Skip to content

not worked example #63

@katkoffff

Description

@katkoffff

with the command 'asap gen_desc -f sps_all.xyz -p B-RSS soap' you can generate a file B-RSS.xyz
then we run the command: 'asap map -f B-RSS.xyz -dm '[*]' -nbs pca' and a message pops up:
load xyz file: B-RSS.xyz , a total of 5038 frames , a total of 97554 atoms , with elements: [5] .
Find the following descriptor names that match the specifications: ['SOAP-n4-l3-c2.4-g0.3']
Cannot find the specified descriptors from xyz
0
Remove raw desciptors..
removing the global descriptors from output xyz with the names: ['SOAP-n4-l3-c2.4-g0.3']
removing the atomic descriptors from output xyz with the names: []
Perform standard scaling of the design matrix. To turn it off use --no-scale
Using PCA ...
Start PCA for a design matrix with shape (0,)
Traceback (most recent call last):
File "", line 198, in _run_module_as_main
File "", line 88, in run_code
File "C:\ProgramData\miniconda3\envs\asap\Scripts\asap.exe_main
.py", line 7, in
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\click\core.py", line 1161, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\click\core.py", line 1082, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\click\core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\click\core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\click\core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\click\core.py", line 788, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\click\decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\asaplib\cli\cmd_asap.py", line 577, in pca
map_process(ctx.obj, reduce_dict, axes, map_name)
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\asaplib\cli\func_asap.py", line 137, in map_process
proj = dreducer.fit_transform(obj['design_matrix'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\asaplib\reducedim\dim_reducer.py", line 123, in fit_transform
X = self.engines[element].fit_transform(X)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\asaplib\reducedim\ml_pca.py", line 132, in fit_transform
self.fit(desc)
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\asaplib\reducedim\ml_pca.py", line 75, in fit
C_desc = self.scalecenter_matrix(desc)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\asaplib\reducedim\ml_pca.py", line 47, in scalecenter_matrix
print(self.scaler.fit(desc))
^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\sklearn\preprocessing_data.py", line 894, in fit
return self.partial_fit(X, y, sample_weight)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\sklearn\base.py", line 1389, in wrapper
return fit_method(estimator, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\sklearn\preprocessing_data.py", line 930, in partial_fit
X = validate_data(
^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\sklearn\utils\validation.py", line 2944, in validate_data
out = check_array(X, input_name="X", **check_params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\miniconda3\envs\asap\Lib\site-packages\sklearn\utils\validation.py", line 1093, in check_array
raise ValueError(msg)
ValueError: Expected 2D array, got 1D array instead:
array=[].
Reshape your data either using array.reshape(-1, 1) if your data has a single feature or array.reshape(1, -1) if it contains a single sample.

that is, apparently, descriptors are not being read. How can this problem be fixed?

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions