HTOCSP

This is a public repository that aims to automate the high-throughput organic crystals prediction by integrating various existing tools such as PyXtal, pyocse, RDKit, AmberTools, and CHARMM.

Python Setup

git clone this repository and then go to the root directory

conda install -c conda-forge mamba
mamba env create -n htocsp 
conda activate htocsp

If you want to update the existing ost enviroment

conda activate htocsp
mamba env update --file environment.yml

CHARMM Setup

One can request a free academic version of CHARMM and then install it via the following commands. Note, make sure you compile charmm with the simplest option with qchem, openmm, quantum and colfft.

$ ./configure --without-mpi --without-qchem --without-openmm --without-quantum --without-colfft -p ~/CHARMM
$ make -j 8
$ make install

After a few minutes, you should see the following messages

[  0%] Built target charmm_c
[ 99%] Built target charmm_fortran
[100%] Built target charmm_cxx
[100%] Built target charmm
Install the project...
-- Install configuration: "Release"
     Installing into $HOME/CHARMM
-- Up-to-date: $HOME/CHARMM/bin/charmm

Then add the path of charmm executable to your .bashrc file and source it.

export PATH=$HOME/CHARMM/bin:$PATH

To check if the installation is successful, go to /HTOCSP/tests/CHARMM and run the example:

$ charmm < charmm.in

                    NORMAL TERMINATION BY NORMAL STOP
                    MOST SEVERE WARNING WAS AT LEVEL  1

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     2.44  SECONDS
                         CPU TIME:     2.40  SECONDS

You should see quickly see the output of NORMAL TERMINATION.

Quick Test

After the environment is correctly setup, you can run the follow script directly from your terminal. This will quickly run 2 generations of sampling with a total of 8 structures.

from pyxtal.optimize import WFS
# Sampling
go = WFS(smiles="CC(=O)OC1=CC=CC=C1C(=O)O",
         wdir="apirin-quick",
         sg=[14],
         tag = 'aspirin',
         N_gen = 2,
         N_pop = 4,
         N_cpu = 1,
         ff_style = 'gaff',
        )
go.run()

The output should look like the following

Method    : Stochastic Width First Sampling
Generation:    2
Population:    4
Fraction  : 0.60 0.40 0.00

Generation 0 starts
  0  83 18.91  3.89 12.92 107.6 1 0 0.96 0.95 0.73   19.9   68.8    0.5 -111.4   -4.9   10.1 0     -85.745 Random  
  1  83  9.07 17.01  5.62  80.4 1 0 0.77 0.37 0.84   81.8   16.1  -56.3 -128.7   -4.1 -157.3 0     -87.927 Random  
  2  82  5.69 12.06 12.31  79.8 1 0 0.42 0.29 0.10   -5.6  -21.3  126.5  -65.3   -2.6  152.8 0     -88.225 Random  
  3  81 21.82  8.30  7.59  68.8 1 0 0.90 0.87 0.26 -102.3  -21.1 -147.9   90.1    0.0 -180.0 0    2500.000 Random  
Generation 0 finishes: 4 strucs
  0  82  5.69 12.06 12.31  79.8 1 0 0.42 0.29 0.10   -5.6  -21.3  126.5  -65.3   -2.6  152.8 0     -88.225 Random   Top
  0  83  9.07 17.01  5.62  80.4 1 0 0.77 0.37 0.84   81.8   16.1  -56.3 -128.7   -4.1 -157.3 0     -87.927 Random   Top
  0  83 18.91  3.89 12.92 107.6 1 0 0.96 0.95 0.73   19.9   68.8    0.5 -111.4   -4.9   10.1 0     -85.745 Random   Top
Gen  0 time usage:  47.7[Calc]   0.0[Proc]

Generation 1 starts
  0  83 13.54 10.84  7.54  50.4 1 0 0.40 0.97 0.19   86.8   14.8 -105.8  -90.0   -0.0  180.0 0    2500.000 Random  
  1  82 14.33  8.12  7.21  98.3 1 0 0.51 0.06 0.27   92.9   16.8    1.7  155.8    9.4  160.8 0     -82.825 Random  
  2  83 13.30  5.61 11.48  96.0 1 0 0.99 0.05 0.73  -17.7   34.3  132.6 -120.7  -16.8   18.5 0     -89.025 Mutation
  3  81 18.70  6.76 16.85 112.9 1 0 0.54 0.84 0.65  -61.9   62.4   -1.3   85.8    1.1    3.2 0     -77.307 Random  
Generation 1 finishes: 8 strucs
  1  83 13.30  5.61 11.48  96.0 1 0 0.99 0.05 0.73  -17.7   34.3  132.6 -120.7  -16.8   18.5 0     -89.025 Mutation Top
  1  82 14.33  8.12  7.21  98.3 1 0 0.51 0.06 0.27   92.9   16.8    1.7  155.8    9.4  160.8 0     -82.825 Random   Top
  1  81 18.70  6.76 16.85 112.9 1 0 0.54 0.84 0.65  -61.9   62.4   -1.3   85.8    1.1    3.2 0     -77.307 Random   Top
Gen  1 time usage:  44.2[Calc]   0.0[Proc]

In this example, the structure ended with 2500.000 means an invalid structure. Make sure you don't see all structures ends up with 2500.000.

Productive Examples

Please ref to the examples folder to run more productive examples.

Citation

Zhu Q, Hattori S. (2024). Automated High-throughput Organic Crystal Structure Prediction via Population-based Sampling

@misc{zhu2024-htocsp,
      title={Automated High-throughput Organic Crystal Structure Prediction via Population-based Sampling}, 
      author={Qiang Zhu and Shinnosuke Hattori},
      year={2024},
      eprint={2408.08843},
      archivePrefix={arXiv},
      primaryClass={cond-mat.mtrl-sci},
      doi={https://doi.org/10.48550/arXiv.2408.08843},
      url={https://arxiv.org/abs/2408.08843},
}

Contacts:

• Qiang Zhu ([email protected])
• Shinnosuke Hattori ([email protected])