Example for 'neb' showing error 'Cannot use NEB with a single replica '

LAMMPS LAMMPS Mailing List Mirror
1

Respected Developer,
I am interested in using ‘NEB’. Going through its example the following error occurred 'Cannot use NEB with a single replica '.

I ran for ‘in.nebsivac’ and ‘in.neb.hop1’

I understand the error but it seems there is one more replica is given that is final.sivac OR final.hop1.

I have no idea about how to create final Replica or what should be the co-ordinates for final replica.

It will be helpful , if this error is fixed or guide me the the way to fix it .
Thankfully.

2

.before posting to the mailing list, please always carefully study the
available documentation and readme files.

axel.

3

Respected Sir,
I read README doc and it says that it needs at least 4 replicas. Whether is it expected from the user to make those or Am I missing some important information or clue?

4

Respected Sir,
I read README doc and it says that it needs at least 4 replicas. Whether is it expected from the user to make those or Am I missing some important information or clue?

you are missing several clues. but you only read the readme. that is a
start but not sufficient, keep reading the documentation.

5

Sir, I read fix neb and neb command but I am not getting any clue regarding error from these docs.

Only difference I am finding is in execution command.
In example: mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac
I used : mpirun -machinefile $PBS_NODEFILE -n 01 /home/anilman/lammps_jul17/new/lammps-6Jul17/src/lmp_mpi < in.neb.sivac > sivac.dat

Sir, Is it the reason behind the error i received?

6

Sir, I read fix neb and neb commandbut I am not getting any
clue regardingerror from these docs.

Only difference I am finding is in execution command.
In example: mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac
I used : mpirun -machinefile $PBS_NODEFILE -n 01
/home/anilman/lammps_jul17/new/lammps-6Jul17/src/lmp_mpi <
in.neb.sivac > sivac.dat

Sir, Is it the reason behind the error i received?

yes! Why are you not using a similar command?
As a general recommendation: never leave out a command or an option,
just because you do not understand it. It is there most probably for
good reasons.

Look at:
https://lammps.sandia.gov/doc/Howto_replica.html

Also, I recommend to test your script/simulations in a local environment
(your workstation), that is not on a cluster. The submission system (PBS
in your case) add additional complexity.

Julien

7

Thank you Sir, for your reply. I will attempt this.