input script or read_data?

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1

Dear Andrew,

I tried diff -b and I got something similar, and I don’t know what’s reason.

in VMD part I tried to use this command in lammps

dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz

but I got this error

ERROR: Dumping an atom property that isn’t allocated (…/dump_custom.cpp:1029)

and I tried some thing else, by using
dump 1 all xyz 100000 *.xyz

in both of codes and I got these

from read_data file:

0.xyz

1
Atoms. Timestep: 0
1 0.5 0.99 0

900000000.xyz

1
Atoms. Timestep: 900000000
1 0.5 0.826027 0

and from input script:

0.xyz

1
Atoms. Timestep: 0
1 0.5 0.99 0

900000000.xyz

1
Atoms. Timestep: 900000000
1 0.5 0.012498 0

the difference is distinct

Regards,

David

Dear lammps users,
So sorry for disturbing you, I’m new in lammps and I have a problem, I checked mail list and manual but I cant solve it. could you please tell me what is difference between these to scripts? (I get different results from them)

Try typing this into the shell

diff -b file1.in file2.in

(change “file1.in”, “file2.in” to the names of your input script files).

When I do this with your input scripts (after changing the line order) I see:

file1.in:
fix 5 all wall/gran 24487562190 29670922496 8688783570 1000000 0.9 1
yplane 0.0 NULL
pair_style gran/hertz/history 24487562190 29670922496 868878350 1000000 0.0 1

file2.in:
fix 5 all wall/gran 24487562190 29670922496 8688783570 1000000 0.9 1
yplane 0 1.0
pair_style gran/hertz/history 24487562190 29670922496 868878350 1000000 0.1 1

I don’t know what effect these changes would have on your system.

Additionally, one of the script reads a data file and the other does
not. You will have to visualize the system with VMD to make sure the
data file you are reading is equivalent to the input script commands
you were using. (Attached file has instructions for viewing data
files with VMD&topotools.)

Andrew

2

dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz

but I got this error

ERROR: Dumping an atom property that isn’t allocated (…/dump_custom.cpp:1029)

I imagine this error is b/c you are using “mol” when

you don’t have an atom_style defined that defines

molecule IDs.

Steve

3

Dear David

Steve is correct.
Sorry about giving you the wrong instructions. I forgot that you were using “atom_style sphere”. The default atom style is “full”. The “full” atom style assigns a molecule-ID number to each atom. (…to keep track of which molecule it belongs to. One way that can be useful is that, when VMD reads the dump file you created in LAMMPS, it can prevent molecules from being cut-in-half when molecules lie on the edge of the periodic boundaries of the simulation. But if you aren’t simulating molecules, then you don’t need this.) The “sphere” atom style does not know about molecule-ID numbers.

How to fix the problem:
In my old instructions, I recommended you use:

dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz

Try using this instead (get rid of “mol”)

dump 1 all custom 5000 DUMP_FILE.lammpstrj id type x y z ix iy iz

Also, in VMD, my old instructions recommended you try this:

topo readlammpsdata system.data full
animate write psf system.psf

Try changing the first line to:
topo readlammpsdata system.data sphere

If that does not work, then try
topo readlammpsdata system.data atomic

VMD should be able to read your data files.

Everything else in my instructions was probably okay.