Can anyone tell me what's the problem in the following 'fix deform'
input file. This was changing the box size perfectly, but now it does
not work with the same data file, although the increase in pressure
can be seen? .. Monojoy
units lj
special_bonds fene
atom_style bond
atom_modify map hash
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 1
#read_data dataD.chain
read_restart restart.dat
#group C type 1
#displace_box all x final -10.844961 10.844961 y final -10.844961
10.844961 z final -10.844961 10.844961 units box
bond_style fene
bond_coeff 1 30.0 1.5 2.0 1.0
pair_style lj/cut 1.12
pair_coeff 1 1 2.0 1.0 1.12
pair_modify shift yes
fix 1 all deform 1 x final -10.844961 10.844961 y final
-10.844961 10.844961 z final -10.844961 10.844961 units box
fix 2 all nve
fix 3 all langevin 1.0 1.0 10.0 904297
write_restart restart2.dat
thermo 1000
dump 1 all xyz 100000 dump03.xyz
timestep 0.005
run 100000
monojoy,
computer software, if correct, acts predictable.
so it is more likely than not, that there is some
kind of difference between what you are doing now
and what you were doing before. nobody but you
can tell what is the difference, so you yourself are
in the best position to find it out.
systematic debugging of problems is a basic
skill in using computational tools. this is a perfect
opportunity to improve your skills in this field.
just sending random input file fragments without
any chance for anybody else to reproduce your
calculation has an extremely low probability of
generating any useful response. you may be better
off playing the lottery.
cheers,
axel.
Hi Axel,
After working for years on MD simulation, I must agree with you that
computer software acts predictably. As this code is not written by me
and also after doing systematically debugging for last two days, when
it didn't work, I asked for help from people who are developing the
same. The answer you gave, I suppose, is not exactly the reply of the
question.
It's true, I started working on LAMMPS recently, but I also wrote my
own small-scale MD code (you can check out my papers on web of
science), so your comment on "improve your computer skills" is not the
answer I was looking for the question I asked. The answer I was
looking for from the expert was whether the input file looks correct,
or there might be a problem in my current data-file (while converting
from restart bin file) or the model is incorrect. Then I have to
correct those.
Thanks once again Axel..
Monojoy
monojoy,
It's true, I started working on LAMMPS recently, but I also wrote my
own small-scale MD code (you can check out my papers on web of
science), so your comment on "improve your computer skills" is not the
answer I was looking for the question I asked. The answer I was
well, i stand corrected and you can replace "computer skills"
with "communication skills".
rule number one for getting help on a mailing list is:
make it easy for people to help you. and you definitely
need to improve in that respect.
outside of people that are extremely bored, how can
you expect anybody to be interested to be looking at
your input fragments, which on top of being incomplete
also are hard to read due to all the commented out lines?
looking for from the expert was whether the input file looks correct,
or there might be a problem in my current data-file (while converting
from restart bin file) or the model is incorrect. Then I have to
correct those.
actually, the input file you posted reads a
restart file not a data file. it is really hard
to follow what you are asking and what you are
expecting the simulation to do and what it does
instead and particularly how you detect it.
most of your failure descriptions are of the type
"it doesn't work".
your question to check the validity of the input
is easily done by checking the documentation yourself,
and perhaps do a few simple input examples to confirm
your expectations.
it doesn't look like you are doing anything complicated
that would require an expect to look at it.
cheers,
axel.
Excellent, your help is highly appreciated, Axel..
Thanks
Monojoy
Your previous email said you converted the restart file
to a data file and the box size hadn't changed. You are
writing a restart file before your run command (not during).
The fix deform command doesn't do anything until
a run takes place, and then it gradually changes the
box size during the run.
Steve
Thanks Steve, it was exactly the same problem you said, writing the
restart file before run command. It works perfect now.
Monojoy