/Fcst_sys_public

To be added soon

Primary LanguagePython

A Forecasting System under the Multiverse ansatz via Machine Learning and Cheminformatics

Specific scope : Computational Time of DFT/TDDFT Calculations for this version

1. Catalogue

  • database :
    • DrugBank : DrugBank all-in-one sdf file, and the scripts for generating the training and the testing suits
    • polyfitted : Fitted ploynormal equations for selected 89 reference DFT functionals
    • rawdata : The assembled Gaussuian09-D.01 timing data, and the separated sdf files with added H atoms
    • trained-models : Trained models for few DFT functional/basis set combinations
  • example : The sample molecule to be predicted
  • src : source code folder
  • tools : Independent scripts
    • experimental : Some scripts in developing or experimental stage
  • TRmod_kernel_A1.py : Training script sample
  • Fcst_kernel_A1.py : Predicting script sample

2. Installation

  • Prerequisities
    • python3 with numpy, scipy, scikit-learn
    • pytorch, with CUDA, cudatoolkit, torchvision, dgl, gensim
    • basis_set_exchange, libxc
    • rdkit, openbabel
    • optional: xlsxwriter, pillow
  • Installation example (recommended with conda):
    • git clone git@github.com:yingjin-ma/Fcst_sys_public.git Fcst_sys_public
    • cd Fcst_sys_public
    • conda create -n Fcst_sys_public python=3.8 (3.7 is also tested)
    • conda activate Fcst_sys_public
    • conda install rdkit pytorch gensim torchvision numpy scipy xlsxwriter scikit-learn basis_set_exchange libxc matplotlib tqdm
      • Suggested installing order:
      • conda install rdkit
      • conda install pytorch=1.11.0=cuda112py38habe9d5a_1
      • conda install gensim torchvision numpy scipy xlsxwriter scikit-learn basis_set_exchange libxc matplotlib tqdm
    • install dgl cuda version (notice at least the major version should match that of installed cudatoolkit)
      • conda install -c dglteam dgl-cuda11.3
      • now: python TRmod_kernel_A1.py should work
    • Install the pylibxc (Please see https://www.tddft.org/programs/libxc/installation/)
      • now: python Fcst_kernel_A1.py should work

3. Usage

  • python TRmod_kernel_A1.py for training
  • python Fcst_kernel_A1.py for predicting
  • python Fcst_kernel_A1_LB_wrapper.py for load-balancing
    • The "Predicted_Loads.txt" will be generated for later usage
  • More will be added

4. Citation

5. Acknowledgement

  • National Key Research and Development Program of China (Grant No.2018YFB0203805)
  • National Natural Science Foundation of China (Grant No.21703260)
  • Informationization Program of the Chinese Academy of Science (Grant No.XXH13506-403)
  • Guangdong Provincial Key Laboratory of Biocomputing (Grant No.2016B030301007)

6. Corresponding authors