Dear Everyone,
I am simulating crack propagation in polymers in Lammps with period boundaries along 3 directions. I read the crack example provided in Lammps package.
I have 2 questions regarding the crack example and my polymers:
(1) I am using periodic boundaries, does it mean that if I create an initial crack in the simulation box, then as a result of the periodic condition, I will get infinite many cracks in the whole polymer system??
(2) As in the crack example dealing with metal, for my long-molecule polymers, can I simply use the “group” command to group the upper part and lower part of the polymer system in order to create the crack?
My concern is that if I do so, I might have broken polymer molecules due to the crack, is lammps able to adjust this?? for example reassign the molecule ID…
Thank you very much for any comments and help,
Lili Zhang
Dear Everyone,
I am simulating crack propagation in polymers in Lammps with period
boundaries along 3 directions. I read the crack example provided in Lammps
package.
I have 2 questions regarding the crack example and my polymers:
(1) I am using periodic boundaries, does it mean that if I create an initial
crack in the simulation box, then as a result of the periodic condition, I
will get infinite many cracks in the whole polymer system??
of course, your system is replicated, what else would you expect?
just do a non-periodic system and pull on both sides, if you don't
want that.
(2) As in the crack example dealing with metal, for my long-molecule
polymers, can I simply use the "group" command to group the upper part and
lower part of the polymer system in order to create the crack?
no. how would it propagate?
My concern is that if I do so, I might have broken polymer molecules due
to the crack, is lammps able to adjust this?? for example reassign the
molecule ID...
this is not what will happen. the crack example turns
off the non-bonded(!) interactions between atoms labeled
as type 2 and 3. if you visualize the trajectory, you'll see
that this is only a subset of the atoms of the system. it
is done just to initiate a crack. this part is somewhat
unphysical, since you cannot do this in real life. but it
doesn't matter, since you care about how it propagates.
with a molecular system, bonds will remain.
axel.
Thanks Axel for your commons.
I want to make sure I understand them correctly: You said " with a molecular system, bonds will remain," do you mean that during the crack propagation in a polymer, the crack won’t break the bonds of the molecules, the crack just “separates” the polymer chains keeping the bonds unbroken? What if the polymer has a single long chain?
Is the method used in the crack example to “initiate the crack” can be used for polymer system? I am still looking for a way to initiate the crack for my polymer.
Thanks again,
Lili
Thanks Axel for your commons.
I want to make sure I understand them correctly: You said " with a molecular
system, bonds will remain," do you mean that during the crack propagation
in a polymer, the crack won't break the bonds of the molecules, the crack
just "separates" the polymer chains keeping the bonds unbroken? What if the
polymer has a single long chain?
in a non-reactive model, bonds cannot break.
please update your knowledge about how
classical force fields are constructed from
one of the many textbooks on MD simulations.
it seems to me, that you have not thought
enough about what you are trying to model
and how this can be achieved with the model
that you are using. if this is right, you have
a big problem. the result of computer simulations
is very much dependent on understanding
the strengths and limitations of the models
employed and what you can learn from them.
in short, if you don't plan well, you will be
wasting a lot of your time and may only find
it out when it is too late.
a computer simulation program just bounces
numbers around. it does it equally well for a
good or a bad model and it cannot tell the
difference. this is your job and that can be
very complicated.
Is the method used in the crack example to "initiate the crack" can be used
for polymer system? I am still looking for a way to initiate the crack for
"polymer system" is *far* too vague a description.
it may or may not be right and classical MD
may even be the wrong model. the best way
to start such a thing is usually to survey the
literature and look up what others have done
to do similar things.
axel.
If you put small "cracks" in a large 3d periodic system and pull
it apart using fix deform, for example, to expand the box, then
you will see crack propagation.
Steve