Error while running NEB simulation

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1

Hi,

I am running an NEB simulation for determination of energy barrier during dislocation motion with the following command line: mpiexec -localonly 8 lmp_mpi -partition 8x1 -in NEB.txt.

But I am an getting an error message like:
Error posting readv, An existing connection was forcibly closed by the remote host.(10054)
unable to read the cmd header on the pmi context, Error = -1

Kindly suggest me some solutions.

For reference I am posting here the input script:

NEB simulation for peierls barrier

units metal
dimension 3
boundary p p f
atom_style atomic
atom_modify map array sort 0 0.0

read_data dislocation_initial.dat

pair_style eam/alloy
pair_coeff * * Fe_Mishin2006.eam.alloy Fe
neighbor 2.0 bin
neigh_modify delay 1 check yes

compute eng all pe/atom
compute eatoms all reduce sum c_eng
compute csym all centro/atom fcc

define groups

region whole block -0.239454 126.163 -0.462324 250.88 -0.0341002 19.821
group sample region whole
region lower block INF INF INF 180 INF INF
group lb region lower
region upper block INF INF 194 INF INF INF
group ub region upper
group boundary union lb ub
group middle subtract sample boundary

region lwer block INF 55 INF INF INF INF
group wb region lwer
region uper block 71 INF INF INF INF INF
group qb region uper
group bdary union qb wb
group nebatoms subtract middle bdary

group nonneb subtract all nebatoms

fix 1 all nve
fix 2 nebatoms neb 10.0 perp 1
fix 3 nonneb setforce 0.0 0.0 0.0

thermo 100

variable u uloop 20

dump 1 nebatoms atom 10 ./datafiles/dump.neb.$u
dump 2 nonneb atom 10 ./datafiles/dump.nonneb.$u

min_style quickmin

neb 1e-6 1e-6 10000 10000 100 final dislocation.final

Thanks in advance
Rakesh

2

Hi,

I am running an NEB simulation for determination of energy barrier during dislocation motion with the following command line: mpiexec -localonly 8 lmp_mpi -partition 8x1 -in NEB.txt.

But I am an getting an error message like:
Error posting readv, An existing connection was forcibly closed by the remote host.(10054)
unable to read the cmd header on the pmi context, Error = -1

impossible to say from remote. kindly inspect your various log and screen files and look for error messages.
please also first make sure your system can run as a single replica without NEB.

axel.

3

In both the log and screen files the following error is showing:
ERROR: Incorrect atom format in neb file (…/neb.cpp:454)
Last command: neb 1e-6 1e-6 10000 10000 100 final dislocation.final

And the system is also running as a single replica without NEB.

4

well, there you have the reason for the failure and what you need to correct.

axel.

5

sorry, Could not figure out. Would you kindly explain me where is the fault?

6

the error message tells you! it cannot get more obvious.
the file with the final configuration used on the neb command line is not correctly formatted.
axel.

7

Ok. Thanks. I will check and rectify the final file format.