doc - OpenGrok history log for /honee/doc

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0c608af5	26-Aug-2025	James Wright <james@jameswright.xyz>	Merge MR !142, 'jrwrigh/smartsim_solution', into 'main' feat(smarsim): Add solution writing for smartsim See merge request phypid/honee!142 /honee/CHANGELOG.md auxiliary.md /honee/include/honee.h /honee/include/log_events.h /honee/include/navierstokes.h /honee/include/smartsim-impl.h /honee/include/smartsim.h /honee/problems/bc_freestream.c /honee/problems/bc_outflow.c /honee/problems/blasius.c /honee/problems/channel.c /honee/problems/densitycurrent.c /honee/problems/newtonian.c /honee/problems/sgs_dd_model.c /honee/problems/stg_shur14.c /honee/problems/taylorgreen.c /honee/qfunctions/advection.h /honee/qfunctions/bc_freestream.h /honee/qfunctions/bc_freestream_type.h /honee/qfunctions/bc_outflow.h /honee/qfunctions/bc_slip.h /honee/qfunctions/blasius.h /honee/qfunctions/channel.h /honee/qfunctions/densitycurrent.h /honee/qfunctions/differential_filter.h /honee/qfunctions/gaussianwave.h /honee/qfunctions/monitor_cfl.h /honee/qfunctions/monitor_totalkineticenergy.h /honee/qfunctions/newtonian.h /honee/qfunctions/newtonian_state.h /honee/qfunctions/newtonian_types.h /honee/qfunctions/riemann_solver.h /honee/qfunctions/sgs_dd_model.h /honee/qfunctions/sgs_dd_training.h /honee/qfunctions/spanstats/cflpe.h /honee/qfunctions/spanstats/turbulence.h /honee/qfunctions/stabilization.h /honee/qfunctions/stabilization_types.h /honee/qfunctions/stg_shur14.h /honee/qfunctions/stg_shur14_type.h /honee/qfunctions/taylorgreen.h /honee/qfunctions/velocity_gradient_projection.h /honee/src/differential_filter.c /honee/src/log_events.c /honee/src/setuplibceed.c /honee/src/setupts.c /honee/src/smartsim/sgs_dd_training.c /honee/src/smartsim/smartsim.c /honee/src/smartsim/solution.c /honee/src/smartsim_weak.c /honee/src/spanstats/cflpe.c /honee/src/spanstats/turbulence.c /honee/tests/output/y0flow_solution_output.npy /honee/tests/smartsim_regression_framework.py
8fc6ab98	19-Aug-2025	James Wright <james@jameswright.xyz>	doc(smartsim): Documentation /honee/.gitlab-ci.yml /honee/CHANGELOG.md /honee/Makefile auxiliary.md /honee/examples/advection.yaml /honee/examples/advection_bl.yaml /honee/examples/advection_wave.yaml /honee/examples/navierstokes.c /honee/include/honee.h /honee/include/log_events.h /honee/include/navierstokes.h /honee/include/petsc-ceed-utils.h /honee/include/smartsim-impl.h /honee/include/smartsim.h /honee/include/spanstats.h /honee/problems/advection.c /honee/problems/bc_freestream.c /honee/problems/bc_outflow.c /honee/problems/blasius.c /honee/problems/channel.c /honee/problems/densitycurrent.c /honee/problems/eulervortex.c /honee/problems/newtonian.c /honee/problems/shocktube.c /honee/src/cloptions.c /honee/src/diff_flux_projection.c /honee/src/honee-file.c /honee/src/log_events.c /honee/src/monitor_cfl.c /honee/src/monitor_totalkineticenergy.c /honee/src/setupdm.c /honee/src/setuplibceed.c /honee/src/setupts.c /honee/src/smartsim/sgs_dd_training.c /honee/src/smartsim/smartsim.c /honee/src/smartsim/solution.c /honee/src/smartsim_weak.c /honee/src/spanstats/cflpe.c /honee/src/spanstats/spanstats.c /honee/src/spanstats/turbulence.c /honee/tests/junit.py /honee/tests/junit_common.py /honee/tests/output/cflpe-spanstats-stats.bin /honee/tests/output/y0flow_solution_output.npy /honee/tests/smartsim_regression_framework.py /honee/tests/stats_test.yaml
f0df98c0	22-Aug-2025	James Wright <james@jameswright.xyz>	refactor: Remove c_tau from Newtonian options It isn't implemented anyways. TODO: Need to edit documentation to reflect the change (if Newtonian has any lingering references to c_tau) /honee/.gitlab-ci.yml /honee/CHANGELOG.md /honee/Makefile examples.md runtime_options.md /honee/examples/advection.yaml /honee/examples/advection_bl.yaml /honee/examples/advection_wave.yaml /honee/examples/navierstokes.c /honee/include/navierstokes.h /honee/include/petsc-ceed-utils.h /honee/include/spanstats.h /honee/problems/advection.c /honee/problems/bc_freestream.c /honee/problems/bc_outflow.c /honee/problems/blasius.c /honee/problems/channel.c /honee/problems/densitycurrent.c /honee/problems/eulervortex.c /honee/problems/gaussianwave.c /honee/problems/newtonian.c /honee/problems/sgs_dd_model.c /honee/problems/shocktube.c /honee/problems/stg_shur14.c /honee/problems/taylorgreen.c /honee/qfunctions/newtonian.h /honee/qfunctions/newtonian_state.h /honee/qfunctions/newtonian_types.h /honee/qfunctions/stabilization.h /honee/qfunctions/stg_shur14_type.h /honee/qfunctions/utils.h /honee/src/cloptions.c /honee/src/diff_flux_projection.c /honee/src/differential_filter.c /honee/src/honee-file.c /honee/src/honee.c /honee/src/mat-ceed.c /honee/src/monitor_cfl.c /honee/src/monitor_totalkineticenergy.c /honee/src/setupdm.c /honee/src/setuplibceed.c /honee/src/setupts.c /honee/src/smartsim/sgs_dd_training.c /honee/src/spanstats/cflpe.c /honee/src/spanstats/spanstats.c /honee/src/spanstats/turbulence.c /honee/src/strong_boundary_conditions.c /honee/tests/junit.py /honee/tests/junit_common.py /honee/tests/output/cflpe-spanstats-stats.bin /honee/tests/stats_test.yaml
b30619f6	30-Mar-2025	James Wright <james@jameswright.xyz>	feat: Add spanstats for CFL and Peclet number - Add CalculatePe* to numerics.h /honee/.gitlab-ci.yml /honee/AUTHORS /honee/CHANGELOG.md /honee/Makefile /honee/conf.py auxiliary.md /honee/examples/navierstokes.c /honee/include/bc_definition.h /honee/include/differential_filter.h /honee/include/honee.h /honee/include/navierstokes.h /honee/include/nodal_projection.h /honee/include/petsc-ceed-utils.h /honee/include/smartsim.h /honee/include/spanstats.h /honee/problems/advection.c /honee/problems/bc_freestream.c /honee/problems/bc_outflow.c /honee/problems/bc_slip.c /honee/problems/blasius.c /honee/problems/channel.c /honee/problems/densitycurrent.c /honee/problems/eulervortex.c /honee/problems/gaussianwave.c /honee/problems/newtonian.c /honee/problems/sgs_dd_model.c /honee/problems/shocktube.c /honee/problems/stg_shur14.c /honee/problems/stg_shur14.h /honee/problems/taylorgreen.c /honee/qfunctions/advection_types.h /honee/qfunctions/bc_freestream.h /honee/qfunctions/bc_slip.h /honee/qfunctions/blasius.h /honee/qfunctions/differential_filter.h /honee/qfunctions/mass.h /honee/qfunctions/monitor_cfl.h /honee/qfunctions/newtonian_types.h /honee/qfunctions/numerics.h /honee/qfunctions/setupgeo_helpers.h /honee/qfunctions/spanstats/cflpe.h /honee/qfunctions/spanstats/turbulence.h /honee/qfunctions/stabilization_types.h /honee/qfunctions/utils.h /honee/src/bc_definition.c /honee/src/boundary_condition.c /honee/src/cloptions.c /honee/src/diff_flux_projection.c /honee/src/differential_filter.c /honee/src/dm_utils.c /honee/src/grid_anisotropy_tensor.c /honee/src/honee-config.c /honee/src/honee-mass.c /honee/src/honee.c /honee/src/honee_versioning.c /honee/src/mat-ceed.c /honee/src/misc.c /honee/src/monitor_cfl.c /honee/src/monitor_totalkineticenergy.c /honee/src/setupdm.c /honee/src/setuplibceed.c /honee/src/setupts.c /honee/src/smartsim/sgs_dd_training.c /honee/src/smartsim/smartsim.c /honee/src/smartsim_weak.c /honee/src/spanstats/cflpe.c /honee/src/spanstats/spanstats.c /honee/src/spanstats/turbulence.c /honee/src/strong_boundary_conditions.c /honee/tests/output/taylorgreen_totalke.csv
43f5052d	11-Jun-2025	James Wright <james@jameswright.xyz>	fix(doc): Missing parathesis And also demonstration for how to do an MR /honee/README.md examples.md /honee/include/dm-utils.h /honee/include/navierstokes.h /honee/problems/bc_freestream.c /honee/problems/bc_outflow.c /honee/qfunctions/bc_freestream.h /honee/qfunctions/bc_outflow.h /honee/qfunctions/blasius.h /honee/src/dm_utils.c /honee/src/qdata.c
c52fa185	31-Mar-2025	James Wright <james@jameswright.xyz>	Merge MR !108, 'jrwrigh/spanstats_tsmonitor', into 'main' refactor: Make spanwise statistics generic See merge request phypid/honee!108 /honee/CHANGELOG.md auxiliary.md /honee/examples/blasius.yaml /honee/examples/navierstokes.c /honee/include/honee.h /honee/include/navierstokes.h /honee/include/spanstats.h /honee/src/cloptions.c /honee/src/setuplibceed.c /honee/src/setupts.c /honee/src/spanstats.c /honee/src/turb_spanstats.c /honee/tests/output/taylor-green-IC.bin /honee/tests/stats_test.yaml
78c5b8e5	30-Mar-2025	James Wright <james@jameswright.xyz>	refactor: Use TSMonitorSetFromOptions for spanstats /honee/CHANGELOG.md auxiliary.md /honee/examples/blasius.yaml /honee/examples/navierstokes.c /honee/include/honee.h /honee/include/navierstokes.h /honee/include/spanstats.h /honee/src/cloptions.c /honee/src/setuplibceed.c /honee/src/setupts.c /honee/src/spanstats.c /honee/src/turb_spanstats.c /honee/tests/stats_test.yaml
d9f57b1c	25-Mar-2025	James Wright <james@jameswright.xyz>	tg: Add background_velocity option for TaylorGreen IC /honee/CHANGELOG.md examples.md /honee/problems/taylorgreen.c /honee/qfunctions/taylorgreen.h
881dd9b7	28-Mar-2025	James Wright <james@jameswright.xyz>	fix: Documentation formatting error /honee/.gitlab-ci.yml /honee/CHANGELOG.md examples.md /honee/include/bc_definition.h /honee/src/bc_definition.c
0fb1909e	24-Mar-2025	James Wright <james@jameswright.xyz>	doc: Rearrange documentation auxiliary.md examples.md runtime_options.md theory.md /honee/index.md /honee/qfunctions/advection.h
7c69a229	24-Mar-2025	James Wright <james@jameswright.xyz>	doc: Convert docs to single sentence-per-line theory.md /honee/src/cloptions.c
ef55efad	24-Mar-2025	James Wright <james@jameswright.xyz>	feat: Change default checkpoint_interval to 0 Binary files are no longer the standard restart file format (CGNS is), therefore this should be avoided. /honee/CHANGELOG.md runtime_options.md /honee/src/cloptions.c
4e1dcb99	16-Feb-2025	James Wright <james@jameswright.xyz>	feat: Add -ts_eval_solutions_view for -ts_eval_times Writes out intermediate solutions specified by `-ts_eval_times` /honee/.gitlab-ci.yml /honee/CHANGELOG.md runtime_options.md /honee/examples/navierstokes.c /honee/include/navierstokes.h /honee/src/honee-file.c /honee/src/monitor_totalkineticenergy.c /honee/src/setupts.c /honee/src/turb_spanstats.c
71f2ed29	12-Dec-2024	James Wright <james@jameswright.xyz>	feat: Add -mass_ksp_view_pre_ts_solve Views mass ksp once before solve. Also sets up the KSP so that the information is complete. /honee/CHANGELOG.md runtime_options.md /honee/examples/navierstokes.c /honee/include/navierstokes.h /honee/problems/advection.c /honee/problems/channel.c /honee/problems/newtonian.c /honee/qfunctions/newtonian.h /honee/src/setuplibceed.c /honee/src/setupts.c /honee/tests/channel_divdiff_verify.yaml /honee/tests/output/channel_div_diff_verify_indirect_explicit.bin
16cb6b6b	09-Dec-2024	James Wright <james@jameswright.xyz>	feat: Add -ksp_post_solve_residual /honee/CHANGELOG.md runtime_options.md /honee/examples/navierstokes.c /honee/include/log_events.h /honee/include/navierstokes.h /honee/problems/advection.c /honee/problems/densitycurrent.c /honee/problems/newtonian.c /honee/problems/sgs_dd_model.c /honee/problems/shocktube.c /honee/problems/torch/sgs_model_torch.cpp /honee/qfunctions/advection.h /honee/qfunctions/blasius.h /honee/qfunctions/channel.h /honee/qfunctions/densitycurrent.h /honee/qfunctions/eulervortex.h /honee/qfunctions/mass.h /honee/qfunctions/newtonian.h /honee/qfunctions/setupgeo.h /honee/qfunctions/setupgeo2d.h /honee/qfunctions/setupgeo_helpers.h /honee/qfunctions/shocktube.h /honee/src/cloptions.c /honee/src/diff_flux_projection.c /honee/src/differential_filter.c /honee/src/honee-file.c /honee/src/honee-ksp.c /honee/src/log_events.c /honee/src/monitor_cfl.c /honee/src/petsc_ops.c /honee/src/setupdm.c /honee/src/setuplibceed.c /honee/src/setupts.c /honee/src/smartsim/sgs_dd_training.c /honee/src/smartsim/smartsim.c /honee/src/strong_boundary_conditions.c /honee/src/velocity_gradient_projection.c /honee/tests/output/adv-rotation-cosine.bin /honee/tests/output/adv-rotation-implicit-stab-supg.bin /honee/tests/output/adv-skew.bin /honee/tests/output/adv-translation-implicit-stab-su.bin /honee/tests/output/adv2d-boundary-layer-ic.bin /honee/tests/output/adv2d-rotation-explicit-stab-supg-consistent-mass.bin /honee/tests/output/adv2d-rotation-explicit-strong.bin /honee/tests/output/adv2d-rotation-implicit-stab-supg.bin /honee/tests/output/adv2d-wave-sine.bin /honee/tests/output/adv2d-wave-square-direct_divdiff.bin /honee/tests/output/adv2d-wave-square-indirect_divdiff.bin /honee/tests/output/blasius-bc_slip.bin /honee/tests/output/blasius-bc_slip_indirect.bin /honee/tests/output/blasius-sgs-data-driven.bin /honee/tests/output/blasius.bin /honee/tests/output/blasius_STG.bin /honee/tests/output/blasius_STG_strongBC.bin /honee/tests/output/blasius_STG_weakT.bin /honee/tests/output/blasius_diff_filter_aniso_vandriest.bin /honee/tests/output/blasius_diff_filter_iso.bin /honee/tests/output/channel-prim.bin /honee/tests/output/channel.bin /honee/tests/output/dc-explicit.bin /honee/tests/output/dc-implicit-stab-none.bin /honee/tests/output/euler-explicit.bin /honee/tests/output/euler-implicit.bin /honee/tests/output/flatplate-STG.bin /honee/tests/output/gaussianwave-IDL-entropy.bin /honee/tests/output/gaussianwave-IDL.bin /honee/tests/output/gaussianwave-cgns-load.bin /honee/tests/output/gaussianwave-explicit.bin /honee/tests/output/gaussianwave-shell.bin /honee/tests/output/shocktube-explicit-su-yzb.bin /honee/tests/output/taylor-green-IC.bin /honee/tests/output/taylor-green.bin /honee/tests/output/turb-spanstats-IC.bin /honee/tests/output/turb-spanstats-stats.bin /honee/tests/stats_test.yaml
87fd7f33	07-Dec-2024	James Wright <james@jameswright.xyz>	feat: Add -ts_monitor_cfl /honee/CHANGELOG.md runtime_options.md /honee/examples/navierstokes.c /honee/include/navierstokes.h /honee/problems/newtonian.c /honee/qfunctions/monitor_cfl.h /honee/src/monitor_cfl.c /honee/src/monitor_totalkineticenergy.c /honee/src/setupdm.c /honee/src/setupts.c /honee/tests/output/adv2d-wave-square-direct_divdiff_cfl.csv
78a26750	05-Dec-2024	James Wright <james@jameswright.xyz>	doc: Rearrange runtime options documentation runtime_options.md /honee/examples/navierstokes.c /honee/src/setupdm.c /honee/tests/gaussianwave_cgns_load.yaml /honee/tests/gaussianwave_test_5.cgns /honee/tests/junit.py /honee/tests/output/fluids-navierstokes-gaussianwave-cgns-load.bin
eb9b4fe1	18-Nov-2024	James Wright <james@jameswright.xyz>	feat: Enable CGNS restarts /honee/CHANGELOG.md runtime_options.md /honee/include/navierstokes.h /honee/src/cloptions.c /honee/src/honee-file.c /honee/src/setupdm.c /honee/src/setupts.c /honee/tests/junit.py
354560d1	02-Dec-2024	James Wright <james@jameswright.xyz>	feat: Add max_wall_time PostStep /honee/CHANGELOG.md runtime_options.md /honee/examples/navierstokes.c /honee/include/navierstokes.h /honee/src/cloptions.c /honee/src/setupts.c
8b774af8	29-Nov-2024	James Wright <james@jameswright.xyz>	feat: Add -honee_check_step runtime_options.md /honee/examples/navierstokes.c /honee/examples/taylor_green_vortex.yaml /honee/include/navierstokes.h /honee/problems/stg_shur14.c /honee/src/cloptions.c /honee/src/setupts.c /honee/tests/junit.py /honee/tests/junit_common.py /honee/tests/output/fluids-navierstokes-taylor-green.bin /honee/tests/output/taylorgreen_totalke.csv
25125139	22-Nov-2024	James Wright <james@jameswright.xyz>	feat: Add monitor for total kinetic energy balance /honee/CHANGELOG.md runtime_options.md /honee/examples/navierstokes.c /honee/include/honee-file.h /honee/include/navierstokes.h /honee/qfunctions/monitor_totalkineticenergy.h /honee/qfunctions/sgs_dd_model.h /honee/src/cloptions.c /honee/src/diff_flux_projection.c /honee/src/grid_anisotropy_tensor.c /honee/src/honee-file.c /honee/src/honee-mass.c /honee/src/misc.c /honee/src/monitor_totalkineticenergy.c /honee/src/setuplibceed.c /honee/src/setupts.c /honee/src/turb_spanstats.c /honee/src/velocity_gradient_projection.c
481d14cb	17-Nov-2024	James Wright <james@jameswright.xyz>	refactor: Remove -continue, add use_continue_file internally runtime_options.md /honee/examples/navierstokes.c /honee/include/navierstokes.h /honee/src/cloptions.c /honee/src/misc.c /honee/tests/stats_test.yaml
2136baaa	17-Nov-2024	James Wright <james@jameswright.xyz>	refactor: -continue_filename has no default value runtime_options.md /honee/src/cloptions.c
ea2beb2d	16-Nov-2024	James Wright <james@jameswright.xyz>	refactor: Remove -continue_time_filename option runtime_options.md /honee/include/honee-file.h /honee/include/mat-ceed-impl.h /honee/include/mat-ceed.h /honee/include/navierstokes.h /honee/include/petsc-ceed-utils.h /honee/problems/sgs_dd_model.c /honee/qfunctions/advection.h /honee/qfunctions/advection_types.h /honee/qfunctions/blasius.h /honee/qfunctions/channel.h /honee/qfunctions/densitycurrent.h /honee/qfunctions/diff_flux_projection.h /honee/qfunctions/differential_filter.h /honee/qfunctions/eulervortex.h /honee/qfunctions/gaussianwave.h /honee/qfunctions/grid_anisotropy_tensor.h /honee/qfunctions/inverse_multiplicity.h /honee/qfunctions/mass.h /honee/qfunctions/newtonian.h /honee/qfunctions/newtonian_state.h /honee/qfunctions/newtonian_types.h /honee/qfunctions/setupgeo.h /honee/qfunctions/setupgeo2d.h /honee/qfunctions/setupgeo_helpers.h /honee/qfunctions/sgs_dd_model.h /honee/qfunctions/sgs_dd_training.h /honee/qfunctions/sgs_dd_utils.h /honee/qfunctions/shocktube.h /honee/qfunctions/stabilization.h /honee/qfunctions/stg_shur14.h /honee/qfunctions/stg_shur14_type.h /honee/qfunctions/strong_boundary_conditions.h /honee/qfunctions/taylorgreen.h /honee/qfunctions/turb_spanstats.h /honee/qfunctions/utils.h /honee/qfunctions/utils_eigensolver_jacobi.h /honee/qfunctions/velocity_gradient_projection.h /honee/src/cloptions.c /honee/src/honee-file.c /honee/src/mat-ceed.c /honee/src/petsc_ops.c /honee/src/setupts.c /honee/src/smartsim/sgs_dd_training.c /honee/src/turb_spanstats.c
80e9ac5b	15-Oct-2024	James Wright <james@jameswright.xyz>	refactor: Rename advection flags to `-advection_ic_*` runtime_options.md /honee/examples/advection.yaml /honee/examples/advection_wave.yaml /honee/examples/navierstokes.c /honee/problems/advection.c
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