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Critsium-xyclaude
Critsium-xy
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claude
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Fix: some easy-to-fix problems in [Code scan] issues (#7582)
* fix(tools): correct syntax error in RT-TDDFT projection tool Line 9 contained the invalid expression `fdir suffix + s_dir`, which made projection.py unparseable. Use `fdir + s_dir` to match the working example copy. Closes #7541 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix(tools): repair empty else branch in generate_orbital_mixstru.sh `bash -n` failed on the empty `else` branch before `fi`. Add a `:` no-op so the example script is syntactically valid. Closes #7542 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix(nao): reject one-past angular momentum index in TwoCenterTable index_map_ is allocated with final dimension length bra.lmax()+ket.lmax()+1, so valid indices are 0..dim_size(6)-1. The bounds check used `l <= dim_size(6)`, allowing a one-past read. Use `l < dim_size(6)` to match the neighboring dimension checks. Closes #7552 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix(container): copy innermost dimension when slicing 3D tensors Each 3D row is placed at offset_out advancing by size[2], so the contiguous copy length must also be size[2]. The copy used size[1], corrupting non-cubic slices where size[1] != size[2]. Closes #7551 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix(esolver): delete OFDFT KEDF_Manager with scalar delete kedf_manager_ is allocated with scalar `new KEDF_Manager()`, but the reinitialization path in before_all_runners() freed it with `delete[]`, which is undefined behavior. Use scalar `delete` to match the allocation. Closes #7548 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix(ci): use consistent SuperLU_DIST32_ROOT variable in path exports LD_LIBRARY_PATH, PKG_CONFIG_PATH and CPATH referenced the misspelled SUPERLU32_DIST_ROOT while CMAKE_PREFIX_PATH used SUPERLU_DIST32_ROOT (the name defined in Dockerfile.intel). Align the path exports to SUPERLU_DIST32_ROOT so SuperLU_DIST is not silently omitted. Closes #7572 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix(io): read LATTICE_PARAMETER blocks consistently in STRU parsers The Multiwfn and pyabacus STRU parsers checked for a LATTICE_PARAMETER block but then read blocks['LATTICE_PARAMETERS'] with an extra S, and treated the list of lines as a string. Read blocks['LATTICE_PARAMETER'][0].split() to match the neighboring LATTICE_CONSTANT idiom, so STRU files using LATTICE_PARAMETER parse instead of raising KeyError. The identical fix for the ASE AbacusLite parser is intentionally left out of this PR and will be handled separately. Refs #7555 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
1 parent 0b7a266 commit 12515e5

9 files changed

Lines changed: 14 additions & 14 deletions

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‎.github/workflows/ase_plugin_test.yml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -48,9 +48,9 @@ jobs:
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- name: Configure & Build ABACUS (GNU)
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run: |
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git config --global --add safe.directory `pwd`
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export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU32_DIST_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH}
52-
export PKG_CONFIG_PATH=${GKLIB_ROOT}/lib/pkgconfig:${METIS32_ROOT}/lib/pkgconfig:${PARMETIS32_ROOT}/lib/pkgconfig:${SUPERLU32_DIST_ROOT}/lib/pkgconfig:${PEXSI32_ROOT}/lib/pkgconfig:${PKG_CONFIG_PATH}
53-
export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
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export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU_DIST32_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH}
52+
export PKG_CONFIG_PATH=${GKLIB_ROOT}/lib/pkgconfig:${METIS32_ROOT}/lib/pkgconfig:${PARMETIS32_ROOT}/lib/pkgconfig:${SUPERLU_DIST32_ROOT}/lib/pkgconfig:${PEXSI32_ROOT}/lib/pkgconfig:${PKG_CONFIG_PATH}
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export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU_DIST32_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
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export CMAKE_PREFIX_PATH=${PEXSI32_ROOT}:${SUPERLU_DIST32_ROOT}:${PARMETIS32_ROOT}:${METIS32_ROOT}:${GKLIB_ROOT}:${CMAKE_PREFIX_PATH}
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source toolchain/install/setup
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rm -rf build

‎.github/workflows/build_test_cmake.yml‎

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@@ -70,9 +70,9 @@ jobs:
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- name: Build
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run: |
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git config --global --add safe.directory `pwd`
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export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU32_DIST_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH}
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export PKG_CONFIG_PATH=${GKLIB_ROOT}/lib/pkgconfig:${METIS32_ROOT}/lib/pkgconfig:${PARMETIS32_ROOT}/lib/pkgconfig:${SUPERLU32_DIST_ROOT}/lib/pkgconfig:${PEXSI32_ROOT}/lib/pkgconfig:${PKG_CONFIG_PATH}
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export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
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export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU_DIST32_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH}
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export PKG_CONFIG_PATH=${GKLIB_ROOT}/lib/pkgconfig:${METIS32_ROOT}/lib/pkgconfig:${PARMETIS32_ROOT}/lib/pkgconfig:${SUPERLU_DIST32_ROOT}/lib/pkgconfig:${PEXSI32_ROOT}/lib/pkgconfig:${PKG_CONFIG_PATH}
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export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU_DIST32_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
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export CMAKE_PREFIX_PATH=${PEXSI32_ROOT}:${SUPERLU_DIST32_ROOT}:${PARMETIS32_ROOT}:${METIS32_ROOT}:${GKLIB_ROOT}:${CMAKE_PREFIX_PATH}
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source toolchain/install/setup
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rm -rf build

‎interfaces/Multiwfn_interface/molden.py‎

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Original file line numberDiff line numberDiff line change
@@ -841,7 +841,7 @@ def read_stru(fpath):
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if 'LATTICE_VECTORS' in blocks:
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stru['lat']['vec'] = [[float(x) for x in line.split()] for line in blocks['LATTICE_VECTORS']]
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elif 'LATTICE_PARAMETER' in blocks:
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stru['lat']['param'] = [float(x) for x in blocks['LATTICE_PARAMETERS'].split()]
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stru['lat']['param'] = [float(x) for x in blocks['LATTICE_PARAMETER'][0].split()]
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#============ ATOMIC_SPECIES ============
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stru['species'] = [ dict(zip(['symbol', 'mass', 'pp_file', 'pp_type'], line.split())) for line in blocks['ATOMIC_SPECIES'] ]

‎python/pyabacus/src/pyabacus/io/stru.py‎

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Original file line numberDiff line numberDiff line change
@@ -134,7 +134,7 @@ def _trim(line):
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for line in blocks['LATTICE_VECTORS']]
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elif 'LATTICE_PARAMETER' in blocks:
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stru['lat']['param'] = [float(x)
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for x in blocks['LATTICE_PARAMETERS'].split()]
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for x in blocks['LATTICE_PARAMETER'][0].split()]
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#============ ATOMIC_SPECIES ============
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stru['species'] = [_atomic_species_from_file(line)

‎source/source_base/module_container/ATen/core/tensor.cpp‎

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Original file line numberDiff line numberDiff line change
@@ -196,7 +196,7 @@ Tensor Tensor::slice(const std::vector<int> &start, const std::vector<int> &size
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int offset_out = i * size[1] * size[2] + j * size[2];
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TEMPLATE_ALL_2(this->data_type_, this->device_,
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kernels::synchronize_memory<T_, DEVICE_, DEVICE_>()(
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output.data<T_>() + offset_out, this->data<T_>() + offset, size[1]))
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output.data<T_>() + offset_out, this->data<T_>() + offset, size[2]))
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}
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}
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}

‎source/source_basis/module_nao/two_center_table.cpp‎

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Original file line numberDiff line numberDiff line change
@@ -135,7 +135,7 @@ bool TwoCenterTable::is_present(const int itype1,
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return itype1 >= 0 && itype1 < index_map_.shape().dim_size(0) && l1 >= 0 && l1 < index_map_.shape().dim_size(1)
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&& izeta1 >= 0 && izeta1 < index_map_.shape().dim_size(2) && itype2 >= 0
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&& itype2 < index_map_.shape().dim_size(3) && l2 >= 0 && l2 < index_map_.shape().dim_size(4) && izeta2 >= 0
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&& izeta2 < index_map_.shape().dim_size(5) && l >= 0 && l <= index_map_.shape().dim_size(6)
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&& izeta2 < index_map_.shape().dim_size(5) && l >= 0 && l < index_map_.shape().dim_size(6)
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&& index_map_.get_value<int>(itype1, l1, izeta1, itype2, l2, izeta2, l) >= 0;
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}
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‎source/source_esolver/esolver_of.cpp‎

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Original file line numberDiff line numberDiff line change
@@ -115,7 +115,7 @@ void ESolver_OF::before_all_runners(UnitCell& ucell, const Input_para& inp)
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this->nelec_[0] = this->pelec->nelec_spin[0];
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this->nelec_[1] = this->pelec->nelec_spin[1];
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}
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delete[] this->kedf_manager_;
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delete this->kedf_manager_;
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this->kedf_manager_ = new KEDF_Manager();
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this->kedf_manager_->init(inp, this->pw_rho, this->dV_, this->nelec_[0]);
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ModuleBase::GlobalFunc::DONE(GlobalV::ofs_running, "INIT KEDF");

‎tools/01_NAO_generation/examples/example_opt_lcao_bash/generate_orbital_mixstru.sh‎

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Original file line numberDiff line numberDiff line change
@@ -651,8 +651,8 @@ if [ "${EXE_orbital:0-3:3}" != ".py" ];
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then
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echo ok ;
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else
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else
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:
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fi
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‎tools/02_postprocessing/rt-tddft-tools/projection.py‎

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Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ def __init__(self, stepref, klist, steps, fdir='./OUT.ABACUS', wfc_dir='', s_dir
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self.klist = klist
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self.steps = steps
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self.wfc_dir = fdir + wfc_dir
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self.s_dir = fdir suffix + s_dir
9+
self.s_dir = fdir + s_dir
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wfc_ref, Ocp_ref = self.read_wfc(klist[0]+1, stepref+1, dir=self.wfc_dir)
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self.nband = len(Ocp_ref)
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self.nlocal = len(wfc_ref[0])

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