Mat Melting Point

Melting Point

<!-- mcp-tools-note -->

[!NOTE] Steps written server.tool are MCP tool calls: mace.run_md is the run_md tool of the mace server (mcp__mace__run_md, or mcp__plugin_atomistic-skills_mace__run_md 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 mlip python -m src.mcp_server.cli mace run_md key=value relax_structure key=value
${CLAUDE_SKILL_DIR}/../../venv/run cpu python -m src.mcp_server.cli base visualize_structure key=value

Goal

To determine the thermodynamic melting temperature ($T_m$) of a bulk material by equilibrating a solid-liquid interface in an NVE ensemble.

Instructions

1. Background Research:

   • Search for the approximate melting point ($T_m$) and boiling/evaporation point ($T_{vap}$) of the material.
   • Choose a melting temperature $T_{melt}$ where $T_m < T_{melt} \ll T_{vap}$.
   • MD Parameters: Refer to the mat-md-monitors skill for best practices on timesteps and monitors. In general, use a 2.0 fs timestep for systems without Hydrogen.

2. Phase Preparation:

   • Solid: Create a supercell using create_supercell.py.

   ${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/create_supercell.py [input_structure.cif] [solid_supercell.cif] --min_length 20.0

   • Liquid: Melt a block using 1D-NPT (with mask) to ensure matching dimensions.

   mace.run_md(
       structure_data="solid_supercell.cif",
       temperature=2000,  # REPLACE with T_melt from Step 1
       ensemble="npt",
       steps=5000,
       timestep=2.0,      # Use 2.0 fs for most inorganic systems
       pressure=1.0,      # Apply positive pressure (1-2 bar) to prevent evaporation
       pressure_mask=[1, 0, 0], # REQUIRED: Must match the stacking axis (e.g., x-axis)
       output_dir="melt_stage"
   )

   • Visual Inspection (CRITICAL): Sometimes the cell does not fully melt within the specified MD steps. You MUST use the base.visualize_structure tool to generate an image of the final liquid.cif structure (or trajectory) and have the VLM visually inspect the image to confirm that the long-range crystalline order has been destroyed and the cell is completely melted. If it has not, you must run the MD with a higher temperature or for more steps.

3. Interface Creation: Use create_interface.py to concatenate the two phases.

   ${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/create_interface.py solid.cif liquid.cif --axis 0 --output interface.cif

4. Relaxation: Perform an ionic relaxation using the relax_structure MCP tool with relax_cell=True. This allows the unit cell to adjust (shrink/expand) to match the density, and remove the interface energy created by stacking the two cells.

   mace.relax_structure(structure_data="interface.cif", relax_cell=True)

5. Phase Verification: Before running production MD, verify solid-liquid coexistence in all structures.

   First, extract reference atomic features:

   # (or venv/mlip)
   # Extract from pure solid - use explicit output path
   mace.predict_atomic_features(
       structure_data="solid_supercell.cif",
       output_path="<research_dir>/solid_features.json"
   )
   
   # Extract from pure liquid - use explicit output path
   mace.predict_atomic_features(
       structure_data="liquid_supercell.cif",
       output_path="<research_dir>/liquid_features.json"
   )

   Then verify phases:

   # Solid should be ~100% solid
   ${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/check_phase.py <research_dir>/solid_features.json \
       --solid_features <research_dir>/solid_features.json \
       --liquid_features <research_dir>/liquid_features.json
   
   # Liquid should be ~100% liquid
   ${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/check_phase.py <research_dir>/liquid_features.json \
       --solid_features <research_dir>/solid_features.json \
       --liquid_features <research_dir>/liquid_features.json
   
   # Interface should show ~50% solid/liquid coexistence
   # (Requires predicting features for the relaxed interface first)
   mace.predict_atomic_features(
       structure_data="interface_relax/relaxed_structure.cif",
       output_path="<research_dir>/interface_features.json"
   )
   ${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/check_phase.py <research_dir>/interface_features.json \
       --solid_features <research_dir>/solid_features.json \
       --liquid_features <research_dir>/liquid_features.json

   Expected:

   • Solid: ≥95% solid
   • Liquid: ≥95% liquid
   • Interface: 40-60% solid (coexistence maintained)

   If interface lost coexistence: Adjust melting temperature or relaxation parameters.

6. Thermalization (Equilibration): Start from the 0 K relaxed structure and run a short NVT thermalization at the expected $T_m$ to properly distribute kinetic and potential energy.

   mace.run_md(
       structure_data="interface_relax/relaxed_structure.cif",
       temperature=933, # Target expected Tm
       ensemble="nvt",
       steps=5000,
       timestep=2.0,
       output_dir="thermalization_md"
   )

7. Production: Run an NVE MD simulation starting from the full .traj file of the thermalized structure with the monitor=True parameter. Passing the .traj file is critical because it preserves the velocities from the NVT run, providing a continuous MD sequence. bash mace.run_md( structure_data="thermalization_md/<formula>_<temp>K_nvt.traj", # Pass .traj to preserve velocities temperature=933, ensemble="nve", steps=100000, timestep=2.0, monitor=True, monitor_type="melting", output_dir="production_md" )

8. Auto-Termination: The integrated monitor will:

   • Check for temperature and potential energy stability.
   • Automatically stop the MD simulation when the melting point is reached.
   • Log termination status in the research log.
   • mace.run_md will return once the simulation stops (either by finishing all steps or by monitor termination).

9. Phase Validation: Verify that the solid and liquid phases still coexist at the end of the simulation. First, predict the atomic features of the final structure:

   mace.predict_atomic_features(
       structure_data="production_md/final_structure.cif",
       output_path="production_md/final_structure_features.json"
   )

   Then, classify the phase:

   ${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/check_phase.py production_md/final_structure_features.json \
     --solid_features solid_features.json \
     --liquid_features liquid_features.json

   • Fully Solidified: The NVE starting temperature was too low.
   • Fully Melted: The NVE starting temperature was too high.

10. Analysis: If coexistence is verified, calculate $T_m$ by averaging the temperature over the last 5 ps of the simulation.