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mohanchenmohanchen
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Merge branch 'develop' into 2026-07-01
2 parents a657a6e + 69e2b1e commit fa4ece7

10 files changed

Lines changed: 23 additions & 23 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:
4848
- name: Configure & Build ABACUS (GNU)
4949
run: |
5050
git config --global --add safe.directory `pwd`
51-
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}
51+
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}
53+
export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU_DIST32_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
5454
export CMAKE_PREFIX_PATH=${PEXSI32_ROOT}:${SUPERLU_DIST32_ROOT}:${PARMETIS32_ROOT}:${METIS32_ROOT}:${GKLIB_ROOT}:${CMAKE_PREFIX_PATH}
5555
source toolchain/install/setup
5656
rm -rf build

‎.github/workflows/build_test_cmake.yml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -70,9 +70,9 @@ jobs:
7070
- name: Build
7171
run: |
7272
git config --global --add safe.directory `pwd`
73-
export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU32_DIST_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH}
74-
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}
75-
export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
73+
export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU_DIST32_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH}
74+
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}
75+
export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU_DIST32_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
7676
export CMAKE_PREFIX_PATH=${PEXSI32_ROOT}:${SUPERLU_DIST32_ROOT}:${PARMETIS32_ROOT}:${METIS32_ROOT}:${GKLIB_ROOT}:${CMAKE_PREFIX_PATH}
7777
source toolchain/install/setup
7878
rm -rf build

‎interfaces/Multiwfn_interface/molden.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -841,7 +841,7 @@ def read_stru(fpath):
841841
if 'LATTICE_VECTORS' in blocks:
842842
stru['lat']['vec'] = [[float(x) for x in line.split()] for line in blocks['LATTICE_VECTORS']]
843843
elif 'LATTICE_PARAMETER' in blocks:
844-
stru['lat']['param'] = [float(x) for x in blocks['LATTICE_PARAMETERS'].split()]
844+
stru['lat']['param'] = [float(x) for x in blocks['LATTICE_PARAMETER'][0].split()]
845845

846846
#============ ATOMIC_SPECIES ============
847847
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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -134,7 +134,7 @@ def _trim(line):
134134
for line in blocks['LATTICE_VECTORS']]
135135
elif 'LATTICE_PARAMETER' in blocks:
136136
stru['lat']['param'] = [float(x)
137-
for x in blocks['LATTICE_PARAMETERS'].split()]
137+
for x in blocks['LATTICE_PARAMETER'][0].split()]
138138

139139
#============ ATOMIC_SPECIES ============
140140
stru['species'] = [_atomic_species_from_file(line)

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

Lines changed: 1 addition & 1 deletion
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
196196
int offset_out = i * size[1] * size[2] + j * size[2];
197197
TEMPLATE_ALL_2(this->data_type_, this->device_,
198198
kernels::synchronize_memory<T_, DEVICE_, DEVICE_>()(
199-
output.data<T_>() + offset_out, this->data<T_>() + offset, size[1]))
199+
output.data<T_>() + offset_out, this->data<T_>() + offset, size[2]))
200200
}
201201
}
202202
}

‎source/source_basis/module_nao/two_center_table.cpp‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -135,7 +135,7 @@ bool TwoCenterTable::is_present(const int itype1,
135135
return itype1 >= 0 && itype1 < index_map_.shape().dim_size(0) && l1 >= 0 && l1 < index_map_.shape().dim_size(1)
136136
&& izeta1 >= 0 && izeta1 < index_map_.shape().dim_size(2) && itype2 >= 0
137137
&& itype2 < index_map_.shape().dim_size(3) && l2 >= 0 && l2 < index_map_.shape().dim_size(4) && izeta2 >= 0
138-
&& izeta2 < index_map_.shape().dim_size(5) && l >= 0 && l <= index_map_.shape().dim_size(6)
138+
&& izeta2 < index_map_.shape().dim_size(5) && l >= 0 && l < index_map_.shape().dim_size(6)
139139
&& index_map_.get_value<int>(itype1, l1, izeta1, itype2, l2, izeta2, l) >= 0;
140140
}
141141

‎source/source_esolver/esolver_of.cpp‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -115,7 +115,7 @@ void ESolver_OF::before_all_runners(UnitCell& ucell, const Input_para& inp)
115115
this->nelec_[0] = this->pelec->nelec_spin[0];
116116
this->nelec_[1] = this->pelec->nelec_spin[1];
117117
}
118-
delete[] this->kedf_manager_;
118+
delete this->kedf_manager_;
119119
this->kedf_manager_ = new KEDF_Manager();
120120
this->kedf_manager_->init(inp, this->pw_rho, this->dV_, this->nelec_[0]);
121121
ModuleBase::GlobalFunc::DONE(GlobalV::ofs_running, "INIT KEDF");

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -651,8 +651,8 @@ if [ "${EXE_orbital:0-3:3}" != ".py" ];
651651
then
652652
echo ok ;
653653

654-
else
655-
654+
else
655+
:
656656
fi
657657

658658

‎tools/02_postprocessing/rt-tddft-tools/projection.py‎

Lines changed: 1 addition & 1 deletion
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
66
self.klist = klist
77
self.steps = steps
88
self.wfc_dir = fdir + wfc_dir
9-
self.s_dir = fdir suffix + s_dir
9+
self.s_dir = fdir + s_dir
1010
wfc_ref, Ocp_ref = self.read_wfc(klist[0]+1, stepref+1, dir=self.wfc_dir)
1111
self.nband = len(Ocp_ref)
1212
self.nlocal = len(wfc_ref[0])

‎tools/03_code_analysis/agent_governance_check.py‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -241,14 +241,14 @@ def check_global_dependencies(findings: List[Finding], lines: Iterable[DiffLine]
241241
continue
242242
if pattern.search(line.content):
243243
add_finding(
244-
findings,
245-
"No new cross-layer globals",
246-
BLOCK,
247-
line.path,
248-
line.line,
249-
"Added line introduces GlobalV, GlobalC, or PARAM as a dependency.",
250-
"Prefer explicit parameters or a narrow local interface. Document any required exception in the PR.",
251-
)
244+
findings,
245+
"No new cross-layer globals",
246+
WARN,
247+
line.path,
248+
line.line,
249+
"Added line introduces GlobalV, GlobalC, or PARAM as a dependency.",
250+
"Prefer explicit parameters or a narrow local interface. Document any required exception in the PR.",
251+
)
252252

253253

254254
def check_default_parameters(findings: List[Finding], lines: Iterable[DiffLine]) -> None:
@@ -518,7 +518,7 @@ def check_pr_metadata(findings: List[Finding], body: Optional[str]) -> None:
518518
add_finding(
519519
findings,
520520
"PR metadata completeness",
521-
BLOCK,
521+
WARN,
522522
"pull_request.body",
523523
None,
524524
"; ".join(reason_parts),

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