Merge pull request #122 from Zikkying/devel-1.3.0

Add APEX Skill and Update Gamma Surface with New Features

Author: kevinwenminion

.gitignore

@@ -35,6 +35,20 @@ elastic_*
 template
 potential
 all_result.json
+usage
+confs
+
+# Keep packaged skill reference docs (overrides the bare `reference` rule above)
+!apex/skills/
+!apex/skills/**/
+!apex/skills/**/reference/
+!apex/skills/**/reference/**
 
 # dflow debug folders generated by examples or local runs
-**/dflow_debug/
+**/dflow_debug/
+# Generated MatMaster skill archive
+apex-flow.zip
+
+# Large DeePMD checkpoints (fetch with scripts/fetch_models.py; keep frozen *.pb in git)
+apex/skills/apex-flow/models/**/*.pt
+apex/skills/apex-flow/models/**/*.partial

README.md

@@ -237,7 +237,7 @@ Create `global_bohrium.json` to submit workflows to the Bohrium cloud platform:
 
 ```json
 {
-  "lammps_image_name": "registry.dp.tech/dptech/prod-11045/deepmdkit-phonolammps:2.1.1",
+  "lammps_image_name": "registry.dp.tech/dptech/dp/native/prod-397637/deepmd-kit-phonolammps:3.1.3",
   "lammps_run_command":"lmp -in in.lammps",
   "scass_type":"c8_m31_1 * NVIDIA T4"
 }
@@ -455,7 +455,7 @@ When you run `apex submit -c global_bohrium.json`, APEX auto-fills these default
 - `k8s_api_server`: `https://workflows.deepmodeling.com`
 - `batch_type`: `Bohrium`
 - `context_type`: `Bohrium`
-- `apex_image_name`: `registry.dp.tech/dptech/dp/native/prod-397637/apex:1.3.0`
+- `apex_image_name`: `registry.dp.tech/dptech/dp/native/prod-397637/apex-flow:1.3.0.post`
 
 Priority rule: values in your `-c` json file override account defaults.
 
@@ -638,12 +638,31 @@ Property selection behavior:
 
 ### 4.5 Decohesive energy line
 
+Decohesive builds a rigid-separation series on one user-specified Miller plane via pymatgen `SlabGenerator`. It does **not** auto-enumerate planes (unlike `surface`) and has **no** crystal-type nested overrides (unlike `gamma`). Any structure that can form that slab is supported; set `miller_index` explicitly.
+
+Recommended default planes by crystal family (JSON `miller_index` uses **3-index** Miller notation):
+
+| Crystal structure | Recommended planes | JSON `miller_index` examples |
+|-------------------|--------------------|------------------------------|
+| **FCC** | $(100)$, $(110)$, $(111)$ | `[1,0,0]`, `[1,1,0]`, `[1,1,1]` |
+| **BCC** | $(100)$, $(110)$, $(111)$ | `[1,0,0]`, `[1,1,0]`, `[1,1,1]` |
+| **Diamond** | $(100)$, $(110)$, $(111)$ | `[1,0,0]`, `[1,1,0]`, `[1,1,1]` |
+| **Zinc blende** | $(100)$, $(110)$, $(111)$ | `[1,0,0]`, `[1,1,0]`, `[1,1,1]` |
+| **Rocksalt** | $(100)$, $(110)$, $(111)$ | `[1,0,0]`, `[1,1,0]`, `[1,1,1]` |
+| **HCP** | $(0001)$, $(10\bar{1}0)$, $(11\bar{2}0)$ | `[0,0,1]`, `[1,0,0]`, `[1,1,0]` |
+| **Perovskite** | $(001)$, $(110)$, $(111)$ | `[0,0,1]`, `[1,1,0]`, `[1,1,1]` |
+
+Notes:
+
+- HCP must use the **3-index** values above. Four-index Miller–Bravais vectors (e.g. `[0,0,0,1]`) are **not** accepted by `decohesive` (no Bravais conversion).
+- Polar / multi-termination faces (common for zinc blende $(111)$ and some perovskite cuts) still generate; APEX takes the first matching slab termination from pymatgen.
+
 | Key | Type | Example | Description |
 |-----|------|---------|-------------|
 | `min_slab_size` | Integer | `10` | Minimum slab thickness. |
 | `max_vacuum_size` | Integer | `11` | Maximum vacuum width. |
 | `pert_xz` | Float | `0.01` | Perturbation along xz plane for surface energy. |
-| `miller_miller` | List[Int] | `[1, 1, 0]` | Miller indices of the target plane. |
+| `miller_index` | List[Int] | `[1, 1, 0]` | Miller indices of the target plane (**required**, 3-index). |
 
 ### 4.6 Elastic
 
@@ -733,6 +752,7 @@ Key parameters:
 | `vacuum_size` | Float | `0` | Added vacuum layer thickness (Å). |
 | `supercell_size` | Sequence[Int] | `[1, 1, 5]` | Slab supercell size. |
 | `add_fix` | Sequence[String] | `["true","true","false"]` | Position constraints along x/y/z. |
+| `closed_loop` | Bool | `false` |  when `true`, derive two periodic in-plane translation vectors from the generated slab. and slip_length or slip_length_y will be **ignored** |
 
 Example:
 
@@ -778,6 +798,7 @@ adds vacuum along the selected fault normal for slab/free-surface calculations.
             "slip_direction": [1, -1, -1],
             "supercell_size": [1, 1, 20],
             "vacuum_size": 15,
+            "closed_loop": false,
             "add_fix": ["true", "true", "false"],
             "n_steps_x": 20,
             "n_steps_y": 20
@@ -788,15 +809,15 @@ adds vacuum along the selected fault normal for slab/free-surface calculations.
 
 APEX integrates parts of [dflow-phonon](https://github.com/Chengqian-Zhang/dflow-phonon) and wraps [Phonopy](https://github.com/phonopy/phonopy) / [phonoLAMMPS](https://github.com/abelcarreras/phonolammps). [SeeK-path](https://seekpath.readthedocs.io/en/latest/index.html) automatically generates high-symmetry k-paths.
 
-> **Important:** Ensure the `run_image` (or local environment in debug mode) contains `phonoLAMMPS` when running LAMMPS-based phonon workflows.
+> **Important:** LAMMPS phonon and Grüneisen workflows always use `registry.dp.tech/dptech/dp/native/prod-397637/deepmd-kit-phonolammps:3.1.3`. During `apex submit`, APEX overrides any other configured LAMMPS image for these properties.
 
 | Key | Type | Default | Description |
 |-----|------|---------|-------------|
 | `primitive` | Bool | `false` | Reduce to primitive cell before phonon calculation. |
 | `approach` | String | `"linear"` | VASP phonon method: `"linear"` or `"displacement"`. |
 | `supercell_size` | Sequence[Int] | `[2, 2, 2]` | Supercell dimensions. |
 | `MESH` | Sequence[Int] | `None` | Reciprocal-space mesh (e.g., `[8, 8, 8]`). |
-| `PRIMITIVE_AXES` | String | `None` | Custom primitive axes definition (`"0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0"`). |
+| `PRIMITIVE_AXES` | String | `"P"` | Primitive axes used consistently by phonopy and phonoLAMMPS; accepts `"P"`, `"AUTO"`, or a 3×3 matrix. |
 | `BAND` | String | `None` | Band path definition (falls back to SeeK-path when omitted). |
 | `BAND_LABELS` | String | `None` | Labels for band segments. |
 | `BAND_POINTS` | Integer | `51` | Number of sampling points per segment. |
@@ -820,8 +841,8 @@ APEX supports Grüneisen workflows based on phonon calculations at multiple stra
 | `primitive` | Bool | `false` | Reduce to primitive cell before phonon calculation. |
 | `approach` | String | `"linear"` | Phonon workflow approach; VASP Grüneisen currently uses linear response. |
 | `supercell_size` | Sequence[Int] | `[2, 2, 2]` | Phonon supercell dimensions. |
-| `MESH` | Sequence[Int] | `None` | Reciprocal-space mesh for mode summation. |
-| `PRIMITIVE_AXES` | String | `None` | Custom primitive axes definition. |
+| `MESH` | Sequence[Int] | `[20, 20, 20]` | Three positive reciprocal-space mesh dimensions for mode summation. |
+| `PRIMITIVE_AXES` | String | `"P"` | Primitive axes used consistently for displacement generation and post-processing. |
 | `BAND` | String | `None` | Band path definition (falls back to SeeK-path when omitted). |
 | `BAND_LABELS` | String | `None` | Labels for band segments. |
 | `BAND_POINTS` | Integer | `51` | Number of sampling points per segment. |

apex/__init__.py

@@ -1,5 +1,5 @@
 import os
-__version__ = '1.3.0.post1'
+__version__ = '1.3.0.post5'
 LOCAL_PATH = os.getcwd()
 
 

apex/account.py

@@ -13,7 +13,7 @@
     "k8s_api_server": BOHRIUM_WORKFLOWS_HOST,
     "batch_type": "Bohrium",
     "context_type": "Bohrium",
-    "apex_image_name": "registry.dp.tech/dptech/dp/native/prod-397637/apex:1.3.0",
+    "apex_image_name": "registry.dp.tech/dptech/dp/native/prod-397637/apex-flow:1.3.0.post",
 }
 SENSITIVE_KEYS = {"password"}
 ACCOUNT_FILE_ENV = "APEX_ACCOUNT_FILE"

apex/config.py

@@ -60,7 +60,10 @@ class Config:
     pool_size: int = None
     upload_python_packages: list = field(default_factory=list)
     exclude_upload_files: list = field(default_factory=list)
-    lammps_image_name: str = None
+    lammps_image_name: str = (
+        "registry.dp.tech/dptech/dp/native/prod-397637/"
+        "deepmd-kit-phonolammps:3.1.3"
+    )
     lammps_run_command: str = None
     phonolammps_run_command: str = None
     vasp_image_name: str = None

apex/core/calculator/Lammps.py

@@ -123,8 +123,12 @@ def _apply_gamma_fix_to_lammps_input(contents, add_fix):
         elif line.split()[:4] == ["variable", "N", "equal", "count(all)"]:
             upper_id = idx
             break
-    if lower_id is None or upper_id is None:
-        return contents
+    if lower_id is None or upper_id is None or lower_id >= upper_id:
+        raise RuntimeError(
+            "Gamma add_fix was requested, but the generated LAMMPS input does "
+            "not contain a compatible minimization block with 'min_style cg' "
+            "and 'variable N equal count(all)' markers"
+        )
     del lines[lower_id + 1 : upper_id - 1]
     lines.insert(lower_id + 1, add_fix_str)
     return "".join(lines)
@@ -386,6 +390,18 @@ def make_input_file(self, output_dir, task_type, task_param):
                 else:
                     raise RuntimeError("not supported calculation setting for LAMMPS")
 
+            elif cal_type == "static":
+                fc = lammps_utils.make_lammps_eval(
+                    "conf.lmp", self.type_map, self.inter_func, self.model_param
+                )
+            elif cal_type == "finite_t_elastic":
+                fc = lammps_utils.make_lammps_FiniteTelastic(
+                    "conf.lmp",
+                    self.type_map,
+                    self.inter_func,
+                    self.model_param,
+                    output_dir,
+                )
             elif task_type in ["annealing", "Annealing"]:
                 # MD annealing schedule: equilibrate -> ramp -> hold -> cool
                 fc = lammps_utils.make_lammps_annealing(
@@ -396,34 +412,22 @@ def make_input_file(self, output_dir, task_type, task_param):
                     cal_setting,
                 )
 
-            elif cal_type == "static":
-                fc = lammps_utils.make_lammps_eval(
-                    "conf.lmp", self.type_map, self.inter_func, self.model_param
-                )
-            elif cal_type == "npt+ave/time":
+            elif task_type == "finite_t_latt":
                 fc = lammps_utils.make_lammps_FiniteTlatt(
                     "conf.lmp",
                     self.type_map,
                     self.inter_func,
                     self.model_param,
                     cal_setting,
                 )
-            elif cal_type == "finite_t_elastic":
-                fc = lammps_utils.make_lammps_FiniteTelastic(
-                    "conf.lmp",
-                    self.type_map,
-                    self.inter_func,
-                    self.model_param,
-                    output_dir,
-                )
 
             else:
                 raise RuntimeError("not supported calculation type for LAMMPS")
 
         if (
             prop_type in {"gamma", "gamma_surface"}
             and cal_type == "relaxation"
-            and "add_fix" in task_param
+            and task_param.get("add_fix") is not None
         ):
             fc = _apply_gamma_fix_to_lammps_input(fc, task_param["add_fix"])
 

apex/core/property/Decohesive.py

@@ -258,17 +258,50 @@ def __gen_slab_pmg(
         sorted_frac_coords, sorted_species = zip(*ordered)
 
         a_vec, b_vec, c_vec = slab.lattice.matrix
-        slab_height = abs(c_vec[2])
+        # ``reorient_lattice=False`` preserves the input orientation, so the
+        # slab-normal c vector is not necessarily aligned with Cartesian z.
+        # Using c_vec[2] therefore produces a zero divisor for valid surfaces
+        # such as bcc (100) and (110), yielding NaNs in the LAMMPS data file.
+        slab_height = np.linalg.norm(c_vec)
+        if slab_height <= np.finfo(float).eps:
+            raise RuntimeError("Generated slab has a zero-length c lattice vector")
         self.is_flip = c_vec[2] < 0
         elong_scale = 1 + (abs(vacuum_size) / slab_height)
 
-        new_lattice = [a_vec, b_vec, elong_scale * c_vec]
+        new_lattice = np.array([a_vec, b_vec, elong_scale * c_vec], dtype=float)
         new_frac_coords = []
         for frac in sorted_frac_coords:
-            coord = frac.copy()
+            coord = np.array(frac, dtype=float)
             coord[2] = coord[2] / elong_scale
             new_frac_coords.append(coord)
 
+        # LAMMPS requires a right-handed box: det([a, b, c]) > 0.
+        # Slab construction (odd axis permutations / mirroring) can produce a
+        # left-handed cell; swapping a↔b restores chirality without changing
+        # the physical slab.
+        new_lattice, new_frac_coords = _ensure_right_handed_cell(
+            new_lattice, new_frac_coords
+        )
+
         return Structure(
-            lattice=np.array(new_lattice), coords=new_frac_coords, species=sorted_species
+            lattice=new_lattice, coords=new_frac_coords, species=sorted_species
+        )
+
+
+def _ensure_right_handed_cell(lattice, frac_coords):
+    """Swap a↔b when det([a, b, c]) ≤ 0 so the cell is right-handed."""
+    lattice = np.array(lattice, dtype=float)
+    det = np.linalg.det(lattice)
+    if det > 0:
+        return lattice, [np.array(fc, dtype=float) for fc in frac_coords]
+    if abs(det) <= np.finfo(float).eps:
+        raise RuntimeError(
+            "Generated slab has a singular lattice (det ≈ 0); cannot convert to LAMMPS"
         )
+    lattice = lattice[[1, 0, 2]]
+    fixed_frac = []
+    for frac in frac_coords:
+        coord = np.array(frac, dtype=float)
+        coord[0], coord[1] = coord[1], coord[0]
+        fixed_frac.append(coord)
+    return lattice, fixed_frac