LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] BOX EXPANSION DURING EQUILIBRATION
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] BOX EXPANSION DURING EQUILIBRATION


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 18 Dec 2017 17:55:26 -0500

there were many more, important questions i have asked that are still unanswered.
...and here is one more: why do you use atom style molecular, even though you are using airebo, where bonds/angles/dihedrals are implicit?
the error message about long bonds suggests, that you have bonds defined in your topology. why?

axel.

On Mon, Dec 18, 2017 at 4:30 PM, Γρηγορης Δεδες <degrigor@...447...> wrote:
Hello Dr Axel,
I am using these specific box dimensions because they were created like this by vmd when i wrote the file in the lammps input form. 
I have tried using a box that matches the dimensions of the nanotube but i get the same results. The box increases in size in a large amount.
I am using npt in order to equilibrate my system at zero pressure and temperature 300 K so i can later compute the young modulus with a strain rate of 0.01.
This is the script i am using :



units  metal
dimension 3
boundary p p p
newton on
atom_style molecular



# ----------------------- ATOM DEFINITION ----------------------------

read_data cnttopology



# ------------------------ FORCE FIELDS ------------------------------
pair_style airebo 3
pair_coeff  * * ../potentials/CH.airebo C 


# ------------------------- SETTINGS ---------------------------------
compute 1 all ke
compute 0 all pair airebo
variable REBO     equal c_0[1]
variable LJ       equal c_0[2]
variable TORSION  equal c_0[3]
######################################
# EQUILIBRATION
reset_timestep 0
timestep 0.001
velocity all create 300 12345 
fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1

# Set thermo output
thermo 30000
thermo_style custom step lx ly lz press pxx pyy pzz pe temp  v_REBO v_LJ v_TORSION


run 400000
unfix 1

# Store final cell length for strain calculations
variable tmp equal "lz"
variable L0 equal ${tmp}
print "Initial Length, L0: ${L0}"


######################################
# DEFORMATION
reset_timestep 0

fix 1 all npt temp 300 300 1 y 0 0 1 x 0 0 1 drag 1

fix 2 all deform 1 z erate 0.01


variable strain equal "(lz - v_L0)/v_L0"
variable p1 equal "v_strain"
variable p2 equal "pxx"
variable p3 equal "pyy"
variable p4 equal "pzz"

fix def1 all print 5 "${p1} ${p2} ${p3} ${p4} " file results.txt screen no



# Display thermo
thermo  300
thermo_style custom step v_strain temp v_p2 v_p3 v_p4 ke pe press

run 4000

######################################
# SIMULATION DONE
print "All done"

I hope i managed to explain my problem more thoroughly
If you have any advice please let me know

Thank you very much in advance


Στις 11:45 μ.μ. Κυριακή, 17 Δεκεμβρίου 2017, ο/η Axel Kohlmeyer <akohlmey@...24...> έγραψε:




On Sun, Dec 17, 2017 at 1:17 PM, Γρηγορης Δεδες via lammps-users <lammps-users@...429...96...sourceforge.net> wrote:
Dear users,

I have modeled a cnt through vmd with a molecular atom style(bonds,angles, dihedrals included). 
I am using periodic boundary conditions and a box that is quite larger(10 times) than the dimensions of the cnt in x,y directions and equal to the dimension of cnt in z direction. 

​why so large in x and y? why not using fixed boundaries there?
why so tight in z? ​
 
During equilibration i use an npt fix 300 300 1 iso 0 0 1 drag 1

​why couple the the box size in x and y to the box size in z and only allow isotropic box changes?
why use fix npt in the first place? ​
 
I run it for 400000 time steps and although the potential energy equilibrates and the temperature somewhat does the box is expanding 5 times its size and does not stabilize.
I also get a warning : bond/angle/dihedral extent >half of periodic box size.
If you any idea about the cause of the problem or any suggestion regarding its fix please let me know.

​well, do you have one or more bonds with that extreme length?​ e.g. by adding bonds across periodic boundaries.

it is difficult to make any specific suggestions, since you don't provide any specific information, but only rather vague descriptions and no explanations for rather unexpected choices.

axel.

 

Thank you very much,
D.G


------------------------------ ------------------------------ ------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
______________________________ _________________
lammps-users mailing list
lammps-users@...396... sourceforge.net
https://lists.sourceforge.net/ lists/listinfo/lammps-users





--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.





--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.