llnl / llnl/USER-EPH

Cutoff issue from different LAMMPS versions

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Dominant language
C++
Stars
22
Forks
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PR merge metrics
No merged PRs in 30d

Description

I've installed latest LAMMPS version, "29 Aug 2024 - Update 2". These are the instructions I followed:
```
git clone -b stable https://github.com/lammps/lammps.git mylammps
cd mylammps/src
git clone https://github.com/LLNL/USER-EPH.git
vim Makefile # Add user-eph at the end of `PACKAGE` variable
make yes-manybody yes-extra-fix yes-extra-dump yes-extra-compute yes-extra-command yes-python yes-openmp yes-user-eph
make mpi mode=shlib -j8
make install-python
export LD_LIBRARY_PATH=$HOME/mylammps/src:$LD_LIBRARY_PATH
```

This is my input script in LAMMPS:
```
units metal
atom_style atomic
boundary p p p
atom_modify map yes
lattice fcc 3.5365
region full_box block -15 15 -15 15 -15 15
region inner_material block -13 13 -13 13 -13 13
create_box 1 full_box
create_atoms 1 region full_box
group full_box region full_box
group inner_box region inner_material
group thermoboundary subtract full_box inner_box
fix integrate all nve
fix reset all dt/reset 10 1e-05 0.001 0.028664999 units box
pair_style eam/fs
pair_coeff * * eam.Ni.Ni.in_lammps Ni
compute ke all ke/atom
compute pe all pe/atom
compute cna all cna/atom 3.0187
compute coord all coord/atom cutoff 3.0187
velocity all create 600.0 1 loop geom mom yes rot yes
thermo 100
thermo_style custom step dt time temp etotal ke pe
dump dump all custom 1000 simulation.xyz id element x y z c_pe c_ke c_cna c_coord
dump_modify dump element 28
run 1000
unfix integrate
fix eph all eph 1 7 4 1.0 3.5e-6 0.1248 300.0 3 3 3 NULL 1000 egrid/egrid Ni_PRB2019_High_Rho.beta Ni
run 1000
```
I get this error on the second run:
```
run 1000
ERROR: Custom neighbor list cutoff too large for communication cutoff (../neighbor.cpp:864)
Last command: run 1000
```

The script works on "28 Mar 2023 - Development" (some colleague is using it) but I don't feel comfortable using an old development version.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the failure with the provided input script and the listed LAMMPS versions. Start at neighbor.cpp:864 and inspect how the EPH fix changes the neighbor-list or communication cutoff during the second run. Done means identifying the version-dependent cause and documenting or implementing a compatible resolution without requiring the old development version.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp
Domain
hpc
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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