Experience with autodE

autodE is a Python module designed for the automated calculation of reaction profiles from just SMILES strings of reactant(s) and product(s) by the Tom Young and the duarte group.(http://fduartegroup.org/)
I tried to run it on Hoffman2 for some weird TSs.

https://github.com/duartegroup/autodE

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Install

• anaconda3
  For Hoffman2 a user installed conda is needed due to the permission problem.
  Download the .sh file from the anaconda website. (https://www.anaconda.com/products/individual)
  install with bash *.sh. It will also write the .bashrc for initilization.

• autodE
  make a new environment with conda

  $ conda create -n autode
  $ conda activate autode

  Install autodE

  $ git clone https://github.com/duartegroup/autodE.git
  $ cd autodE
  $ conda config --append channels conda-forge --append channels omnia
  $ conda install --file requirements.txt
  $ python setup.py install

  run test (https://duartegroup.github.io/autodE/install.html#quick-test)

Job submission

• Using conda with the submission script requires initialization. Copy what’s in the .bashrc like this:

  # >>> conda initialize >>>
  # !! Contents within this block are managed by 'conda init' !!
  __conda_setup="$('~/bin/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
  if [ $? -eq 0 ]; then
      eval "$__conda_setup"
  else
      if [ -f "~/bin/anaconda3/etc/profile.d/conda.sh" ]; then
          . "~/bin/anaconda3/etc/profile.d/conda.sh"
      else
          export PATH="~/bin/anaconda3/bin:$PATH"
      fi
  fi
  unset __conda_setup
  # <<< conda initialize <<<

  Or just source a file containing these lines.

  and then activate

  conda activate autode

• load gaussian

  . /u/local/Modules/default/init/modules.sh
  module load gaussian/g16_sse4
  export GAUSS_SCRDIR=$TMPDIR

• load XTB

  source /u/home/${initial}/${USER}/bin/XTB/Config_xtb_env.bash

  Not necessary if xtb is installed with conda

• run autodE

  python input.py

Also notice that the submission script is strict with unix file format. Windows user can use doc2unix or :set ff=unix in vi to change the format.

Input Script

In version 1.0.0a2 Config.max_cores is set directly to %mem in the gaussian input. This leads to errors running on TaiYi and slow down the job on Hoffman2.