csp_pyxtal_dftb

Crytal structure prediction using PyXtal and DFTB+

Requirements

1. [Miniconda Python] (https://docs.conda.io/en/latest/miniconda.html)
2. [PyXtal] (https://github.com/qzhu2017/PyXtal)
3. [DFTB+] (https://dftbplus.org/)
4. [rdkit] (https://anaconda.org/rdkit/rdkit)
5. [ASE] (https://pypi.org/project/ase/)
6. [pymatgen] (https://anaconda.org/conda-forge/pymatgen)
7. [numpy] (https://anaconda.org/conda-forge/numpy)
8. [scipy] (https://anaconda.org/conda-forge/scipy)
9. [matplotlib] (https://anaconda.org/conda-forge/matplotlib)
10. [pandas] (https://anaconda.org/conda-forge/pandas)
11. [acpype] (https://anaconda.org/conda-forge/acpype)
12. [zipp] (https://anaconda.org/conda-forge/zipp)
13. [llvmlite] (https://anaconda.org/conda-forge/llvmlite)
14. [py3Dmol] (https://anaconda.org/conda-forge/py3Dmol)
15. [numba] (https://anaconda.org/conda-forge/numba)
16. [importlib-metadata] (https://anaconda.org/conda-forge/importlib-metadata)

Optional

1. [CP2K] (https://www.cp2k.org/)
2. [QuantumEspressso] (https://www.quantum-espresso.org/)
3. [Critic2] (https://aoterodelaroza.github.io/critic2/)

Installation of python envriromntent for csp_pyxtal_dftb

1. Install anaconda3 or miniconda3

2. Creaate python 3.10 virtual environment

$ conda create -n py310-molcryspred python=3.10
$ conda activate py310-molcryspred  
$ conda install -c conda-forge pyyaml openbabel rdkit ambertools lammps dftbplus qe cp2k ase pymatgen sssp  
$ pip install pyxtal  
$ pip install git+https://github.com/shirtsgroup/InterMol.git
$ pip install git+https://github.com/mkatouda/csp_pyxtal_dftb.git

How to run csp_pyxtal sample job

Crystal prediction of benzene

1. Get sample input files

$ git clon https://github.com/mkatouda/csp_pyxtal_dftb.git

2. Move working dirctory

$ cd .csp_pyxtal_dftb/tests/benzene  

3. Activate miniconda virtual environment

$ conda activate py310-molcryspred

4. Run python script csp_pyxtal_dftb.py with input yaml file (benzene.yml)

$ bash ./run.sh