Ni Sigma5(310)[001] periodic bicrystal:Atomsk ->fixedcellCG ->PTM/excessenergy.

bash build.sh         2actualAtomsk orientedcrystals;assemble/prune;deduplicate
bash run.sh           8freshGPUminimizations and4samegeometry/FDprocesses
bash analyze.sh work  reanalyze your completed data without new jobs
bash analyze.sh       analyze supplied actual data without new jobs
bash plot.sh reference redraw supplied actual source data

Full comparison needs both P100 and V10016 permissions;2minimization jobs and
1V10016static job,each1GPU2allocatedCPUcores1MPI1OMP. No directGPU SSH.
TCdynamicmembers andV10032 excluded. CPU preparation/OVITOanalysis singlethread.
Inspect work/SUBMISSIONS.json and work/CROSS-SUBMISSION.json if interrupted;
never resubmit into existing work. Use fresh extraction to start over.

Ni a3.52,orientationsA[1-30][310][001],B[130][-310][001],4x8x4nativecells.
Perfectcells1280atoms;each bicrystal1248after32B removals. Two intended pruning
thresholds1.4/1.8A produce identicaldata for eachtranslation and are not rerun.
Two X translations0/half5.56560868A nativeperiod are starting variants,not a
complete grainboundarysearch. FullxyzPBC implies2interfaces;referencearea2LxLz.
EAM Ni_u3.eam Foiles etal PhysRevB33,7983(1986),notDFT orfiniteTfreeenergy.
CG fixedbox ftol.002,dmax.05,8000iter/80000eval. No MD.

PTM nativefloat32 orientations retained. Convert tofloat64 andexplicitly
normalize quaternions before rotationmatrices;derived unitnorm and crystal
orientation checks are separate from the original rawunitnorm1e-8 mismatch.
24proper cubic symmetries used;no naive quaternionaverage. LabelsOther do not
independently define a phase. FCC plot colors use initial grainprovenance tags.

LAMMPS30Sep2026 GCC13.3/CUDA12.8/OpenMPI5.0.10/Kokkos5.2.1.
Atomsk0.13.1 GFortran13.3;OVITO3.16.1;existingNumPy/Matplotlib analysis.
