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Refactor: normalize and shorten source filenames for consistency - #7797

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mohanchen merged 28 commits into
deepmodeling:developfrom
mohanchen:2026-08-10-b
Aug 13, 2026
Merged

Refactor: normalize and shorten source filenames for consistency#7797
mohanchen merged 28 commits into
deepmodeling:developfrom
mohanchen:2026-08-10-b

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@mohanchen mohanchen commented Aug 10, 2026

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Summary

This PR systematically renames source files under source/ to follow
consistent naming conventions:

  1. Shorten overly long filenames (≥25 chars) using standard abbreviations
  2. Remove uppercase letters from filenames (e.g., LCAO_ → lcao_,
    ORB_ → orb_, FORCE_ → force_, H_ → h_)
  3. Replace dashes with underscores (e.g., exx_abfs-io.cpp →
    exx_abfs_io.cpp, matrix-inl.h → matrix_inl.h)

Motivation

The codebase had inconsistent filename conventions: mixed case
(LCAO_set.cpp vs lcao_set_fs.cpp), dashes (exx_abfs-io.cpp),
and excessively long names (charge_mixing_preconditioner.cpp).
This made file discovery harder and broke the KISS principle.

Changes

Phase 1–5: Shorten long filenames (61 files)

  • charge_mixing_preconditioner.cpp → mix_precond.cpp
  • spherical_bessel_transformer.{cpp,h} → sph_bessel_tf.{cpp,h}
  • gint_vl_metagga_nspin4_gpu.{cpp,h} → gint_vl_mgga_n4_gpu.{cpp,h}
  • read_input_item_* → read_inp_* (8 files)
  • ... and 46 more

Phase A: LCAO_ → lcao_ (16 files)

  • LCAO_deepks.{cpp,h} → lcao_deepks.{cpp,h}
  • LCAO_set.{cpp,h} → lcao_set.{cpp,h}
  • LCAO_domain.h → lcao_domain.h
  • ... and 13 more

Phase B: ORB_ → orb_ (18 files)

  • ORB_atomic.{cpp,h} → orb_atomic.{cpp,h}
  • ORB_read.{cpp,h} → orb_read.{cpp,h}
  • ORB_unittest.{cpp,h} → orb_unittest.{cpp,h}
  • ... and 15 more

Phase C–G: Remaining normalization (planned)

  • H_Ewald_pw.{cpp,h} → h_ewald_pw.{cpp,h}
  • FORCE_STRESS.{cpp,h} → force_stress.{cpp,h}
  • Matrix_Orbs11.{cpp,h} → matrix_orbs11.{cpp,h}
  • ABFs_Construct-PCA.{cpp,h} → abfs_construct_pca.{cpp,h}
  • Inverse_Matrix.{h,hpp} → invmat_ri.{h,hpp} (avoid name clash)
  • ... and ~115 more

What is preserved

  • Function names, class names, namespace names (e.g., LCAO_domain::,
    ORB_gaunt_table)
  • Header guard macro names
  • CMake target identifiers
  • esolver_ks_lcao_tddft, two_center_integrator, blas_connector_*
    intentionally kept unchanged

Verification

  • All #include paths updated
  • All CMakeLists.txt and Makefile.Objects entries updated
  • Python pyabacus references updated where applicable
  • Each phase compiled and tested before proceeding to the next

abacus_fixer added 9 commits August 10, 2026 16:36
abacus_fixer
refactor: shorten long filenames in source (phase 1)
b31ed6a 
Rename 7 files (32-29 chars → 12-22 chars):
- charge_mixing_preconditioner.cpp → mix_precond.cpp
- spherical_bessel_transformer.{cpp,h} → sph_bessel_tf.{cpp,h}
- read_input_item_postprocess.cpp → read_inp_postproc.cpp
- gint_vl_metagga_nspin4_gpu.{cpp,h} → gint_vl_mgga_n4_gpu.{cpp,h}
- snap_projector_half_tddft.{cpp,h} → snap_proj_half_tddft.{cpp,h}

Update all #include references, CMakeLists.txt, Makefile.Objects,
header guards, and code comments. Function names (e.g.
snap_projector_half_tddft) are preserved unchanged.
abacus_fixer
refactor: shorten long filenames in source (phase 2)
334391a 
Rename 15 files (29-25 chars → 12-21 chars):
- read_input_item_elec_stru.cpp → read_inp_estruc.cpp
- gint_precision_controller.{cpp,h} → gint_prec_ctrl.{cpp,h}
- global_function-func_each_2.h → glob_fn_each2.h
- snap_phialpha_half_tddft.{cpp,h} → snap_pha_half_tddft.{cpp,h}
- snap_psibeta_half_tddft.{cpp,h} → snap_psb_half_tddft.{cpp,h}
- symmetry_rotation_output.cpp → symm_rot_out.cpp
- read_input_item_exx_dftu.cpp → read_inp_exx_dftu.cpp
- write_mlkedf_descriptors.{cpp,h} → write_mlkedf_desc.{cpp,h}
- global_function_ddotreal.cpp → glob_fn_ddotreal.cpp
- exx_abfs-construct_orbs.{cpp,h} → exx_abfs_ctor_orbs.{cpp,h}

Update all #include references, CMakeLists.txt, Makefile.Objects,
and header guards. Function and variable names preserved unchanged.
abacus_fixer
refactor: shorten long filenames in source (phase 3)
cf02d81 
Rename 8 files (27-25 chars → 12-21 chars):
- to_wannier90_lcao_in_pw.{cpp,h} → to_w90_lcao_pw.{cpp,h}
- dist_matrix_transformer.{cpp,h} → dist_mat_tf.{cpp,h}
- element_basis_index-ORB.{cpp,h} → elem_basis_idx_orb.{cpp,h}
- sph_bessel_recursive-d1.cpp → sph_bessel_rec_d1.cpp
- sph_bessel_recursive-d2.cpp → sph_bessel_rec_d2.cpp

Update all #include references, CMakeLists.txt, Makefile.Objects,
and header guards. Function and class names preserved unchanged.
abacus_fixer
refactor: shorten long filenames in source (phase 4)
1d72486 
Rename 20 files (26 chars → 12-20 chars), including 6 .cpp/.h pairs:
- lattice_change_methods.{cpp,h} → lat_change_method.{cpp,h}
- vec_mul_vec_complex_op.{cpp,h} → vec_mul_cx_op.{cpp,h}
- psi_init_atomic_random.{cpp,h} → psi_init_atom_rand.{cpp,h}
- cal_mlkedf_descriptors.{cpp,h} → cal_mlkedf_desc.{cpp,h}
- gint_vl_metagga_nspin4.{cpp,h} → gint_vl_mgga_n4.{cpp,h}
- symmetry_rotation_spin.{cpp,h} → symm_rot_spin.{cpp,h}
- irreducible_sector_bvk.cpp → irred_sec_bvk.cpp
- read_input_item_{system,output,deepks}.cpp → read_inp_{sys,out,deepks}.cpp
- charge_mixing_residual.cpp → mix_resid.cpp
- elecstate_energy_terms.cpp → estate_e_terms.cpp
- pw_distributeg_method{1,2}.cpp → pw_distg_method{1,2}.cpp

Update all #include references, CMakeLists.txt, Makefile.Objects,
Makefile, header guards, and WARNING string literals. Function,
class, and struct names preserved unchanged.
abacus_fixer
refactor: shorten long filenames in source (phase 4)
301c118 
Rename 20 files (26 chars → 12-20 chars), including 6 .cpp/.h pairs:
- lattice_change_methods.{cpp,h} → lat_change_method.{cpp,h}
- vec_mul_vec_complex_op.{cpp,h} → vec_mul_cx_op.{cpp,h}
- psi_init_atomic_random.{cpp,h} → psi_init_atom_rand.{cpp,h}
- cal_mlkedf_descriptors.{cpp,h} → cal_mlkedf_desc.{cpp,h}
- gint_vl_metagga_nspin4.{cpp,h} → gint_vl_mgga_n4.{cpp,h}
- symmetry_rotation_spin.{cpp,h} → symm_rot_spin.{cpp,h}
- irreducible_sector_bvk.cpp → irred_sec_bvk.cpp
- read_input_item_{system,output,deepks}.cpp → read_inp_{sys,out,deepks}.cpp
- charge_mixing_residual.cpp → mix_resid.cpp
- elecstate_energy_terms.cpp → estate_e_terms.cpp
- pw_distributeg_method{1,2}.cpp → pw_distg_method{1,2}.cpp

Update all #include references, CMakeLists.txt, Makefile.Objects,
Makefile, header guards, and WARNING string literals. Function,
class, and struct names preserved unchanged.
abacus_fixer
refactor: shorten long filenames in source (phase 5, revised)
8c336be 
Rename 11 files (25 chars → 14-20 chars), including 3 .cpp/.h pairs:
- LCAO_deepks_interface.{cpp,h} → lcao_deepks_iface.{cpp,h}
- para_linear_transform.{cpp,h} → para_lin_tf.{cpp,h}
- read_input_item_{tddft,relax,other,ofdft,model}.cpp → read_inp_{...}.cpp
- vdwd3_autoset_xcparam.cpp → vdwd3_auto_xcpar.cpp
- element_covalent_radius.h → elem_cov_rad.h

Update all #include references, CMakeLists.txt, Makefile.Objects,
header guards, and python pyabacus references. Function, class, and
variable names preserved unchanged.

Note: esolver_ks_lcao_tddft, two_center_integrator, and blas_connector
files are intentionally kept unchanged per user request.
abacus_fixer
refactor: normalize LCAO_ prefix filenames to lowercase (phase A)
82f448b 
Rename 16 files from LCAO_* to lcao_* (remove uppercase letters):
- LCAO_allocate.cpp → lcao_allocate.cpp
- LCAO_domain.h → lcao_domain.h
- LCAO_HS_arrays.hpp → lcao_hs_arrays.hpp
- LCAO_init_basis.cpp → lcao_init_basis.cpp
- LCAO_nl_mu.cpp → lcao_nl_mu.cpp
- LCAO_nonlocal_info.h → lcao_nonlocal_info.h
- LCAO_set.{cpp,h} → lcao_set.{cpp,h}
- LCAO_set_{fs,mat2d,st,zero}.cpp → lcao_set_{...}.cpp
- LCAO_deepks.{cpp,h} → lcao_deepks.{cpp,h}
- LCAO_deepks_io.{cpp,h} → lcao_deepks_io.{cpp,h}

Update all #include references, CMakeLists.txt, Makefile.Objects,
and code comments. Namespace names (LCAO_domain::), class names,
and header guards preserved unchanged.
abacus_fixer
refactor: normalize ORB_ prefix filenames to lowercase (phase B)
829da33 
Rename 18 files from ORB_* to orb_* (remove uppercase letters):
- ORB_atomic.{cpp,h} → orb_atomic.{cpp,h}
- ORB_atomic_lm.{cpp,h} → orb_atomic_lm.{cpp,h}
- ORB_gaunt_table.{cpp,h} → orb_gaunt_table.{cpp,h}
- ORB_nonlocal.{cpp,h} → orb_nonlocal.{cpp,h}
- ORB_nonlocal_lm.{cpp,h} → orb_nonlocal_lm.{cpp,h}
- ORB_read.{cpp,h} → orb_read.{cpp,h}
- ORB_{atomic_lm,nonlocal_lm,nonlocal,read}_test.cpp → orb_{...}_test.cpp
- ORB_unittest.{cpp,h} → orb_unittest.{cpp,h}

Update all #include references, CMakeLists.txt, Makefile.Objects,
and README. Class names, header guards, and CMake target identifiers
preserved unchanged.
abacus_fixer
refactor: normalize ORB_ prefix filenames to lowercase (phase B)
5d7c566 
Rename 18 files from ORB_* to orb_* (remove uppercase letters):
- ORB_atomic.{cpp,h} → orb_atomic.{cpp,h}
- ORB_atomic_lm.{cpp,h} → orb_atomic_lm.{cpp,h}
- ORB_gaunt_table.{cpp,h} → orb_gaunt_table.{cpp,h}
- ORB_nonlocal.{cpp,h} → orb_nonlocal.{cpp,h}
- ORB_nonlocal_lm.{cpp,h} → orb_nonlocal_lm.{cpp,h}
- ORB_read.{cpp,h} → orb_read.{cpp,h}
- ORB_{atomic_lm,nonlocal_lm,nonlocal,read}_test.cpp → orb_{...}_test.cpp
- ORB_unittest.{cpp,h} → orb_unittest.{cpp,h}

Update all #include references, CMakeLists.txt, Makefile.Objects,
and README. Class names, header guards, and CMake target identifiers
preserved unchanged.
@mohanchen
mohanchen requested a review from AsTonyshment August 10, 2026 11:14
@mohanchen mohanchen added Refactor Refactor ABACUS codes The Absolute Zero Reduce the "entropy" of the code to 0 labels Aug 10, 2026
abacus_fixer added 9 commits August 10, 2026 19:37
abacus_fixer
refactor: normalize H_/FORCE_/forces_ filenames (phase C)
c8a98dd 
Rename 21 files, add module suffixes for force files, and
update header guards:

Correction abbreviation:
- H_correction_pw.cpp → h_corr_pw.cpp

Hamiltonian uppercase prefixes (H_* → h_*):
- H_Ewald_pw.{cpp,h} → h_ewald_pw.{cpp,h}
- H_Hartree_pw.{cpp,h} → h_hartree_pw.{cpp,h}
- H_TDDFT_pw.{cpp,h} → h_tddft_pw.{cpp,h}

LCAO force files (FORCE_* → force_lcao_*, FORCE_STRESS → force_stress_lcao):
- FORCE.h → force_lcao.h
- FORCE_gamma.cpp → force_lcao_gamma.cpp
- FORCE_k.cpp → force_lcao_k.cpp
- FORCE_STRESS.{cpp,h} → force_stress_lcao.{cpp,h}

PW force files (forces_* → force_pw_*, distinguish from LCAO):
- forces.{cpp,h} → force_pw.{cpp,h}
- forces_nl.cpp → force_pw_nl.cpp
- forces_onsite.cpp → force_pw_onsite.cpp
- forces_scc.cpp → force_pw_scc.cpp
- forces_us.cpp → force_pw_us.cpp
- forces_cc.cpp → force_pw_cc.cpp

Test files:
- opt_CG_test.cpp → opt_cg_test.cpp
- opt_TN_test.cpp → opt_tn_test.cpp

Header guards updated: HHARTREEPW_H → H_HARTREE_PW_H,
FORCES_H → FORCE_PW_H. Update all #include references,
CMakeLists.txt, and Makefile.Objects. Class/variable names preserved.
abacus_fixer
refactor: normalize Matrix_/Mix_/RI_/RPA_/LRI_ filenames (phase D)
c0317b7 
Rename 24 files to lowercase in source_lcao/module_ri/:
- Matrix_Orbs{11,21,22}.{cpp,h,hpp} → matrix_orbs{11,21,22}.{cpp,h,hpp}
- Mix_DMk_2D.{cpp,h} → mix_dmk_2d.{cpp,h}
- RI_2D_Comm.{cpp,h,hpp} → ri_2d_comm.{cpp,h,hpp}
- RI_Util.{h,hpp} → ri_util.{h,hpp}
- RPA_LRI.{h,hpp} → rpa_lri.{h,hpp}
- LRI_CV.{h,hpp} → lri_cv.{h,hpp}
- LRI_CV_Tools.{h,hpp} → lri_cv_tools.{h,hpp}
- make_gaunt_table-unittest.h → make_gaunt_table_unittest.h

Update all #include references, CMakeLists.txt, and Makefile.Objects.
Class names, namespace names, and header guards preserved unchanged.
abacus_fixer
refactor: replace dashes with underscores in filenames (phase E)
efab52d 
Rename 22 files, replacing '-' with '_' and normalizing case:
- ABFs_Construct-PCA.{cpp,h} → abfs_construct_pca.{cpp,h}
- abfs-vector3_order.{h} → abfs_vector3_order.{h}
- abfs-vector3_order_test.cpp → abfs_vector3_order_test.cpp
- center2_orb-orb{11,21,22}.{cpp,h} → center2_orb_orb{11,21,22}.{cpp,h}
- exx_abfs-io.{cpp,h} → exx_abfs_io.{cpp,h}
- exx_abfs-jle.{cpp,h} → exx_abfs_jle.{cpp,h}
- exx_opt_orb-print.cpp → exx_opt_orb_print.cpp
- exx_abfs-construct_orbs-test.h → exx_abfs_construct_orbs_test.h
- gram_schmidt_orth-inl.h → gram_schmidt_orth_inl.h
- matrix-inl.h → matrix_inl.h
- scalapack-test.cpp → scalapack_test.cpp
- element_basis_index-{test.h,unittest.cpp} → element_basis_index_{test.h,unittest.cpp}
- Inverse_Matrix-test.h → invmat_ri_test.h

Update all #include references, CMakeLists.txt, Makefile.Objects,
and code comments. Class names and header guards preserved unchanged.
abacus_fixer
refactor: normalize remaining uppercase filenames to lowercase (phase F)
8814e96 
Rename 44 files, converting uppercase letters to lowercase:
- Cblacs.h → cblacs.h
- cal_pLpR.{cpp,h} → cal_plpr.{cpp,h}
- cal_r_overlap_R.{cpp,h} → cal_r_overlap_r.{cpp,h}
- ewald_Vq.{h,hpp} → ewald_vq.{h,hpp}
- ExxLriDetail.{cpp,h} → exx_lri_detail.{cpp,h}
- Exx_LRI.{h,hpp} → exx_lri.{h,hpp}
- Exx_LRI_interface.{h,hpp} → exx_lri_interface.{h,hpp}
- fR_overlap.{cpp,h} → fr_overlap.{cpp,h}
- Inverse_Matrix.{h,hpp} → invmat_ri.{h,hpp}
- opt_TN.hpp → opt_tn.hpp
- single_R_io.{cpp,h} → single_r_io.{cpp,h}
- symmetry_rotation_R{,_hcontainer}.hpp → symmetry_rotation_r{,_hcontainer}.hpp
- write_dH{,_terms}.{cpp,h} → write_dh{,_terms}.{cpp,h}
- write_HS{,_R,_sparse}.{cpp,h} → write_hs{,_r,_sparse}.{cpp,h}
- write_H_terms.{cpp,h} → write_h_terms.{cpp,h}
- pw_basis_{C2C,C2R}.cpp → pw_basis_{c2c,c2r}.cpp
- pw_basis_k_C2C.cpp → pw_basis_k_c2c.cpp
- test_T_NL_cd.cpp → test_t_nl_cd.cpp
- test-{big,other}.cpp → test_{big,other}.cpp
- test_hcontainer_readCSR.cpp → test_hcontainer_read_csr.cpp
- test_{cal_dm_R,dm_R_init}.cpp → test_{cal_dm_r,dm_r_init}.cpp

Update all #include references, CMakeLists.txt, Makefile.Objects,
CMake target names, and code comments. Class names, function names,
namespace names, and header guards preserved unchanged.
abacus_fixer
Rename test files to follow source file renames
7569c7b 
Rename 6 test files to match their already-renamed source files:
- spherical_bessel_transformer_test → sph_bessel_tf_test
- gint_precision_controller_test → gint_prec_ctrl_test
- snap_psibeta_half_tddft_test → snap_psb_half_tddft_test
- lattice_change_methods_test → lat_change_method_test
- symmetry_rotation_spin_test → symm_rot_spin_test
- symmetry_rho_soc_test → symm_rho_soc_test

Update CMakeLists.txt entries and log file references accordingly.
abacus_fixer
update
9b00acc
abacus_fixer
Simplify test file names using standard abbreviations (Phase G2)
8d83710 
Apply KISS abbreviation rules to 15 test files:
- construct→ctor, radial→rad, interpolation→interp
- integrator→integ, initializer→init, recursive→rec
- clebsch_gordan→cg (math standard), element→elem, index→idx
- vector3→vec3, algorithms→algo, helper→hlp
- system→sys, variable→var, chebyshev→cheby
- operator→op

Update CMakeLists.txt entries, #include paths, and header guards accordingly.
abacus_fixer
Replace dashes with underscores in test file names (Phase G3)
4d8bba8 
Rename 42 numbered test files in source_basis/module_pw/test/:
- test1-1-1.cpp → test1_1_1.cpp
- test1-2.cpp → test1_2.cpp
- ... (all test*-*.cpp files)

Update CMakeLists.txt references accordingly.
Follows project naming convention: filenames must use underscores, not dashes.
abacus_fixer
Rename: normalize source file naming across modules
6335265 
- source_base: lowercase opt_CG/opt_DCsrch → opt_cg/opt_dcsrch (4 files)
- symmetry modules: unify symmetry_ → symm_ prefix (16 renamed,
  61 total files updated across source_cell/symmetry, source_estate,
  source_lcao/module_ri/module_exx_symmetry, and all call sites;
  module entry points symmetry.h / symmetry.cpp unchanged, class
  names Symmetry_Basic / Symmetry_rho / Symmetry_rotation preserved)
- source_cell: unify read_pseudo → read_pp_ucell to match read_pp
  series (2 renamed, 18 total files updated across CMake targets,
  Makefile.Objects, and callers; function names untouched)
- test files: unify _unittest suffix → _test (4 files: orb_test,
  element_basis_index_test, make_gaunt_table_test; include paths
  and header guards synced)
- source_lcao: disambiguate duplicate dftu_lcao name — rename
  dftu_lcao.{cpp,h} → setup_dftu_lcao.{cpp,h} (init/finish helpers);
  module_operator_lcao/dftu_lcao (DFTU operator implementation)
  retains original name
@mohanchen
mohanchen requested a review from Critsium-xy August 10, 2026 15:16
AsTonyshment
AsTonyshment reviewed Aug 11, 2026
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There are some conflicts need to be resolved.

Comment thread source/source_basis/module_pw/test/Makefile Outdated
abacus_fixer added 2 commits August 11, 2026 11:56
abacus_fixer
Merge upstream/develop into 2026-08-10-b
4918f95 
Sync with latest upstream develop to resolve conflicts with PR deepmodeling#7797.
All conflicts auto-resolved.
abacus_fixer
update makefile in module_pw
7732d83
@mohanchen mohanchen changed the title refactor: normalize and shorten source filenames for consistency Refactor: normalize and shorten source filenames for consistency Aug 11, 2026
abacus_fixer added 3 commits August 11, 2026 12:33
abacus_fixer
solve conflict
50d5f88
abacus_fixer
Merge upstream/develop into 2026-08-10-b
3da00cb 
Resolve conflicts:
- Keep HEAD file renaming (psi_init_atom_rand instead of psi_init_atomic_random)
- Use correct include paths (sph_bessel_tf.h and psi_base.h)
- Keep psi_init_unit_test.cpp as the test file name
- Resolve rename/rename conflict by keeping HEAD's psi_init_unit_test.cpp
abacus_fixer
Fix psi_init_atom_rand to match updated base class interface
b661c39 
- Update initialize() signature to match psi_init_atomic's new interface
- Use this->npol_ instead of PARAM.globalv.npol
- Remove unnecessary includes (vnl_pw.h, parameter.h)
abacus_fixer added 5 commits August 11, 2026 17:03
abacus_fixer
Add missing pw_basis_k.h include to psi_init_atom_rand.cpp
762819d 
The init_psig() method accesses pw_wfc_->npwk_max which requires the
complete type of ModulePW::PW_Basis_K, not just the forward declaration.
abacus_fixer
Merge upstream/develop into 2026-08-10-b
5117591 
Resolve conflicts caused by both branches moving files from source_io
to source_base/source_cell and renaming filenames to lowercase.

Resolution strategy:
- Keep our lowercase filename renames (write_hs.h, write_hs_r.h, etc.)
- Use upstream's correct include paths for moved files
  (source_base/module_out/, source_cell/)
- Remove duplicate entries in Makefile.Objects for files already
  moved to OBJS_BASE/OBJS_CELL
- Remove unnecessary explicit source compilation of orb_io.cpp and
  sparse_matrix.cpp in tests (now provided by base library)
abacus_fixer
Merge remote-tracking branch 'upstream/develop' into 2026-08-10-b
6821497
abacus_fixer
Merge remote-tracking branch 'upstream/develop' into 2026-08-10-b
d3b5bb8
abacus_fixer
Merge remote-tracking branch 'upstream/develop' into 2026-08-10-b
0be2efa
@mohanchen
mohanchen merged commit 3b22343 into deepmodeling:develop Aug 13, 2026
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@AsTonyshment AsTonyshment mentioned this pull request Aug 13, 2026
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Refactor Refactor ABACUS codes The Absolute Zero Reduce the "entropy" of the code to 0

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