Gradually increasing the density of a polymer system

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1

Hello all,

I am trying to achieve a certain density (rho_desired) of crosslinked epoxy system. My initial system is at lower density (rho_initial ~ 6*rho_desired).

Case 1. I am using change_box command to decrease the box dimensions and achieving denser system. I am observing that instead of decreasing the box size over given “run period”, box size is changing at the start of each “run period”, which means box is changing suddenly.

Case 2. I am using press/berendsen command to apply some guessed hydrostatic pressure to bring the density of the system to rho_desired. This time, density seems to be changing gradually until a certain value, ~1.8*rho_initial. After this, I am observing that density is increasing but is fluctuating too much.

I am using reaxff potential. Following is my input script:

REAX potential for CHON system

…

units real

atom_style charge
boundary p p p
read_data datapress3.txt

pair_style reax/c lmp_control lgvdw yes
pair_coeff * * ffield.reax.EPON H C N O

neighbor 2 bin
neigh_modify every 10 delay 0 check no

timestep 0.01 # 0.25

fix 1 all nve

fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq

fix 3 all temp/berendsen 300.0 300.0 1000.0

reset_timestep 0

T=10 K

fix 5 all nvt temp 300.0 300.0 1000.0
fix 4 all press/berendsen iso 0.0 100.0 1000.0

change_box all x final -14.50 14.50 y final -14.50 14.50 z final -14.50 14.50 remap

thermo 100
thermo_style custom step temp pe etotal press pxx pyy pzz density
dump 2 all custom 100 trypress4.xyz id type x y z
run 100000

write_data datapress4.txt

Please provide some suggestions.

Thanks!,
Rajni Chahal

2

Hello all,

I am trying to achieve a certain density (rho_desired) of crosslinked
epoxy system. My initial system is at lower density (rho_initial ~
6*rho_desired).

*Case 1.* I am using change_box command to decrease the box dimensions
and achieving denser system. I am observing that instead of decreasing the
box size over given "run period", box size is changing at the start of each
"run period", which means box is changing suddenly.

​which is not really a big problem, if you do short chunks of runs and
change the box frequently. however, the simpler solution is to simply use
fix deform, which *does* do a gradual deformation during a dynamics run.​

*Case 2. *I am using press/berendsen command to apply some
guessed hydrostatic pressure to bring the density of the system to
rho_desired. This time, density seems to be changing gradually until a
certain value, ~1.8*rho_initial. After this, I am observing that density is
increasing but is fluctuating too much.

​once you get to high enough density, you will get large pressure
fluctuations, which in turn will result in box fluctuations and thus
density fluctuations.
the only way to reduce pressure fluctuations (and many other fluctuations),
is to use a larger system.​

​axel.​

3

Hello all,

I am trying to achieve a certain density (rho_desired) of crosslinked epoxy system. My initial system is at lower density (rho_initial ~ 6*rho_desired).

Case 1. I am using change_box command to decrease the box dimensions and achieving denser system. I am observing that instead of decreasing the box size over given "run period", box size is changing at the start of each "run period", which means box is changing suddenly.

which is not really a big problem, if you do short chunks of runs and change the box frequently. however, the simpler solution is to simply use fix deform, which *does* do a gradual deformation during a dynamics run.

Thanks for your suggestions Axel.
Using box_deform, I did followed running in chunks and changing the box size frequently. At the end, I ended up getting large values of residual stress. So, I changed the command to press/berendsen, which is giving reasonable residual stress.
I will look into fix deform too, it seems like a good option.

Case 2. I am using press/berendsen command to apply some guessed hydrostatic pressure to bring the density of the system to rho_desired. This time, density seems to be changing gradually until a certain value, ~1.8*rho_initial. After this, I am observing that density is increasing but is fluctuating too much.

once you get to high enough density, you will get large pressure fluctuations, which in turn will result in box fluctuations and thus density fluctuations.
the only way to reduce pressure fluctuations (and many other fluctuations), is to use a larger system.

This means, I should discontinue increasing density if could not make my system larger?
axel.

I am using reaxff potential. Following is my input script:

# REAX potential for CHON system
# .....

units real

atom_style charge
boundary p p p
read_data datapress3.txt

pair_style reax/c lmp_control lgvdw yes
pair_coeff * * ffield.reax.EPON H C N O

neighbor 2 bin
neigh_modify every 10 delay 0 check no

timestep 0.01 # 0.25

# fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
# fix 3 all temp/berendsen 300.0 300.0 1000.0

# reset_timestep 0

# T=10 K
fix 5 all nvt temp 300.0 300.0 1000.0
fix 4 all press/berendsen iso 0.0 100.0 1000.0
# change_box all x final -14.50 14.50 y final -14.50 14.50 z final -14.50 14.50 remap

thermo 100
thermo_style custom step temp pe etotal press pxx pyy pzz density
dump 2 all custom 100 trypress4.xyz<http://trypress4.xyz> id type x y z
run 100000

write_data datapress4.txt

Please provide some suggestions.

Thanks!,
Rajni Chahal

4

*From:* Axel Kohlmeyer <[email protected]>
*Sent:* Friday, May 19, 2017 6:46 PM
*To:* Chahal, Rajni
*Cc:* [email protected]
*Subject:* Re: [lammps-users] Gradually increasing the density of a
polymer system

Hello all,

I am trying to achieve a certain density (rho_desired) of crosslinked
epoxy system. My initial system is at lower density (rho_initial ~
6*rho_desired).

*Case 1.* I am using change_box command to decrease the box dimensions
and achieving denser system. I am observing that instead of decreasing the
box size over given "run period", box size is changing at the start of each
"run period", which means box is changing suddenly.

which is not really a big problem, if you do short chunks of runs and
change the box frequently. however, the simpler solution is to simply use
fix deform, which *does* do a gradual deformation during a dynamics run.

Thanks for your suggestions Axel.
Using box_deform, I did followed running in chunks and changing the box
size frequently. At the end, I ended up getting large values of residual
stress. So, I changed the command to press/berendsen, which is giving
reasonable residual stress.
I will look into fix deform too, it seems like a good option.

dense liquids and solids are not very compressible​, and compressing a
system too quickly can create large stress. equilibrating such a system is
non-trivial due to what is called "jamming". there is a lot of literature
on this. you should read up on it. using press/berendsen doesn't change
that.

*Case 2. *I am using press/berendsen command to apply some

guessed hydrostatic pressure to bring the density of the system to
rho_desired. This time, density seems to be changing gradually until a
certain value, ~1.8*rho_initial. After this, I am observing that density is
increasing but is fluctuating too much.

once you get to high enough density, you will get large pressure
fluctuations, which in turn will result in box fluctuations and thus
density fluctuations.
the only way to reduce pressure fluctuations (and many other
fluctuations), is to use a larger system.

This means, I should discontinue increasing density if could not make my
system larger?

​it primarily means, that you need to read up on statistical mechanics and
learn how microscopic, atomic scale properties are connected to
macroscopic, continuum properties.​

​axel.​