[pull] develop from lammps:develop#171
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The test generators mark new YAML files with a "generated" tag that is to be removed once the reference data is reviewed and validated. These files from the recently merged test PRs had passed review and CI with the marker still in place.
fix ffl sets scalar_flag without declaring whether its cumulative thermostat energy is extensive, which aborts any thermo output that accesses the scalar. It is extensive, like the equivalent quantity of fix langevin. Found by the new fix-timestep-ffl.yaml test.
nlevels_respa was declared but never assigned, so any r-RESPA run with this fix used an uninitialized level index in setup() and crashed or corrupted the per-level force arrays. Initialize it in init() like its sibling fix electron/stopping does. Found by the new fix-timestep-electron_stopping_fit.yaml test.
The base class constructor of fix wall/reflect allocates the graphics objects for rendering walls with dump image based on the wall count of ITS argument parser. fix wall/reflect/stochastic does not use that parser: it resets nwall and parses its own arguments, so the arrays stayed sized for zero walls (a null pointer) while post_integrate() updates them for every parsed wall. Every run with this fix style crashed since the wall rendering support was added. Factor the allocation into a helper that derived classes re-run after parsing. Found by the new fix-timestep-wall_reflect_stochastic.yaml test.
- no_restart: stochastic fixes that do not store their RNG state in restart files (e.g. langevin, qtb) cannot reproduce the reference trajectory from a restarted run; the tag skips the restart and rmass legs of the test - no_t_target: fixes that compute their target temperature internally (e.g. the nphug hugoniostat) cannot satisfy the check of the extracted t_target against the input variable
langevin (plus tally variant), ffl, qtb, baoab, viscous/nonlinear, dt/reset, thermal/conductivity, ehex, msst, nphug, nvt/uef, electron/stopping/fit, ti/spring, propel/self, brownian, wall/harmonic/outside, wall/reflect/stochastic, and wall/flow. Stochastic fixes use fixed seeds and the new no_restart tag (their RNG state is not preserved across restarts); most also skip the r-RESPA leg where the different force evaluation pattern changes the drawn random stream. msst and nphug are tagged no_restart pending a closer look at the completeness of their restart data. nvt/uef runs on a triclinic box via change_box. brownian and viscous/nonlinear run on the sphere test system of the existing brownian/sphere test.
The fix implemented only post_force(), so under r-RESPA it was never invoked and the propulsion force silently vanished. Add the standard post_force_respa()/init()/setup() pattern applying the force at the outermost level (or the level selected with fix_modify respa).
The tag marks reference data that has not been reviewed and validated yet and is removed manually after validation. Previously it was only added when a test file had no tags at all, so regenerating a file with functional tags (like no_respa) did not mark it as unreviewed.
The TMD target geometry is the fourmol data file with all positions randomly displaced by up to 0.4 Angstrom. The fix computes its distance-to-target schedule at fix creation time and stores no restart data, so the restarted-run comparison is skipped via the no_restart tag. Also regenerate the propel/self reference: with its new r-RESPA support the fix now runs under respa, but its velocity-proportional force legitimately diverges from the verlet reference trajectory, so the test keeps the no_respa tag.
Also clarify that the generated tag is now always added when reference data is written and must be removed manually after validation.
Fix-timestep test additions: 21 new fix style tests (+4 bug fixes)
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