Cont damage fix

[ChrisZYJ]

Description

Bug fix; closes #1673.

Following #1673, this PR made the following major changes to the continuous damage model:

• Instead of the scalar D, now it advances the conservative $U_D=m_{solid}D$ with flux $U_D u$ and source $m_{solid} \dot{D}$
• $-p\mathbf{I}$ is included correctly in the maximum principle stress, for 1D/2D/3D
• Energy now tracks energy related to undamaged modulus $G_0$, so the states remain finite and stable as D->1
• D is carefully clipped to [0,1] (and projects $U_D$) after each stage

Testing

Regenerated the affected continuous damage golden files.

All CI passed on CPU and GPU.

Shock-cylinder interaction - damage evolution in the cylinder:

Checklist

Check these like this [x] to indicate which of the below applies.

• I added or updated tests for new behavior
• I updated documentation if user-facing behavior changed

See the developer guide for full coding standards.

GPU changes (expand if you modified src/simulation/)

• GPU results match CPU results
• Tested on NVIDIA GPU or AMD GPU

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[ChrisZYJ]

Almost done. Will update very soon.

[codecov]

Codecov Report

❌ Patch coverage is 51.28205% with 57 lines in your changes missing coverage. Please review.
✅ Project coverage is 61.64%. Comparing base (30e7004) to head (fd1f7ce).

Files with missing lines	Patch %	Lines
src/simulation/m_data_output.fpp	3.44%	28 Missing ⚠️
src/common/m_variables_conversion.fpp	44.44%	6 Missing and 4 partials ⚠️
src/simulation/m_hypoelastic.fpp	82.00%	0 Missing and 9 partials ⚠️
src/simulation/m_riemann_solver_hllc.fpp	0.00%	5 Missing and 1 partial ⚠️
src/simulation/m_riemann_solver_hll.fpp	62.50%	0 Missing and 3 partials ⚠️
src/simulation/m_riemann_state.fpp	66.66%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1723      +/-   ##
==========================================
- Coverage   61.68%   61.64%   -0.04%     
==========================================
  Files          84       84              
  Lines       21613    21674      +61     
  Branches     3196     3210      +14     
==========================================
+ Hits        13331    13362      +31     
- Misses       6090     6111      +21     
- Partials     2192     2201       +9     

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[sbryngelson]

Merged master to resolve the conflicts from #1762, which moved the elastic-energy term into f_hypoelastic_energy. The resolution keeps this PR's physics under that API: the elastic energy uses the undamaged modulus (G_K in m_variables_conversion, G_undamaged in m_data_output) and the sound speed the damaged one. That leaves master's G_damaged block in s_convert_conservative_to_primitive dead, so it is removed, together with the stress_cons copies the new API no longer needs; the Riemann private lists are master's plus solid_partial_density_L/R. Please check the G_K choice there matches your intent. Verified on the Hypoelasticity set (61 passed).

[github-actions]

Lines of Code

File	Lines	Diff
src/simulation/m_hypoelastic.fpp	628	+37
src/simulation/m_data_output.fpp	1336	+26
src/simulation/m_riemann_solver_hll.fpp	615	+20
src/common/m_variables_conversion.fpp	1144	+16
src/simulation/m_riemann_solver_hllc.fpp	1284	+16
src/simulation/m_time_steppers.fpp	829	+2

Directory	Lines	Diff
common	9962	+16
simulation	27769	+101
total	45555	+117