pablopiaggi / environmentfinder Goto Github PK

I am learning metadynamics and trying to use MTMB, as I need to use a custom lattice, I saw it is recommended to use environment finder for this method. I have followed the instruction to install environment finder. When I hit "environmentfinder", a broswer pops up and shows "Firefox can’t find the file at /tmp/tmpe3d8dkan.html.".

I also tried the jupyter one on https://mybinder.org/v2/gh/PabloPiaggi/EnvironmentFinder/master?urlpath=apps%2FApp.ipynb, and got "404 : Not Found". Did I make a mistake or the server is outdated?

Thanks!

The numbering of atoms starts from zero in the output environments in PDB format. This is incompatible with PLUMED according to the manual.

The part of the code that prints the PDB files uses ASE and therefore is not easy to change from the EnvironmentFinder. I submitted a pull request to ASE to start the numbering from one and it was merged into the master branch. Therefore when the ASE version is updated this bug will be solved.

Useful information about the unique environments should be printed.

• The degeneracy of each environment
• The average number of atoms in the environments

Hello,
Recently, I used anaconda3 to install environmentfinder but when I typed environmentfinder, nothing was open.
My installation method is
...
conda create --name env_finder python=3.8
conda activate env_finder
pip install environmentfinder
...
Successfully installed anyio-4.4.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 ase-3.22.1 asttokens-2.4.1 async-lru-2.0.4 attrs-23.2.0 babel-2.15.0 backcall-0.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 certifi-2024.7.4 cffi-1.16.0 charset-normalizer-3.3.2 comm-0.2.2 contourpy-1.1.1 cycler-0.12.1 debugpy-1.8.2 decorator-5.1.1 defusedxml-0.7.1 environmentfinder-1.1.6 exceptiongroup-1.2.2 executing-2.0.1 fastjsonschema-2.20.0 fonttools-4.53.1 fqdn-1.5.1 h11-0.14.0 httpcore-1.0.5 httpx-0.27.0 idna-3.7 importlib-metadata-8.0.0 importlib-resources-6.4.0 ipykernel-6.29.5 ipython-8.12.3 ipywidgets-8.1.3 isoduration-20.11.0 jedi-0.19.1 jinja2-3.1.4 json5-0.9.25 jsonpointer-3.0.0 jsonschema-4.23.0 jsonschema-specifications-2023.12.1 jupyter-client-8.6.2 jupyter-core-5.7.2 jupyter-events-0.10.0 jupyter-lsp-2.2.5 jupyter-server-2.14.2 jupyter-server-terminals-0.5.3 jupyterlab-4.2.4 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.3 jupyterlab-widgets-3.0.11 kiwisolver-1.4.5 markdown-3.6 markupsafe-2.1.5 matplotlib-3.7.5 matplotlib-inline-0.1.7 mistune-3.0.2 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nest-asyncio-1.6.0 nglview-3.1.2 notebook-7.2.1 notebook-shim-0.2.4 numpy-1.24.2 overrides-7.7.0 packaging-24.1 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 pickleshare-0.7.5 pillow-10.4.0 pkgutil-resolve-name-1.3.10 platformdirs-4.2.2 prometheus-client-0.20.0 prompt-toolkit-3.0.47 psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.2 pycparser-2.22 pygments-2.18.0 pyparsing-3.1.2 python-dateutil-2.9.0.post0 python-json-logger-2.0.7 pytz-2024.1 pyyaml-6.0.1 pyzmq-26.0.3 referencing-0.35.1 requests-2.32.3 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.19.0 scipy-1.10.1 send2trash-1.8.3 six-1.16.0 sniffio-1.3.1 soupsieve-2.5 stack-data-0.6.3 terminado-0.18.1 tinycss2-1.3.0 tomli-2.0.1 tornado-6.4.1 tqdm-4.66.4 traitlets-5.14.3 types-python-dateutil-2.9.0.20240316 typing-extensions-4.12.2 uri-template-1.3.0 urllib3-2.2.2 voila-0.5.7 wcwidth-0.2.13 webcolors-24.6.0 webencodings-0.5.1 websocket-client-1.8.0 websockets-12.0 widgetsnbextension-4.0.11 zipp-3.19.2

when I typed environmentfinder
/data/home/soft/anaconda3/envs/env_finder/lib/python3.8/site-packages/traitlets/traitlets.py:3541: DeprecationWarning: --VoilaConfiguration.file_whitelist=['.*download.zip'] for containers is deprecated in traitlets 5.0. You can pass --VoilaConfiguration.file_whitelist item ... multiple times to add items to a list.
warn(
/data/home/soft/anaconda3/envs/env_finder/lib/python3.8/site-packages/traitlets/traitlets.py:1241: DeprecationWarning: Deprecated, use VoilaConfiguration.file_allowlist instead.
return self.func(*args, **kwargs)
[Voila] Using /tmp to store connection files
[Voila] Storing connection files in /tmp/voila_08y9rb6i.
[Voila] Serving static files from /data/home/yc37810/soft/anaconda3/envs/env_finder/lib/python3.8/site-packages/voila/static.
[Voila] Voilà is running at:
http://localhost:8866/
START /usr/bin/geany "/tmp/tmp3s5hmxv2.html"
MoTTY X11 proxy: Authorisation not recognised

In case you are trying to start a graphical application with "sudo", read this article in order to avoid this issue:
https://blog.mobatek.net/post/how-to-keep-X11-display-after-su-or-sudo/

Geany: cannot open display

xdg-open: no method available for opening 'file:///tmp/tmp3s5hmxv2.html'

Did I make a mistake during the installation process? Thank you for your help.

Setup regression tests to make the code robust against different versions of python (e.g., 3.8 to 3.11), numpy, and ase.

Testing appmode, voila, ipywidgets, and nglview may be harder.