marsalekgroup / aml Goto Github PK

Dear AML Team,

I just want to use the aml to generate a NNP potential of water. When I used the script of "create-model.py" prepared in the examples, I encountered an issue like below:

Traceback (most recent call last):
File "/lustre1/u/u3004964/using_n2p2/aml-committee/water-cheng/create-model.py", line 35, in
n2p2.train(structures, n_epoch=2)
File "/lustre1/u/u3004964/software/aml/aml/mlp.py", line 206, in train
self._read_parameters(directories)
File "/lustre1/u/u3004964/software/aml/aml/mlp.py", line 160, in _read_parameters
model_parameters.append(self._read_output_train(directory))
File "/lustre1/u/u3004964/software/aml/aml/mlp.py", line 449, in _read_output_train
raise Exception(f'No weights file found for element: {element:s}')
Exception: No weights file found for element: O

I carefully prepared the input files (including input.data, input.nn and scaling,data) for training the NNP by using n2p2, and I also tested and found that it is correct if I directly run 'nnp-train' in the path of 'final-training/train-000'. Could you tell me what should I do for this issue? Many thanks.

I am also confused about the aml function, does aml can be sued to train the NNP potential? or we need to use the n2p2 to train and then use the aml to generate the C-NNP?

Cheers,
zezhu

Hello,
I was playing around with the example to run a Qbc for a system of mine. My energy and force files are in CP2K format, and when I run the run-Qbc.py it generates the RuNNer format file properly. However, when I look at the "eval_train" and "predict" folders, I can see that the values of energy and forces in the "input.data" file are zero. Would you please help me find out what could go wrong?

Thank you

Hello, I am trying to use the "score-all.py" to validate my trajectories but this error pops up
" ModuleNotFoundError: No module named 'mdtraj' "
I tried to replace the line " import mdtraj as mdt " with " from aml.io import mdtraj as mdt ", but then I get another error
"AttributeError: module 'aml.io.mdtraj' has no attribute 'load_frame' "
I was wondering if you could help me fix this issue.

Cheers
Mozhdeh

Hello,

I have been trying to run QbC jobs with AML, but have found that long jobs stop halfway through with no errors or logs explaining why.

I have yet to find the cause of this issue.

I was wondering if there is some way that I can continue an incomplete QbC job.

For example, the most recent job stopped at iteration 8 of 10. Is there some way that I can rerun the QbC for just the last 3 iterations?

Thanks,
Oliver