Changes

Summary

1. Cleaned up test case (details)
2. Added updated gmsh reader test (details)
3. Reader change (details)
4. Added a control test case (details)
5. Added plate test case (details)
6. Fixed tandem sphere normalization (details)
7. Fixed vara and compiler warnings (details)
8. Refactored indexing in IBL (details)
9. Removed redundant IBL auxiliary equation implementation (details)
10. Refactored IBL to include placeholders for the amplification factor (details)
11. Refactored/fixed panel method to accommodate changes in PDEIBL.  Patched (details)
12. Removed more unnecessary files (details)
13. Turned off verbose printout (details)
14. Delta wing case to dump metrics for ODU (details)
15. Added IBL PDE indexing checks.  Added a var interpreter method.  Fixed a (details)
16. Added equations to IBL: amplification factor growth and shear stress (details)
17. Added 4th order Lagrange Basis Functions for Hexs and Unit Tests (details)
18. patched some unit tests, but still working progress (details)
19. Cleaned up IO files in sandbox (details)
20. Refactored to use line-based parsing when reading initial IBL solutions. (details)
21. Added more quantities to IBL output list (details)
22. Added pressure gradient parameter beta to IBL output list (details)
23. 1. Refactored/debugged IBL PDE's transition and lag implementation; 2. (details)
24. Refactored profile selection.  Minor working update on lag equation (details)
25. Cleaned up IBL transition and lag source terms (details)
26. Changed primary unknown from G to ctau.  Updated naming. (details)
27. More fix on VarType naming (details)
28. 1. Cleaned up template types; 2. Refactored lag equation formulation: (details)
29. Minor refactoring on IBL pde (details)
30. tweaks to read in ODU grids (details)
31. Refactored secondary var calculations: now supporting multiple (details)
32. Added ctau_eq to IBL output list (details)
33. Fixed a bug in ctau_eq calculation (details)
34. a possible bug fix for FeFloa (details)
35. stuff to read in the ODU grids (details)
36. Fixed system test on coupled IBL/panel.  Verified that newly added (details)
37. Avoided dividing by zero when calculating pressure gradient parameter (details)
38. Fixed XFOIL-lag closure (details)
39. Completed IBL3 lag/dissipation formulation and add that of XFOIL (details)
40. refactored ctau transition fitting: forced transition at airfoil TE now (details)
41. Refactored transition fitting of ctau for transition that happens on the (details)
42. tweaks to read in the ODU grids (details)
43. minor edit (details)
44. First solution of forced transition at a grid node (details)
45. Fixed typos in comments (details)
46. Renamed velocity profile class (details)
47. Renamed secondary var class (details)
48. Fixed IBL unit tests compilation (details)
49. Modularized fluid parameters into a dedicated model class (details)
50. refactored and unit tested gas model in IBL (details)
51. Removed Pr in IBL (details)
52. Refactored IBL edge viscosity model/parameter (details)
53. A solve case for running a sequence of grids (details)
54. increased the PTC max iter and use the final solution from the previous (details)
55. always starts from a p0 solve, now has lots of Newton steps allowed (details)
56. Generalized abstractions of flow parameters and compressibility types. (details)
57. Added more velocity profile unit tests. Updated function name (details)
58. Fixed an insidious bug in IBL source term (details)
59. Passed all the IBL unit tests (details)
60. Added instantiation.  Fixed panel method unit tests. (details)
61. minor fix (details)
62. Removed files that popped up again in the last merge.  Fix for last (details)
63. Abstracted transition model into a dedicated class (details)
64. Replaced DBL_EPSILON with std::numeric_limits<Real>::epsilon() (details)
65. Fixed missing typename and template keywords (details)
66. Fixed panel method system testing dump.  Refactored transition model (details)
67. Updating delta wing (details)
68. Updated linesearch names (details)
69. Refactored transition model: 1. ensures profile and intermittency is (details)
70. Refactored control statements to avoid compiler warnings (details)
71. Fixed uncoupled IBL test cases.  Airfoil+wake may be refactored after (details)
72. Fixed system tests for IBL. Deleted obsolete ones (details)
73. Moved the TE thickness treatment from integrand to PDEIBL (details)
74. Covered fluid models with more extensive unit tests.  Turned off some (details)
75. Refactored transition model profile choice logic.  Fixed PDEIBL unit (details)
76. Fixed system test.  More unit tests.  Some cleanup (details)
77. Updated TE matching condition for amp factor eqn (details)
78. Minor refactoring (details)
79. Refactored secondary variable class in IBL and added more unit tests (details)
80. Minor update.  Added a system test (details)
81. Added a system test for forced transition case (details)
82. Fixed some double semicolons (details)
83. Overhauled IBL with 6-unknown cut-cell formulation.  All unit test (details)
84. Went on fixing PanelMethod unit tests that are affected by IBL (details)
85. Fixed missing keywords: typename and template (details)
86. Refactored IBL-related fluxAdvectiveUpwind to fix compiling errors. (details)
87. Fixed uncoupled IBL system test case on airfoil only.  [TBD] (details)
88. Fixed block 4x4 jacobian ping test.  Minor refactoring (details)
89. Fixed the uncoupled IBL airfoil+wake case.  Previously failing due to a (details)
90. Updated IBL output functions and unit tests (details)
91. Put new IBL output function to work in a system test (details)
92. updated forced transition coordinate default (details)
93. (1) Debugged and refactored hubtrace matching conditions (eqns) and (details)
94. Debugged and refactored IBL hubtrace equation/flux formulation. (details)
95. Refactored IBL-related machinery involving profile determination at (details)
96. Initial solution matters in IBL cases!  Tweaked it to make test cases (details)
97. pre merge (details)
98. Fixed a runtime error.  The problem was caused by using the same name (details)
99. Cleaned PDEIBL a bit and added unit tests on hubtrace fluxes/sources (details)
100. Relaxed IBL output unit tests given that I am currently hacking p1 for (details)
101. Fixed error. Lesson: cannot use static members without instantiating the (details)
102. Relaxed pyrite tolerance for clang on reynolds (details)
103. Added high-level machinery (higher than elemental Galerkin weighted (details)
104. Refactored logic: use cut-cell transition Galerkin weighted integral (details)
105. Completed an initial version of cut-cell transition IBL residual --> (details)
106. Added specialized jacobian clasess for cut-cell transition IBL (details)
107. Got new Jacobian machinery to compile with existing no-transition IBL (details)
108. Added a new ping test for cut-cell transition IBL.  [To be completed] (details)
109. Fixed a bug in cut-cell elemental jacobian.  Ping test passes now :) (details)
110. Got cut-cell machinery to work for forced transition at an element (details)
111. Fixed interface flux at transition front.  Updated system test pyrite (details)
112. Fix for a jacobian ping test (details)
113. Refactored cut-cell integrandCell class. Updated system test initial (details)
114. Fixed a bug in cut-cell transition Galerkin weighted integral: missing (details)
115. Some cleanup (details)
116. updated a pyrite file since the Auxi equation upwind flux changed in two (details)
117. Added a system test case [Only works for intra cell force transition (details)
118. Intra-cell transition is working with no explicit mass conservation at (details)
119. Got intra-cell transition to work with explicit mass conservation. (details)
120. Verified that forced transition at element interface still works will (details)
121. Fixed asymmetric solution with explicit mass conservation.  [TBD] needs (details)
122. Adding Bernstein BF for triangles and Tets (details)
123. Cleaned up a system test (details)
124. Added a toy case for examing volume ratio's effect on system (details)
125. Renamed file.  Separated cut-cell hack of integrand cell out to a (details)
126. Mostly cleanup and restoration (details)
127. Switched weighting function is DG weighted residuals from original (details)
128. Updated gitignore (details)
129. Fixed the ill-conditioning issue with cut-cell transition IBL (when cut (details)
130. Fixed the ill-conditioning issue with cut-cell transition IBL (when cut (details)
131. Refactored indexing usage (details)
132. Some cleanup (details)
133. pre merge (details)
134. Revived hacks for explicit mass conservation at transition front (details)
135. Refactored IBL transition treatment with or without explicit mass (details)
136. Renaming for clarity (details)
137. Refactored IBL elemental weighted residual computation so that it can (details)
138. Minor refactoring (details)
139. Started working on explicit mass conservation at transition front via an (details)
140. Refactoring so that  residual machinery compiles.   Jacobian stuff to be (details)
141. Minor refactoring for speedup (details)
142. Implemented coupling jacobian between matching conditions/variables and (details)
143. Fixed a bug in DOF mapping call.  Completed dummy equation/jacobian for (details)
144. Completed jacobian w.r.t. parameters.  Jacobian ping test underway (details)
145. minor edits (details)
146. minor refactoring (details)
147. Bug fix in residual cell. Other minor refactoring (details)
148. minor refactoring (details)
149. Fixefd a bug in jacobian param (details)
150. Verified the new transition IBL formulation works with no explicit mass (details)
151. Fixed ping test for transition IBL (details)
152. Updated pyrite files.  Minor refactoring (details)
153. cleanup (details)
154. added windowed output (details)
155. changed to pressure squared output (details)
156. Minor refactoring (details)
157. Refactored cut-cell determination logic to include natural transition (details)
158. first steps toward general harmonic balance (details)
159. prints whether using solve or project now (details)
160. have a harmonic balance algebraic equation set, trying to fill out (details)
161. forgot to include extra typedef (details)
162. trying to add NS field-weighted/basis-weighted comparison (details)
163. fixed but in stabilized CG, field-weighted consistency check for NS (details)
164. enable nitsche parameters (details)
165. incremental HB changes (details)
166. working on HB residual, took lifting operator out of CG flat plate (details)
167. full VMS in place, bug in flux mitstate fieldweighted (details)
168. harmonic balance still not compiling.. (details)
169. Various fixes (details)
170. Fixed compile errors (details)
171. Updated transition IBL algebraic equation set to use SystemMatrixView (details)
172. galerkin output functional now uses linearization on g, nitsche params (details)
173. HB getting there, just need to sort out element associativity (details)
174. forgot jacobian file (details)
175. HB working?? (details)
176. Working on Surrealized reference coordinate sRef for IBL transition (details)
177. bug fixes for wake-cut (details)
178. minor mods to CG tecplot output (not active) (details)
179. added PX-to-SANS ordering for P1 quad; added better developer exception (details)
180. //#define --> #undef (details)
181. added ordering option for all applicable preconditioners (details)
182. the HB solution looks correct! (details)
183. Allows IBL parameter field (Qauxv) to be surrealized based on IBL (details)
184. Now able to propagate Surrealized reference coordinate sRef through some (details)
185. unit tests for linearized stabilized cg output passing (details)
186. Completed propagation of jacobian calculation for solution-dependent (details)
187. moved HB toy to asymptotic unit test (details)
188. Refactored cut-cell elemental residual logic a little bit.  Ping tested (details)
189. Added a test case to examine natural transition [working progress] (details)
190. Added a BCList BoundaryGroups consistency checker (details)
191. Added pressure output (details)
192. Fixed dimension and added dimension checker (details)
193. Refactored IBL and GalerkinWeightedIntegral_TransitionIBL (details)
194. added nEqn() (details)
195. Refactored IBL for simplicity and cleanness (details)
196. Adding Restart Hack files (details)
197. Adding correct restart files (details)
198. unit tests passing for Galerkin mitstate w DC term and nitsche params (details)
199. Unit tests for BC input check. More MatrixDView fixes (details)
200. updated Galerkin unit test nb (details)
201. Fixed instantiations (details)
202. Fixed nightly error? (details)
203. fixed a typo (details)
204. First success in cut-cell solution-dependent natural transition (details)
205. generated genuine algebraic equation set for IPTF; moved explicit Ax=b (details)
206. Trying to fix Jenkins errors (details)
207. Adding tests for LIP sensitivities. Fixed missing check in MDF ordering (details)
208. Added Roe1D (details)
209. Updates to Burgers BCs (details)
210. Forgot files (details)
211. added checks for pow(0,b) (details)
212. Fixed ternary operator compile problem (details)
213. Various fixes (details)
214. Updated unit tests (details)
215. added checks for pow(0,b) in Surreals (details)
216. Updated porous media test cases (details)
217. generalized IPTF solver to allow for non-L2 functional minimization; (details)
218. Updates for Burgers (details)
219. Fixed compile errors and Lagrange P4 CG Hex field construction (details)
220. removed line-length warning (details)
221. Updated amplification factor equation source term (details)
222. More BC tests for Burgers and Buckley-Leverett (details)
223. Fixed hubtrace AES residual norm calculation for transitional IBL (details)
224. Fixed formatting (details)
225. Clean up (details)
226. Re-push (details)
227. Unit tests for LIP sensitivity calculations (details)
228. Fixed compile error (details)
229. Link error fixes (details)
230. Fixed missing includes (details)
231. new linesearch dump files for comparison; appears that corrected Surreal (details)
232. Forgot mpiexec (details)
233. added p6 and p7 lagrange node points (details)
234. trying to get thru Jenkins (details)
235. Added an exception (details)
236. Actual nightly fix (details)
237. added output jacobians (details)
238. Adding unit test for restart hack as well as trying to get though (details)
239. clang complains of a missing include that defines sparse-matrix (details)
240. made IPTF unit tests consistent with generalized Lp norm minimization (details)
241. preliminary avro interface (details)
242. removed copied test, guard SANS_AVRO (details)
243. oops (details)
244. forgot copyright...its been a while since i committed to sans (details)
245. changed ifld accumulation to be sqrt of a sum of squares (details)
246. moving to hypersonic (details)
247. undoing p6 and p7, don't have all the functions right now (details)
248. modified left BC data (from Sw=1 to Sw=0.9) to avoid machine precision (details)
249. Upwinding Kutta condition. Jenkins tweaks (details)
250. Added missing include (details)
251. changed left BC to (SwL=0.9) to avoid machine precision issues in BL (details)
252. some domain work (details)
253. Tangentual Us for Kutta LIP (details)
254. Added std::remove for partitioning test (details)
255. Fixed for correct std::accumulate include (details)
256. Fixed warnings (details)
257. Played with a toy case (details)
258. Removed duplicate instantiations (details)
259. Minor fixes (details)
260. Updated ccache path on testing machines (details)
261. retention of point markers and map to egads entities in EGTriangle (details)
262. construction of a domain (&xfield) from avro mesh (details)
263. changes to avro interface with XFieldDomain (details)
264. eLfld works, removed the comment about turning it off. (details)
265. guard AvroEGModel in instantiation (details)
266. added pringle function (details)
267. asan needs to be turned on in sans if turned on in avro, otherwise apple (details)
268. libmeshb library linked in tests for EGTess (details)
269. Working on full potential (details)
270. More full potential work (details)
271. conversion between sans XFieldDomain and avro::Mesh (details)
272. apparently i changed a space in MeshAdapter (details)
273. Fixed warning and compile error (details)
274. Fixed clang analyzer warning (details)
275. Bumped up unit testing time (details)
276. Making CG and DG field constructors consistent (details)
277. Tweaks to jenkins scripts (details)
278. renaming Estimate Galerkin to Estimate_StrongForm_Galerkin. This (details)
279. changing to camel case (details)
280. renaming cell and interior trace (details)
281. Simplifed Newton solver and added unit test (details)
282. Fixed warning (details)
283. Fixes to LIP and FP for Kutta and Wake (details)
284. changed FieldWeighted integrand to allow efldElem basis functions. (details)
285. more special cases for Surreal::pow (details)
286. Finished up making CG and DG Field constructors consistent (details)
287. Added vector cast multiplication (details)
288. changed back to absolute values for collecting LO and PDE errors. Should (details)
289. missing use of VectorD.h (details)
290. renamed old tests to StrongForm, started work on ErrorEstimate with (details)
291. Removed optimization and debug information from header compile check (details)
292. experimental changes to GLS tau (details)
293. added pow(0,b) tests for SurrealD (details)
294. new linesearch pyrite files for DG Buckley-Leverett consistent with (details)
295. moving to lab box (details)
296. convert Interior Trace to use efldElems (details)
297. added a second type of consistency check, recovers BasisWeighted with (details)
298. more consistency checks (details)
299. poundif back to conventional tau, to get thru Jenkins (details)
300. Nightly fixes (details)
301. Increased ccache size (details)
302. Another MKL valgrind suppression (details)
303. changed galerkin mitstate integrand to nitsche, updated unit test (details)
304. changed over a lot of integrands to the new field weighted, the (details)
305. turned off tecplot dump in galerkin moess (details)
306. Fixed compiler warnings (details)
307. pre merge (details)
308. Surreal cleanup with new pow around 0 logic (details)
309. bug fix for dK/dUx term in stabilized CG (details)
310. experimental GLS tau (details)
311. sandbox tweak (details)
312. CG local solves extract sub-matrix (details)
313. Refactored ping test function error logic (details)
314. Updates for new homebrew boost-python naming convention (details)
315. Fixes for OSX (details)
316. Only set boost-python suffix on APPLE (details)
317. More intel valgrind suppressions (details)
318. stabilized cell works, added estimate vary consistency check (details)
319. Galerkin disc folder working again (details)
320. Error Estimate folder passing (details)
321. moved disc object out of fieldbundle. every AES will have a disc (details)
322. forgot generic disc for Galerkin, DGAdv (details)
323. abs to fabs (details)
324. More tests for Vector-Vector multiplication (details)
325. Removed PROCESSOR_COUNT and CMake is way faster on OSX now (details)
326. Some more CMake cleanup (details)
327. forgot to change an interface (details)
328. Fixed ProcessorCount for OSX, but we don't use it at the moment (details)
329. camel case bug (details)
330. unsigned int comparison warnings (details)
331. reverting src/Meshing to the main branch versions (details)
332. Fixed intel optimization uninitialized data bug (bug in intel compiler) (details)
333. forgot another one (details)
334. sandbox tests compiling (details)
335. Suppress analyzier warning (details)
336. removed the memory leak (details)
337. Removed unnessesary includes (details)
338. Fixed one more memory leak (details)
339. put back constructors without disc object (details)
340. reverted unit test to not use disc (details)
341. Added more checks for finding refine, and the optional automatic build (details)
342. removing loop over pde index (details)
343. Better EGADS specification for refine (details)
344. Fixed logic whether to build refine (details)
345. added mach number derived quantity output for 3D NS (details)
346. Fixed link problems when building refine (details)
347. Fixes for DeltaWing (details)
348. Reverted PETSc build back to 3.8.4 as the transpose solve broke in 3.9.* (details)
349. new stabilizationMatrix seems to be working! no PDE template (details)
350. Added missing ifdef SANS_PETSC (details)
351. some function calls changed to references (details)
352. reverting to develop (details)
353. filing system tweaks and petsc parameters (details)
354. minor tweaks to get thru Jenkins (details)
355. Added warnings to not use PETSc 3.9 for now (details)
356. Added jzavala@mit.edu to DeveloperEmailAddresses (details)
357. Extrapolated nt growth source term in turbulent sub-element.  Working (details)
358. minor cleanup (details)
359. Updated initial guess.  Enabled restarted solution from a previous (details)
360. BuildREFINE uses new --with-OpenCASCADE flag (details)
361. Fixed memory leak (details)
362. Updated pyrite files (details)
363. IBL PDE cleanup.  Started working on upwinding at transition (details)
364. Implemented upwinding at transition front.  Added/update pyrite check (details)
365. Fixed warnings about uninitialized data (details)
366. minor cleanup (details)
367. Added unit tets for reference element mesh (details)
368. Fixed array out of bounds error for reference element mesh (details)
369. Refactored PDEIBL implementation.  In particular, relocated hubtrace (details)
370. Cleaning up Restart file read in to not need two reads, added Partition (details)
371. Refactored PDEIBL and added plenty of unit tests (details)
372. Patch unit tests for IBL BC (details)
373. Cleaned up more IBL unit tests (details)
374. FIxed a bug in panel equation residual norm calculation.  Plenty of (details)
375. Retired some unit tests.  Added missing include (details)
376. Turned off some old unit tests (details)
377. minor cleanup, added some interfaces to ndconverts (details)
378. Refactored ctau numerical flux when transition happens at an interior (details)
379. Disentangled cut-cell transition IBL machinery with the rest so that (details)
380. Fixed a test case (details)
381. relaxed torlerance (details)
382. relaxed tolerances (details)
383. Revived the stagnation flow test for laminar BL (details)
384. Refactored stagnation flow laminar BL cases (details)
385. Turned off a verbose printout (details)
386. Cleaned up CodeConsistency system test cases for IBL (details)
387. Fixed warnings etc. (details)
388. Relaxed tolerances.  Fixed warnings (details)
389. Removed an obsolete toy case (details)
390. Relaxed tolerance (details)
391. Fixed warning (details)
392. Added explicit instantiations to fix gnu compiler errors (details)
393. Separated template methods into implementation header (details)
394. Removed template keywords (details)
395. Minor refactoring (details)
396. Added missing template to the delight of gnu8 (details)
397. Added explicit instantiations.  Fixed unused variable warnings (details)
398. One more attempt (details)
399. Added a missing instantiation (details)
400. Missed typename keyword (details)
401. missed template keyword (details)
402. Removed an troublesome solution order case (details)
403. sans interface to avro complete, sandbox case for AD, doesnt really work (details)
404. Added missing instantiations for python Dict parameter get (details)
405. Fixed warnings/errors (details)
406. added instantiations (details)
407. Relaxed tolerances for intel (details)
408. fixed warnings and style (details)
409. moved order of links in CMakeLists for AFLR (details)
410. missing link to avroLib in Adaptation/MOESS (details)
411. Relaxed tolerances for release_intel18 (details)
412. Replaced M_PI with PI (details)
413. AdaptationLib needs link to TetGenLib too since XFieldDomain uses it (details)
414. more missing links, this time in system/adaptation (details)
415. more missing links (details)
416. bumped EGTessLib before SANS_TETGENLIB (details)
417. setting geometry in domain (details)
418. link in TAO optimizer too......... (details)
419. Minor naming refactoring (details)
420. minor cleanup (details)
421. setting up a case to examine whether cut-cell IBL residual is smooth (details)
422. changed Euclidian to the more typical spelling Euclidean (details)
423. forgot two (details)
424. Added printout in Newton solver (details)
425. minor changes in soln function, output. changed tau inverse to LUP (details)
426. Added ugrid reader. Fixed some cmake bugs (details)
427. Fixed warning (details)
428. Updates for the latest version of EPIC. NodeMovement is now effective in (details)
429. Dissable AFLR4 for LIPSolver (details)
430. Added and tried full upwinding in IBL pde flux and and transition front (details)
431. Gmsh can now copy partitions (details)
432. Small fix for gmsh (details)
433. Various updates and fixes (details)
434. Fixes for runing Q2 HCH (details)
435. HCH updates for new EPIC (details)
436. completed ns jacobian flux viscous unit test (details)
437. Fixed parallel tecplot dumps (details)
438. fixes to errororder nightly (details)
439. Tweaks for MinGW (details)
440. Updated gmsh writer so each BC is displayed independently in gmsh GUI (details)
441. Added directory creation for HCH (details)
442. Updated dummy variable values.  Added and turned off some hacks (details)
443. Updated toy case that examines residual smoothness of cut-cell (details)
444. added LUP solve for surreal1 (details)
445. Different initial qualeties for EPIC 2D vs 3D (details)
446. Updated toy case to examine cut-cell IBL residual smoothness (details)
447. turned off a state validity check that is being developed (details)
448. Updates for compiling with mingw (details)
449. Refafored IBL upwind flux to accommodate mit-state inflow BC, along with (details)
450. Reverted a pyrite file (details)
451. BOOST_DATA_TEST_CASE is not available on older versions of BOOST (e.g. (details)
452. Forgot that some outdated pyrite files were deleted (details)
453. Reorded matching conditions at transition front (details)
454. relaxed tolerance (details)
455. minor tweaks (details)
456. Tweaks to boost and cblas (details)
457. Reorded matching equations in unit test (details)
458. Updated assertion (details)
459. playing with toy case (details)
460. Renamed a function to avoid misuse (details)
461. Added MKL as an option to sansLIP solver (details)
462. Fixed unit test (details)
463. Added ugrid reader unit test (details)
464. Fixed missing call to base class constructor in XField_ugrid (details)
465. minor refactoring (details)
466. mod'd solution fcn, test cases (details)
467. format error fixed (details)
468. another stupid format error (details)
469. minor refactoring (details)
470. revert BN BC to original formulation (details)
471. added HB unit test, fixed format (details)
472. order of cmake file wrong? (details)
473. new hb unit tests (details)
474. modified ojeda soln fcn (details)
475. remove adjoint dumps from CG MOESS (details)

Cleaned up test case

Added updated gmsh reader test

Reader change

Added a control test case

Added plate test case

Fixed tandem sphere normalization

Fixed vara and compiler warnings

Refactored indexing in IBL

Removed redundant IBL auxiliary equation implementation

Refactored IBL to include placeholders for the amplification factor
(transition) and lag equations.  Refactored much of the old IBL PDE
implementation

Refactored/fixed panel method to accommodate changes in PDEIBL.  Patched
missing instantiations.

Removed more unnecessary files

Turned off verbose printout

Delta wing case to dump metrics for ODU

Added IBL PDE indexing checks.  Added a var interpreter method.  Fixed a
benign typo

Added equations to IBL: amplification factor growth and shear stress
lag. [Not yet tested!!!]  Updated variable mu naming

Added 4th order Lagrange Basis Functions for Hexs and Unit Tests

patched some unit tests, but still working progress

Cleaned up IO files in sandbox

Refactored to use line-based parsing when reading initial IBL solutions.

Added more quantities to IBL output list

Added pressure gradient parameter beta to IBL output list

1. Refactored/debugged IBL PDE's transition and lag implementation; 2.
Added the transition toy case to indexing

Refactored profile selection.  Minor working update on lag equation

Cleaned up IBL transition and lag source terms

Changed primary unknown from G to ctau.  Updated naming.

More fix on VarType naming

1. Cleaned up template types; 2. Refactored lag equation formulation:
prescribing ctau in laminar region and convecting ctau in turbulent
region

Minor refactoring on IBL pde

tweaks to read in ODU grids

Refactored secondary var calculations: now supporting multiple
dissipation closures.  [Haven't fixed affected unit tests yet!!!]

Added ctau_eq to IBL output list

Fixed a bug in ctau_eq calculation

a possible bug fix for FeFloa

stuff to read in the ODU grids

Fixed system test on coupled IBL/panel.  Verified that newly added
transition+lag equation didn't affect previous solution.  Minor bug
fixes in PDEIBL.  Added ctau_eq for SANS-IBL formulation.

Avoided dividing by zero when calculating pressure gradient parameter
beta

Fixed XFOIL-lag closure

Completed IBL3 lag/dissipation formulation and add that of XFOIL

refactored ctau transition fitting: forced transition at airfoil TE now
uses fluxMatching to carry out fitting

Refactored transition fitting of ctau for transition that happens on the
airfoil --> [TBD] robustness and effectiveness still to be examined

tweaks to read in the ODU grids

minor edit

First solution of forced transition at a grid node

Fixed typos in comments

Renamed velocity profile class

Renamed secondary var class

Fixed IBL unit tests compilation

Modularized fluid parameters into a dedicated model class

refactored and unit tested gas model in IBL

Removed Pr in IBL

Refactored IBL edge viscosity model/parameter

A solve case for running a sequence of grids

increased the PTC max iter and use the final solution from the previous
solve as the initial condition for the next

always starts from a p0 solve, now has lots of Newton steps allowed

Generalized abstractions of flow parameters and compressibility types. 
Fixed FluidModel unit test

Added more velocity profile unit tests. Updated function name

Fixed an insidious bug in IBL source term

Passed all the IBL unit tests

Added instantiation.  Fixed panel method unit tests.

minor fix

Removed files that popped up again in the last merge.  Fix for last
merge

Abstracted transition model into a dedicated class

Replaced DBL_EPSILON with std::numeric_limits<Real>::epsilon()

Fixed missing typename and template keywords

Fixed panel method system testing dump.  Refactored transition model
dictionary and PDEIBL constructor

Updating delta wing

Updated linesearch names

Refactored transition model: 1. ensures profile and intermittency is
consistent; 2. extensible to various transition mechanisms

Refactored control statements to avoid compiler warnings

Fixed uncoupled IBL test cases.  Airfoil+wake may be refactored after
the coupled IBL case is fully restored

Fixed system tests for IBL. Deleted obsolete ones

Moved the TE thickness treatment from integrand to PDEIBL

Covered fluid models with more extensive unit tests.  Turned off some
unused code that could be used later.

Refactored transition model profile choice logic.  Fixed PDEIBL unit
test

Fixed system test.  More unit tests.  Some cleanup

Updated TE matching condition for amp factor eqn

Minor refactoring

Refactored secondary variable class in IBL and added more unit tests

Minor update.  Added a system test

Added a system test for forced transition case

Fixed some double semicolons

Overhauled IBL with 6-unknown cut-cell formulation.  All unit test
passing.  [TBD] more comprehensive unit tests are necessary as the
formulation settles down

Went on fixing PanelMethod unit tests that are affected by IBL
refactoring

Fixed missing keywords: typename and template

Refactored IBL-related fluxAdvectiveUpwind to fix compiling errors. 
Added instantiations to compile an IBL system test. [TBD] runtime error
to be fixed

Fixed uncoupled IBL system test case on airfoil only.  [TBD]
airfoil+wake solution being debugged

Fixed block 4x4 jacobian ping test.  Minor refactoring

Fixed the uncoupled IBL airfoil+wake case.  Previously failing due to a
bug in the TE matching flux

Updated IBL output functions and unit tests

Put new IBL output function to work in a system test

updated forced transition coordinate default

(1) Debugged and refactored hubtrace matching conditions (eqns) and
matching fluxes. (2) Turned off amplification and lag eqns for now.  (3)
Revived all IBL system tests without amp and lag eqns

Debugged and refactored IBL hubtrace equation/flux formulation. 
Refactored inflow bc source of IBL amp factor eqn [more work needed]. 
Revived all the IBL system test cases with lag+amp, except forced
transition.  Updated initial solution so that nonlinear solver can
converge.

Refactored IBL-related machinery involving profile determination at
transition front.  [Some are hacky currently; to be fixed].  Revived
forced transition with the new 6-unknown IBL formulation

Initial solution matters in IBL cases!  Tweaked it to make test cases
happy

pre merge

Fixed a runtime error.  The problem was caused by using the same name
(i.e. GasModel) for two different classes.  The compiler was probably
confused as to which instantiations of the class it should use and
likely threw its dice instead of throwing an error. --> Lesson: don't
use the same class name (esp. in the same namespace)

Cleaned PDEIBL a bit and added unit tests on hubtrace fluxes/sources

Relaxed IBL output unit tests given that I am currently hacking p1 for
transition. [TBD: to be fixed later]

Fixed error. Lesson: cannot use static members without instantiating the
class.

Relaxed pyrite tolerance for clang on reynolds

Added high-level machinery (higher than elemental Galerkin weighted
integral) for cut-cell transition of IBL.

Refactored logic: use cut-cell transition Galerkin weighted integral
only when transition model is active

Completed an initial version of cut-cell transition IBL residual -->
compiled with the forced transition system test case.  [TBD] now need to
complete Jacobian

Added specialized jacobian clasess for cut-cell transition IBL

Got new Jacobian machinery to compile with existing no-transition IBL
case.  Still passed that system test

Added a new ping test for cut-cell transition IBL.  [To be completed]

Fixed a bug in cut-cell elemental jacobian.  Ping test passes now :)

Got cut-cell machinery to work for forced transition at an element
interface

Fixed interface flux at transition front.  Updated system test pyrite
file.  Removed IBL output hack

Fix for a jacobian ping test

Refactored cut-cell integrandCell class. Updated system test initial
solution get converge faster.  Verified system test on forced transition
still passes

Fixed a bug in cut-cell transition Galerkin weighted integral: missing
scaling terms in grid jacobian for subelement.  Added LF flux to Auxi
equations

Some cleanup

updated a pyrite file since the Auxi equation upwind flux changed in two
commits ealier

Added a system test case [Only works for intra cell force transition
without explicit mass conservation]

Intra-cell transition is working with no explicit mass conservation at
transition front

Got intra-cell transition to work with explicit mass conservation.
Updated/added pyrite files

Verified that forced transition at element interface still works will
explicit mass conservation