Dear LAMMPS users ,
I want to calculate RDF for long cutoff range so I use rerun command .
This is a part of my input file :
…
dump 1 all atom 100 dump.atom
compute RDF all rdf 100 1 1
fix 1 all ave/time 100 1 100 c_RDF file output.rdf mode vector
run 10000
reset_timestep 100
rerun dump.atom dump x y
My system is 2D !
I get an error : ERROR: Invalid timestep reset for fix ave/time (…/fix_ave_time.cpp:555)
Can you please let me know How I can solve it ?
I would be grateful If you can send me one example of this kind of calculation.
Best,
Dear LAMMPS users ,
I want to calculate RDF for long cutoff range so I use rerun command .
This is a part of my input file :
...
dump 1 all atom 100 dump.atom
compute RDF all rdf 100 1 1
fix 1 all ave/time 100 1 100 c_RDF file output.rdf mode vector
run 10000
reset_timestep 100
rerun dump.atom dump x y
My system is 2D !
I get an error : ERROR: Invalid timestep reset for fix ave/time
(../fix_ave_time.cpp:555)
Can you please let me know How I can solve it ?
the error message already tells you where the problem is: you cannot keep
fix ave/time open while you reset the timestep and change settings and
rerun. that simply doesn't make sense.
I would be grateful If you can send me one example of this kind of
calculation.
there is really not much to it, and it just requires a minimal amount of
thinking and common sense to get it working. 1) do a run and record the
trajectory. 2) set up a second input that is essentially the same , but has
changed settings, e.g. a longer cutoff and then use rerun instead of run.
easy as pie.
axel.
Dear Axel ,
I did exactly what you told me !
My system is 2D , when I choose a very long cutoff I got this error :
ERROR: Cannot use neighbor bins - box size << cutoff (…/neighbor.cpp:1715)
I changed the neighbor command to neighbor 2.0 nsq
But now I get one another error :
ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (…/neigh_half_nsq.cpp:356)
As I understood I should use " neigh_modify one " for solving this error but I don’t have any idea about “N = max number of neighbors of one atom” .
How can I get it ?!
Best,
Dear Axel ,
I did exactly what you told me !
My system is 2D , when I choose a very long cutoff I got this error :
ERROR: Cannot use neighbor bins - box size << cutoff (../neighbor.cpp:1715)
I changed the neighbor command to neighbor 2.0 nsq
But now I get one another error :
ERROR on proc 0: Neighbor list overflow, boost neigh_modify one
(../neigh_half_nsq.cpp:356)
As I understood I should use " neigh_modify one " for solving this error
but I don't have any idea about "N = max number of neighbors of one atom"
.
How can I get it ?!
ouch! are you serious??
the cutoff defines a sphere around the central atom, right? now, how many
atoms of a given type are in a sphere of a given volume? you know your
overall atom density, you can determine the volume of the sphere (plus
neighbor list skin) and if you multiply those, you get the average number
of neighbors. crank that up some for safety, and you should be done.
axel.