Hi all,
I am working on a perovskite-based system. I want to know how you visualize the neb file dump.neb, I tried with VMD and ASE, but I am not able to visualize it. Can you please help me out?
Thanks in advance!
Hi,
Are you sure that .neb is a standard format ? What command did you use to print it ?
Simon
There is not enough information here for any meaningful suggestions.
- How did you generate that dump.neb file with LAMMPS exactly?
- What are its contents?
- What is it that you want to see from it?
- How did you try read the file into the visualization software? Note that most visualization tools try to infer the file format from the file name.
Hi Simon,
I am doing the neb simulation in which the snapshots are written to a dump. neb from command dump:dump 1 nebatoms atom 10 dump. neb, the problem is I am unable to visualize this file as this is not the standard format.
I am also attaching my input file:
units metal
atom_style atomic
atom_modify map yes
newton on
boundary p p p
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
minimize 1.0e-6 1.0e-4 1000 1000
reset_timestep 0
timestep 0.001 # ps (in units metal)
group nebatoms id 217
#set group nebatoms type 4
fix 1 nebatoms neb 10.0
thermo 100
dump 1 nebatoms atom 10 dump.neb
min_style quickmin
neb 0.0 0.1 600 12000 12 final final.hop
Sorry, but I disagree. This is in the canonical LAMMPS dump trajectory format, which is supported by VMD. I know this for certain because I wrote most of the VMD plugin for reading this type of file.
I you want to load this file into VMD you have to tell VMD that it is in “lammpstrj” format or change the output file name in your dump command so that it ends in “.lammpstrj” and then VMD will auto-detect the file format.
Hi Alex,
I apologize for the oversight. I am doing the neb simulation in which the snapshots are written to a dump. neb from command dump:dump 1 nebatoms atom 10 dump. neb, the problem is I am unable to visualize this file, I want to see my system going from initial state to final state along MEP.
I am attaching my input file:
units metal
atom_style atomic
atom_modify map yes
newton on
boundary p p p
read_data poscar_a_initial.data
pair_style mace no_domain_decomposition
pair_coeff * * /home/parul.goel/mace/mace_matpes.model-lammps.pt La Sr Ni Fe O
mass 1 55.845 # Fe
mass 2 138.905 # La
mass 3 58.6934 # Ni
mass 4 15.9994 # O
mass 5 87.62 # Sr
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
minimize 1.0e-6 1.0e-4 1000 1000
reset_timestep 0
timestep 0.001 # ps (in units metal)
group nebatoms id 217
#set group nebatoms type 4
fix 1 nebatoms neb 10.0
thermo 100
dump 1 nebatoms atom 10 dump.neb
min_style quickmin
neb 0.0 0.1 600 12000 12 final final.hop
Thanks, Alex. It worked after changing the file name to .lammpstrj, and I have one more question. In my trajectory file, I can’t see the whole system. I can only see the oxygen whose coordinates I specified in my final.hop file, and I am also getting only 2 frames instead of 16.
I am trying to perform oxygen vacancy diffusion in my pervoksite system, so in my final file final.hop contains the coordinates and oxygen ID to be hopped. What am I doing wrong?
You are not reading the LAMMPS manual.
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