Nanocar Builder - Avogadro 2 Plug-in

Nanocar Builder for Avogadro 2

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Installation


Mac OS X

1. Install Avogadro 2

2. Configure the Python environment

3. Set the Python environment

We need to help Avogadro find our Python environment. While the nanocar environment is activated type

which python

and copy the path which should look like /usr/local/miniconda3/envs/nanocar/bin/python.

Open Avogadro and go to Quantum -> Input Generators -> Set Python Path. Paste this path here. Now Avogadro knows which Python to use for our plug-in!

4. Install the Nanocar builder plug-in

Lastly, we need to install our plug-in. For Mac, the plug-ins directory will be present at Applications -> Avogadro2.app -> Contents -> lib -> avogadro2 -> scripts. Copy the path for this directory which should look like /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts. Enter the nanocar-avogadro repository and run the installer Python script:

python install_plugin.py /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts

Congratulations! Now you should see the Nanocar option under Build in Avogadro.

Last tested: March 28, 2019 on MacOS Mojave 10.14.2 (18C54)


Linux

1. Install Avogadro 2

First build Avogadro 2 from the openchemistry supermodule.

git clone --recursive https://github.com/OpenChemistry/openchemistry.git
mkdir openchemistry-build
cd openchemistry-build
cmake ../openchemistry
cmake --build . --config Release

More build and updating instructions can be found here.

2. Configure the Python environment

3. Set the Python environment

We need to help Avogadro find our Python environment. While the nanocar environment is activated type

which python

and copy the path which should look something like /home/<username>/miniconda3/envs/nanocar/bin/python.

Open Avogadro and go to Quantum -> Input Generators -> Set Python Path. Paste this path here. Now Avogadro knows which Python to use for our plug-in!

4. Install the Nanocar builder plug-in

Lastly, we need to install our plug-in. For linux the plug-ins directory should be under /home/<username>/.local/share/OpenChemistry/Avogadro where <username> is your username. Copy that path and run the Python installer:

python install_plugin.py /home/<username>/.local/share/OpenChemistry/Avogadro

Congratulations! Now you should see the Nanocar option under Build in Avogadro.

Last tested: Oct 8, 2018 on Ubuntu 16.08


Configuring the Python environment

  1. Install miniconda for Python >= 3.6 here.

  2. Create a new environment in conda.
    conda create -n nanocar python=3.6
    

    Activate the environment:

    conda activate nanocar
    

    Depending on your conda installation / system you might need to use:

    source activate nanocar
    
  3. Clone the nanocar-avogadro repository:
    git clone https://github.com/kbsezginel/nanocar-avogadro.git
    cd nanocar-avogadro
    
  4. Install requirements:
    pip install -r requirements.txt
    

Notes

If you are planning to use other plug-ins make sure to install their dependencies to the same Python environment. Currently, Avogadro uses the same Python environment for all the plug-ins.

For debugging purposes you can run Avogadro from the command line:

Depending on your Avogadro version the plug-in directory might be different. When you run Avogadro from the command line, it will print the directories it’s checking for scripts. If you see Checking for "commands" scripts instead of Checking for "workflows" scripts then you need to run the installation script as:

python install_plugin.py /path/to/avogadro/plugin/directory --subfolder commands