Fix rigid molecule in liggghts

Submitted by leila khajenoori on Wed, 04/08/2015 - 15:31

Hi everybody

I am trying to make a complex shape particle by using fix rigid molecule command. I used following scripts in lammps and it run well. but once I wanted excutive it in liggghts I saw this ERROR: Illegal fix property/atom command, not enough arguments (../fix_property_atom.cpp:65)

units si
atom_style sphere
boundary f f f
newton off
communicate single vel yes

fix addMolecule all property/atom mol ghost yes
read_data mybag.rigid fix addMolecule Null Molecules

neigh_modify delay 0
pair_style gran/hertz/history
pair_coeff * *

fix 1 all rigid molecule 1

neigh_modify exclude molecule 1

I used fix property/atom in lammps to define molecule but in liggghts I do not know how to use this command and fix rigid molecule . Should fix property/atom be used or not if yes, how?

I would really appreciate any help.
Leila

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ckloss's picture

ckloss | Mon, 04/13/2015 - 11:41

Hi Leila,

>>I used fix property/atom in lammps to define molecule but in liggghts I do not know how to use this command and fix rigid molecule
LIGGGHTS is not LAMMPS - there is no guarantee that something you did in LAMMPS will work in LIGGGHTS. FIx property/atom is simply a different command - see doc for details

Best wishes
Christoph

leila khajenoori | Wed, 06/17/2015 - 12:12

Hi Christoph,
Thanks so much for replying me. Actually my problem is how to use fix rigid molecule in liggghts. it seems to me before using fix rigid molecule, it should be define by another command that we use molecule ID in our data file . ( for example like fix property/atom in lammps).
I really appreciate any help.
Kind regards
Leila

ma | Thu, 06/18/2015 - 22:32

Hi,
I am using the same command, however not so successfuly.
Following the doc, it is mentioned in the doc that first of all the molecular package should be added to liggghts by typing these two commands in a terminal in the /src folder
"make yes-molecule"
"make g++"

then you should rebuild LAMMPS, (I think it should be done by typing) :
"make clean-all"
"make fedora" in the /src

then type this line in the input file:
"atom_style hybrid granular molecule"

and the data file should contain the following commands:
atom-ID atom-type x y z diameter density molecule-ID

however, by running the commands this error emerges

atom_style hybrid granular molecule
ERROR: Invalid atom style (atom.cpp:343)

I was wondering if the procedure and commands are OK? and how can I fix the error?

best regards
ma

ma | Thu, 06/18/2015 - 22:40

Hi,
sorry the command should be as follows and it works
"atom_style hybrid granular molecular"

then assign mass to particles
the commands may help you proceed
best regards

leila khajenoori | Thu, 06/25/2015 - 10:57

Hi ma,
Thanks very much for your message. I tried exactly whatever you mentioned step by step but the error: invalid atom style happened.
Leila

ma | Thu, 06/25/2015 - 13:57

Sorry that I do not know the problem and cannot help more.

leila khajenoori | Wed, 07/01/2015 - 18:13

Hi ma,
I sorted out the problem with adding molecule package and I made my model with 9 rigid body but when I increased the number of rigid body to 10 this error happened: Segmentation fault (core dumped). Is there any restriction on the number of rigid body using atom style hybrid granular molecular?
kind regards,
Leila

ma | Tue, 07/14/2015 - 13:38

Hi leila
I have the same problem and it seems that it can be solved by using the commerical support (premium). However, I myself did not try it.
best regards
ma