"""Pull mechanical properties (elastic moduli) for MP entries via MP API. For entries from Materials Project, this script queries the MP API for elastic tensor data (bulk modulus, shear modulus, Young's modulus, Poisson ratio). For non-MP entries, it attempts a geometric proxy based on bond density. Fills the ssb_screening block with: - bulk_modulus_GPa - shear_modulus_GPa - youngs_modulus_GPa - poisson_ratio - elastic_source: "MP_API" | "geometric_proxy" | null - dendrite_suppression_flag: shear_modulus > 6 GPa (Monroe-Newman criterion) Usage: python scripts/compute_mechanical_properties.py python scripts/compute_mechanical_properties.py --api-key YOUR_KEY python scripts/compute_mechanical_properties.py --mp-only python scripts/compute_mechanical_properties.py --proxy-only python scripts/compute_mechanical_properties.py --dry-run """ import json, os, sys, time, argparse, warnings from pathlib import Path import numpy as np warnings.filterwarnings("ignore") WIDTH = 60 # Monroe-Newman criterion: G_solid > ~2x G_Li for dendrite suppression LI_SHEAR_MODULUS = 4.25 # GPa at room temp (varies 3.4-4.8) DENDRITE_THRESHOLD = 6.0 # GPa conservative threshold def compute_density_proxy(structure): """Compute geometric proxy for elastic moduli from structure. Based on bond density and packing fraction correlations. Returns approximate bulk_modulus and shear_modulus in GPa. """ try: density = structure.density n_atoms = len(structure) volume = structure.volume if volume <= 0 or n_atoms < 2: return None, None, "insufficient_data" # Atomic packing density proxy # Sum of approximate atomic volumes (using covalent radii) atomic_vol = 0.0 for site in structure: el = site.specie.symbol r_cov = { "Li": 1.28, "Na": 1.66, "Mg": 1.41, "Al": 1.21, "Si": 1.11, "P": 1.07, "S": 1.05, "Cl": 1.02, "K": 2.03, "Ca": 1.76, "Ti": 1.47, "V": 1.34, "Cr": 1.27, "Mn": 1.26, "Fe": 1.25, "Co": 1.24, "Ni": 1.21, "Cu": 1.22, "Zn": 1.20, "Ga": 1.22, "Ge": 1.21, "As": 1.21, "Se": 1.17, "Br": 1.14, "Y": 1.78, "Zr": 1.57, "Nb": 1.45, "Mo": 1.38, "Ru": 1.33, "Rh": 1.31, "Pd": 1.30, "Ag": 1.34, "Cd": 1.36, "In": 1.42, "Sn": 1.40, "Sb": 1.40, "Te": 1.37, "I": 1.33, "La": 1.87, "Ce": 1.82, "Pr": 1.82, "Nd": 1.81, "Sm": 1.80, "Eu": 1.80, "Gd": 1.79, "Tb": 1.76, "Dy": 1.75, "Ho": 1.74, "Er": 1.73, "Tm": 1.72, "Yb": 1.71, "Lu": 1.70, "Ta": 1.45, "W": 1.39, "Pb": 1.44, "Bi": 1.50, "O": 0.66, "N": 0.71, "F": 0.64, "H": 0.31, }.get(el, 1.5) atomic_vol += (4.0/3.0) * np.pi * (r_cov ** 3) packing_fraction = atomic_vol / volume if volume > 0 else 0.3 # Correlation: denser packing -> higher moduli # Bulk modulus roughly scales with cohesive energy density coh_energy_density = density * 100 # rough proxy in GPa-like units bulk_modulus = coh_energy_density * (packing_fraction ** 1.5) shear_modulus = bulk_modulus * (packing_fraction ** 0.5) * 0.5 # Clamp to realistic ranges bulk_modulus = max(5.0, min(400.0, bulk_modulus)) shear_modulus = max(2.0, min(300.0, shear_modulus)) return round(bulk_modulus, 2), round(shear_modulus, 2), "geometric_proxy" except Exception: return None, None, "error" def main(): parser = argparse.ArgumentParser(description="Compute mechanical properties") parser.add_argument("--api-key", type=str, default=None, help="Materials Project API key (optional, for live API queries)") parser.add_argument("--mp-only", action="store_true", help="Only process MP entries (skip geometric proxy)") parser.add_argument("--proxy-only", action="store_true", help="Only use geometric proxy (skip MP API)") parser.add_argument("--limit", type=int, default=None) parser.add_argument("--dry-run", action="store_true") parser.add_argument("--output", type=str, default=None) args = parser.parse_args() BASE_DIR = Path(__file__).resolve().parent.parent DATASET_PATH = BASE_DIR / "dataset" print("=" * WIDTH) print(" MECHANICAL PROPERTIES — ELASTIC MODULI") print(f" Dendrite suppression threshold: G > {DENDRITE_THRESHOLD} GPa") print("=" * WIDTH) print("\nLoading entries...") t0 = time.time() with open(DATASET_PATH / "entries_final_v3.json") as f: all_entries = json.load(f) print(f" {len(all_entries):,} entries ({time.time()-t0:.1f}s)") if args.limit: all_entries = all_entries[:args.limit] print(f" Limited to {args.limit} entries") # Try MP API for MP entries mp_elastic_data = {} if args.api_key and not args.proxy_only: print("\n Querying MP API for elastic data...") try: from mp_api.client import MPRester with MPRester(args.api_key) as mpr: mp_ids = [e.get("source_id") for e in all_entries if e.get("source") == "mp" and e.get("source_id")] print(f" MP entries with source_ids: {len(mp_ids):,}") for i in range(0, len(mp_ids), 50): batch = mp_ids[i:i+50] try: results = mpr.elasticity.search(material_ids=batch) for doc in results: if doc.material_id in batch: mp_elastic_data[doc.material_id] = { "bulk_modulus": doc.bulk_modulus, "shear_modulus": doc.shear_modulus, "youngs_modulus": doc.youngs_modulus, "poisson_ratio": doc.poisson_ratio, } except Exception: pass if (i+1) % 500 == 0: print(f" Queried {i+1}/{len(mp_ids)} MP IDs") print(f" Retrieved elastic data for {len(mp_elastic_data):,} MP entries") except ImportError: print(" mp-api not installed. Skipping MP API query.") except Exception as exc: print(f" MP API error: {exc}") # Process entries print(f"\n{'─' * WIDTH}") print(" Computing mechanical properties...") print(f"{'─' * WIDTH}") processed = 0 mp_api_found = 0 proxy_computed = 0 errors = 0 dendrite_suppression = 0 from pymatgen.core import Structure import json as _json for idx, e in enumerate(all_entries): if "ssb_screening" not in e: e["ssb_screening"] = {} ss = e["ssb_screening"] source = e.get("source", "") source_id = e.get("source_id", "") # Try MP API data first if source == "mp" and source_id in mp_elastic_data: mp_data = mp_elastic_data[source_id] ss["bulk_modulus_GPa"] = mp_data.get("bulk_modulus") ss["shear_modulus_GPa"] = mp_data.get("shear_modulus") ss["youngs_modulus_GPa"] = mp_data.get("youngs_modulus") ss["poisson_ratio"] = mp_data.get("poisson_ratio") ss["elastic_source"] = "MP_API" mp_api_found += 1 elif not args.mp_only and e.get("structure_json"): # Use geometric proxy try: struct_dict = _json.loads(e["structure_json"]) structure = Structure.from_dict(struct_dict) K, G, proxy_source = compute_density_proxy(structure) if K is not None and G is not None: ss["bulk_modulus_GPa"] = K ss["shear_modulus_GPa"] = G ss["youngs_modulus_GPa"] = round(9 * K * G / (3 * K + G), 2) if (3*K+G) > 0 else None ss["poisson_ratio"] = round((3*K - 2*G) / (2*(3*K + G)), 3) if (3*K+G) > 0 else None ss["elastic_source"] = proxy_source proxy_computed += 1 except Exception: errors += 1 # Set dendrite suppression flag shear_mod = ss.get("shear_modulus_GPa") if shear_mod is not None: ss["dendrite_suppression_flag"] = bool(shear_mod >= DENDRITE_THRESHOLD) if ss["dendrite_suppression_flag"]: dendrite_suppression += 1 processed += 1 if (idx + 1) % 5000 == 0: print(f" {idx+1}/{len(all_entries)} | MP_API:{mp_api_found} Proxy:{proxy_computed} Dendrite:{dendrite_suppression}") print(f"\n{'─' * WIDTH}") print(f" Complete: {processed} processed") print(f" MP API data: {mp_api_found:,}") print(f" Geometric proxy: {proxy_computed:,}") print(f" Errors: {errors:,}") print(f" Dendrite suppression (G > {DENDRITE_THRESHOLD} GPa): {dendrite_suppression:,}") # Save if args.dry_run: print(f"\n (dry-run — not saved)") else: output_path = DATASET_PATH / "entries_final_v3.json" print(f"\n Writing to {output_path}...") t_write = time.time() with open(args.output or output_path, "w") as f: json.dump(all_entries, f) print(f" Done ({time.time()-t_write:.1f}s)") print("=" * WIDTH) if __name__ == "__main__": main()