a possible bug in hb2skf.py #32
Description
Hi
I am using the hb2skf.py code to convert the hotbit parameter to the skf file.
Here is the procedure:
1. I went to the example folder AuAu_parametrization
2. I renamed the Au_Au_repulsion.par file to Au_Au.par
3. then I copied the hb2skf.py from the source code to the current example folder AuAu_parametrization
4. run the python code by 'python hb2skf.py Au Au'
Then I encountered an error like this:
Fitting a spline basis function in the range between 0.494382851691 and 0.594382851691
DEBUG t=[0.49438285 0.51438285 0.53438285 0.55438285 0.57438285 0.59438285]
DEBUG start=0.494382851691
Traceback (most recent call last):
File "hb2skf.py", line 276, in <module>
generate_DFTBplus_repulsion(tmp,
File "hb2skf.py", line 129, in generate_DFTBplus_repulsion
splParams, fitCovariances = curve_fit(splinefit, [t, start], data)
File "/u/home/g/gengsun/anaconda3/lib/python3.8/site-packages/scipy/optimize/minpack.py", line 742, in curve_fit
xdata = np.asarray_chkfinite(xdata, float)
File "/u/home/g/gengsun/anaconda3/lib/python3.8/site-packages/numpy/lib/function_base.py", line 486, in asarray_chkfinite
a = asarray(a, dtype=dtype, order=order)
File "/u/home/g/gengsun/anaconda3/lib/python3.8/site-packages/numpy/core/_asarray.py", line 102, in asarray
return array(a, dtype, copy=False, order=order)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part.
In which, I modified the hb2skf.py to print the two lines starting with DEBUG.
It seems that the curve_fit function complains about the input [t, start]. 't' is a numpy array, but 'start' is a float. This is a little bit strange to me.
Is there anything wrong in my usage of the code? or is this a bug?
Thanks.
Best,
Geng