Refactor Parallel_Grid::init to separate serial/parallel initialization

.ci/slurm/config.ini

@@ -491,7 +491,7 @@ runner = autotest_gpu
 
 [case.080]
 suite = 01_PW
-name = 035_PW_15_SO
+name = scf_spin4
 resource = pw_gpu1
 runner = autotest_gpu
 

.github/instructions/abacus-governance.instructions.md

@@ -22,6 +22,8 @@ Apply these instructions when reviewing or changing ABACUS code:
   usually warnings unless the PR records a narrow reason.
 - Require LF line endings for text files. `.bat` and `.cmd` files are the CRLF
   exceptions.
+- Flag new `#pragma once` in header files as a blocker-level governance issue.
+  Require traditional `#ifndef`/`#define`/`#endif` include guards instead.
 - For INPUT parameter behavior changes, require synchronized updates to
   `docs/parameters.yaml` and `docs/advanced/input_files/input-main.md`, or a
   clear no-update explanation in the PR.

.github/workflows/ase_plugin_test.yml

@@ -74,3 +74,17 @@ jobs:
           cd interfaces/ASE_interface/tests
           chmod +x xtest.sh
           ./xtest.sh
+
+      # When a test fails, every integration test script (scf/relax/md/band/
+      # magnetic) preserves its whole ABACUS run directory under
+      # /tmp/abacus_ase_failure (see preserved_tmpdir in tests/common.py,
+      # overridable via ASE_ABACUS_KEEP_DIR). Upload it so remote-CI-only
+      # failures (e.g. issue #7794) can be root-caused without runner access.
+      - name: Upload ASE failure artifacts
+        if: failure()
+        uses: actions/upload-artifact@v7
+        with:
+          name: ase-failure-${{ github.run_id }}-${{ github.run_attempt }}
+          path: /tmp/abacus_ase_failure/**
+          if-no-files-found: ignore
+          retention-days: 14

.github/workflows/build_test_cmake.yml

@@ -24,11 +24,11 @@ jobs:
 
           - tag: gnu
             external_toolchain_args: ""
-            build_args: "-DENABLE_LIBXC=ON -DENABLE_MLALGO=ON -DENABLE_LIBRI=ON -DENABLE_DFTD4=ON -DENABLE_PEXSI=ON"
+            build_args: "-DENABLE_LIBXC=ON -DENABLE_MLALGO=ON -DENABLE_LIBRI=ON -DENABLE_DFTD4=ON -DENABLE_PEXSI=ON -DENABLE_JSON=ON"
             name: "Build extra components with GNU toolchain"
           - tag: intel
             external_toolchain_args: "--with-intel"
-            build_args: "-DENABLE_LIBXC=ON -DENABLE_MLALGO=ON -DENABLE_LIBRI=ON -DENABLE_DFTD4=ON"
+            build_args: "-DENABLE_LIBXC=ON -DENABLE_MLALGO=ON -DENABLE_LIBRI=ON -DENABLE_DFTD4=ON -DENABLE_JSON=ON"
             name: "Build extra components with Intel toolchain"
 
           - tag: cuda

.github/workflows/build_test_makefile.yml

@@ -22,7 +22,9 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v7.0.1
       - name: Build
+        # TODO: Remove nlohmann-json installation here since Dockerfile will have installed it.
         run: |
+          apt update && apt install -y nlohmann-json3-dev
           export I_MPI_CXX=icpx
           chmod a+x generate_build_info.sh
           cd source

.github/workflows/coverage.yml

@@ -62,8 +62,8 @@ jobs:
           -DENABLE_MLALGO=ON \
           -DENABLE_LIBXC=ON \
           -DENABLE_LIBRI=ON \
-          -DENABLE_GOOGLEBENCH=ON \
-          -DENABLE_RAPIDJSON=ON \
+          -DENABLE_GOOGLEBENCH=OFF \
+          -DENABLE_JSON=ON \
           -DCMAKE_BUILD_TYPE=Debug \
           -DCMAKE_CXX_FLAGS="--coverage -fprofile-arcs -ftest-coverage" \
           -DCMAKE_EXE_LINKER_FLAGS="--coverage"
@@ -83,7 +83,7 @@ jobs:
 
         lcov --directory . --capture --output-file coverage.info
 
-        lcov --remove coverage.info '/usr/*' '*/test/*' '*/external/*' '*/build/*' --output-file coverage.filtered.info
+        lcov --remove coverage.info '/usr/*' '*/test/*' '*/unittests/*' '*/external/*' '*/build/*' --output-file coverage.filtered.info
 
         genhtml coverage.filtered.info --output-directory coverage-report
 

.github/workflows/cuda.yml

@@ -28,6 +28,12 @@ jobs:
       CCACHE_BASEDIR: ${{ github.workspace }}
       CCACHE_COMPRESS: "true"
       CCACHE_MAXSIZE: 8G
+      # Test cases to run side by side. The runner has 12 cores and one
+      # V100-32GB; a GPU case is a few atoms and takes about 2 s, so these
+      # suites are bound by process startup, not by the device. Four leaves
+      # every rank a core of its own and keeps the concurrent CUDA contexts
+      # far inside the card's memory.
+      GPU_TEST_JOBS: "4"
     steps:
       - name: Checkout
         uses: actions/checkout@v7.0.1
@@ -46,7 +52,7 @@ jobs:
           echo "fingerprint=${fingerprint}" >> "${GITHUB_OUTPUT}"
 
       - name: Restore compiler cache
-        uses: actions/cache@v6
+        uses: actions/cache/restore@v6
         with:
           path: ${{ env.CCACHE_DIR }}
           key: abacus-cuda-ccache-v1-${{ runner.os }}-${{ runner.arch }}-${{ steps.compiler.outputs.fingerprint }}-${{ github.sha }}
@@ -72,6 +78,7 @@ jobs:
           source toolchain/install/setup
           rm -rf build
           cmake -B build -G Ninja -DUSE_CUDA=ON -DBUILD_TESTING=ON -DENABLE_FLOAT_FFTW=ON \
+            -DENABLE_GOOGLEBENCH=OFF \
             -DCMAKE_CUDA_ARCHITECTURES=70
           cmake --build build -j "$(nproc)"
           cmake --install build
@@ -82,6 +89,17 @@ jobs:
           ccache --show-stats
           ccache --show-stats >> "${GITHUB_STEP_SUMMARY}"
 
+      # Only develop writes the cache. A cache saved from a pull request is
+      # scoped to that pull request's ref, so no other branch can ever read
+      # it, while it still counts against the repository's 10 GB budget and
+      # evicts the develop entry that every pull request does restore from.
+      - name: Save compiler cache
+        if: github.ref == 'refs/heads/develop'
+        uses: actions/cache/save@v6
+        with:
+          path: ${{ env.CCACHE_DIR }}
+          key: abacus-cuda-ccache-v1-${{ runner.os }}-${{ runner.arch }}-${{ steps.compiler.outputs.fingerprint }}-${{ github.sha }}
+
       - name: Module_LCAO CUDA Unittests
         env:
           GTEST_COLOR: 'yes'
@@ -92,17 +110,17 @@ jobs:
       - name: Test 11_PW_GPU
         run: |
           cd tests/11_PW_GPU
-          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+          bash ../integrate/Autotest.sh -n 2 -j "$GPU_TEST_JOBS" -f CASES_GPU.txt
 
       - name: Test 12_NAO_Gamma_GPU
         run: |
           cd tests/12_NAO_Gamma_GPU
-          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+          bash ../integrate/Autotest.sh -n 2 -j "$GPU_TEST_JOBS" -f CASES_GPU.txt
 
       - name: Test 13_NAO_multik_GPU
         run: |
           cd tests/13_NAO_multik_GPU
-          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+          bash ../integrate/Autotest.sh -n 2 -j "$GPU_TEST_JOBS" -f CASES_GPU.txt
 
       - name: Test 02_NAO_Gamma on GPU
         run: |
@@ -114,7 +132,7 @@ jobs:
                   echo "device    gpu" >> "$f"
               fi
           done
-          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+          bash ../integrate/Autotest.sh -n 2 -j "$GPU_TEST_JOBS" -f CASES_GPU.txt
 
       - name: Test 03_NAO_multik on GPU
         run: |
@@ -126,17 +144,17 @@ jobs:
                   echo "device    gpu" >> "$f"
               fi
           done
-          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+          bash ../integrate/Autotest.sh -n 2 -j "$GPU_TEST_JOBS" -f CASES_GPU.txt
 
       - name: Test 15_rtTDDFT_GPU
         run: |
           cd tests/15_rtTDDFT_GPU
-          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+          bash ../integrate/Autotest.sh -n 2 -j "$GPU_TEST_JOBS" -f CASES_GPU.txt
 
       - name: Test 16_SDFT_GPU
         run: |
           cd tests/16_SDFT_GPU
-          bash ../integrate/Autotest.sh -n 2 -f CASES_GPU.txt
+          bash ../integrate/Autotest.sh -n 2 -j "$GPU_TEST_JOBS" -f CASES_GPU.txt
 
       - name: Test 01_PW on GPU
         run: |
@@ -148,4 +166,4 @@ jobs:
                   echo "device    gpu" >> "$f"
               fi
           done
-          bash ../integrate/Autotest.sh -n 1 -a abacus -f CASES_GPU.txt
+          bash ../integrate/Autotest.sh -n 1 -j "$GPU_TEST_JOBS" -a abacus -f CASES_GPU.txt

.github/workflows/test.yml

@@ -63,7 +63,7 @@ jobs:
           echo "fingerprint=${fingerprint}" >> "${GITHUB_OUTPUT}"
 
       - name: Restore compiler cache
-        uses: actions/cache@v6
+        uses: actions/cache/restore@v6
         with:
           path: ${{ env.CCACHE_DIR }}
           key: abacus-gnu-ccache-v1-${{ runner.os }}-${{ runner.arch }}-${{ steps.compiler.outputs.fingerprint }}-${{ github.sha }}
@@ -92,8 +92,8 @@ jobs:
             -DENABLE_MLALGO=ON \
             -DENABLE_LIBXC=ON \
             -DENABLE_LIBRI=ON \
-            -DENABLE_GOOGLEBENCH=ON \
-            -DENABLE_RAPIDJSON=ON \
+            -DENABLE_GOOGLEBENCH=OFF \
+            -DENABLE_JSON=ON \
             -DENABLE_FLOAT_FFTW=ON \
             -DENABLE_DFTD4=ON \
             -DENABLE_PEXSI=ON \
@@ -121,6 +121,17 @@ jobs:
           ccache --show-stats
           ccache --show-stats >> "${GITHUB_STEP_SUMMARY}"
 
+      # Only develop writes the cache. A cache saved from a pull request is
+      # scoped to that pull request's ref, so no other branch can ever read
+      # it, while it still counts against the repository's 10 GB budget and
+      # evicts the develop entry that every pull request does restore from.
+      - name: Save compiler cache
+        if: github.ref == 'refs/heads/develop'
+        uses: actions/cache/save@v6
+        with:
+          path: ${{ env.CCACHE_DIR }}
+          key: abacus-gnu-ccache-v1-${{ runner.os }}-${{ runner.arch }}-${{ steps.compiler.outputs.fingerprint }}-${{ github.sha }}
+
       - name: Check documentation consistency
         run: |
           ABACUS_BIN=$(find build -name "abacus_*" -type f -executable | head -1)
@@ -175,7 +186,7 @@ jobs:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          ctest --test-dir build -V --timeout 1700 -R MODULE_HSOLVER -E PERF_MODULE_HSOLVER_KERNELS
+          ctest --test-dir build -V --timeout 1700 -R MODULE_HSOLVER
 
       - name: Module_Cell Unittests
         env:
@@ -212,6 +223,13 @@ jobs:
         run: |
           ctest --test-dir build -V --timeout 1700 -R MODULE_ESTATE
 
+      - name: Module_Charge Unittests
+        env:
+          GTEST_COLOR: 'yes'
+          OMP_NUM_THREADS: '2'
+        run: |
+          ctest --test-dir build -V --timeout 1700 -R MODULE_CHARGE
+
       - name: Module_Hamilt Unittests
         env:
           GTEST_COLOR: 'yes'
@@ -310,12 +328,12 @@ jobs:
         run: |
           ctest --test-dir build -V --timeout 1700 -R 07_OFDFT
 
-      - name: 08_EXX Test
+      - name: 08_RI Test
         env:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          ctest --test-dir build -V --timeout 1700 -R 08_EXX
+          ctest --test-dir build -V --timeout 1700 -R 08_RI
 
       - name: 09_DeePKS Test
         env:
@@ -343,4 +361,4 @@ jobs:
           GTEST_COLOR: 'yes'
           OMP_NUM_THREADS: '2'
         run: |
-          ctest --test-dir build -V --timeout 1700 -E 'integrate_test|01_PW|02_NAO_Gamma|03_NAO_multik|04_FF|05_rtTDDFT|06_SDFT|07_OFDFT|08_EXX|09_DeePKS|10_others|11_PW_GPU|12_NAO_Gamma_GPU|13_NAO_multik_GPU|15_rtTDDFT_GPU|16_SDFT_GPU|17_DS_DFTU|MODULE_BASE|MODULE_IO|MODULE_HSOLVER|MODULE_CELL|MODULE_MD|MODULE_PSI|MODULE_ESTATE|MODULE_RI|MODULE_HAMILT|MODULE_PW|MODULE_LCAO|MODULE_AO|MODULE_NAO|MODULE_RELAX|MODULE_LR'
+          ctest --test-dir build -V --timeout 1700 -E 'integrated_test|01_PW|02_NAO_Gamma|03_NAO_multik|04_FF|05_rtTDDFT|06_SDFT|07_OFDFT|08_RI|09_DeePKS|10_others|11_PW_GPU|12_NAO_Gamma_GPU|13_NAO_multik_GPU|15_rtTDDFT_GPU|16_SDFT_GPU|17_DS_DFTU|MODULE_BASE|MODULE_IO|MODULE_HSOLVER|MODULE_CELL|MODULE_MD|MODULE_PSI|MODULE_ESTATE|MODULE_CHARGE|MODULE_RI|MODULE_HAMILT|MODULE_PW|MODULE_LCAO|MODULE_AO|MODULE_NAO|MODULE_RELAX|MODULE_LR'

.readthedocs.yaml

@@ -9,17 +9,32 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
+  # Toolchain for the `latexpdf` output (latex_engine = 'xelatex' in conf.py).
+  # Note: none of these come with the default image — each package below
+  # fixed a real build failure encountered during local verification.
+  jobs:
+    pre_build:
+      # RTD builds PR (external) versions as HTML only, so PDF failures would
+      # not surface until post-merge. Run the same latex->PDF chain here as a
+      # pre-merge gate. `latexpdf` is a make-mode target, not a -b builder,
+      # hence the two-step latex build + make all-pdf.
+      - |
+        if [ "$READTHEDOCS_VERSION_TYPE" = "external" ]; then
+          sphinx-build -b latex docs/ _latex_prcheck --fail-on-warning
+        fi
 
+
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/conf.py
   # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
   # builder: "dirhtml"
   # Fail on all warnings to avoid broken references
-  # fail_on_warning: true
+  fail_on_warning: true
 
 # Optionally build your docs in additional formats such as PDF and ePub
-formats: all
+formats:
+  - pdf
 
 # Optional but recommended, declare the Python requirements required
 # to build your documentation

AGENTS.md

@@ -50,6 +50,14 @@ rules. Read the complete governance document before making or reviewing changes:
       initializer list to direct parameter passthrough. Perform multi-step
       computations in the constructor body instead, so failures are easy to
       debug and each intermediate result is inspectable.
+  14. Do not write conditional or computed expressions in a function's
+      argument list; first assign the value to a named local variable, then
+      pass that variable. This keeps each argument inspectable and makes the
+      call site self-documenting. For example, prefer
+      `const int isk = (nspin == 2 && isk_ptr) ? isk_ptr[ik] : 0;`
+      followed by `f(..., isk, ...)` over inlining the ternary into the call.
+  15. Do not use `#pragma once` in header files; use traditional
+      `#ifndef`/`#define`/`#endif` include guards instead.
 - Use LF line endings for text files. Only `.bat` and `.cmd` files may use CRLF.
 - Keep source file additions deterministic: update the relevant `CMakeLists.txt`
   or explain why the file is generated or included indirectly.
@@ -157,6 +165,12 @@ full mixed-line-ending hook only for intentional repository-wide normalization.
 - Pull requests: https://github.com/deepmodeling/abacus-develop/pulls
 - Upstream PRs are opened from personal fork branches
   (`<fork-owner>:<branch>` into `develop`).
+- When synchronizing a local branch with `upstream/develop`, prefer
+  `git merge upstream/develop` over `git rebase upstream/develop`. Merge
+  preserves the original commit SHAs of the local work, keeps the branch
+  pushable without `--force`, and avoids re-applying a long patch series
+  when conflicts arise. Use rebase only when the user explicitly asks for
+  a linear history.
 - `workflow_dispatch`-only workflows (e.g. `.github/workflows/interface.yml`)
   are not triggered by push/PR events; PR CI cannot verify such fixes, so
   state "manual dispatch run required" in the PR verification notes.