125 lines
4.5 KiB
Markdown
125 lines
4.5 KiB
Markdown
---
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license: llama3.1
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base_model: meta-llama/Llama-3.1-8B-Instruct
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library_name: transformers
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pipeline_tag: text-generation
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language:
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- en
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tags:
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- chemistry
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- molecular-geometry
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- conformer-generation
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- smiles
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- z-matrix
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- geom
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- llama
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- axolotl
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- arxiv:2607.13350
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datasets:
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- GEOM
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---
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# Llama-3.1-8B-GeomLlama-zmatrix
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**Built with Llama. Built with Axolotl.**
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GeomLlama-zmatrix is a fine-tune of **Llama-3.1-8B-Instruct** that generates
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3D molecular conformer geometries directly from a SMILES string, emitting each
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structure as a **Fenske–Hall Z-matrix** (internal coordinates: bond length, bond
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angle, dihedral, referenced to previously placed atoms). It is one of two models
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from our paper; the companion model, [Llama-3.1-8B-GeomLlama-xyz](https://huggingface.co/THGLab/Llama-3.1-8B-GeomLlama-xyz),
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emits Cartesian XYZ coordinates instead.
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The model was trained jointly ("hybrid") on **GEOM-QM9** and **GEOM-Drugs**, so it
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covers both small molecules and larger drug-like molecules with a single set of
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weights.
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## Quick start
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The model was trained in the Alpaca instruction format. Reproduce the exact
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inference prompt used for the paper's numbers:
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```python
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import torch
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from transformers import AutoModelForCausalLM, AutoTokenizer
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model_id = "THGLab/Llama-3.1-8B-GeomLlama-zmatrix"
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tok = AutoTokenizer.from_pretrained(model_id)
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model = AutoModelForCausalLM.from_pretrained(model_id, torch_dtype=torch.bfloat16, device_map="auto")
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smiles = "Cc1cccc(CSc2nnnn2-c2ccccc2)c1"
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prompt = (
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"### Instruction:\n"
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"You can generate accurate molecular coordinates from a prompt "
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"containing a SMILES string.\n\n"
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"### Input:\n"
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"Generate a realistic equilibrium geometry for the molecule with the "
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f"following SMILES string in Fenske-Hall Z-matrix format: {smiles}\n\n"
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"### Response:\n"
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)
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inputs = tok(prompt, return_tensors="pt").to(model.device)
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out = model.generate(**inputs, max_new_tokens=3072, do_sample=True, temperature=1.0, top_p=0.95)
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print(tok.decode(out[0][inputs.input_ids.shape[1]:], skip_special_tokens=True))
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```
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Sample many completions per SMILES (each is one candidate conformer) to build a
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conformer ensemble. `T=1.0, top_p=0.95` and `T=1.2, top_p=0.95` are good defaults.
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### Output format
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Each line places one atom. The first token is the element; the remaining tokens
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are the internal coordinates relative to earlier atoms:
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```
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O 1 # atom 1: reference origin
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C 1 1.388 # atom 2: bonded to atom 1 at 1.388 Å
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H 2 1.090 1 105.769 # atom 3: bond to 2, angle to 1
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C 2 1.547 1 117.304 3 129.0 # atom 4: bond, angle, dihedral
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...
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```
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Atoms are emitted in an arbitrary order with **no atom labels or connectivity
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block** — the model learns geometry from the SMILES alone. Parse the Z-matrix back
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to Cartesian coordinates with a standard NeRF/internal-to-Cartesian routine.
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> View z-matrix or xyz coordinates easily at
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> [doublemolview.streamlit.app](https://doublemolview.streamlit.app).
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## Training
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- **Base:** meta-llama/Llama-3.1-8B-Instruct
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- **Framework:** [Axolotl](https://github.com/axolotl-ai-cloud/axolotl)
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- **Method:** LoRA (r = 32, α = 16, dropout 0.05, all linear layers), merged into the base weights
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- **Epochs:** 4 · **LR:** 3e-4, cosine · **Optimizer:** adamw_bnb_8bit
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- **Sequence length:** 4096, sample packing · **Precision:** bf16
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- **Data:** GEOM-QM9 + GEOM-Drugs, Fenske–Hall Z-matrix targets (`ori_fh`), plus the
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[Alpaca](https://huggingface.co/datasets/tatsu-lab/alpaca) instruction dataset for
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general-instruction rehearsal
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## Citation
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Paper: *How Well Can Frontier Large Language Models Generate Structures? High Quality
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Prediction of Molecular Geometries with Help from Fine-Tuning* —
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[arXiv:2607.13350](https://arxiv.org/abs/2607.13350). Please cite the paper and the
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underlying GEOM dataset (Axelrod & Gómez-Bombarelli, *Scientific Data*, 2022) if you
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use this model.
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```bibtex
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@misc{cavanagh2026geomllama,
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title = {How Well Can Frontier Large Language Models Generate Structures?
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High Quality Prediction of Molecular Geometries with Help from Fine-Tuning},
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author = {Cavanagh, Joseph M. and Arnold, Jonathan B. and Alteri, Giovanni Battista
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and Gritsevskiy, Andrew and Head-Gordon, Teresa},
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year = {2026},
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eprint = {2607.13350},
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archivePrefix = {arXiv},
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url = {https://arxiv.org/abs/2607.13350}
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}
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```
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## License
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Governed by the [Llama 3.1 Community License](https://github.com/meta-llama/llama-models/blob/main/models/llama3_1/LICENSE).
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By using this model you agree to its terms. Built with Llama.
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