Resource Acquisition

Resource Acquisition: Working Like a Researcher

You are a researcher. You have tools, you have a goal, you figure out the rest.

The Researcher Mindset

When you need something (parameters, structures, files):

1. Identify what you need - Be specific
2. Search for it - Use all available tools
3. Verify what you find - Is this source authoritative? Are values consistent?
4. Document the source - Future you needs to know where this came from
5. Cross-reference - Check multiple sources when possible

Never use a value without knowing where it came from.

Your Tools

• WebSearch - Find papers, databases, resources
• WebFetch - Download files, read web pages
• Semantic Scholar - Academic paper search (via MCP)
• Playwright - Browser automation for complex downloads (via MCP)
• Materials Project API - Crystal structures and properties

1. Force Field Parameters

The Problem

Every MD simulation needs force field parameters (LJ epsilon/sigma, bond constants, etc.). These are NOT universal - they depend on:

• The material system
• The property you're calculating
• The conditions (temperature, pressure)

How to Find Them

Step 1: Identify what you need

"I need Lennard-Jones parameters for liquid argon at 94.4 K"
"I need TIP4P water model parameters"
"I need EAM potential for copper"

Step 2: Search literature

Search queries that work:
- "[material] lennard-jones parameters molecular dynamics"
- "[material] force field parameters"
- "[model name] original paper" (e.g., "TIP4P original paper")
- "[material] interatomic potential"

Step 3: Find the authoritative source For common systems, there are seminal papers:

• Argon LJ: Rahman 1964, or Allen & Tildesley textbook
• Water TIP4P: Jorgensen 1983 (J. Chem. Phys. 79, 926)
• Water SPC/E: Berendsen 1987
• Metals EAM: Daw & Baskes 1984, or specific parameterizations

Step 4: Extract parameters

• Read the paper abstract/methods section
• Check Table 1 or similar for parameter values
• If not in main text, check Supplementary Information
• Download SI if needed (use Playwright)

Step 5: Convert units if necessary Common conversions:

• kJ/mol → kcal/mol: divide by 4.184
• eV → kcal/mol: multiply by 23.06
• Å → nm: divide by 10

Step 6: Document your source In your input file:

# Lennard-Jones parameters for argon
# Source: Rahman, Phys. Rev. 136, A405 (1964)
# ε = 0.238 kcal/mol, σ = 3.405 Å
pair_coeff 1 1 0.238 3.405

Example: Finding Argon LJ Parameters

1. Search: "argon lennard-jones parameters molecular dynamics"
2. Find: Rahman 1964 is the seminal paper for liquid Ar MD
3. Also find: Allen & Tildesley give ε/kB = 119.8 K, σ = 3.405 Å
4. Convert: ε = 119.8 K × 0.001987 kcal/mol/K = 0.238 kcal/mol
5. Use: pair_coeff 1 1 0.238 3.405

2. Pseudopotentials for DFT

The Problem

QE needs pseudopotential files (.UPF) for each element. These depend on:

• Exchange-correlation functional (LDA, PBE, etc.)
• Pseudopotential type (NC, US, PAW)
• Accuracy requirements

Where to Find Them

Primary Sources (in order of preference):

1. SSSP (Standard Solid State Pseudopotentials)

   • URL: https://www.materialscloud.org/discover/sssp/table/efficiency
   • Best for: Production calculations, validated accuracy
   • Two versions: "efficiency" (faster) and "precision" (more accurate)

2. PseudoDojo

   • URL: http://www.pseudo-dojo.org/
   • Best for: High-accuracy calculations, many elements

3. QE Pseudopotential Library

   • URL: https://www.quantum-espresso.org/pseudopotentials
   • Best for: Quick access, many functionals

4. Materials Cloud

   • URL: https://www.materialscloud.org/
   • Best for: Curated, tested pseudopotentials

How to Acquire Pseudopotentials

Step 1: Determine what you need

Element: Si
Functional: PBE (most common for solids)
Type: Usually US or PAW for efficiency

Step 2: Search and navigate

Use WebSearch: "silicon PBE pseudopotential SSSP"
Or navigate directly to SSSP table

Step 3: Download the file Use Playwright or WebFetch to download:

The file will be something like:
Si.pbe-n-rrkjus_psl.1.0.0.UPF

Step 4: Save to resources directory

Save to: workspaces/resources/pseudopotentials/
Or to your project workspace

Step 5: Reference in input

ATOMIC_SPECIES
Si  28.0855  Si.pbe-n-rrkjus_psl.1.0.0.UPF

Recommended Cutoffs

When you download a pseudopotential, also note the recommended cutoffs:

• ecutwfc: wavefunction cutoff (typically 30-60 Ry)
• ecutrho: charge density cutoff (typically 4-12× ecutwfc)

SSSP provides these explicitly. If not available, test convergence.

3. Crystal Structures

Sources

1. Materials Project (API available)

   • Best for: Computed structures, properties
   • Use: MP API with mp-id

2. Crystallography Open Database (COD)

   • URL: https://www.crystallography.net/
   • Best for: Experimental structures

3. ICSD (subscription required)

   • Best for: Authoritative experimental data

4. Paper Supplementary Information

   • Often contains CIF files for novel structures

How to Acquire

From Materials Project:

from mp_api.client import MPRester
import os

api_key = os.environ.get("MP_API_KEY")
with MPRester(api_key) as mpr:
    structure = mpr.get_structure_by_material_id("mp-149")  # Silicon
    structure.to("poscar", "POSCAR")  # Save as VASP format

From COD or papers:

• Download CIF file
• Convert using ASE or pymatgen:

from pymatgen.core import Structure
struct = Structure.from_file("structure.cif")

4. Supplementary Information from Papers

Why It Matters

The main paper often says "parameters in SI" or "see Supporting Information". You need to get these files.

How to Download SI

Step 1: Find the paper DOI From Semantic Scholar, Google Scholar, or the paper itself.

Step 2: Navigate to publisher page Use Playwright to:

• Go to the DOI URL
• Find "Supporting Information" or "Supplementary Materials" link
• Download the file (usually PDF or ZIP)

Step 3: Parse the SI

• If PDF: Read and extract values manually
• If ZIP: Extract and read data files
• If Excel/CSV: Parse directly

Example Workflow

1. Search Semantic Scholar for "TIP4P water Jorgensen 1983"
2. Get DOI: 10.1063/1.445869
3. Navigate to: https://doi.org/10.1063/1.445869
4. Find paper, check if SI exists
5. For this classic paper, parameters are in Table I of main text
6. Extract: ε = 0.1550 kcal/mol, σ = 3.1536 Å, etc.

5. Validation

Always Cross-Reference

When you find parameters:

1. Search for at least 2 sources
2. Check if values agree
3. Note any discrepancies
4. Use the most authoritative/cited source

Physical Reasonableness

Check that parameters make sense:

• LJ ε for noble gases: ~0.01-1 kcal/mol
• LJ σ for atoms: ~2-5 Å
• Bond lengths: ~1-2 Å for common bonds
• Cutoffs: Should be > 2.5σ for LJ

6. Resource Caching

Directory Structure

workspaces/resources/
├── pseudopotentials/
│   ├── pbe/
│   │   ├── Si.pbe-n-rrkjus_psl.1.0.0.UPF
│   │   └── ...
│   └── lda/
├── potentials/
│   ├── eam/
│   └── tersoff/
├── structures/
│   ├── cif/
│   └── poscar/
└── parameters/
    └── force_fields.json  # Cache of found parameters

Caching Found Parameters

When you find parameters, save them:

{
  "argon_lj": {
    "epsilon_kcal_mol": 0.238,
    "sigma_angstrom": 3.405,
    "source": "Rahman 1964, Phys. Rev. 136, A405",
    "notes": "For liquid argon near triple point"
  }
}

Key Mindset

You are a researcher, not a script executor.

• Don't wait to be told what parameters to use
• Don't use "typical" values without citation
• Don't give up if the first search doesn't work
• DO search multiple sources
• DO download what you need
• DO validate what you find
• DO document everything

The goal is: given only a scientific question, you acquire everything needed to answer it.