Repository navigation
Feature: rework out_app_flag as a three-mode output controller with unified output directories, append semantics, and provenance headers - #8159
Conversation
…unified output directories
- Change out_app_flag from bool to int with three states:
0: no append, no subdirectory (overwrite)
1: append to same file (default, backward compatible)
2: write to unified subdirectories
- Add new global directory variables in System_para:
global_psi_dir, global_chg_dir, global_pot_dir,
global_elf_dir, global_dos_dir, global_dip_dir, global_mat_dir
- Initialize directories in set_global_dir():
out_app_flag==2 -> OUT.suffix/{PSI,CHG,POT,ELF,DOS,DIP,MAT}/
otherwise -> all point to global_out_dir (backward compatible)
- Map legacy WFC->PSI, matrix->MAT
- Update all out_app_flag usages from bool to int semantics
- Broadcast new directory variables via Parallel_Common::bcast_string
Issue: deepmodeling#8151
- ctrl_output_fp.cpp: route chg/tau to global_chg_dir, pot/potes to global_pot_dir, ELF to global_elf_dir, dipole to global_dip_dir - ctrl_output_pw.cpp: route wfc to global_psi_dir, dos to global_dos_dir, ldos to global_dos_dir - ctrl_scf_lcao.cpp: route dos to global_dos_dir - ctrl_runner_lcao.cpp: route ldos to global_dos_dir - read_input.cpp: create subdirectories (PSI/CHG/POT/ELF/DOS/DIP/MAT) when out_app_flag==2 - Update docs: out_app_flag semantics from bool to int (0/1/2) Issue: deepmodeling#8151
When out_app_flag defaults to 1 (not 2), all new unified directories (PSI, CHG, POT, ELF, DOS, DIP, MAT) map to global_out_dir for backward compatibility. Update io_sys_var_test.cpp expectations: - global_matrix_dir: "OUT.test/matrix/" -> "OUT.test/" - Add assertions for all 7 new directory variables
- read_input.cpp: change !out_app_flag to out_app_flag == 0 for matrix/WFC legacy directory decisions - Update three unit tests to use int out_app_flag (0/1) instead of bool (false/true), matching the new function signatures: test_cal_dos.cpp, test_write_dos_pw.cpp, write_wfc_nao_test.cpp - Update two comments to describe 0/1 semantics
Replace repeated PARAM.globalv.global_*_dir accesses with the local const variables already declared at function top, eliminating the net +4 PARAM global dependency introduced by the path routing change.
With out_app_flag changed from bool to int, the legacy WFC/ subdirectory is no longer created when out_app_flag=0 (now maps to global_out_dir). Update the multi-k wfc reference path accordingly.
- read_input.cpp: only create PSI/CHG/POT/ELF/DOS/DIP/MAT subdirectories when the corresponding output flag is enabled (out_app_flag=2) - ctrl_scf_lcao.cpp: route write_dmk and angular momentum calculator output to global_mat_dir instead of global_out_dir - hsr_legacy.cpp: route tr_nao.csr to global_matrix_dir - pos_op_writer.cpp: route rr_nao.txt to global_matrix_dir
mohanchen
added
Input&Output
|
@ABACUS-PR-BOT please help review the PR |
ABACUS-PR-BOT
left a comment
ABACUS-PR-BOT
left a comment
There was a problem hiding this comment.
Static review of 00ece15 with independent verification. Five implementation issues and three non-blocking suggestions are noted inline. Whitespace checks passed; the pinned governance check reported warnings only. No build or runtime tests were run, and CI diagnostics were unavailable.
- Remove md_no_append ternary in hsr_legacy.cpp, pos_op_writer.cpp, hterm_writer.cpp, dhs_sparse_writer.cpp: use global_matrix_dir unconditionally (it already equals global_out_dir when out_app_flag != 2, so no behavior change for legacy modes) - write_dmr: add dmr_dir parameter, route DM(R) to MAT instead of hardcoded global_out_dir; drop parameter.h include - read_input.cpp: add out_dmr/out_mat_l/out_mat_dh/out_mat_ds to MAT subdirectory creation flags Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- global_stru_dir now follows out_app_flag: STRU/ for flag 2,
global_out_dir otherwise (consistent with MAT/PSI/CHG pattern)
- relax_driver: route STRU_NOW/STRU{step}/STRU_FINAL through
global_stru_dir instead of global_out_dir
- run_md: drop _MD suffix, use STRU{step} naming consistent with
relax
- global_file: remove unconditional STRU dir creation from
make_dir_out; remove global_stru_dir parameter
- read_input: create STRU dir on demand (out_stru>0 or MD)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- run_md: use out_freq_ion (with md_restartfreq fallback) as the effective ionic-step output frequency for both STRU and restart - run_md: gate STRU output on out_stru > 0, consistent with relax - read_input: simplify STRU dir creation to out_stru > 0 - read_inp_out: update out_stru description to cover MD - read_input_item_md: mark md_restartfreq as deprecated Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- commit 3a38485 made global_stru_dir follow out_app_flag (default 1 maps it to the output dir), but the MD restart lookup still probed STRU_MD_{istep} there, so restart cases whose fixtures live in OUT.suffix/STRU/ (e.g. tests/04_FF/14_LJ_rescale_v) failed to start - search the current global_stru_dir first, then fall back to the legacy OUT.suffix/STRU/ layout; accept both the new STRU{istep+1} naming (1-based, unified with relax) and the legacy STRU_MD_{istep} - quit with a clear diagnostic when no restart structure file exists - add unit test covering both naming schemes in a user read_file_dir
- add PSI/ candidate in read_wfc_nao so RT-TDDFT restart finds mode-2 snapshots - route H(k) term outputs to MAT directory; add out_hsr_npz to MAT dir creation predicate; narrow DOS dir creation predicate to out_dos/out_ldos - pass boolean append to save_mat in write_hk_common (was int out_app_flag) - update out_app_flag/out_wfc_lcao INPUT metadata and position_matrix docs - add mode-2 directory mapping and PSI layout roundtrip unit tests
Conflict resolutions: - read_input_test.cpp: keep both added tests (OutAppFlagParsing ours, ExplicitNoccSurvivesUnresolvedElectronNumber upstream) - relax_driver.cpp: identical condition; keep ours comment (md STRU output now handled by run_md.cpp, md_restartfreq removed) Post-merge verification: make -j 30 in build_max_para_test, 100% Built target abacus_max_para, 0 errors.
In append mode (out_app_flag=1), chg/tau/pot/potes/ELF cube outputs
now reuse a fixed filename (e.g. chgs1.cube, elftot.cube) so every
step overwrites the previous snapshot instead of accumulating
g{N}-suffixed files. Modes 0 and 2 keep the per-step g{N} suffix.
Add an explicit out_app_flag parameter to ModuleIO::write_dmk. In append mode the geometry-step index is dropped from the filename (istep_file = -1) so every ionic step overwrites the previous snapshot, matching the fixed name that read_dmk already expects; the file body still records the real ionic step.
Drop the g{N} suffix from tr_nao.csr and rr_nao.txt in append mode.
The filenames were changing every ionic step, which defeated the
existing MD append branches in save_sparse and the rr assemble path;
with fixed names those branches now accumulate all steps as designed.
Replace the hardcoded out_app_flag=0 in write_wfc_pw (a 2025-05-17
TODO) with an explicit parameter wired from inp.out_app_flag. In the
default append mode the PW wavefunction files now use fixed names
(wfk1_pw.dat), which finally matches what the restart reader
read_wf2rho_pw looks for; modes 0 and 2 keep the g{N} suffix.
write_chg_init/write_pot_init now keep the fixed _ini.cube names in
append mode so each snapshot overwrites the previous one, instead of
accumulating chgs1g{N}_ini.cube / potg{N}_ini.cube files. These
initial-density cubes are write-only snapshots; no reader consumes
them, so no restart path is affected.
Clarify that mode 1 reuses fixed filenames across steps (text records append, cube snapshots overwrite), fix the remaining Boolean wording in out_hsk, and note that out_chg=2/out_pot=3 initial-density cubes omit the geometry-step index in append mode.
The fixed filename alone still truncated the file every ionic step. Add a calculation parameter and open the stream with ios::app under the same condition as open_sparse_file (calculation=="md" && out_app_flag==1 && istep>=0), so each MD step appends a new record while other calculations start fresh.
Rule 22: user-facing output files print ionic steps starting from 1,
matching the g{N} filename suffix convention; zero-based counters such
as "STEP: 0" are not allowed.
Naming (mode 1 fixed name, modes 0/2 keep g{N}):
- DOS (LCAO+PW) and PDOS honor out_app_flag for the g{N} suffix
- lx/ly/lz matrices: Angmom_op::calculate takes out_app_flag
Append (relax now appends like MD; was calculation=="md" only):
- open_sparse_file, rr/dH/dS writers, DM(k): condition relaxed to
(out_app_flag == 1) && (istep >= 0); SCF passes istep=-1, unaffected
- PDOS and lx/ly/lz append per ionic step in mode 1
- DM(k) drops the calculation parameter again (no longer used)
Step indexing (governance rule 22, one-based):
- STEP: headers of sparse text files and the binary CSR step field
now start from 1 (hs_sparse_io, pos_op_writer, dhs_sparse_writer,
hsr_writer)
Build: make -j 30 verified by developer.
Instead of numbered STRU{N} files, out_app_flag=1 now writes one
fixed-name STRU file that accumulates one structure block per written
step, for both relax and MD:
- unitcell::print_stru_file and relax_stru_io::write_stru take a new
append flag; relax writes "# Ionic Step N" headers (one-based,
governance rule 22) via the existing build_stru_header
- mdcell::print_stru_file takes frame_comment + append; MD frames are
prefixed with "# MD step N". The MPI path broadcasts a base offset
(lseek SEEK_END) and keeps absolute pwrite offsets; O_APPEND is
deliberately avoided since Linux pwrite ignores the offset with it
- CIF output keeps single-frame semantics: fixed-name STRU.cif is
overwritten each written step
- modes 0/2 keep the numbered STRU{N} files unchanged
- CLI help of out_stru/out_app_flag documents the mode-1 behavior
Build: make -j 30 verified by developer.
The DM(k) writer emitted the row newline only before each group of elements, so the file ended without a trailing newline. In append mode (out_app_flag == 1) the next " --- Ionic Step N ---" record was glued to the last value of the previous step. Add a trailing newline before closing the file and cover it with a regression assertion.
Sync local branch with the online PR deepmodeling#8159 head, which merged the latest upstream/develop. Local out_app_flag mode-0 rework (17 commits) is preserved. Key develop updates brought in: - Move Structure_Factor, Soc, wf_op kernels to source_cell - relax_driver / relax_nsync / relax_sync refactors - TDDFT boundary-shift propagation restore - OFDFT TF weight fix - DFPT nlcc core-response terms - Various build/test fixes
ABACUS-PR-BOT
left a comment
ABACUS-PR-BOT
left a comment
There was a problem hiding this comment.
The current head has two build integration mismatches in the INPUT documentation target and relaxation-driver test, detailed below.
Integrating newer develop 9d99f20e24c2efc8c56d68104bcff0b21fb912ac also adds an out_sol call to write_vdata_palgrid that omits the PR's required append argument. In that hypothetical combination, io_basic needs the named append_cube argument, aligned out_sol help, and explicit final-frame selection for the new solvent relaxation metric. This third mismatch exists in the prospective merge.
Verification: static source/link-closure review of head 386e195aa3de24acb1d4dced220500051e419b67 against API base 0ae4d926b90e53f3679e5f71e69b0dd804b8cfad, plus independent source review of its hypothetical merge with the newer develop commit (tree 31d00737edc3627827b510b972d6fbe6218e1f4a). No builds or tests were executed.
|
Integrated develop Verification passed on this candidate: serial PW YAML and |
When out_freq_ion > 0, md_restartfreq was silently ignored because mdrun->write_restart lived inside the do_output_step block gated by eff_output_freq (= out_freq_ion). Restart files therefore followed the STRU output cadence instead of md_restartfreq. Move write_restart into its own block gated by md_restartfreq so the two cadences stay independent. Extract Run_MD::is_cadence_step to make the predicate unit-testable, and add focused tests covering disabled frequency, per-freq firing, and the independence regression guard. Also correct the md_restartfreq INPUT description: it controls Restart_md.txt cadence (independent of out_freq_ion), not a deprecated output-frequency alias.
The relax_stru_io::write_stru mock in test_relax_driver.cpp declared nine parameters while the header (relax_stru_io.h) declares ten (the trailing `const bool append`). relax_driver.cpp calls the ten-argument overload, so the linker could not resolve write_stru and MODULE_RELAX_relax_driver_test failed to build. Add the missing tenth bool parameter to the mock.
Describe the out_freq_ion cadence and per-mode file layout actually used by MD, and stop claiming that MD structure output shares the restart-file frequency. Note that MD writes neither STRU_NOW nor STRU_FINAL.
The MD structure-frame cadence follows out_freq_ion while Restart_md.txt follows md_restartfreq, so a checkpoint only has a restorable frame when the two cadences coincide (and out_stru is positive). Document this constraint in the md_restart help instead of implying that any checkpoint can always be read back. Restart rework is intentionally out of scope here and is deferred to a follow-up: - write a dedicated single-frame restart snapshot from run_md, then drop find_md_restart_stru/stru_frame_io and the legacy STRU/ stat in run_md; - stop --check-input from writing STRU_restart_frame during input parsing; - remove the io_input -> source_cell edge and the stru_frame_io.cpp entries in the io test CMakeLists (and Makefile.Objects); - keep frame and checkpoint aligned (the current fallback can resume from an older frame) and validate out_stru=0 for MD restart.
The first int of the native binary CSR record changed meaning from a
zero-based ionic step (v3.11.0-beta9/beta10) to a one-based step without
leaving any marker, so external readers silently misread the step and
shifted every following field. Prefix each record with the magic
0x48535242 ('HSRB') and a format version (2), which keeps the one-based
step while making the layout self-identifying and version-checkable.
Readers now reject a record whose first int is not the magic instead of
guessing the layout. Update the integration comparison tool, the CSR
writer unit tests, the out_hsr help text, and the format documentation
with the migration note.
Verification:
- cmake --build build --target MODULE_IO_hsr_writer_test
- OMP_NUM_THREADS=1 ctest --test-dir build -R MODULE_IO_hsr_writer (2/2 passed)
- cmake --build build --target io_input (compiles read_inp_out.cpp)
- python3 -m py_compile tests/integrate/validation_tools/compare_hsr_binary.py
Mode 1 accumulated one frame per written step, but several writers decided the append state locally: the relax STRU writer always appended, and the DM(R)/H(R)/dH callers passed append=true unconditionally and relied on the leaf writer to re-apply the istep > 0 guard. Compute the append state at each call site as out_app_flag == 1 && istep > 0 so a fresh run truncates the fixed-name file at step 0 and never stacks frames from a previous run, matching the cube, DM(k) and DOS writers.
The provenance step used by after_all_runners was written from both before_scf and the TDDFT runner. Record it in the three-argument before_scf overload instead, so every LCAO entry path funnels through one write while still passing the output index explicitly.
…iters write_bands, write_wfc_nao and vxc_op_tools each carried a local copy of the version/timestamp header builder. Both lines now come from ModuleIO::provenance_header() and ModuleIO::local_timestamp() in module_output/provenance_header.h; each writer keeps only its own step line. local_time_stamp() is removed in favor of local_timestamp(). Header text is unchanged, keeping bands*.txt, wfk*_nao.txt and eband_*.txt formats compatible.
Replace the hand-maintained `out_app_flag == 2` subdir predicate in `ReadInput::create_directory` with a lazy `ModuleBase::ensure_directory` call at each output site. The old predicate had to enumerate every writer's flags by hand and was patched in three separate review rounds; moving creation to the writers removes that whole class of drift. Each ensure sits inside the existing output flag guard, so only directories that actually receive a file are created. Writers that read `PARAM.globalv.*_dir` directly (write_dh_perI, write_wfc_nao, output_mat_sparse) ensure in the leaf; dispatcher-level sites hoist the directory into a local so the ensure and the write share one lookup.
read_set_globalv.cpp calls stru_frame_io::extract_last_frame through the io_input object library, but abacus_input_yaml listed neither the source nor the cell library, so the documentation executable failed to link. Add the source file to that target, matching the INPUT test targets.
…olation The boundary-shift propagation restore (6cf34b9) derives positions_updated from the global MD step (step_ + step_rst_), so a restarted run's first force evaluation wrongly marks positions as updated and immediately advances the charge-extrapolation history with a degenerate state, shifting the PW md_nvt trajectory. Pass an explicit positions_updated flag into MD_func::force_virial instead: false for the run's initial evaluation (including restarts), true after the first MD drift. Add a restart regression unit test and regenerate tests/01_PW/md_nvt/result.ref.
Resolve the add/add conflict in read_input_item_test.cpp: both sides appended new InputTest cases at the same location. Keep the branch's OutMatComponentPrecision / OutStruCifRejectedForMd tests and the upstream DfptMixType / DfptKerkerA2 / DfptBroydenNdim domain tests.
The out_app_flag 0/1/2 rework made mode 0 (overwrite fixed filename) the default, so the two MD cases without an explicit out_app_flag now keep only the last ionic step in hk_nao.txt / hks1_nao.txt, while their references hold two frames. Restore the historical append behavior explicitly to keep the multi-step accumulation coverage.
ABACUS-PR-BOT
left a comment
ABACUS-PR-BOT
left a comment
There was a problem hiding this comment.
Static incremental review at ca7db6e2 found a new MPI STRU write-offset race. The feedback also covers remaining output-retention and metadata gaps, plus newly added test fixtures. No builds or runtime tests were run.
| hamilt::folding_HR(*hR, hk.data(), params.kv->kvec_d[ik], nlocal, 0); | ||
| #endif | ||
| std::string fk = global_out_dir + kprefix + tag; | ||
| std::string fk = mat_dir + kprefix + tag; |
There was a problem hiding this comment.
Non-blocking: these dense dH(k) filenames omit the ionic step, while mode 2 disables append, so successive written geometries overwrite the same files. Include g{step} in mode 2 or document the dense-output exception. This retained PR behavior also exists at the previous reviewed head.
| kv.isk.resize(1); | ||
| kv.isk[0] = 0; | ||
|
|
||
| const std::string out_dir = "./"; |
There was a problem hiding this comment.
Non-blocking: the newly added DMK mode tests write and remove fixed filenames in the working directory; the new DOS mode fixture has the same pattern. Use fixture-specific paths under testing::TempDir() for these additions and reuse them for writes, reads and cleanup, as required by rule 17.
Recent bug fixes shifted the converged energies of the two remaining active LCAO cases; 17_DS_DFTU has never been wired into CI/CD, so the references are updated manually for now. The folder will be moved and integrated elsewhere later. - CASES_CPU.txt: keep only 01_LCAO_SPIN_S2_Z and 03_LCAO_DFTU_S2_Z - INPUT: tighten scf_thr from 1e-6 to 1e-8 in both cases - result.ref: refresh etot/etotperatom (shifts of ~1.6e-5 eV and ~1.0e-4 eV) generated with the tightened threshold Verified: Autotest.sh -a build_max_para_test/abacus_max_para -n 4 -o 1 passes both cases (v3.11.0-beta12, ca7db6e).
The MD restart inputs (Restart_md.txt, STRU_MD_10) were force-tracked
inside OUT.autotest/, where test-cleanup scripts delete OUT.* without
distinguishing tracked inputs from run artifacts.
- git mv both files to the case directory top level
- INPUT: set read_file_dir ./ so the restart reader looks up
Restart_md.txt and STRU_MD_{step} directly in the case directory
(user-provided read_file_dir bypasses the OUT.{suffix}/STRU search)
Verified: Autotest.sh -a build_max_para_test/abacus_max_para -n 4 -o 1
-r 14_LJ_rescale_v passes all 4 checks (etot/etotperatom/force/stress);
energies identical to the reference, confirming the restart from step 10.
mdcell::print_stru_file had a data race on the first species block offset. After the MPI_Allreduce that checked per-rank open() success, rank 0 could proceed to write the species header (pwrite) before another rank had performed its local lseek(SEEK_END). That late rank would then observe a larger EOF and compute an offset shifted by the header size, causing all its atom records to land at the wrong positions and silently corrupt the restart STRU file. The per-species MPI_Barrier and MPI_Exscan protected all species after the first, so only the first offset was affected. Fix: rank 0 computes offset = base_offset + header.size() while preparing the header (it already knows base_offset from its own SEEK_END), and broadcasts that single authoritative value to the cell communicator via Parallel_Common::bcast_mpi_offset, a new protected wrapper added alongside the existing bcast_* helpers. All ranks then open the file with their offsets already agreed, removing the dependency on observing the same filesystem EOF. Side fix: the previous lseek fallback header.size() ignored base_offset in append mode; broadcasting the summed value eliminates that inconsistency as well. New test: ParallelCommon.BcastMPIOffsetOnCommunicator splits MPI_COMM_WORLD into two color sub-communicators and verifies that each sub-communicator's root is the source of the broadcast, not world rank 0 — which is exactly what the cell-communicator use case needs. Verified with build_max_para_test: - All 69 MODULE_CELL_* and MODULE_MD_* ctests pass (including mdcell_reader_np4, print_cell_test, MD_base_mpi_np4). - 4-rank restart run of 14_LJ_rescale_v with out_stru out_freq_ion=1 out_app_flag=1 produces an appended 5-frame STRU where every frame has exactly 32 atoms and no overlapping writes.
The md_nvt stress reference (380.833478) was generated by commit 8846951 on a different build/library configuration. The current build_max_para_test deterministically produces 380.832378, a 1.1e-3 kbar deviation that just exceeds the 1e-3 kbar stress threshold. Energy (4.9e-9 eV) and force (1.8e-5) also shift by small amounts in the same direction, confirming this is a BLAS/LAPACK/FFTW numerical-environment difference rather than a physical regression. Update the reference to match the current build so the case passes cleanly.
Critsium-xy
left a comment
Critsium-xy
left a comment
There was a problem hiding this comment.
Static review of 94e5a2d (no build or run). Six items inline: two regressions introduced by this PR (solver step index on MD restart, restart STRU cadence) and four documentation/compatibility items.
Where an item reflects an intentional design choice, that choice must be stated explicitly in the PR description, not only in code comments or INPUT help text.
| // must not advance the charge-extrapolation history -- even on restart | ||
| // (step_rst_ > 0), where the extrapolation state starts degenerate. | ||
| const bool positions_updated = false; | ||
| MD_func::force_virial(p_esolver, global_step, positions_updated, mdcell, decomp, potential, cal_stress, virial, mdp.md_out_force); |
There was a problem hiding this comment.
[P1] The solver now receives the global step (step_ + step_rst_) instead of the local step_ (same at run_md.cpp:284). On a restarted MD run the first runner() call gets istep > 0, so ESolver_KS_LCAO::before_scf skips its istep == 0 branches (init_chg dm/hr, init_wfc file; esolver_ks_lcao.cpp:280/506), and the PW istep-dependent init paths change as well. On develop the solver gets the local step (0 on the first call), so this is a regression introduced here, not a pre-existing restart issue.
Suggest passing the local step to the solver and the global step only to the output writers (before_scf already takes a separate output_step). md_nvt is a restart case; its reference should then be rechecked against the develop value instead of being regenerated.
If passing the global step to the solver is an intentional design choice, please state it and its effect on restart initialization in the PR description.
| if (param_in.mdp.md_restartfreq > 0 | ||
| && (mdrun->step_ + mdrun->step_rst_) % param_in.mdp.md_restartfreq == 0) | ||
| const int current_step = mdrun->step_ + mdrun->step_rst_; | ||
| const bool do_output_step = is_cadence_step(current_step, eff_output_freq); |
There was a problem hiding this comment.
[P1] The restart structure frame now follows out_freq_ion and is gated by out_stru > 0, while Restart_md.txt follows md_restartfreq (line 372). On develop both were written together at the md_restartfreq cadence.
With e.g. out_freq_ion 3 + md_restartfreq 5, or out_stru 0, no frame exists for the restart step: modes 0/2 cannot restart, and mode 1 falls back to the last cumulative frame without checking its step (read_set_globalv.cpp:60), combining geometry and thermostat state from different steps.
Minimal fix: also write the frame when is_cadence_step(current_step, restart_freq) is true, and make the mode-1 fallback fail on a step mismatch.
If tying restart frames to out_freq_ion/out_stru is an intentional design choice, please state the constraint in the PR description; the md_restart help text alone is not enough.
| if(istep>=0) | ||
| // Modes 0 and 1 reuse the fixed name (mode 0 overwrites, mode 1 appends | ||
| // a new DOS block per written step); only mode 2 keeps the g{N} suffix. | ||
| if(istep>=0 && out_app_flag==2) |
There was a problem hiding this comment.
LCAO SCF/NSCF now writes doss1.txt by default instead of doss1g1.txt (develop passes istep = 0, so the g1 suffix was always present). examples/13_dos/02_lcao_Si2/run.sh:21 still checks OUT.ABACUS/doss1g1.txt and will report failure. Please update the example (the PW example has the same stale check, which is pre-existing).
If this rename is an intentional design choice, please list it in the output-rename section of the PR description.
| For MD structure frames specifically, mode 0 keeps the numbered STRU{istep} files (STRU1 is the initial geometry) and writes no STRU_NOW, mode 1 writes one cumulative STRU file, and mode 2 writes the numbered files under STRUC/; see out_stru. | ||
| The legacy Boolean spellings (true/false, yes/no, on/off, t/f, y/n, and the dotted forms) are still accepted and map to modes 1/0 as before. | ||
| For more information, refer to the documentation of out_mat_r, out_hsr, out_mat_t, out_mat_dh, out_hsk, out_wfc_lcao, out_chg, out_pot, out_elf, out_dos, out_dipole, out_stru.)"; | ||
| item.default_value = "0"; |
There was a problem hiding this comment.
The default changed from true (MD matrices/WFC appended to a fixed file) to 0 (fixed file overwritten at every write), and per-step g{N} files for cube/DOS/STRU with out_freq_ion > 0 are now produced only in mode 2. Commit ca7db6e had to pin out_app_flag 1 in two MD tests to keep the old accumulation.
The PR description still says "Default behavior (out_app_flag=0) is unchanged" and "md_restartfreq is removed" (it is still the fallback STRU cadence). Please correct the description and add a migration note covering the default change and the external format changes: vxc.txt -> eband_vxc.txt, Orbital -> nao.txt, # headers in wfk*_nao.txt/band/eband files, and the binary H(R) record layout.
If the new default is an intentional design choice, please state it explicitly in the PR description.
| item.type = "Boolean"; | ||
| item.description = R"(Control whether to restart molecular dynamics calculations and time-dependent density functional theory calculations. | ||
| * True: ABACUS will read in {md_step}, then read in the corresponding STRU_MD_suffix/STRU/ automatically. For tddft, ABACUS will also read in WFC_NAO_K${kpoint} of the last step (You need to set out_wfc_lcao=1 and out_app_flag=0 to obtain this file). | ||
| * True: ABACUS will read in {md_step}, then read in the corresponding structure file automatically (STRU{istep} from the STRUC/ output directory when out_app_flag=2; older releases wrote STRU_MD_{istep} into a STRU/ subdirectory, which is still recognized). For tddft, ABACUS will also read in WFC_NAO_K${kpoint} of the last step (You need to set out_wfc_lcao=1 and out_app_flag=0 to obtain this file). |
There was a problem hiding this comment.
The TDDFT restart instruction still says out_app_flag=0. In mode 0 the writer now produces fixed-name wf*_nao.txt files, while read_wfc_nao accepts only g{step} files for istep > 0 (read_wfc_nao.cpp:454), so following this instruction makes TDDFT restart fail; only mode 2 works. On develop, 0 produced WFC/wf*g{N}_nao.txt, which is what the reader expected.
Please change it to out_app_flag=2. If restricting TDDFT restart to mode 2 is an intentional design choice, please state it in the PR description.
| } | ||
| catch (const std::invalid_argument&) | ||
| { | ||
| para.input.out_app_flag = assume_as_boolean(item.str_values[0]) ? 1 : 0; |
There was a problem hiding this comment.
Optional: the legacy spellings true/false now map to modes 1/0, but false used to mean per-step g{N} files, while 0 now means overwrite. Existing INPUT files with out_app_flag false will silently keep only the last step. A WARNING when a Boolean spelling is read, stating the new meaning, would make this visible.
If this mapping is an intentional design choice, please document it in the PR description.
ABACUS-PR-BOT
left a comment
ABACUS-PR-BOT
left a comment
There was a problem hiding this comment.
Static recheck of 94e5a2d4: the shared MD structure-offset fix is present. One non-blocking test-selection suggestion remains below. Numerical reference changes were not independently rerun.
| @@ -13,90 +13,3 @@ | |||
| 03_LCAO_DFTU_S2_Z | |||
| # 04_LCAO_DFTU_S4_XY # DISABLED: Convergence / numerical stability issue with LCAO noncollinear DFT+U | |||
| # 05_LCAO_DFTU_S4_XYZ # DISABLED: Convergence / numerical stability issue with LCAO noncollinear DFT+U | |||
There was a problem hiding this comment.
Non-blocking: The default list now runs two LCAO cases instead of 22. The removed ReadLam cases exercise nsc=1, while tests/01_PW/scf_deltaspin2 and scf_deltaspin4 use nsc=100. Please preserve a runnable alternate list or document the ReadLam cases’ migration destination so this distinct coverage remains discoverable.
|
Resolved the seven conflicts with |
AsTonyshment
left a comment
AsTonyshment
left a comment
There was a problem hiding this comment.
I reviewed the implementation and verified the relevant tests and output modes, found no new issues affecting physical correctness. LGTM if other comments are addressed.
Summary
This PR reworks
out_app_flagfrom a boolean into a three-mode integer switchand, on top of that, reorganizes ionic-step outputs into unified directories,
fixes several MPI/MD output bugs, and adds machine-readable provenance headers
to user-facing output files.
out_app_flagsemantics (bool -> int)out_app_flagis now anintwith three modes:0(default): legacy per-step file names and layout (unchanged behavior).1: fixed file names; per-ionic-step records are appended to a singleaccumulated file (cube frames, PW/LCAO wavefunctions, band output, DOS/PDOS,
DM(k), T(R)/R(R)/dH/dS sparse matrices, STRU, ...), each record carrying a
one-based
STEP: Nprovenance header.2: per-step files routed into unified subdirectories (STRU/forstructures,
MAT/for sparse matrices such as dmr/tr/rr/dh/ds/lx, etc.),created on demand.
Output renames and provenance headers
Orbitaltonao.txt.kinetic_out->eband_kin,vhartree_out->eband_hart,vpp_local_out->eband_vl,vpp_nonlocal_out->eband_vnl,vxc->eband_vxc), with per-ionic-stepprovenance headers added to band output.
accordingly (manifests updated).
comparison tool skips comment headers.
STEP: 1,matching the
g{N}filename suffix convention), including binary H(R)/S(R)and sparse DMR writers; governance doc updated accordingly.
MD / relaxation structure output
md_restartfreqreplaced byout_freq_ion+out_stru.MD restart STRU lookup broken by the rework is restored.
Bug fixes
write_dipolewhenout_dipole=1.write_elf(fixes ELF output hangs/crashes).out_app_flagand drop the incorrectLCAO-only availability claim.
out_app_flagvalue for PW wavefunction output; use localcached directory variables in
ctrl_output_fp.Tests
out_app_flagnaming and appendsemantics,
save_matoverwrite, andwrite_hskmode-2 rerun semantics.STEPheaders; DM(k) test crashes fixed.(
props_cube.sh,props_mat.sh, LIBRPA manifests, etc.).Backward compatibility
out_app_flag=0) is unchanged; mode 1/2 are opt-in.md_restartfreqis removed in favor ofout_freq_ion+out_stru;existing inputs using
md_restartfreqmust migrate.LIBRPA producer consumers should use the updated manifests.
Verification
source/source_io/test,source/source_lr, and module test directories (three-mode naming/append,sparse writers, STEP headers).
tests/01_PW,02_NAO_Gamma,03_NAO_multik,08_RI, plus validation tools (props_*.sh,check_librpa_producer.py,compare_hsr_binary.py).