Installation of TurboGenius

The following is an instruction to install TurboGenius. If you have any problem on the installation, please visit TurboGenius Discussions and please post your problem.

Prerequisites

Before installing the packages, ensure you have the following prerequisites:

TurboRVB
Python 3.8 or later
Conda (optional, recommended for Python environment management)

TurboGenius also depends on the following Python packages, which will be automatically installed during the installation process:

numpy (version 1.x)
pandas
matplotlib
trexio
trexio-tools
basis-set-exchange
ase
pymatgen
click
tqdm
psutil
pytest (for developers)
setuptools_scm (for developers)

To run the tutorials, the users also need to install the following software:

PySCF

Installation procedure

Let’s make a conda environment to install turbogenius (if you prefer)

% conda create -n turborvb python=3.8
% conda activate turborvb

Please download the source codes from the GitHub repository.

% cd ~/applications
% git clone https://github.com/kousuke-nakano/turbogenius.git

Let’s install turbogenius via pip

% cd turbogenius
% pip install -e .    # Install in development mode

Test if it works.

% turbogenius --help

If you see the help output, TurboGenius has been successfully installed!

Troubleshooting

Common issues and solutions:

If the help output is not shown, and the following error messages are produced instead:

$ turbogenius --help
Traceback (most recent call last):
  File "/envs/turborvb/lib/python3.11/site-packages/turbogenius/pyturbo/utils/env.py", line 46, in <module>
    os.path.dirname(subprocess.check_output(cmd, shell=True, env=sys_env))
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/envs/turborvb/lib/python3.11/subprocess.py", line 466, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/envs/turborvb/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'which readalles.x' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/envs/turborvb/bin/turbogenius", line 3, in <module>
    from turbogenius.turbo_genius_cli import cli
  File "/envs/turborvb/lib/python3.11/site-packages/turbogenius/__init__.py", line 11, in <module>
    from . import *
  File "/envs/turborvb/lib/python3.11/site-packages/turbogenius/correlated_sampling_genius.py", line 21, in <module>
    from turbogenius.pyturbo.vmc import VMC
  File "/envs/turborvb/lib/python3.11/site-packages/turbogenius/pyturbo/__init__.py", line 10, in <module>
    from . import *
  File "/envs/turborvb/lib/python3.11/site-packages/turbogenius/pyturbo/lrdmc.py", line 20, in <module>
    from turbogenius.pyturbo.namelist import Namelist
  File "/envs/turborvb/lib/python3.11/site-packages/turbogenius/pyturbo/namelist.py", line 23, in <module>
    from turbogenius.pyturbo.utils.utility import get_str_variable_type_auto
  File "/envs/turborvb/lib/python3.11/site-packages/turbogenius/pyturbo/utils/utility.py", line 29, in <module>
    from .env import pyturbo_root
  File "/envs/turborvb/lib/python3.11/site-packages/turbogenius/pyturbo/utils/env.py", line 50, in <module>
    raise ValueError(
ValueError: Set TURBORVB_ROOT (e.g., export TURBORVB_ROOT=XXX in ~.bashrc)

it occurs when TurboRVB is not installed or the executables of TurboRVB are not included in the command search paths. Please make sure that you have installed TurboRVB following the inststruction turborvb_installation. Then, add the directory to the PATH environment variable where the TurboRVB executables are installed, or set it to TURBORVB_ROOT as shown in the error message.

Python environment issues

If you have problems with the Python environment:
- Ensure you’re using the correct Python version
- Try creating a fresh conda environment
- Check that pip is up to date: pip install --upgrade pip

For additional help, please visit the discussion forums linked above or open an issue on the respective GitHub repositories.