[lammps-users] Alignment of dump file quantities

I would like to transfer the atom id, and coordinates data from the dump text file into excel, in order to plot atom id’s versus different quantities such as positions, velocities ect.

however after transfer all of the lammps output is only going into one column.

Is there a way to force lammps to output dumpfile data in an alignment/column spacing of your choice?

Can you also force the output to be sorted with respect to atom id?

Finally, is there a built in option in lammps to output plots of velocity, and or position distributions of the atoms in your simulation?

v/r,

Comments below.

Steve

I would like to transfer the atom id, and coordinates data from the dump
text file into excel, in order to plot atom id's versus different quantities
such as positions, velocities ect.

however after transfer all of the lammps output is only going into one
column.

Is there a way to force lammps to output dumpfile data in an
alignment/column spacing of your choice?

You can use dump_modify format to specify a C-style format
string that will print each dump line however you like.

Can you also force the output to be sorted with respect to atom id?

The dump and dump_modify doc pages explains sorting, and which
styles support it and which don't. You can always sort a dump
file via post-processing. For example,
in tools/python, there is a script that sorts each snapshot.

Finally, is there a built in option in lammps to output plots of velocity,
and or position distributions of the atoms in your simulation?

There is no plotting, but there is fix ave/histo which will histogram
various quantities and output them to a file. Plotting is best
left for post processings. Again in tools/python there is a script
that will use GnuPlot to make a simple plot of 2 columns from
a log file.

More generally, the Pizza,py toolkit can be scripted to automate
dump sorting or create a set of plots very easily, if you know a
bit of Python.