feat: Use correct reduction for GSAS and pass base parameters via a embedded comment the .cif file

Author: Linked-Liszt

configs/simulator.yaml

@@ -15,7 +15,11 @@ worker_base_dir: "/data/workers"
 parallel_jobs: 10
 sims_per_file: 2
 master_seed: 42           # Reproducible parameter sampling
-cleanup_worker_dirs: true # If false, worker directories will be kept
+cleanup_worker_dirs: true
+ 
+# If true, read SG from "# _original_symmetry_space_group_name_H-M" comment in CIF
+# If using custom CIFs without this comment, set to false to use standard tags
+parse_from_comment: true  
 
 # --- Simulation Parameter Ranges ---
 # The format is ALWAYS (smaller_number, larger_number)

docker/downloader.Dockerfile

@@ -10,6 +10,8 @@ WORKDIR /app
 COPY src/downloader/requirements.txt /tmp/requirements.txt
 RUN pip install --no-cache-dir -r /tmp/requirements.txt
 
+ENV MPLCONFIGDIR=/app/.cache/matplotlib
+
 # Code and configs are mounted at runtime via docker-compose volumes:
 #   - ./src/downloader -> /app
 #   - ./configs -> /configs

src/downloader/downloader.py

@@ -36,46 +36,28 @@ def _write_cif_from_struct(
     out_path: Path,
     sg_num: Optional[int] = None,
     sg_symbol: Optional[str] = None,
-    symprec: float = 0.01,
-    angle_tolerance: float = 5.0,
 ) -> None:
     """
-    Write structure to CIF using pymatgen's CifWriter, ensuring symmetry metadata (_symmetry_* tags)
-    are present and reflect the detected space group from SpacegroupAnalyzer.
+    Write structure to CIF using pymatgen's CifWriter without forcing symmetry detection (emit P1/minimal symmetry).
+    Then annotate the file with original space group/crystal system as comment lines so downstream tools ignore them.
     """
     try:
-        # Write CIF with symmetry detection enabled
-        CifWriter(structure, symprec=symprec, angle_tolerance=angle_tolerance).write_file(out_path)
+        # Write CIF without forcing symmetry detection (emit P1/minimal symmetry with fully expanded sites)
+        CifWriter(structure).write_file(out_path)
     except Exception as e:
         raise RuntimeError(f"Failed to write CIF to {out_path}: {e}")
 
-    # Post-process CIF to force writing of symmetry tags
-    try:
-        with open(out_path, "r", errors="ignore") as f:
-            lines = f.readlines()
-
-        def set_or_insert(tag: str, value: Any, quote: bool = False) -> None:
-            val_str = f"'{value}'" if quote else str(value)
-            for i, line in enumerate(lines):
-                if line.strip().startswith(tag):
-                    lines[i] = f"{tag}   {val_str}\n"
-                    break
-            else:
-                # Insert after the first line (typically the data_ line)
-                insert_idx = 1 if len(lines) >= 1 else 0
-                lines.insert(insert_idx, f"{tag}   {val_str}\n")
-
-        if sg_num is not None:
-            set_or_insert("_symmetry_Int_Tables_number", sg_num, quote=False)
-        if sg_symbol:
-            set_or_insert("_symmetry_space_group_name_H-M", sg_symbol, quote=True)
-
-        with open(out_path, "w") as f:
-            f.writelines(lines)
-    except Exception:
-        # Non-fatal if symmetry tag insertion fails; CIF already written
-        pass
+    # Post-process CIF to add original symmetry as comments (ignored by CIF parsers)
+    with open(out_path, "r", errors="ignore") as f:
+        lines = f.readlines()
+
+    comment = f"# _original_symmetry_space_group_name_H-M   '{str(sg_symbol)}'\n"
+
+    insert_idx = 1 if len(lines) >= 1 else 0
+    lines.insert(insert_idx, comment)
 
+    with open(out_path, "w") as f:
+        f.writelines(lines)
 
 def niggli_reduce(
     structure: Structure,
@@ -348,9 +330,7 @@ def download_cifs_entire_db(
                         std_struct,
                         out_path,
                         sg_num=sg_num,
-                        sg_symbol=sga_conv.get_space_group_symbol(),
-                        symprec=symprec,
-                        angle_tolerance=angle_tolerance,
+                        sg_symbol=sga_conv.get_space_group_symbol()
                     )
                     summary["downloaded"] += 1
 

src/simulator/diffraction_generator.py

@@ -85,6 +85,7 @@ def _generate_simulation_tasks(self, n_sims_per_file, master_seed, cleanup_worke
                     'constant_noise_range': param_ranges['constant_noise_range'],
                     'cleanup_worker_dir': cleanup_worker_dirs,
                     'output_filename': f"{stem}-{variation_index}.npy",
+                    'parse_from_comment': bool(kwargs.get('parse_from_comment', False)),
                 }
                 tasks_to_run.append(params)
                 job_id_counter += 1
@@ -164,6 +165,7 @@ def main() -> None:
     sims_per_file = int(cfg["sims_per_file"])
     master_seed = int(cfg["master_seed"])
     cleanup_worker_dirs = bool(cfg["cleanup_worker_dirs"])
+    parse_from_comment = bool(cfg.get("parse_from_comment", False))
 
     # Parameter ranges
     ranges = {
@@ -192,6 +194,7 @@ def main() -> None:
     print(f"Sims per file:              {sims_per_file}")
     print(f"Master seed:                {master_seed}")
     print(f"Cleanup worker dirs:        {cleanup_worker_dirs}")
+    print(f"Parse from comment:         {parse_from_comment}")
     print("Parameter ranges:")
     for k, v in ranges.items():
         print(f"  {k}: {v}")
@@ -211,6 +214,7 @@ def main() -> None:
             n_sims_per_file=sims_per_file,
             master_seed=master_seed,
             cleanup_worker_dirs=cleanup_worker_dirs,
+            parse_from_comment=parse_from_comment,
             **ranges,
         )
     except Exception as e:

src/simulator/simulation_worker.py

@@ -87,25 +87,40 @@ def get_sg_num_from_symbol(sg_symbol):
         try: return SpaceGroup.sg_encoding[sg_symbol]['int_number']
         except KeyError: return None
 
-def _parse_cif_file(file_path):
+def _parse_cif_file(file_path, parse_from_comment: bool = False):
     """Parses a CIF file to get the space group number."""
     sg_num = None
     with open(file_path, 'r', errors='ignore') as f:
-        for line in f:
-            if '_symmetry_Int_Tables_number' in line or '_space_group_IT_number' in line:
-                try:
-                    sg_num = int(line.split()[-1])
+        for raw_line in f:
+            line = raw_line.strip()
+
+            if parse_from_comment:
+                # Prefer provenance comment inserted by downloader, e.g.:
+                # # _original__symmetry_space_group_name_H-M   'I-43m'
+                if line.startswith("# _original_symmetry_space_group_name_H-M"):
+                    if '"' in line:
+                        sg_sym = line.split('"')[1].replace(' ', '')
+                    elif "'" in line:
+                        sg_sym = line.split("'")[1].replace(' ', '')
+                    sg_num = get_sg_num_from_symbol(sg_sym)
                     return sg_num, get_crystal_system(sg_num)
-                except (ValueError, IndexError): continue
+                
+            else:
+                # Standard CIF tags (non-comment)
+                if '_symmetry_Int_Tables_number' in line or '_space_group_IT_number' in line:
+                    try:
+                        sg_num = int(line.split()[-1])
+                        return sg_num, get_crystal_system(sg_num)
+                    except (ValueError, IndexError): continue
 
-            # H-M name tag with quoted values: handle original double quotes and the provided single-quote example
-            if '_symmetry_space_group_name_H-M' in line:
-                if '"' in line:
-                    sg_sym = line.split('"')[1].replace(' ', '')
-                elif "'" in line:
-                    sg_sym = line.split("'")[1].replace(' ', '')
-                sg_num = get_sg_num_from_symbol(sg_sym)
-                return sg_num, get_crystal_system(sg_num)
+                # H-M name tag with quoted values (ignore commented lines)
+                if '_symmetry_space_group_name_H-M' in line and not line.startswith("#"):
+                    if '"' in line:
+                        sg_sym = line.split('"')[1].replace(' ', '')
+                    elif "'" in line:
+                        sg_sym = line.split("'")[1].replace(' ', '')
+                    sg_num = get_sg_num_from_symbol(sg_sym)
+                    return sg_num, get_crystal_system(sg_num)
 
     return None, None
 
@@ -212,7 +227,7 @@ def run_single_simulation(params):
     try:
         if input_file.suffix.lower() == '.cif':
             file_type = 'cif'
-            sg_num, cs = _parse_cif_file(input_file)
+            sg_num, cs = _parse_cif_file(input_file, parse_from_comment=params['parse_from_comment'])
             if sg_num is None: raise ValueError("Could not parse space group number from CIF.")
         elif input_file.suffix.lower() in ['.dif', '.txt']:
             file_type = 'dif'