fix ave/chunk with ave running

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1

When I use fix ave/chunk with ‘ave running,’ the output file only contains the header lines and a line for each timestep, but the line for each timestep says that there are 0 chunks and 0 atoms, like so:

Chunk-averaged data for fix chunkFix and group all

Timestep Number-of-chunks Total-count

Chunk Coord1 Coord2 Ncount temp

0 0 0
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
7 0 0
8 0 0
9 0 0
10 0 0

I have the newest version of lammps from git. I have attached an example script which reproduces the problem.
Thanks, Steve Strong

in.test (553 Bytes)

2

I suggest you first define compute chunk/atom and dump

the per-atom chunk assignments to a dump file to see

if they are what you intend. If that works, then

use fix ave/chunk.

Steve

3

Thanks for the reply. When I use the fix ave/chunk without ‘ave running’ it works exactly as expected. When I use the exact same command, but tack on ‘ave running’ it gives the output below. So I don’t think the problem is with the compute.
Thanks, Steven

4

Think I fixed this. Will be in next patch …

thanks for the test script,

Steve

5

Thanks, that did fix that issue, but now I get a segfault when I use compute chunk/atom with the region keyword. The error message is below, and the test script that generated it is also attached.

[enemy:17752] *** Process received signal ***
[enemy:17752] Signal: Segmentation fault (11)
[enemy:17752] Signal code: Address not mapped (1)
[enemy:17752] Failing at address: 0x104
[enemy:17752] [ 0] /lib64/libpthread.so.0 [0x384200e7c0]
[enemy:17752] [ 1] lammps(_ZN9LAMMPS_NS6Region8prematchEv+0x5) [0xab77a5]
[enemy:17752] [ 2] lammps(_ZN9LAMMPS_NS16ComputeChunkAtom16assign_chunk_idsEv+0xb2) [0x563262]
[enemy:17752] [ 3] lammps(_ZN9LAMMPS_NS16ComputeChunkAtom12setup_chunksEv+0x6dc) [0x56282c]
[enemy:17752] [ 4] lammps(_ZN9LAMMPS_NS11FixAveChunkC1EPNS_6LAMMPSEiPPc+0x1231) [0x6263a1]
[enemy:17752] [ 5] lammps(_ZN9LAMMPS_NS6Modify11fix_creatorINS_11FixAveChunkEEEPNS_3FixEPNS_6LAMMPSEiPPc+0x5e) [0x7edd9e]
[enemy:17752] [ 6] lammps(_ZN9LAMMPS_NS6Modify7add_fixEiPPci+0xd7d) [0x7fc71d]
[enemy:17752] [ 7] lammps(_ZN9LAMMPS_NS5Input15execute_commandEv+0x178a) [0x7b7c5a]
[enemy:17752] [ 8] lammps(_ZN9LAMMPS_NS5Input4fileEv+0x15e) [0x7b5bae]
[enemy:17752] [ 9] lammps(main+0xad) [0x7d297d]
[enemy:17752] [10] /lib64/libc.so.6(__libc_start_main+0xf4) [0x384141d994]
[enemy:17752] [11] lammps [0x4b9ca9]
[enemy:17752] *** End of error message ***
Segmentation fault

Thanks, Steven

in.test (707 Bytes)

6

Here is a very slightly simpler test script. I accidentally left a few other lines in.

in.test (660 Bytes)

7

I see the problem - will be fixed in a patch later today.

thanks for another test script

Steve