Not able to establish the enviroment for running the first python file

[qqlovekerry]

Hello,
I followed the instructions to create the environment,

1. I installed conda first
2. run conda env create -f environment.yml at the root folder.
3. run conda activate slitpore37 in the terminal
4. run pip3 install -e . to install the packages

But after all the steps, I still failed to run the first Python file to build the vapor and liquid box by using python GEMC_NVT_Psat_water_298K.py

I tried to import the packages in the terminal one by one and I found I was not able to import the Forcefield module of the foyer package. The following are the details.

Python 3.9.16 | packaged by conda-forge | (main, Feb  1 2023, 21:39:03) 
[GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

>>> import mbuild
/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/mdtraj/geometry/order.py:25: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  from pkg_resources import parse_version
/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
  declare_namespace(pkg)
/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
  declare_namespace(pkg)
>>> from foyer import Forcefield
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/foyer/__init__.py", line 2, in <module>
    from foyer.forcefield import Forcefield
  File "/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/foyer/forcefield.py", line 37, in <module>
    from foyer.atomtyper import find_atomtypes
  File "/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/foyer/atomtyper.py", line 6, in <module>
    from gmso import Topology
  File "/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/gmso/__init__.py", line 2, in <module>
    from .core.angle import Angle
  File "/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/gmso/core/angle.py", line 6, in <module>
    from gmso.abc.abstract_connection import Connection
  File "/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/gmso/abc/abstract_connection.py", line 5, in <module>
    from gmso.abc.abstract_site import Site
  File "/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/gmso/abc/abstract_site.py", line 10, in <module>
    from gmso.abc.gmso_base import GMSOBase
  File "/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/gmso/abc/gmso_base.py", line 8, in <module>
    from pydantic.validators import dict_validator
ImportError: cannot import name 'dict_validator' from 'pydantic.validators' (/storage/programs/miniconda3/envs/slitpore37/lib/python3.9/site-packages/pydantic/validators.py)

Could you please tell me how to solve this problem?

I also tried to use pip3 to install the packages and tried to run the Python file with the default Python executable. E.g. at the folder mosdef_slitpore/simulations/Psat_SPCE_298K/gomc/build_liq_vap_boxes I run /usr/bin/python3 GEMC_NVT_Psat_water_298K.py, but I got the following errors

/usr/lib/python3/dist-packages/apport/report.py:13: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses   import fnmatch, glob, traceback, errno, sys, atexit, locale, imp, stat
 
Traceback (most recent call last):
 
  File "GEMC_NVT_Psat_water_298K.py", line 2, in <module>
 
    from foyer import Forcefield
 
  File "/home/wenqiang/.local/lib/python3.6/site-packages/foyer/__init__.py", line 1, in <module>
 
    from foyer.forcefield import Forcefield
 
  File "/home/wenqiang/.local/lib/python3.6/site-packages/foyer/forcefield.py", line 14, in <module>
 
    import simtk.openmm.app.element as elem
 ModuleNotFoundError: No module named 'simtk.openmm'

Could you please help me with this problem? I am trying to run the Psat_SPCE_298K example and trying to get more values of vapor saturation pressure at different temperatures.

Any help would be greatly appreciated!