Addign editor to fix atomic positions in x,y,z and to add constraints

src/aiidalab_qe/app/result/components/summary/model.py

@@ -193,20 +193,41 @@ def _generate_report_parameters(self):
             "cell_lengths": "{:.3f} {:.3f} {:.3f}".format(*structure.cell_lengths),
             "cell_angles": "{:.0f} {:.0f} {:.0f}".format(*structure.cell_angles),
         }
+
 
         relax_value_mapping = {
             "none": "off",
             "positions": "atomic positions",
             "positions_cell": "full geometry",
         }
-
+
+        # check for fixed atoms
+        constraints = ''
+        fixed_atoms = structure.base.attributes.all.get('fixed_atoms', None)
+        other_constraints = structure.base.attributes.all.get('CONSTRAINTS', None)
+
+        if fixed_atoms is not None:
+            has_fixed = any(
+                any((int(v) == 0) for v in row if v is not None)
+                for row in fixed_atoms
+            )
+            # True if any element equals 0 (works for (N,3), (N,), or nested lists)
+            if has_fixed:
+                constraints += "There are fixed atoms."
+
+        if other_constraints is not None:
+            constraints += '; '.join(other_constraints['list'])
+        if not constraints:
+            constraints = "None"
+
         report |= {
             "basic_settings": {
                 "relaxed": relax_value_mapping.get(basic["relax_type"], "off"),
                 "protocol": basic["protocol"],
                 "spin_type": "off" if basic["spin_type"] == "none" else "on",
                 "electronic_type": basic["electronic_type"],
                 "periodicity": PERIODICITY_MAPPING.get(structure.pbc, "xyz"),
+                "constraints": constraints
             },
             "advanced_settings": {},
         }

src/aiidalab_qe/app/result/components/summary/schema.json

@@ -94,6 +94,11 @@
     "type": "text",
     "description": "The periodicity of the structure"
   },
+  "constraints": {
+    "title": "Constraints",
+    "type": "text",
+    "description": "The constraints applied to the structure"
+  },
   "functional": {
     "title": "Functional",
     "type": "link",

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

@@ -1,5 +1,8 @@
 from __future__ import annotations
+from pydoc import html
 
+from aiida_quantumespresso.tools import data
+from matplotlib import legend
 import traitlets as tl
 from ase.formula import Formula
 
@@ -74,30 +77,154 @@ def _get_structure_info(self):
             </div>
         """
 
+    # def _get_atom_table_data(self):
+    #     """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 = self.structure.base.attributes.all.get('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_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 AiiDA StructureData attributes (or ASE arrays),
+        add a 'Free x,y,z' column showing '✓' for free (1) and 'x' for fixed (0).
+        - If constraints exist (CONSTRAINTS block), add a 'Constr.' column with
+        star labels (*1, *2, …) for atoms involved in each constraint.
+        """
+        # --- source data ---
+        attrs_all = getattr(getattr(getattr(self.structure, "base", None), "attributes", None), "all", {}) or {}
+        fixed_atoms = attrs_all.get("fixed_atoms", None)
+
+        ase_atoms = self.structure.get_ase()
+
+        # Try also to read fixed mask from ASE arrays if attributes missing
+        if fixed_atoms is None and "fixed_atoms" in getattr(ase_atoms, "arrays", {}):
+            fixed_atoms = ase_atoms.arrays["fixed_atoms"].tolist()
+
+        # constraints: prefer attributes, else ASE info
+        constraints_info = attrs_all.get("CONSTRAINTS")
+        if constraints_info is None:
+            constraints_info = ase_atoms.info.get("CONSTRAINTS", None) if hasattr(ase_atoms, "info") else None
+        # normalize constraints_info
+        if not isinstance(constraints_info, dict):
+            constraints_info = {"number": 0, "tolerance": "1e-6", "list": []}
+        constraints_list = constraints_info.get("list", []) or []
+
+        # Build star marks per atom and a legend (legend not returned here)
+        def build_marks(n_atoms, entries):
+            marks = {i: [] for i in range(n_atoms)}
+            legend = []
+            for k, entry in enumerate(entries, start=1):
+                legend.append(f"*{k} {entry}")
+                parts = str(entry).strip().split()
+                if len(parts) >= 4 and parts[0] == "distance":
+                    try:
+                        i1 = int(parts[1]) - 1
+                        i2 = int(parts[2]) - 1
+                    except Exception:
+                        continue
+                    label = f"*{k}"
+                    if 0 <= i1 < n_atoms:
+                        marks[i1].append(label)
+                    if 0 <= i2 < n_atoms:
+                        marks[i2].append(label)
+            return marks, legend
+
+        marks_map, legend = build_marks(len(ase_atoms), constraints_list)
+
+        # --- 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")
+        # add constraints column if any constraints exist
+        if constraints_list:
+            data[0].append("Constr.")
+
+        positions = ase_atoms.positions
+        chemical_symbols = ase_atoms.get_chemical_symbols()
+        tags = ase_atoms.get_tags()
+
+        def fmt_free(mask):
+            """mask: 3-tuple/list of 0/1; 1=free → '✓', 0=fixed → 'x'."""
+            try:
+                x, y, z = mask
+            except Exception:
+                x = y = z = 1  # default free if malformed
+            return f"({'✓' if int(x)==1 else 'x'} {'✓' if int(y)==1 else 'x'} {'✓' if int(z)==1 else 'x'})"
+
+        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:
+                # robustly fetch mask; default to all free if missing
+                mask = (1, 1, 1)
+                try:
+                    if 0 <= (idx - 1) < len(fixed_atoms):
+                        mask = fixed_atoms[idx - 1]
+                except Exception:
+                    pass
+                row.append(fmt_free(mask))
+
+            if constraints_list:
+                stars = " ".join(marks_map.get(idx - 1, []))
+                row.append(stars)
+
+            data.append(row)
+        # temporary quick fix to show teh legend of constraints
+        if legend:
+            ncols = len(data[0])
+            legend_text = "; ".join(legend)
+
+            injected = (
+                # close the last normal row
+                f'</td></tr>'
+                # add a non-interactive full-width legend row
+                f'<tr class="constraints-legend-row" '
+                f'style="pointer-events:none; user-select:none;">'
+                f'<td colspan="{ncols}" style="text-align:right;">{html.escape(legend_text)}</td>'
+                f'</tr>'
+                # open a dummy row/cell so the renderer’s trailing </td></tr> stays balanced
+                f'<tr><td>'
+            )
+            data.append([injected])
+
+
 
         return data
 
+
     def get_model_state(self):
         return {
             "selected_view": self.selected_view,

src/aiidalab_qe/app/structure/__init__.py

@@ -10,6 +10,7 @@
 from aiidalab_qe.app.structure.model import StructureStepModel
 from aiidalab_qe.app.utils import get_entry_items
 from aiidalab_qe.common import (
+    AddingConstraintsEditor,
     AddingTagsEditor,
     LazyLoadedOptimade,
     LazyLoadedStructureBrowser,
@@ -105,6 +106,7 @@ def _render(self):
             BasicCellEditor(title="Edit cell"),
             BasicStructureEditor(title="Edit structure"),
             AddingTagsEditor(title="Edit atom tags"),
+            AddingConstraintsEditor(title="Edit constraints"),
             PeriodicityEditor(title="Edit periodicity"),
             ShakeNBreakEditor(title="ShakeNBreak"),
         ]

src/aiidalab_qe/common/__init__.py

@@ -2,6 +2,7 @@
 from .node_view import CalcJobNodeViewerWidget  # noqa: F401
 from .process import QeAppWorkChainSelector, WorkChainSelector
 from .widgets import (
+    AddingConstraintsEditor,
     AddingTagsEditor,
     LazyLoadedOptimade,
     LazyLoadedStructureBrowser,
@@ -10,6 +11,7 @@
 )
 
 __all__ = [
+    "AddingConstraintsEditor",
     "AddingTagsEditor",
     "LazyLoadedOptimade",
     "LazyLoadedStructureBrowser",