Thanks !. I was trying to achieve something else with fix deposit (which it was not intended to). I will figure this out later.
I have another question now. Lets consider the deposition of molecule say water in to a system (I am using atomstyle full). I am turning of all the bonded interactions by using the delete bonds command
delete_bonds all multi any
Now the deposited molecule belongs to the group all and also the group mentioned in the fix deposit according to the manual.
But the bond, angle potentials are not turned off for the deposited molecule why is this so ?. You can check thus by using
compute 1 all pe bond
I can get around this problem by zeroing out the coefficients for the deposited molecule but I dont want to .
The group command in lammps is incremental and I thought group all would be internally updated and any restrictions/constraints placed on group all would be respected by fix deposit.
Also I am concerned about how the fix deposit is going to handle conflicting group restrictions since the deposited molecule belongs to group all and the group mentioned in the fix deposit.
Right now the fix deposit seems to ignore any group restrictions on the group “all”.
Thanks
Arun
Thanks !. I was trying to achieve something else with fix deposit (which it
was not intended to). I will figure this out later.
I have another question now. Lets consider the deposition of molecule say
water in to a system (I am using atomstyle full). I am turning of all the
bonded interactions by using the delete bonds command
delete_bonds all multi any
before or after the simulation with fix deposit?
Now the deposited molecule belongs to the group all and also the group
mentioned in the fix deposit according to the manual.
But the bond, angle potentials are not turned off for the deposited
molecule why is this so ?. You can check thus by using
all commands in LAMMPS act immediately on the system as it is. if you
deposit molecules *after* running delete_bonds
compute 1 all pe bond
i cannot reproduce it by modifying the deposit example.
I can get around this problem by zeroing out the coefficients for the
deposited molecule but I dont want to .
The group command in lammps is incremental and I thought group all would be
internally updated and any restrictions/constraints placed on group all
would be respected by fix deposit.
*all* atoms are part of group all, they don't need to be added. a one
time command doesn't place a constraint on groups. deposited atoms or
molecules only come into existence during the run, so running
delete_bonds before has no effect on the deposition and running it
after a run works just fine for me.
if you have an input that demonstrates where LAMMPS doesn't behave as
it is documented, please post it.
axel.