how to visualize structure results with colored lattices

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1

Dear experts,

After exploring the list and LAMMPS manual, I finally built my first model on melting. Thank everyone contributing to community.
The thing is, when a solid melts, the lattice structures melt from fcc or bcc etc into disordered particles.
Is there any command or tool to visualize the melting process and solidification proecess by recognizing lattice structures and marking them with different colors?
I read in papers that some researchers can do this, but I am not sure how they did that.
I have checked atomeye, but did not find how to get what I want with it yet.

Thank you for any help.

2

Dear experts,

After exploring the list and LAMMPS manual, I finally built my first model
on melting. Thank everyone contributing to community.
The thing is, when a solid melts, the lattice structures melt from fcc or
bcc etc into disordered particles.
Is there any command or tool to visualize the melting process and
solidification proecess by recognizing lattice structures and marking them
with different colors?
I read in papers that some researchers can do this, but I am not sure how
they did that.
I have checked atomeye, but did not find how to get what I want with it yet.

please have a look at the dump image command included in LAMMPS. it
can do visualizations internally *and* utilize computed properties for
coloring. there are multiple computes in LAMMPS that indicate the kind
and degree of ordering around individual atoms.

computed per atom properties can also be stored in dump files and used
in more generic visualization tools.

please also see the mailing list archives for more detailed
discussions on specific issues.

axel.

3

Axel,

Thanks for advice.

I checked manual for dump image and dump cfg. Looks like I can define colors according to any atom attributes.
Then would you please detail on what attributes are able to identify lattice structures? As the common per atom attributes seem not able to recognize lattice structures.
And another thing, anyone knows how to render in Atomeye with any specified atom attribute (or the given options are enough in my case)?

Thanks a lot.

Best,

4

Have you checked this out?

http://lammps.sandia.gov/doc/fix_orient_fcc.html

Ray

5

Axel,

Thanks for advice.

I checked manual for dump image and dump cfg. Looks like I can define colors
according to any atom attributes.
Then would you please detail on what attributes are able to identify lattice
structures? As the common per atom attributes seem not able to recognize
lattice structures.

of course not. such information would have to be computed first.
please see the list of available computes in the LAMMPS manual. what
comes to mind is cna/atom, centro/atom, ackland/atom. there may be
more.

And another thing, anyone knows how to render in Atomeye with any specified
atom attribute (or the given options are enough in my case)?

i don't use atomeye, so i don't know. but this kind of discussion is
off-topic for this mailing list, anyway. please see the atomeye
documentation or their corresponding user forum or mailing list.
...and have you asked your colleagues?

axel.

6

Hi,

14.07.2015, 21:28, “Zheng Kang” <kang214@…132…>:

And another thing, anyone knows how to render in Atomeye with any specified atom attribute (or the given options are enough in my case)?

http://li.mit.edu/Archive/Graphics/A/#auxiliary_property_coloring

You may also probably use http://li.mit.edu/Archive/Graphics/A/#central_symm_coloring as an indicator of melting. Anyway, it is all on Atomeye doc page.

Oleg

7

Thanks everyone for help.
I will explore more then come back.

To Axel, the sad truth is, I myself is looking for colleagues around. In my lab, I am the first on this topic.