nileshjchoudhary / genstride Goto Github PK

## Contributors: Ryan DeFever, Colin Targonski, Steven Hall 
## Sarupria Research Group, Smith Research Group
## Clemson University
## 2019 Jun 22

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## REQUIREMENTS:  
- Python 3 [tested with 3.6.6]  
- Tensorflow [tested with 1.12.0]  
- Cython [tested with 0.29.3]  
- MDAnalysis (only required for reading .gro/.xtc files) [tested with 0.19.0]   
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## OVERVIEW:

scripts/ --> Example scripts for training and evaluation  
models/ --> PointNet model in tensorflow  
utils/ --> Definition of datacontainer for PointNet  
datasets/ --> Example training data and example trajectory  
mda_custom/ --> Custom edits of MDAnalysis neighbor search  
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## RELATED WORK:

This software would not be possible without the work of previous 
researchers. The neighbor search functionality is adapted from 
MDAnalysis (https://mdanalysis.org). The PointNet architecture is taken
from arXiv:1612.00593. Also see http://stanford.edu/~rqi/pointnet/
and https://github.com/charlesq34/pointnet. 


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## COMPILING CUSTOM MDANALYSIS NEIGHBOR SEARCH:

cd mda_custom/nsgrid/  
python setup.py build_ext --inplace  
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## EXAMPLES:  

### TRAINING POINTNET:  
 
python scripts/train.py --dataset datasets/lj-r2.0_scaled_shuffled_equal_samples.npy
                        --labels  datasets/lj-r2.0_scaled_shuffled_equal_labels.npy
                        --weights PATH_TO_SAVE_WEIGHTS/weights  

Comments:

- See prepare_train.py for example of how samples and labels .npy files were prepared  
- WARNING, running train.py takes ~4 hours on one NVIDIA V100 GPU  


### USING POINTNET TO CLASSIFY CRYSTAL STRUCTURES:  

python scripts/mda_cluster.py --weights PATH_TO_SAVE_WEIGHTS/weights
                              --nclass 4
                              --trjpath datasets/lj-seed
                              --cutoff 2.0
                              --maxneigh 43
                              --outname example  

Comments:

- nclass = 4, the network was trained to recognize four classes (liq,fcc,hcp,bcc)  
- maxneigh = 43, each point cloud has 43 points in training set. The number of points in  
  each point cloud affects the network architecture.
- cutoff = 2.0, same as used for training

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## GENERAL PROCEDURE FOR CRYSTAL STRUCTURE IDENTIFICATION:  

- Run simulations of pure phases at a range of (T,P) conditions  
- Pick a cutoff distance (targeting avg of ~30--50 points appears to give accurate classification)  
- Calculate mean and stdev number of points within cutoff distance for all phases  
- Choose the max number of points in each point cloud (mu+2*stdev seems to work well)  
- Extract training examples from pure phase simulations -- create .npy structures (see prepare_train.py for an example)
  with training point clouds and labels in the SAME ORDER  
    (a) Shape of numpy array for training point clouds should be [NEXAMPLES,NPOINTS,3]  
    (b) Labels are one-hot encoded: Shape of numpy array for training labels should be [NEXAMPLES,NCLASSES]  
    (c) Central atom for point clouds always translated to (0,0,0)  
    (d) Points in point cloud scaled such that closest point to central atom is at a distance of 1.0  
- Train PointNet (see train.py)  
- Use PointNet for classification (see mda_cluster.py)   
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