How to read/load simulation/universe from LAMMPS?

[0x90]

I have this input file:

units lj
dimension 2
boundary p p p
atom_style atomic
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no

lattice hex 0.5
region simbox block 0 100 0 50 -0.1 0.1
create_box 2 simbox

lattice hex 0.5
create_atoms 1 region simbox

lattice hex 0.5 origin 0.5 0.5 0
create_atoms 2 region simbox

mass 1 1
mass 2 1000.0

velocity all create 5 78554
pair_style hybrid lj/cut 2.5 soft 0.5
pair_coeff 1 1 lj/cut 1.0 1.0 2.5
pair_coeff 1 2 soft 0.5
pair_coeff 2 2 soft 0.5


fix 1 all nvt temp 0.25 0.25 1.0


dump 1 all atom 10 dump.lammpstrj
thermo 200
run 100

The output head will look something like this:

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
20000
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+000 1.5196713713031852e+002
0.0000000000000000e+000 1.3160740129524925e+002
-1.5196713713031854e-001 1.5196713713031854e-001
ITEM: ATOMS id type xs ys zs
1 1 0 0 0.5
2 1 0.005 0.01 0.5
10001 2 0 0 0.5
10102 2 0.005 0.01 0.5
3 1 0.01 0 0.5
4 1 0.015 0.01 0.5
10002 2 0.01 0 0.5
10104 2 0.015 0.01 0.5
5 1 0.02 0 0.5
6 1 0.025 0.01 0.5
10003 2 0.02 0 0.5

I tried these 2 functions, the first didn't work at all. I am not sure how to work with the object returned from the second option and if it's the right way to go.

u = MDAnalysis.Universe('out.lammps', 'in.lammps', format="LAMMPS")

u = MDAnalysis.topology.LAMMPSParser.DATAParser('out.lammps')

[0x90]

One of my problems is that the documentation says the following approach is deprecated:

d=MDAnalysis.topology.LAMMPSParser.DATAParser(trajectory)

d.writePSF("lammps.psf")

d.writePDB("lammps.pdb")

u = MDAnalysis.Unverse("lammps.psf", "lammps.dcd", format="LAMMPS")

[Oliver Beckstein]

Hi 0x90,

It’s been a while since I worked with LAMMPS… so anyone else (Richard, Sean?) please correct me.

1) LAMMPSDataConverter is really old code and it’s not really maintained; ideally it should not be necessary. (But if it works for you, good… just be careful)

2) MDAnalysis cannot parse LAMMPS input “scripts” (such as your input file). It reads DATA files.

3) What format is your output? It does not look like the DATA file http://lammps.sandia.gov/doc/2001/data_format.html (or http://lammps.sandia.gov/doc/read_data.html) . MDAnalysis parses this DATA file format. (If you have a data file then you should be able to do u = mda.Universe(“lamps.data”)  and this should give you both topology information and coordinates.)

I *think* your output is a LAMMPS dump trajectory. If you write it as DCD or XTC instead then you’ll be able to read it in MDA. We don’t have a parser for LAMMPS dump format.

I can’t remember how to create the DATA file, probably http://lammps.sandia.gov/doc/write_data.html – someone with more LAMMPS experience should chime in, please.

(It might be useful to update https://www.mdanalysis.org/docs/documentation_pages/topology/LAMMPSParser.html with the information on how to create DATA files if this is not something that is commonly done in a typical LAMMPS workflow.)

Oliver

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