ValueError: Expected 2D array, got 1D array instead: #62
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I think asap was not able to find the computed descriptors that match the pattern SOAP*. Can you try: |
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Same error occurs: |
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Can you check the asapdesc.xyz to see if the descriptors are there?
…On Tue, May 14, 2024 at 8:38 PM BIAN Tieyuan ***@***.***> wrote:
Same error occurs:
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.
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And does the xyz file contains multiple frames? If it only has one frame it
doesn’t make sense to do pca on global descriptors.
…On Tue, May 14, 2024 at 8:40 PM Bingqing Cheng ***@***.***> wrote:
Can you check the asapdesc.xyz to see if the descriptors are there?
On Tue, May 14, 2024 at 8:38 PM BIAN Tieyuan ***@***.***>
wrote:
> Same error occurs:
> 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.
>
> —
> Reply to this email directly, view it on GitHub
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> or unsubscribe
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I think ASAP.desc.xyz has descriptors part |
Yes it has multiple frames. It shows 728 frames after loading it into OVITO. |
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I am having the same problem... |
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That's strange. I never had this problem.
Can you send a few frames of your xyz so I can test?
…On Fri, May 17, 2024 at 10:53 PM Yingze Wang ***@***.***> wrote:
I am having the same problem...
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test.zip |
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asap works. I used:
asap map -f ASAP-desc.xyz -dm '[*]' pca
The issue was that if you specify using energy to color the points (-c
energy), but the xyz file doesn't contain energy information, asap raises
an error:
Traceback (most recent call last):
File
"/Users/tc/miniconda3/envs/asap/lib/python3.8/site-packages/asaplib/data/xyz.py",
line 542, in get_property
y_all.append(frame.info[y_key])
KeyError: 'energy'
…On Sun, May 19, 2024 at 12:05 AM Tieyuan BIAN ***@***.***> wrote:
test.zip <https://github.com/BingqingCheng/ASAP/files/15368457/test.zip>
Here is a .exyz file containing 31 frames. Thanks!
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It is very strange that I used the same command |
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If you remove the single quotation marks, i.e. use
asap map -f ASAP-desc.xyz -dm [*] pca
does it work?
…On Sun, May 19, 2024 at 10:58 PM Tieyuan BIAN ***@***.***> wrote:
It is very strange that I used the same command asap map -f ASAP-desc.xyz
-dm '[*]' pca but still has error
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.
I installed asaplib by pip install asaplib.
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Still same error. I paste the whole error message here: (MDA2) [polyucmp@localhost 282ab895-d12b-4248-8357-261397bf73a6]$ asap map -f ASAP-desc.xyz -dm [*] pca
load xyz file: ASAP-desc.xyz , a total of 31 frames , a total of 10360 atoms , with elements: [1, 6, 7, 53, 82] .
Find the following descriptor names that match the specifications: ['SOAP-n4-l3-c3.9-g0.48']
Cannot find the specified descriptors from xyz
0
Remove raw desciptors..
removing the global descriptors from output xyz with the names: ['SOAP-n4-l3-c3.9-g0.48']
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 "/run/media/polyucmp/282ab895-d12b-4248-8357-261397bf73a6/software/anaconda3/envs/MDA2/bin/asap", line 8, in <module>
sys.exit(asap())
...
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. |
First I generate descriptors using
asap gen_desc -f train.xyz soapThen I tried to plot PCA map using
asap map -f ASAP-desc.xyz -dm '[SOAP*]' -c energy pca. But it raise an error: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.Did I miss something? I noticed that in ./examples/ice-phases there is a file named ice-properties.dat. Should I generate this file?
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