neb calculation

Dear LAMMPS community,
I’m trying to find the saddle point of a gas phase chemical reaction using the neb command and the ReaxFF force field, but I constantly get the following error: Unknown identifier in data file: 1 5.0000000 5.0000000 5.0000000

This is the input file I’m using:

Neb calculation

units real
boundary p p p
atom_style atomic
atom_modify map array sort 0 0.0
read_data replica1
read_data replica2
read_data replica3
read_data replica4
read_data replica5
read_data replica6
read_data replica7
region box block 0 25 0 25 0 25
create_box 2 box
pair_style reax/c lmp_control checkqeq yes safezone 1.8 mincap 150
pair_coeff * * ffield.reax H O

timestep 1.0
min_style fire
set mass 1 1.0080
set mass 2 15.9994
set mass 3 15.9994
set mass 4 1.0080
set mass 5 15.9994
set mass 6 15.9994
group term id 1 2 3 4 5 6

fix 1 term neb 1.0
neb 1e-4 1e-6 1000 500 50 each replica1
neb 1e-4 1e-6 1000 500 50 each replica2
neb 1e-4 1e-6 1000 500 50 each replica3
neb 1e-4 1e-6 1000 500 50 each replica4
neb 1e-4 1e-6 1000 500 50 each replica5
neb 1e-4 1e-6 1000 500 50 each replica6
neb 1e-4 1e-6 1000 500 50 each replica7

And this is the format of the data files with the replicas (where x, y and z are the Cartesian coordinates):

6
1 x1 y1 z1
2 x2 y2 z2
3 x3 y3 z3
4 x4 y4 z4
5 x5 y5 z5
6 x6 y6 z6

Since the format of the data file is the format suggested in the manual, I guess I’m missing something in the input file. I would appreciate any suggestion.

Thank you very much for your time

That error is coming from the read_data command, not NEB. The

format you list for your “data files”, are not the format

for a LAMMPS data file, as read by the read_data command.

They are the format for the files read by the neb command.

Steve

Steve, thanks for your answer.
Right, but I should use the format for a NEB calculation. Then, I assume I should read the files in a different way or I’m missing something so that LAMMPS doesn’t know I’m trying to run a NEB calculation.

Manuel Monge-Palacios
Postdoctoral Fellow
Department of Theoretical Chemistry
University of Missouri-Columbia

Dear LAMMPS community,
I'm trying to find the saddle point of a gas phase chemical reaction using
the neb command and the ReaxFF force field, but I constantly get the
following error: Unknown identifier in data file: 1 5.0000000 5.0000000
5.0000000

This is the input file I'm using:

# Neb calculation

units real
boundary p p p
atom_style atomic

reaxff calculations require atom style charge, not atomic. if you are
reading a data file formatted for atom style charge with atom style
atomic, you have too many entries and that would produce exactly the
kind of error message you see.

atom_modify map array sort 0 0.0
read_data replica1
read_data replica2
read_data replica3
read_data replica4
read_data replica5
read_data replica6
read_data replica7

this *cannot* work. you cannot read different data files like this
into the same instance of LAMMPS. when running with the neb command
only the first replica is read from the data file with read_data, the
rest is either read or generated with the neb command.

axel.

Steve, thanks for your answer.
Right, but I should use the format for a NEB calculation. Then, I assume I
should read the files in a different way or I'm missing something so that
LAMMPS doesn't know I'm trying to run a NEB calculation.

LAMMPS only knows that you are doing a NEB calculation when you invoke
the neb command. before that, each replica is set up as a concurrent
multi partition calculation.
you propagate the various initial replica configurations with the neb
command. please see the each option:
http://lammps.sandia.gov/doc/neb.html