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):

•Identify what you need - Be specific
•Search for it - Use all available tools
•Verify what you find - Is this source authoritative? Are values consistent?
•Document the source - Future you needs to know where this came from
•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

code

"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

code

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:

lammps

# 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

code

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):

•
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)
•
PseudoDojo
- •URL: http://www.pseudo-dojo.org/
- •Best for: High-accuracy calculations, many elements
•
QE Pseudopotential Library
- •URL: https://www.quantum-espresso.org/pseudopotentials
- •Best for: Quick access, many functionals
•
Materials Cloud
- •URL: https://www.materialscloud.org/
- •Best for: Curated, tested pseudopotentials

How to Acquire Pseudopotentials

Step 1: Determine what you need

code

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

Step 2: Search and navigate

code

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

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

code

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

Step 4: Save to resources directory

code

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

Step 5: Reference in input

fortran

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

•
Materials Project (API available)
- •Best for: Computed structures, properties
- •Use: MP API with mp-id
•
Crystallography Open Database (COD)
- •URL: https://www.crystallography.net/
- •Best for: Experimental structures
•
ICSD (subscription required)
- •Best for: Authoritative experimental data
•
Paper Supplementary Information
- •Often contains CIF files for novel structures

How to Acquire

From Materials Project:

python

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:

python

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

code

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:

•Search for at least 2 sources
•Check if values agree
•Note any discrepancies
•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

code

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:

json

{
  "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.