Added posisbility to fix atoms in x,y,z. Updated tables accordingly

Author: cpignedoli

src/aiidalab_qe/app/result/components/viewer/structure/model.py

@@ -75,29 +75,48 @@ def _get_structure_info(self):
         """
 
     def _get_atom_table_data(self):
-        structure = self.structure.get_ase()
-        data = [
-            [
-                "Atom index",
-                "Chemical symbol",
-                "Tag",
-                "x (Å)",
-                "y (Å)",
-                "z (Å)",
-            ]
-        ]
-        positions = structure.positions
-        chemical_symbols = structure.get_chemical_symbols()
-        tags = structure.get_tags()
-
-        for index, (symbol, tag, position) in enumerate(
-            zip(chemical_symbols, tags, positions), start=1
-        ):
-            formatted_position = [f"{coord:.2f}" for coord in position]
-            data.append([index, symbol, tag, *formatted_position])
+        """Build table data; if 'fixed_atoms' is present in structure attributes,
+        add a 'Free x,y,z' column showing '✓' for free (1) and 'x' for fixed (0)."""
+        # Try to get fixed_atoms from AiiDA StructureData attributes
+        fixed_atoms = None
+        try:
+            fixed_atoms = self.structure.base.attributes.all['fixed_atoms']
+        except KeyError:
+            fixed_atoms = None
+
+        ase_atoms = self.structure.get_ase()
+
+        # Header
+        data = [["Atom index", "Chemical symbol", "Tag", "x (Å)", "y (Å)", "z (Å)"]]
+        if fixed_atoms is not None:
+            data[0].append("Free x,y,z")
+
+        positions = ase_atoms.positions
+        chemical_symbols = ase_atoms.get_chemical_symbols()
+        tags = ase_atoms.get_tags()
+
+        def fmt_free(mask):
+            """mask: tuple/list of three 0/1; 0=free -> 'X', 1=fixed -> ' '."""
+            try:
+                x, y, z = mask
+            except Exception:
+                x = y = z = 0
+            # If your UI collapses spaces, replace ' ' with '·' or '\u00A0' (NBSP).
+            return f"({'x' if x == 0 else '✓'} {'x' if y == 0 else '✓'} {'x' if z == 0 else '✓'})"
+
+        for idx, (symbol, tag, pos) in enumerate(zip(chemical_symbols, tags, positions), start=1):
+            formatted_position = [f"{coord:.2f}" for coord in pos]
+            row = [idx, symbol, tag, *formatted_position]
+
+            if fixed_atoms is not None:
+                mask = fixed_atoms[idx - 1] if idx - 1 < len(fixed_atoms) else (0, 0, 0)
+                row.append(fmt_free(mask))
+
+            data.append(row)
 
         return data
 
+
     def get_model_state(self):
         return {
             "selected_view": self.selected_view,

src/aiidalab_qe/workflows/__init__.py

@@ -206,7 +206,10 @@ def get_builder_from_protocol(
             relax_builder.pop("structure", None)
             relax_builder.pop("clean_workdir", None)
             relax_builder.pop("base_final_scf", None)  # never run a final scf
-            builder.relax = relax_builder
+            if 'fixed_atoms' in structure.base.attributes.all:
+                
+                relax_builder.base.pw.settings = orm.Dict({'FIXED_COORDS':[[v == 0 for v in row] for row in structure.base.attributes.all['fixed_atoms']]})
+            builder.relax = relax_builder            
         else:
             builder.pop("relax")