Mat Xrd Refinement

Rietveld Refinement

Goal

Perform quantitative Rietveld refinement of powder X-ray diffraction (XRD) patterns using DARA (Data-driven Automated Rietveld Analysis) with BGMN. Use when you have an experimental (or theoretical) pattern in .xy format and candidate phase CIFs.

Requirements

• Conda environment: xrd-agent (see conda-envs/xrd-agent).
• Dependencies: dara-xrd, pymatgen. Optional: kaleido for PNG export (use kaleido>=0.2.1,<0.3 to avoid needing Chrome).
• BGMN: DARA uses BGMN; ensure it is installed. On HPC without network, set --bgmn_dir or DARA_BGMN_DIR to a local BGMN directory.

Scripts

Instructions

1. Prepare XRD data (.xy format)

Two columns (2θ and intensity), space-separated. Options:

• From xrd-spectrum JSON: use convert_xrd_to_xy.py with --input_file your_xrd.json. Output is written next to the input as your_xrd.xy.
• From experimental DIF: use convert_xrd_to_xy.py with --input_file your_data.txt (or .dif). Format is auto-detected if the file contains a header with 2-THETA and INTENSITY.

# From JSON (e.g. xrd-spectrum output)
python .agents/skills/mat-xrd-refinement/scripts/convert_xrd_to_xy.py --input_file path/to/xrd.json

# From DIF
python .agents/skills/mat-xrd-refinement/scripts/convert_xrd_to_xy.py --input_file path/to/scan.txt

Convert arguments:

• --input_file: Path to JSON or DIF file.
• --format: auto (default), json, or dif to force format.

2. Run refinement (refine.py)

Refinement uses DARA’s do_refinement_no_saving (no BGMN working files left on disk). Output is written to refinement_results/ under the same directory as the XRD file (no --output_dir argument).

Refine arguments:

• --xrd_data: (Required.) Path to the .xy pattern. Quote the path in the shell if it contains parentheses or spaces, e.g. --xrd_data "./path/with(Chem).xy".
• --cifs: (Optional.) List of CIF paths. If omitted, CIFs are auto-discovered: first from a cifs/ subfolder next to the XRD file, then from the XRD directory. Example layout: examples/LiFePO4/LiFePO4_xrd.xy and examples/LiFePO4/cifs/LiFePO4.cif, Li3PO4.cif.
• --instrument_profile: Default Aeris-fds-Pixcel1d-Medipix3.
• --phase_params: Path to a JSON file with phase refinement parameters (e.g. lattice_range, b1, k1, gewicht). See DARA tutorial.
• --refinement_params: Path to JSON for refinement options (e.g. wmin, wmax).
• --bgmn_dir: Local BGMN directory (avoids download). Or set DARA_BGMN_DIR.
• --quiet: Suppress progress output.

Normalized intensity: If the pattern’s maximum intensity is < 10, the script scales intensities to ~1000 before refinement so Rwp is comparable to the DARA tutorial; the applied scale is printed and stored in refinement_result.json as intensity_scale_applied.

Output files (refine.py)

All under <xrd_directory>/refinement_results/<stem>/ (e.g. refinement_results/LiFePO4/):

No BGMN working files (.str, .par, .lst, etc.) are saved; DARA runs in a temporary directory.

Examples

Example 1: LiFePO4 (CIFs in cifs/ subfolder)

Layout: examples/LiFePO4/LiFePO4_xrd.xy and examples/LiFePO4/cifs/LiFePO4.cif, Li3PO4.cif. No --cifs needed.

# Env: xrd-agent
python .agents/skills/mat-xrd-refinement/scripts/refine.py \
  --xrd_data .agents/skills/mat-xrd-refinement/examples/LiFePO4/LiFePO4_xrd.xy

Results: examples/LiFePO4/refinement_results/LiFePO4/ (refinement_result.json, HTML/PNG, peak_data CSV).

Example 2: CaNi(PO3)4 (path with parentheses — must quote)

# Env: xrd-agent. Quote the path because of (PO3), (OH), (NH4).
python .agents/skills/mat-xrd-refinement/scripts/refine.py \
  --xrd_data ".agents/skills/mat-xrd-refinement/examples/CaNi(PO3)4_800_240_Ca(OH)2_(NH4)2HPO4_NiO/CaNi(PO3)4_800_240_Ca(OH)2_(NH4)2HPO4_NiO.xy"

# If your shell or conda run still has trouble with parentheses in the path,
# you can invoke the environment's Python explicitly instead of using `conda run`:
/home/USER/.conda/envs/xrd-agent/bin/python .agents/skills/mat-xrd-refinement/scripts/refine.py \
  --xrd_data ".agents/skills/mat-xrd-refinement/examples/CaNi(PO3)4_800_240_Ca(OH)2_(NH4)2HPO4_NiO/CaNi(PO3)4_800_240_Ca(OH)2_(NH4)2HPO4_NiO.xy"

CIFs are taken from examples/CaNi(PO3)4_.../cifs/ (NiO_225_sym.cif, CaNi(PO3)4_15_sym.cif). Results under that example’s refinement_results/.

Example 3: Explicit CIFs and optional parameters

python .agents/skills/mat-xrd-refinement/scripts/refine.py \
  --xrd_data pattern.xy \
  --cifs phase1.cif phase2.cif \
  --phase_params phase_params.json \
  --refinement_params refinement_params.json

Standalone Plotting (plot.py)

If you want to adjust the visualization (e.g. dimensions, font sizes, legend position) without re-running the heavy DARA refinement process, you can use the standalone plot.py script. This script reads the *_curve_data.csv exported by refine.py.

python .agents/skills/mat-xrd-refinement/scripts/plot.py \
  --data_dir refinement_results/my_pattern \
  --output refinement_results/my_pattern/reformatted_plot

You can independently edit plot.py directly to adjust any of the matplotlib/plotly formatting rules.

Constraints

• BGMN: Must be installed and on PATH, or provide --bgmn_dir / DARA_BGMN_DIR on restricted networks.
• Paths: In the shell, quote any path that contains ( ) or spaces.
• Rwp: Good fits often < 15%. High Rwp with a good-looking plot can occur if the pattern is normalized (low intensity); the script auto-scales in that case. You can also try --phase_params (e.g. lattice_range, b1, k1, gewicht) per the DARA tutorial.
• Instrument profile: Default is Aeris-fds-Pixcel1d-Medipix3; change with --instrument_profile if needed for your diffractometer.

Related skills

• mat-xrd-digitizer:
  • Use this skill to digitize an image or screenshot of an XRD plot into an .xy file if you do not have raw experimental data.
• mat-xrd-calculator:
  • Calculate theoretical XRD patterns from crystal structures.
• foundation-potentials:
  • Relax structures before XRD for better agreement with experiment.

Author: Nofit Segal Contact: GitHub @nofitsegal