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MDIL-SNU / SIMPLE-NN

SIMPLE-NN(SNU Interatomic Machine-learning PotentiaL packagE – version Neural Network)
GNU General Public License v3.0
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Fingerprinting Seg Faults #60

Closed bencomer closed 5 years ago

bencomer commented 5 years ago

I've been using simple_nn and have run into a few instances where the code terminates in a segmentation fault during fingerprint calculations. I am unable to find the origin of this issue. I've attached a google drive folder that contains the inputs I'm using along with the error message I get in log.

https://drive.google.com/drive/folders/128VUgF4QL0Pb-w8U6-TAzaKCpyhaas0H?usp=sharing

Nanco-L commented 5 years ago

In the current version of the code, we assume the PBC cell for x-, y-, and z-direction. In your example, there is no PBC for z-direction and the coordinates of some atoms are out of the cell boundary. That leads to some problems in our neighboring atom searching algorithm. Thus, if you want no periodicity for z-direction, we recommend increasing the lattice parameter of z-direction (>cutoff radius) and turning on PBC for all direction. To handle this problem, we will add the code for automatically adding vacuum layer for the non-PBC direction of the cell soon.

Kyuhyun

bencomer commented 5 years ago

The z-direction actually does have periodicity in the original calculation! (or at least it should, looks like it got messed up somehow.) When I change the periodicity it everything seems to work!