feature: get kpath from structure file

src/abacusagent/modules/symmetry.py

@@ -1,8 +1,26 @@
 from pathlib import Path
-from typing import Dict, Any
+from typing import Dict, Any, Literal
 
 from abacusagent.init_mcp import mcp
 
+@mcp.tool()
+def get_high_symm_points_from_stru(stru_file: Path,
+                                   stru_type: Literal['cif', 'poscar', 'abacus/stru'] = 'cif'
+) -> Dict[str, Any]:
+    """
+    Get high symmetry points and kpath from structure file.
+    Args:
+        stru_file (Path): Absolute path to the structure file.
+        stru_type (Literal): Type of the structure file, can be 'cif', 'poscar', or 'abacus/stru'.
+    Returns:
+        A Dictionary with keys:
+        - high_symm_points: A list of dictionary, where the key is the label of the point, and the value is the fractional coordinates of the point.
+        - kpath: A list of tuples, where each tuple is a pair of labels of the two points in the kpath.
+    """
+    from abacusagent.modules.util.symmetry import get_high_symm_points_from_stru as _get_high_symm_points_from_stru
+
+    return _get_high_symm_points_from_stru(stru_file, stru_type)
+
 @mcp.tool()
 def get_high_symm_points_from_abacus_inputs_dir(abacusjob_dir: Path) -> Dict[str, Any]:
     """

src/abacusagent/modules/util/symmetry.py

@@ -2,94 +2,28 @@
 
 from pathlib import Path
 from typing import Literal, Dict, Any
-from abacustest.lib_prepare.abacus import AbacusStru, ReadInput
+from abacustest import AbacusSTRU, ReadInput
 
 def get_high_symm_points_from_stru(stru_file: Path,
                                    stru_type: Literal['cif', 'poscar', 'abacus/stru'] = 'cif'
-) -> Any:
+) -> Dict[str, Any]:
     """
     Get high symmetry points and kpath from structure file.
     Args:
         stru_file (Path): Absolute path to the structure file.
         stru_type (Literal): Type of the structure file, can be 'cif', 'poscar', or 'abacus/stru'.
     Returns:
-        A tuple containing high symmetry points and kpath.
+        A Dictionary with keys:
+        - high_symm_points: A list of dictionary, where the key is the label of the point, and the value is the fractional coordinates of the point.
+        - kpath: A list of tuples, where each tuple is a pair of labels of the two points in the kpath.
     """
-    import seekpath
-    from ase.io import read
-
-    if stru_type in ['cif', 'poscar']:
-        stru = read(stru_file)
-        cell = stru.get_cell()
-        coord = stru.get_positions()
-        labels = stru.get_chemical_symbols()
-        label = []
-        for i in labels:
-            if i not in label:
-                label.append(i)
-        number = [label.index(i) for i in labels]
-        stru_final = (cell, coord, number)
-    elif stru_type == 'abacus/stru':
-        stru = AbacusStru.ReadStru(stru_file)
-        cell = stru.get_cell(bohr=True)
-        coord = stru.get_coord(bohr=True)
-        labels = stru.get_label()
-        number = stru.get_label()
-        label = []
-        for i in labels: 
-            if i not in label:
-                label.append(i)
-        number = [label.index(i) for i in labels]
-        stru_final = (cell,coord,number)
+    if stru_type in ['cif', 'poscar', 'abacus/stru']:
+        stru = AbacusSTRU.read(stru_file, stru_type)
     else:
         raise ValueError("stru_type should be 'cif', 'poscar', or 'abacus/stru'")
 
-    sym_prec = 1e-5
-    while sym_prec <= 1e-2:
-        try:
-            kpath = seekpath.get_path_orig_cell(stru_final,
-                                                with_time_reversal=True,
-                                                recipe='hpkot',
-                                                threshold=1e-5,
-                                                symprec=sym_prec,
-                                                angle_tolerance=-1.0)
-            break
-        except:
-            print("WARNING: get_path failed, increase symprec to %e" % (sym_prec*10))
-            sym_prec *= 10
-
-    if sym_prec > 1e-2:
-        print(f"Symmetry precision {sym_prec} is too large")
-
-    concatenated_kpath, path = [], None
-    for path_idx, path_line in enumerate(kpath['path']):
-        path_line_start, path_line_end = path_line[0], path_line[1]
-        if path is None:
-            path = [path_line_start, path_line_end]
-        else:
-            if path_idx == len(kpath['path']) - 1:
-                if path is None:
-                    path.append(path_line_start)
-                path.append(path_line_end)
-                concatenated_kpath.append(path)
-                path = None
-            elif path_idx < len(kpath['path']) - 1:
-                if path is None:
-                    path.append(path_line_start)
-                path.append(path_line_end)
-                next_line_start = kpath['path'][path_idx+1][0]
-                if path_line_end != next_line_start:
-                    concatenated_kpath.append(path)
-                    path = None
-            else:
-                if path is None:
-                    path = [path_line_start, path_line_end]
-                else:
-                    path.append(path_line_end)
-                concatenated_kpath.append(path)
-
-    kpath['path'] = concatenated_kpath
-    return kpath
+    high_symm_points, kpath = stru.get_kline()
+    return {"high_symm_points": high_symm_points, "kpath": kpath}
 
 def get_high_symm_points_from_abacus_inputs_dir(abacus_inputs_dir: Path) -> Dict[str, Any]:
     """