Issues with compute com: "compute used in variable between runs is not current"

LAMMPS LAMMPS General Discussion
1

I’m running LAMMPS Nov 3 2022 version.

There is a previous question that seems relevant, but it appears the code parts of the answer/question are missing, so I am posting my own version of the question.

I’m trying to use the compute com command to find the center of mass for a group of atoms, so I can center indents around this point. In particular, I am indenting Z-planes, so I want the Z-coordinate in particular. I’m trying to figure out how to properly call this, and I seem to be having trouble. The following are relevant lines. I’m wondering what I’m doing wrong, to (A) set a variable with the Z coordinate of the center-of-mass, and (B) print that variable.

Here are (I think) the relevant bits for the code:

group		chrom type 1 2 
fix 6 all adapt 1 pair soft a * * v_prefactor
fix 1 all nve/dotc/langevin 1.0 1.0 50.0 100 angmom 10
run                   10000
unfix		1

compute		CHCRM chrom com
variable	centr equal c_CHCRM[3]
print	"${centr}"

Error:

ERROR: Variable centr: Compute used in variable between runs is not current (src/variable.cpp:1452)
Last command: ${centr

My suspicion is that the following commands are much less correct (although obviously there is an issue in the code as it is). Still, I tried them, here are the alternatives:

compute		CHCRM chrom com
variable	centr equal c_CHCRM
print	"${centr}"

Error:

ERROR: Variable centr: Compute global vector in equal-style variable formula (src/variable.cpp:1500)
Last command: ${centr

compute		CHCRM chrom com
variable	centr equal c_CHCRM  (or c_CHCRM[3])
print	"${centr}"

Error:

ERROR on proc 0: Substitution for illegal variable v_centr (src/input.cpp:650)
Last command: ${v_centr
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor

2

That is very relevant and you would just need to follow the explanation.

The problem is that you are using the wrong “tool” for this particular task. Rather than using an “external” compute and accessing its result after it was triggered (the triggering part is what you are missing), you should just use the “xcm()” function of the variable command — LAMMPS documentation, because this is not subject to the restrictions of computes (i.e. need a “consumer” and need to be triggered during a run).

Try

variable centr equal xcm(CHCRM,z)

instead.

1 Like
3

That worked, thank you!