}|
3291
element mesh {
3292
attribute name { "VelocityMesh" }
3293
}|
3294
element mesh {
3295
attribute name { "PressureMesh" }
3296
}
3297
)
3298
3299
# Not really a choice, for fields that have to be on the velocity mesh
3300
# currently that's all scalar fields, except pressure
3301
# and of course velocity itself
3302
# If you want to implement scalar fields on other meshes, feel free to do so
3303
# but bare in mind you need to make sure the field stays outside RMEM.
3304
# Currently all scalar fields are packed in RMEM with length nonods
3305
velocity_mesh_choice =
3306
(
3307
(
3308
element mesh {
3309
attribute name { "VelocityMesh" }
3310
}|
3311
element mesh {
3312
attribute name { "PressureMesh" }
3313
}|
3314
element mesh {
3315
attribute name { "CoordinateMesh" }
3316
}|
3317
element mesh {
3318
attribute name { string }
3319
}
3320
)
3321
)
3322
3323
pressure_mesh_choice =
3324
(
3325
(
3326
element mesh {
3327
attribute name { "PressureMesh" }
3328
}|
3329
element mesh {
3330
attribute name { "VelocityMesh" }
3331
}|
3332
element mesh {
3333
attribute name { "CoordinateMesh" }
3334
}|
3335
element mesh {
3336
attribute name { string }
3337
}
3338
)
3339
)
3340
3341
# This is the choice of additional scalar field to be solved for
3342
scalar_field_choice =
3343
(
3344
# The first is a generic field, which may be used for any user-defined field
3345
# that FLUIDITY knows nothing about, or a generic diagnostic
3346
(
3347
element scalar_field {
3348
attribute rank { "0" },
3349
attribute name { xsd:string },
3350
## Field type
3351
(
3352
element prognostic {
3353
velocity_mesh_choice,
3354
prognostic_scalar_field
3355
}|
3356
element prescribed {
3357
velocity_mesh_choice,
3358
prescribed_scalar_field
3359
}|
3360
element diagnostic {
3361
scalar_diagnostic_algorithms,
3362
velocity_mesh_choice,
3363
python_diagnostic_field_code?,
3364
diagnostic_scalar_field
3365
}|
3366
element aliased {
3367
generic_aliased_field
3368
}
3369
)
3370
}|
3371
## Prognostic scalar fields below this
3372
element ___Prognostic_Fields_Below___ {
3373
empty
3374
}|
3375
3376
# This is the long list of fields that FLUIDITY knows about
3377
# -- First is a list of fields that are primarily prognostic,
3378
# but can be set to prescribed, or aliased...
3379
# -- The list is in order of most frequently used.
3380
3381
## Salinity
3382
element scalar_field {
3383
attribute rank { "0" },
3384
attribute name { "Salinity" },
3385
attribute replaces { "IDENT = 42" },
3386
(
3387
element prognostic {
3388
velocity_mesh_choice,
3389
prognostic_scalar_field
3390
}|
3391
element prescribed {
3392
velocity_mesh_choice,
3393
prescribed_scalar_field
3394
}|
3395
element aliased {
3396
generic_aliased_field
3397
}
3398
)
3399
}|
3400
## Temperature
3401
element scalar_field {
3402
attribute rank { "0" },
3403
attribute name { "Temperature" },
3404
attribute replaces { "IDENT = -1" },
3405
(
3406
element prognostic {
3407
velocity_mesh_choice,
3408
prognostic_scalar_field
3409
}|
3410
element prescribed {
3411
velocity_mesh_choice,
3412
prescribed_scalar_field
3413
}|
3414
element aliased {
3415
generic_aliased_field
3416
}
3417
)
3418
}|
3419
## Background Temperature
3420
element scalar_field {
3421
attribute rank { "0" },
3422
attribute name { "BackgroundTemperature" },
3423
(
3424
element prescribed {
3425
velocity_mesh_choice,
3426
prescribed_scalar_field
3427
}
3428
)
3429
}|
3430
## Passive Tracer
3431
element scalar_field {
3432
attribute rank { "0" },
3433
attribute name { "Tracer" },
3434
attribute replaces { "IDENT = 666" },
3435
(
3436
element prognostic {
3437
velocity_mesh_choice,
3438
prognostic_scalar_field
3439
}|
3440
element prescribed {
3441
velocity_mesh_choice,
3442
prescribed_scalar_field
3443
}|
3444
element aliased {
3445
generic_aliased_field
3446
}
3447
)
3448
}|
3449
## Free Surface
3450
## NOTE: the prognostic FreeSurface field only works with the
3451
## legacy_continuous_galerkin code path
3452
## NOTE: if you are using the free_surface boundary condition
3453
## applied to the Velocity field (recommended), you should not
3454
## use the prognostic FreeSurface field. In this case you may
3455
## (optionally) add a diagnostic FreeSurface field.
3456
element scalar_field {
3457
attribute rank { "0" },
3458
attribute name { "FreeSurface" },
3459
(
3460
## Free Surface
3461
## NOTE: the prognostic FreeSurface field only works with the
3462
## legacy_continuous_galerkin code path
3463
element prognostic {
3464
## Note that this is not the quadratic mesh balance pressure is
3465
## actually calculated on, but the linear mesh it is projected back
3466
## on for output purposes.
3467
element mesh {
3468
attribute name { "VelocityMesh" }
3469
},
3470
prognostic_free_surface_field
3471
}|
3472
## Free Surface
3473
## NOTE: the diagnostic FreeSurface field only works in combination
3474
## with the free_surface boundary condition applied to the Velocity
3475
## field. It gives you a 3D field (constant over the vertical)
3476
## of the free surface elevation.
3477
element diagnostic {
3478
internal_algorithm,
3479
# this is hard-coded on the PressureMesh as long as the Pressure is
3480
# if this is no longer true, it should be option-checked to be on the
3481
# same mesh as Pressure
3482
## Must be on the same mesh as Pressure
3483
element mesh {
3484
attribute name { "PressureMesh" }
3485
},
3486
diagnostic_scalar_field
3487
}
3488
3489
)
3490
}|
3491
## Second Fluid
3492
element scalar_field {
3493
attribute rank { "0" },
3494
attribute name { "SecondFluid" },
3495
attribute replaces { "IDENT = 56" },
3496
(
3497
element prognostic {
3498
velocity_mesh_choice,
3499
prognostic_scalar_field
3500
}|
3501
element prescribed {
3502
velocity_mesh_choice,
3503
prescribed_scalar_field
3504
}|
3505
element aliased {
3506
generic_aliased_field
3507
}
3508
)
3509
}|
3510
## Diffuse Interface
3511
element scalar_field {
3512
attribute rank { "0" },
3513
attribute name { "DiffuseInterface" },
3514
attribute replaces { "IDENT = 57" },
3515
(
3516
element prognostic {
3517
velocity_mesh_choice,
3518
prognostic_scalar_field
3519
}|
3520
element prescribed {
3521
velocity_mesh_choice,
3522
prescribed_scalar_field
3523
}|
3524
element aliased {
3525
generic_aliased_field
3526
}
3527
)
3528
}|
3529
element scalar_field {
3530
attribute rank { "0" },
3531
attribute name { "BalancePressure" },
3532
attribute replaces { "IDENT = -2003" },
3533
(
3534
element prognostic {
3535
# Note the assumptions about quadratic/linear below and hard-coding
3536
# of the mesh, this is because of restrictions of the
3537
# current code, will change in the near future.
3538
## Note that this is not the quadratic mesh balance pressure is
3539
## actually calculated on, but the linear mesh it is projected back
3540
## on for output purposes.
3541
element mesh {
3542
attribute name { "VelocityMesh" }
3543
},
3544
prognostic_balance_pressure_field
3545
}
3546
)
3547
}|
3548
## If enabled, decomposes Pressure by solving for the balanced part of
3549
## Pressure using a "geopressure" solver:
3550
##
3551
## f = - grad p_gp + g
3552
##
3553
## By choosing an appropriate mesh (typically velocity mesh order + 1)
3554
## for the balanced part of pressure, physical balance can be
3555
## represented to a higher degree of accuracy.
3556
##
3557
## Expanded BalancePressure field. As BalancePressure, but with
3558
## additional options, including the ability to choose a general
3559
## mesh for the geopressure solver.
3560
element scalar_field {
3561
attribute rank { "0" },
3562
attribute name { "GeostrophicPressure" },
3563
attribute replaces { "IDENT = -2003" },
3564
(
3565
element prognostic {
3566
## The GeostrophicPressure mesh
3567
##
3568
## <b>WARNING: It is usual for this to be a higher degree
3569
## mesh than the velocity mesh</b>
3570
element mesh {
3571
attribute name { xsd:string },
3572
comment
3573
},
3574
prognostic_geostrophic_pressure_field
3575
}
3576
)
3577
}|
3578
element scalar_field {
3579
attribute rank { "0" },
3580
attribute name { "VerticalBalancePressure" },
3581
(
3582
element prognostic {
3583
## This needs to be a quadratic DG mesh
3584
mesh_choice,
3585
prognostic_vertical_balance_pressure_field
3586
}
3587
)
3588
}|
3589
## MaterialVolumeFraction field:
3590
##
3591
## Volume fraction of this material.
3592
## Required in multimaterial simulations.
3593
## - if prognostic solves for the volume fraction
3594
## - if prescribed uses a specified volume fraction
3595
## - if diagnostic solves for the final material volume fraction
3596
## Only 1 diagnostic MaterialVolumeFraction field allowed per
3597
## simulation or solves for all the volume fractions based on
3598
## the SumMaterialVolumeFractions field.
3599
##
3600
## A diagnostic MaterialVolumeFraction field is currently required for
3601
## compressible multimaterial simulations (even if only 1 material).
3602
## Generally also requires a MaterialDensity field.
3603
element scalar_field {
3604
attribute rank { "0" },
3605
attribute name { "MaterialVolumeFraction" },
3606
(
3607
element prognostic {
3608
velocity_mesh_choice,
3609
prognostic_scalar_field,
3610
cap_option?,
3611
surface_tension_option?
3612
}|
3613
element diagnostic {
3614
internal_algorithm,
3615
velocity_mesh_choice,
3616
diagnostic_scalar_field,
3617
cap_option?
3618
}|
3619
element prescribed {
3620
velocity_mesh_choice,
3621
prescribed_scalar_field,
3622
cap_option?
3623
}|
3624
element aliased {
3625
generic_aliased_field
3626
}
3627
)
3628
}|
3629
## MaterialDensity field:
3630
##
3631
## Field for the density of this material.
3632
## Required in multimaterial simulations.
3633
## - prescribed if an incompressible simulation
3634
## - diagnostic if using a linear equation of state
3635
## - prognostic if a compressible simulation
3636
## (note that if you set a multimaterial
3637
## equation of state and this field is
3638
## prognostic then its initial condition
3639
## will be overwritten by the density that
3640
## satisfies the initial pressure and
3641
## the equation of state)
3642
element scalar_field {
3643
attribute rank { "0" },
3644
attribute name { "MaterialDensity" },
3645
(
3646
element prognostic {
3647
velocity_mesh_choice,
3648
prognostic_scalar_field
3649
}|
3650
element diagnostic {
3651
internal_algorithm,
3652
velocity_mesh_choice,
3653
diagnostic_scalar_field
3654
}|
3655
element prescribed {
3656
velocity_mesh_choice,
3657
prescribed_scalar_field
3658
}|
3659
element aliased {
3660
generic_aliased_field
3661
}
3662
)
3663
}|
3664
## MaterialInternalEnergy field:
3665
##
3666
## Field for the internal energy of this material.
3667
## Required in multimaterial compressible simulations
3668
## with full miegrunneisen (perfect gas) eos.
3669
element scalar_field {
3670
attribute rank { "0" },
3671
attribute name { "MaterialInternalEnergy" },
3672
(
3673
element prognostic {
3674
velocity_mesh_choice,
3675
prognostic_scalar_field
3676
}|
3677
element aliased {
3678
generic_aliased_field
3679
}
3680
)
3681
}|
3682
## SumMaterialVolumeFractions field:
3683
##
3684
## Sums the prognostic MaterialVolumeFraction fields.
3685
## - diagnostic: sums all the volume fractions in the other
3686
## material phases
3687
element scalar_field {
3688
attribute rank { "0" },
3689
attribute name { "SumMaterialVolumeFractions" },
3690
(
3691
element diagnostic {
3692
internal_algorithm,
3693
velocity_mesh_choice,
3694
diagnostic_scalar_field
3695
}|
3696
element aliased {
3697
generic_aliased_field
3698
}
3699
)
3700
}|
3701
## CopiedField - This field copies the previous timesteps
3702
## values from another (specified) field at every iteration
3703
## and then solves the field using different (again, specified)
3704
## scheme and solution options.
3705
## For instance, this field can be used to create a diffused
3706
## field to adapt to.
3707
## Unless someone requests otherwise this is only currently possible
3708
## for fields within the same material_phase.
3709
element scalar_field {
3710
attribute rank { "0" },
3711
attribute name { "CopiedField" },
3712
(
3713
element prognostic {
3714
velocity_mesh_choice,
3715
attribute copy_from_field { string },
3716
prognostic_scalar_field
3717
}
3718
)
3719
}|
3720
## Calculate the stream function of 2D incompressible flow. Note
3721
## that this *only* makes sense for proper 2D (not pseudo-2D) simulations.
3722
## Requires a continuous mesh.
3723
element scalar_field {
3724
attribute rank { "0" },
3725
attribute name { "StreamFunction" },
3726
(
3727
element prognostic {
3728
mesh_choice,
3729
prognostic_stream_function_field
3730
}
3731
)
3732
}|
3733
## Phytoplankton
3734
element scalar_field {
3735
attribute rank { "0" },
3736
attribute name { "Phytoplankton" },
3737
(
3738
element prognostic {
3739
velocity_mesh_choice,
3740
prognostic_scalar_field
3741
}|
3742
element prescribed {
3743
velocity_mesh_choice,
3744
prescribed_scalar_field
3745
}
3746
)
3747
}|
3748
## Zooplankton
3749
element scalar_field {
3750
attribute rank { "0" },
3751
attribute name { "Zooplankton" },
3752
(
3753
element prognostic {
3754
velocity_mesh_choice,
3755
prognostic_scalar_field
3756
}|
3757
element prescribed {
3758
velocity_mesh_choice,
3759
prescribed_scalar_field
3760
}
3761
)
3762
}|
3763
## Nutrient
3764
element scalar_field {
3765
attribute rank { "0" },
3766
attribute name { "Nutrient" },
3767
(
3768
element prognostic {
3769
velocity_mesh_choice,
3770
prognostic_scalar_field
3771
}|
3772
element prescribed {
3773
velocity_mesh_choice,
3774
prescribed_scalar_field
3775
}
3776
)
3777
}|
3778
## Detritus
3779
element scalar_field {
3780
attribute rank { "0" },
3781
attribute name { "Detritus" },
3782
(
3783
element prognostic {
3784
velocity_mesh_choice,
3785
prognostic_scalar_field
3786
}|
3787
element prescribed {
3788
velocity_mesh_choice,
3789
prescribed_scalar_field
3790
}
3791
)
3792
}|
3793
3794
## PhaseVolumeFraction:
3795
## Required in porous_media problem type
3796
element scalar_field {
3797
attribute rank { "0" },
3798
attribute name { "PhaseVolumeFraction" },
3799
(
3800
element prognostic {
3801
velocity_mesh_choice,
3802
prognostic_scalar_field
3803
}|
3804
element prescribed {
3805
velocity_mesh_choice,
3806
prescribed_scalar_field
3807
}
3808
)
3809
}|
3810
3811
## Electrical Potential:
3812
## Required in electrokinetic, electrothermal
3813
## and electrochemical problems
3814
## (sub-option of porous_media problem type)
3815
element scalar_field {
3816
attribute rank { "0" },
3817
attribute name { "ElectricalPotential" },
3818
(
3819
element prognostic {
3820
velocity_mesh_choice,
3821
prognostic_scalar_field
3822
}
3823
)
3824
}|
3825
3826
# Insert new prognostic scalar fields here using the template:
3827
# element scalar_field {
3828
# attribute rank { "0" },
3829
# attribute name { "NewFieldName" },
3830
# (
3831
# element prognostic {
3832
# velocity_mesh_choice,
3833
# prognostic_scalar_field
3834
# }|
3835
# element prescribed {
3836
# velocity_mesh_choice,
3837
# prescribed_scalar_field
3838
# }|
3839
# element aliased {
3840
# generic_aliased_field
3841
# }
3842
# )
3843
# }
3844
3845
# -- Second is a list of fields that are primarily prescribed,
3846
# but can be aliased. An example is wind velocity.
3847
# -- The list is in order of most frequently used.
3848
3849
## Prescribed scalar fields below this
3850
element ___Prescribed_fields_below___ {
3851
empty
3852
}|
3853
element scalar_field {
3854
attribute rank { "0" },
3855
attribute name { "DistanceToSideBoundaries" },
3856
attribute replaces { "IDENT = -144" },
3857
(
3858
element prescribed {
3859
velocity_mesh_choice,
3860
prescribed_scalar_field
3861
}|
3862
element aliased {
3863
generic_aliased_field
3864
}
3865
)
3866
}|
3867
## MaterialFrictionAngle for multimaterial
3868
## plasticity problems
3869
##
3870
## Requires a diagnostic bulk FrictionAngle field
3871
## - not tested yet
3872
element scalar_field {
3873
attribute rank { "0" },
3874
attribute name { "MaterialFrictionAngle" },
3875
(
3876
element prescribed {
3877
velocity_mesh_choice,
3878
prescribed_scalar_field
3879
}|
3880
element aliased {
3881
generic_aliased_field
3882
}
3883
)
3884
}|
3885
## MaterialCohesion for multimaterial
3886
## plasticity problems
3887
##
3888
## Requires a diagnostic bulk Cohesion field
3889
## - not tested yet
3890
element scalar_field {
3891
attribute rank { "0" },
3892
attribute name { "MaterialCohesion" },
3893
(
3894
element prescribed {
3895
velocity_mesh_choice,
3896
prescribed_scalar_field
3897
}|
3898
element aliased {
3899
generic_aliased_field
3900
}
3901
)
3902
}|
3903
#
3904
# Insert new prescribed scalar fields here using the template:
3905
# element scalar_field {
3906
# attribute rank { "0" },
3907
# attribute name { "NewFieldName" },
3908
# (
3909
# element prescribed {
3910
# velocity_mesh_choice,
3911
# prescribed_scalar_field
3912
# }|
3913
# element aliased {
3914
# generic_aliased_field
3915
# }
3916
# )
3917
# }
3918
#
3919
# -- Last is a list of fields that are primarily diagnostic,
3920
# but can be aliased. An example is Tidal Range.
3921
# -- The list is in order of most frequently used.
3922
#
3923
## Diagnostic scalar fields below this
3924
element ___Diagnostic_Fields_Below___ {
3925
empty
3926
}|
3927
element scalar_field {
3928
attribute rank { "0" },
3929
attribute name { "PerturbationDensity" },
3930
attribute replaces { "IDENT = -143" },
3931
(
3932
element diagnostic {
3933
internal_algorithm,
3934
velocity_mesh_choice,
3935
diagnostic_scalar_field
3936
}|
3937
element aliased {
3938
generic_aliased_field
3939
}
3940
)
3941
}|
3942
## ControlVolumeDivergence:
3943
##
3944
## div field
3945
##
3946
## Divergence of the velocity field where
3947
## the divergence operator is defined using
3948
## the control volume C^T matrix.
3949
## This assumes that the test space is discontinuous
3950
## control volumes.
3951
element scalar_field {
3952
attribute rank { "0" },
3953
attribute name { "ControlVolumeDivergence" },
3954
(
3955
element diagnostic {
3956
internal_algorithm,
3957
attribute field_name { string },
3958
velocity_mesh_choice,
3959
diagnostic_cv_divergence_scalar_field
3960
}|
3961
element aliased {
3962
generic_aliased_field
3963
}
3964
)
3965
}|
3966
3967
## FiniteElementDivergence:
3968
##
3969
## div field
3970
##
3971
## Divergence of the velocity field where
3972
## the divergence operator is defined using
3973
## the finite element C^T matrix.
3974
element scalar_field {
3975
attribute rank { "0" },
3976
attribute name { "FiniteElementDivergence" },
3977
(
3978
element diagnostic {
3979
internal_algorithm,
3980
attribute field_name { string },
3981
velocity_mesh_choice,
3982
element integrate_divergence_by_parts {
3983
empty
3984
}?,
3985
diagnostic_fe_divergence_scalar_field
3986
}|
3987
element aliased {
3988
generic_aliased_field
3989
}
3990
)
3991
}|
3992
## Diffusive dissipation
3993
element scalar_field {
3994
attribute rank { "0" },
3995
attribute name { "DiffusiveDissipation" },
3996
(
3997
element diagnostic {
3998
internal_algorithm,
3999
velocity_mesh_choice,
4000
diagnostic_scalar_field
4001
}|
4002
element aliased {
4003
generic_aliased_field
4004
}
4005
)
4006
}|
4007
## Viscous dissipation
4008
element scalar_field {
4009
attribute rank { "0" },
4010
attribute name { "ViscousDissipation" },
4011
(
4012
element diagnostic {
4013
internal_algorithm,
4014
velocity_mesh_choice,
4015
diagnostic_scalar_field
4016
}|
4017
element aliased {
4018
generic_aliased_field
4019
}
4020
)
4021
}|
4022
## Richardson Number:
4023
##
4024
## Ri = \frac{N^2}{(\frac{\partial u}{\partial z})^2 + (\frac{\partial u}{\partial z})^2}
4025
## with
4026
## N^2 = -\frac{g}{\rho_0}\frac{\partial \rho}{\partial z}
4027
##
4028
## Limitations:
4029
## - Gravity must be constant.
4030
## - Assumes gravity is in -ve final coordinate direction.
4031
element scalar_field {
4032
attribute rank { "0" },
4033
attribute name { "RichardsonNumber" },
4034
attribute depends { "Velocity,PerturbationDensity" },
4035
(
4036
element diagnostic {
4037
internal_algorithm,
4038
velocity_mesh_choice,
4039
diagnostic_richardson_number_field
4040
}|
4041
element aliased {
4042
generic_aliased_field
4043
}
4044
)
4045
}|
4046
## CFLNumber
4047
##
4048
## See http://amcg.ese.ic.ac.uk/index.php?title=Local:Diagnostics#CFL_Number
4049
##
4050
## Adapting to this field is not recommended
4051
element scalar_field {
4052
attribute rank { "0" },
4053
attribute name { "CFLNumber" },
4054
attribute replaces { "IDENT = -601" },
4055
(
4056
element diagnostic {
4057
internal_algorithm,
4058
velocity_mesh_choice,
4059
diagnostic_scalar_field
4060
}|
4061
element aliased {
4062
generic_aliased_field
4063
}
4064
)
4065
}|
4066
## ControlVolumeCFLNumber
4067
##
4068
## Courant Number as defined on a control volume mesh
4069
##
4070
## Adapting to this field is not recommended
4071
element scalar_field {
4072
attribute rank { "0" },
4073
attribute name { "ControlVolumeCFLNumber" },
4074
(
4075
element diagnostic {
4076
internal_algorithm,
4077
velocity_mesh_choice,
4078
diagnostic_scalar_field
4079
}|
4080
element aliased {
4081
generic_aliased_field
4082
}
4083
)
4084
}|
4085
## DG_CourantNumber
4086
##
4087
## Courant Number as defined on a DG mesh
4088
##
4089
## Adapting to this field is not recommended
4090
element scalar_field {
4091
attribute rank { "0" },
4092
attribute name { "DG_CourantNumber" },
4093
(
4094
element diagnostic {
4095
internal_algorithm,
4096
velocity_mesh_choice,
4097
diagnostic_scalar_field
4098
}|
4099
element aliased {
4100
generic_aliased_field
4101
}
4102
)
4103
}|
4104
## CVMaterialDensityCFLNumber
4105
##
4106
## Courant Number as defined on a control volume mesh and
4107
## incorporating the MaterialDensity.
4108
## Requires a MaterialDensity field!
4109
##
4110
## Adapting to this field is not recommended
4111
element scalar_field {
4112
attribute rank { "0" },
4113
attribute name { "CVMaterialDensityCFLNumber" },
4114
(
4115
element diagnostic {
4116
internal_algorithm,
4117
velocity_mesh_choice,
4118
diagnostic_scalar_field
4119
}|
4120
element aliased {
4121
generic_aliased_field
4122
}
4123
)
4124
}|
4125
element scalar_field {
4126
attribute rank { "0" },
4127
attribute name { "SolidConcentration" },
4128
(
4129
element diagnostic {
4130
internal_algorithm,
4131
velocity_mesh_choice,
4132
diagnostic_scalar_field
4133
}|
4134
element aliased {
4135
generic_aliased_field
4136
}
4137
)
4138
}|
4139
## This scalar field is meant to replace DENTRAF.
4140
## Basically, if you use new options, DENTRAF is no longer needed
4141
## No repointing is done from this field to DENTRAF.
4142
element scalar_field {
4143
attribute rank { "0" },
4144
attribute name { "CopyofDensity" },
4145
attribute replaces { "DENTRAF" },
4146
(
4147
element diagnostic {
4148
internal_algorithm,
4149
velocity_mesh_choice,
4150
diagnostic_scalar_field
4151
}
4152
)
4153
}|
4154
## Add field to be used by Solid_configuration to
4155
## Visualize the solids and MaterialVolumeFraction together
4156
element scalar_field {
4157
attribute rank { "0" },
4158
attribute name { "VisualizeSolidFluid" },
4159
(
4160
element diagnostic {
4161
internal_algorithm,
4162
velocity_mesh_choice,
4163
diagnostic_scalar_field
4164
}
4165
)
4166
}|
4167
## Add field to be used by Solid_configuration to
4168
## Visualize the solid_Concentration
4169
element scalar_field {
4170
attribute rank { "0" },
4171
attribute name { "VisualizeSolid" },
4172
(
4173
element diagnostic {
4174
internal_algorithm,
4175
velocity_mesh_choice,
4176
diagnostic_scalar_field
4177
}
4178
)
4179
}|
4180
## Add field to be used by Solid_configuration to
4181
## map the solid_Concentration from particle mesh to
4182
## the fluid mesh.
4183
element scalar_field {
4184
attribute rank { "0" },
4185
attribute name { "ParticleScalar" },
4186
(
4187
element diagnostic {
4188
internal_algorithm,
4189
mesh_choice,
4190
diagnostic_scalar_field
4191
}
4192
)
4193
}|
4194
## Add field to be used by Explicit_ALE to
4195
## visualize functional values before iterations start.
4196
element scalar_field {
4197
attribute rank { "0" },
4198
attribute name { "FunctionalBegin" },
4199
(
4200
element diagnostic {
4201
internal_algorithm,
4202
mesh_choice,
4203
diagnostic_scalar_field
4204
}
4205
)
4206
}|
4207
## Add field to be used by Explicit_ALE to
4208
## visualize functional values at each iteration.
4209
element scalar_field {
4210
attribute rank { "0" },
4211
attribute name { "FunctionalIter" },
4212
(
4213
element diagnostic {
4214
internal_algorithm,
4215
mesh_choice,
4216
diagnostic_scalar_field
4217
}
4218
)
4219
}|
4220
## add a MaterialVolume scalar_field to calculate the spatially varying
4221
## volume of a material (requires a MaterialVolumeFraction)
4222
element scalar_field {
4223
attribute rank { "0" },
4224
attribute name { "MaterialVolume" },
4225
(
4226
element diagnostic {
4227
internal_algorithm,
4228
velocity_mesh_choice,
4229
diagnostic_scalar_field
4230
}|
4231
element aliased {
4232
generic_aliased_field
4233
}
4234
)
4235
}|
4236
## add a MaterialMass scalar_field to calculate the spatially varying
4237
## mass of a material (requires a MaterialVolumeFraction and a MaterialDensity)
4238
element scalar_field {
4239
attribute rank { "0" },
4240
attribute name { "MaterialMass" },
4241
(
4242
element diagnostic {
4243
internal_algorithm,
4244
velocity_mesh_choice,
4245
diagnostic_scalar_field
4246
}|
4247
element aliased {
4248
generic_aliased_field
4249
}
4250
)
4251
}|
4252
## Calculates the MaterialDensity based on the bulk Pressure
4253
## (and MaterialInternalEnergy if appropriate) for the equation
4254
## of state of this material.
4255
element scalar_field {
4256
attribute rank { "0" },
4257
attribute name { "MaterialEOSDensity" },
4258
(
4259
element diagnostic {
4260
internal_algorithm,
4261
velocity_mesh_choice,
4262
diagnostic_scalar_field
4263
}|
4264
element aliased {
4265
generic_aliased_field
4266
}
4267
)
4268
}|
4269
## Calculates the MaterialPressure based on the MaterialDensity
4270
## (and MaterialInternalEnergy if appropriate) for the equation
4271
## of state of this material.
4272
element scalar_field {
4273
attribute rank { "0" },
4274
attribute name { "MaterialPressure" },
4275
(
4276
element diagnostic {
4277
internal_algorithm,
4278
velocity_mesh_choice,
4279
diagnostic_scalar_field
4280
}|
4281
element aliased {
4282
generic_aliased_field
4283
}
4284
)
4285
}|
4286
## Calculates the BulkMaterialPressure based on the MaterialDensity
4287
## and MaterialVolumeFraction (and MaterialInternalEnergy if appropriate)
4288
## for the equation of state of all materials.
4289
element scalar_field {
4290
attribute rank { "0" },
4291
attribute name { "BulkMaterialPressure" },
4292
(
4293
element diagnostic {
4294
internal_algorithm,
4295
velocity_mesh_choice,
4296
diagnostic_scalar_field
4297
}|
4298
element aliased {
4299
generic_aliased_field
4300
}
4301
)
4302
}|
4303
## Grid Reynolds number
4304
element scalar_field {
4305
attribute rank { "0" },
4306
attribute name { "GridReynoldsNumber" },
4307
(element diagnostic {
4308
internal_algorithm,
4309
element mesh {
4310
attribute name { "VelocityMesh" }
4311
},
4312
diagnostic_scalar_field
4313
}
4314
| element aliased { generic_aliased_field })
4315
}|
4316
## GridPecletNumber
4317
##
4318
## Peclet Number Pe = U*dx/2*diffusivity
4319
##
4320
## Also see the test case 'grid_peclet_number'
4321
## if you wish to see the effect of changing the
4322
## diffusivity on a 1D, cg-discretised tracer-field
4323
##
4324
## Adapting to this field is not recommended
4325
element scalar_field {
4326
attribute rank { "0" },
4327
attribute name { "GridPecletNumber" },
4328
(
4329
element diagnostic {
4330
internal_algorithm,
4331
## Mesh on which to calculate dx
4332
mesh_choice,
4333
## This is the name of the scalar field
4334
## to calculate the Peclet number for
4335
## Note this field needs to have a diffusivity
4336
element field_name { string },
4337
diagnostic_scalar_field
4338
}|
4339
element aliased {
4340
generic_aliased_field
4341
}
4342
)
4343
}|
4344
## Horizontal velocity divergence:
4345
##
4346
## div_H velocity
4347
##
4348
## Uses the gravity field direction to determine the horizontal plane.
4349
element scalar_field {
4350
attribute rank { "0" },
4351
attribute name { "HorizontalVelocityDivergence" },
4352
(
4353
element diagnostic {
4354
internal_algorithm,
4355
velocity_mesh_choice,
4356
diagnostic_scalar_field
4357
}|
4358
element aliased {
4359
generic_aliased_field
4360
}
4361
)
4362
}|
4363
4364
## Velocity divergence:
4365
##
4366
## div velocity
4367
##
4368
element scalar_field {
4369
attribute rank { "0" },
4370
attribute name { "VelocityDivergence" },
4371
(
4372
element diagnostic {
4373
internal_algorithm,
4374
velocity_mesh_choice,
4375
diagnostic_scalar_field
4376
}|
4377
element aliased {
4378
generic_aliased_field
4379
}
4380
)
4381
}|
4382
4383
## Vorticity for a 2D field:
4384
##
4385
## du dv
4386
## -- - --
4387
## dy dx
4388
element scalar_field {
4389
attribute rank { "0" },
4390
attribute name { "Vorticity2D" },
4391
(
4392
element diagnostic {
4393
internal_algorithm,
4394
mesh_choice,
4395
diagnostic_scalar_field
4396
}|
4397
element aliased {
4398
generic_aliased_field
4399
}
4400
)
4401
}|
4402
4403
## Kinetic energy density:
4404
##
4405
## 1/2 rho_0*|u|^2
4406
##
4407
## where rho_0 is the (reference) density
4408
##
4409
## Limitations:
4410
## - The Density, PerturbationDensity, KineticEnergyDensity and Velocity fields must be on the same mesh.
4411
element scalar_field {
4412
attribute rank { "0" },
4413
attribute name { "KineticEnergyDensity" },
4414
(
4415
element diagnostic {
4416
internal_algorithm,
4417
velocity_mesh_choice,
4418
diagnostic_scalar_field
4419
}|
4420
element aliased {
4421
generic_aliased_field
4422
}
4423
)
4424
}|
4425
4426
## Gravitational potential energy density:
4427
##
4428
## rho_0*(1.0 + rho')*(g dot (r - r_0))
4429
##
4430
## where rho_0 is the (reference) density, rho' is the perturbation density and r_0 is the potential energy zero point.
4431
##
4432
## Limitations:
4433
## - Requires a constant gravity direction.
4434
## - The Density, PerturbationDensity and GravitationalPotentialEnergyDensity fields must be on the same mesh.
4435
element scalar_field {
4436
attribute rank { "0" },
4437
attribute name { "GravitationalPotentialEnergyDensity" },
4438
(
4439
element diagnostic {
4440
internal_algorithm,
4441
velocity_mesh_choice,
4442
diagnostic_scalar_field,
4443
## Coordinate of a point with a potential energy of zero.
4444
element zero_point {
4445
real_dim_vector
4446
}
4447
}|
4448
element aliased {
4449
generic_aliased_field
4450
}
4451
)
4452
}|
4453
## Isopycnal coordinate
4454
##
4455
## z_star(x,t) = 1/A int_V' H(rho(x',t)-rho(x,t)) dV'
4456
##
4457
## where rho is the density, A is the width/area of the domain
4458
##
4459
## Limitations:
4460
## - You need to specify a (fine) mesh to redistribute the PerturbationDensity onto
4461
## - Requires a constant gravity direction.
4462
## - The Density, PerturbationDensity and GravitationalPotentialEnergyDensity fields must be on the same mesh.
4463
element scalar_field {
4464
attribute rank { "0" },
4465
attribute name { "IsopycnalCoordinate" },
4466
(
4467
element diagnostic {
4468
internal_algorithm,
4469
velocity_mesh_choice,
4470
## This is the mesh onto which we redistribute the PerturbationDensity
4471
element fine_mesh {
4472
attribute name { string }
4473
},
4474
diagnostic_scalar_field
4475
}|
4476
element aliased {
4477
generic_aliased_field
4478
}
4479
)
4480
}|
4481
## Background potential energy density:
4482
##
4483
## PE_b = rho*z_star
4484
##
4485
## where rho is the density, z_star is the isopycnal coordinate
4486
##
4487
## Limitations:
4488
## - Requires a constant gravity direction.
4489
## - The Density, PerturbationDensity and
4490
## GravitationalPotentialEnergyDensity fields must be on the
4491
## same mesh.
4492
element scalar_field {
4493
attribute rank { "0" },
4494
attribute name { "BackgroundPotentialEnergyDensity" },
4495
(
4496
element diagnostic {
4497
internal_algorithm,
4498
velocity_mesh_choice,
4499
diagnostic_scalar_field
4500
}|
4501
element aliased {
4502
generic_aliased_field
4503
}
4504
)
4505
}|
4506
4507
## Ertel potential vorticity:
4508
##
4509
## (f + curl u) dot grad rho'
4510
##
4511
## Limitations:
4512
## - Requires a geometry dimension of 3.
4513
element scalar_field {
4514
attribute rank { "0" },
4515
attribute name { "PotentialVorticity" },
4516
attribute depends { "Velocity,PerturbationDensity" },
4517
(
4518
element diagnostic {
4519
internal_algorithm,
4520
velocity_mesh_choice,
4521
diagnostic_scalar_field
4522
}|
4523
element aliased {
4524
generic_aliased_field
4525
}
4526
)
4527
}|
4528
## Relative potential vorticity:
4529
##
4530
## curl u dot grad rho'
4531
element scalar_field {
4532
attribute rank { "0" },
4533
attribute name { "RelativePotentialVorticity" },
4534
attribute depends { "Velocity,PerturbationDensity" },
4535
(
4536
element diagnostic {
4537
internal_algorithm,
4538
velocity_mesh_choice,
4539
diagnostic_scalar_field
4540
}|
4541
element aliased {
4542
generic_aliased_field
4543
}
4544
)
4545
}|
4546
## Local average mesh edge lengths
4547
element scalar_field {
4548
attribute rank { "0" },
4549
attribute name { "MeshEdgeLengths" },
4550
(
4551
element diagnostic {
4552
internal_algorithm,
4553
element mesh {
4554
attribute name { "CoordinateMesh" }
4555
},
4556
diagnostic_scalar_field
4557
}|
4558
element aliased {
4559
generic_aliased_field
4560
}
4561
)
4562
}|
4563
## Calculate the horizontal stream function psi where:
4564
## \partial_x \psi = -v
4565
## \partial_y \psi = u
4566
## where u and v are perpendicular to the gravity direction. Applies a
4567
## strong Dirichlet boundary condition of 0 on all boundaries.
4568
element scalar_field {
4569
attribute rank { "0" },
4570
attribute name { "HorizontalStreamFunction" },
4571
attribute depends { "Velocity" },
4572
(
4573
element diagnostic {
4574
internal_algorithm,
4575
velocity_mesh_choice,
4576
## Solver
4577
element solver {
4578
linear_solver_options_sym
4579
},
4580
diagnostic_scalar_field
4581
}|
4582
element aliased {
4583
generic_aliased_field
4584
}
4585
)
4586
}|
4587
## Speed:
4588
##
4589
## |u|
4590
##
4591
## Limitations:
4592
## - The Speed and Velocity fields must be on the same mesh.
4593
element scalar_field {
4594
attribute rank { "0" },
4595
attribute name { "Speed" },
4596
(
4597
element diagnostic {
4598
internal_algorithm,
4599
velocity_mesh_choice,
4600
diagnostic_scalar_field
4601
}|
4602
element aliased {
4603
generic_aliased_field
4604
}
4605
)
4606
}|
4607
4608
## Volume of the vehicles
4609
##
4610
## used in Traffic Modelling
4611
element scalar_field {
4612
attribute rank { "0" },
4613
attribute name { "SolidPhase" },
4614
attribute raplaces { "IDENT = -42"},
4615
(
4616
element diagnostic {
4617
internal_algorithm,
4618
velocity_mesh_choice,
4619
diagnostic_scalar_field
4620
}|
4621
element aliased {
4622
generic_aliased_field
4623
}
4624
)
4625
}|
4626
## Absolute Difference between two scalar fields.
4627
##
4628
## Both fields must be in this material_phase.
4629
## Assumes both fields are on the same mesh as the AbsoluteDifference field.
4630
element scalar_field {
4631
attribute rank { "0" },
4632
attribute name { "AbsoluteDifference" },
4633
(
4634
element diagnostic {
4635
internal_algorithm,
4636
attribute field_name_a { string },
4637
attribute field_name_b { string },
4638
mesh_choice,
4639
diagnostic_scalar_field,
4640
## Evaluate the absolute difference once the average difference has been removed?
4641
element relative_to_average {
4642
empty
4643
}?,
4644
## Ignore boundary nodes (i.e. zero them when calculating the difference)
4645
element ignore_boundaries {
4646
empty
4647
}?
4648
}|
4649
element aliased {
4650
generic_aliased_field
4651
}
4652
)
4653
}|
4654
4655
## Absolute Difference between two scalar fields.
4656
##
4657
## Both fields must be in this material_phase.
4658
## Assumes both fields are on the same mesh as the AbsoluteDifference field.
4659
element scalar_field {
4660
attribute rank { "0" },
4661
attribute name { "ScalarAbsoluteDifference" },
4662
(
4663
element diagnostic {
4664
internal_algorithm,
4665
attribute field_name_a { string },
4666
attribute field_name_b { string },
4667
mesh_choice,
4668
diagnostic_scalar_field,
4669
## Evaluate the absolute difference once the average difference has been removed?
4670
element relative_to_average {
4671
empty
4672
}?,
4673
## Ignore boundary nodes (i.e. zero them when calculating the difference)
4674
element ignore_boundaries {
4675
empty
4676
}?
4677
}|
4678
element aliased {
4679
generic_aliased_field
4680
}
4681
)
4682
}|
4683
## Galerkin projection of one field onto another mesh.
4684
##
4685
## The field must be in this material_phase.
4686
##
4687
## NOTE: you need the solver options if the mesh
4688
## of this field is continuous.
4689
element scalar_field {
4690
attribute rank { "0" },
4691
attribute name { "GalerkinProjection" },
4692
(
4693
element diagnostic {
4694
internal_algorithm,
4695
element source_field_name { string },
4696
mesh_choice,
4697
## Lump the mass matrix of the galerkin projection
4698
## less accurate but faster and might give smoother result.
4699
element lump_mass {
4700
empty
4701
}?,
4702
element solver {
4703
linear_solver_options_sym
4704
}?,
4705
diagnostic_scalar_field
4706
}|
4707
element aliased {
4708
generic_aliased_field
4709
}
4710
)
4711
}|
4712
## Primary production of Phytoplankton. This is calculated by
4713
## the ocean biology module and will not be calculated unless
4714
## ocean biology is being simulated.
4715
element scalar_field {
4716
attribute rank { "0" },
4717
attribute name { "PrimaryProduction" },
4718
(
4719
element diagnostic {
4720
internal_algorithm,
4721
velocity_mesh_choice,
4722
diagnostic_scalar_field
4723
}|
4724
element aliased {
4725
generic_aliased_field
4726
}
4727
)
4728
}|
4729
## Grazing of Phytoplankton by Zooplankton. This is calculated by
4730
## the ocean biology module and will not be calculated unless
4731
## ocean biology is being simulated.
4732
element scalar_field {
4733
attribute rank { "0" },
4734
attribute name { "PhytoplanktonGrazing" },
4735
(
4736
element diagnostic {
4737
internal_algorithm,
4738
velocity_mesh_choice,
4739
diagnostic_scalar_field
4740
}|
4741
element aliased {
4742
generic_aliased_field
4743
}
4744
)
4745
4746
}|
4747
element scalar_field {
4748
attribute rank { "0" },
4749
attribute name { "TidalRange" },
4750
attribute replaces { "IDENT = -32" },
4751
(
4752
element diagnostic {
4753
internal_algorithm,
4754
velocity_mesh_choice,
4755
diagnostic_scalar_field_tidal_range
4756
}|
4757
element aliased {
4758
generic_aliased_field
4759
}
4760
)
4761
}|
4762
element scalar_field {
4763
attribute rank { "0" },
4764
attribute name { "MaxFreeSurface" },
4765
attribute replaces { "IDENT = -33" },
4766
(
4767
element diagnostic {
4768
internal_algorithm,
4769
velocity_mesh_choice,
4770
diagnostic_scalar_field
4771
}|
4772
element aliased {
4773
generic_aliased_field
4774
}
4775
)
4776
}|
4777
element scalar_field {
4778
attribute rank { "0" },
4779
attribute name { "MinFreeSurface" },
4780
attribute replaces { "IDENT = -34" },
4781
(
4782
element diagnostic {
4783
internal_algorithm,
4784
velocity_mesh_choice,
4785
diagnostic_scalar_field
4786
}|
4787
element aliased {
4788
generic_aliased_field
4789
}
4790
)
4791
}|
4792
element scalar_field {
4793
attribute rank { "0" },
4794
attribute name { "HarmonicAmplitudeM2" },
4795
(
4796
element diagnostic {
4797
internal_algorithm,
4798
velocity_mesh_choice,
4799
diagnostic_scalar_field
4800
}|
4801
element aliased {
4802
generic_aliased_field
4803
}
4804
)
4805
}|
4806
element scalar_field {
4807
attribute rank { "0" },
4808
attribute name { "HarmonicPhaseM2" },
4809
(
4810
element diagnostic {
4811
internal_algorithm,
4812
velocity_mesh_choice,
4813
diagnostic_scalar_field
4814
}|
4815
element aliased {
4816
generic_aliased_field
4817
}
4818
)
4819
}|
4820
element scalar_field {
4821
attribute rank { "0" },
4822
attribute name { "HarmonicAmplitudeS2" },
4823
(
4824
element diagnostic {
4825
internal_algorithm,
4826
velocity_mesh_choice,
4827
diagnostic_scalar_field
4828
}|
4829
element aliased {
4830
generic_aliased_field
4831
}
4832
)
4833
}|
4834
element scalar_field {
4835
attribute rank { "0" },
4836
attribute name { "HarmonicPhaseS2" },
4837
(
4838
element diagnostic {
4839
internal_algorithm,
4840
velocity_mesh_choice,
4841
diagnostic_scalar_field
4842
}|
4843
element aliased {
4844
generic_aliased_field
4845
}
4846
)
4847
}|
4848
element scalar_field {
4849
attribute rank { "0" },
4850
attribute name { "HarmonicAmplitudeN2" },
4851
(
4852
element diagnostic {
4853
internal_algorithm,
4854
velocity_mesh_choice,
4855
diagnostic_scalar_field
4856
}|
4857
element aliased {
4858
generic_aliased_field
4859
}
4860
)
4861
}|
4862
element scalar_field {
4863
attribute rank { "0" },
4864
attribute name { "HarmonicPhaseN2" },
4865
(
4866
element diagnostic {
4867
internal_algorithm,
4868
velocity_mesh_choice,
4869
diagnostic_scalar_field
4870
}|
4871
element aliased {
4872
generic_aliased_field
4873
}
4874
)
4875
}|
4876
element scalar_field {
4877
attribute rank { "0" },
4878
attribute name { "HarmonicAmplitudeK2" },
4879
(
4880
element diagnostic {
4881
internal_algorithm,
4882
velocity_mesh_choice,
4883
diagnostic_scalar_field
4884
}|
4885
element aliased {
4886
generic_aliased_field
4887
}
4888
)
4889
}|
4890
element scalar_field {
4891
attribute rank { "0" },
4892
attribute name { "HarmonicPhaseK2" },
4893
(
4894
element diagnostic {
4895
internal_algorithm,
4896
velocity_mesh_choice,
4897
diagnostic_scalar_field
4898
}|
4899
element aliased {
4900
generic_aliased_field
4901
}
4902
)
4903
}|
4904
element scalar_field {
4905
attribute rank { "0" },
4906
attribute name { "HarmonicAmplitudeK1" },
4907
(
4908
element diagnostic {
4909
internal_algorithm,
4910
velocity_mesh_choice,
4911
diagnostic_scalar_field
4912
}|
4913
element aliased {
4914
generic_aliased_field
4915
}
4916
)
4917
}|
4918
element scalar_field {
4919
attribute rank { "0" },
4920
attribute name { "HarmonicPhaseK1" },
4921
(
4922
element diagnostic {
4923
internal_algorithm,
4924
velocity_mesh_choice,
4925
diagnostic_scalar_field
4926
}|
4927
element aliased {
4928
generic_aliased_field
4929
}
4930
)
4931
}|
4932
element scalar_field {
4933
attribute rank { "0" },
4934
attribute name { "HarmonicAmplitudeO1" },
4935
(
4936
element diagnostic {
4937
internal_algorithm,
4938
velocity_mesh_choice,
4939
diagnostic_scalar_field
4940
}|
4941
element aliased {
4942
generic_aliased_field
4943
}
4944
)
4945
}|
4946
element scalar_field {
4947
attribute rank { "0" },
4948
attribute name { "HarmonicPhaseO1" },
4949
(
4950
element diagnostic {
4951
internal_algorithm,
4952
velocity_mesh_choice,
4953
diagnostic_scalar_field
4954
}|
4955
element aliased {
4956
generic_aliased_field
4957
}
4958
)
4959
}|
4960
element scalar_field {
4961
attribute rank { "0" },
4962
attribute name { "HarmonicAmplitudeP1" },
4963
(
4964
element diagnostic {
4965
internal_algorithm,
4966
velocity_mesh_choice,
4967
diagnostic_scalar_field
4968
}|
4969
element aliased {
4970
generic_aliased_field
4971
}
4972
)
4973
}|
4974
element scalar_field {
4975
attribute rank { "0" },
4976
attribute name { "HarmonicPhaseP1" },
4977
(
4978
element diagnostic {
4979
internal_algorithm,
4980
velocity_mesh_choice,
4981
diagnostic_scalar_field
4982
}|
4983
element aliased {
4984
generic_aliased_field
4985
}
4986
)
4987
}|
4988
element scalar_field {
4989
attribute rank { "0" },
4990
attribute name { "HarmonicAmplitudeQ1" },
4991
(
4992
element diagnostic {
4993
internal_algorithm,
4994
velocity_mesh_choice,
4995
diagnostic_scalar_field
4996
}|
4997
element aliased {
4998
generic_aliased_field
4999
}
5000
)
5001
}|
5002
element scalar_field {
5003
attribute rank { "0" },
5004
attribute name { "HarmonicPhaseQ1" },
5005
(
5006
element diagnostic {
5007
internal_algorithm,
5008
velocity_mesh_choice,
5009
diagnostic_scalar_field
5010
}|
5011
element aliased {
5012
generic_aliased_field
5013
}
5014
)
5015
}|
5016
element scalar_field {
5017
attribute rank { "0" },
5018
attribute name { "HarmonicAmplitudeMf" },
5019
(
5020
element diagnostic {
5021
internal_algorithm,
5022
velocity_mesh_choice,
5023
diagnostic_scalar_field
5024
}|
5025
element aliased {
5026
generic_aliased_field
5027
}
5028
)
5029
}|
5030
element scalar_field {
5031
attribute rank { "0" },
5032
attribute name { "HarmonicPhaseMf" },
5033
(
5034
element diagnostic {
5035
internal_algorithm,
5036
velocity_mesh_choice,
5037
diagnostic_scalar_field
5038
}|
5039
element aliased {
5040
generic_aliased_field
5041
}
5042
)
5043
}|
5044
element scalar_field {
5045
attribute rank { "0" },
5046
attribute name { "HarmonicAmplitudeMm" },
5047
(
5048
element diagnostic {
5049
internal_algorithm,
5050
velocity_mesh_choice,
5051
diagnostic_scalar_field
5052
}|
5053
element aliased {
5054
generic_aliased_field
5055
}
5056
)
5057
}|
5058
element scalar_field {
5059
attribute rank { "0" },
5060
attribute name { "HarmonicPhaseMm" },
5061
(
5062
element diagnostic {
5063
internal_algorithm,
5064
velocity_mesh_choice,
5065
diagnostic_scalar_field
5066
}|
5067
element aliased {
5068
generic_aliased_field
5069
}
5070
)
5071
}|
5072
element scalar_field {
5073
attribute rank { "0" },
5074
attribute name { "HarmonicAmplitudeSSa" },
5075
(
5076
element diagnostic {
5077
internal_algorithm,
5078
velocity_mesh_choice,
5079
diagnostic_scalar_field
5080
}|
5081
element aliased {
5082
generic_aliased_field
5083
}
5084
)
5085
}|
5086
## Output the universal numbering of the mesh on which this field is based.
5087
element scalar_field {
5088
attribute rank { "0" },
5089
attribute name { "UniversalNumber" },
5090
(
5091
element diagnostic {
5092
internal_algorithm,
5093
mesh_choice,
5094
diagnostic_scalar_field
5095
}|
5096
element aliased {
5097
generic_aliased_field
5098
}
5099
)
5100
}|
5101
## Output the processors which own the nodes of the mesh on which this field is based.
5102
element scalar_field {
5103
attribute rank { "0" },
5104
attribute name { "NodeOwner" },
5105
(
5106
element diagnostic {
5107
internal_algorithm,
5108
mesh_choice,
5109
diagnostic_scalar_field
5110
}|
5111
element aliased {
5112
generic_aliased_field
5113
}
5114
)
5115
}|
5116
## Output the processors which own the elements of the mesh on which this field is based.
5117
element scalar_field {
5118
attribute rank { "0" },
5119
attribute name { "ElementOwner" },
5120
(
5121
element diagnostic {
5122
internal_algorithm,
5123
mesh_choice,
5124
diagnostic_scalar_field
5125
}|
5126
element aliased {
5127
generic_aliased_field
5128
}
5129
)
5130
}|
5131
## Primary production of Phytoplankton. This is calculated by
5132
## the ocean biology module and will not be calculated unless
5133
## ocean biology is being simulated.
5134
element scalar_field {
5135
attribute rank { "0" },
5136
attribute name { "HarmonicPhaseSSa" },
5137
(
5138
element diagnostic {
5139
internal_algorithm,
5140
velocity_mesh_choice,
5141
diagnostic_scalar_field
5142
}|
5143
element aliased {
5144
generic_aliased_field
5145
}
5146
)
5147
}
5148
5149
# Insert new diagnostic scalar fields here using the template:
5150
# element scalar_field {
5151
# attribute rank { "0" },
5152
# attribute name { "NewFieldName" },
5153
# (
5154
# element diagnostic {
5155
# internal_algorithm,
5156
# velocity_mesh_choice,
5157
# diagnostic_scalar_field
5158
# }|
5159
# element aliased {
5160
# generic_aliased_field
5161
# }
5162
# )
5163
# }
5164
)
5165
)
5166
5167
# This is the choice of additional vector field to be solved for
5168
vector_field_choice =
5169
(
5170
# The first is a generic field, which may be used for any user-defined field
5171
# that FLUIDITY knows nothing about, or a generic diagnostic
5172
# Prognostic vector fields are not possible (other than velocity and those known fields below).
5173
(
5174
## Generic field variable (vector)
5175
element vector_field {
5176
attribute rank { "1" },
5177
attribute name { xsd:string },
5178
## Field type
5179
(
5180
element prescribed {
5181
mesh_choice,
5182
prescribed_vector_field
5183
}|
5184
element aliased {
5185
generic_aliased_field
5186
}|
5187
element diagnostic {
5188
vector_diagnostic_algorithms,
5189
velocity_mesh_choice,
5190
python_diagnostic_field_code?,
5191
diagnostic_vector_field
5192
}
5193
)
5194
}|
5195
#
5196
# -- List of fields that are primarily prognostic,
5197
# but can be aliased.
5198
# -- The list is in order of most frequently used.
5199
#
5200
## Prescribed vector fields below this
5201
element ___Prognostic_fields_below___ {
5202
empty
5203
}|
5204
5205
#
5206
# -- List of fields that are primarily prescribed,
5207
# but can be aliased. An example is Maximum bed shear stress.
5208
# -- The list is in order of most frequently used.
5209
#
5210
## Prescribed vector fields below this
5211
element ___Prescribed_fields_below___ {
5212
empty
5213
}|
5214
5215
## Gradient of a scalar field evaluated using the C gradient
5216
## matrix constructed using finite elements.
5217
## Field must be in this material_phase.
5218
element vector_field {
5219
attribute rank { "1" },
5220
attribute name { "FiniteElementGradient" },
5221
(
5222
element diagnostic {
5223
internal_algorithm,
5224
attribute field_name { string },
5225
mesh_choice,
5226
element integrate_gradient_by_parts {
5227
empty
5228
}?,
5229
diagnostic_gradient_vector_field
5230
}|
5231
element aliased {
5232
generic_aliased_field
5233
}
5234
)
5235
}|
5236
5237
## Gradient of a scalar field evaluated using the transpose
5238
## of the C^T divergence matrix constructed using finite
5239
## elements.
5240
## Field must be in this material_phase.
5241
element vector_field {
5242
attribute rank { "1" },
5243
attribute name { "FiniteElementDivergenceTransposed" },
5244
(
5245
element diagnostic {
5246
internal_algorithm,
5247
attribute field_name { string },
5248
mesh_choice,
5249
element integrate_divergence_by_parts {
5250
empty
5251
}?,
5252
diagnostic_gradient_vector_field
5253
}|
5254
element aliased {
5255
generic_aliased_field
5256
}
5257
)
5258
}|
5259
5260
## Relative vorticity field - curl of the velocity field
5261
element vector_field {
5262
attribute rank { "1" },
5263
attribute name { "Vorticity" },
5264
(
5265
element diagnostic {
5266
internal_algorithm,
5267
### Relative vorticity
5268
#element algorithm {
5269
# attribute name { "curl" },
5270
# attribute material_phase_support { "single" },
5271
# attribute source_field_name { "Velocity" }
5272
#},
5273
element mesh {
5274
attribute name { "VelocityMesh" }
5275
},
5276
diagnostic_vector_field
5277
}|
5278
element aliased {
5279
generic_aliased_field
5280
}
5281
)
5282
}|
5283
## Planetary vorticity
5284
##
5285
## Limitations:
5286
## - Requires geometry dimension of 3.
5287
element vector_field {
5288
attribute rank { "1" },
5289
attribute name { "PlanetaryVorticity" },
5290
(
5291
element diagnostic {
5292
internal_algorithm,
5293
velocity_mesh_choice,
5294
diagnostic_vector_field
5295
}|
5296
element aliased {
5297
generic_aliased_field
5298
}
5299
)
5300
}|
5301
## Absolute vorticity:
5302
##
5303
## f + curl u
5304
##
5305
## Limitations:
5306
## - Requires a geometry dimension of 3.
5307
element vector_field {
5308
attribute rank { "1" },
5309
attribute name { "AbsoluteVorticity" },
5310
attribute depends { "Velocity" },
5311
(
5312
element diagnostic {
5313
internal_algorithm,
5314
velocity_mesh_choice,
5315
diagnostic_vector_field
5316
}|
5317
element aliased {
5318
generic_aliased_field
5319
}
5320
)
5321
}|
5322
5323
## Gradient of a scalar field evaluated using the transpose
5324
## of the C^T matrix constructed using control volumes.
5325
## Field must be in this material_phase.
5326
element vector_field {
5327
attribute rank { "1" },
5328
attribute name { "ControlVolumeDivergenceTransposed" },
5329
(
5330
element diagnostic {
5331
internal_algorithm,
5332
attribute field_name { string },
5333
velocity_mesh_choice,
5334
diagnostic_cv_gradient_vector_field
5335
}|
5336
element aliased {
5337
generic_aliased_field
5338
}
5339
)
5340
}|
5341
## Full velocity in an
5342
## inner element SGS treatment of momentum
5343
##
5344
## Limitations:
5345
## - Requires a geometry dimension of 3.
5346
## - Requires inner element active for momentum
5347
element vector_field {
5348
attribute rank { "1" },
5349
attribute name { "InnerElementFullVelocity" },
5350
(
5351
element diagnostic {
5352
internal_algorithm,
5353
element mesh {
5354
attribute name { "InnerElementMesh" }
5355
},
5356
diagnostic_vector_field
5357
}|
5358
element aliased {
5359
generic_aliased_field
5360
}
5361
)
5362
}|
5363
## Vorticity of the full velocity in an
5364
## inner element SGS treatment of momentum
5365
##
5366
## Limitations:
5367
## - Requires a geometry dimension of 3.
5368
## - Requires inner element active for momentum
5369
element vector_field {
5370
attribute rank { "1" },
5371
attribute name { "InnerElementFullVorticity" },
5372
(
5373
element diagnostic {
5374
internal_algorithm,
5375
element mesh {
5376
attribute name { "InnerElementMesh" }
5377
},
5378
diagnostic_vector_field
5379
}|
5380
element aliased {
5381
generic_aliased_field
5382
}
5383
)
5384
}|
5385
## Vorticity of the SGS velocity in an
5386
## inner element SGS treatment of momentum
5387
##
5388
## Limitations:
5389
## - Requires a geometry dimension of 3.
5390
## - Requires inner element active for momentum
5391
element vector_field {
5392
attribute rank { "1" },
5393
attribute name { "InnerElementVorticity" },
5394
(
5395
element diagnostic {
5396
internal_algorithm,
5397
element mesh {
5398
attribute name { "InnerElementMesh" }
5399
},
5400
diagnostic_vector_field
5401
}|
5402
element aliased {
5403
generic_aliased_field
5404
}
5405
)
5406
}|
5407
## The continuous solution mapped to a discontinuous mesh
5408
##
5409
## Limitations:
5410
## - Requires a geometry dimension of 3.
5411
## - Requires inner element active for momentum
5412
element vector_field {
5413
attribute rank { "1" },
5414
attribute name { "DgMappedVelocity" },
5415
(
5416
element diagnostic {
5417
internal_algorithm,
5418
element mesh {
5419
attribute name { "InnerElementMesh" }
5420
},
5421
diagnostic_vector_field
5422
}|
5423
element aliased {
5424
generic_aliased_field
5425
}
5426
)
5427
}|
5428
## Vorticity of the DG mapped Velocity
5429
## Note vorticity is actually calculated over a DG field
5430
##
5431
## Limitations:
5432
## - Requires a geometry dimension of 3.
5433
## - Requires inner element active for momentum
5434
element vector_field {
5435
attribute rank { "1" },
5436
attribute name { "DgMappedVorticity" },
5437
(
5438
element diagnostic {
5439
internal_algorithm,
5440
element mesh {
5441
attribute name { "InnerElementMesh" }
5442
},
5443
diagnostic_vector_field
5444
}|
5445
element aliased {
5446
generic_aliased_field
5447
}
5448
)
5449
}|
5450
## Solid Velocity field. Used to generate the momentum source
5451
element vector_field {
5452
attribute rank { "1" },
5453
attribute replaces {"UTRAF,VTRAF,WTRAF"},
5454
attribute name { "SolidVelocity" },
5455
(
5456
element diagnostic {
5457
internal_algorithm,
5458
mesh_choice,
5459
diagnostic_vector_field
5460
}
5461
)
5462
}|
5463
## Same as Solid Velocity field but it is on the Particle mesh.
5464
## It is used to map the velocities coming from an external program like
5465
## FEMDEM or DEM to the fluid mesh.
5466
element vector_field {
5467
attribute rank { "1" },
5468
attribute name { "ParticleVector" },
5469
(
5470
element diagnostic {
5471
internal_algorithm,
5472
mesh_choice,
5473
diagnostic_vector_field
5474
}
5475
)
5476
}|
5477
## Same as Solid Velocity field but it is on the Particle mesh.
5478
## It is used to map the velocities coming from an external program like
5479
## FEMDEM or DEM to the fluid mesh.
5480
element vector_field {
5481
attribute rank { "1" },
5482
attribute name { "ParticleForce" },
5483
(
5484
element diagnostic {
5485
internal_algorithm,
5486
mesh_choice,
5487
diagnostic_vector_field
5488
}
5489
)
5490
}|
5491
5492
## Same as Solid Velocity field but it is on the Particle mesh.
5493
## It is used to map the velocities coming from an external program like
5494
## FEMDEM or DEM to the fluid mesh.
5495
element vector_field {
5496
attribute rank { "1" },
5497
attribute name { "SolidForce" },
5498
(
5499
element diagnostic {
5500
internal_algorithm,
5501
velocity_mesh_choice,
5502
diagnostic_vector_field
5503
}
5504
)
5505
}|
5506
element vector_field {
5507
attribute rank { "1" },
5508
attribute name { "VelocityPlotForSolids" },
5509
(
5510
element diagnostic {
5511
internal_algorithm,
5512
velocity_mesh_choice,
5513
diagnostic_vector_field
5514
}
5515
)
5516
}|
5517
## Same as Solid Velocity field but it is on the Particle mesh.
5518
## It is used to map the velocities coming from an external program like
5519
## FEMDEM or DEM to the fluid mesh.
5520
element vector_field {
5521
attribute rank { "1" },
5522
attribute name { "FunctionalGradient" },
5523
(
5524
element diagnostic {
5525
internal_algorithm,
5526
velocity_mesh_choice,
5527
diagnostic_vector_field
5528
}
5529
)
5530
}|
5531
## LinearMomentum field.
5532
## p = \rho*u
5533
## (where p is the linear momentum, \rho the density and u the velocity)
5534
element vector_field {
5535
attribute rank { "1" },
5536
attribute name { "LinearMomentum" },
5537
(
5538
element diagnostic {
5539
internal_algorithm,
5540
velocity_mesh_choice,
5541
diagnostic_vector_field
5542
}|
5543
element aliased {
5544
generic_aliased_field
5545
}
5546
)
5547
}|
5548
## Calculate the control volume auxiliary gradient for a particular field.
5549
## The related field must be a scalar field in this material_phase.
5550
element vector_field {
5551
attribute rank { "0" },
5552
attribute name { "ControlVolumeAuxiliaryGradient" },
5553
(
5554
element diagnostic {
5555
internal_algorithm,
5556
velocity_mesh_choice,
5557
attribute gradient_of_field { string },
5558
diagnostic_vector_field
5559
}|
5560
element aliased {
5561
generic_aliased_field
5562
}
5563
)
5564
}|
5565
## Calculate the dg (Bassi Rebay) auxiliary gradient for a particular field.
5566
## The related field must be a scalar field in this material_phase.
5567
element vector_field {
5568
attribute rank { "0" },
5569
attribute name { "DGAuxiliaryGradient" },
5570
(
5571
element diagnostic {
5572
internal_algorithm,
5573
velocity_mesh_choice,
5574
attribute gradient_of_field { string },
5575
diagnostic_vector_field
5576
}|
5577
element aliased {
5578
generic_aliased_field
5579
}
5580
)
5581
}|
5582
## Experimental geostrophic source field to be used in combination with
5583
## a free surface. Does not solve a vertical balance yet.
5584
element vector_field {
5585
attribute rank { "1" },
5586
attribute name { "GeostrophicSource" },
5587
(
5588
element diagnostic {
5589
internal_algorithm,
5590
mesh_choice,
5591
diagnostic_vector_field
5592
}
5593
)
5594
}|
5595
5596
## Absolute Difference between two vector fields.
5597
##
5598
## Both fields must be in this material_phase.
5599
## Assumes both fields are on the same mesh as the AbsoluteDifference field.
5600
element vector_field {
5601
attribute rank { "1" },
5602
attribute name { "AbsoluteDifference" },
5603
(
5604
element diagnostic {
5605
internal_algorithm,
5606
attribute field_name_a { string },
5607
attribute field_name_b { string },
5608
mesh_choice,
5609
diagnostic_vector_field
5610
}|
5611
element aliased {
5612
generic_aliased_field
5613
}
5614
)
5615
}|
5616
5617
## Absolute Difference between two vector fields.
5618
##
5619
## Both fields must be in this material_phase.
5620
## Assumes both fields are on the same mesh as the AbsoluteDifference field.
5621
element vector_field {
5622
attribute rank { "1" },
5623
attribute name { "VectorAbsoluteDifference" },
5624
(
5625
element diagnostic {
5626
internal_algorithm,
5627
attribute field_name_a { string },
5628
attribute field_name_b { string },
5629
mesh_choice,
5630
diagnostic_vector_field
5631
}|
5632
element aliased {
5633
generic_aliased_field
5634
}
5635
)
5636
}|
5637
5638
## Bed Shear Stress = density*drag_coeff*|u|*u
5639
##
5640
## at the moment this assumes the density and drag coefficients are constants.
5641
## This diagnostic vector field is only calculated over surface elements/nodes,
5642
## interior nodes will have zero value.
5643
element vector_field {
5644
attribute rank { "1" },
5645
attribute name { "BedShearStress" },
5646
(
5647
element diagnostic {
5648
internal_algorithm,
5649
velocity_mesh_choice,
5650
diagnostic_vector_field_bed_shear_stress
5651
}|
5652
element aliased {
5653
generic_aliased_field
5654
}
5655
)
5656
}|
5657
## Max Bed Shear Stress.
5658
##
5659
## Note that you need BedShearStress turned on for this to work.
5660
element vector_field {
5661
attribute rank { "1" },
5662
attribute name { "MaxBedShearStress" },
5663
(
5664
element diagnostic {
5665
internal_algorithm,
5666
velocity_mesh_choice
5667
#diagnostic_vector_field_max_bed_shear_stress
5668
}|
5669
element aliased {
5670
generic_aliased_field
5671
}
5672
),
5673
## This is the time after which the max operator is
5674
## applied to the bed shear stress.
5675
element spin_up_time {
5676
real
5677
}
5678
}|
5679
5680
## Displacement
5681
element vector_field {
5682
attribute rank { "1" },
5683
attribute name { "Displacement" },
5684
(
5685
element diagnostic {
5686
internal_algorithm,
5687
velocity_mesh_choice,
5688
diagnostic_vector_field
5689
}|
5690
element aliased {
5691
generic_aliased_field
5692
}
5693
)
5694
}|
5695
## Galerkin projection of one field onto another mesh.
5696
##
5697
## The field must be in this material_phase.
5698
##
5699
## NOTE: you need the solver options if the mesh
5700
## of this field is continuous.
5701
element vector_field {
5702
attribute rank { "1" },
5703
attribute name { "GalerkinProjection" },
5704
(
5705
element diagnostic {
5706
internal_algorithm,
5707
element source_field_name { string },
5708
mesh_choice,
5709
## Lump the mass matrix of the galerkin projection
5710
## less accurate but faster and might give smoother result.
5711
element lump_mass {
5712
empty
5713
}?,
5714
element solver {
5715
linear_solver_options_sym
5716
}?,
5717
diagnostic_vector_field
5718
}|
5719
element aliased {
5720
generic_aliased_field
5721
}
5722
)
5723
}|
5724
## Compute the imbalanced component of velocity,
5725
## that is,
5726
## u - u_bal
5727
## where u_bal is the velocity that puts the state in geostrophic
5728
## balance.
5729
## Note: if your VelocityMesh is continuous, then the solver option
5730
## is necessary.
5731
element vector_field {
5732
attribute rank { "1" },
5733
attribute name { "ImbalancedVelocity" },
5734
(
5735
element diagnostic {
5736
internal_algorithm,
5737
velocity_mesh_choice,
5738
element solver {
5739
linear_solver_options_sym
5740
}?,
5741
diagnostic_vector_field
5742
}|
5743
element aliased {
5744
generic_aliased_field
5745
}
5746
)
5747
}|
5748
## Compute the balanced component of velocity,
5749
## that is, the velocity that puts the state in geostrophic
5750
## balance.
5751
## This diagnostic depends on ImbalancedVelocity.
5752
element vector_field {
5753
attribute rank { "1" },
5754
attribute name { "BalancedVelocity" },
5755
(
5756
element diagnostic {
5757
internal_algorithm,
5758
velocity_mesh_choice,
5759
diagnostic_vector_field
5760
}|
5761
element aliased {
5762
generic_aliased_field
5763
}
5764
)
5765
}
5766
5767
# Insert new diagnostic vector field here using the template:
5768
# element vector_field {
5769
# attribute rank { "1" },
5770
# attribute name { "NewFieldName" },
5771
# (
5772
# element diagnostic {
5773
# internal_algorithm,
5774
# mesh_choice,
5775
# diagnostic_vector_field
5776
# }|
5777
# element aliased {
5778
# generic_aliased_field
5779
# }
5780
# )
5781
# }
5782
)
5783
)
5784
5785
# This is the choice of additional tensor fields
5786
tensor_field_choice =
5787
(
5788
# The first is a generic field, which may be used for any user-defined field
5789
# that FLUIDITY knows nothing about, or a generic diagnostic
5790
# Prognostic tensor fields are not possible.
5791
(
5792
## Generic field variable (tensor)
5793
element tensor_field {
5794
attribute rank { "2" },
5795
attribute name { xsd:string },
5796
## Field type
5797
(
5798
element prescribed {
5799
mesh_choice,
5800
prescribed_tensor_field
5801
}|
5802
element aliased {
5803
generic_aliased_field
5804
}|
5805
element diagnostic {
5806
tensor_diagnostic_algorithms,
5807
velocity_mesh_choice,
5808
python_diagnostic_field_code?,
5809
diagnostic_tensor_field
5810
}
5811
)
5812
}|
5813
#
5814
# -- Second is a list of tensor fields that are primarily prescribed,
5815
# but can be aliased.
5816
# -- The list is in order of most frequently used.
5817
#
5818
## Prescribed scalar fields below this
5819
element ___Prescribed_fields_below___ {
5820
empty
5821
}|
5822
5823
## MaterialViscosity field:
5824
##
5825
## Field for the viscosity of this material.
5826
## Required if using a diagnostic bulk viscosity
5827
## in a multimaterial simulation.
5828
element tensor_field {
5829
attribute rank { "2" },
5830
attribute name { "MaterialViscosity" },
5831
(
5832
element prescribed {
5833
mesh_choice,
5834
prescribed_tensor_field
5835
}|
5836
element aliased {
5837
generic_aliased_field
5838
}
5839
)
5840
}|
5841
5842
element tensor_field {
5843
attribute rank { "2" },
5844
attribute name { "MaterialElasticity" },
5845
(
5846
element prescribed {
5847
mesh_choice,
5848
prescribed_tensor_field
5849
}|
5850
element aliased {
5851
generic_aliased_field
5852
}
5853
)
5854
}|
5855
5856
#
5857
# Insert new prescribed tensor fields here using the template:
5858
# element tensor_field {
5859
# attribute rank { "2" },
5860
# attribute name { "NewFieldName" },
5861
# (
5862
# element prescribed {
5863
# mesh_choice,
5864
# prescribed_tensor_field
5865
# }|
5866
# element aliased {
5867
# generic_aliased_field
5868
# }
5869
# )
5870
# }|
5871
#
5872
# -- Last is a list of fields that are primarily diagnostic,
5873
# but can be aliased.
5874
# -- The list is in order of most frequently used.
5875
#
5876
## Diagnostic tensor fields below this
5877
element ___Diagnostic_Fields_Below___ {
5878
empty
5879
}|
5880
## From a field on a mesh, diagnose the anisotropic
5881
## interpolation weight that would give the mesh back.
5882
## It is computed as:
5883
## \Eps = M^-1 |H|
5884
element tensor_field {
5885
attribute rank { "2" },
5886
attribute name { "FieldTolerance" },
5887
(
5888
element diagnostic {
5889
internal_algorithm,
5890
element source_field_name { string },
5891
velocity_mesh_choice,
5892
diagnostic_tensor_field
5893
}|
5894
element aliased {
5895
generic_aliased_field
5896
}
5897
)
5898
}
5899
5900
# Insert new diagnostic tensor field here using the template:
5901
# element tensor_field {
5902
# attribute name { "NewFieldName" },
5903
# (
5904
# element diagnostic {
5905
# internal_algorithm,
5906
# mesh_choice,
5907
# diagnostic_tensor_field
5908
# }|
5909
# element aliased {
5910
# generic_aliased_field
5911
# }
5912
# )
5913
# }
5914
)
5915
)
5916
5917
mesh_info =
5918
(
5919
## Read mesh from file.
5920
element from_file {
5921
(
5922
## Triangle mesh format.
5923
##
5924
## Enter the base name without the .edge .ele, .face or
5925
## .node extensions, and without process numbers.
5926
element format {
5927
attribute name { "triangle" },
5928
# string_value elements are used only for backwards compatibility - any new format choices should NOT have these
5929
element string_value {
5930
"triangle"
5931
},
5932
comment
5933
}|
5934
## Read the mesh from a vtu. Note that the mesh will have no surface
5935
## or region IDs.
5936
element format {
5937
attribute name { "vtu" },
5938
comment
5939
}|
5940
## CGNS mesh format (not yet implemented)
5941
element format {
5942
attribute name { "cgns" },
5943
# string_value elements are used only for backwards compatibility - any new format choices should NOT have these
5944
element string_value {
5945
"cgns"
5946
},
5947
comment
5948
}
5949
),
5950
attribute file_name { xsd:string },
5951
from_file_mesh_stat_options,
5952
comment
5953
}|
5954
## Make mesh from existing mesh. The existing mesh cannot itself
5955
## be made from an existing mesh (i.e. it must be read from a
5956
## file).
5957
element from_mesh {
5958
mesh_choice,
5959
element mesh_shape {
5960
element polynomial_degree {
5961
integer
5962
}
5963
}?,
5964
element mesh_continuity {
5965
element string_value{
5966
"continuous" | "discontinuous"
5967
}
5968
}?,
5969
## Make mesh periodic
5970
element periodic_boundary_conditions {
5971
attribute name { xsd:string },
5972
## List of boundary ids that are aliased to
5973
element physical_boundary_ids {
5974
integer_vector
5975
},
5976
## List of boundary ids that are aliased
5977
element aliased_boundary_ids {
5978
integer_vector
5979
},
5980
## Python code which takes coordinate of an aliased
5981
## boundary node and returns the coordinate of a physical
5982
## boundary node
5983
element coordinate_map {
5984
python_code
5985
}
5986
}*,
5987
## Extrude a horizontal (1D or 2D) mesh in the vertical
5988
element extrude {
5989
## Depth over which to extrude
5990
## top will be at z=0
5991
## bottom will be at z=-bottom_depth
5992
element bottom_depth {
5993
real
5994
},
5995
## Constant or function to specify the depth of the
5996
## layers. The function is a function of all coordinates
5997
## (so in 2+1D: x,y and z) to specify a layer depth that
5998
## varies both in the horizontal as in the vertical.
5999
element sizing_function {
6000
input_choice_real
6001
},
6002
## surface_id to assign to the top of the extruded mesh
6003
element top_surface_id {
6004
integer
6005
}?,
6006
## surface_id to assign to the bottom of the extruded mesh
6007
element bottom_surface_id {
6008
integer
6009
}?
6010
}?,
6011
derived_mesh_stat_options,
6012
comment
6013
}
6014
)
6015
6016
# Options for inclusion/exclusion of mesh statistics from the .stat file
6017
include_mesh_in_stat =
6018
(
6019
## Include this mesh in the .stat file
6020
element include_in_stat {
6021
comment
6022
}
6023
)
6024
exclude_mesh_from_stat =
6025
(
6026
## Exclude this mesh from the .stat file
6027
element exclude_from_stat {
6028
comment
6029
}
6030
)
6031
6032
# Diagnostic statistics options for meshed, with enabled by default
6033
mesh_stat_options_enabled_default = include_mesh_in_stat
6034
mesh_stat_options_enabled_default |= exclude_mesh_from_stat
6035
6036
# Diagnostic statistics options for meshed, with disabled by default
6037
mesh_stat_options_disabled_default = exclude_mesh_from_stat
6038
mesh_stat_options_disabled_default |= include_mesh_in_stat
6039
6040
from_file_mesh_stat_options =
6041
(
6042
## Specify what is added to .stat files
6043
element stat {
6044
mesh_stat_options_enabled_default
6045
}
6046
)
6047
derived_mesh_stat_options =
6048
(
6049
## Specify what is added to .stat files
6050
element stat {
6051
mesh_stat_options_disabled_default
6052
}
6053
)
6054
6055
linear_solver_options_asym =
6056
(
6057
## Iterative (Krylov) method to solve the linear discretised equation
6058
## Given are the most frequently used methods. The solution is done
6059
## by the PETSc library. Many more methods are provided.
6060
##
6061
(
6062
## GMRES
6063
##
6064
## Your safest bet for non-symmetric systems.
6065
element iterative_method {
6066
attribute name { "gmres" },
6067
## Restart value for gmres iteration
6068
## Higher values give better convergence but require more memory.
6069
## Suggested value: 30
6070
element restart {
6071
integer
6072
}
6073
}|
6074
## Conjugate gradient method
6075
##
6076
## Only works for symmetric systems.
6077
element iterative_method {
6078
attribute name { "cg" }
6079
}|
6080
## Direct method
6081
##
6082
## This is for non-iterative methods
6083
## Only makes sense in combination with preconditioners that do a complete solve, e.g. lu.
6084
element iterative_method {
6085
attribute name { "preonly" }
6086
}|
6087
## Richardson iteration
6088
##
6089
## Only apply preconditioner each iteration, no krylov acceleration
6090
element iterative_method {
6091
attribute name { "richardson" }
6092
}|
6093
## Other methods
6094
##
6095
## Any method provided by the PETSc library
6096
## http://www-unix.mcs.anl.gov/petsc/petsc-2/snapshots/petsc-dev/docs/manualpages/KSP/KSPType.html
6097
## (available methods may depend on the PETSc library installed on your system)
6098
element iterative_method {
6099
attribute name { xsd:string }
6100
}
6101
),
6102
## Preconditioner to be used in combination with the iterative method.
6103
(
6104
## Succesive Over-Relaxation
6105
##
6106
## This includes SSOR (symmetric sor)
6107
element preconditioner {
6108
attribute name { "sor" }
6109
}|
6110
## The Eisenstat method
6111
##
6112
## This preconditioner is equivalent to SOR but only uses
6113
## half the number of flops,
6114
## i.e. same convergence rate but twice as fast per
6115
## iteration. Because it computes
6116
## a different preconditioned residual the convergence in
6117
## practice may be quite different though.
6118
##
6119
## It does not work in parallel!
6120
element preconditioner {
6121
attribute name { "eisenstat" }
6122
}|
6123
## Incomplete LU decomposition
6124
element preconditioner {
6125
attribute name { "ilu" }
6126
}|
6127
## LU direct solver
6128
##
6129
## This performs a complete, direct solve of the equation and should only be used in combination with preonly as iterative method.
6130
element preconditioner {
6131
attribute name { "lu" }
6132
}|
6133
## Fluidity`s own multigrid method
6134
##
6135
## Especially suited for ill-conditioned, large aspect ratio problems.
6136
element preconditioner {
6137
attribute name { "mg" }
6138
}|
6139
## Prometheus multigrid method
6140
element preconditioner {
6141
attribute name { "prometheus" }
6142
}|
6143
## Hypre preconditioners (includes boomeramg)
6144
element preconditioner {
6145
attribute name { "hypre" },
6146
(
6147
## BoomerAMG multigrid method
6148
element hypre_type {
6149
attribute name { "boomeramg" }
6150
}|
6151
## Other Hypre preconditioners
6152
element hypre_type {
6153
attribute name { string }
6154
}
6155
)
6156
}|
6157
## Complete solve
6158
##
6159
## This only makes sense for solves where a different approximated preconditioner
6160
## matrix is provided. For instance when solving pressure with the
6161
## option full_schur_complement and using a masslumped schur complement
6162
## as preconditioner matrix.
6163
##
6164
## NOTE: If you are using a krylov method (cg/gmres) for this preconditioner
6165
## solve you either need to set your tolerances much stricter for it
6166
## than in the outer solve (so that the preconditioner is close to an
6167
## exact matrix inversion), or use fgmres in the outer solve.
6168
element preconditioner {
6169
attribute name { "ksp" },
6170
(
6171
## Solver options for the full solve done by this preconditioner
6172
element solver {
6173
pc_ksp_solver_options
6174
}
6175
)
6176
}|
6177
## Other preconditioners
6178
##
6179
## Any preconditioner provided by the PETSc library
6180
## http://www-unix.mcs.anl.gov/petsc/petsc-2/snapshots/petsc-dev/docs/manualpages/PC/PCType.html
6181
## (available preconditiors may depend on the PETSc library installed on your system)
6182
element preconditioner {
6183
attribute name { string }
6184
}
6185
),
6186
generic_solver_options
6187
)
6188
6189
linear_solver_options_sym =
6190
(
6191
## Iterative (Krylov) method to solve the linear discretised equation
6192
## Given are the most frequently used methods. The solution is done
6193
## by the PETSc library. Many more methods are provided.
6194
##
6195
(
6196
## Conjugate gradient method
6197
##
6198
## Only works for symmetric systems.
6199
element iterative_method {
6200
attribute name { "cg" }
6201
}|
6202
## GMRES
6203
##
6204
## Your safest bet for non-symmetric systems.
6205
element iterative_method {
6206
attribute name { "gmres" },
6207
## Restart value for gmres iteration
6208
## Higher values give better convergence but require more memory.
6209
## Suggested value: 30
6210
element restart {
6211
integer
6212
}
6213
}|
6214
## Direct method
6215
##
6216
## This is for non-iterative methods
6217
## Only makes sense in combination with preconditioners that do a complete solve, e.g. lu.
6218
element iterative_method {
6219
attribute name { "preonly" }
6220
}|
6221
## Richardson iteration
6222
##
6223
## Only apply preconditioner each iteration, no krylov acceleration
6224
element iterative_method {
6225
attribute name { "richardson" }
6226
}|
6227
## Other methods
6228
##
6229
## Any method provided by the PETSc library
6230
## http://www-unix.mcs.anl.gov/petsc/petsc-2/snapshots/petsc-dev/docs/manualpages/KSP/KSPType.html
6231
## (available methods may depend on the PETSc library installed on your system)
6232
element iterative_method {
6233
attribute name { xsd:string }
6234
}
6235
),
6236
## Preconditioner to be used in combination with the iterative method.
6237
(
6238
## Succesive Over-Relaxation
6239
##
6240
## This includes SSOR (symmetric sor)
6241
element preconditioner {
6242
attribute name { "sor" }
6243
}|
6244
## The Eisenstat method
6245
##
6246
## This preconditioner is equivalent to SOR but only uses
6247
## half the number of flops,
6248
## i.e. same convergence rate but twice as fast per
6249
## iteration. Because it computes
6250
## a different preconditioned residual the convergence in
6251
## practice may be quite different though.
6252
## It does not work in parallel!
6253
element preconditioner {
6254
attribute name { "eisenstat" }
6255
}|
6256
## Incomplete LU decomposition
6257
element preconditioner {
6258
attribute name { "ilu" }
6259
}|
6260
## Incomplete Cholesky decomposition (only works for symmetric matrices)
6261
element preconditioner {
6262
attribute name { "icc" }
6263
}|
6264
## LU direct solver
6265
##
6266
## This performs a complete, direct solve of the equation and should only be used in combination with preonly as iterative method.
6267
element preconditioner {
6268
attribute name { "lu" }
6269
}|
6270
## Fluidity`s own multigrid method
6271
##
6272
## Especially suited for ill-conditioned, large aspect ratio problems.
6273
element preconditioner {
6274
attribute name { "mg" },
6275
## apply vertical lumping from the full mesh to the surface mesh
6276
## as the first coarsening step instead of the default
6277
## aggregation method.
6278
element vertical_lumping {
6279
## Does additional smoothing by solving the equation but with
6280
## a dirichilet boundary condition on top given by the last iteration
6281
## of the multigrid cycle. May be quite expensive per iteration
6282
## but improves the solution quite a lot for difficult meshes.
6283
element internal_smoother {
6284
empty
6285
}?
6286
}?
6287
}|
6288
## Prometheus multigrid method
6289
element preconditioner {
6290
attribute name { "prometheus" }
6291
}|
6292
## Hypre preconditioners (includes boomeramg)
6293
element preconditioner {
6294
attribute name { "hypre" },
6295
(
6296
## BoomerAMG multigrid method
6297
element hypre_type {
6298
attribute name { "boomeramg" }
6299
}|
6300
## Other Hypre preconditioners
6301
element hypre_type {
6302
attribute name { string }
6303
}
6304
)
6305
}|
6306
## Complete solve
6307
##
6308
## This only makes sense for solves where a different approximated preconditioner
6309
## matrix is provided. For instance when solving pressure with the
6310
## option full_schur_complement and using a masslumped schur complement
6311
## as preconditioner matrix.
6312
##
6313
## NOTE: If you are using a krylov method (cg/gmres) for this preconditioner
6314
## solve you either need to set your tolerances much stricter for it
6315
## than in the outer solve (so that the preconditioner is close to an
6316
## exact matrix inversion), or use fgmres in the outer solve.
6317
element preconditioner {
6318
attribute name { "ksp" },
6319
(
6320
## Solver options for the full solve done by this preconditioner
6321
element solver {
6322
pc_ksp_solver_options
6323
}
6324
)
6325
}|
6326
## Other preconditioners
6327
##
6328
## Any preconditioner provided by the PETSc library
6329
## http://www-unix.mcs.anl.gov/petsc/petsc-2/snapshots/petsc-dev/docs/manualpages/PC/PCType.html
6330
## (available preconditiors may depend on the PETSc library installed on your system)
6331
element preconditioner {
6332
attribute name { string }
6333
}
6334
),
6335
generic_solver_options
6336
)
6337
6338
# this is a copy linear_solver_options_sym, but with preconditioner "ksp"
6339
# removed to avoid infinite recursion
6340
pc_ksp_solver_options =
6341
(
6342
## Iterative (Krylov) method to solve the linear discretised equation
6343
## Given are the most frequently used methods. The solution is done
6344
## by the PETSc library. Many more methods are provided.
6345
##
6346
(
6347
## Conjugate gradient method
6348
##
6349
## Only works for symmetric systems.
6350
element iterative_method {
6351
attribute name { "cg" }
6352
}|
6353
## GMRES
6354
##
6355
## Your safest bet for non-symmetric systems.
6356
element iterative_method {
6357
attribute name { "gmres" },
6358
## Restart value for gmres iteration
6359
## Higher values give better convergence but require more memory.
6360
## Suggested value: 30
6361
element restart {
6362
integer
6363
}
6364
}|
6365
## Direct method
6366
##
6367
## This is for non-iterative methods
6368
## Only makes sense in combination with preconditioners that do a complete solve, e.g. lu.
6369
element iterative_method {
6370
attribute name { "preonly" }
6371
}|
6372
## Richardson iteration
6373
##
6374
## Only apply preconditioner each iteration, no krylov acceleration
6375
element iterative_method {
6376
attribute name { "richardson" }
6377
}|
6378
## Other methods
6379
##
6380
## Any method provided by the PETSc library
6381
## http://www-unix.mcs.anl.gov/petsc/petsc-2/snapshots/petsc-dev/docs/manualpages/KSP/KSPType.html
6382
## (available methods may depend on the PETSc library installed on your system)
6383
element iterative_method {
6384
attribute name { xsd:string }
6385
}
6386
),
6387
## Preconditioner to be used in combination with the iterative method.
6388
(
6389
## Succesive Over-Relaxation
6390
##
6391
## This includes SSOR (symmetric sor)
6392
element preconditioner {
6393
attribute name { "sor" }
6394
}|
6395
## The Eisenstat method
6396
##
6397
## This preconditioner is equivalent to SOR but only uses
6398
## half the number of flops,
6399
## i.e. same convergence rate but twice as fast per
6400
## iteration. Because it computes
6401
## a different preconditioned residual the convergence in
6402
## practice may be quite different though.
6403
## It does not work in parallel!
6404
element preconditioner {
6405
attribute name { "eisenstat" }
6406
}|
6407
## Incomplete LU decomposition
6408
element preconditioner {
6409
attribute name { "ilu" }
6410
}|
6411
## Incomplete Cholesky decomposition (only works for symmetric matrices)
6412
element preconditioner {
6413
attribute name { "icc" }
6414
}|
6415
## LU direct solver
6416
##
6417
## This performs a complete, direct solve of the equation and should only be used in combination with preonly as iterative method.
6418
element preconditioner {
6419
attribute name { "lu" }
6420
}|
6421
## Fluidity`s own multigrid method
6422
##
6423
## Especially suited for ill-conditioned, large aspect ratio problems.
6424
element preconditioner {
6425
attribute name { "mg" },
6426
## apply vertical lumping from the full mesh to the surface mesh
6427
## as the first coarsening step instead of the default
6428
## aggregation method.
6429
element vertical_lumping {
6430
## Does additional smoothing by solving the equation but with
6431
## a dirichilet boundary condition on top given by the last iteration
6432
## of the multigrid cycle. May be quite expensive per iteration
6433
## but improves the solution quite a lot for difficult meshes.
6434
element internal_smoother {
6435
empty
6436
}?
6437
}?
6438
}|
6439
## Prometheus multigrid method
6440
element preconditioner {
6441
attribute name { "prometheus" }
6442
}|
6443
## Hypre preconditioners (includes boomeramg)
6444
element preconditioner {
6445
attribute name { "hypre" },
6446
(
6447
## BoomerAMG multigrid method
6448
element hypre_type {
6449
attribute name { "boomeramg" }
6450
}|
6451
## Other Hypre preconditioners
6452
element hypre_type {
6453
attribute name { string }
6454
}
6455
)
6456
}|
6457
## Other preconditioners
6458
##
6459
## Any preconditioner provided by the PETSc library
6460
## http://www-unix.mcs.anl.gov/petsc/petsc-2/snapshots/petsc-dev/docs/manualpages/PC/PCType.html
6461
## (available preconditiors may depend on the PETSc library installed on your system)
6462
element preconditioner {
6463
attribute name { string }
6464
}
6465
),
6466
generic_solver_options
6467
)
6468
6469
generic_solver_options =
6470
(
6471
## Relative error
6472
##
6473
## The solver finishes if the preconditioned error becomes smaller than the original preconditioned error times this value.
6474
## Suggested value: 1.0e-7
6475
element relative_error {
6476
real
6477
},
6478
## Absolute error bound
6479
##
6480
## The solver finishes if the preconditioned error becomes smaller than this value.
6481
element absolute_error {
6482
real
6483
}?,
6484
## Maximum number of iterations allowed in the linear solver
6485
## before giving up.
6486
element max_iterations {
6487
integer
6488
},
6489
## Switch on to not use an initial guess from a previous solve but
6490
## start with a zero vector. Note that some of the solves always
6491
## start at zero in which case this switch will have no effect (see the log output).
6492
element start_from_zero {
6493
empty
6494
}?,
6495
## Remove Null-space from residual after applying preconditioner.
6496
## This often leads to better convergence rates, when compared to
6497
## imposing a reference_node to pin the solution.
6498
element remove_null_space {
6499
empty
6500
}?,
6501
## Miscellaneous PETSc options
6502
##
6503
## Any options not included above can be set using the PETSc option syntax
6504
## For example: -ksp_dtol 1e5 -ksp_monitor_draw
6505
element petsc_options {
6506
string
6507
}?,
6508
(
6509
## Solver failures are always treated as fatal errors. The
6510
## model stops at the end of the time step in order to allow
6511
## for the latest output to be written.
6512
element never_ignore_solver_failures {
6513
empty
6514
}|
6515
## Allow for an initial period in which solver failures
6516
## caused by non-convergence in the maximum number of
6517
## iterations are ignored.
6518
element ignore_non_convergence_during_spin_up {
6519
## As long as current_time < spin_up_time, solver failures
6520
## due to non-convergence in the maximum number of
6521
## iterations are ignored. This might be used for spinning
6522
## up the model. As there is no guarantee we're actually
6523
## solving the flow equations to any accuracy, the results
6524
## in this period should not be trusted.
6525
element spin_up_time {
6526
real
6527
}
6528
}|
6529
## Ignore all solver failures. This is a dangerous option
6530
## that should only be used in exceptional cases.
6531
element ignore_all_solver_failures {
6532
empty
6533
}
6534
),
6535
## Extra diagnostics to help debug solver problems
6536
element diagnostics {
6537
## Print out the norm of vectors and matrices before the
6538
## solve, and that of the solution vector afterwards.
6539
## Norms are printed at verbosity level 2, so run fluidity with -v2 or -v3
6540
element print_norms {
6541
empty
6542
}?,
6543
## Options to give extra information for each iteration of the
6544
## the solve. Some of those may really slow down your computation!
6545
element monitors {
6546
## Prints the preconditioned residual for each iteration of the solve.
6547
## This is the error estimation PETSc uses during the solve.
6548
element preconditioned_residual {
6549
empty
6550
}?,
6551
## Prints the "true" residual for each iteration of the solve,
6552
## i.e. PETSc computes the L2-norm of r=A-bx. This may mean
6553
## PETSc has to do extra computations.
6554
element true_residual {
6555
empty
6556
}?,
6557
## Draws a graph over the convergence of the preconditioned residual
6558
## during the solve. This option only works for systems where PETSc
6559
## has been linked with the X library.
6560
element preconditioned_residual_graph {
6561
empty
6562
}?,
6563
## Prints the error by computing the difference with the provided
6564
## exact solution each time step.
6565
element true_error {
6566
## Give the field name of the field that contains the exact
6567
## solution to be compared with each iteration
6568
attribute exact_solution_field {
6569
string
6570
}
6571
}?
6572
}
6573
}
6574
)
6575
6576
6577
input_choice_tensor_field =
6578
(
6579
(
6580
## An isotropic tensor, i.e.
6581
## one with no directional variation.
6582
## Can be represented as a scalar real.
6583
element isotropic {
6584
input_choice_real
6585
}|
6586
## A symmetric tensor, i.e.
6587
## A^T = A
6588
element anisotropic_symmetric {
6589
input_choice_real_dim_symmetric_tensor
6590
}|
6591
## A general asymmetric tensor.
6592
element anisotropic_asymmetric {
6593
input_choice_real_dim_tensor
6594
}
6595
)
6596
)
6597
6598
constitutive_laws =
6599
(
6600
(
6601
## Constitutive laws for fluids
6602
element constitutive_law {
6603
attribute name { "fluid" }
6604
}|
6605
## Constitutive laws for solids
6606
element constitutive_law {
6607
attribute name { "solid" }
6608
}
6609
)
6610
)
6611
6612
region_ids =
6613
(
6614
## Optional region ids to associate different values
6615
## to different regions of the mesh.
6616
## Leave unselected if you`re not using multiple regions or
6617
## region_ids.
6618
## Currently only works with triangle files created by gmsh2triangle.
6619
element region_ids {
6620
integer_vector
6621
}?
6622
)
6623
6624
temporal_control_volume_options =
6625
(
6626
## Temporal discretisation options that are only relevant if a control volume or mixed control volume - continuous galerkin spatial discretisation is selected for this field.
6627
element control_volumes {
6628
## Number of iterations within an advection solve.
6629
## This increases the accuracy of the face values and ensures that
6630
## the pivoted solution is cancelled out.
6631
## Defaults to 1 if unselected.
6632
element number_advection_iterations {
6633
attribute replaces { "INT(ABS(NDISOT)/10)" },
6634
integer,
6635
## Cut short advection_iterations if the specified tolerance
6636
## is reached.
6637
## This only works for pure control volume discretisations.
6638
element tolerance {
6639
real,
6640
(
6641
## Select the norm with which you want the tolerance to be tested.
6642
##
6643
## The infinity norm.
6644
element infinity_norm {
6645
empty
6646
}|
6647
## Select the norm with which you want the tolerance to be tested.
6648
##
6649
## The l2 norm.
6650
element l2_norm {
6651
empty
6652
}|
6653
## Select the norm with which you want the tolerance to be tested.
6654
##
6655
## The l2 norm evaluated on a control volume mesh.
6656
element cv_l2_norm {
6657
empty
6658
}
6659
)
6660
}?
6661
}?,
6662
(
6663
## Use timestep subcycling to solve this equation.
6664
## Specify the maximum courant number per subcycle.
6665
## This only works for pure control volume discretisations.
6666
element maximum_courant_number_per_subcycle {
6667
real,
6668
field_based_cfl_number_options
6669
}|
6670
## Use timestep subcycling to solve this equation.
6671
## Specify the number of subcycles.
6672
## This only works for pure control volume discretisations.
6673
element number_advection_subcycles {
6674
integer
6675
}
6676
)?,
6677
## Only works if a control volume or mixed control volume -
6678
## continuous galerkin spatial discretisation is selected.
6679
## If not active then the theta specified above will be used.
6680
## Otherwise use variable limited theta on individual faces.
6681
element limit_theta {
6682
attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 1,3,5,7,9 (odd)" },
6683
empty
6684
}?,
6685
## Only works if a control volume or mixed control volume -
6686
## continuous galerkin spatial discretisation is selected.
6687
## Time discretisation of upwind discretisation off which the
6688
## higher order solution is pivotted.
6689
## - pivot_theta = 1 - implicit pivot (default if not set and
6690
## best choice if not intentionally modifying
6691
## scheme to be explicit)
6692
## - pivot_theta = 0 - explicit pivot
6693
element pivot_theta {
6694
real
6695
}?
6696
}
6697
)
6698
6699
temporal_discontinuous_galerkin_options =
6700
(
6701
## This enables DG-specific timestepping options, such as
6702
## explicit advection subcycling.
6703
element discontinuous_galerkin {
6704
(
6705
## Use timestep subcycling to solve this equation.
6706
## Specify the maximum courant number per subcycle.
6707
element maximum_courant_number_per_subcycle {
6708
real
6709
}|
6710
## Use timestep subcycling to solve this equation.
6711
## Specify the number of subcycles.
6712
element number_advection_subcycles {
6713
integer
6714
}
6715
)?
6716
}
6717
)
6718
6719
legacy_mixed_cv_cg_options =
6720
(
6721
## Use a mixed control volume - continuous galerkin
6722
## discretisation.
6723
##
6724
## This uses a control volume discretisation of the advective
6725
## terms and a continuous galerkin representation of the
6726
## diffusion, source and absorption terms.
6727
## Clearly, in terms of discretisation this does the same thing
6728
## as a pure control volume discretisation if diffusion terms
6729
## are zero.
6730
## However it still follows a partially legacy code path.
6731
element legacy_mixed_cv_cg {
6732
attribute replaces { "NDISOT >= 10, DISOTT = -7, TLUMP = .TRUE." },
6733
spatial_control_volume_options,
6734
6735
## Allows legacy options to be set.
6736
## BE WARNED: this probably means you're using inconsistent discretisations
6737
## on different terms - make sure you're happy with what your code path is doing
6738
## before selecting this.
6739
element legacy_disott {
6740
attribute replaces { "DISOTT" },
6741
integer
6742
}?
6743
}
6744
)
6745
6746
pure_cv_options =
6747
(
6748
## Use a pure control volume discretisations.
6749
## Follows a new control volume code path.
6750
element control_volumes {
6751
spatial_control_volume_options,
6752
(
6753
## Use the gradient of the field constructed using the
6754
## basis functions of the parent finite element mesh to
6755
## form the divergence.
6756
##
6757
## DOES NOT CURRENTLY WORK WITH ROBIN OR WEAK DIRICHLET BOUNDARY CONDITIONS!
6758
##
6759
## Based on schemes in Handbook of Numerical Analysis,
6760
## P.G. Ciarlet, J.L. Lions eds, vol 7, pp 713-1020
6761
element diffusion_scheme {
6762
attribute name{"ElementGradient"}
6763
}|
6764
## Use an auxiliary gradient equation to find the gradient of the field.
6765
##
6766
## DOES NOT CURRENTLY WORK WITH ROBIN BOUNDARY CONDITIONS!
6767
##
6768
## Based on scheme proposed in Bassi, F. & Rebay, S., A
6769
## high-order accurate discontinuous finite element method
6770
## for the numerical solution of the compressible
6771
## Navier-Stokes equations, Journal Of Computational
6772
## Physics, 1997, 131, 267-279
6773
element diffusion_scheme {
6774
attribute name{"BassiRebay"}
6775
}
6776
)
6777
}
6778
)
6779
6780
coupled_cv_options =
6781
(
6782
## Use a pure control volume discretisations with face value
6783
## restrictions between different fields in different material_phases.
6784
##
6785
## THIS DOES NOT WORK WITH DIFFUSION!
6786
##
6787
## Follows a new control volume code path.
6788
element coupled_cv {
6789
coupled_spatial_control_volume_options,
6790
## Set the maximum and minimum bounds for the sum up to and including this field.
6791
## This defines the limiter used to enforce boundedness on this field.
6792
element parent_sum {
6793
element target_maximum {
6794
real
6795
},
6796
element target_minimum {
6797
real
6798
}
6799
}
6800
}
6801
)
6802
6803
spatial_control_volume_options = standard_control_volume_options
6804
spatial_control_volume_options |= compressive_control_volume_options
6805
6806
standard_control_volume_options =
6807
(
6808
## First Order Upwind face value discretisation
6809
## face_value = donor_value,
6810
## where
6811
## donor_value = income*val_1 + (1.-income)*val_2,
6812
## where val_i is the value on the ith node neighbouring the face and
6813
## income = [0, 1] depending on whether the flow is coming from node 1 or 2
6814
## First order upwinding is monotonic so no limiting is ever required
6815
element face_value {
6816
attribute name { "FirstOrderUpwind" },
6817
attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 0,1" },
6818
empty
6819
}|
6820
## Trapezoidal face value discretisation
6821
## face_value = 0.5*(val_1 + val_2),
6822
## where
6823
## val_i is the value on the ith node neighbouring the face
6824
##
6825
## Trapezoidal discretisation is unbounded so limiting is compulsory
6826
element face_value {
6827
attribute name { "Trapezoidal" },
6828
attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 2,3" },
6829
limiter_options
6830
}|
6831
## Finite Element face value discretisation
6832
## face_value = finite element interpolation from surrounding nodes
6833
##
6834
## Finite element discretisation may become unbounded so limiting is often necessary.
6835
element face_value {
6836
attribute name { "FiniteElement" },
6837
attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 4,5,6,7" },
6838
limiter_options?
6839
}
6840
)
6841
6842
coupled_spatial_control_volume_options = coupled_control_volume_options
6843
coupled_spatial_control_volume_options |= compressive_control_volume_options
6844
6845
# coupled control volume options are the same as the standard ones (annoyingly copied and pasted)
6846
# except that firstorderupwind gets limiter options
6847
coupled_control_volume_options =
6848
(
6849
## First Order Upwind face value discretisation
6850
## face_value = donor_value,
6851
## where
6852
## donor_value = income*val_1 + (1.-income)*val_2,
6853
## where val_i is the value on the ith node neighbouring the face and
6854
## income = [0, 1] depending on whether the flow is coming from node 1 or 2
6855
## First order upwinding is monotonic so no limiting is ever required
6856
element face_value {
6857
attribute name { "FirstOrderUpwind" },
6858
attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 0,1" },
6859
limiter_options?
6860
}|
6861
## Trapezoidal face value discretisation
6862
## face_value = 0.5*(val_1 + val_2),
6863
## where
6864
## val_i is the value on the ith node neighbouring the face
6865
##
6866
## Trapezoidal discretisation is unbounded so limiting is compulsory
6867
element face_value {
6868
attribute name { "Trapezoidal" },
6869
attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 2,3" },
6870
limiter_options
6871
}|
6872
## Finite Element face value discretisation
6873
## face_value = finite element interpolation from surrounding nodes
6874
##
6875
## Finite element discretisation may become unbounded so limiting is often necessary.
6876
element face_value {
6877
attribute name { "FiniteElement" },
6878
attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 4,5,6,7" },
6879
limiter_options?
6880
}
6881
)
6882
6883
compressive_control_volume_options =
6884
(
6885
## HyperC face value discretisation
6886
##
6887
## face_value calculated from upper bound of explicit TVD zone of NVD diagram
6888
## Normally used for MaterialVolumeFraction fields
6889
element face_value {
6890
attribute name { "HyperC" },
6891
attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 8,9" },
6892
upwind_value_options?,
6893
cv_face_cfl_number_options
6894
}|
6895
## UltraC face value discretisation
6896
##
6897
## face_value calculated from extended upper bound of
6898
## explicit TVD zone of NVD diagram assuming
6899
## values bounded by target_maximum and target_minimum.
6900
element face_value {
6901
attribute name { "UltraC" },
6902
attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 8,9, with ULTRAC = TRUE from solidity_options.inp" },
6903
## Specifiy the upper bound which UltraC will use to
6904
## calculate the maximum flux.
6905
element target_maximum {
6906
real
6907
},
6908
## Specifiy the lower bound which UltraC will use to
6909
## calculate the minimum flux.
6910
element target_minimum {
6911
real
6912
},
6913
upwind_value_options?,
6914
cv_face_cfl_number_options
6915
}|
6916
## **UNDER TESTING**
6917
##
6918
## PotentialUltraC face value discretisation
6919
##
6920
## face_value calculated from extended upper bound of
6921
## explicit TVD zone of NVD diagram if potential
6922
## value of field is sufficient (as specified by
6923
## target_maximum) to ensure the correct front advection
6924
## velocity.
6925
##
6926
## If not then either switch to HyperC or use a modified flux
6927
## based on the potential function.
6928
element face_value {
6929
attribute name { "PotentialUltraC" },
6930
## Specifiy the upper bound which PotentialUltraC will use
6931
## to calculate the maximum flux if the potential function
6932
## value is sufficient to maintain the correct front
6933
## advection velocity.
6934
element target_maximum {
6935
real
6936
},
6937
## Specifiy the lower bound which PotentialUltraC will use to calculate the minimum flux.
6938
element target_minimum {
6939
real
6940
},
6941
(
6942
## Select what PotentialUltraC should do if the
6943
## potential function value does not reach the required
6944
## value specified by the target_maximum.
6945
##
6946
## Switch to using HyperC face values. This ensures
6947
## that the advection velocity is correct however may
6948
## create isolated regions beneath the target_maximum.
6949
element switch_to_hyperc {
6950
empty
6951
}|
6952
## Select what PotentialUltraC should do if the
6953
## potential function value does not reach the required
6954
## value specified by the target_maximum.
6955
##
6956
## Modify the maximum nodal values (both downwind and
6957
## upwind) so that the fluxes are at their maximum
6958
## possible without affecting the front advection
6959
## velocity.
6960
element use_potential_flux {
6961
empty
6962
}
6963
),
6964
upwind_value_options?,
6965
cv_face_cfl_number_options
6966
}
6967
)
6968
6969
#Select the type of dynamic control to be used
6970
#Note: DEM and FEMDEM require the respective libraries
6971
#to be compiled.
6972
input_solid_dynamics_choice =
6973
(
6974
## Obtain values from point and radius file.
6975
##
6976
## First line of file is free to use (for comments)
6977
## Second line must contain the number of particles
6978
## Third and fourth line are again for comments.
6979
## Following lines include 10 columns, corresponding to
6980
## the particle's x, y, and z positions, followed by the radius, then
6981
## velocities in x, y, and z directions, followed by angular velocities
6982
## in the x, y, and z directions.
6983
element dynamic_type {
6984
attribute name {"from_input_file"},
6985
attribute file_name {xsd:string}
6986
}|
6987
## Two python scripts must be provided. The script is cycled over each particle.
6988
## One script for particle position (output is tuple of position coords)
6989
## Second script is for particle radius (output is tuple of position coords)
6990
## Third script is for particle translational velocity.
6991
## Fourth script is for particle angular velocity. (Note: particles
6992
## have a no slip boundary condition at the surface, so this angular velocity
6993
## WILL matter to the flow.)
6994
## Python functions should be of the form:
6995
## def val(X, t):
6996
## Function code
6997
## return # Return value
6998
## where X is a tuple of length geometry dimension.
6999
## X[0] contains the number of the particle (in real format)
7000
element dynamic_type {
7001
attribute name {"python_script"}
7002
}|
7003
element dynamic_type {
7004
attribute name {"use_simple_dynamics"},
7005
element set_bottom{real},
7006
element set_xmin{real},
7007
element set_ymin{real},
7008
element set_zmin{real},
7009
element set_xmax{real},
7010
element set_ymax{real},
7011
element set_zmax{real}
7012
}|
7013
## Using y3D to model dynamics. Filename of input file for y3D must
7014
## be specified.
7015
element dynamic_type {
7016
attribute name {"use_y3D"},
7017
attribute file_name {xsd:string}
7018
}|
7019
## Using femdem 2D to model dynamics. Filename of input file must
7020
## be specified.
7021
element dynamic_type {
7022
attribute name {"use_2Dfemdem"},
7023
attribute file_name {xsd:string}
7024
}|
7025
## Using femdem 3D to model dynamics. Filename of input file must
7026
## be specified.
7027
element dynamic_type {
7028
attribute name {"use_3Dfemdem"},
7029
attribute file_name {xsd:string},
7030
element quad2lin {
7031
attribute file_name {xsd:string}
7032
}
7033
}
7034
)
7035
7036
cap_option =
7037
(
7038
## Cap the min and max values of this field when using
7039
## it as a volume fraction to work out bulk material
7040
## properties.
7041
## No capping used if not selected.
7042
element cap_values {
7043
## Set the upper bound on the field.
7044
## Defaults to huge(0.0)*epsilon(0.0) if not set.
7045
element upper_cap {
7046
real
7047
}?,
7048
## Set the lower bound on the field.
7049
## Defaults to -huge(0.0)*epsilon(0.0) if not set.
7050
element lower_cap {
7051
real
7052
}?
7053
}
7054
)
7055
7056
surface_tension_option =
7057
(
7058
element surface_tension {
7059
## Surface tension coefficient
7060
element surface_tension_coefficient {
7061
real
7062
},
7063
## The equilibrium contact angle (in radians) with the boundaries identified by the surface ids
7064
element equilibrium_contact_angle {
7065
real,
7066
## Surface ids:
7067
element surface_ids {
7068
integer_vector
7069
}
7070
}?
7071
}
7072
)
7073
7074
limiter_options =
7075
(
7076
## Limit the face value to satisfy a boundedness criterion.
7077
element limit_face_value{
7078
(
7079
sweby_limiter|
7080
ultimate_limiter
7081
)
7082
}
7083
)
7084
7085
sweby_limiter =
7086
## See "High-Resolution Schemes Using Flux Limiters for
7087
## Hyperblic Conservation-Laws", P. K. Sweby, 1984, Siam
7088
## Journal on Numerical Analysis, 21, 995-1011
7089
element limiter {
7090
attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 2,3,4,5" },
7091
attribute name {"Sweby"},
7092
slope_options?,
7093
upwind_value_options?
7094
}
7095
7096
ultimate_limiter =
7097
## See "The Ultimate Conservative Difference Scheme Applied
7098
## to Unsteady One-Dimensional Advection", B. P. Leonard,
7099
## 1991, Computer Methods in Applied Mechanics and
7100
## Engineering, 88, 17-74
7101
element limiter {
7102
attribute name {"Ultimate"},
7103
field_based_cfl_number_options,
7104
upwind_value_options?
7105
}
7106
7107
slope_options =
7108
(
7109
## Control the upper and lower slopes of the NVD limiter
7110
element slopes {
7111
## Defaults to Sweby, 1984 limiter (= 1.0) if unselected
7112
element lower {
7113
real
7114
}?,
7115
## Defaults to Sweby, 1984 limiter (= 2.0) if unselected
7116
element upper {
7117
real
7118
}?
7119
}
7120
)
7121
7122
upwind_value_options =
7123
(
7124
(
7125
## Select the method to be used for calculating the upwind value.
7126
## If not selected will default to project_upwind_value_from_point for
7127
## simplex element meshes and to a locally_bound_upwind_value for cube
7128
## element meshes.
7129
##
7130
## This method projects the upwind value from a point in the element just
7131
## upwind of the node pair straddling the face. It is otherwise known as
7132
## anisotropic limiting.
7133
## This is only available on simplex meshes as it involes a search around
7134
## the donor node to find the upwind element.
7135
element project_upwind_value_from_point {
7136
attribute replaces { "NDISOT > 0 on simplex meshes" },
7137
## When the donor node is on a domain boundary reflect the projection
7138
## back into the mesh.
7139
element reflect_off_domain_boundaries {
7140
empty
7141
}?,
7142
## Constrain the projected value to be between the min and max of the
7143
## element values which it was found from.
7144
element bound_projected_value_locally {
7145
empty
7146
}?,
7147
## Store the locations of the elements where the upwind values
7148
## are projected from for each node pair.
7149
## This inserts an integer csr matrix into state so is memory expensive but
7150
## saves a significant amount of time (searching around the neighbouring elements).
7151
## This is unsafe for moving meshes but should be ok for adaptive meshes.
7152
element store_upwind_elements {
7153
attribute replaces { "ABS(NDISOT) >= 1000" },
7154
## Store the quadrature locations within the elements
7155
## where the upwind values
7156
## are projected from for each node pair.
7157
## This inserts a real block csr matrix into state so is even more memory
7158
## expensive than just storing the upwind elements and
7159
## only saves a comparitively
7160
## marginal amount of time (as actually searching the
7161
## neighbouring elements is the
7162
## slowest bit, finding the quadrature is relatively easy).
7163
element store_upwind_quadrature {
7164
attribute replaces { "ABS(NDISOT) >= 1000" },
7165
empty
7166
}?
7167
}?
7168
}|
7169
## Select the method to be used for calculating the upwind value.
7170
## If not selected will default to project_upwind_value_from_point for
7171
## simplex element meshes and to a locally_bound_upwind_value for cube
7172
## element meshes.
7173
##
7174
## Projects the value of the advected variable from the downwind or donor node
7175
## using the interpolated gradient at the donor node in the
7176
## direction of the vector
7177
## connecting the node pair straddling the face.
7178
## This is available on all meshes (except if bounding the values).
7179
element project_upwind_value_from_gradient {
7180
(
7181
## Select which node to project from:
7182
## Project from the downwind node (Jasak et al., 1999) so that:
7183
## upwind_value = downwind_value - 2*gradient.vector
7184
element project_from_downwind_value {
7185
comment
7186
}|
7187
## Select which node to project from:
7188
## Project from the donor node so that:
7189
## upwind_value = donor_value - gradient.vector
7190
element project_from_donor_value {
7191
comment
7192
}
7193
),
7194
## When the donor node is on a domain boundary reflect the projection
7195
## back into the mesh.
7196
element reflect_off_domain_boundaries {
7197
empty
7198
}?,
7199
## Constrain the projected value to be between the min and max of the
7200
## element values which surround it.
7201
## This is only available on simplex meshes as it involes a search around
7202
## the donor node to find the upwind element.
7203
element bound_projected_value_locally {
7204
## Store the locations of the elements closest to the project value.
7205
## This inserts an integer csr matrix into state so is
7206
## memory expensive but
7207
## saves a significant amount of time (searching around
7208
## the neighbouring elements).
7209
## This is unsafe for moving meshes but should be ok for adaptive meshes.
7210
element store_upwind_elements {
7211
comment
7212
}?
7213
}?
7214
}|
7215
## Select the method to be used for calculating the upwind value.
7216
## If not selected will default to project_upwind_value_from_point for
7217
## simplex element meshes and to a locally_bound_upwind_value for cube
7218
## element meshes.
7219
##
7220
## Chooses an upwind value by selecting the maximum or minimum of the neighbouring
7221
## nodes depending on the local slope of the donor and downwind values.
7222
## Otherwise known as isotropic limiting.
7223
## This is available on all meshes.
7224
element locally_bound_upwind_value {
7225
attribute replaces { "all cube elements, NDISOT < 0 on simplex elements" },
7226
empty
7227
}|
7228
## Select the method to be used for calculating the upwind value.
7229
## If not selected will default to project_upwind_value_from_point for
7230
## simplex element meshes and to a locally_bound_upwind_value for cube
7231
## element meshes.
7232
##
7233
## Chooses an upwind value by selecting the value at the node most directy
7234
## upwind from the vector connecting the donor and downwind nodes.
7235
## This is available on all meshes.
7236
element pseudo_structured_upwind_value {
7237
empty
7238
}
7239
)
7240
)
7241
7242
field_based_cfl_number_options =
7243
(
7244
(
7245
## Select the Courant Number definition to be used.
7246
##
7247
## This uses the control volume definition of the CFL Number.
7248
element courant_number {
7249
attribute name { "ControlVolumeCFLNumber" },
7250
empty
7251
}|
7252
## ***UNDER TESTING***
7253
##
7254
## Select the Courant Number definition to be used.
7255
##
7256
## This uses the control volume definition of the CFL Number.
7257
element courant_number {
7258
attribute name { "CVMaterialDensityCFLNumber" },
7259
empty
7260
}|
7261
## Select the Courant Number definition to be used.
7262
##
7263
## This uses the finite element approximation of the CFL Number.
7264
element courant_number {
7265
attribute name { "CFLNumber" },
7266
empty
7267
}|
7268
## Select the Courant Number definition to be used.
7269
element courant_number {
7270
attribute name { string },
7271
empty
7272
}
7273
)
7274
)
7275
7276
cv_face_cfl_number_options =
7277
(
7278
(
7279
## Select the Courant Number definition to be used in the slope of
7280
## the NVD diagram upper bound.
7281
## This uses the finite difference definition of the CFL Number
7282
## consistent with the 1D version of HyperC (Leonard, 1981).
7283
## This is the default that reproduces old behaviour.
7284
## All others are under testing or construction.
7285
element courant_number {
7286
attribute name { "FiniteDifferenceCFLNumber" },
7287
empty
7288
}|
7289
## Select the Courant Number definition to be used in the slope of
7290
## the NVD diagram upper bound.
7291
## This uses the control volume definition of the CFL Number.
7292
element courant_number {
7293
attribute name { "ControlVolumeCFLNumber" },
7294
empty
7295
}|
7296
## ***UNDER TESTING***
7297
##
7298
## Select the Courant Number definition to be used in the slope of
7299
## the NVD diagram upper bound.
7300
## This uses a control volume definition of the CFL Number
7301
## that incorporates the MaterialDensity.
7302
## Requires a MaterialDensity field in this material_phase!
7303
element courant_number {
7304
attribute name { "CVMaterialDensityCFLNumber" },
7305
empty
7306
}|
7307
## ***UNDER TESTING***
7308
##
7309
## Select the Courant Number definition to be used in the slope of
7310
## the NVD diagram upper bound.
7311
## This uses the finite element approximation of the CFL Number.
7312
element courant_number {
7313
attribute name { "CFLNumber" },
7314
empty
7315
}|
7316
## ***UNDER TESTING***
7317
##
7318
## Select the Courant Number definition to be used in the slope of
7319
## the NVD diagram upper bound.
7320
element courant_number {
7321
attribute name { string },
7322
empty
7323
}
7324
)
7325
)
7326
7327
timestep_cfl_number_options =
7328
(
7329
(
7330
## Select the Courant Number definition to be used for adaptive timestepping.
7331
## This uses the finite element approximation of the CFL Number.
7332
element courant_number {
7333
attribute name { "CFLNumber" },
7334
## Select the mesh on which you wish to evaluate the CFLNumber.
7335
velocity_mesh_choice
7336
}|
7337
## Select the Courant Number definition to be used for adaptive timestepping.
7338
## This uses the control volume definition of the CFL Number.
7339
element courant_number {
7340
attribute name { "ControlVolumeCFLNumber" },
7341
## Select the mesh on which you wish to evaluate the ControlVolumeCFLNumber.
7342
velocity_mesh_choice
7343
}
7344
)
7345
)
7346
7347
mixing_stats =
7348
(
7349
## Enable to include in the .stat file the fractions of the
7350
## scalar field contained in
7351
## bins specified by the user. This allows mixing of the field to be quantified.
7352
## Replaces and expands upon the old heaviside.dat file
7353
element include_mixing_stats{
7354
attribute name { xsd:string },
7355
attribute replaces { "heaviside.dat file" },
7356
(
7357
## Select whether to evaluate the volume fraction over the finite element
7358
## (continuous galerkin) or within the control volume (control_volumes).
7359
##
7360
## NOTE: continuous_galerkin only works with linear tets
7361
##
7362
## NOTE: continuous_galerkin is not fully validated yet
7363
element continuous_galerkin {
7364
## if select normalise the volume fractions will be
7365
## divided by the total volume of the domain
7366
element normalise {
7367
empty
7368
}?
7369
}|
7370
## Select whether to evaluate the volume fraction over the finite element
7371
## (continuous galerkin) or within the control volume (control_volumes).
7372
element control_volumes {
7373
## if select normalise the volume fractions will be divided by the total volume of the domain
7374
element normalise {
7375
empty
7376
}?
7377
}
7378
),
7379
## The values of the bounds of the bins
7380
## e.g. the values 0 1 2 3 will return 4 bins
7381
## and the fraction of the field in each bin with,
7382
## 0<=field<1, 1<=field<2, 2<=field<3, 3<=field,
7383
## will be calculated.
7384
element mixing_bin_bounds {
7385
real_vector
7386
},
7387
## Define the tolerance beneath the specified bins that should be included.
7388
## Defaults to zero at machine tolerance (epsilon(0.0)) if not selected.
7389
element tolerance {
7390
real
7391
}?
7392
}
7393
)
7394
7395
cv_stats =
7396
(
7397
## Include statistics evaluated on the control volume mesh.
7398
element include_cv_stats {
7399
empty
7400
}
7401
)
7402
7403
# Options for inclusion of calculations of surface integrals in the .stat file
7404
surface_integral_stats_base.surface_integral =
7405
(
7406
attribute name { xsd:string },
7407
## Surface IDs defining the surface over which to integrate. If disabled, integrates over the whole surface.
7408
element surface_ids {
7409
integer_vector
7410
}?,
7411
## Enable to normalise the integral by dividing by the surface area
7412
element normalise {
7413
comment
7414
}?
7415
)
7416
surface_integral_stats_scalar =
7417
(
7418
## Surface integral calculations. The following integral types are available:
7419
## value: Integrates the field
7420
## gradient_normal: Integrates the normal component of the gradient of the field
7421
element surface_integral {
7422
surface_integral_stats_scalar.surface_integral
7423
}
7424
)
7425
surface_integral_stats_scalar.surface_integral = surface_integral_stats_base.surface_integral
7426
surface_integral_stats_scalar.surface_integral &=
7427
(
7428
attribute type { "value" | "gradient_normal" }
7429
)
7430
surface_integral_stats_vector =
7431
(
7432
## Surface integral calculations. The following integral types are available:
7433
## normal: Integrates the normal component of the field
7434
element surface_integral {
7435
surface_integral_stats_vector.surface_integral
7436
}
7437
)
7438
surface_integral_stats_vector.surface_integral = surface_integral_stats_base.surface_integral
7439
surface_integral_stats_vector.surface_integral &=
7440
(
7441
attribute type { "normal" }
7442
)
7443
7444
velocity_equation_choice =
7445
(
7446
## Select the equation used to solve for velocity.
7447
## LinearMomentum is the norm and works for all discretisation types.
7448
element equation {
7449
attribute name { "LinearMomentum" }
7450
}|
7451
## Select the equation used to solve for velocity.
7452
## Boussinesq only works for continuous_galerkin and discontinuous_galerkin.
7453
element equation {
7454
attribute name { "Boussinesq" }
7455
}|
7456
## Select the equation used to solve for velocity.
7457
## Drainage only works for continuous_galerkin and discontinuous_galerkin.
7458
element equation {
7459
attribute name { "Drainage" }
7460
}
7461
)
7462
7463
scalar_equation_choice =
7464
(
7465
(
7466
## Select the equation used to solve for this field.
7467
## Advection Diffusion is the norm for scalar fields.
7468
## Works for all discretisation types.
7469
element equation {
7470
attribute name { "AdvectionDiffusion" }
7471
}|
7472
## ***UNDER TESTING***
7473
##
7474
## Select the equation used to solve for this field.
7475
## Conservation of Mass equation - requires the selection of a Density field.
7476
## ONLY WORKS FOR CONTROL VOLUME DISCRETISATIONS WITHOUT A
7477
## DIFFUSIVITY, SOURCE OR ABSORPTION.
7478
element equation {
7479
attribute name { "ConservationOfMass" },
7480
(
7481
## Select density to use in the Conservation of Mass Equation
7482
## Use the MaterialDensity - useful for multimaterial simulations
7483
## Clearly this requires a MaterialDensity field to be present
7484
element density {
7485
attribute name { "MaterialDensity" }
7486
}|
7487
## Select density to use in the Conservation of Mass Equation
7488
## Use the bulk Density
7489
## Clearly this requires a Density field to be present
7490
element density {
7491
attribute name { "Density" }
7492
}|
7493
## Select density to use in the Conservation of Mass Equation
7494
element density {
7495
attribute name { string }
7496
}
7497
)
7498
}|
7499
## ***UNDER TESTING***
7500
##
7501
## Select the equation used to solve for this field.
7502
## Reduced Conservation of Mass equation - requires the selection of a Density field.
7503
##
7504
## ONLY WORKS FOR CONTROL VOLUME DISCRETISATIONS WITHOUT A
7505
## DIFFUSIVITY, SOURCE OR ABSORPTION.
7506
##
7507
## This equation is very similar to a standard conservation of mass equation
7508
## except that the time discretisation uses only a single time level of density.
7509
## This enables consistency between the
7510
## MaterialVolumeFraction (ReducedConservationOfMass) and
7511
## MaterialDensity (Advection) equations in compressible multimaterial simulations.
7512
element equation {
7513
attribute name { "ReducedConservationOfMass" },
7514
(
7515
## Select density to use in the Reduced Conservation of Mass Equation
7516
## Use the MaterialDensity - useful for multimaterial simulations
7517
## Clearly this requires a MaterialDensity field to be present
7518
element density {
7519
attribute name { "MaterialDensity" }
7520
}|
7521
## Select density to use in the Reduced Conservation of Mass Equation
7522
## Use the bulk Density
7523
## Clearly this requires a Density field to be present
7524
element density {
7525
attribute name { "Density" }
7526
}|
7527
## Select density to use in the Reduced Conservation of Mass Equation
7528
element density {
7529
attribute name { string }
7530
}
7531
)
7532
}|
7533
## ***UNDER TESTING***
7534
##
7535
## Select the equation used to solve for this field.
7536
## Internal Energy equation - requires the selection of a Density field.
7537
## ONLY WORKS FOR CONTROL VOLUME DISCRETISATIONS WITHOUT A
7538
## DIFFUSIVITY, SOURCE OR ABSORPTION.
7539
## Solve the internal energy equation for this field.
7540
## Requires pressure and velocity fields to be present.
7541
## Uses a nonconservative time discretisation.
7542
element equation {
7543
attribute name { "InternalEnergy" },
7544
(
7545
## Select density to use in the Internal Energy Equation
7546
## Use the MaterialDensity - useful for multimaterial simulations
7547
## Clearly this requires a MaterialDensity field to be present
7548
## Whatever field is selected must be present.
7549
element density {
7550
attribute name { "MaterialDensity" }
7551
}|
7552
## Select density to use in the Internal Energy Equation
7553
## Use the bulk Density
7554
## Clearly this requires a Density field to be present
7555
## Whatever field is selected must be present.
7556
element density {
7557
attribute name { "Density" }
7558
}|
7559
## Select density to use in the Internal Energy Equation
7560
## Whatever field is selected must be present.
7561
element density {
7562
attribute name { string }
7563
}
7564
)
7565
}|
7566
## Option to solve for electrical potential from
7567
## electrokinetic, electrochemical or electrothermal sources
7568
element equation {
7569
attribute name { "ElectricalPotential" }
7570
}
7571
)
7572
)
7573
7574
inner_element_scalar =
7575
(
7576
## Inner element sub-grid scale model (Candy and Pain)
7577
## Requires continuous galerkin selected above.
7578
element inner_element {
7579
attribute replaces { "NSUBTLOC, NSUBNTLOC" },
7580
## Inner element solution of the scalar field.
7581
element scalar_field {
7582
attribute rank { "0" },
7583
attribute name { "InnerElement" },
7584
element prognostic {
7585
element mesh {
7586
attribute name { "InnerElementMesh" }
7587
},
7588
prognostic_scalar_output_options,
7589
prognostic_scalar_stat_options,
7590
prognostic_detector_options
7591
}
7592
}
7593
}
7594
)
7595
7596
inner_element_velocity =
7597
(
7598
## Inner element sub-grid scale model (Candy and Pain)
7599
## Requires continuous galerkin selected above.
7600
element inner_element {
7601
attribute replaces { "NSUBVLOC, NSUBNVLOC" },
7602
## SGS velocity in an inner element SGS treatment of momentum
7603
##
7604
## Limitations:
7605
## - Requires a geometry dimension of 3.
7606
## - Requires inner element active for momentum
7607
element vector_field {
7608
attribute rank { "1" },
7609
attribute name { "InnerElement" },
7610
element prognostic {
7611
element mesh {
7612
attribute name { "InnerElementMesh" }
7613
},
7614
prognostic_vector_output_options,
7615
prognostic_vector_stat_options,
7616
vector_convergence_options
7617
}
7618
},
7619
## A filter for the sub-grid scale equations
7620
## Add diffusion to matrix D of the Inner Element model
7621
element use_filter {
7622
## Strength of the diffusion term
7623
## Suggested value: 0.01
7624
element strength {
7625
real
7626
},
7627
empty
7628
}?,
7629
element use_quadratic_pressure {
7630
attribute replaces { "PREOPT=PREOPT+1000" }
7631
}?,
7632
element apply_full_discontinuous_Galerkin {
7633
attribute replaces { "PREOPT=PREOPT+10000" }
7634
}?
7635
}?
7636
)
7637
forcing =
7638
(
7639
## Add forcing from ocean data
7640
## If you enable this you MUST enable the /geometry/ocean_boundaries option too
7641
element ocean_forcing{
7642
## The netCDF data file downloaded from ERA-40 reanalysis
7643
element input_file {
7644
attribute file_name {xsd:string}
7645
},
7646
element mesh_choice {
7647
velocity_mesh_choice
7648
},
7649
element surface_stress {
7650
empty
7651
}?,
7652
element temperature_flux {
7653
empty
7654
}?,
7655
element salinity_flux {
7656
empty
7657
}?,
7658
element solar_radiation {
7659
empty
7660
}?
7661
}
7662
)
7663
7664
biology =
7665
(
7666
## Model of biological processes in the ocean.
7667
element ocean_biology{
7668
## A simple model of phytoplankton, zooplankton, general nutrient and detritus.
7669
element pznd {
7670
(
7671
## Python code specifying the source and sink relationships
7672
## between the biological tracers. This is usually achieved by
7673
## importing fluidity.ocean_biology and calling a scheme from there.
7674
element source_and_sink_algorithm {
7675
python_code
7676
}|
7677
## Do not calculate sources and sinks.
7678
## This option is generally only useful for testing.
7679
element disable_sources_and_sinks {
7680
empty
7681
}
7682
),
7683
# ## Phytoplankton
7684
# element scalar_field {
7685
# attribute rank { "0" },
7686
# attribute name { "Phytoplankton" },
7687
# (
7688
# element prognostic {
7689
# velocity_mesh_choice,
7690
# prognostic_scalar_field
7691
# }|
7692
# element prescribed {
7693
# velocity_mesh_choice,
7694
# prescribed_scalar_field
7695
# }
7696
# )
7697
# },
7698
# ## Zooplankton
7699
# element scalar_field {
7700
# attribute rank { "0" },
7701
# attribute name { "Zooplankton" },
7702
# (
7703
# element prognostic {
7704
# velocity_mesh_choice,
7705
# prognostic_scalar_field
7706
# }|
7707
# element prescribed {
7708
# velocity_mesh_choice,
7709
# prescribed_scalar_field
7710
# }
7711
# )
7712
# },
7713
# ## Nutrient
7714
# element scalar_field {
7715
# attribute rank { "0" },
7716
# attribute name { "Nutrient" },
7717
# (
7718
# element prognostic {
7719
# velocity_mesh_choice,
7720
# prognostic_scalar_field
7721
# }|
7722
# element prescribed {
7723
# velocity_mesh_choice,
7724
# prescribed_scalar_field
7725
# }
7726
# )
7727
# },
7728
# ## Detritus
7729
# element scalar_field {
7730
# attribute rank { "0" },
7731
# attribute name { "Detritus" },
7732
# (
7733
# element prognostic {
7734
# velocity_mesh_choice,
7735
# prognostic_scalar_field
7736
# }|
7737
# element prescribed {
7738
# velocity_mesh_choice,
7739
# prescribed_scalar_field
7740
# }
7741
# )
7742
# },
7743
## Photosynthetically Active Radiation (PAR)
7744
element scalar_field {
7745
attribute rank { "0" },
7746
attribute name { "PhotosyntheticRadiation" },
7747
(
7748
element prognostic {
7749
velocity_mesh_choice,
7750
prognostic_photosynthetic_radiation
7751
}|
7752
element prescribed {
7753
velocity_mesh_choice,
7754
prescribed_scalar_field
7755
}
7756
)
7757
}
7758
}
7759
}
7760
)
7761
7762
7763
prognostic_photosynthetic_radiation =
7764
(
7765
## PAR equation.
7766
element equation {
7767
attribute name { "PhotosyntheticRadiation" }
7768
},
7769
## Spatial discretisation options
7770
element spatial_discretisation {
7771
(
7772
## Discontinuous galerkin formulation. You can also use this
7773
## formulation with a continuous field in which case a simple
7774
## galerkin formulation will result.
7775
element discontinuous_galerkin {
7776
empty
7777
}
7778
)
7779
},
7780
(
7781
## Solver
7782
element solver {
7783
linear_solver_options_asym
7784
}
7785
),
7786
## Coefficients of absorption of photosynthetically active
7787
## radiation for water and phytoplankton.
7788
element absorption_coefficients {
7789
## Photosynthetically active radiation absorption coefficient for water.
7790
element water {
7791
real
7792
},
7793
## Photosynthetically active radiation absorption coefficient for water.
7794
element phytoplankton {
7795
real
7796
}
7797
},
7798
## Boundary conditions
7799
element boundary_conditions {
7800
attribute replaces { "boundary, TTPER1 TTPER2 TTPERI" },
7801
attribute name { string },
7802
## Surface id:
7803
element surface_ids {
7804
integer_vector
7805
},
7806
## Type
7807
(
7808
element type {
7809
attribute name { "dirichlet" },
7810
## Apply the dirichlet bc weakly. Only available with
7811
## discontinuous_galerkin, control_volume and
7812
## legacy_mixed_cv_cg spatial_discretisations.
7813
##
7814
## If not selected boundary conditions are applied strongly.
7815
element apply_weakly {
7816
empty
7817
},
7818
input_choice_real
7819
}|
7820
element type {
7821
attribute name { "neumann" },
7822
input_choice_real
7823
}|
7824
element type {
7825
attribute name { "robin" },
7826
element order_zero_coefficient {
7827
input_choice_real
7828
},
7829
element order_one_coefficient {
7830
input_choice_real
7831
}
7832
}
7833
)
7834
}+,
7835
prognostic_scalar_output_options,
7836
prognostic_scalar_stat_options,
7837
scalar_convergence_options,
7838
prognostic_detector_options,
7839
scalar_steady_state_options,
7840
adaptivity_options_scalar_field,
7841
## Set the priority of this field
7842
## This determines the order in which scalar_fields are solved for:
7843
## - higher numbers have the highest priority
7844
## - lower numbers (including negative) have the lowest priority
7845
## - default if not set is 0
7846
element priority {
7847
integer
7848
}?
7849
)
7850
7851
recalculation_options =
7852
(
7853
## Prevent this field from being recalculated at every timestep.
7854
## This is cheaper especially if you are enforcing discrete properties on the field.
7855
element do_not_recalculate {
7856
empty
7857
}
7858
)
7859
7860
discrete_properties_algorithm_scalar =
7861
(
7862
## Select discrete properties to enforce on the field
7863
## either after being prescribed or interpolated
7864
element enforce_discrete_properties {
7865
## Update this field using the lagrangian multiplier
7866
## calculated in the solenoidal projection of a
7867
## scalar field.
7868
##
7869
## Note this field must be specified as the update field
7870
## underneath that vector field too.
7871
##
7872
## Note also this only really makes sense for coupled
7873
## fields like velocity and pressure.
7874
element solenoidal_lagrange_update {
7875
empty
7876
}?
7877
}
7878
)
7879
7880
discrete_properties_algorithm_vector =
7881
(
7882
## Select discrete properties to enforce on the field
7883
## either after being prescribed or interpolated
7884
element enforce_discrete_properties {
7885
solenoidal_options?
7886
}
7887
)
7888
7889
interpolation_algorithm_disabled =
7890
(
7891
## Disable interpolation
7892
element no_interpolation {
7893
comment
7894
}
7895
)
7896
7897
interpolation_algorithm_scalar =
7898
(
7899
## Basis function interpolation.
7900
## The standard algorithm. It is quick
7901
## and bounded, but non-conservative and dissipative.
7902
## All other algorithms require construction of a supermesh.
7903
element consistent_interpolation {
7904
empty
7905
}|
7906
## Galerkin projection. By default, conservative, non-dissipative and
7907
## non-bounded. The most accurate choice, in the sense of minimising
7908
## the L2 norm of the residual
7909
element galerkin_projection {
7910
galerkin_projection_scalar
7911
}
7912
)
7913
7914
interpolation_algorithm_scalar_full = interpolation_algorithm_scalar
7915
interpolation_algorithm_scalar_full |= interpolation_algorithm_disabled
7916
7917
interpolation_algorithm_vector =
7918
(
7919
## Basis function interpolation.
7920
## The standard algorithm. It is quick
7921
## and bounded, but non-conservative and dissipative.
7922
## All other algorithms require construction of a supermesh.
7923
element consistent_interpolation {
7924
consistent_interpolation_vector
7925
}|
7926
## Galerkin projection. By default, conservative, non-dissipative and
7927
## non-bounded. The most accurate choice, in the sense of minimising
7928
## the L2 norm of the residual
7929
element galerkin_projection {
7930
galerkin_projection_vector
7931
}
7932
)
7933
7934
consistent_interpolation_vector =
7935
(
7936
balanced_interpolation?
7937
)
7938
7939
galerkin_projection_vector =
7940
(
7941
continuous_discontinuous_projection,
7942
balanced_interpolation?,
7943
supermesh_free?,
7944
supermesh_conservation?
7945
)
7946
7947
galerkin_projection_scalar =
7948
(
7949
continuous_discontinuous_projection,
7950
supermesh_free?,
7951
supermesh_conservation?
7952
)
7953
7954
continuous_discontinuous_projection =
7955
(
7956
## Continuous field Galerkin projection.
7957
## If the field you are interpolating is continuous, then
7958
## a linear solver is required to invert the mass matrix.
7959
element continuous {
7960
(
7961
## Use a bounded Galerkin projection. Conservative, bounded in the
7962
## limit, and minimally dissipative. This algorithm starts with the
7963
## Galerkin projection and dissipates it until it achieves
7964
## boundedness.
7965
## If it does not converge, it may not be exactly bounded.
7966
## Note well: this only works for linear fields.
7967
element bounded {
7968
attribute name {"Diffuse"},
7969
## The number of dissipation iterations attempted to bound the
7970
## Galerkin projection.
7971
element boundedness_iterations {
7972
integer,
7973
## Specify the tolerance to which boundedness is to be tested.
7974
## Defaults to computer precision if unspecified.
7975
element tolerance {
7976
real
7977
}?
7978
},
7979
## If the bounds on this field are known then they can be set here.
7980
## These can either further constrain the limits worked out by the
7981
## lumped version of the projection (i.e. to make sure that errors
7982
## don't accumulate with succesive interpolations) or if apply_globally
7983
## is set they are just made to be bounded within the bounds globally
7984
## (i.e. anything between those bounds is not smoothed).
7985
element bounds {
7986
element upper_bound {
7987
real,
7988
## If this is set the upper_bound is used everywhere.
7989
## If left unset the upper_bound is only used to constrain
7990
## the smoothed bounds calculated by the code
7991
element apply_globally {
7992
empty
7993
}?,
7994
## This field is to be considered as being coupled to another field
7995
## such that the sum of the two fields is constrained to be less than
7996
## the upper_bound specified above.
7997
##
7998
## The relationships between fields are worked out according to their
7999
## priority ordering.
8000
##
8001
## This method is akin to the coupled_cv advection method.
8002
element coupled {
8003
empty
8004
}?
8005
}?,
8006
element lower_bound {
8007
real,
8008
## If this is set the upper_bound is used everywhere.
8009
## If left unset the upper_bound is only used to constrain
8010
## the smoothed bounds calculated by the code
8011
element apply_globally {
8012
empty
8013
}?
8014
}?
8015
}?,
8016
## If, after performing all the boundedness_iterations, the field
8017
## is still not bounded then perform surgery to redistribute the
8018
## deviations to nodes that have less than their bounds.
8019
element repair_deviations {
8020
empty
8021
}?
8022
}|
8023
## Use a bounded Galerkin projection. Conservative, bounded in the
8024
## limit, and hopefully minimally dissipative. This algorithm starts with the
8025
## Galerkin projection and uses the optimisation library Algencan to bound
8026
## it by minimising a functional within constraints on boundedness and conservation.
8027
## Note well: this only works for linear fields.
8028
element bounded {
8029
attribute name {"Algencan"},
8030
(
8031
element functional {
8032
attribute name {"L2"},
8033
element weight {
8034
real
8035
}?
8036
}|
8037
element functional {
8038
attribute name {"LumpedMassL2"},
8039
element weight {
8040
real
8041
}?
8042
}|
8043
element functional {
8044
attribute name {"IntegralL2"},
8045
element weight {
8046
real
8047
}?
8048
}|
8049
element functional {
8050
attribute name { string },
8051
element weight {
8052
real
8053
}?
8054
}
8055
),
8056
## If the bounds on this field are known then they can be set here.
8057
## These can either further constrain the limits worked out by the
8058
## lumped version of the projection (i.e. to make sure that errors
8059
## don't accumulate with succesive interpolations) or if apply_globally
8060
## is set they are just made to be bounded within the bounds globally
8061
## (i.e. anything between those bounds is not smoothed).
8062
element bounds {
8063
element upper_bound {
8064
real,
8065
## If this is set the upper_bound is used everywhere.
8066
## If left unset the upper_bound is only used to constrain
8067
## the smoothed bounds calculated by the code
8068
element apply_globally {
8069
empty
8070
}?,
8071
## This field is to be considered as being coupled to another field
8072
## such that the sum of the two fields is constrained to be less than
8073
## the upper_bound specified above.
8074
##
8075
## The relationships between fields are worked out according to their
8076
## priority ordering.
8077
##
8078
## This method is akin to the coupled_cv advection method.
8079
element coupled {
8080
empty
8081
}?
8082
}?,
8083
element lower_bound {
8084
real,
8085
## If this is set the upper_bound is used everywhere.
8086
## If left unset the upper_bound is only used to constrain
8087
## the smoothed bounds calculated by the code
8088
element apply_globally {
8089
empty
8090
}?
8091
}?
8092
}?
8093
}
8094
)?,
8095
(
8096
## Solver options for the linear solve.
8097
## This method requires the inversion of a mass matrix. Note that
8098
## conservation properties are affected by the tolerance of the
8099
## linear solve.
8100
element solver {
8101
linear_solver_options_sym
8102
}|
8103
## Lump the mass matrix on the left hand side of the galerkin projection.
8104
## Hence solver options aren't necessary.
8105
element lump_mass_matrix {
8106
empty
8107
}
8108
)
8109
}|
8110
## Discontinuous field Galerkin projection
8111
## In this case, no linear solver is required to invert the mass matrix.
8112
element discontinuous {
8113
empty
8114
}
8115
)
8116
8117
solenoidal_options =
8118
## Constrained divergence-free projection.
8119
## This adds an additional constraint that ensures that the field
8120
## is solenoidal, i.e. divergence-free.
8121
## This is equivalent in cost to a pressure solve.
8122
## This is expensive, and thus best left until
8123
## needed.
8124
##
8125
## Note well: this only makes sense for nondivergent
8126
## vector fields, such as incompressible velocity!
8127
element solenoidal {
8128
## Options for the mass matrix of the field being interpolated
8129
element interpolated_field {
8130
(
8131
element continuous {
8132
## Lump the mass matrix for the assembly of the projection matrix
8133
## (not for the initial galerkin projection)
8134
##
8135
## Required when using interpolating continuous fields
8136
element lump_mass_matrix {
8137
## Lump on the submesh.
8138
## This only works for simplex meshes and is only
8139
## strictly valid on 2d meshes.
8140
element use_submesh {
8141
empty
8142
}?
8143
}
8144
}|
8145
element discontinuous {
8146
## Lump the mass matrix for the assembly of the projection matrix
8147
## (not for the initial galerkin projection)
8148
element lump_mass_matrix {
8149
empty
8150
}?
8151
}
8152
)
8153
},
8154
## Options for the lagrange multiplier
8155
##
8156
## Must be on a continuous mesh!
8157
element lagrange_multiplier {
8158
pressure_mesh_choice,
8159
element spatial_discretisation {
8160
(
8161
element continuous_galerkin {
8162
## Remove the stabilisation term from the projection operator.
8163
##
8164
## Automatic when not using P1P1.
8165
element remove_stabilisation_term {
8166
empty
8167
}?,
8168
## Integrate the divergence operator by parts.
8169
##
8170
## Automatic when projecting a discontinuous field
8171
element integrate_divergence_by_parts {
8172
empty
8173
}?
8174
}|
8175
element control_volumes {
8176
empty
8177
}
8178
)
8179
},
8180
element reference_node {
8181
integer
8182
}?,
8183
(
8184
## Update a scalar field using the lagrange multiplier from
8185
## the divergence free projection of this field. The selected
8186
## scalar field must have solenoidal selected in its interpolation
8187
## options too and it must be on the same mesh as used for the
8188
## solenoidal projection above.
8189
##
8190
## Note well: this only really makes sense for scalar fields linked to nondivergent
8191
## vector fields, such as pressure to incompressible velocity!
8192
element update_scalar_field {
8193
attribute name { "Pressure" },
8194
empty
8195
}|
8196
## Update a scalar field using the lagrange multiplier from
8197
## the divergence free projection of this field. The selected
8198
## scalar field must have solenoidal selected in its interpolation
8199
## options too and it must be on the same mesh as used for the
8200
## solenoidal projection above.
8201
##
8202
## Note well: this only really makes sense for scalar fields linked to nondivergent
8203
## vector fields, such as pressure to incompressible velocity!
8204
element update_scalar_field {
8205
attribute name { string },
8206
empty
8207
}
8208
)?,
8209
## Solver options for the linear solve.
8210
## This method requires the inversion of a projection matrix.
8211
element solver {
8212
linear_solver_options_sym
8213
}
8214
}
8215
}
8216
8217
8218
balanced_interpolation =
8219
## Geostrophically-balanced interpolation.
8220
## During the interpolation, the velocity is split into
8221
## balanced and imbalanced parts. The imbalanced part is
8222
## interpolated whereas the balanced part is recovered
8223
## on the other side of the interpolation from the pressure.
8224
## This means that if your velocity field is balanced before
8225
## interpolation, it will be balanced afterwards also.
8226
##
8227
## Note well: this only makes sense for velocity.
8228
element balanced_interpolation {
8229
## The solver options for computing the balanced velocity to subtract.
8230
element solver {
8231
linear_solver_options_sym
8232
}
8233
}
8234
8235
supermesh_free =
8236
## Enables a supermesh free Galerkin projection. Uses incomplete
8237
## quadrature, and hence is not conservative.
8238
element supermesh_free {
8239
empty
8240
}
8241
8242
represcribe_before_interpolation =
8243
## Represcribe the field before interpolation.
8244
##
8245
## This means the interpolation will not be conservative from the previous mesh so be careful what you're trying to achieve!
8246
element represcribe_before_interpolation {
8247
empty
8248
}
8249
8250
supermesh_conservation =
8251
## Options for checking the supermesh conservation properties
8252
element supermesh_conservation {
8253
## Specify the fraction of the original elemental area/volume
8254
## to be used to check the conservation of the supermesh.
8255
##
8256
## Since all fields are supermeshed together the minimum tolerance
8257
## specified over all fields will be used.
8258
##
8259
## Defaults to 0.001 if unspecified.
8260
## i.e. 0.1% of the area/volume of an element in the new mesh may
8261
## be lost without warning or attempts to fix (if compiled with cgal)
8262
## during the construction of the supermesh between the old
8263
## and new meshes.
8264
element tolerance {
8265
real
8266
}?,
8267
## Compute the field integral after the interpolation and print the relative
8268
## mass loss to the logfile (level 2 verbosity).
8269
##
8270
## Note this is a post interpolation step and offers no chance of
8271
## fixing the conservation error (unlike the tolerance above if compiled
8272
## with cgal)
8273
element print_field_integral {
8274
## Relative tolerance with which to test the conservation of the field
8275
## integral. If the conservation fails this tolerance a warning is issued
8276
## (level 0 verbosity) and vtus containing the field are output.
8277
element tolerance {
8278
real
8279
}
8280
}?
8281
}
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Version: 2.0.1