Bmad conversion bugfixes -- take 2 for #663

CHANGELOG.md

@@ -11,6 +11,8 @@
 
 ### 🐛 Bug fixes
 
+- Fix Bmad lattice conversion issues with overlay and group definitions, wildcard element references, scientific notation in expressions, unary signs, and mapping of `type` and `alias` fields to element `metadata` (see #663) (@roussel-ryan, @jank324)
+
 ### 🐆 Other
 
 - Update openPMD dependency to renamed package (see #684) (@jank324)

cheetah/converters/bmad.py

@@ -40,6 +40,11 @@ def convert_element(
         "dtype": dtype or torch.get_default_dtype(),
     }
     bmad_parsed = context[name]
+    metadata = (
+        {k: bmad_parsed[k] for k in ["alias", "type"] if k in bmad_parsed}
+        if isinstance(bmad_parsed, dict)
+        else {}
+    )
 
     shared_properties = ["element_type", "alias", "type"]
 
@@ -55,27 +60,35 @@ def convert_element(
     elif isinstance(bmad_parsed, dict) and "element_type" in bmad_parsed:
         if bmad_parsed["element_type"] == "marker":
             validate_understood_properties(shared_properties, bmad_parsed)
-            return cheetah.Marker(name=name, sanitize_name=sanitize_name)
+            return cheetah.Marker(
+                name=name, sanitize_name=sanitize_name, metadata=metadata
+            )
         elif bmad_parsed["element_type"] == "monitor":
             validate_understood_properties(shared_properties + ["l"], bmad_parsed)
             if "l" in bmad_parsed:
                 return cheetah.Drift(
                     length=torch.tensor(bmad_parsed["l"], **factory_kwargs),
                     name=name,
                     sanitize_name=sanitize_name,
+                    metadata=metadata,
                 )
             else:
-                return cheetah.Marker(name=name, sanitize_name=sanitize_name)
+                return cheetah.Marker(
+                    name=name, sanitize_name=sanitize_name, metadata=metadata
+                )
         elif bmad_parsed["element_type"] == "instrument":
             validate_understood_properties(shared_properties + ["l"], bmad_parsed)
             if "l" in bmad_parsed:
                 return cheetah.Drift(
                     length=torch.tensor(bmad_parsed["l"], **factory_kwargs),
                     name=name,
                     sanitize_name=sanitize_name,
+                    metadata=metadata,
                 )
             else:
-                return cheetah.Marker(name=name, sanitize_name=sanitize_name)
+                return cheetah.Marker(
+                    name=name, sanitize_name=sanitize_name, metadata=metadata
+                )
         elif bmad_parsed["element_type"] == "pipe":
             validate_understood_properties(
                 shared_properties + ["l", "descrip"], bmad_parsed
@@ -84,6 +97,7 @@ def convert_element(
                 length=torch.tensor(bmad_parsed["l"], **factory_kwargs),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "drift":
             validate_understood_properties(
@@ -93,6 +107,7 @@ def convert_element(
                 length=torch.tensor(bmad_parsed["l"], **factory_kwargs),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "hkicker":
             validate_understood_properties(shared_properties + ["kick"], bmad_parsed)
@@ -101,6 +116,7 @@ def convert_element(
                 angle=torch.tensor(bmad_parsed.get("kick", 0.0), **factory_kwargs),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "vkicker":
             validate_understood_properties(shared_properties + ["kick"], bmad_parsed)
@@ -109,6 +125,7 @@ def convert_element(
                 angle=torch.tensor(bmad_parsed.get("kick", 0.0), **factory_kwargs),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "sbend":
             validate_understood_properties(
@@ -120,7 +137,7 @@ def convert_element(
                 length=torch.tensor(bmad_parsed["l"], **factory_kwargs),
                 gap=torch.tensor(2 * bmad_parsed.get("hgap", 0.0), **factory_kwargs),
                 angle=torch.tensor(bmad_parsed.get("angle", 0.0), **factory_kwargs),
-                dipole_e1=torch.tensor(bmad_parsed["e1"], **factory_kwargs),
+                dipole_e1=torch.tensor(bmad_parsed.get("e1", 0.0), **factory_kwargs),
                 dipole_e2=torch.tensor(bmad_parsed.get("e2", 0.0), **factory_kwargs),
                 tilt=torch.tensor(bmad_parsed.get("ref_tilt", 0.0), **factory_kwargs),
                 fringe_integral=torch.tensor(
@@ -133,6 +150,7 @@ def convert_element(
                 ),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "quadrupole":
             validate_understood_properties(
@@ -144,6 +162,7 @@ def convert_element(
                 tilt=torch.tensor(bmad_parsed.get("tilt", 0.0), **factory_kwargs),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "sextupole":
             validate_understood_properties(
@@ -155,6 +174,7 @@ def convert_element(
                 tilt=torch.tensor(bmad_parsed.get("tilt", 0.0), **factory_kwargs),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "solenoid":
             validate_understood_properties(shared_properties + ["l", "ks"], bmad_parsed)
@@ -163,6 +183,7 @@ def convert_element(
                 k=torch.tensor(bmad_parsed["ks"], **factory_kwargs),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "lcavity":
             validate_understood_properties(
@@ -181,6 +202,21 @@ def convert_element(
                 cavity_type=bmad_parsed["cavity_type"],
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
+            )
+        elif bmad_parsed["element_type"] == "crab_cavity":
+            validate_understood_properties(
+                shared_properties + ["l", "rf_frequency", "voltage", "phi0"],
+                bmad_parsed,
+            )
+            return cheetah.TransverseDeflectingCavity(
+                length=torch.tensor(bmad_parsed["l"], **factory_kwargs),
+                voltage=torch.tensor(bmad_parsed.get("voltage", 0.0), **factory_kwargs),
+                phase=-(torch.tensor(bmad_parsed.get("phi0", 0.0), **factory_kwargs)),
+                frequency=torch.tensor(bmad_parsed["rf_frequency"], **factory_kwargs),
+                name=name,
+                sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "rcollimator":
             validate_understood_properties(
@@ -210,6 +246,7 @@ def convert_element(
                 ],
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "ecollimator":
             validate_understood_properties(
@@ -239,6 +276,7 @@ def convert_element(
                 ],
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "wiggler":
             validate_understood_properties(
@@ -252,6 +290,7 @@ def convert_element(
                 period=torch.tensor(bmad_parsed["l_period"], **factory_kwargs),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         elif bmad_parsed["element_type"] == "patch":
             # TODO: Does this need to be implemented in Cheetah in a more proper way?
@@ -260,6 +299,7 @@ def convert_element(
                 length=torch.tensor(bmad_parsed.get("l", 0.0), **factory_kwargs),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
         else:
             warnings.warn(
@@ -272,6 +312,7 @@ def convert_element(
                 length=torch.tensor(bmad_parsed.get("l", 0.0), **factory_kwargs),
                 name=name,
                 sanitize_name=sanitize_name,
+                metadata=metadata,
             )
     else:
         raise ValueError(f"Unknown Bmad element type for {name = }")  # noqa: E202, E251

cheetah/converters/utils/fortran_namelist.py

@@ -28,13 +28,7 @@
 )
 LINE_DEFINITION_PATTERN = f"({ELEMENT_NAME_PATTERN})" + r"\s*\:\s*line\s*=\s*\((.*)\)"
 USE_LINE_PATTERN = r'use\s*\,\s*([a-z0-9_]+|"[a-z0-9_\-\.\:]+")'
-OVERLAY_DEFINITION_PATTERN = (
-    f"({ELEMENT_NAME_PATTERN})" r"\s*\:\s*overlay\s*=\s*\{(.*)\}\s*\,\s*var\s*=\s*"
-)
-OVERLAY_KNOT_BASED_PATTERN = (
-    OVERLAY_DEFINITION_PATTERN + r"\{\s*([a-z0-9_]+)\s*\}\s*\,\s*x_knot\s*=\s*\{(.*)\}"
-)
-OVERLAY_EXPRESSION_BASED_PATTERN = OVERLAY_DEFINITION_PATTERN + r"\{(.*)\}\s*(\,.*)*"
+CONTROL_DEFINITION_PATTERN = rf"({ELEMENT_NAME_PATTERN})\s*:\s*(?:overlay|group)\b.*"
 
 
 def read_clean_lines(lattice_file_path: Path) -> list[str]:
@@ -143,6 +137,12 @@ def evaluate_expression(expression: str, context: dict) -> Any:
     except ValueError:
         pass
 
+    # Check against string literals enclosed in quotes
+    if (expression.startswith('"') and expression.endswith('"')) or (
+        expression.startswith("'") and expression.endswith("'")
+    ):
+        return expression[1:-1]
+
     # Check against allowed keywords
     if expression in ["open", "electron", "t", "f", "traveling_wave", "full"]:
         return expression
@@ -168,28 +168,26 @@ def evaluate_expression(expression: str, context: dict) -> Any:
             return expression
 
 
-def resolve_object_name_wildcard(wildcard_pattern: str, context: dict) -> list:
+def resolve_object_name_wildcard(wildcard_pattern: str, context: dict) -> list[str]:
     """
-    Return a list of object names that match the given wildcard pattern.
-
-    :param wildcard_pattern: Wildcard pattern to match.
-    :param context: Dictionary of variables among which to search for matching object.
-    :return: List of object names that match the given wildcard pattern, both in terms
-        of name and element type.
+    Return a list of element names in context matching a name pattern and/or type
+    prefix.
     """
-    object_type, object_name = wildcard_pattern.split("::")
+    if "::" in wildcard_pattern:
+        object_type, object_name = wildcard_pattern.split("::", maxsplit=1)
+    else:
+        object_type, object_name = None, wildcard_pattern
 
     pattern = object_name.replace("*", ".*").replace("%", ".")
-    name_matching_keys = [key for key in context.keys() if re.fullmatch(pattern, key)]
-    type_matching_keys = [
-        key
-        for key in name_matching_keys
-        if isinstance(context[key], dict)
-        and "element_type" in context[key]
-        and context[key]["element_type"] == object_type
-    ]
 
-    return type_matching_keys
+    return [
+        name
+        for name, element in context.items()
+        if isinstance(element, dict)
+        and "element_type" in element
+        and (object_type is None or element["element_type"] == object_type)
+        and re.fullmatch(pattern, name)
+    ]
 
 
 def assign_property(line: str, context: dict) -> dict:
@@ -207,7 +205,7 @@ def assign_property(line: str, context: dict) -> dict:
     property_name = match.group(2).strip()
     property_expression = match.group(3).strip()  # TODO: Evaluate expression first
 
-    if "*" in object_name or "%" in object_name:
+    if "*" in object_name or "%" in object_name or "::" in object_name:
         object_names = resolve_object_name_wildcard(object_name, context)
     else:
         object_names = [object_name]
@@ -271,7 +269,7 @@ def define_element(line: str, context: dict) -> dict:
         for property_string in property_matches:
             property_string = property_string.strip()
 
-            property_name, property_expression = property_string.split("=")
+            property_name, property_expression = property_string.split("=", maxsplit=1)
             property_name = property_name.strip()
             property_expression = property_expression.strip()
 
@@ -310,50 +308,6 @@ def define_line(line: str, context: dict) -> dict:
     return context
 
 
-def define_overlay(line: str, context: dict) -> dict:
-    """
-    Define an overlay in the context.
-
-    :param line: Line of an overlay definition to be parsed.
-    :param context: Dictionary of variables to define the overlay in and from which to
-        read variables.
-    :return: Updated context.
-    """
-
-    expression_match = re.fullmatch(OVERLAY_EXPRESSION_BASED_PATTERN, line)
-    knot_match = re.fullmatch(OVERLAY_KNOT_BASED_PATTERN, line)
-
-    if knot_match:
-        overlay_name = knot_match.group(1).strip()
-        overlay_definition = knot_match.group(2).strip()
-        overlay_variable = knot_match.group(3).strip()
-        overlay_x_knot = knot_match.group(4).strip()
-
-        context[overlay_name] = {
-            "overlay_definition": overlay_definition,
-            "overlay_variable": overlay_variable,
-            "overlay_x_knot": overlay_x_knot,
-        }
-    elif expression_match:
-        overlay_name = expression_match.group(1).strip()
-        overlay_definition = expression_match.group(2).strip()
-        overlay_variables = expression_match.group(3).strip()
-        if expression_match.group(4) is not None:
-            overlay_parameters = expression_match.group(4).strip()[1:].strip()
-        else:
-            overlay_parameters = None
-
-        context[overlay_name] = {
-            "overlay_definition": overlay_definition,
-            "overlay_variables": overlay_variables,
-            "overlay_parameters": overlay_parameters,
-        }
-    else:
-        raise ValueError(f"Overlay definition {line} not understood.")
-
-    return context
-
-
 def parse_use_line(line: str, context: dict) -> dict:
     """
     Parse a use line.
@@ -410,8 +364,9 @@ def parse_lines(lines: str) -> dict:
             context = assign_variable(line, context)
         elif re.fullmatch(LINE_DEFINITION_PATTERN, line):
             context = define_line(line, context)
-        elif re.fullmatch(OVERLAY_DEFINITION_PATTERN, line):
-            context = define_overlay(line, context)
+        elif re.fullmatch(CONTROL_DEFINITION_PATTERN, line):
+            # Overlay and group definitions are control entries; skip for simplicity.
+            continue
         elif re.fullmatch(ELEMENT_DEFINITION_PATTERN, line):
             context = define_element(line, context)
         elif re.fullmatch(USE_LINE_PATTERN, line):