Open GattiMh opened 10 months ago
Hello, I think you were doing it correctly. I can think of 2 reasons for the speed differences, mainly:
ANI2xt
and ANI2x
are generally faster, you can sepcify isomer_engine=ANI2xt
if you want to try one of them. Model | Elements Covered | Charge | Training Dataset Size | Target DFT | Input | Output |
---|---|---|---|---|---|---|
ANI2x | H, C, N, O, F, S, Cl | only neutral molecules | ~ 4.5M | ωB97X/6-31G* | elements, coordinates | energy, forces |
ANI2xt | H, C, N, O, F, S, Cl | only neutral molecules, with enhancement for tautomers | ~ 13M | B97-3c | elements, coordinates | energy, forces |
AIMNET | H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, I | both neutral and charged molecules | ~ 20 M | wB97M/Def2-TZVPP | elements, coordinates, molecular charge | energy, forces |
Please let me know if you have additional questions :-)
That's really useful, thanks. I think it's a matter of using GPUs then, probably those timelines are related to having GPU performance accounted. Maybe you should update the comment on the notebook? As it stands, it implies the CPU version will be very fast.
When running the thermodynamic_calculator
notebook, the first stage is fine generate low energy conformers
but the second part # Calculate thermodynamic properties with the 3D structures
I get this error:
0%| | 0/4 [00:00<?, ?it/s]
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[5], line 14
10 t = 298
11 return (id, t)
---> 14 out_thermo = calc_thermo(out, "AIMNET", get_mol_idx_t, opt_tol=0.003)
15 print(out_thermo)
File ~/mambaforge/envs/auto3d/lib/python3.12/site-packages/Auto3D/ASE/thermo.py:264, in calc_thermo(path, model_name, get_mol_idx_t, gpu_idx, opt_tol, opt_steps)
262 T = 298
263 else:
--> 264 idx, T = get_mol_idx_t(mol)
265 print(idx)
267 try:
Cell In[5], line 9, in get_mol_idx_t(mol)
8 def get_mol_idx_t(mol):
----> 9 id = mol.data["ID"]
10 t = 298
11 return (id, t)
AttributeError: 'Mol' object has no attribute 'data'
Change out_thermo = calc_thermo(out, "AIMNET", get_mol_idx_t, opt_tol=0.003)
to out_thermo = calc_thermo(out, "AIMNET", opt_tol=0.003)
will solve the problem.
Sorry that the examples are outdated. I already updated them :-)
Hello!
I'm working on M2 Mac and I had no issue with installation. Currently, testing your tutorial notebooks optimising the 4 smiles from the
smiles.smi
file provided.Upon running these lines:
The notebook mentions taking it less than 1 minute. In my case is quite slow and seems to take multiple minutes. Am I the only one that has these issue?
Many thanks