How to get all bond angles and bond distances for all atoms in sheet

LAMMPS LAMMPS Mailing List Mirror
1

Dear all,

How can we get bond angles and bond length distribution in lammps. Is there any processing tool for getting distribution of bond angles and lengths all over the sheet.

Thanking you

Thanks & Regards,
Venkata Pavan Kumar. Miriyala
pavan.kumar9111@…24…,
contact number: +91-9032307746

2

Dear all,
          How can we get bond angles and bond length distribution in lammps.
Is there any processing tool for getting distribution of bond angles and
lengths all over the sheet.

that is best done with a custom post processing tool. you can take the
bond and angle definitions from a data file and then compute them and
histogram them. should be straightforward with a little bit of python
scripting.

if you are more into Tcl, you can use VMD which can read and parse
data files via the topotools plugin and can do time series of bond
lengths and angles via the label command or can use the measure
command for bonds and angles.
of course, that requires some script programming, too, but that is the
normal way of computational research... :wink:

axel.

3

Actually LAMMPS can compute this on the fly as well.

The compute bond/local or angle/local commands
calculate bond lengths and angles. That output
can be histogrammed via the fix ave/histo command.

Steve

4

Thank you axel, In my experiment of tensile test, I want to know how the angles and bond lengths are distributed over a system of atoms at particular time intervals. So, I shouldn’t use data file for angle and bond length distributions.

I want to load xyz dump files of particular time intervals into vmd and check the distribution (some bonds will be stretched) of angles and bond lengths.

But, I’m using graphene sheet with airebo potential by creating data file without bonds :frowning:

Is custom a separate post processing tool ?

5

Thank you steve, I will try now :slight_smile:

6

Thank you axel, In my experiment of tensile test, I want to know how the
angles and bond lengths are distributed over a system of atoms at particular
time intervals. So, I shouldn't use data file for angle and bond length
distributions.

I want to load xyz dump files of particular time intervals into vmd and
check the distribution (some bonds will be stretched) of angles and bond
lengths.

But, I'm using graphene sheet with airebo potential by creating data file
without bonds :frowning:
Is custom a separate post processing tool ?

not unless you write one yourself. it should be simple enough for a
simple system like yours.

7

Thank you steve, I will try now :slight_smile:

i don't think that that will work for a setup like yours, where you
don't have a bond or angle style defined. you would have to create a
special topology for that and post-process with the rerun command.

if you had spent the time programming instead of asking, you might
have a usable code already...

8

Thank you axel.

9

Dear axel,
Just asking with bit of anxiety, how can we use measure command to know bond angles and bond lengths in VMD.

10

Dear axel,
              Just asking with bit of anxiety, how can we use measure
command to know bond angles and bond lengths in VMD.

that is a) a question that is better asked on the VMD mailing list and
b) explained in the VMD user's guide.