Dear all,
I have a pb with move command : I lost atoms.
In the attached files, adding (or removing) fix n°6 makes the calculation KO (or OK).
It is a dummy example where I set the velocity of a given group (move_top_group) to zero and then I apply or not the move command. To the best of my understanding, the fix n°6 should not change anything (I set an initial velocity to NULL NULL 0.0 and move at a velocity of NULL NULL 0.0) but it makes the calculation crash with lost atoms.
I have checked where the lost atoms are, there are located in the top of the box, and are part of the move_top_group group. I suspect that the escape through top fixed boundary, but 1) they should be trapped by the move command with Vz=0.0 and 2) they should be trapped by the fix/wall command.
I would not understand they escape through x or y boundary.
Do you have any suggestions ?
PS : in the real case, fix n°6 has a velocity Z component different from 0.0
Alexandre BARTHELEMY
move.zip (363 KB)
Dear all,
I have a pb with move command : I lost atoms.
In the attached files, adding (or removing) fix n°6 makes the calculation KO
(or OK).
It is a dummy example where I set the velocity of a given group
(move_top_group) to zero and then I apply or not the move command. To the
best of my understanding, the fix n°6 should not change anything (I set an
initial velocity to NULL NULL 0.0 and move at a velocity of NULL NULL 0.0)
but it makes the calculation crash with lost atoms.
I have checked where the lost atoms are, there are located in the top of the
box, and are part of the move_top_group group. I suspect that the escape
through top fixed boundary, but 1) they should be trapped by the move
command with Vz=0.0 and 2) they should be trapped by the fix/wall command.
I would not understand they escape through x or y boundary.
Do you have any suggestions ?
yes. you need to remove the image flags in your data file.
write out a dump with xu yu zu coordinates and you'll see.
why specifically fix move triggers this is a bit of a mystery to me,
but after running:
sed -i 's/ -*[0-9]\+ -*[0-9]\+ -*[0-9]\+$//' data_bonding.silicon1
your input is running smoothly.
axel.
omg
I would have *never* figured this out.
Axel, I thank you a lot
Have a nice day
Alexandre
-----Message d'origine-----
This paragrpah on the fix move doc page is
probably relevant:
IMPORTANT NOTE: As dicsussed below, atoms are moved relative to their
initial position at the time the fix is specified. These initial
coordinates are stored by the fix in “unwrapped” form, by using the
image flags associated with each atom. See the “dump
custom”_dump.html command for a discussion of “unwrapped” coordinates.
See the Atoms section of the “read_data”_read_data.html command for a
discussion of image flags and how they are set for each atom. You can
reset the image flags (e.g. to 0) before invoking this fix by using
the “set image”_set.html command.
Steve