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AMP-USERS  July 2017

AMP-USERS July 2017

Subject:

Re: Amp "NodePlot" function and Gaussian descriptor

From:

"El Khatib Rodriguez, Muammar" <[log in to unmask]>

Reply-To:

Amp Users List <[log in to unmask]>

Date:

Mon, 31 Jul 2017 10:25:21 -0400

Content-Type:

text/plain

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Parts/Attachments

text/plain (47 lines)

On Mon, Jul 31, 2017 at 9:56 AM, Chen, Xi <[log in to unmask]> wrote:
> Hello all,
>
> I am using Amp Gaussian training for a potential surface for a gas phase
> combination reaction (with 'C' and 'H' two elements).
> However, when I try to test different parameters in the gaussian descriptor
> and visualize, I came through some problems.
>
> 1. For some reason, I can only plot the node information ('NodePlot'
> fucntion)  for 'H' element, when the code start to plot "C" element, it
> always gave me the following error while calling 'violinplot' function:
> ------------------------------------------------
>   File
> "/gpfs/runtime/opt/python/2.7.3/lib/python2.7/site-packages/numpy/linalg/linalg.py",
> line 90, in _raise_linalgerror_singular
>     raise LinAlgError("Singular matrix")
> numpy.linalg.linalg.LinAlgError: Singular matrix
> --------------------------------------------------
> I also came through the same problem when I using the 'FingerprintPlot'
> function. Tried less images (using 2 images), got the same error.
> I am wondering have you ever came through this problem and know why this
> happens and fix it?
>
> 2. Gaussian descriptor can be specified by:
> calc = Amp(descriptor = Gaussian(Gs = Gs)).(Gs is the dictionary)
>
> For the customized Gs, could we have a different number of Gaussian feature
> subvectors for different elements? More broadly, I am wondering is there any
> rules that I should stick to when I manipulate the descriptor?
>

I haven't stumbled upon the problem you described on 1. But, regarding
your second question, you may take a look at this page in Amp's
documentation: http://amp.readthedocs.io/en/latest/gaussian.html.
There you will find an example on how you may add more elements to
your fingerprint vectors.

Best,

-- 
Muammar W El Khatib Rodriguez
Postdoctoral Research Associate
Brown University School of Engineering
184 Hope Street
Providence, RI, 02912, USA
http://brown.edu/go/catalyst

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