Getting different results in rerun

I calculated radius of gyration of a molecule by this command in the main run:

dump main all custom 10000 dump.lammpstrj id mol type element mass q xu yu zu x y z ix iy iz

compute g011 P1 gyration
fix gr011 P1 ave/time 5 99 500 c_g011 file tmp.gr011

and later in the rerun:

compute g P1 gyration
fix gr1 P1 ave/time 10000 1 10000 c_g file tmp.gr1

I did it as a test and obtained invalid results (values are impossible, and always increasing)! Thus, I’m worried about the values that I didn’t calculate in the main run, but am going to calculate for the first time in the rerun.

What may be the reason for bad results in rerun, while the command are the same? (lammps 15 May 2015)
If you need further info, please tell me.

I calculated radius of gyration of a molecule by this command in the main
run:

dump main all custom 10000 dump.lammpstrj id mol type element mass q xu
yu zu x y z ix iy iz

compute g011 P1 gyration
fix gr011 P1 ave/time 5 99 500 c_g011 file tmp.gr011

and later in the rerun:

compute g P1 gyration
fix gr1 P1 ave/time 10000 1 10000 c_g file tmp.gr1

I did it as a test and obtained invalid results (values are impossible,
and always increasing)! Thus, I'm worried about the values that I didn't
calculate in the main run, but am going to calculate for the first time in
the rerun.

What may be the reason for bad results in rerun, while the command are the
same? (lammps 15 May 2015)
If you need further info, please tell me.

you are comparing apples with oranges, i.e. numbers that have been averaged
over 99 steps each 5 steps apart, with numbers from a single step.​ why
*should* they be the same?

axel.

Yes. That’s true regarding averaging.
However, the fact is that, during rerun, I get values that are far larger than the possible values! The trend and the range of numbers are impossible.

Yes. That's true regarding averaging.
However, the fact is that, during rerun, I get values that are far larger
than the possible values! The trend and the range of numbers are impossible.

​well, nobody can do something about this with such limited information and
no information to quickly and easily reproduce it.
if you believe that there is something wrong with LAMMPS, you have to do
better than just stating "i do something and i get some numbers that i
don't believe".

axel.​

Thank you Axel,

I guess the reason for bad results for radius of gyration (Rg) during rerun is because the molecule crosses the boundaries of the periodic cell. This caused some sudden steps in the trend of Rg vs time.
My dump file contains: id mol type element mass q xu yu zu x y z ix iy iz
I tried to calculate Rg for unwrapped coordinates by “wrapped no” in rerun. However, the results are the same as “wrapped yes”.
How can I tell lammps read the xu yu zu coordinates instead of x y z in my data file in rerun?

I have uploaded the main run and the rerun data here for examination:

https://drive.google.com/folderview?id=0B2ErBBVDJB6GR1U3OFlyVTkxNUU&usp=sharing

From the read_dump doc page, which also applies to rerun:

For dump files in native format, each column of per-atom data has a text label listed in the file. A matching label for each field must appear, e.g. the label “vy” for the field vy. For the x, y, z fields any of the following labels are considered a match:

x, xs, xu, xsu for field *x*
y, ys, yu, ysu for field *y*
z, zs, zu, zsu for field *z* 

The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and unwrapped) is explained on the dump command doc page. These labels are searched for in the list of column labels in the dump file, in order, until a match is found.

So long as you also read the image flags, LAMMPS should do the right thing.

The compute byration commands calculate using unwrapped coords (see the doc pages),

which they do by using the images flags. So if those are correct, you should get

the write answer.

Steve

Thanks Steve,

I have read the doc page, and tried other keys and args.
Although it doesn’t say in the syntax section of the read_dump command, I already tried xu yu zu, and received: ERROR: Illegal read_dump command.
Tried ix iy iz, and obtained pressure in the order of 1E+8, and a constant value for Rg versus time.
While the results for other computes seem to be good in rerun, I wonder why Rg compute is behaving in other ways.
You are welcome to test with the files I shared.
Anyway, thank you so much for your time.

I think you misunderstood the doc page.

In the input script command you always use x,y,z.

But the dump file can list x,xs,xu,etc. LAMMPS will interpret

that column as x-coordinate data and convert it to the right

value internally. However if you don’t have image flags in

your dump file, LAMMPS cannot restore them correctly

in the rerun to what they were in the original run.

Steve