NEB path

[baizq]

Dear all,

I would like to set up an NEB path between two geometries (in both geometries there is a MgO slab with one oxygen vacancy inside. A carbon atom is diffusing from the surface (initial) into the vacancy in the slab (final)). However, when I put the two geometries into the VNL NEB builder, it complains "invalid". I have tried both relaxed and unrelaxed pairs.

Could anyone suggest me what happens here and how to solve the problem? I have attached the relaxed geometries for your reference.

Thanks in advance!
baizq

[Anders Blom]

The problem is that your carbon atom has different index in the two configurations. Delete it from both initial and final (remember the coordinates!) and then add it again, so it's last in both configs.

I have added two "fixed" configs.

[baizq]

Thank you, Anders. Yes, the script you attached works for setting up the NEB run. However, when the job runs, it complaints the following strange error:

Assertion failed in file src/mpid/ch3/channels/nemesis/netmod/tcp/socksm.c at line 591: hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_ID_INFO || hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_TMPVC_INFO
internal ABORT - process 0

I am wondering what it is... I have attached the log file and input file for your reference.

Thanks,
baizq

[Umberto Martinez]

can  you check the individual log files neb_image.0, neb_image.1, ....
It can be that one of the parallel taks failed, perhaps because of a license issue.

[Anders Blom]

It's either a hardware error or perhaps as Umberto wrote a license error on one of the slave processes. Once a slave terminates, the master will terminate the entire job and it typically looks like these error messages.