Add atst examples in ASE interfaces examples

interfaces/ASE_interface/README.md

@@ -32,6 +32,7 @@ Please refer to the example scripts in the `examples` folder. Recommended learni
 7. **constraintmd.py** - Constrained molecular dynamics simulation
 8. **metadynamics.py** - Metadynamics simulation
 9. **neb.py** - Nudged Elastic Band (NEB) calculation
+10. **examples/atst_tools/README.md** - optional ATST-Tools workflow examples that use abacuslite for relax, NEB, Sella, CCQN, MD, and ABACUS input helpers
 
 More usage examples will be provided in future versions.
 
@@ -54,4 +55,4 @@ Thanks to the ABACUS development team for their support and contributions.
 
 If you have any questions or suggestions, please contact us through:
 
-- GitHub: [deepmodeling/abacus-develop](https://github.com/deepmodeling/abacus-develop)
+- GitHub: [deepmodeling/abacus-develop](https://github.com/deepmodeling/abacus-develop)

interfaces/ASE_interface/examples/atst_tools/README.md

@@ -0,0 +1,51 @@
+# Optional ATST-Tools Workflow Examples
+
+These examples show how ATST-Tools can use abacuslite as the ABACUS ASE
+calculator backend. They are an optional workflow layer on top of abacuslite:
+abacuslite itself does not depend on ATST-Tools.
+
+Install the optional workflow package in an environment where this checkout is
+available:
+
+```bash
+pip install atst-tools
+```
+
+Each case is intentionally small and uses pseudopotential and orbital files from
+`tests/PP_ORB`. Run commands from the case directory so relative structure and
+PP/ORB paths resolve as written.
+
+| Case | Workflow | Purpose |
+| --- | --- | --- |
+| `relax_si` | `calculation.type: relax` | Basic geometry optimization through `atst run`. |
+| `neb_si` | `calculation.type: neb` | Generated Si path with a short two-stage NEB setup. |
+| `sella_h2` | `calculation.type: sella` | Standalone single-ended saddle search syntax. |
+| `ccqn_h2` | `calculation.type: ccqn` | CCQN with an explicit reactive bond. |
+| `md_si` | `calculation.type: md` | ASE-driven MD and ABACUS-native MD templates. |
+| `abacus_helper` | `atst abacus prepare/collect` | INPUT/KPT/STRU preparation and conservative output collection. |
+
+General workflow:
+
+```bash
+cd interfaces/ASE_interface/examples/atst_tools/relax_si
+python make_inputs.py
+atst config validate config.yaml --print-normalized
+atst run --dry-run config.yaml
+atst run config.yaml
+```
+
+For SAI GPU runs, keep the same YAML structure but change
+`calculator.abacus.parameters.ks_solver` from `genelpa` to `cusolver` if the
+loaded ABACUS build requires the GPU solver.
+
+The helper case does not launch ABACUS:
+
+```bash
+cd interfaces/ASE_interface/examples/atst_tools/abacus_helper
+python make_inputs.py
+atst abacus prepare config.yaml --structure inputs/init.extxyz --output-dir prepared_abacus --force
+atst abacus collect prepared_abacus --output abacus_results.json
+```
+
+`collect` is normally useful after ABACUS has populated a run directory; using it
+on `prepared_abacus` only exercises the conservative file-summary path.

interfaces/ASE_interface/examples/atst_tools/abacus_helper/config.yaml

@@ -0,0 +1,34 @@
+calculation:
+  type: relax
+  init_structure: inputs/init.extxyz
+  fmax: 0.10
+  max_steps: 1
+  optimizer: BFGS
+  trajectory: helper_relax.traj
+  logfile: helper_relax.log
+
+calculator:
+  name: abacus
+  abacus:
+    command: abacus
+    mpi: 1
+    omp: 1
+    directory: helper_abacus_run
+    kpts: [1, 1, 1]
+    parameters:
+      calculation: scf
+      basis_type: lcao
+      ks_solver: genelpa
+      ecutwfc: 100
+      dft_functional: pbe
+      symmetry: 0
+      scf_thr: 1e-6
+      scf_nmax: 100
+      cal_force: 1
+      cal_stress: 0
+      pseudo_dir: ../../../../../tests/PP_ORB
+      orbital_dir: ../../../../../tests/PP_ORB
+      pseudopotentials:
+        Si: Si_ONCV_PBE-1.0.upf
+      basissets:
+        Si: Si_gga_8au_100Ry_2s2p1d.orb

interfaces/ASE_interface/examples/atst_tools/abacus_helper/make_inputs.py

@@ -0,0 +1,19 @@
+from pathlib import Path
+
+from ase.build import bulk
+from ase.io import write
+
+
+HERE = Path(__file__).resolve().parent
+INPUTS = HERE / "inputs"
+
+
+def main():
+    INPUTS.mkdir(exist_ok=True)
+    atoms = bulk("Si", "diamond", a=5.43)
+    write(INPUTS / "init.extxyz", atoms)
+    print(f"Wrote {INPUTS / 'init.extxyz'}")
+
+
+if __name__ == "__main__":
+    main()

interfaces/ASE_interface/examples/atst_tools/ccqn_h2/config.yaml

@@ -0,0 +1,45 @@
+calculation:
+  type: ccqn
+  init_structure: inputs/ts_guess.extxyz
+  fmax: 0.05
+  max_steps: 5
+  trajectory: ccqn_h2.traj
+  logfile: ccqn_h2.log
+  final_structure: ccqn_h2_final.extxyz
+  artifact_manifest: atst_artifacts_ccqn_h2.json
+  e_vector_method: ic
+  reactive_bonds: "1-2"
+  ic_mode: democratic
+  cos_phi: 0.5
+  trust_radius_uphill: 0.05
+  trust_radius_saddle_initial: 0.03
+  accept_initial_converged: false
+  mode_manifest: ccqn_h2_mode_manifest.json
+  diagnostics_file: ccqn_h2_diagnostics.json
+  directory: run_ccqn_h2
+
+calculator:
+  name: abacus
+  abacus:
+    command: abacus
+    mpi: 1
+    omp: 1
+    directory: run_ccqn_h2
+    kpts: [1, 1, 1]
+    parameters:
+      calculation: scf
+      basis_type: lcao
+      ks_solver: genelpa
+      ecutwfc: 100
+      dft_functional: pbe
+      symmetry: 0
+      scf_thr: 1e-6
+      scf_nmax: 100
+      cal_force: 1
+      cal_stress: 0
+      pseudo_dir: ../../../../../tests/PP_ORB
+      orbital_dir: ../../../../../tests/PP_ORB
+      pseudopotentials:
+        H: H_ONCV_PBE-1.0.upf
+      basissets:
+        H: H_gga_8au_100Ry_2s1p.orb

interfaces/ASE_interface/examples/atst_tools/ccqn_h2/make_inputs.py

@@ -0,0 +1,24 @@
+from pathlib import Path
+
+from ase import Atoms
+from ase.io import write
+
+
+HERE = Path(__file__).resolve().parent
+INPUTS = HERE / "inputs"
+
+
+def main():
+    INPUTS.mkdir(exist_ok=True)
+    atoms = Atoms(
+        "H2",
+        positions=[(4.0, 4.0, 3.50), (4.0, 4.0, 4.50)],
+        cell=[8.0, 8.0, 8.0],
+        pbc=True,
+    )
+    write(INPUTS / "ts_guess.extxyz", atoms)
+    print(f"Wrote {INPUTS / 'ts_guess.extxyz'}")
+
+
+if __name__ == "__main__":
+    main()

interfaces/ASE_interface/examples/atst_tools/md_si/config_abacus_native.yaml

@@ -0,0 +1,54 @@
+calculation:
+  type: md
+  driver: abacus_native
+  init_structure: inputs/init.traj
+  steps: 5
+  directory: run_md_si_abacus_native
+  trajectory: md_si_abacus_native.traj
+  summary_file: md_si_abacus_native_summary.json
+  final_structure: md_si_abacus_native_final.traj
+  artifact_manifest: atst_artifacts_md_si_abacus_native.json
+  poll_interval_seconds: 5.0
+  postprocess:
+    summary:
+      enabled: true
+      output: md_si_abacus_native_post_summary.json
+    convert:
+      enabled: false
+      format: extxyz
+      output_prefix: md_si_abacus_native_post
+
+calculator:
+  name: abacus
+  abacus:
+    command: abacus
+    mpi: 1
+    omp: 1
+    directory: run_md_si_abacus_native
+    kpts: [1, 1, 1]
+    parameters:
+      calculation: md
+      basis_type: lcao
+      ks_solver: genelpa
+      ecutwfc: 100
+      dft_functional: pbe
+      symmetry: 0
+      scf_thr: 1e-6
+      scf_nmax: 100
+      smearing_method: gaussian
+      smearing_sigma: 0.001
+      mixing_type: broyden
+      cal_force: 1
+      cal_stress: 1
+      init_wfc: atomic
+      init_chg: atomic
+      md_type: nvt
+      md_nstep: 5
+      md_dt: 0.5
+      md_tfirst: 300
+      pseudo_dir: ../../../../../tests/PP_ORB
+      orbital_dir: ../../../../../tests/PP_ORB
+      pseudopotentials:
+        Si: Si_ONCV_PBE-1.0.upf
+      basissets:
+        Si: Si_gga_8au_100Ry_2s2p1d.orb

interfaces/ASE_interface/examples/atst_tools/md_si/config_ase_abacus.yaml

@@ -0,0 +1,53 @@
+calculation:
+  type: md
+  driver: ase
+  init_structure: inputs/init.traj
+  ensemble: nvt
+  algorithm: langevin
+  steps: 5
+  timestep_fs: 0.5
+  temperature_K: 300.0
+  friction_fs_inv: 0.01
+  seed: 7
+  trajectory: md_si_ase_abacus.traj
+  logfile: md_si_ase_abacus.log
+  summary_file: md_si_ase_abacus_summary.json
+  final_structure: md_si_ase_abacus_final.traj
+  artifact_manifest: atst_artifacts_md_si_ase_abacus.json
+  postprocess:
+    summary:
+      enabled: true
+      output: md_si_ase_abacus_post_summary.json
+    convert:
+      enabled: false
+      format: extxyz
+      output_prefix: md_si_ase_abacus_post
+
+calculator:
+  name: abacus
+  abacus:
+    command: abacus
+    mpi: 1
+    omp: 1
+    directory: run_md_si_ase_abacus
+    kpts: [1, 1, 1]
+    parameters:
+      calculation: scf
+      basis_type: lcao
+      ks_solver: genelpa
+      ecutwfc: 100
+      dft_functional: pbe
+      symmetry: 0
+      scf_thr: 1e-6
+      scf_nmax: 100
+      smearing_method: gaussian
+      smearing_sigma: 0.001
+      mixing_type: broyden
+      cal_force: 1
+      cal_stress: 1
+      pseudo_dir: ../../../../../tests/PP_ORB
+      orbital_dir: ../../../../../tests/PP_ORB
+      pseudopotentials:
+        Si: Si_ONCV_PBE-1.0.upf
+      basissets:
+        Si: Si_gga_8au_100Ry_2s2p1d.orb

interfaces/ASE_interface/examples/atst_tools/md_si/make_inputs.py

@@ -0,0 +1,19 @@
+from pathlib import Path
+
+from ase.build import bulk
+from ase.io import write
+
+
+HERE = Path(__file__).resolve().parent
+INPUTS = HERE / "inputs"
+
+
+def main():
+    INPUTS.mkdir(exist_ok=True)
+    atoms = bulk("Si", "diamond", a=5.43, cubic=True)
+    write(INPUTS / "init.traj", atoms)
+    print(f"Wrote {INPUTS / 'init.traj'}")
+
+
+if __name__ == "__main__":
+    main()

interfaces/ASE_interface/examples/atst_tools/neb_si/config.yaml

@@ -0,0 +1,42 @@
+calculation:
+  type: neb
+  init_chain: inputs/init_neb_chain.traj
+  climb: true
+  two_stage: true
+  stage1_steps: 2
+  stage1_fmax: 0.20
+  fmax: 0.10
+  k: 0.1
+  algorism: improvedtangent
+  parallel: false
+  optimizer: FIRE
+  max_steps: 5
+  trajectory: neb_si.traj
+  artifact_manifest: atst_artifacts_neb_si.json
+  endpoint_singlepoint: auto
+
+calculator:
+  name: abacus
+  abacus:
+    command: abacus
+    mpi: 1
+    omp: 1
+    directory: run_neb_si
+    kpts: [1, 1, 1]
+    parameters:
+      calculation: scf
+      basis_type: lcao
+      ks_solver: genelpa
+      ecutwfc: 100
+      dft_functional: pbe
+      symmetry: 0
+      scf_thr: 1e-6
+      scf_nmax: 100
+      cal_force: 1
+      cal_stress: 0
+      pseudo_dir: ../../../../../tests/PP_ORB
+      orbital_dir: ../../../../../tests/PP_ORB
+      pseudopotentials:
+        Si: Si_ONCV_PBE-1.0.upf
+      basissets:
+        Si: Si_gga_8au_100Ry_2s2p1d.orb

interfaces/ASE_interface/examples/atst_tools/neb_si/make_inputs.py

@@ -0,0 +1,31 @@
+from pathlib import Path
+
+from ase.build import bulk
+from ase.io import write
+from ase.mep import NEB
+
+
+HERE = Path(__file__).resolve().parent
+INPUTS = HERE / "inputs"
+
+
+def main():
+    INPUTS.mkdir(exist_ok=True)
+    initial = bulk("Si", "diamond", a=5.43)
+    final = initial.copy()
+    final.positions[1, 0] += 0.35
+
+    images = [initial.copy()]
+    images.extend(initial.copy() for _ in range(3))
+    images.append(final.copy())
+    neb = NEB(images, method="improvedtangent")
+    neb.interpolate(method="linear")
+
+    write(INPUTS / "init.extxyz", initial)
+    write(INPUTS / "final.extxyz", final)
+    write(INPUTS / "init_neb_chain.traj", images)
+    print(f"Wrote {INPUTS / 'init_neb_chain.traj'}")
+
+
+if __name__ == "__main__":
+    main()