Output Orientorder/atom vector as file

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1

Dear all

I am running simulation of 5120 Ni atoms doped with Fe, I have used the compute command to compute the bond orientation order by using the “compute orientorder/atom” but am unable to dump it using the dump custom command I am including the log for the input file and the error. Is there any other way for getting the output of this per atom without the use of user packages. Does it Depend on the file type?

Thank you

units real
boundary p p p
atom_style atomic
#log log.$rsimname}.txt
read_data ni3fe.txt

pair_style eam/alloy
pair_coeff * * NiFe.set Ni Fe
neighbor 1.0 bin
neigh_modify every 1 delay 5 check yes

#Equilibration
velocity all create 300.0 492825 dist gaussian

timestep 1
thermo 1000
thermo_style multi

fix 1 all nvt temp 300.0 300.0 100.0

compute myBond all orientorder/atom degrees 2 4 6

compute myRDF all rdf 100 1 1 1 2 2 1 2 2

fix 3 all ave/time 100 10 5000 c_myRDF file tmp.rdf mode vector
dump 1 all xyz 5000 300_MC_swap_MD_ni3fe.xyz

dump 2 all custom 1000000 dump.123.xyz id type c_myBond

restart 1000000 ni3fe1.restart
run 5000000

ERROR: Dump custom compute does not calculate per-atom vector (…/dump_custom.cpp:1228)

PS: I have also included the text file for my initial configuration to be used in the input file

Joydeep Datta
Indian Institute of Technology, Kanpur

ni3fe.txt (211 KB)

2

Dear all

I am running simulation of 5120 Ni atoms doped with Fe, I have used the
compute command to compute the bond orientation order by using the "compute
orientorder/atom" but am unable to dump it using the dump custom command I
am including the log for the input file and the error. Is there any other
way for getting the output of this per atom without the use of user
packages. Does it Depend on the file type?

no, it depends on correctly specifying what you want to output.

since you request 2 (two!) lvalues in your compute (4 and 6), the
compute doesn't produce a per-atom vector, but a per-atom array.
to correct for that, you need to tell the dump command, which of the
two columns you want to output.

dump 2 all custom 100 dump.123.xyz id type c_myBond[1] c_myBond[2]

as of LAMMPS version 1 Aug 2016, you can now automatically output all
columns using the following, new syntax.

dump 2 all custom 100 dump.123.xyz id type c_myBond[*]

axel.