Mat Magnetic Density

Magnetic Density

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[!NOTE] Steps written server.tool are MCP tool calls: atomate2.run_atomate2_vasp_calculation is the run_atomate2_vasp_calculation tool of the atomate2 server (mcp__atomate2__run_atomate2_vasp_calculation, or mcp__plugin_atomistic-skills_atomate2__run_atomate2_vasp_calculation when installed as a plugin). Without a connected server, run the same tools from the shell. Tools named in one command share a process, so a model loaded by load_model stays loaded:

${CLAUDE_SKILL_DIR}/../../venv/run cpu python -m src.mcp_server.cli atomate2 run_atomate2_vasp_calculation key=value get_atomate2_job_status key=value
${CLAUDE_SKILL_DIR}/../../venv/run cpu python -m src.mcp_server.cli base search_materials_project_by_formula key=value

Goal

To calculate the magnetic moments and optionally extract the spin density ($\rho_{\text{spin}}$) of magnetic materials using spin-polarized DFT calculations. This skill enables the characterization of magnetic ordering, local magnetic moments on individual atoms, and spatial distribution of spin density.

Instructions

1. Structure Preparation

Obtain or prepare the structure of the magnetic material you want to study. You can:

• Query from Materials Project using the base MCP tools (recommended - already DFT-optimized)
• Load from a local CIF/POSCAR file
• Use a previously relaxed structure

Note on relaxation: For magnetic moment calculations, relaxation is optional if using high-quality experimental or Materials Project structures. Magnetic moments are relatively insensitive to small structural variations. However, relaxation is recommended for:

• New/hypothetical structures
• Surfaces, interfaces, or defects
• Systems where you need accurate total energies (not just magnetic moments)
• Strongly correlated oxides with significant magnetic-structural coupling

2. Run Spin-Polarized DFT Calculation

Use the atomate2 MCP tool to run a spin-polarized static calculation. The mp preset (MPStaticSet) automatically enables spin polarization and applies appropriate settings for magnetic systems.

atomate2.run_atomate2_vasp_calculation(
    structures_path="structure.cif",  # Path to your structure file
    output_dir="magnetic_calc",       # Directory to save results
    preset_type="mp",  # MPStaticSet with PBE (includes spin polarization)
    calculation_type="static",         # Static calculation
)

Important - Functional Selection:

• For metallic ferromagnets (Fe, Co, Ni): Use mp preset (MPStaticSet with PBE). PBE provides excellent accuracy for magnetic moments (typically within ~2% of experimental values)[1].
• For strongly correlated oxides (NiO, CoO, FeO): Use mp preset (see Example 2 below). MPStaticSet automatically applies appropriate GGA+U corrections for transition metal oxides. Standard PBE fails to predict the correct insulating antiferromagnetic ground state and severely underestimates band gaps[3]. Note: +U corrections improve electronic structure but do not guarantee better magnetic moments (e.g., GGA+U may overestimate for NiO or underestimate for CoO due to missing orbital contributions)[4].
• Avoid r2SCAN for metallic ferromagnets: r2SCAN significantly overestimates magnetic moments in itinerant ferromagnets like Fe (by ~24% compared to experimental values)[2].

References: [1] PBE underestimates Fe magnetization by only 1.8%: Zhang et al., Phys. Rev. Materials 6, 013801 (2022). DOI: 10.1103/PhysRevMaterials.6.013801 [2] r2SCAN and SCAN overestimate Fe magnetization by 24% and 17% respectively: ibid. [3] PBE+U opens band gaps and corrects ground state in transition metal oxides: Kulik, J. Chem. Phys. 142, 240901 (2015). DOI: 10.1063/1.4922693 [4] CoO magnetic moments: PBE+U underestimates due to missing orbital contributions: Radi et al., Z. Naturforsch. A 70, 789 (2015). DOI: 10.1515/zna-2015-0216

See the "Functional Selection Guide" section below for detailed recommendations.

3. Monitor Job Status

After submitting the calculation, monitor its progress:

atomate2.get_atomate2_job_status(
    job_id="<job_id_from_step_2>"  # Job ID returned from step 2
)

4. Extract Magnetic Moments

Once the calculation is complete, retrieve the results to extract magnetic moments:

atomate2.get_atomate2_results_by_id(
    job_ids=["<job_id>"],  # List of job IDs
    save_to_file="magnetic_results.json"  # Save results to file
)

The results will include:

• Total magnetization: Net magnetic moment of the unit cell
• Site magnetic moments: Magnetic moment on each atom
• Energy: Total energy of the magnetic configuration

5. Parse and Analyze Results

Use the provided script to parse the magnetic moments from the results:

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/parse_magnetic_moments.py magnetic_results.json --output magnetic_analysis.json

This script will:

• Extract site-resolved magnetic moments
• Calculate the total magnetization
• Identify the magnetic ordering pattern
• Generate a summary report

6. Extract Spin Density (Optional)

For detailed analysis of spin density distribution, use the spin density extraction script:

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/extract_spin_density.py <output_dir> --output spin_density.json

This requires access to the CHGCAR file from the VASP calculation and will:

• Read the spin density from CHGCAR
• Calculate integrated spin moments
• Optionally generate 3D visualization data