running error "MPI_ABORT"

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1

Dear Lammps users.

I am running the lammps (version:lmp-31Mar17).
However, I received some warnings and output error information like below.
Can anyone figure out what happened?
The first three warnings I faced in my previous simulation for other system,but it simulation runs well.So I just ignored.
For the last warnings, " Bond/angle/dihedral extent > half of periodic box length". I NOT sure how to deal with this.
And the output error information shown “MPI_ABORT” (see bottom figure for details)
Thank you very much for any help in this matter.

best regards

Liyi

PPPM initialization …
extracting TIP4P info from pair style
WARNING: Using 12-bit tables for long-range coulomb (…/kspace.cpp:321)
G vector (1/distance) = 0.288434
grid = 30 30 48
stencil order = 5
estimated absolute RMS force accuracy = 0.0376551
estimated relative force accuracy = 0.000113397
using double precision FFTs
3d grid and FFT values/proc = 15004 5400
WARNING: One or more atoms are time integrated more than once (…/modify.cpp:274)
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (…/neighbor.cpp:472)
Neighbor list info …
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.3092
ghost atom cutoff = 11.3092
binsize = 5.6546, bins = 9 10 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/tip4p/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
WARNING: Bond/angle/dihedral extent > half of periodic box length (…/domain.cpp:906)

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2

Dear Lammps users.

I am running the lammps (version:lmp-31Mar17).

that is 3 years old. there have been significant improvements to LAMMPS since.

However, I received some warnings and output error information like below.
Can anyone figure out what happened?

no. you are missing to provide the actual error message. MPI_Abort is caused by some condition where LAMMPS detects that it cannot continue the simulation and aborts. but it prints what condition that is. this is missing here.

The first three warnings I faced in my previous simulation for other system,but it simulation runs well.So I just ignored.

the first one is an informational message and has been changed to represent this.

WARNING: One or more atoms are time integrated more than once (…/modify.cpp:274)

this one you should not ignore. this is bad and possibly the cause for the abort, as it can lead to diverging time integration.

For the last warnings, " Bond/angle/dihedral extent > half of periodic box length". I NOT sure how to deal with this.

if you have a periodic systems with bonds across periodic boundaries, this is acceptable. if not, then your bond topology is wrong.

axel.

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3

Dear Dr.Axel and lammps users

Yes, you are correct. My topology was wrong. Now It can run but terminated with only 2 timesteps.

The system consists of two solutes (SiO2 tip and SiOH plate which only the surface Si atom hydroxylated) and tip4p/2005 water.

SiO2 tip set to fixed without charge via "fix 4 tip setforce 0.0 0.0 0.0 " (partial input shown below)

For SiOH plate, only the Si on surface and OH with charge. All Si and O are fixed, but H on the surface can move with fixed bond lengths(OH bond) and bond angles(SI-O-H). To deal with the movemrnt of H atom , I use "fix 5 Hydr nvt temp {Text} {Text} 200.0 "

However, I got the error " ERROR: Out of range atoms - cannot compute PPPM (…/pppm_tip4p.cpp:107)"( see below for details)"
The error means water molecules move very fast. I have checked there is no overlap water molecules. And the force on the water is very large (thousands or ever larger in the unit of Kcal/mole-Angstrom) . I am not sure why these force so large and water suddenly move out of box.

Thank you very much for any help in this matter.

Liyi

partial input :

pair_style lj/cut/tip4p/long 2 1 1 1 0.1546 12.0 8.5
#pair_style lj/cut/tip4p/cut 2 1 1 1 0.1546 12.0 8.5
pair_modify mix arithmetic tail yes
kspace_style pppm/tip4p 0.0001

bond_style harmonic
angle_style harmonic

neighbor 2.0 bin

group water type 1 2
group tip type 3 4
group surface type 5 6
group Hydr type 7
group bottom type 5 6 7

neigh_modify delay 2 exclude type 3 4
neigh_modify delay 2 exclude molecule/intra bottom

fix 1 water shake 0.0001 20 0 b 1 a 1
fix 2 water nvt temp {Text} {Text} 200.0

fix 5 Hydr nvt temp {Text} {Text} 200.0
fix 3 surface setforce 0.0 0.0 0.0
fix 4 tip setforce 0.0 0.0 0.0

ini.png

WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (…/neighbor.cpp:472)
Neighbor list info …
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 8 27
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/tip4p/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.29 | 17.11 | 18.3 Mbytes
Step Temp f_TempAve Press f_PressAve f_PEAve_Mol f_DensAve TotEng
0 442.80653 0 9430440.8 0 0 0 26205254
ERROR: Out of range atoms - cannot compute PPPM (…/pppm_tip4p.cpp:107)

Axel Kohlmeyer <[email protected]> 于2020年4月12日周日 下午11:20写道：

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