midas-hkls 0.1.0__tar.gz

midas_hkls-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: midas-hkls
+Version: 0.1.0
+Summary: Pure-Python crystallography & HKL list generator. sginfo-equivalent: 230 space groups via Hall-symbol parser.
+Author: MIDAS contributors
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/marinerhemant/MIDAS
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.22
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == "dev"
+Requires-Dist: pandas>=1.5; extra == "dev"
+Provides-Extra: cif
+Requires-Dist: pycifrw>=4.4; extra == "cif"
+
+# midas-hkls
+
+Pure-Python crystallography & HKL list generator. **sginfo-equivalent**: all 230
+space groups via Hall-symbol parsing, no C dependencies at runtime.
+
+## What it provides
+
+- `SpaceGroup` — load by number, Hermann-Mauguin symbol, or Hall symbol; expose
+  symmetry operations, systematic absences, equivalent reflections, multiplicities,
+  Laue class, centering.
+- `Lattice` — direct/reciprocal metric tensors, d-spacings, Bragg 2θ, with
+  per-crystal-system convenience constructors.
+- `generate_hkls()` — enumerate Laue-unique allowed reflections within a
+  d-spacing or 2θ cutoff, sorted by d-descending, with multiplicities.
+- CLI: `midas-hkls gen|info|list` (drop-in for `GetHKLList`).
+
+## Quick start
+
+```python
+from midas_hkls import SpaceGroup, Lattice, generate_hkls
+
+sg  = SpaceGroup.from_number(225)              # CeO₂ / Cu / Au / NaCl  (Fm-3m)
+lat = Lattice.for_system("cubic", a=5.411)     # Å
+refs = generate_hkls(sg, lat, wavelength_A=0.173, two_theta_max_deg=15.0)
+
+for r in refs:
+    print(r.ring_nr, (r.h, r.k, r.l), r.d_spacing, r.two_theta_deg, r.multiplicity)
+```
+
+## CLI
+
+```
+midas-hkls gen --sg 225 --lat 5.411 5.411 5.411 90 90 90 --wavelength 0.173 \
+               --two-theta-max 15.0 -o ceo2.csv
+midas-hkls info --sg "Fm-3m" --ops
+midas-hkls list
+```
+
+## Parity with sginfo C library
+
+`midas-hkls` is parity-tested byte-for-byte against MIDAS's `GetHKLList` (sginfo):
+
+- Ring count, ring d-spacing, ring 2θ, ring multiplicity match exactly across
+  CeO₂, LaB₆, Si, α-Fe, α-Ti, calcite, Pnma, P21/c.
+- All 230 space groups parse without error and have correct Friedel-corrected
+  Laue-class group orders.
+
+Run `pytest` to exercise the parity matrix.
+
+## Conventions
+
+- Lattice constants in Å; angles in degrees.
+- Wavelengths in Å.
+- Symmetry operations stored as integer Seitz matrices over translation base
+  STBF=12 (so 1/2 → 6, 1/3 → 4, 1/4 → 3, etc.) — exact-arithmetic absence
+  detection, no float fuzz.
+- Equivalent HKLs include Friedel pairs (centric structure factor under X-ray
+  Laue symmetry).
+
+## Roadmap (post v0.1.0)
+
+- CIF reader (`io/cif.py`).
+- Atomic form factors (Cromer-Mann) and structure factors.
+- Anomalous scattering (Henke / Cromer tables).
+- Wyckoff positions tables (currently only general position is exposed).
+- Origin-choice and alternate-setting transformations beyond what sginfo's
+  `extension` field provides.
+
+## Origin
+
+The 530-entry Hall-symbol table is extracted verbatim from sginfo
+(© 1994-96 Ralf W. Grosse-Kunstleve, public domain) so that midas-hkls and
+MIDAS's existing C tools resolve the same standard setting for every space
+group.

midas_hkls-0.1.0/README.md

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+# midas-hkls
+
+Pure-Python crystallography & HKL list generator. **sginfo-equivalent**: all 230
+space groups via Hall-symbol parsing, no C dependencies at runtime.
+
+## What it provides
+
+- `SpaceGroup` — load by number, Hermann-Mauguin symbol, or Hall symbol; expose
+  symmetry operations, systematic absences, equivalent reflections, multiplicities,
+  Laue class, centering.
+- `Lattice` — direct/reciprocal metric tensors, d-spacings, Bragg 2θ, with
+  per-crystal-system convenience constructors.
+- `generate_hkls()` — enumerate Laue-unique allowed reflections within a
+  d-spacing or 2θ cutoff, sorted by d-descending, with multiplicities.
+- CLI: `midas-hkls gen|info|list` (drop-in for `GetHKLList`).
+
+## Quick start
+
+```python
+from midas_hkls import SpaceGroup, Lattice, generate_hkls
+
+sg  = SpaceGroup.from_number(225)              # CeO₂ / Cu / Au / NaCl  (Fm-3m)
+lat = Lattice.for_system("cubic", a=5.411)     # Å
+refs = generate_hkls(sg, lat, wavelength_A=0.173, two_theta_max_deg=15.0)
+
+for r in refs:
+    print(r.ring_nr, (r.h, r.k, r.l), r.d_spacing, r.two_theta_deg, r.multiplicity)
+```
+
+## CLI
+
+```
+midas-hkls gen --sg 225 --lat 5.411 5.411 5.411 90 90 90 --wavelength 0.173 \
+               --two-theta-max 15.0 -o ceo2.csv
+midas-hkls info --sg "Fm-3m" --ops
+midas-hkls list
+```
+
+## Parity with sginfo C library
+
+`midas-hkls` is parity-tested byte-for-byte against MIDAS's `GetHKLList` (sginfo):
+
+- Ring count, ring d-spacing, ring 2θ, ring multiplicity match exactly across
+  CeO₂, LaB₆, Si, α-Fe, α-Ti, calcite, Pnma, P21/c.
+- All 230 space groups parse without error and have correct Friedel-corrected
+  Laue-class group orders.
+
+Run `pytest` to exercise the parity matrix.
+
+## Conventions
+
+- Lattice constants in Å; angles in degrees.
+- Wavelengths in Å.
+- Symmetry operations stored as integer Seitz matrices over translation base
+  STBF=12 (so 1/2 → 6, 1/3 → 4, 1/4 → 3, etc.) — exact-arithmetic absence
+  detection, no float fuzz.
+- Equivalent HKLs include Friedel pairs (centric structure factor under X-ray
+  Laue symmetry).
+
+## Roadmap (post v0.1.0)
+
+- CIF reader (`io/cif.py`).
+- Atomic form factors (Cromer-Mann) and structure factors.
+- Anomalous scattering (Henke / Cromer tables).
+- Wyckoff positions tables (currently only general position is exposed).
+- Origin-choice and alternate-setting transformations beyond what sginfo's
+  `extension` field provides.
+
+## Origin
+
+The 530-entry Hall-symbol table is extracted verbatim from sginfo
+(© 1994-96 Ralf W. Grosse-Kunstleve, public domain) so that midas-hkls and
+MIDAS's existing C tools resolve the same standard setting for every space
+group.

midas_hkls-0.1.0/midas_hkls/__init__.py

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+"""midas-hkls — pure-Python crystallography & HKL list generator.
+
+sginfo-equivalent (Ralf W. Grosse-Kunstleve, 1994-96) via Hall-symbol parsing.
+Public API:
+
+    from midas_hkls import SpaceGroup, Lattice, generate_hkls, Reflection
+
+    sg = SpaceGroup.from_number(225)        # CeO2 / NaCl / Cu / Au
+    lat = Lattice.for_system("cubic", a=5.411)
+    refs = generate_hkls(sg, lat, wavelength_A=0.173, two_theta_max_deg=20.0)
+"""
+from .hkl_gen import Reflection, generate_hkls, reflections_to_dataframe
+from .lattice import Lattice
+from .space_group import SpaceGroup, list_space_groups
+from .symops import SymOp
+
+__version__ = "0.1.0"
+
+__all__ = [
+    "Lattice",
+    "Reflection",
+    "SpaceGroup",
+    "SymOp",
+    "generate_hkls",
+    "list_space_groups",
+    "reflections_to_dataframe",
+]

midas_hkls-0.1.0/midas_hkls/cli.py

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+"""Command-line interface — drop-in replacement for GetHKLList."""
+from __future__ import annotations
+
+import argparse
+import csv
+import sys
+from pathlib import Path
+from typing import Sequence
+
+from .hkl_gen import generate_hkls
+from .lattice import Lattice
+from .space_group import SpaceGroup, list_space_groups
+
+
+def _build_parser() -> argparse.ArgumentParser:
+    p = argparse.ArgumentParser(prog="midas-hkls", description="Generate HKL list (sginfo replacement)")
+    sub = p.add_subparsers(dest="cmd", required=True)
+
+    g = sub.add_parser("gen", help="Generate an HKL list")
+    g.add_argument("--sg", required=True, help="Space group: number, HM symbol, or Hall symbol")
+    g.add_argument("--lat", nargs=6, type=float, metavar=("a", "b", "c", "alpha", "beta", "gamma"),
+                   required=True, help="Lattice constants (Å, Å, Å, deg, deg, deg)")
+    g.add_argument("--wavelength", type=float, required=True, help="X-ray wavelength (Å)")
+    g.add_argument("--two-theta-max", type=float, default=None, help="Maximum 2θ in degrees")
+    g.add_argument("--d-min", type=float, default=None, help="Minimum d-spacing in Å")
+    g.add_argument("--output", "-o", type=Path, default=None, help="CSV output path (default: stdout)")
+    g.add_argument("--ext", default="", help="Setting extension (sginfo extension code)")
+
+    sub.add_parser("list", help="List all 230 space groups in the canonical table")
+
+    info = sub.add_parser("info", help="Print space group info (operations, centering, Laue)")
+    info.add_argument("--sg", required=True, help="Space group: number, HM, or Hall")
+    info.add_argument("--ops", action="store_true", help="Print all symmetry operations")
+
+    return p
+
+
+def _resolve_space_group(spec: str, ext: str = "") -> SpaceGroup:
+    spec = spec.strip()
+    if spec.isdigit():
+        return SpaceGroup.from_number(int(spec), extension=ext)
+    if " " in spec or spec.startswith("-"):
+        return SpaceGroup.from_hall(spec)
+    try:
+        return SpaceGroup.from_hm(spec)
+    except ValueError:
+        return SpaceGroup.from_hall(spec)
+
+
+def _emit_csv(refs, fp) -> None:
+    w = csv.writer(fp)
+    w.writerow(["ring_nr", "h", "k", "l", "d_spacing", "two_theta_deg", "multiplicity"])
+    for r in refs:
+        w.writerow([r.ring_nr, r.h, r.k, r.l, f"{r.d_spacing:.8g}",
+                    f"{r.two_theta_deg:.8g}", r.multiplicity])
+
+
+def main(argv: Sequence[str] | None = None) -> int:
+    args = _build_parser().parse_args(argv)
+
+    if args.cmd == "list":
+        for num, hall, hm in list_space_groups():
+            print(f"{num:>3}  {hall:<28}  {hm}")
+        return 0
+
+    if args.cmd == "info":
+        sg = _resolve_space_group(args.sg)
+        print(f"Number       : {sg.number}")
+        print(f"Hall symbol  : {sg.hall_symbol!r}")
+        print(f"HM symbol    : {sg.hm_symbol!r}")
+        print(f"Crystal sys  : {sg.crystal_system}")
+        print(f"Laue class   : {sg.laue_class}")
+        print(f"Centering    : {sg.centering}")
+        print(f"Order        : {sg.order}")
+        print(f"Centric      : {sg.is_centrosymmetric()}")
+        if args.ops:
+            for i, op in enumerate(sg.operations):
+                print(f"  {i + 1:3d}: {op.to_xyz()}")
+        return 0
+
+    if args.cmd == "gen":
+        sg = _resolve_space_group(args.sg, ext=args.ext)
+        lat = Lattice(*args.lat)
+        refs = generate_hkls(
+            sg, lat,
+            wavelength_A=args.wavelength,
+            d_min=args.d_min,
+            two_theta_max_deg=args.two_theta_max,
+        )
+        if args.output is None:
+            _emit_csv(refs, sys.stdout)
+        else:
+            with args.output.open("w", newline="") as fp:
+                _emit_csv(refs, fp)
+            print(f"Wrote {len(refs)} reflections to {args.output}", file=sys.stderr)
+        return 0
+
+    return 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())