@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

package/bin/skills/pymatgen/scripts/phase_diagram_generator.py

@@ -0,0 +1,233 @@
+#!/usr/bin/env python3
+"""
+Phase diagram generator using Materials Project data.
+
+This script generates phase diagrams for chemical systems using data from the
+Materials Project database via pymatgen's MPRester.
+
+Usage:
+    python phase_diagram_generator.py chemical_system [options]
+
+Examples:
+    python phase_diagram_generator.py Li-Fe-O
+    python phase_diagram_generator.py Li-Fe-O --output li_fe_o_pd.png
+    python phase_diagram_generator.py Fe-O --show
+    python phase_diagram_generator.py Li-Fe-O --analyze "LiFeO2"
+"""
+
+import argparse
+import os
+import sys
+from pathlib import Path
+
+try:
+    from pymatgen.core import Composition
+    from pymatgen.analysis.phase_diagram import PhaseDiagram, PDPlotter
+except ImportError:
+    print("Error: pymatgen is not installed. Install with: pip install pymatgen")
+    sys.exit(1)
+
+try:
+    from mp_api.client import MPRester
+except ImportError:
+    print("Error: mp-api is not installed. Install with: pip install mp-api")
+    sys.exit(1)
+
+
+def get_api_key() -> str:
+    """Get Materials Project API key from environment."""
+    api_key = os.environ.get("MP_API_KEY")
+    if not api_key:
+        print("Error: MP_API_KEY environment variable not set.")
+        print("Get your API key from https://next-gen.materialsproject.org/")
+        print("Then set it with: export MP_API_KEY='your_key_here'")
+        sys.exit(1)
+    return api_key
+
+
+def generate_phase_diagram(chemsys: str, args):
+    """
+    Generate and analyze phase diagram for a chemical system.
+
+    Args:
+        chemsys: Chemical system (e.g., "Li-Fe-O")
+        args: Command line arguments
+    """
+    api_key = get_api_key()
+
+    print(f"\n{'='*60}")
+    print(f"PHASE DIAGRAM: {chemsys}")
+    print(f"{'='*60}\n")
+
+    # Get entries from Materials Project
+    print("Fetching data from Materials Project...")
+    with MPRester(api_key) as mpr:
+        entries = mpr.get_entries_in_chemsys(chemsys)
+
+    print(f"✓ Retrieved {len(entries)} entries")
+
+    if len(entries) == 0:
+        print(f"Error: No entries found for chemical system {chemsys}")
+        sys.exit(1)
+
+    # Build phase diagram
+    print("Building phase diagram...")
+    pd = PhaseDiagram(entries)
+
+    # Get stable entries
+    stable_entries = pd.stable_entries
+    print(f"✓ Phase diagram constructed with {len(stable_entries)} stable phases")
+
+    # Print stable phases
+    print("\n--- STABLE PHASES ---")
+    for entry in stable_entries:
+        formula = entry.composition.reduced_formula
+        energy = entry.energy_per_atom
+        print(f"  {formula:<20} E = {energy:.4f} eV/atom")
+
+    # Analyze specific composition if requested
+    if args.analyze:
+        print(f"\n--- STABILITY ANALYSIS: {args.analyze} ---")
+        try:
+            comp = Composition(args.analyze)
+
+            # Find closest entry
+            closest_entry = None
+            min_distance = float('inf')
+
+            for entry in entries:
+                if entry.composition.reduced_formula == comp.reduced_formula:
+                    closest_entry = entry
+                    break
+
+            if closest_entry:
+                # Calculate energy above hull
+                e_above_hull = pd.get_e_above_hull(closest_entry)
+                print(f"Energy above hull:    {e_above_hull:.4f} eV/atom")
+
+                if e_above_hull < 0.001:
+                    print(f"Status:               STABLE (on convex hull)")
+                elif e_above_hull < 0.05:
+                    print(f"Status:               METASTABLE (nearly stable)")
+                else:
+                    print(f"Status:               UNSTABLE")
+
+                    # Get decomposition
+                    decomp = pd.get_decomposition(comp)
+                    print(f"\nDecomposes to:")
+                    for entry, fraction in decomp.items():
+                        formula = entry.composition.reduced_formula
+                        print(f"  {fraction:.3f} × {formula}")
+
+                    # Get reaction energy
+                    rxn_energy = pd.get_equilibrium_reaction_energy(closest_entry)
+                    print(f"\nDecomposition energy: {rxn_energy:.4f} eV/atom")
+
+            else:
+                print(f"No entry found for composition {args.analyze}")
+                print("Checking stability of hypothetical composition...")
+
+                # Analyze hypothetical composition
+                decomp = pd.get_decomposition(comp)
+                print(f"\nWould decompose to:")
+                for entry, fraction in decomp.items():
+                    formula = entry.composition.reduced_formula
+                    print(f"  {fraction:.3f} × {formula}")
+
+        except Exception as e:
+            print(f"Error analyzing composition: {e}")
+
+    # Get chemical potentials
+    if args.chemical_potentials:
+        print("\n--- CHEMICAL POTENTIALS ---")
+        print("(at stability regions)")
+        try:
+            chempots = pd.get_all_chempots()
+            for element, potentials in chempots.items():
+                print(f"\n{element}:")
+                for potential in potentials[:5]:  # Show first 5
+                    print(f"  {potential:.4f} eV")
+        except Exception as e:
+            print(f"Could not calculate chemical potentials: {e}")
+
+    # Plot phase diagram
+    print("\n--- GENERATING PLOT ---")
+    plotter = PDPlotter(pd, show_unstable=args.show_unstable)
+
+    if args.output:
+        output_path = Path(args.output)
+        plotter.write_image(str(output_path), image_format=output_path.suffix[1:])
+        print(f"✓ Phase diagram saved to {output_path}")
+
+    if args.show:
+        print("Opening interactive plot...")
+        plotter.show()
+
+    print(f"\n{'='*60}\n")
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Generate phase diagrams using Materials Project data",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Requirements:
+  - Materials Project API key (set MP_API_KEY environment variable)
+  - mp-api package: pip install mp-api
+
+Examples:
+  %(prog)s Li-Fe-O
+  %(prog)s Li-Fe-O --output li_fe_o_phase_diagram.png
+  %(prog)s Fe-O --show --analyze "Fe2O3"
+  %(prog)s Li-Fe-O --analyze "LiFeO2" --show-unstable
+        """
+    )
+
+    parser.add_argument(
+        "chemsys",
+        help="Chemical system (e.g., Li-Fe-O, Fe-O)"
+    )
+
+    parser.add_argument(
+        "--output", "-o",
+        help="Output file for phase diagram plot (PNG, PDF, SVG)"
+    )
+
+    parser.add_argument(
+        "--show", "-s",
+        action="store_true",
+        help="Show interactive plot"
+    )
+
+    parser.add_argument(
+        "--analyze", "-a",
+        help="Analyze stability of specific composition (e.g., LiFeO2)"
+    )
+
+    parser.add_argument(
+        "--show-unstable",
+        action="store_true",
+        help="Include unstable phases in plot"
+    )
+
+    parser.add_argument(
+        "--chemical-potentials",
+        action="store_true",
+        help="Calculate chemical potentials"
+    )
+
+    args = parser.parse_args()
+
+    # Validate chemical system format
+    elements = args.chemsys.split("-")
+    if len(elements) < 2:
+        print("Error: Chemical system must contain at least 2 elements")
+        print("Example: Li-Fe-O")
+        sys.exit(1)
+
+    # Generate phase diagram
+    generate_phase_diagram(args.chemsys, args)
+
+
+if __name__ == "__main__":
+    main()

package/bin/skills/pymatgen/scripts/structure_analyzer.py

@@ -0,0 +1,266 @@
+#!/usr/bin/env python3
+"""
+Structure analysis tool using pymatgen.
+
+Analyzes crystal structures and provides comprehensive information including:
+- Composition and formula
+- Space group and symmetry
+- Lattice parameters
+- Density
+- Coordination environment
+- Bond lengths and angles
+
+Usage:
+    python structure_analyzer.py structure_file [options]
+
+Examples:
+    python structure_analyzer.py POSCAR
+    python structure_analyzer.py structure.cif --symmetry --neighbors
+    python structure_analyzer.py POSCAR --export json
+"""
+
+import argparse
+import json
+import sys
+from pathlib import Path
+
+try:
+    from pymatgen.core import Structure
+    from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+    from pymatgen.analysis.local_env import CrystalNN
+except ImportError:
+    print("Error: pymatgen is not installed. Install with: pip install pymatgen")
+    sys.exit(1)
+
+
+def analyze_structure(struct: Structure, args) -> dict:
+    """
+    Perform comprehensive structure analysis.
+
+    Args:
+        struct: Pymatgen Structure object
+        args: Command line arguments
+
+    Returns:
+        Dictionary containing analysis results
+    """
+    results = {}
+
+    # Basic information
+    print("\n" + "="*60)
+    print("STRUCTURE ANALYSIS")
+    print("="*60)
+
+    print("\n--- COMPOSITION ---")
+    print(f"Formula (reduced):    {struct.composition.reduced_formula}")
+    print(f"Formula (full):       {struct.composition.formula}")
+    print(f"Formula (Hill):       {struct.composition.hill_formula}")
+    print(f"Chemical system:      {struct.composition.chemical_system}")
+    print(f"Number of sites:      {len(struct)}")
+    print(f"Number of species:    {len(struct.composition.elements)}")
+    print(f"Molecular weight:     {struct.composition.weight:.2f} amu")
+
+    results['composition'] = {
+        'reduced_formula': struct.composition.reduced_formula,
+        'formula': struct.composition.formula,
+        'hill_formula': struct.composition.hill_formula,
+        'chemical_system': struct.composition.chemical_system,
+        'num_sites': len(struct),
+        'molecular_weight': struct.composition.weight,
+    }
+
+    # Lattice information
+    print("\n--- LATTICE ---")
+    print(f"a = {struct.lattice.a:.4f} Å")
+    print(f"b = {struct.lattice.b:.4f} Å")
+    print(f"c = {struct.lattice.c:.4f} Å")
+    print(f"α = {struct.lattice.alpha:.2f}°")
+    print(f"β = {struct.lattice.beta:.2f}°")
+    print(f"γ = {struct.lattice.gamma:.2f}°")
+    print(f"Volume:               {struct.volume:.2f} ų")
+    print(f"Density:              {struct.density:.3f} g/cm³")
+
+    results['lattice'] = {
+        'a': struct.lattice.a,
+        'b': struct.lattice.b,
+        'c': struct.lattice.c,
+        'alpha': struct.lattice.alpha,
+        'beta': struct.lattice.beta,
+        'gamma': struct.lattice.gamma,
+        'volume': struct.volume,
+        'density': struct.density,
+    }
+
+    # Symmetry analysis
+    if args.symmetry:
+        print("\n--- SYMMETRY ---")
+        try:
+            sga = SpacegroupAnalyzer(struct)
+
+            spacegroup_symbol = sga.get_space_group_symbol()
+            spacegroup_number = sga.get_space_group_number()
+            crystal_system = sga.get_crystal_system()
+            point_group = sga.get_point_group_symbol()
+
+            print(f"Space group:          {spacegroup_symbol} (#{spacegroup_number})")
+            print(f"Crystal system:       {crystal_system}")
+            print(f"Point group:          {point_group}")
+
+            # Get symmetry operations
+            symm_ops = sga.get_symmetry_operations()
+            print(f"Symmetry operations:  {len(symm_ops)}")
+
+            results['symmetry'] = {
+                'spacegroup_symbol': spacegroup_symbol,
+                'spacegroup_number': spacegroup_number,
+                'crystal_system': crystal_system,
+                'point_group': point_group,
+                'num_symmetry_ops': len(symm_ops),
+            }
+
+            # Show equivalent sites
+            sym_struct = sga.get_symmetrized_structure()
+            print(f"Symmetry-equivalent site groups: {len(sym_struct.equivalent_sites)}")
+
+        except Exception as e:
+            print(f"Could not determine symmetry: {e}")
+
+    # Site information
+    print("\n--- SITES ---")
+    print(f"{'Index':<6} {'Species':<10} {'Wyckoff':<10} {'Frac Coords':<30}")
+    print("-" * 60)
+
+    for i, site in enumerate(struct):
+        coords_str = f"[{site.frac_coords[0]:.4f}, {site.frac_coords[1]:.4f}, {site.frac_coords[2]:.4f}]"
+        wyckoff = "N/A"
+
+        if args.symmetry:
+            try:
+                sga = SpacegroupAnalyzer(struct)
+                sym_struct = sga.get_symmetrized_structure()
+                wyckoff = sym_struct.equivalent_sites[0][0].species_string  # Simplified
+            except:
+                pass
+
+        print(f"{i:<6} {site.species_string:<10} {wyckoff:<10} {coords_str:<30}")
+
+    # Neighbor analysis
+    if args.neighbors:
+        print("\n--- COORDINATION ENVIRONMENT ---")
+        try:
+            cnn = CrystalNN()
+
+            for i, site in enumerate(struct):
+                neighbors = cnn.get_nn_info(struct, i)
+                print(f"\nSite {i} ({site.species_string}):")
+                print(f"  Coordination number: {len(neighbors)}")
+
+                if len(neighbors) > 0 and len(neighbors) <= 12:
+                    print(f"  Neighbors:")
+                    for j, neighbor in enumerate(neighbors):
+                        neighbor_site = struct[neighbor['site_index']]
+                        distance = site.distance(neighbor_site)
+                        print(f"    {neighbor_site.species_string} at {distance:.3f} Å")
+
+        except Exception as e:
+            print(f"Could not analyze coordination: {e}")
+
+    # Distance matrix (for small structures)
+    if args.distances and len(struct) <= 20:
+        print("\n--- DISTANCE MATRIX (Å) ---")
+        distance_matrix = struct.distance_matrix
+
+        # Print header
+        print(f"{'':>4}", end="")
+        for i in range(len(struct)):
+            print(f"{i:>8}", end="")
+        print()
+
+        # Print matrix
+        for i in range(len(struct)):
+            print(f"{i:>4}", end="")
+            for j in range(len(struct)):
+                if i == j:
+                    print(f"{'---':>8}", end="")
+                else:
+                    print(f"{distance_matrix[i][j]:>8.3f}", end="")
+            print()
+
+    print("\n" + "="*60)
+
+    return results
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Analyze crystal structures using pymatgen",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+
+    parser.add_argument(
+        "structure_file",
+        help="Structure file to analyze (CIF, POSCAR, etc.)"
+    )
+
+    parser.add_argument(
+        "--symmetry", "-s",
+        action="store_true",
+        help="Perform symmetry analysis"
+    )
+
+    parser.add_argument(
+        "--neighbors", "-n",
+        action="store_true",
+        help="Analyze coordination environment"
+    )
+
+    parser.add_argument(
+        "--distances", "-d",
+        action="store_true",
+        help="Show distance matrix (for structures with ≤20 atoms)"
+    )
+
+    parser.add_argument(
+        "--export", "-e",
+        choices=["json", "yaml"],
+        help="Export analysis results to file"
+    )
+
+    parser.add_argument(
+        "--output", "-o",
+        help="Output file for exported results"
+    )
+
+    args = parser.parse_args()
+
+    # Read structure
+    try:
+        struct = Structure.from_file(args.structure_file)
+    except Exception as e:
+        print(f"Error reading structure file: {e}")
+        sys.exit(1)
+
+    # Analyze structure
+    results = analyze_structure(struct, args)
+
+    # Export results
+    if args.export:
+        output_file = args.output or f"analysis.{args.export}"
+
+        if args.export == "json":
+            with open(output_file, "w") as f:
+                json.dump(results, f, indent=2)
+            print(f"\n✓ Analysis exported to {output_file}")
+
+        elif args.export == "yaml":
+            try:
+                import yaml
+                with open(output_file, "w") as f:
+                    yaml.dump(results, f, default_flow_style=False)
+                print(f"\n✓ Analysis exported to {output_file}")
+            except ImportError:
+                print("Error: PyYAML is not installed. Install with: pip install pyyaml")
+
+
+if __name__ == "__main__":
+    main()

package/bin/skills/pymatgen/scripts/structure_converter.py

@@ -0,0 +1,169 @@
+#!/usr/bin/env python3
+"""
+Structure file format converter using pymatgen.
+
+This script converts between different structure file formats supported by pymatgen.
+Supports automatic format detection and batch conversion.
+
+Usage:
+    python structure_converter.py input_file output_file
+    python structure_converter.py input_file --format cif
+    python structure_converter.py *.cif --output-dir ./converted --format poscar
+
+Examples:
+    python structure_converter.py POSCAR structure.cif
+    python structure_converter.py structure.cif --format json
+    python structure_converter.py *.vasp --output-dir ./cif_files --format cif
+"""
+
+import argparse
+import sys
+from pathlib import Path
+from typing import List
+
+try:
+    from pymatgen.core import Structure
+except ImportError:
+    print("Error: pymatgen is not installed. Install with: pip install pymatgen")
+    sys.exit(1)
+
+
+def convert_structure(input_path: Path, output_path: Path = None, output_format: str = None) -> bool:
+    """
+    Convert a structure file to a different format.
+
+    Args:
+        input_path: Path to input structure file
+        output_path: Path to output file (optional if output_format is specified)
+        output_format: Target format (e.g., 'cif', 'poscar', 'json', 'yaml')
+
+    Returns:
+        True if conversion succeeded, False otherwise
+    """
+    try:
+        # Read structure with automatic format detection
+        struct = Structure.from_file(str(input_path))
+        print(f"✓ Read structure: {struct.composition.reduced_formula} from {input_path}")
+
+        # Determine output path
+        if output_path is None and output_format:
+            output_path = input_path.with_suffix(f".{output_format}")
+        elif output_path is None:
+            print("Error: Must specify either output_path or output_format")
+            return False
+
+        # Write structure
+        struct.to(filename=str(output_path))
+        print(f"✓ Wrote structure to {output_path}")
+
+        return True
+
+    except Exception as e:
+        print(f"✗ Error converting {input_path}: {e}")
+        return False
+
+
+def batch_convert(input_files: List[Path], output_dir: Path, output_format: str) -> None:
+    """
+    Convert multiple structure files to a common format.
+
+    Args:
+        input_files: List of input structure files
+        output_dir: Directory for output files
+        output_format: Target format for all files
+    """
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    success_count = 0
+    for input_file in input_files:
+        output_file = output_dir / f"{input_file.stem}.{output_format}"
+        if convert_structure(input_file, output_file):
+            success_count += 1
+
+    print(f"\n{'='*60}")
+    print(f"Conversion complete: {success_count}/{len(input_files)} files converted successfully")
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Convert structure files between different formats using pymatgen",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Supported formats:
+  Input:  CIF, POSCAR, CONTCAR, XYZ, PDB, JSON, YAML, and many more
+  Output: CIF, POSCAR, XYZ, PDB, JSON, YAML, XSF, and many more
+
+Examples:
+  %(prog)s POSCAR structure.cif
+  %(prog)s structure.cif --format json
+  %(prog)s *.cif --output-dir ./poscar_files --format poscar
+        """
+    )
+
+    parser.add_argument(
+        "input",
+        nargs="+",
+        help="Input structure file(s). Supports wildcards for batch conversion."
+    )
+
+    parser.add_argument(
+        "output",
+        nargs="?",
+        help="Output structure file (ignored if --output-dir is used)"
+    )
+
+    parser.add_argument(
+        "--format", "-f",
+        help="Output format (e.g., cif, poscar, json, yaml, xyz)"
+    )
+
+    parser.add_argument(
+        "--output-dir", "-o",
+        type=Path,
+        help="Output directory for batch conversion"
+    )
+
+    args = parser.parse_args()
+
+    # Expand wildcards and convert to Path objects
+    input_files = []
+    for pattern in args.input:
+        matches = list(Path.cwd().glob(pattern))
+        if matches:
+            input_files.extend(matches)
+        else:
+            input_files.append(Path(pattern))
+
+    # Filter to files only
+    input_files = [f for f in input_files if f.is_file()]
+
+    if not input_files:
+        print("Error: No input files found")
+        sys.exit(1)
+
+    # Batch conversion mode
+    if args.output_dir or len(input_files) > 1:
+        if not args.format:
+            print("Error: --format is required for batch conversion")
+            sys.exit(1)
+
+        output_dir = args.output_dir or Path("./converted")
+        batch_convert(input_files, output_dir, args.format)
+
+    # Single file conversion
+    elif len(input_files) == 1:
+        input_file = input_files[0]
+
+        if args.output:
+            output_file = Path(args.output)
+            convert_structure(input_file, output_file)
+        elif args.format:
+            convert_structure(input_file, output_format=args.format)
+        else:
+            print("Error: Must specify output file or --format")
+            parser.print_help()
+            sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()