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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 10:52:53 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (46 lines)

On Mon, Jul 31, 2017 at 10:47 AM, Chen, Xi <[log in to unmask]> wrote:
> Yes. That's where I got my initial try. But, When I change the descriptor
> for the different element, the amp does not start to train.
> For example,  I keep the descriptor for 'H' unchanged as default and delete
> some vector for 'C', after the amp interprete the fingerprints it hang
> there,
> and the error file, it shows:
>
>  Step                Time   Loss (SSD)   EnergyRMSE     MaxResid
> ===== =================== ============ ============ ============
> Traceback (most recent call last):
>   File "/gpfs/runtime/opt/python/2.7.3/lib/python2.7/runpy.py", line 162, in
> _run_module_as_main
>     "__main__", fname, loader, pkg_name)
>   File "/gpfs/runtime/opt/python/2.7.3/lib/python2.7/runpy.py", line 72, in
> _run_code
>     exec code in run_globals
>   File "/gpfs_home/xc13/amp/amp/model/__main__.py", line 113, in <module>
>     lossprime=lossprime)
>   File "/users/xc13/amp/amp/model/__init__.py", line 517, in get_loss
>     self._send_data_to_fortran()
>   File "/users/xc13/amp/amp/model/__init__.py", line 475, in
> _send_data_to_fortran
>     self.d)
>   File "/users/xc13/amp/amp/model/__init__.py", line 1083, in
> send_data_to_fortran
>     _fmodules.fingerprint_props.raveled_fingerprints = raveled_fingerprints
> ValueError: setting an array element with a sequence.
>
>

I think I understand now the problem. Probably the
`make_default_symmetry_functions()` method _is only called_ by the
Gaussian descriptor class if Gs=None, otherwise it will assume that
all elements want to have a custom set of symmetry functions that are
fed by Gs?.


-- 
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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