ReaxFF and evaluation using Pizza.py

Dear LAMMPS-users,

I'm an absolute newbie regarding LAMMPS, so my question is likely trivial, though I am overwhelmed at this point.

I'm trying to simulate the behaviour of a Si-crystal using the Reax force field. I created the initial topology from a unit cell with the ReaxFF simulation package and altered the resulting fort.85 into a LAMMPS readable format (http://lammps.sandia.gov/doc/2001/data_format.html). Example files I looked at do not include information regarding bonds, angles etc., which I assume to be treated by the ReaxFF implicitly. My simulation completes, though I have problems evaluating the simulation, using the Pizza.py script. When I call e.g. the block.py command, I get the warning

"StandardError: unique log vector E_bond not found"

which correctly tells me that there are no bond energies in my log.lammps file. How should I evaluate my simulation? At the beginning, I'm just interested in the lattice structure and basic information, like different energy terms, density etc. My in.reax.rdx file looks like this

Dear LAMMPS-users,

I'm an absolute newbie regarding LAMMPS, so my question is likely
trivial, though I am overwhelmed at this point.

I'm trying to simulate the behaviour of a Si-crystal using the Reax
force field. I created the initial topology from a unit cell with the
ReaxFF simulation package and altered the resulting fort.85 into a
LAMMPS readable format
(http://lammps.sandia.gov/doc/2001/data_format.html). Example files I

this is the documentation for the format compatible with the fortran
95 version of LAMMPS.
the format for the current version of LAMMPS is described in the
documentation for the "read_data" command.

looked at do not include information regarding bonds, angles etc., which
I assume to be treated by the ReaxFF implicitly. My simulation

yes, that is how ReaxFF works.

completes, though I have problems evaluating the simulation, using the
Pizza.py script. When I call e.g. the block.py command, I get the warning

"StandardError: unique log vector E_bond not found"

which correctly tells me that there are no bond energies in my
log.lammps file. How should I evaluate my simulation? At the beginning,
I'm just interested in the lattice structure and basic information, like
different energy terms, density etc. My in.reax.rdx file looks like this

your input is using the deprecated and no longer maintained fortran
version of reax in LAMMPS. please update to the USER-REAXC package
instead. it is faster and is maintained.

also, the column header output format changed recently, so Pizza.py
may need to see some updates.

axel.

The easiest way to evaluate a simulation of this type is to visualize snapshots using a package such vmd, atomeye, or ovito. For typical structures, these packages usually do a good job of identifying changes in bonding topology.

http://lammps.sandia.gov/viz.html

You can also learn a lot by looking at the per-atom energy of each atom, and also the itemized breakdown of the potential energy (see examples/reax/in.reaxc.rdx for an example). Note also that rdx refers to the particular molecular crystal called RDX, so you should probably rename your script something like in.reaxc.si

Aidan