mat-intercalation-voltage

Intercalation Voltage

Goal

To calculate the average open-circuit voltage (OCV) of an intercalation cathode material (e.g., Li$_x$M$_y$O$_z$) by computing the energy difference between the fully intercalated (charged) and de-intercalated (discharged) states.

The average voltage $V$ is given by: $$V = -\frac{E(\text{full}) - E(\text{empty}) - n \mu_{\text{metal}}}{n}$$ where $E$ is the total energy, $n$ is the number of intercalated ions, and $\mu_{\text{metal}}$ is the chemical potential per atom of the bulk metal.

Instructions

1. Prepare Structures:

   • Obtain the fully intercalated structure (e.g., LiFePO$_4$)
   • Create the de-intercalated structure by removing intercalating ions:

   # Env: base-agent
   python .agents/skills/mat-intercalation-voltage/scripts/remove_atoms.py \
       LiFePO4.cif \
       --remove Li \
       --output FePO4.cif
   

   • Get the bulk metal structure from resources/ (e.g., Li_metal.cif)

2. Select Foundation Potential: Choose an appropriate MLIP based on the system (see foundation-potentials.md). For cathode materials, MACE-MH-1 with matpes_r2scan head or CHGNet-MatPES-r2SCAN are recommended.

3. Relax Structures Using MCP Tools:

   Load the model and relax all three structures:

   # Load the model (example with MACE)
   mcp_mace_load_model(model_name="MACE-MH-1", task_name="matpes_r2scan")
   
   # Relax full structure
   mcp_mace_relax_structure(
       structure_data="LiFePO4.cif",
       output_dir="voltage_calc/full_relax"
   )
   
   # Relax empty structure
   mcp_mace_relax_structure(
       structure_data="FePO4.cif",
       output_dir="voltage_calc/empty_relax"
   )
   
   # Relax bulk metal
   mcp_mace_relax_structure(
       structure_data=".agents/skills/mat-intercalation-voltage/resources/Li_metal.cif",
       output_dir="voltage_calc/metal_relax"
   )
   

4. Extract Energies: From each relaxation output directory, extract:

   • E_full: Energy from full_relax/result.json
   • E_empty: Energy from empty_relax/result.json
   • E_metal: Energy from metal_relax/result.json
   • n_metal: Number of atoms in the relaxed metal structure
   • n_ions: Count difference of intercalating ions between full and empty structures