Open Matheus-Novoa opened 2 years ago
Hello!
The warning tells you that these atoms have only 1 neighbor in their neighbor list but some of your symmetry functions need at least 2 neighbors to be non-zero. This is usually the case when you have used all element combinations of angular symmetry functions (e.g. for central C atoms: H-H, H-C, C-C neighbors) but then within the cutoff sphere there are no atoms of all types. This is very likely to happen in your 1-D nanomaterial and not per se a problem (zero is also a valid input for a neural network input node). If you are sure that your symmetry function setup is ok, you can turn off these warnings if you recompile the entire code with
PROJECT_OPTIONS+= -DN2P2_NO_NEIGH_CHECK
Just remove the comment sign #
in the corresponding line in makefile.<comp>
(around line 43).
Best,
Andreas
Hello!
I have similar issues when running lammps calling n2p2. I run for a simple 3D atomic model using pbc. After the initial 100 steps, I start to see most of atoms showing this warning for most later steps, and this produces a huge output file. I wonder if it is possible to silence this warning from lammps without recompiling?
Also, when will this be an issue? From visualization I see nothing wrong, and for short-range interacting atoms that are far away (in gas phase), the angular functions shall be zero. Maybe we could consider this situation and incorporate into the code?
Thanks
I'm trying to build an NNP for a 1-D nanomaterial. However, i'm facing some issues about the training stage.
In nnp-train.log file, there are some warning lines like that:
WARNING: Structure 1 Atom 2 : 1 neighbors. WARNING: Structure 1 Atom 3 : 1 neighbors. WARNING: Structure 1 Atom 8 : 1 neighbors. WARNING: Structure 1 Atom 9 : 1 neighbors. WARNING: Structure 1 Atom 10 : 1 neighbors. WARNING: Structure 1 Atom 11 : 1 neighbors. WARNING: Structure 1 Atom 16 : 1 neighbors. WARNING: Structure 1 Atom 17 : 1 neighbors. WARNING: Structure 1 Atom 18 : 1 neighbors. WARNING: Structure 1 Atom 19 : 1 neighbors. WARNING: Structure 1 Atom 22 : 1 neighbors.
Even so, i decided to test the model obtained from this training in a MD simulation. In simulation output, i got the same warnings and soon after a lost atoms error occurred.
I would like to know the origin of these warnings. Thanks in advance for your help
input.nn.txt nnp-train.log.txt