Change output format to custom lammps/data from hoomd-blue gsd file

OVITO
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1

Hi,

I have a .gsd system file created with hoomd-blue and now I want to change the format to lammps/data using a python script with ovito. In the .gsd file the particle type indices start at “0” and have to be incremented by 1 to work with lammps. Additionally I use a custom hybrid bond charge pair style in lammps, so the data file should look like this:

LAMMPS data file via write_data, version 29 Oct 2020
1000 atoms
988 bonds
4 atom types
1 bond types
-12.0 12.0 xlo xhi
-12.0 12.0 ylo yhi
-12.0 12.0 zlo zhi

Masses

1 1
2 1
3 1
4 1

Atoms # hybrid

1 1 -4.8904447556 -9.0006971359 -4.4801688194 1 0.0 0 0 0
2 2 1.0052903891 1.9645963907 -10.9656629562 1 0.0 0 0 0
3 3 3.8270976543 -1.3371047974 -8.0224752426 1 0.0 0 0 0
4 4 2.8785529137 -1.7345225811 -7.4386529922 1 0.0 0 0 0

If i use the export file function of ovito:
export_file(pipeline, “test.data”, “lammps/data”, atom_style=“hybrid”, atom_substyles=(“bond”, “charge”))

the data file looks like this:

LAMMPS data file written by Ovito 3.7.12

1000 atoms
988 bonds
4 atom types
1 bond types
-12.0 12.0 xlo xhi
-12.0 12.0 ylo yhi
-12.0 12.0 zlo zhi

Atoms # hybrid bond charge

1 0 -4.8904447556 -9.0006971359 -4.4801688194 1 0.0
2 1 1.0052903891 1.9645963907 -10.9656629562 1 0.0
3 2 3.8270976543 -1.3371047974 -8.0224752426 1 0.0
4 3 2.8785529137 -1.7345225811 -7.4386529922 1 0.0
…

I tried to define some custom particle property “lammps particle type” and use something like
export_file(pipeline, “outputfile.dump”, “lammps/dump”,
columns = [“Position.X”, “Position.Y”, “Position.Z”, “My Property”])

or

export_file(pipeline, “FENE.xyz”, “xyz”, columns =
[“Particle Identifier”, “Particle Type”, “Position.X”, “Position.Y”, “Position.Z”])

to achive the right format for the columns, without success. I would be glad for any help you can give.
Best,
Hendrik

2

In the next release, OVITO 3.8.0, the LAMMPS data file writer will provide the option to renumber the atom types during export. This will solve the problem of zero-based type IDs from a GSD file.

In the meantime, you can insert a custom modifier into the pipeline to adjust the type IDs from 0-based to 1-based:

def increment_type_ids(frame: int, data: DataCollection):
    ptype_prop = data.particles_.particle_types_
    ptype_prop[...] += 1
    for t in ptype_prop.types:
        ptype_prop.make_mutable(t).id += 1

pipeline.modifiers.append(increment_type_ids)

This modifier function changes the numeric IDs of the ParticleType objects and increments the values stored in the per-atom type array.

3

Thank you again Dr Stukowski,

I tried it and it works perfectly. Of course the same change has to be done for bonds:

def increment_bondtype_ids(frame: int, data: DataCollection):
    btype_prop = data.particles_.bonds_.bond_types_
    btype_prop[...] += 1
    for t in btype_prop.types:
        btype_prop.make_mutable(t).id += 1

pipeline.modifiers.append(increment_bondtype_ids)

and I assume in other cases for angles, too.

4

Is it possible to include the masses with “export_file”? And is it possible to append the extra " 0 0 0" at the end of each line in the Atoms - section of the data file?