Hi,

I’m using the compute pair/local command to get the distances from a particular set of atoms of the system using the python interface. I’m using the 23Jun2022 (Update 1) release.

I set up two compute commands as:

lmp.command(“compute ids all property/local patom1 patom2”)

lmp.command(“compute dist all pair/local dx dy dz”)

lmp.command(“run 0”)

to get the id pairs of all interactions, and the distances associated to those interactions. lmp is the LAMMPS object.

Then I extract the information from those computes:

ids = gather_compute(“ids”,lmp,MPI.COMM_WORLD,2,np.int32)

dist = gather_compute(“dist”,lmp,MPI.COMM_WORLD,3)

gather_compute is a small function that I made to collect the information with MPI:

```
def gather_compute(computeid,lmp,comm,vec_size,datatype=np.float64):
array = lmp.numpy.extract_compute(computeid,LMP_STYLE_LOCAL,LMP_TYPE_ARRAY).astype(datatype,copy=False)
farray = array.flatten()
array_sizes = np.array(comm.gather(farray.shape[0],root=0))
if(master):
recvbf = np.empty(array_sizes.sum(),dtype=datatype)
else:
recvbf = None
comm.Gatherv(farray,(recvbf,array_sizes),root=0)
if(master):
return recvbf.reshape((int(array_sizes.sum()/vec_size),vec_size))
else:
return None
```

According to the LAMMPS documentation for both the latest stable release and the version I’m using the vectors in ‘dist’ should always be defined from the smallest id to the biggest id (“This value [dx,dy,dz] is always the distance from the atom of lower to the one with the higher id.”) but I find that the opposite is true. Outputting a couple i,j pairs of the previously defined ‘ids’ and their corresponding ‘dist’ vectors I get:

1539 562 [-3.94407078 8.67170072 0.98916273]

1542 562 [-2.12934197 8.51996973 2.73700122]

The positions of the atoms with these ids are:

562 -0.1641226737947051 8.984665968777039 -0.9482579825615813

1539 3.7799481076267973 0.31296524725565583 -1.9374207112908028

1542 1.9652192984527783 0.4646962400097415 -3.6852592019084223

As you can see for the 1539 562 pair if we did the vector from 562 (smaller id) to 1539 (bigger) we would get pos(1539)-pos(562) = 3.94407078, -8.67170072, -0.98916273, the opposite sing. This is easy to fix from my python script but I would like to know if this is the intended output.

Unless I’m misunderstanding the LAMMPS documentation it appears this is a bug? I have not found in the release notes if this has been fixed, but sorry if this is known/fixed in some later release.

Thanks.