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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

Merged

mohanchen merged 122 commits into

deepmodeling:developfrom

mohanchen:2026-10-16-b

Nov 4, 2026

Merged

Feature: rework out_app_flag as a three-mode output controller with unified output directories, append semantics, and provenance headers#8159
mohanchen merged 122 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
- refactor(io): rename mode-2 structure output dir STRU/ -> STRUC/
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  dfbcbbb
- fix(lcao): skip Hartree gint on grid-parallel ranks with no local grid
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  0d295c4
- fix(lcao): guard local/XC gint on grid-parallel ranks with no local grid
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  a6650e3
- fix(lcao): keep gint collective matched on empty-grid ranks
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  ec9ebf9
- fix(lcao): drop doubled 'k' in potential matrix filenames
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  3ed18db
- fix(md): restore MD restart from mode-1 cumulative STRU file
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  a6c3a17
- fix(tddft): reject cumulative WFC file on positive restart step
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  de91422
- build(cell): link device lib into MODULE_CELL_stru_frame_io test
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  7076eaf
- build(io): link stru_frame_io into io_input test targets
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  5c76699
- fix(output): truncate fixed-name files on first step of a fresh run
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  e146c47
- fix(output): decouple PW wfc append decision from the filename sentinel
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  1ce77a9
- fix(input): create mode-2 subdirectories for out_hsr/out_pchg/out_wfc_norm
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  720f830
Commits on Oct 26, 2026
- Merge develop and retain both serial INPUT test dependencies
  ABACUS-PR-BOT
  committed
  241386f
Commits on Oct 28, 2026
- test(output): reuse cached MPI pool globals in WriteWfcAppendMode
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  1699b10
- refactor(hs): pass output_mat_sparse config via parameters, not PARAM
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  a2d5de8
- Merge branch 'develop' into 2026-10-16-b
  mohanchen
  authored
  a5b1b42
- Merge branch 'pr-8159' into 2026-10-16-b
  
  abacus_fixer
  authored and
  trae-solo-agent [origin=trae-ide]
  committed
  551dd94
- fix(test): link stru_frame_io.cpp into MODULE_IO_input_error_mpi
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  0d62a96
Commits on Oct 29, 2026
- Merge branch 'develop' into 2026-10-16-b
  abacus_fixer
  committed
  7fa01a6
- fix(tddft): allow istep==0 to fall back to fixed-name WFC file
  abacus_fixer
  committed
  738ba4e
- fix(md): use global step index for output writers on restarted runs
  abacus_fixer
  committed
  2e29441
- fix(io): truncate accumulators at fresh first frame in append mode
  abacus_fixer
  committed
  4a83ef6
Commits on Oct 30, 2026
- fix(md): pass local step index to electronic solver on restarted runs
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  2d702fd
- fix(io): pick MD restart STRU by frame step to avoid stale shadowing
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  cd00c72
- fix(input): restore out_eband_terms alias and create dirs for out_hsr=3
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  5547b89
- fix(io): decouple DM(R) filename selection from append decision in mode 1
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  f5c6235
- refactor(io): share compact spin tag helper across band/wfc headers
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  d252e75
- fix(test): replace direct MPI calls with wrappers in io/cell tests
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  a7c7c3e
- test(integrate): harden eband and wfc comparisons in validation scripts
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  37cd4c0
Commits on Oct 31, 2026
- Revert "fix(md): pass local step index to electronic solver on restarted runs"
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  941eb05
- fix(input): reject out_stru=2 for MD and align its help text
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  421c36c
- fix(io): forward the selected precision to the H(k) component writers
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  84f5274
- test(integrate): fail the multi-k wfc comparison when preprocessing fails
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  1dd2630
- feat(io): rework out_app_flag into 0/1/2 output controller
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  89aaa48
- test(io): align out_app_flag tests with three-mode semantics
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  1c5bde5
- docs(input): update out_app_flag and output param descriptions for 0/1/2 modes
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  19a7e8c
- docs: align output-file docs with out_app_flag three-mode semantics
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  3488125
- test(integrate): update props_cube.sh for out_app_flag mode-2-only g suffix
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  c97211d
- fix(io): mode 1 writes only the last electronic iteration per ionic step for PW wfc
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  115184b
Commits on Nov 1, 2026
- Merge branch 'develop' into 2026-10-16-b
  mohanchen
  authored
  386e195
- Merge branch 'develop' (via origin/2026-10-16-b) into 2026-10-16-b
  abacus_fixer
  committed
  5ca451a
- Merge develop for PR8159 integration baseline
  ABACUS-PR-BOT
  committed
  28e17b3
- Fix PR8159 build and solvent output integration
  ABACUS-PR-BOT
  committed
  7811506
- fix(md): decouple restart cadence from output cadence
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  0d77820
- test(relax): match write_stru mock signature to header
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  81a76e4
- docs(io): align structure-output descriptions with MD behavior
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  0f3b05a
- docs(input): state the structure-frame requirement for MD restart
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  3a35430
- fix(io): version the native binary H(R)/S(R) record header
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  b9ed06f
- fix(io): truncate mode-1 fixed-name outputs on the first ionic step
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  83f4afd
- refactor(esolver): record the LCAO ionic step in a single place
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  a30fb4a
- refactor(io): share provenance header helper across band/wfc/eband writers
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  48b7bc1
- refactor(io): create mode-2 output subdirectories at write time
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  82d0a97
- build(io): link stru_frame_io into the INPUT YAML target
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  dd1c1b2
Commits on Nov 2, 2026
- fix(md): keep restarted initial force evaluation out of charge extrapolation
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  8846951
- Merge remote-tracking branch 'origin/2026-10-16-b' into 2026-10-16-b
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  500536d
- Merge upstream/develop into 2026-10-16-b
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  218d302
- test: pin out_app_flag=1 for md_out_hk multi-frame references
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  ca7db6e
- test(dftu): slim 17_DS_DFTU to two LCAO cases and refresh refs
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  64a0697
- test(ff): move 14_LJ_rescale_v restart inputs out of OUT.autotest
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  d5c128d
Commits on Nov 3, 2026
- fix(md): broadcast MDCell STRU write offset instead of seeking EOF
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  ed00c48
- test(pw): refresh md_nvt stress reference for build_max_para_test
  
  abacus_fixer
  authored and
  trae-solo-agent
  committed
  94e5a2d
- Merge develop into PR 8159 and preserve IO collector semantics
  Critsium-xy
  committed
  e20431c
Commits on Nov 4, 2026
- fix(md): pass local step index to electronic solver on restarted runs
  abacus_fixer
  committed
  34bb07f
- fix(md): pair checkpoint STRU frames with Restart_md.txt on every
  abacus_fixer
  committed
  0bbb7c5
- fix(example): align DOS example scripts and helpers with out_app_flag default
  abacus_fixer
  committed
  3c4bac8
- fix(io): align md_restart/out_app_flag docs with the mode-2-only g{step} reader
  abacus_fixer
  committed
  ca57099
- Merge branch 'develop' into 2026-10-16-b
  mohanchen
  authored
  0a30ec7
- Merge remote-tracking branch 'origin/2026-10-16-b' into 2026-10-16-b
  abacus_fixer
  committed
  de0fe37
- fix(test): align MD restart cumulative STRU fixture with 1-based frames
  abacus_fixer
  committed
  c2ad2fd

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

Commits on Oct 26, 2026

Commits on Oct 28, 2026

Commits on Oct 29, 2026

Commits on Oct 30, 2026

Commits on Oct 31, 2026

Commits on Nov 1, 2026

Commits on Nov 2, 2026

Commits on Nov 3, 2026

Commits on Nov 4, 2026