Llama-3.1-8B-GeomLlama-zmat-QM9-Large

Llama-3.1-8B-GeomLlama-zmat-QM9-Large

Built with Llama. Built with Axolotl.

GeomLlama-zmat-QM9-Large is a fine-tune of Llama-3.1-8B-Instruct that generates 3D molecular conformer geometries directly from a SMILES string, emitting each structure as a Fenske–Hall Z-matrix (internal coordinates: bond length, bond angle, dihedral, referenced to previously placed atoms).

Unlike the jointly-trained "hybrid" GeomLlama models (zmatrix, xyz), this is a specialized model trained on GEOM-QM9 alone, focusing it on small-molecule (QM9-scale) geometries. It is one of a family of four specialized models (Fenske–Hall Z-matrix or Cartesian XYZ, on GEOM-QM9 or GEOM-Drugs-Large); the others are:

• Llama-3.1-8B-GeomLlama-xyz-QM9-Large
• Llama-3.1-8B-GeomLlama-zmat-Drugs-Large
• Llama-3.1-8B-GeomLlama-xyz-Drugs-Large

Quick start

The model was trained in the Alpaca instruction format. Reproduce the exact inference prompt used for the paper's numbers:

import torch
from transformers import AutoModelForCausalLM, AutoTokenizer

model_id = "THGLab/Llama-3.1-8B-GeomLlama-zmat-QM9-Large"
tok = AutoTokenizer.from_pretrained(model_id)
model = AutoModelForCausalLM.from_pretrained(model_id, torch_dtype=torch.bfloat16, device_map="auto")

smiles = "Cc1cccc(CSc2nnnn2-c2ccccc2)c1"
prompt = (
    "### Instruction:\n"
    "You can generate accurate molecular coordinates from a prompt "
    "containing a SMILES string.\n\n"
    "### Input:\n"
    "Generate a realistic equilibrium geometry for the molecule with the "
    f"following SMILES string in Fenske-Hall Z-matrix format: {smiles}\n\n"
    "### Response:\n"
)

inputs = tok(prompt, return_tensors="pt").to(model.device)
out = model.generate(**inputs, max_new_tokens=3072, do_sample=True, temperature=1.0, top_p=0.95)
print(tok.decode(out[0][inputs.input_ids.shape[1]:], skip_special_tokens=True))

Sample many completions per SMILES (each is one candidate conformer) to build a conformer ensemble. T=1.0, top_p=0.95 and T=1.2, top_p=0.95 are good defaults.

Output format

Each line places one atom. The first token is the element; the remaining tokens are the internal coordinates relative to earlier atoms:

O 1                          # atom 1: reference origin
C 1 1.388                    # atom 2: bonded to atom 1 at 1.388 Å
H 2 1.090 1 105.769          # atom 3: bond to 2, angle to 1
C 2 1.547 1 117.304 3 129.0  # atom 4: bond, angle, dihedral
...

Atoms are emitted in an arbitrary order with no atom labels or connectivity block — the model learns geometry from the SMILES alone. Parse the Z-matrix back to Cartesian coordinates with a standard NeRF/internal-to-Cartesian routine.

View z-matrix or xyz coordinates easily at doublemolview.streamlit.app.

Training

• Base: meta-llama/Llama-3.1-8B-Instruct
• Framework: Axolotl
• Method: LoRA (r = 32, α = 16, dropout 0.05, all linear layers), merged into the base weights
• Epochs: 4 · LR: 3e-4, cosine · Optimizer: adamw_bnb_8bit
• Sequence length: 4096, sample packing · Precision: bf16
• Data: the full GEOM-QM9 split (with hydrogens), Fenske–Hall Z-matrix targets (ori_fh), plus a ~393k-example subset of the Tulu-3 SFT mixture for general-instruction rehearsal

Citation

Paper: How Well Can Frontier Large Language Models Generate Structures? High Quality Prediction of Molecular Geometries with Help from Fine-Tuning — arXiv:2607.13350. Please cite the paper and the underlying GEOM dataset (Axelrod & Gómez-Bombarelli, Scientific Data, 2022) if you use this model.

@misc{cavanagh2026geomllama,
  title         = {How Well Can Frontier Large Language Models Generate Structures?
                   High Quality Prediction of Molecular Geometries with Help from Fine-Tuning},
  author        = {Cavanagh, Joseph M. and Arnold, Jonathan B. and Alteri, Giovanni Battista
                   and Gritsevskiy, Andrew and Head-Gordon, Teresa},
  year          = {2026},
  eprint        = {2607.13350},
  archivePrefix = {arXiv},
  url           = {https://arxiv.org/abs/2607.13350}
}

License

Governed by the Llama 3.1 Community License. By using this model you agree to its terms. Built with Llama.