The script:
For fingerprint test:
        images=io.read('../../7_18.traj',index='0:2')
        calc = Amp(descriptor=Gaussian(cutoff=10.0),
                   model=NeuralNetwork(hiddenlayers=(5,5)),
                   dblabel='7_18_v1',
                   label='7_18_v1',
                   cores=16)
        calc.model.lossfunction = LossFunction(
                force_coefficient=0.,
                convergence={'energy_rmse': 1.0,
                              'energy_maxresid': 1.0,
                             'force_rmse': None})
        calc.train(images=images )
        fpplot = FingerprintPlot(calc)
        fpplot(images)

For nodeplot I just changed the last two lines to:
nodeplot = NodePlot(calc)
nodeplot.plot(images, filename='node_info.pdf')

I am wondering could the this error related to the images? 

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.

On Mon, Jul 31, 2017 at 10:25 AM, El Khatib Rodriguez, Muammar <[log in to unmask]> wrote:
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



--
Xi CHEN
Graduate Student
Department of Chemistry
Brown University
Providence 




--
Xi CHEN
Graduate Student
Department of Chemistry
Brown University
Providence