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Feature: rework out_app_flag as a three-mode output controller with unified output directories, append semantics, and provenance headers - #8159

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mohanchen wants to merge 53 commits into

deepmodeling:developfrom

mohanchen:2026-10-16-b

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Feature: rework out_app_flag as a three-mode output controller with unified output directories, append semantics, and provenance headers#8159
mohanchen wants to merge 53 commits into
deepmodeling:developfrom
mohanchen:2026-10-16-b

Commits on Oct 16, 2026
- refactor(out_app_flag): change out_app_flag from bool to int and add unified output directories
  abacus_fixer
  committed
  ae461dd
- feat(output): use unified subdirectories when out_app_flag=2
  abacus_fixer
  committed
  2545b1b
- test(io): update directory expectations for out_app_flag default
  abacus_fixer
  committed
  1beabad
- refactor(io): migrate remaining out_app_flag bool usage to int
  abacus_fixer
  committed
  a4ce9a3
- chore: remove accidentally committed quality report file
  abacus_fixer
  committed
  5adf04b
- fix(io): use local cached directory variables in ctrl_output_fp
  abacus_fixer
  committed
  e734403
- test(integrate): fix WFC file path in props_cube.sh for out_app_flag=0
  abacus_fixer
  committed
  9254e95
- feat(io): create subdirs on demand and route dmk/lx/rr/tr to MAT
  abacus_fixer
  committed
  00ece15
Commits on Oct 18, 2026
- feat(io): route dmr/tr/rr/dh/ds/lx outputs to MAT directory
  
  abacus_fixer
  and
  claude
  committed
  a77e356
- feat(io): unify STRU output directory and naming for relax and MD
  
  abacus_fixer
  and
  claude
  committed
  3a38485
- feat(md): replace md_restartfreq with out_freq_ion + out_stru
  
  abacus_fixer
  and
  claude
  committed
  aabef5f
- fix(md): start MD STRU numbering from 1 (like relax)
  
  abacus_fixer
  and
  claude
  committed
  443c337
Commits on Oct 19, 2026
- fix(io): restore MD restart STRU lookup after out_app_flag rework
  abacus_fixer
  committed
  b106783
Commits on Oct 20, 2026
- fix(io): address review comments on out_app_flag mode-2 rework
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  432649c
- Merge upstream/develop into 2026-10-16-b
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  108b2b7
- feat(io): honor out_app_flag=1 for realspace cube outputs
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  7e0ac77
- feat(io): write DM(k) to fixed filename when out_app_flag=1
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  ca73e2e
- feat(io): keep fixed T(R)/R(R) filenames when out_app_flag=1
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  0a8c069
- fix(io): use real out_app_flag for PW wavefunction output
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  9342534
- feat(io): omit geometry index in init cube names when out_app_flag=1
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  d0274b9
- docs(input): describe fixed-name behavior of out_app_flag=1
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  b8236ec
- fix(io): append DM(k) records in MD when out_app_flag=1
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  8c9091d
- docs(governance): require one-based ionic-step indices in outputs
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  a9cba38
- feat(io): full out_app_flag=1 semantics for DOS/PDOS/L/matrices
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  a658239
- feat(io): single accumulated STRU file when out_app_flag=1
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  9b2b4ac
- fix(io): terminate DM(k) matrix body with a newline
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  0933cf5
- feat(io): append PW wavefunction frames when out_app_flag=1
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  65a4a61
- feat(io): add per-ionic-step provenance header to band output
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  c14f0c8
- fix(io): use compact spin label in band provenance header
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  747646c
- test(out_app_flag): three-mode unit test coverage for naming and append semantics
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  9876bf4
- fix(test): add missing link libs and K_Vectors/precision args
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  40c8bcd
Commits on Oct 21, 2026
- test(io): align step assertions and fix DM(k) test crashes
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  d5781b1
- test(io): update STEP header in sparse-matrix references to one-based
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  5ac2adf
- fix(io): align binary H(R)/S(R) step check and docs with one-based header
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  a61b91a
- fix(io): route per-atom dH component outputs through global_mat_dir
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  613d6e8
- fix(io): include H/dH component flags in MAT dir creation predicate
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  2f33b8a
- fix(io): route remaining PW outputs and drop LCAO-only availability for out_app_flag
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  8c4ebb0
- test(io): cover save_mat overwrite and write_hsk mode-2 rerun semantics
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  4ca63db
- fix(md): keep legacy STRU directory layout when writing MD structures
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  7cc8eb0
- fix(io): resolve MPI crashes in write_dipole when out_dipole=1
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  13b21fb
- Merge branch 'develop' into 2026-10-16-b
  mohanchen
  authored
  1a552f8
- fix(elf): keep all ranks on the FFT path in write_elf
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  43c09cd
- refactor(io): rename orbital info output from Orbital to nao.txt
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  e141cc2
- feat(io): add provenance header to text LCAO wavefunction output
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  5f944ea
- test(lr): expect one-based STEP header in sparse DMR writer test
  
  authored and
  trae-solo-agent
  committed
  fe2b62f
- feat(io): append cube frames per ionic step under out_app_flag 1
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  603824f
- feat(io): rename band-energy-term outputs and add provenance headers
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  d73fe29
- Merge remote-tracking branch 'upstream/develop' into 2026-10-16-b
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  406c8fe
- Merge remote-tracking branch 'origin/2026-10-16-b' into 2026-10-16-b
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  99c1eb9
Commits on Oct 22, 2026
- fix(io): reuse fixed dH/dS CSR filename in append mode and log every write
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  0475b92
Commits on Oct 23, 2026
- fix(test): skip provenance comment header when comparing LCAO wfc output
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  1eb4483
- refactor(io): rename band-decomposed XC output and relocate LIBRPA reference files
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  f26d911
- refactor(io): rename LCAO k-space matrix output params and fix misleading docs
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  964455d

Commits

Commits on Oct 16, 2026

Commits on Oct 18, 2026

Commits on Oct 19, 2026

Commits on Oct 20, 2026

Commits on Oct 21, 2026

Commits on Oct 22, 2026

Commits on Oct 23, 2026