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Merge branch 'deepmodeling:develop' into develop
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‎.gitattributes‎

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.gitattributes export-ignore
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.gitignore export-ignore
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.gitmodules export-ignore
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.pre-commit-config.yaml export-ignore
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.github/ export-ignore

‎.github/workflows/ase_plugin_test.yml‎

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uses: actions/checkout@v6
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- name: Set up Miniconda
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uses: conda-incubator/setup-miniconda@v3
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uses: conda-incubator/setup-miniconda@v4
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with:
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miniconda-version: 'latest'
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activate-environment: abacuslite

‎.github/workflows/doxygen.yml‎

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uses: actions/configure-pages@v6
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- name: Upload artifact
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uses: actions/upload-pages-artifact@v4
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uses: actions/upload-pages-artifact@v5
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with:
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path: './doxygen/html'
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‎.github/workflows/interface.yml‎

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name: interface
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on:
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workflow_dispatch:
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jobs:
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wannier-interface:
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name: "wannier interface — ${{ matrix.name }}"
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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- name: basic (LCAO)
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script: example_basic.py
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prefix: Bi2Se3_basic
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basis: lcao
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- name: pw (Plane Wave)
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script: example_pw.py
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prefix: Bi2Se3_pw
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basis: pw
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- name: advance (LCAO)
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script: example_advance.py
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prefix: Bi2Se3_advanced
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basis: lcao
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defaults:
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run:
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working-directory: interfaces/Wannier90_interface/examples_python
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steps:
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- name: Checkout repository
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uses: actions/checkout@v6
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- name: Set up Python 3.10
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uses: actions/setup-python@v6
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with:
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python-version: "3.10"
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- name: Install abacusw90
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run: |
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python -m pip install --upgrade pip
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pip install -e ..
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- name: Confirm no wannier90.x in environment
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run: |
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if command -v wannier90.x 2>/dev/null; then
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echo "::error::wannier90.x found — CI must test WITHOUT external binaries"
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exit 1
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fi
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echo "OK: no wannier90.x (dryrun mode)"
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- name: Create mock data & patch script
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env:
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SCRIPT: ${{ matrix.script }}
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PREFIX: ${{ matrix.prefix }}
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run: |
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python3 << 'PYEOF'
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import os, re, textwrap
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script = os.environ["SCRIPT"]
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prefix = os.environ["PREFIX"]
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# ── 1. Patch the example script ────────────────────────
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with open(script) as f:
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src = f.read()
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src = src.replace("DRY_RUN = False", "DRY_RUN = True")
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src = re.sub(
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r"\s*job\.step0_run_scf\([^)]*\)",
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" # [CI:skip] step0_run_scf — no ABACUS in this environment",
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src,
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flags=re.DOTALL,
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)
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src = src.replace(
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"job.step1_generate_wannier_win()",
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"# [CI:skip] step1_generate_wannier_win — no wannier90.x in this environment",
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)
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with open(script, "w") as f:
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f.write(src)
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print(f"[patch] {script}")
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# ── 2. Create work directories ─────────────────────────
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for d in [f"{prefix}/scf", f"{prefix}/wannier"]:
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os.makedirs(d, exist_ok=True)
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# ── 3. Mock STRU (scf/ + wannier/) ────────────────────
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if basis == "pw":
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atom_species = (
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"ATOMIC_SPECIES\n"
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"Bi 208.980 Bi_pbe_fr.upf\n"
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"Se 78.960 Bi_pbe_fr.upf\n"
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"\n"
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)
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else:
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atom_species = (
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"ATOMIC_SPECIES\n"
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"Bi 208.980 Bi_pbe_fr.upf Bi_gga_10au_100Ry_2s2p2d.orb\n"
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"Se 78.960 Bi_pbe_fr.upf Se_gga_10au_100Ry_2s2p2d.orb\n"
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"\n"
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)
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lattice_block = textwrap.dedent("""\
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LATTICE_CONSTANT
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1.0
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LATTICE_VECTORS
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-2.069 -3.583614 0.0
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2.069 -3.583614 0.0
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0.000 2.389075 9.546667
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ATOMIC_POSITIONS
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Direct
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Bi
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0.399 0.399 0.697 1 1 1
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0.601 0.601 0.303 1 1 1
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Se
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0.000 0.000 0.500 1 1 1
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0.206 0.206 0.118 1 1 1
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0.794 0.794 0.882 1 1 1
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""")
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stru = atom_species + lattice_block
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for d in [f"{prefix}/scf", f"{prefix}/wannier"]:
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p = os.path.join(d, "STRU")
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with open(p, "w") as f:
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f.write(stru)
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print(f"[mock] {p}")
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# ── 4. Mock wannier90.nnkp ────────────────────────────
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nbands = 20
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nk = 64 # 4 × 4 × 4
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nntot = 14
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lines = [
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f" {nbands}", "! num_bands",
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f" {nk}", "! num_kpts",
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" 4 4 4", "! mp_grid",
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]
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for ix in range(4):
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for iy in range(4):
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for iz in range(4):
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lines.append(f" {ix/4:.15f} {iy/4:.15f} {iz/4:.15f}")
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lines.append(f" {nntot}")
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lines.append("! nntot")
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for ik in range(nk):
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lines.append(f" {nntot}")
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for ib in range(nntot):
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lines.append(f" {(ik + ib) % nk + 1}")
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lines.append(f" {nntot}")
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for ib in range(nntot):
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lines.append(" 0 0 0")
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lines += [
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f" {nbands}", "! num_exclude_bands",
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" 30", "! num_wann",
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" 6", "! num_proj",
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]
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for proj in ["Bi : pz","Bi : px","Bi : py",
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"Se : pz","Se : px","Se : py"]:
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lines.append(f" {proj}")
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nnkp = os.path.join(prefix, "wannier", "wannier90.nnkp")
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with open(nnkp, "w") as f:
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f.write("\n".join(lines) + "\n")
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print(f"[mock] {nnkp} ({len(lines)} lines)")
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# ── 5. Mock PP & ORB files ─────────────────────────────
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orb_dir = os.path.abspath("../../../tests/PP_ORB/")
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os.makedirs(orb_dir, exist_ok=True)
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for name in ["Bi_pbe_fr.upf", "Se_pbe_fr.upf", "Bi_gga_10au_100Ry_2s2p2d.orb", "Se_gga_10au_100Ry_2s2p2d.orb"]:
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p = os.path.join(orb_dir, name)
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with open(p, "w") as f:
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f.write("# mock for CI dryrun\n")
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print(f"[mock] {p}")
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print("\n[done] all mocks ready")
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PYEOF
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- name: Run ${{ matrix.script }} — dryrun
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run: python ${{ matrix.script }} 2>&1 | tee run.log
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- name: Check dryrun completion banner
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run: |
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if grep -q "DRY RUN COMPLETE" run.log; then
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echo " [OK] dryrun banner found"
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else
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echo " [FAIL] 'DRY RUN COMPLETE' not found — script may have crashed"
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exit 1
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fi
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- name: Validate generated files (${{ matrix.name }})
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run: |
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W="${{ matrix.prefix }}/wannier"
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ERR=0
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check() {
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if [ -f "$1" ]; then
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echo " [OK] $1 ($(wc -c < "$1") bytes)"
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else
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echo " [FAIL] $1 (not found)"
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ERR=1
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fi
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}
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echo "=========================================="
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echo " NSCF input files (from step2)"
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echo "=========================================="
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check "$W/INPUT"
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check "$W/KPT"
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check "$W/STRU"
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if [ -f "$W/INPUT" ]; then
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echo ""
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echo "--- INPUT keyword checks ---"
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for key in "calculation" "towannier90" "nspin"; do
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if grep -qi "$key" "$W/INPUT"; then
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echo " [OK] INPUT contains '$key'"
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else
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echo " [FAIL] INPUT missing '$key'"
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ERR=1
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fi
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done
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if grep -qi "gamma_only" "$W/INPUT"; then
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echo " [FAIL] INPUT contains 'gamma_only' — forbidden!"
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ERR=1
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else
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echo " [OK] INPUT does NOT contain 'gamma_only'"
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fi
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fi
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echo ""
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echo "--- Basis-specific checks (${{ matrix.basis }}) ---"
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if [ "${{ matrix.basis }}" = "pw" ]; then
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if grep -qi "orbital_file\|orbital_dir" "$W/INPUT"; then
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echo " [FAIL] PW INPUT contains orbital_file/orbital_dir"
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ERR=1
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else
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echo " [OK] PW INPUT does NOT contain orbital_file/orbital_dir"
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fi
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else
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if grep -qi "orbital_file\|orbital_dir" "$W/INPUT"; then
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echo " [OK] LCAO INPUT contains orbital_file/orbital_dir"
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else
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echo " [WARN] LCAO INPUT missing orbital references (may be in STRU)"
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fi
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fi
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if [ -f "$W/KPT" ]; then
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echo ""
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klines=$(wc -l < "$W/KPT")
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if [ "$klines" -gt 5 ]; then
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echo " [OK] KPT has $klines lines (reasonable)"
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else
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echo " [FAIL] KPT too short ($klines lines)"
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ERR=1
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fi
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fi
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echo ""
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if [ "$ERR" -ne 0 ]; then
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echo "=========================================="
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echo " VALIDATION FAILED"
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echo "=========================================="
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exit 1
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fi
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echo "=========================================="
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echo " ALL CHECKS PASSED (${{ matrix.name }})"
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echo "=========================================="
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- name: Show full script output
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if: always()
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run: cat run.log
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- name: Show generated INPUT
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if: always()
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run: |
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f="${{ matrix.prefix }}/wannier/INPUT"
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if [ -f "$f" ]; then echo "=== $f ==="; cat "$f"; else echo "$f not found"; fi
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- name: Show generated KPT (first 20 lines)
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if: always()
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run: |
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f="${{ matrix.prefix }}/wannier/KPT"
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if [ -f "$f" ]; then echo "=== $f (first 20 lines) ==="; head -20 "$f"; else echo "$f not found"; fi
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- name: List all generated files
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if: always()
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run: find ${{ matrix.prefix }} -type f | sort

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