txie-93 / gdynet Goto Github PK
View Code? Open in Web Editor NEWUnsupervised learning of atomic scale dynamics from molecular dynamics.
License: MIT License
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cloudac7 aixuan1995py chqlee liunianxuxie kimyujin96 hyzcn jimmy-inl imin-95 zeromtmu lwk205 abhijeetdhakane ruihwang looomo 15garzab zhongpc ritesh001 hanfengzhai mavanish xiangxiang920920 itzme-jp overwhelming01 danielathkgdynet's Issues
What is Variable N0 stand for in _pooling function
def _pooling(inps):
"""
Pool the atom_fea of target atoms together using their indexes.
Parameters
----------
atom_fea: (B, N, atom_fea_len)
target_index: (B, N0)
Returns
-------
crys_fea: (B, N0, atom_fea_len)
"""
atom_fea, target_index = inps
B = tf.shape(atom_fea)[0]
N0 = tf.shape(target_index)[1]
batch_idx = tf.reshape(tf.range(0, B), (B, 1))
batch_idx = tf.tile(batch_idx, (1, N0))
full_idx = tf.stack((batch_idx, target_index), axis=-1)
return tf.gather_nd(atom_fea, full_idx)problem during Visualization
dear doc Xie:
I am trying to use gdynet to identify dynamic processes in a friction MD simulation to get specific bonding state for aimed atom. After training the model , I follow the jupyter notebook to visualize the results. When I try to plot the relaxation timescales, something wrong happens just like:
gdynet/postprocess.py:41: RuntimeWarning: invalid value encountered in log
its_log_std = np.std(np.log(splited_its), axis=0)
/conda/anaconda3/envs/gdynet/lib/python3.6/site-packages/numpy/core/_methods.py:117: RuntimeWarning: invalid value encountered in subtract
x = asanyarray(arr - arrmean)
So I check the koopman_op for the array lags, finding there are a lot of zero arrays (the second one):
[[ 6.7463994e-01 -1.1839467e-01 4.3136746e-01 1.2387081e-02]
[-5.4880998e-06 9.7734249e-01 2.0228788e-02 2.4341424e-03]
[ 2.2197758e-04 9.0464517e-02 9.0913689e-01 1.7680590e-04]
[ 2.5602803e-05 7.5335771e-02 -1.7902499e-02 9.4254106e-01]]
[[0. 0. 0. 0.]
[0. 0. 0. 0.]
[0. 0. 0. 0.]
[0. 0. 0. 0.]]
I am wondering which part goes wrong. Thanks a lot!
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