Error in running Python file using ASE library

Question

I am trying to run a Python script using ASE library, I have installed ASE using this page and run my Python script using this library on my terminal. I have made a virtual env named 'MLC_env' and have already installed the ASE library there.

Python script

from ase import Atoms
atoms = Atoms('N2')
print(atoms.positions)

Error: While trying to run the above python script

(MLC_env) (base) anshumansinha@Anshumans-MacBook-Pro-3 Q1 % python3 struct.py
Traceback (most recent call last):
  File "/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/numpy/compat/py3k.py", line 24, in <module>
    import pickle5 as pickle
  File "/Users/anshumansinha/.local/lib/python3.10/site-packages/pickle5/__init__.py", line 1, in <module>
    from .pickle import *
  File "/Users/anshumansinha/.local/lib/python3.10/site-packages/pickle5/pickle.py", line 33, in <module>
    from struct import pack, unpack
  File "/Users/anshumansinha/Desktop/MLC/HW1/Q1/struct.py", line 1, in <module>
    from ase import Atoms
ImportError: cannot import name 'Atoms' from partially initialized module 'ase' (most likely due to a circular import) (/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/ase/__init__.py)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/numpy/core/__init__.py", line 23, in <module>
    from . import multiarray
  File "/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/numpy/core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/numpy/core/overrides.py", line 8, in <module>
    from numpy.compat._inspect import getargspec
  File "/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/numpy/compat/__init__.py", line 12, in <module>
    from . import py3k
  File "/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/numpy/compat/py3k.py", line 26, in <module>
    import pickle
  File "/Users/anshumansinha/miniforge3/lib/python3.10/pickle.py", line 33, in <module>
    from struct import pack, unpack
  File "/Users/anshumansinha/Desktop/MLC/HW1/Q1/struct.py", line 1, in <module>
    from ase import Atoms
ImportError: cannot import name 'Atoms' from partially initialized module 'ase' (most likely due to a circular import) (/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/ase/__init__.py)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/anshumansinha/Desktop/MLC/HW1/Q1/struct.py", line 1, in <module>
    from ase import Atoms
  File "/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/ase/__init__.py", line 17, in <module>
    from ase.atom import Atom
  File "/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/ase/atom.py", line 3, in <module>
    import numpy as np
  File "/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/numpy/__init__.py", line 141, in <module>
    from . import core
  File "/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/numpy/core/__init__.py", line 49, in <module>
    raise ImportError(msg)
ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.10 from "/Users/anshumansinha/Desktop/MLC/MLC_env/bin/python3"
  * The NumPy version is: "1.24.1"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: cannot import name 'Atoms' from partially initialized module 'ase' (most likely due to a circular import) (/Users/anshumansinha/Desktop/MLC/MLC_env/lib/python3.10/site-packages/ase/__init__.py)

Answer 1

There are few issues here:

You have been calling the constructor to the atom object wrong: If you refer to the ASE manual, and go to Atoms object section, you will see that you need to explicitly set the positions for the atoms in the molecule that you are creating. Consider the example of creating a carbon-monoxide molecule, you will do it as follows:

from ase import Atoms 
d = 1.1 
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)])

The error message in your case is trying to say that you have not set the positions for the atoms, but is then trying to access that property (which the system does not have)

Editing the answer to address the comment by Cavenfish:

Following the link in the error message, it seems that the issue is with the installation of ase. I tried installing ase in a virtualenv using two methods

1. Normal pip install --upgrade --user ase, and
2. pip install --upgrade git+https://gitlab.com/ase/ase.git@master

In the first method, the installation completed, but had errors with the dependencies, particularly numpy. Using the second method, I was able to install and use ase without any issues.

Thus it seems that OP might have used the first method, and inadvertently had some issues with the dependencies.