Hello,
I have a question on “dump” command.
I’d like to dump final configuration (x y z) only at the end of simulation run.
for example, I can use:
dump 1 all custom 10000 final.dump id type x y z
run 10000
but when I use “restart” command (read_restart), time step is continuous.
so, if I use same dump command as above, I will get a dump file containing two configurations at time step=10000 (beginning) and 20000 (end).
Do anyone know how to initialize this, or how to get a dump file only at the end of simulation run (especially when using read_restart)??
Thank you.
Hello,
I have a question on "dump" command.
I'd like to dump final configuration (x y z) only at the end of simulation
run.
for example, I can use:
dump 1 all custom 10000 final.dump id type x y z
run 10000
but when I use "restart" command (read_restart), time step is continuous.
so, if I use same dump command as above, I will get a dump file containing
two configurations at time step=10000 (beginning) and 20000 (end).
Do anyone know how to initialize this, or how to get a dump file only at the
end of simulation run (especially when using read_restart)??
how about this:
don't define a dump during the "regular" run, but rather
define the dump _after_ it is done.
then do a 'dump_modify <dumpid> first yes'
followed by a 'run 0'
axel.
Thank you. That works.
by the way,
MSD output is not continuous when using “read_restart”.
i.e., it starts from 0 every run.
Is there a way to continue MSD output from a value obtained at the end of previous simulation run?
From the compute msd doc page:
IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a restart file, then you should use
the same ID for this compute, as in the original run. This is so that
the created fix will also have the same ID, and thus be initialized
correctly with atom coordinates from the restart file.
Steve
Thank you.
But, I used same ID for MSD calculation.
Actually, I used same input file except replacing read_data with read_restart.
It doesn’t provide continuous MSD result.
Thank you.
But, I used same ID for MSD calculation.
Actually, I used same input file except replacing read_data with
read_restart.
It doesn't provide continuous MSD result.
please provide an example input, as simple as possible,
that reproduces this and somebody will look into it.
it is next to impossible to discuss this kind of issue
without a tangible input.
axel.
I used below input file (for example).
At first run, I used simulation.data file.
At second run, I used simulation.restart file created at the first run.
msdB data are continuous, but msdA data start from 0 at second run.
Thank you.
FYI, according to the documentation, I cannot continue the result from restart file.
But my question is how to make it possible?
Same “fix print” does not work for msd/molecule.
e.g.,
variable msdA equal c_msdA[4]
fix msdA groupA print 100 “${msdA}” file A.msd
In my previous answer, I assumed you were asking
about the compute msd command, so I quoted from
its doc page that you can restart with it. Which your
example below has success with.
For compute msd/molecule, the doc page says:
IMPORTANT NOTE: Unlike the compute msd command, this compute does not
store the initial center-of-mass coorindates of its molecules in a
restart file. Thus you cannot continue the MSD per molecule
calculation of this compute when running from a restart file.
Again, that's what your example shows.
To make this work, there would have to be some additional coding,
to hook up the compute with a fix that would archive the info
to restart files.
Steve