fix: hessian.dat under quiet, LAMMPS dlopen errors, listed-atom file-order - #411
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fix: hessian.dat under quiet, LAMMPS dlopen errors, listed-atom file-order#411HaoZeke wants to merge 7 commits into
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quiet still suppresses the log line. require_loaded now says whether the so is missing, failed dlopen, or has no lammps_open_no_mpi.
from_conframe stores file_to_struct. ListedAtoms retries that map when the raw file-order rows are all frozen.
pbc uses minimage.Cell when installed. neighbor_list_linkcell compares vesin pairs to linkcell.knearest on the same Structure.
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Quiet suppresses the write log line only. The user guide no longer says the matrix file exists only when quiet is false.
copyTestData copies neb_morse/hessian.dat (9 lines) into the unique workdir, so exists() could not prove the job wrote the artifact under quiet=true. Remove the fixture first and require a full matrix.
Ortho and restricted-triclinic wraps agree with the eOn numpy/C++ rules, LAMMPS minimum_image, and GROMACS pbc_dx. linkcell k-NN matches vesin pairs sorted by minimage.dist2. pbc uses minimage when installed; the numpy wrap stays as pbc_eon_legacy.
Benchmark ResultsNote All benchmarks unchanged
8 unchanged benchmark(s)
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Raw asv-spyglass output |
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Four client/server bugs that showed up on an 8788-atom Cu V/SIA AKMC run, plus an optional geometry path so
minimageandlinkcellcan be checked against vesin.[Main] quiet = truestill assembled the FD Hessian and exited 0, butHessian.cppskippedhessian.dat. The Hessian job exists to write that file; quiet now only suppresses the log line.LammpsLoader::available()stays a filesystem probe (no banner).require_loaded()now says whetherliblammps.sois missing, faileddlopen(glibc), or opened withoutlammps_open_no_mpi.liblammps_pot.sois the eOn plugin, not LAMMPS.displace_atom_listin the docs is CON file-order (0, 1, 2). After load,Structuresorts uniqueatom_ids. A movable-first active-volume.conthen listed free file rows that were frozen buffer atoms after the sort (Listed atoms are all frozen).from_conframenow keepsfile_to_struct;ListedAtomsretries that map when the raw list is empty.eon.geometry.pbcusesminimage.Cell.from_vesinwhen that package is installed, else the numpy wrap.neighbor_list_linkcellis a check path againstlinkcell.knearest; productionneighbor_listis still vesin. Tests skip if those packages are not importable.tests/test_listed_atoms_id_sort.pycovers a 4-atom Cu.con(file ids 100,101,0,1; file rows 0,1 free) remapped to Structure rows[2, 3]. The C++ Hessian/LAMMPS cases are inJobIntegrationTest/LammpsLoaderTest.Fixes the quiet Hessian write, the LAMMPS dlopen message, and the listed-atom file-order trap.