Input file too long for fix ave/time?

Axel, please find the attached file. I do not know what other ASCII
characters could look like '&'. Anyway, please help me run the input file
and see what is going on on your machine. Thanks, Ajing

FWIW this input is using syntax that would only work with
a rather old version of LAMMPS.

please update to the current version.

i cannot promise that this will work,
but i can promise that nobody will care
to make an old version work for you.

axel.

in case, you need additional motivation to update:

the new pair_style tersoff/table will run
your input almost twice as fast

also you should add:

processors * 2 1

to have better load distribution.
with 32 processors,that is another ~2x speedup.

also, the input has overlapping integrators.

axel.

final remark (for now):

the attached picture visualizes the molid to atom mapping
and that has made me curious. is there a specific reason
for this unusual mapping, or do i have to chase a bug in
my topotools plugin for VMD that doesn't read it right?

thanks,
     axel.

vmdscene.jpg

I’m not sure what kind of mapping VMD does but looks like VMD gives colors of atoms according to their molecule IDs. Basically, I want to obtain some average values of each molecule so that I can have high resolution of some physical parameter like Temperature over the entire spacial domain. Does that make sense?

Hi axel,

There is sth wrong with the SVN. I downloaded the most updated LAMMPS package via SVN and tried to compile as I always do. It turns out sth is not working properly.

[acao@…3074… src]$ pwd
/home/acao/mylammps/src

[acao@…3074… src]$ make serial
Makefile:20: *** missing separator. Stop.

Obviously, the 20th line in Makefile " <<<<<<< .mine" has “.” separator. I have no idea why the compiler was complaining about? Any idea?

AC

I'm not sure what kind of mapping VMD does but looks like VMD gives
colors of atoms according to their molecule IDs. Basically, I want

yes, that is what i told it to do.

to obtain some average values of each molecule so that I can have
high resolution of some physical parameter like Temperature over the
entire spacial domain. Does that make sense?

yes. that is what i understood, but what
i don't understand is that those domains
are so irregular. have you tested or
validated those somehow?

overall, you have to do a lot of "homework"
to make your input up-to-date with the current
version of lammps and make it work correctly
and only after that, we can talk again about
potential limitations in the input parser,
which nobody currently can even reproduce.

axel.

Hi axel,

There is sth wrong with the SVN. I downloaded the most updated
LAMMPS package via SVN and tried to compile as I always do. It turns
out sth is not working properly.

[[email protected]... src]$ pwd
/home/acao/mylammps/src

[[email protected]... src]$ make serial
Makefile:20: *** missing separator. Stop.

Obviously, the 20th line in Makefile " <<<<<<< .mine" has "."
separator. I have no idea why the compiler was complaining about?
Any idea?

you have a "conflict" in that file.

likely you made some changes that are incompatible
with changes that you downloaded through updating
the svn. so you'll have to "resolve" this. this is
explained in the SVN documentation.

axel.

All right, finally I found where the problem is. IN my input after “&” there is one space " " that is hard to detect, which will make it not recognizable, as Steve pointed out. Steve, thanks for your help.

Axel, as for the irregular shape of the small box in the data file, I think that is not what I specified. I actually specified the box size as 1 nm X 1 nm except those at the boundaries. Most likely because of the different file format used.

Thank, Ajing