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Fix #5021 #5939: warn on ignored x/y magnetization and remove nspin=4 autoset - #8079

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mohanchen merged 25 commits into
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mohanchen:2026-10-06-a
Oct 10, 2026
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Fix #5021 #5939: warn on ignored x/y magnetization and remove nspin=4 autoset#8079
mohanchen merged 25 commits into
deepmodeling:developfrom
mohanchen:2026-10-06-a

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@mohanchen mohanchen commented Oct 5, 2026 •
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Problem Description

Issue #5021: x/y components of magnetization silently zeroed

When nspin=4 and noncolin=0, the x/y components of the initial magnetization
set in STRU are silently zeroed, keeping only the z component. Users who provide
a 3-component magnetization vector (e.g., mag 1.0 0.5 0.3) get no indication
that the x/y components are discarded, which can lead to confusion about why
the final magnetic moment differs from the input.

Issue #5939: nspin=4 auto-assigns (1,1,1) to all atoms

When nspin=4 and no initial magnetization is set in STRU, the code
automatically assigns (1.0, 1.0, 1.0) to all atoms regardless of element
type. This is overly aggressive — non-magnetic elements (e.g., O, H) also get
a magnetic moment, which can alter the SCF convergence path and final results.

Solution

1. Warn when x/y components are

abacus_fixer
Fix deepmodeling#5021 deepmodeling#5939: warn on ignored x/y magnetiz…
98e3f81 
…ation and remove nspin=4 autoset

When nspin=4 with noncolin=0, the x/y components of the initial
magnetization from STRU are silently zeroed. Now a warning is printed
to both stdout and running_scf.log, telling the user that x/y are
ignored and suggesting to set noncolin=1.

When nspin=4 and no initial magnetization is set in STRU, the code
previously auto-assigned (1,1,1) to all atoms. This is removed; the
calculation now starts from zero magnetic moment with a warning,
letting the user decide explicitly.

nspin=2 autoset behavior is unchanged.

Also adds unit tests for both behaviors and updates parameter docs.
@mohanchen
mohanchen requested a review from AsTonyshment October 5, 2026 23:32
@mohanchen mohanchen added Bugs Bugs that only solvable with sufficient knowledge of DFT Refactor Refactor ABACUS codes The Absolute Zero Reduce the "entropy" of the code to 0 collinear/non-collinear/SOC/delta-spin Issues related to SOC labels Oct 5, 2026
abacus_fixer and others added 20 commits October 6, 2026 09:57
abacus_fixer
Fix parameters.yaml sync: add noncolin notes to C++ description source
9d8317c 
docs/parameters.yaml is generated from item.description in C++ source.
Commit 98e3f81 added two noncolin notes to the generated yaml and
input-main.md but omitted the generator source, making the yaml
consistency CI check fail. Add the same two notes to the noncolin
description in read_inp_estruc.cpp so regeneration matches.
abacus_fixer
Test: update ReadAtomPositionsAutosetMag for nspin=4 zero-moment start
ffaeba6 
Follow-up to deepmodeling#5939: nspin=4 with no mag in STRU no longer autosets
(1,1,1); the unit test still expected the old forced moments. Assert
zero magnetization instead and verify the new warning on both stdout
and the running log.
abacus_fixer
Test: split cal_ux tests out of MODULE_CELL_unitcell_test
5306acf 
Move JudgeParallel, CalUx1 and CalUx2 to the new test_cal_ux.cpp /
MODULE_CELL_cal_ux_test target, one test file per source file. The new
target compiles ../cal_ux.cpp directly like the old target did;
unitcell_test no longer needs it.
abacus_fixer
Test: split read_orb tests out of MODULE_CELL_unitcell_test
18fb06b 
Move ReadOrbFile (kept under the __LCAO guard as before) and
ReadOrbFileWarning to the new test_read_orb.cpp /
MODULE_CELL_read_orb_test target. read_orb.cpp is already part of the
test-only cell_info object library, so no extra source is compiled in.
abacus_fixer
Test: move compare_atom_labels/print_unitcell_pseudo tests to readpp …
cda48b0 
…suite

CompareAatomLabel and PrintUnitcellPseudo exercise read_pp_ucell.cpp,
so move them from MODULE_CELL_unitcell_test into the existing
MODULE_CELL_unitcell_test_readpp target. The rebuilt cell needed by
PrintUnitcellPseudo uses the C1H2-Index prepare entry. Drop the now
unused read_pp_ucell.h include from unitcell_test.cpp.
abacus_fixer
Test: split update_cell tests out of MODULE_CELL_unitcell_test
27ae2da 
Move RemakeCell, RemakeCellWarnings, PeriodicBoundaryAdjustment2 and
UpdateVel to the new test_update_cell.cpp /
MODULE_CELL_update_cell_test target. The commented-out
PeriodicBoundaryAdjustment1 block moves as well and stays commented.
update_cell.cpp is already part of the test-only cell_info library.
Drop the now unused update_cell.h include from unitcell_test.cpp.
abacus_fixer
Test: move print_cell/print_tau tests into MODULE_CELL_print_cell_test
974ba84 
PrintCell, PrintTauDirect and PrintTauCartesian exercise print_cell.cpp,
the same source as the PrintSTRU tests already living in
test_print_cell.cpp. Move them into that file/target and reuse the
PrintCellTest fixture. Drop the now unused print_cell.h include and the
stale PrintSTRU navigation comment from unitcell_test.cpp.
abacus_fixer
Test: split cell_tools free-function tests out of MODULE_CELL_unitcel…
016e69e 
…l_test

Add test_cell_tools.cpp / MODULE_CELL_cell_tools_test for the
unitcell:: free functions in cell_tools.cpp:
- new IfCellCanChange truth-table case over the lattice-axis flags
- vector get_atomCounts/get_lnchiCounts cases split out of the mixed
  member/free GetAtomCounts and GetLnchiCounts tests (the member
  get_atom_Counts/get_lnchi_Counts map assertions stay in unitcell_test)
- SelectiveDynamics (if_atoms_can_move) moved verbatim

Setup keeps only the setup_from_input member assertions; its
if_cell_can_change checks are now covered by the dedicated truth table.
Drop the unused cell_tools.h include from unitcell_test.cpp.
abacus_fixer
Test: split read_atom_species tests out of MODULE_CELL_unitcell_test
5d6950f 
Move the 7 STRU header-parsing cases (read_atom_species and
read_lattice_constant, both in read_atom_species.cpp) to the new
test_read_atom_species.cpp / MODULE_CELL_read_atom_species_test target,
kept under the __LCAO guard as before. ReadAtomSpeciesWarning5 uses the
death-test fixture alias; the rest use the new ReadAtomSpeciesTest
fixture. Drop the stale doc entries from unitcell_test.cpp.
abacus_fixer
Test: split read_atoms tests out of MODULE_CELL_unitcell_test
55c4f5f 
Move the 17 read_atom_positions cases (spin/coordinate modes plus the
five warning cases) to the new test_read_atoms.cpp /
MODULE_CELL_read_atoms_test target, kept under the __LCAO guard. This
removes the LCAO block and UcellTestReadStru fixture from
unitcell_test.cpp, which now holds only the 9 UnitCell member-function
tests. Also de-duplicate the triple read_stru.h include. The 6 GlobalV
references are migration-neutral (added = removed).
abacus_fixer
update initialized mag
8c314ef
@mohanchen
Merge branch 'develop' into 2026-10-06-a
67147d0
abacus_fixer
move 057_PW_SO_IW test to scf_in_wf_spin4
7e79a8a
abacus_fixer
move 035_PW_15_SO to scf_spin4
f42d24e
abacus_fixer
add comments about mag for nspin=4 calculations
b8ce15c
abacus_fixer
try to fix bug for nspin=4
3d6bc87
abacus_fixer
Merge branch 'pr8079' into 2026-10-06-a
adca5d3
abacus_fixer
update mag
d8f6322
abacus_fixer
fix bug by change slightly the reference forces of the example 03_NAO…
45afdb8 
…_multik/scf_out_dos_spin4
@mohanchen
Merge branch 'develop' into 2026-10-06-a
93abd5e
@mohanchen
mohanchen requested a review from Critsium-xy October 9, 2026 09:18
Critsium-xy
Critsium-xy reviewed Oct 9, 2026
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@Critsium-xy Critsium-xy left a comment

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Three points on the magnetization changes.

Comment thread docs/advanced/input_files/input-main.md
Comment thread source/source_cell/read_atoms_helper.cpp Outdated
Comment thread source/source_cell/read_atoms_helper.cpp Outdated
Critsium-xy and others added 2 commits October 9, 2026 18:53
@Critsium-xy @claude
fix(cell): report the nspin=4 zero-moment start on every code path
355d2a3 
The zero-moment warning added for deepmodeling#5939 was unreachable in the two cases
that matter most:

* autoset_magnetization() keyed the check on atom.mag, which for a
  three-component "magmom" holds the full norm including x/y. With
  nspin=4 and noncolin=0 the x/y components are projected away, leaving
  m_loc_ = (0,0,0) while mag stays non-zero, so the warning was skipped
  for exactly the silent zero-moment start it was meant to surface.
* read_atom_positions() only calls autoset_magnetization() when
  symmetry != 1, and symmetry defaults to 1 for nspin=4 + noncolin=1 +
  lspinorb=0 scf runs with k-points, so the documented warning never
  appeared there either.

Split the magnetization reporting out of autoset_magnetization():

* is_magnetization_all_zero() shares the all-zero test.
* warn_zero_magnetization_nspin4() keys on m_loc_, the vector cal_ux()
  actually consumes, and read_atom_positions() calls it for every
  symmetry setting.
* autoset_magnetization() now only handles the nspin=2 autoset.

Also stop printing the x/y-discarded warning once per atom. The block
right below it in process_magnetization() throttles its output for the
same reason; a 2000-atom cell with tilted moments produced ~4000 lines
of identical text before SCF started. process_magnetization() now
returns whether the projection discarded anything and
read_atom_positions() aggregates it per atom type, reporting the
affected-atom count once.

Both warnings now also go through ModuleBase::WARNING so they reach
warning.log, and the multi-line text is written straight to ofs_running
instead of through GlobalFunc::OUT, whose setw(40) key/value layout was
broken by the embedded newlines.

Finally, the "initial magmom is all zero and symmetry=1" message is no
longer printed for an explicitly magnetized STRU.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DNd7fpeHXHuL9DKME85J44
@Critsium-xy @claude
docs: align the magnetization autoset docs with the new behavior
c6c6480 
docs/advanced/input_files/stru.md still told users that nspin=4 autosets
"mag 1 1 1" on every atom, which this branch removes; that page is where
the STRU "mag" field is looked up, so it contradicted the notes added to
input-main.md. Rewrite the section to describe the zero-moment start,
the explicit-mag example, the x/y discard under noncolin=0, and the
symmetry=1 case in which the nspin=2 autoset is skipped as well.

Also record the autoset rules under "nspin" itself rather than only
under "noncolin": the behavior is a property of nspin. parameters.yaml
and input-main.md are regenerated from the C++ Input_Item description so
the documentation-consistency check stays satisfied.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DNd7fpeHXHuL9DKME85J44
Critsium-xy and others added 2 commits October 9, 2026 18:54
@Critsium-xy @claude
chore: follow the test rename and separate a shared test log
ee5d253 
* .ci/slurm/config.ini still registered case.080 as 01_PW/035_PW_15_SO,
  a directory this branch renamed to scf_spin4, so that GPU case looked
  for a path that no longer exists. (19 further entries in that file
  already point at missing directories from earlier renames; those are
  left alone.)
* PrintCellTest.PrintCell and UcellTest.PrintUnitcellPseudo both used
  "printcell.log". Before the unitcell_test.cpp split they shared one
  translation unit and ran sequentially; they are now separate
  executables that AddTest runs in the same working directory, so under
  ctest -j each could read or delete the other's file. Give the
  print_cell test its own name.
* Keep the #pragma omp parallel for adjacent to the loop it governs in
  noncolin_rho(): the explanatory comment sat between the two, which
  compiles but invites an edit that drops a statement into the gap.
* Strip the trailing blanks added to the regenerated
  03_NAO_multik/scf_out_dos_spin4 INPUT and STRU.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DNd7fpeHXHuL9DKME85J44
@mohanchen
Merge branch 'develop' into 2026-10-06-a
6313fa8
AsTonyshment
AsTonyshment approved these changes Oct 9, 2026
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@AsTonyshment AsTonyshment left a comment

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I didn't find any obvious issues, LGTM.

@mohanchen
mohanchen merged commit 40f925a into deepmodeling:develop Oct 10, 2026
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Bugs Bugs that only solvable with sufficient knowledge of DFT collinear/non-collinear/SOC/delta-spin Issues related to SOC Refactor Refactor ABACUS codes The Absolute Zero Reduce the "entropy" of the code to 0

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