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newns-anderson's Introduction

  • catchemi (link): A tool to compute energies from the Newns-Anderson model along with different orthogonalization schemes. See this paper for more details on the implementation and this paper for an application to single-atom alloys.
  • coeffnet (link): Predicting activation barriers through a chemically-interpretable, equivariant and physically constrained graph neural network. See this paper for details on implementation.
  • catmap (link): Implementation of the numbers-solver for solving a steady-state micro-kinetic model. See this paper for details about the implementation.
  • tpd-analyse (link): Implementation of a tool to analyse TPD spectra. See this paper for details about the implementation.
  • aiida-ase(link): AiiDA plugin for ASE.

newns-anderson's People

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newns-anderson's Issues

Missing requirements `adjustText` and `CatChemi`

You may wish to update your requirements.txt to the following, as it's missing the bottom two dependencies. After this, and noting that python-flint (a CatChemi dependency) can be installed with conda but not pip (see here), everything is good to go!

numpy
scipy
matplotlib
ase
PyYAML
mpmath
adjustText
git+https://github.com/sudarshanv01/CatChemi.git

Initial guess length mismatch when `eps_a` is of type `list`

When running run_model.py, I get the following traceback. It seems to be that the initial guess list has length 5, but when this is unpacked in CatChemi, it's expecting a length of 3. Changing EPS_A_VALUES to a List[float] rather than List[List[float]] resolves the issue, so it's just related to when one wants to use multiple values for eps_a for a given adsorbate.

Fitting parameters for adsorbate ['CO'] with eps_a [[-7, 2.5]]
Fitting parameters for adsorbate CO with eps_a [-7, 2.5]
Initial guess:  [0.01, 0.01, 1.8849555921538759, 1.8849555921538759, 0.1, 0.1]
Traceback (most recent call last):
  File "run_model.py", line 176, in <module>
    fitting_odr = odr.ODR(data, fitting_model, initial_guess)
  File "/home/arosen/anaconda3/envs/na/lib/python3.8/site-packages/scipy/odr/_odrpack.py", line 784, in __init__
    self._check()
  File "/home/arosen/anaconda3/envs/na/lib/python3.8/site-packages/scipy/odr/_odrpack.py", line 845, in _check
    res = self.model.fcn(*arglist)
  File "/home/arosen/anaconda3/envs/na/lib/python3.8/site-packages/catchemi/NewnsAndersonRepulsion.py", line 72, in fit_parameters
    alpha, beta, constant_offset = args
ValueError: too many values to unpack (expected 3)

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