Extracting a scalar from local compute

Dear LAMMPS users,

I am using the python library interface to interact with Lammps between runs. I run Lammps in parallel and use the “extract_compute” command to retrieve per-molecule properties from each processor, calculated with the “compute rigid/local” command. The input file can be found below. I use Python2.7 and Lammps version 12Dec18.

I can use the extract_compute command without any issue for vector and array type properties. I also want to get the number of molecules at each processor by running extract_compute(“mol”,2,0). This, according to the doc, should return an integer with the length of the local array:

from the source code:
"for local data, accessing scalar data for the compute (type = 0),

returns a pointer that should be cast to (int *) which points to

an int with the number of local rows, i.e. the length of the local array.

returns a void pointer to the compute’s internal data structure

for the entity which the caller can cast to the proper data type

returns a NULL if id is not recognized or style/type not supported"

However, extract_compute(“mol”,2,0) returns None, as shown below:

MOL = lmp.extract_compute(“mol”,2,1) (works fine)


<class ‘lammps.LP_c_double’>

length = lmp.extract_compute(“mol”,2,0) (here is the problem)

<type ‘NoneType’>

What can I do to fix this problem? Any suggestion would be greatly appreciated.

This is the input script I am using:

water box simulation

Units and atom style

units real

atom_style full

atom_modify map array sort 0 0.0

Pair info

pair_style lj/cut/coul/long 9.0 9.0

pair_modify tail yes

kspace_style pppm 1.0e-4

bond_style harmonic

angle_style harmonic

dihedral_style none

improper_style none

read_data restart.dat

Neighbor list

neighbor 2.5 bin

neigh_modify every 2 delay 0 check yes

fix 1 all rigid/nve/small molecule

Compute rigid body molecule ids at each processor

compute mol all rigid/local 1 mol

run 100


Pelin Su Bulutoglu