Changes

Summary

1. Added variable interpreter for primary unknowns = {delta*, theta, G} (details)
2. Refactored IBL profile type identifier (details)
3. Added unit tests to VarInterpret (details)
4. Fixed unit test (details)
5. Added a new class for calculating thicknesses and coeffcients, along with unit tests. (details)
6. Typo fixes (details)
7. Refactored PDEIBLUniField to use genealized thicknesses/coeffcients calculation routines.  Verified uncoupled IBL run with airfoil only (details)
8. Refactoring to get coupled IBLUniField to work without transition.  Caveat: pyrite check is fine with delta & A variables, but mismatches G (maybe numerical precision issue? to be eamined) (details)
9. Cleaned up obsolete stuff (details)
10. Cleanup (details)
11. Renaming/cleanup (details)
12. Preliminary implementation of correlation closure (details)
13. Minor refactoring (details)
14. First run of correlation-closure IBL on an uncoupled airfoil-only case, compared reasonably well with profile-closure results (details)
15. minor edit (details)
16. Added turbulent closure from MSES paper.  Ran coupled IBL on airfoil+wake configuration, comparing reasonably well with IBL based on profile closures (details)
17. Distinguished H from Hk (kinematic). (details)
18. Reduced code repetition (details)
19. Added some XFOIL closures (details)
20. Added more XFOIL closures (details)
21. Typo fixes (details)
22. Refactored Uslip calculation (details)
23. Fixed a typo in xfoil laminar BL closure (details)
24. Added pyrite check for XFOIL laminar BL closure (details)
25. Recovered the correct double dissipation for wake.  Added pyrite files (details)
26. Added output dumping functions for correlation-closure IBL (details)
27. Refactored output function and added a utility function (details)
28. Added XFOIL amplification growth rate closure, which is almost identical to IBL (details)
29. Modified lag equation and CDiss closure a bit. (details)
30. With modified lag equation, laminarBL+turbulentWake results matches XFOIL very closely (details)
31. Added captured transition test case with pyrite file for correlation-based IBL (details)
32. Fixed an innocuous bug (details)
33. Re-enabled LF flux (details)
34. Added machinery for loading up IBL solution from input file (details)
35. Make LF flux a default for IBL (details)
36. Refactored blended intermittency calculation for correlation-based closure (details)
37. Do no apply blending for wake (details)
38. Switched to generalized thickness/coeffcient calculation for duplicate-field IBL as well.  Verified uncoupled airfoil case with full upwind (details)
39. Bug fix (details)
40. Verified coupled case with laminarBL+turbulentWake (details)
41. Minor refactoring (details)
42. minor cleanup (details)
43. Added instantiation and fixed transition test cases (details)
44. Added a missing method (details)
45. Added a pyrite check for NACA0012 case (with flow separation) (details)
46. Added a different set of initial solution.  Allowed for laminar BL to turn turbulent during transient state (details)
47. Added new IBL variable type (details)
48. Added unit tests and fixed bugs (details)
49. Generalized dummy equations in duplicate-field IBL pde class (details)
50. Follow-up fixes for test cases affected by earlier commits (details)
51. Refactored solution initialization (details)
52. Enabled correlation-based two-field IBL formulation.  Added test case of coupled IBL with lamiBL+turbWake and corresponding pyrite file. (details)
53. Refactored updateFraction in PDEIBL and also fixed the sign in solution update (details)
54. Generalized cut-cell machinery to handle two different sets of IBL primary unknowns (details)
55. Added pyrite check (details)
56. Added comments (details)
57. Minor refactoring.  Added missing initial solution file (details)
58. Intermediate commit (details)
59. Cleaned up test cases (details)
60. Refactored updateFraction (details)
61. Added a pyrite check (details)
62. Relaxed tolerance (details)
63. Refactoring updateFraction.  Added an expedient guard against too small Hk (details)
64. Added underrelaxation (details)
65. Added underrelaxation-related stuff (details)
66. Cosmetic edtis (details)
67. Verified pyrite check for fitted-transition IBL on NACA0012 Re=1e5 massively separated laminar BL (details)
68. Added Cf replacement for turbulent BL with too small Retheta (details)
69. Added a pyrite file (details)
70. Added a pyrite file (details)
71. BC refactoring and unit test fix (details)
72. Refactored BC and added unit tests (details)
73. Improved coverage by removing redundant safety guards (details)
74. Just renaming (details)
75. Refactoring and unit testing (details)
76. Fixed a bug in Cf correlation.  Added unit test (details)
77. Type fix (details)
78. Unit tested correlations from XFOIL. (details)
79. Refactored amplification growth correlation calculation for speedup --> changed the floating-point arithmetic a bit  Added unit tests. (details)
80. added comments (details)
81. Cleanup (details)
82. Cleanup (details)
83. Dump additional output files for examination (details)
84. Unit test fixes (details)
85. More unit test fixes (details)
86. Unit test fix (details)
87. Refactored blended intermittency calculation and added unit tests (details)
88. Refactored updateFraction and added unit tests (details)
89. minor fixes (details)
90. matching old system pyrite test: coupled IBLUniField profile-closure lamiBL+turbWake (details)
91. Changed initial solution guess (details)
92. Bug fix.  Equality operator is sensitive to type: std::string vs its reference. (details)
93. Minor refactoring (details)
94. Added comments (details)
95. Refactored unit tests (details)
96. Refactored source terms and added unit tests for PDEIBL2D (details)
97. Refactored ctau_{turb,init}.  Unit tested turbulent sub-cell source term for amplification eqn in cut-cell transition formulation (details)
98. Fix for vera formatting check.  Also a minor refactoring (details)
99. Minor refactoring (details)
100. Refactored ctau_{turb,init} fitting calculation (details)
101. Forgot to save  this in the last commit... (details)
102. Unit-tested upwind advective flux in two-fIeld IBL pde class (details)
103. Minor commenting (details)
104. Minor refactoring (details)
105. minor refactoring (details)
106. Refactored dummy matching equations for fitted transition (details)
107. Forgot to commit this in the last pass (details)
108. Modified artificial amplification source term in fully turbulent elements.  Pluse other minor refactoring (details)
109. Make sure scales are non-negative (details)
110. Enabled G=ln(ctau^0.5) as a primary unknown in place of ctau.  It helps with nonlinear solution. (details)
111. Fixed unit tests (details)
112. Dumping matching variables for transition (details)
113. Refactored underrelaxation to guard against zero G.  Added forced-transition subiteration output dump (details)
114. Turned off limiting on G variable.  Made H validity check tighter (details)
115. Playing with a different form of lag equation in fitted transition approach.  Not much luck though.  So, as of now, using G as the primary unknown is already helpful (details)
116. Playing with point source for setting ctau_{Turb,init} (details)
117. Refactored forced transition point source for ctau jump (details)
118. playing with point source for ctau jump in free transition (details)
119. Tried implementing ctau jump condition via flux modification (details)
120. Got a captured transition result with sharp ctau jump at free transition front (details)
121. Added explicit instantiation (details)
122. Genearalized HubTrace boundary trace integrand by ridding of any PDE/BC dependence (details)
123. Generalized IBL solution DOF setter (details)
124. Implemented a different formulation for captured transition by splitting the amplification and lag equations (details)
125. Added instantiations (details)
126. Fixed amplification and lag source terms in new IBL PDE class (details)
127. Verified NACA0012 Re1e5 results against XFOIL (separated fully laminar BL) (details)
128. Add a lower limit to the modeled turbulent initial ctau (details)
129. Minor refactoring (details)
130. Fixed a bug in solution initialization (details)
131. Refactored masterState calculation from cumulation to assignment (details)
132. minor tidying (details)
133. Refactored smooth intermittency blending to allow for natural and forced transition as the same time (details)
134. Allowed for initializing p0 IBL solution from input file (details)
135. Added H upper limit in validity check (details)
136. SplitAmpLag working on NACA0012 Re 2e5 separation bubble (details)
137. Cosmetic edit (details)
138. Decoupled nt variables of BL from nt of the wake (details)
139. Converged p=0 solution on ne64 and n128 grids for Eppler 387 case (details)
140. minor cleanup (details)
141. renaming (details)
142. Refactored state validity check (details)
143. minor refactoring (details)
144. Added IO files for testing Eppler 387 airfoil (details)
145. Typo fix (details)
146. Tried PTC for IBLSplitAmpLag captured transition case (details)
147. Further simplified amplification equation at hubtrace (details)
148. Added grid and initial solution files (details)
149. minor cleanup (details)
150. added hessian to Joukowski solution (details)
151. bug fix in Joukowski test (details)
152. Minor edit (details)
153. Refactored a case (details)
154. Fixed calls to jacobianTranspose of daisy-chained algebraic equation set (details)
155. Cleanup (details)
156. minor refactoring (details)
157. minor edit to running case (details)
158. Refactored printed normed reisudals when line-search fails. (details)
159. Refactored running case (details)
160. Minor cleanup (details)
161. Minor fix (details)
162. Refactored uncoupled IBL case and added pyrite file (details)
163. Fixed HDG continuous implementation.  Reverted to Var(delta, A, G) to not hacking scaling delta and A.  Cleaned up some system tests (details)
164. Refactored two test cases (details)
165. Added Hk lower limit check when checking state validity for IBLUniField with correlation closures (details)
166. Added pyrite check file.  Refactored test cases and enabled PTC on one of them. (details)
167. Fix pyrite check (details)
168. Fixed undefined variables (details)
169. Updated a pyrite file to be consistent with the latest settings in IBLUniField (details)
170. Deleted a redundant case (details)
171. added some commented out hack for fully turbulent BL simulation with IBLUniField (details)
172. Updated pyrite file (details)
173. Added exceptions as safe guards (details)
174. cosmetic refactoring (details)
175. cosmetic refactoring (details)
176. Added a pyrite file and changed test file name (details)
177. turned on set IBL dofs for p=0 for DsThG (details)
178. Dumped singular jacobian when UMFPACK finds it (details)
179. Refactored system test cases (details)
180. Using a less conservative initial CFL for PTC in a test case (details)
181. Refactored system test case (details)
182. Added some auxiliary functions for system test cases (details)
183. Added some debugging options (details)
184. Minor refactoring (details)
185. Simplified upwind flux in IBL to improve code reuse (details)
186. Commented out hacks.  Added minor guards.  Dumped matrix when UMFPACK linear solve fails. (details)
187. Laminar-turbulent blending works for Eppler 387 now.  Turned on G limiting in updateFraction (details)
188. Cleaned up and refactored projection to Qauxi (details)
189. Removed redundant TopoDim templates following Hugh's recent updates (details)
190. playing with numerical flux and nt growth rate in laminar-turbulent blending formulation (details)
191. Playing with various grid-dependent laminar-turbulent blending strategies (details)
192. minor cleanup (details)
193. Use value instead of reference since equivalence is checked instead of identity (details)
194. Added output (details)
195. Tweaked LF flux dissipation coefficient a bit.  Modified lag source term to prevent ctau to drop with ctau_Tinit after reaching its peak.  Hacking grid dependent blending.  Left system test case unchecked for the moment (details)
196. Added Hs derivatives with unit tests.  Fixed typos in closure unit tests (details)
197. Abstracted Re_theta calculation (details)
198. Added Roe flux based on arithmetic average state (details)
199. Added class for setting qaux field from file (details)
200. Typo fix (details)
201. Minor refactoring (details)
202. Output blended IBL quantities (details)
203. Added an uncoupled IBL case (details)
204. Added qinif initialization to a shared file for setting up IBL case (details)
205. Using qinf initialization from a shared file (details)
206. Refactored Roe flux for IBL (details)
207. Added entropy fix (details)
208. Just hacking around.  The hacky stuff are turned off (details)
209. Reformulated DG-IBL interface flux and finally fixed solution oscillation in transition cases.  Saved other miscellaneous updates (details)
210. cosmetic changes (with hacks being commented out) (details)
211. Normalize KE equation by q^2 (details)
212. editted comments (details)
213. Use pde fluxAdvective function to calculate outflow flux at Hubtrace boundary (details)
214. cleaned up some hacks (details)
215. minor cleanup (details)
216. Accidentally messed up blended source term.  Restore it now. (details)
217. Stashed some intermediate edits (details)
218. Fixed the numerical flux of IBL momentum equations to eliminate solution jumps and/or oscillations.  Also cleaned up temporary hacks. (details)
219. Make intermittency length scale a parameter in the transition model.  Cleaned up old hacks in in PDEIBLSplitAmpLag2D (details)
220. More cleanup (details)
221. minor edits (details)
222. Disable search for boost-cmake; otherwise, runs into conflicts with FindBoost.  Need to resolve this if using boost-cmake in the future (details)
223. Minor cleanup following last merge commit (details)
224. Minor fixes to keep up with changes in the main branch (details)
225. Add pyrite check on E387 airfoil transition separation bubble case (details)
226. Update Solve2D_Coupled4x4_IBLSplitAmpLag_CorrelationClosure_CapturedTransition_PTC_btest.cpp (details)
227. Cleaned up the numerical flux options in Qauxi projection.  All three numerical fluxes produce similar well-behaved results.  Add a sandbox case (details)
228. working on advective field case... (details)
229. asdfasdf (details)
230. working on the advective field and it's broken LOL (details)
231. fix mpi dg (details)
232. trying to figure out idiosyncracy (details)
233. cont'd (details)
234. cont'd pt. ii (details)
235. name fix (details)
236. oopsie (details)
237. working on random field (details)
238. updated random fields, should be working but untested. (details)
239. unit tests for adjoint (details)
240. fixes to compute AR etc. (details)
241. Fix for EPIC 2D without geometry (details)
242. jenkins fix, holdover code. (details)
243. adding block pivoting to ilu (details)
244. a VMSDBR2 version of the DeltaWing Chain toy (details)
245. Enable static condensation with MKL (details)
246. Missed a static condensation step (details)
247. Another MKL static condensation fix (details)
248. Relaxed tolerance (details)
249. a VMSDBR2 Double BL, also lining up the 3 so that they are the same. HOWEVER, Seems to be something very wrong with plain VMSD, the adapt looks crap and the error is enormous.... (details)
250. Updates for latest refine (details)
251. urop fix? (details)
252. jenkins fix, odds and ends. (details)
253. added 2D+T VMSD AD case. (details)
254. minor edit (details)
255. refactored the new PDE IBL class and added unit tests (details)
256. fixed LF flux (details)
257. Relocated blended intermittency to PDE class.  Added unit tests. (details)
258. Added unit tests to VarInterpret (details)
259. Fixed intermittency usage in auxi equation (details)
260. refactored intermittency calculation calling signature across different variants of IBL formulations (details)
261. Fixed type (details)
262. Refactored unit tests to keep up with updates in the thickness class (details)
263. Cleaned up manifold interface integrand implementation.  Minor type corrections for unit tests involving Surreal types. (details)
264. Fixed ping tests by adjusting the reference solution and step size (details)
265. Refactored  PDEIBLSplitAmgLag2D default flux and ctau_min.  Added pyrite check files (details)
266. updated pyrite files (details)
267. Refactored IBL solution file reader.  Cleaned up system tests for various IBL formulations (details)
268. Removed IO file clutter (details)
269. Added variable data constructors.  Fixed types.  File cleanup (details)
270. Fixed IBL solution reader usage (details)
271. Recovered a system test on IBLUniField (details)
272. Cleaned up system tests (details)
273. Fixed IBL solution reader usage (details)
274. Fixed duplicate symbols by inline.  Added a missing pyrite check file (details)
275. Relaxed pyrite tolerance.  Fixed unit tests for IBL soluton file reader (details)
276. Suppressed file output for Jenkins (details)
277. Suppressed one more file output for Jenkins. (details)
278. Fixed unused variable (details)
279. Relaxed pyrite tolerances for gnu (details)
280. Subtle typo in pyrite filename (details)
281. Relaxed tolerances for intel compilers (details)
282. Relaxed pyrite tolerance.  Added explicit instantiation to fix linker error (details)
283. Relaxed tolerance. Fixed timeout on Jenkins (details)
284. Relaxed pyrite tolerances (details)
285. relaxed tolerance on d/dxdy test (details)
286. Replace Joukowski q1 grid (details)
287. coverage improvement (details)
288. hotfix (details)
289. quick fix (details)
290. Attempt to use parallel MKL (does not work yet). Other small cleanups. (details)
291. Added cartesian table lookup for PorusMedia SPE calculations (details)
292. Use atlas blas on rhel7 (details)
293. 2d+t hex solve patch. (details)
294. belated nomenclature fix (details)
295. Consistent delete (details)
296. VMSDBR2 3D+T additions. (details)
297. added squarechannel vmsd br2 changes (details)
298. General PETSc verson on macOZ for jenkins (details)
299. Suppress tetgen CMake warning. Relax tolerance for macOS (details)
300. Allow MKL as BLAS library. Update macOS PETSc. Fix tolerance. (details)
301. Add option to dump per rank matrix market file from PETSc (details)
302. 1st crack at SPE10 test case; compiles but errors out when run; (details)
303. unit tests for PorosityModel_CartTable (details)
304. unit tests for Porosivity and Permeability (details)
305. Fix for PETSc matrix market dump (details)
306. bug fixes in 2-phase porous flow classes/tests; added CartTable unit tests for PDETwoPhase2D (details)
307. updated SPE10 test case to include lookup poro/perm tables; BCs now complaining about CartTable (details)
308. reverted to original functionality on fluxAdvectiveUpwind: no-op rather than developer exception; (details)
309. added "#include <fstream>" in lookup table tests (details)
310. SPE10 testcase: added avro include files and check on SANS_AVRO (details)
311. cppcheck fixes (details)
312. Jenkins updates (details)
313. Added Kyle Anderson k-ordering to PETSc (details)
314. Another jenkins update (details)
315. Fix warnings (details)
316. vmsd sip -> vmsd br2 in sandbox (details)
317. Update CMake build to Nlopt 2.6.1 (details)
318. SPE10 testcase: added needed instantiations for BC parameters, algebraic eq set, error estimates (details)
319. more vmsd sip -> vmsd br2 in sandbox (details)
320. Fix k-ordering (details)
321. Fix for k-ordering with BAIJ PETSc matrices (details)
322. fixed typo in comments; no change in functionality (details)
323. SPE10 testcase: fixed typos/bugs in instantiations (details)
324. SPE10: changed avro check to BOOST_FAIL, so code always compiles even if USE_AVRO not defined (details)
325. Implemented refine 2D API interface (details)
326. SPE10: generalized output functional to sum over a vector of outflow wells (details)
327. SPE10: added multiple wells to output functional (details)
328. SPE10: trying to achieve successful compile when SANS_AVRO not defined (details)
329. SPE10: added checks on porosity & permeability table lookups (details)
330. Upgrade ccache version (details)
331. vmsd -> sip again (details)
332. 2D refine updates to swork with CAD. Not done yet. (details)
333. Fix compile error (details)
334. Suppress some cppcheck warnings (details)
335. Tweak for jenkins Commit script (details)
336. less sharp exact soln, BR2 not SIP (details)
337. and output fix (details)
338. eliminated option to use single/scalar source to initialize OutputTwoPhase2D_Flowrate; (details)
339. added test for 1x1 constant lookup table (details)
340. typo fix in output functional source class name (SourceClass -> SourceOutflowClass) (details)
341. another intel suppression for valgrind (details)
342. cppcheck suppression (details)
343. Added a scaling factor to PermeabilityModel2D_CartTable to fix units in SPE10 case. Added rock compressibility to PorosityModel_CartTable, and updated unit tests. Added phi, Kxx, and Kyy as derived quantities to PDETwoPhase2D for visualization. Added table look-up files with homogeneous data for SPE10. (details)
344. Fixed unused variable warning (details)
345. forcing function adjustment... not improved :( (details)
346. Update for latest refine (details)
347. SingularException destructor instantiation (details)
348. Rename BCEulermitAVDiffusion to BCEulermitAVSensor since the name makes more sense (details)
349. First pass at including artificial viscosity model from Holst (2020) (details)
350. GCC9 caught some unitialized data (details)
351. A few bugs (details)
352. Unit tests and associated bug fixes (details)
353. Fix library ordering for HSM (details)
354. Updated gcc warning regex (details)
355. Increase timout times (details)
356. Slight correction to refine unit test (details)
357. Updates for refine incliding 2D triangle hack. Still need help from Mike. (details)
358. Dissable refine 2D test (details)
359. Refine now works in 2D (details)
360. Add restart interface for refine (details)
361. Increase timeour for refine2D tests (details)
362. Use MPI_sleep for avro execution (details)
363. Only write EGADS file from one processor and reduce iterations in refine2D_btest (details)
364. Add missing include (details)
365. Relax refine timie a bit more (details)
366. Add missing link library (details)
367. refine2D with EGADS still does not quite work. (details)
368. Fix for parallel 2D refine (details)
369. One more refine fix (details)
370. Only remove files on the rank 0 processor (details)
371. Warning fixes (details)
372. Fix up Box Tet WakeCut for adjoint (details)
373. Added Ismail-Roe entropy conservative flux (with optional entropy fix based on Harten) in 2D. Unit tested to ensure: primal and entropy consistency for the entropy conservative formulation, primal consistency and entropy dissipation for version with entropy fix. Extension to RANSSA NOT implemented. (details)
374. Added header: src/pde/NS/Roe.h to src/pde/NS/IsmailRoe.h to it can access datatype: RoeEntropyFix (details)
375. Typo fix in enum RoeEntropyFix: eIsmailRoeEntopyNeutral -> eIsmailRoeEntropyNeutral (details)
376. Added SPE10 permeability datasets with reduced contrast ratios (details)
377. Updated quarter five spot case to use avro (details)
378. lorenz building, not converging. need unit tests. (details)
379. in progress... (details)
380. lorenz in progress, not converging, seems to need stabilization. (details)
381. working on vmsd. (details)
382. added DG, broken. now VMSD and DGBR2 are both broken and CG is unstable :) (details)
383. more of the same. (details)
384. made some fixes, fem of lorenz seems to be working (w/ 4M elements...) (details)
385. trying to figure out what's wrong (details)
386. unit test addition.. (details)
387. hmm looking for valgrid shit now. (details)
388. added exact solution for alpha=0 case. (details)
389. configured for convergence test, convergent. (details)
390. output tricks (details)
391. working on homotopy pde (details)
392. for marshall (details)
393. Some progress for BCHomotopy (details)
394. homotopy in progress (still) (details)
395. on the way to a block 2x2 version of htc... (details)
396. slow but steady. (details)
397. on the curve between the easy solution and the hard one (details)
398. bob loblaw law blog (details)
399. homotopy might be working might be leaking might be a figment of my imagination. (details)
400. fieldbase uninitialized data fix. (details)
401. homotopy running but breaking for chaos :( (details)
402. added dumps (details)
403. fixed homotopy bug i think. (details)
404. added adaptive stepping to homotopy. (details)
405. ready for ben (details)
406. state of the art (details)
407. small changes. (details)
408. Removed PDE template from BCLorenz since it was no longer needed. Generalized the new homotopy integrand so it can be applied to Real and VectorS PDE::ArrayQ types. Updates required adding move construction and move assignment operator to VectorBlock_2 to prevent warnings about using implicit constructors under g++9. Propogated the required changes to unit test and sandbox cases. (details)
409. Statically condensed VMSD with homotopy: Updated the jacobian functions in the the HTC algebraic equation set, added logic for static condensation to Block 2x2 matrix interface with UMFPACK, and also had to expose the types of the vectors in VectorBlock_2. Also updated the Homotopy logic to be more robust, which mostly consists of making sure steps taken in the predictor phase are valid. (details)
410. Added ability to pass q and qp into source term individually for VMSDBR2. This is needed for some of the resolution sensors I am experimenting with for shock capturing. This required an additional source function to be added to PDEs that takes q, qp, gradq, and gradqp. Currently, this new function forwards (q+qp) and (gradq+gradqp) to the original source function. Unit tests have been added to test consistency of this new source term. (details)
411. Added new boundary condition: BCTypeFullStateRadialInflow_mitState. This is a FullState_mitState style boundary condition, except velocity magnitude is specified. The direction is then calculated as radially outward from an origin at (0,0). (details)
412. Added PDESourceOnly2D which implements a pde q - a = 0. This is for use as the auxiliary equation for Homotopy continuation. Unit tests added to applying this PDE to adevction diffusion, Euler and Euler with artificial diffusion. Also found that the jacobianMasterState and jacobianFluxAdvectveTime functions were reversed for the sensor PDE. This has been fixed and unit tests updated. (details)
413. Setting up a bump in a subsonic inviscid flow. Now verbose enables / disables all console output of the halving linesearch. Also added some extra function to PDEEuler2D to forward calls that have params. (details)
414. Added sourceCoarse and sourceFine function calls to VMSDBR2, which are source terms weighted against the coarse and fine space test functions respectively. For the most part these forward calls to the source function in the PDE. These are required because VMSD does not have a unique solution for the PDE q - a = 0 if a is a constant. Since this is the case in the SourceOnly PDE, that PDE now solves (\bar{q} - a) = 0, and q' = 0. (details)
415. Setting up RadialShock problem using VMSDBR2 and Homotopy. This required instantiating objects relating to the Block 2x2 linear algebra for PDEs of dimension 5. It also required adding the new source functions to the Sensor PDE. (details)
416. Renamed eLaplaceViscosity to eLaplaceViscosityEnthalpy in enum EulerArtViscosity. This is a more descriptive name for this option: artificial diffusion is applied to the gradient of total enthalpy (not total internal energy as a pure Laplacian operator would suggest). Now the option eLaplaceViscosityEnergy can be added to the enum EulerArtViscosity to describe the artificial diffusion being applied to the conservation variables. (details)
417. Upgraded to latest AFLR (details)
418. Added eLaplaceViscosityEnergy to enum EulerArtViscosity. This applies a Laplacian operator to the conservation variable gradient (i.e. energy gradient not enthalpy gradient). System tests have been added to ensure that the calculation is correct for Euler2D and RANSSA2D PDEs. (details)
419. Fixed two bugs highlighted by Jenkins. 1) PDELorenz was using abs on a Real. 2) Several lines in SolutionFunction_Euler2D.h were too long. (details)
420. Look for Real Time library for AFLR (details)
421. Fix for last commit (details)
422. A few AFLR fixes (details)
423. Previous commits overwrote some updates to the PETSc interface, so had to revert to commit 8fa5bcb008f4c19ec223d6ebfa628f6d4d9354cd for those files. Also updated files that failed vera checks. (details)
424. Instantiations for Block2x2 systems for a PDE of 5 equations were missing from MKL. Also, the version of UMFPack on Ubuntu 12.04 does not support the new exception types, so have reverted src/LinearAlgebra/SparseLinAlg/Direct/UMFPACK/UMFPACKSolver.cpp back to commit 45d3cd53036a51bccf943d9c5097544bd220d8f8 (details)
425. Relaxed tolerances on JacobianCell_VMSD_BR2_AD_btest for intel. Added #ifdef protection on the new UMFPACk error flags for older versions of UMFPack (pre 5.5) (details)
426. Updated BuildBoost to Boost 1.72 (details)
427. Updated AFLR to 16.30.11. Lots of cppcheck fixes. (details)
428. Add missing include (details)
429. Fixes for AFLR4 farfield mesh generation (details)
430. A few nightly fixes (details)
431. Add continuousGlobalMap for LIP solvers (details)
432. Fix the last fix (details)
433. Use CMake python when building boost (details)
434. Fix for gold linker with MKL (details)
435. Some more nightly fixes (details)
436. One more nightly fix (details)

Added variable interpreter for primary unknowns = {delta*, theta, G}

Refactored IBL profile type identifier

Added unit tests to VarInterpret

Fixed unit test

Added a new class for calculating thicknesses and coeffcients, along with unit tests.

Typo fixes

Refactored PDEIBLUniField to use genealized thicknesses/coeffcients calculation routines.  Verified uncoupled IBL run with airfoil only

Refactoring to get coupled IBLUniField to work without transition.  Caveat: pyrite check is fine with delta & A variables, but mismatches G (maybe numerical precision issue? to be eamined)

Cleaned up obsolete stuff

Cleanup

Renaming/cleanup

Preliminary implementation of correlation closure

Minor refactoring

First run of correlation-closure IBL on an uncoupled airfoil-only case, compared reasonably well with profile-closure results

minor edit

Added turbulent closure from MSES paper.  Ran coupled IBL on airfoil+wake configuration, comparing reasonably well with IBL based on profile closures

Distinguished H from Hk (kinematic).

Reduced code repetition

Added some XFOIL closures

Added more XFOIL closures

Typo fixes

Refactored Uslip calculation

Fixed a typo in xfoil laminar BL closure

Added pyrite check for XFOIL laminar BL closure

Recovered the correct double dissipation for wake.  Added pyrite files

Added output dumping functions for correlation-closure IBL

Refactored output function and added a utility function

Added XFOIL amplification growth rate closure, which is almost identical to IBL

Modified lag equation and CDiss closure a bit.

With modified lag equation, laminarBL+turbulentWake results matches XFOIL very closely

Added captured transition test case with pyrite file for correlation-based IBL

Fixed an innocuous bug

Re-enabled LF flux

Added machinery for loading up IBL solution from input file

Make LF flux a default for IBL

Refactored blended intermittency calculation for correlation-based closure

Do no apply blending for wake

Switched to generalized thickness/coeffcient calculation for duplicate-field IBL as well.  Verified uncoupled airfoil case with full upwind

Bug fix

Verified coupled case with laminarBL+turbulentWake

Minor refactoring

minor cleanup

Added instantiation and fixed transition test cases

Added a missing method

Added a pyrite check for NACA0012 case (with flow separation)

Added a different set of initial solution.  Allowed for laminar BL to turn turbulent during transient state

Added new IBL variable type

Added unit tests and fixed bugs

Generalized dummy equations in duplicate-field IBL pde class

Follow-up fixes for test cases affected by earlier commits

Refactored solution initialization

Enabled correlation-based two-field IBL formulation.  Added test case of coupled IBL with lamiBL+turbWake and corresponding pyrite file.

Refactored updateFraction in PDEIBL and also fixed the sign in solution update

Generalized cut-cell machinery to handle two different sets of IBL primary unknowns

Added pyrite check

Added comments

Minor refactoring.  Added missing initial solution file

Intermediate commit

Cleaned up test cases

Refactored updateFraction

Added a pyrite check

Relaxed tolerance

Refactoring updateFraction.  Added an expedient guard against too small Hk

Added underrelaxation

Added underrelaxation-related stuff

Cosmetic edtis

Verified pyrite check for fitted-transition IBL on NACA0012 Re=1e5 massively separated laminar BL

Added Cf replacement for turbulent BL with too small Retheta

Added a pyrite file

Added a pyrite file

BC refactoring and unit test fix

Refactored BC and added unit tests

Improved coverage by removing redundant safety guards

Just renaming

Refactoring and unit testing

Fixed a bug in Cf correlation.  Added unit test

Type fix

Unit tested correlations from XFOIL.

Refactored amplification growth correlation calculation for speedup --> changed the floating-point arithmetic a bit  Added unit tests.

added comments

Cleanup

Cleanup

Dump additional output files for examination

Unit test fixes

More unit test fixes

Unit test fix

Refactored blended intermittency calculation and added unit tests

Refactored updateFraction and added unit tests

minor fixes

matching old system pyrite test: coupled IBLUniField profile-closure lamiBL+turbWake

Changed initial solution guess

Bug fix.  Equality operator is sensitive to type: std::string vs its reference.

Minor refactoring

Added comments

Refactored unit tests

Refactored source terms and added unit tests for PDEIBL2D

Refactored ctau_{turb,init}.  Unit tested turbulent sub-cell source term for amplification eqn in cut-cell transition formulation

Fix for vera formatting check.  Also a minor refactoring

Minor refactoring

Refactored ctau_{turb,init} fitting calculation

Forgot to save  this in the last commit...

Unit-tested upwind advective flux in two-fIeld IBL pde class

Minor commenting

Minor refactoring

minor refactoring

Refactored dummy matching equations for fitted transition

Forgot to commit this in the last pass

Modified artificial amplification source term in fully turbulent elements.  Pluse other minor refactoring

Make sure scales are non-negative

Enabled G=ln(ctau^0.5) as a primary unknown in place of ctau.  It helps with nonlinear solution.

Fixed unit tests

Dumping matching variables for transition

Refactored underrelaxation to guard against zero G.  Added forced-transition subiteration output dump

Turned off limiting on G variable.  Made H validity check tighter

Playing with a different form of lag equation in fitted transition approach.  Not much luck though.  So, as of now, using G as the primary unknown is already helpful

Playing with point source for setting ctau_{Turb,init}

Refactored forced transition point source for ctau jump

playing with point source for ctau jump in free transition

Tried implementing ctau jump condition via flux modification

Got a captured transition result with sharp ctau jump at free transition front

Added explicit instantiation

Genearalized HubTrace boundary trace integrand by ridding of any PDE/BC dependence

Generalized IBL solution DOF setter

Implemented a different formulation for captured transition by splitting the amplification and lag equations

Added instantiations

Fixed amplification and lag source terms in new IBL PDE class

Verified NACA0012 Re1e5 results against XFOIL (separated fully laminar BL)

Add a lower limit to the modeled turbulent initial ctau

Minor refactoring

Fixed a bug in solution initialization

Refactored masterState calculation from cumulation to assignment

minor tidying

Refactored smooth intermittency blending to allow for natural and forced transition as the same time

Allowed for initializing p0 IBL solution from input file

Added H upper limit in validity check

SplitAmpLag working on NACA0012 Re 2e5 separation bubble

Cosmetic edit

Decoupled nt variables of BL from nt of the wake

Converged p=0 solution on ne64 and n128 grids for Eppler 387 case

minor cleanup

renaming

Refactored state validity check

minor refactoring

Added IO files for testing Eppler 387 airfoil

Typo fix

Tried PTC for IBLSplitAmpLag captured transition case

Further simplified amplification equation at hubtrace

Added grid and initial solution files

minor cleanup

added hessian to Joukowski solution

bug fix in Joukowski test

Minor edit

Refactored a case

Fixed calls to jacobianTranspose of daisy-chained algebraic equation set

Cleanup

minor refactoring

minor edit to running case

Refactored printed normed reisudals when line-search fails.

Refactored running case

Minor cleanup

Minor fix

Refactored uncoupled IBL case and added pyrite file

Fixed HDG continuous implementation.  Reverted to Var(delta, A, G) to not hacking scaling delta and A.  Cleaned up some system tests

Refactored two test cases

Added Hk lower limit check when checking state validity for IBLUniField with correlation closures

Added pyrite check file.  Refactored test cases and enabled PTC on one of them.

Fix pyrite check

Fixed undefined variables

Updated a pyrite file to be consistent with the latest settings in IBLUniField

Deleted a redundant case

added some commented out hack for fully turbulent BL simulation with IBLUniField

Updated pyrite file

Added exceptions as safe guards

cosmetic refactoring

cosmetic refactoring

Added a pyrite file and changed test file name

turned on set IBL dofs for p=0 for DsThG

Dumped singular jacobian when UMFPACK finds it

Refactored system test cases

Using a less conservative initial CFL for PTC in a test case

Refactored system test case

Added some auxiliary functions for system test cases

Added some debugging options

Minor refactoring

Simplified upwind flux in IBL to improve code reuse

Commented out hacks.  Added minor guards.  Dumped matrix when UMFPACK linear solve fails.

Laminar-turbulent blending works for Eppler 387 now.  Turned on G limiting in updateFraction

Cleaned up and refactored projection to Qauxi

Removed redundant TopoDim templates following Hugh's recent updates

playing with numerical flux and nt growth rate in laminar-turbulent blending formulation

Playing with various grid-dependent laminar-turbulent blending strategies

minor cleanup

Use value instead of reference since equivalence is checked instead of identity

Added output

Tweaked LF flux dissipation coefficient a bit.  Modified lag source term to prevent ctau to drop with ctau_Tinit after reaching its peak.  Hacking grid dependent blending.  Left system test case unchecked for the moment

Added Hs derivatives with unit tests.  Fixed typos in closure unit tests

Abstracted Re_theta calculation

Added Roe flux based on arithmetic average state

Added class for setting qaux field from file

Typo fix

Minor refactoring

Output blended IBL quantities

Added an uncoupled IBL case