Tags: solidsgroup/alamo
Tags
Standard update into master branch from development (#96) * Format Documents (Tabs and Spaces) * Fixed errors in compiling * Added a default max_step value * Added default values to ref_threshold and made changes to pp_query naming errors * correctd BMP input verification, added working blade impact dynamics example * Substantial revision to traction boundary conditions for dynamics (they were never actually correct before). Shock tube case and droplet impact all working. * adding dynamicbar test, more minor fixes * fixed uninitialize value issue, and added ignores so that elastic expression BCs work in 2d and 3d * fixing formatting and docs * Fixing formatting and input errors * makefile update * reverting to div(sigma) but still need to check impact test * updating dynamics BCs to account for eigenstrain * fixing clang incompatibilities * updates for multimodel inputs to the mechanics integrator; some small updates to ParmParse * fixed backwards compatibility error from new model parse check, updated laplacian to have a parsed coefficient * fixed depenency error with .cc files during compilation * Removed some warnings * Deleted changes and applied difftool to go back to development's status * Changed pp_query to default/required PART 1 * pp_query changes PART 2 * PART 3 * pp_query changes PART 3 * pp_query changes PART 3 * pp_query changes PART 4 * fixed bug with #83 for dispersion variable bad query * pp_query changes PART 5 * pp_query changes PART 5 * pp_query changes PART 5 * pp_query changes PART 5.2 * pp_query changes PART 6 * pp_query changes PART 6.1 * pp_query changes PART 6.2 * debugging * fixed merge conflict marker * Changes in Integrator.cpp * Changes in Integrator.cpp * Reverted pp_query changes to 4 * pp_changes PART 5.3 * pp_query changes 5.4 * pp_query changes 5.5 * pp_query changes 7.0 * pp_query changes 7.1 * pp_query changes 7.3 * pp_query changes 7.2 * pp_query changes 7.4 * pp_query changes 7.5 * pp_query changes 7.41 * pp_query changes 5.5 * pp_query changes 7.7 * pp_query changes 7.8 * pp_query changes 8.0 * pp_query changes 8.1 * pp_query changes 8.2 * pp_query changes 8.21 * pp_query changes 8.22 * pp_query changes 8.23 * pp_query changes 8.3 * pp_query changes 8.4 * pp_query changes 8.5 * pp_queery changes 8.51 * pp_query changes 8.55 * pp_query changes 8.6 * pp_query changes 8.61 * pp_query changes 8.7 (Flame.cpp) * pp_query changes 8.71 (Fracture.H) * pp_query changes 8.72 (Integrator.cpp) * pp_query changes 8.721 (Integrator.cpp) * pp_query changes 8.73 (PhaseFieldMicrostructure.H) * pp_query changes 8.74 (SutureCrack.H) * updated test scripts to make them more robust * pp_query changes 8.731 (PhaseFieldMicrostructure.H) * pp_query changes 8.5 (Mechanics.H) * pp_query changes 8.51 (Mechanics.H) * pp_query changes 8.52 (Mechanics.H) * pp_query changes 8.74 (SutureCrack.H) * pp_query changes 8.75 (Reverted SutureCrack.H) * pp_query changes 8.76 (testing without validate in mechanics) * pp_query changes 8.77 (😫) * pp_query changes 8.78 (Flame.cpp rmv validate) * pp_query changes 8.781 (re added validate to Flame.cpp - was working before) * Added plot_file variable substitution * pp_query changes 8.783 redoing from the last succesful run * adding anglefmt specifier * Fixed missing anglefmt documentation * test scripts change * pp_query changes - fixed 8.73 * pp_query changes - fixed 8.74 * integrating changes from atgb-twin * renaming some models * fixed compile error in test * reverting Voronoi test * Adding pp_query_validate to Mechanics.H * Added pp_query_validate to Mechanics.H - 1.2 * pp_query FINAL UPDATES * Delete sshfile * Delete sshfile.pub * Resolved formatting changes - AllenCahn.H * Resolved formatting changes - BaseField.H * Resolved formatting changes - CahnHilliard.H * Resolved formatting changes - CahnHilliard.cpp * Reverted to OG file - Fracture.H * Reverted to OG file - SutureCrack.H * Delete sudo * Changes upon comments in Pull Request - Integrator.cpp * Integrator.cpp - Regrid int = 2 // not 10 * Integrator.cpp - PR changes * testing - remove 0 and using required - Flame.cpp * 0 TO 'NAN' changes upon PR comments - Flame.cpp/H * 0 to 'NAN' changes - Flame.cpp/H * 0 to NAN - Flame.cpp/H * retrying Flame.cpp/H fixes * retrying Flame.cpp/H fixes 2 * resetting few values except those with all zeroes in flame.cpp * resetting the same in Flame.H * adding sdf * Removed bmp and png from pp_query_validate - Flame.cpp * removed thermal disperssion from Flame.cpp * Added comments referring to -ve values in Integrator.cpp * Added pp_query_validate line in TopOp.H * Initialized values to NAN in Dendrite.H and TopOp.H. Provided Vol0frac = 0.5 * set non-pp_query values to NAN - testing * Set lower values to NAN - AllenCahn.H * Set lower values to NAN & add timestep in .cpp - Flame.cpp/H * Set lower values to NAN and added timestep in .cpp - Flame.cpp/H * Set lower values to NAN and added timestep to Flame.cpp - Flame.H/cpp * Set lower values as NAN - Integrator.H * Set the lower values to NAN - Mechanics.H * Set lower values to NAN - PhaseFieldMicrostructure.H * Set lower values to NAN - TopOp.H * testing changes in Random.H * reverted NAN changes in PhaseFieldMicroStructure.H * Updated, merged with development, and fixed regridding issue * Removing Random.IC test * Readded Random.IC test * Tried resolving compiling erros after merging * resolving merge conflicts * restoring from merge * reverting merge * trying to fix make error in test.cc and mechanics.cc * fixing make error in test.cc & mechanics.cc * using difftool to crosscheck 62c1cc5 - last successful commit * difftool a6a8654 * merging with development . pt1 * merging with development PT. 2 * fixed Integrator.cpp diff * Testing update for Random.IC in AllenCahn * Restoring AllenCahn Test * Allowing ref in AllenCahn Test * ref = False -- AllenCahn Test * finite crystal plasticity implementation * added random with , in var in allencahn * reverted test and changed input - AllenCahn * reverting to 1 before * changing = to == in AllenCahn.H * changed test - Allen Cahn * type -- alpha.ic.type - AllenCahn Test * added "" to random * removed "" * ref file gen = true * removedd sys.argv[2] * i don't know * added comma to reference = reference * reverting to OG * reverted ref file * set ref * adding reference and generating ref data - Allen Chan * reference for random.ic added * set gen_ref_data = false * added reference for remaining tests * added stop_time=30.0 * replacing NAN with -1 when initializing int * Updating coverage test to use coverage version of code * updating to amrex 24.08, which required some ParmParse fixes * removing coverage test from Linux run * Adding file hasher - wip to do runtime source checking * fixing EC issue - literally just one space * Brining in some updates from viscous2d * adding new required constant values to SCP tests * initial select implementation * wip - input parsing * formatted tabs * adding more IO utils and associated python * fixing compatibility issues * most parts working now * Finalizing alpha builder * compile error fixed * All tests passing locally - ready to merge in * removed docutils - wasn't necessary * REALLY removing docutils this time... * fixed perturbedinterface input file so now tests pass * fixing test script to catch error * Fixing reference for incorrect test * Fixing regtest issue and extending the input builder * Updating thermoelastic test to add el.bc.type * Fixing css formatting * Updating regtest script to include progress updates * updating to avoid status update with backspace on GH actions * Fixing error in run script that was failing to notice if a run crashed * updated run script to force kill a run that has timed out * merging in some of the developments from hydro * updating configure * Added kill to timeout in regtest script, was causing CI to hang on completion because jobs were still running * Cleaning up some of the tests, adding TopOp verification * Upgrading artifact uploading * Updating the pp.select implementation and documentation capability * Modernizing the inputs table formatting * more formatting changes * Formatting and purging some of the code * Code purging * purge and format * additional documentation and purging old code * fix: added Trig back in because a test depends on it * Upgrading to AMReX 25.02 * checking to make sure memcheck FAILS * bugfix: fixed an error in the linear interpolator that was accessing points outside the array * Flame bugfix - eta.ic and pf.eta.ic were both allowed which led to memory leaks. This has been fixed * fixed whitespace warning and added required documentation to Flame * Switching to ASan for memory checking. * adding ASan and MSan options, fixing some of the memory leak issues * fix workflow character error * caught some memory leaks but not all - still work to do * Updating configure script to check mpich version for ASan compatibility * Numerous memory leak fixes. * Cleaning up the test runner - formatting and adding kill * fixing stencil overflow error in Flame * Fixed another stencil overflow error in Integrator::Mechanics. Updated the pressurized hole reference data * Update issue templates * Update issue templates --------- Co-authored-by: Moses Ongole <[email protected]> Co-authored-by: meierms1 <[email protected]> Co-authored-by: Brandon Runnels <Brandon Runnels>