I used the following input file with streitz and eam/alloy potential settings for the simulation with LAMMPS.
variable kb equal 8.617333262e-5
variable t equal 300.0
variable th equal 400.0
variable tc equal 200.0
units metal
dimension 3
newton on
boundary p p p
atom_style atomic
neighbor 2.0 bin
timestep 0.0005
read_data atomic_structure_atomic
#pair_style hybrid vashishta lj/cut 12.0 airebo 3.0
#pair_coeff * * vashishta ./Al2O3.vashishta O Al NULL NULL
pair_style hybrid/overlay coul/streitz 12.0 wolf 0.3 eam/alloy airebo 3.0 lj/cut 12.0
pair_coeff * * coul/streitz ./AlO.streitz O Al NULL NULL
pair_coeff * * eam/alloy ./AlO.eam.alloy O Al NULL NULL
pair_coeff * * airebo ./CH.airebo NULL NULL C C
pair_coeff 1 3 lj/cut 0.006199133907248657 3.692748434432002
pair_coeff 1 4 lj/cut 0.006199133907248657 3.692748434432002
pair_coeff 2 3 lj/cut 0.042256836241015484 3.1764162195782846
pair_coeff 2 4 lj/cut 0.042256836241015484 3.1764162195782846
#fix 11 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
compute ke1 all ke/atom
variable tem atom c_ke1/1.5/${kb}
#thermo 100
thermo 1000
thermo_style custom step temp pxx pyy pzz press vol
velocity all create $t 898758 mom yes rot yes dist gaussian
fix 11 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
min_style cg
minimize 1.0e-8 1.0e-8 1000000 1000000
#1st euqilibrium in NPT ensamble
#thermo 100
thermo 2000
thermo_style custom step temp pe ke etotal vol pxx pyy pzz press
fix 1 all npt temp $t $t 0.05 aniso 0.0 0.0 0.5
#dump xyz_npt all xyz 10 dump_npt.xyz
dump xyz_npt all xyz 1000 dump_npt.xyz
dump_modify xyz_npt element O Al C1 C2
run 500000
#run 1000000
unfix 1
undump xyz_npt
reset_timestep 0
write_data atomic_structure_atomic_npt.dat
#2nd equilibrium in NVT ensamble
#thermo 100
thermo 2000
thermo_style custom temp pe ke etotal vol pxx pyy pzz press
fix 2 all nvt temp $t $t 0.05
#dump xyz_nvt all xyz 10 dump_nvt.xyz
dump xyz_nvt all xyz 1000 dump_nvt.xyz
dump_modify xyz_nvt element O Al C1 C2
run 500000
#run 1000000
unfix 2
undump xyz_nvt
reset_timestep 0
#Dividing the zone
variable zbl equal zlo
variable zbh equal zhi
variable nla equal 100
variable sca equal 1/${nla}
variable len equal ${zbh}-${zbl}
variable dz equal ${len}/${nla}
variable zll equal ${zbl}+${dz}*2
variable zlh equal ${zbl}+${dz}*6
variable zrl equal ${zbh}-${dz}*6
variable zrh equal ${zbh}-${dz}*2
region reg_whole block INF INF INF INF ${zbl} ${zbh} units box
region lef_fixed block INF INF INF INF INF ${zll} units box
region hot block INF INF INF INF ${zll} ${zlh} units box
region cold block INF INF INF INF ${zrl} ${zrh} units box
region rig_fixed block INF INF INF INF ${zrh} INF units box
region fixed_both union 2 lef_fixed rig_fixed
group fixed region fixed_both
group hot region hot
group cold region cold
group move subtract all fixed
reset_timestep 0
change_box all boundary p p f
velocity fixed set 0 0 0
fix fixed fixed setforce 0 0 0
fix 3 hot langevin ${th} ${th} 0.05 14565 tally yes
fix 4 cold langevin ${tc} ${tc} 0.05 16576 tally yes
fix 5 all nve
variable time equal step
variable el equal f_3
variable er equal f_4
compute 6 all chunk/atom bin/1d z lower ${sca} units reduced
#fix 7 all ave/chunk 1 10 10 6 v_tem file profile.heat
fix 7 all ave/chunk 1 10000 10000 6 v_tem file profile.heat
#thermo 100
thermo 2000
thermo_style custom step temp ke pe etotal press vol
#dump xyz_nve all xyz 10 dump_nve.xyz
dump xyz_nve all xyz 1000 dump_nve.xyz
dump_modify xyz_nve element O Al C1 C2
run 500000
#run 1000000
unfix 7
undump xyz_nve
reset_timestep 0
fix 8 all ave/chunk 1 10000 10000 6 v_tem file time_average_temperature.dat
fix eou all print 2000 "${time} ${el} ${er}" file energy.dat title "time e1 e2" screen no
#thermo 200
thermo 20000
thermo_style custom step temp ke pe etotal press vol
#dump fin all xyz 100 fin.xyz
dump fin all xyz 20000 fin.xyz
dump_modify fin element O Al C1 C2
run 500000
#run 2000000
After I launched the simulation, the calculation failed. The log.lammps file was empty and the output file from slurm system shows the following error message.
LAMMPS (17 Apr 2024)
[b08r4n08:32415:0:32415] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n10:24083:0:24083] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n09:26220:0:26220] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32412:0:32412] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32432:0:32432] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32416:0:32416] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32413:0:32413] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32436:0:32436] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32435:0:32435] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32427:0:32427] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32423:0:32423] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32429:0:32429] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32437:0:32437] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32431:0:32431] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32424:0:32424] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32414:0:32414] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32426:0:32426] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n08:32438:0:32438] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n10:24100:0:24100] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
Reading data file ...
orthogonal box = (0 0 0) to (24.7284 23.795 1199.1959)
1 by 1 by 96 MPI processor grid
reading atoms ...
83280 atoms
read_data CPU = 0.465 seconds
Reading coul/streitz potential file ./AlO.streitz with DATE: 2015-02-19
Reading eam/alloy potential file ./AlO.eam.alloy with DATE: 2015-02-19
Reading airebo potential file ./CH.airebo with DATE: 2011-10-25
[b08r4n10:24084:0:24084] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n09:26224:0:26224] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[b08r4n10:24104:0:24104] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
......
......
......
[b08r4n08:32422] [ 5] /public/home/zzs000227/lammps/lammps-17Apr2024/src/lmp_mpi[0x419e66]
[b08r4n08:32422] [ 6] /public/home/zzs000227/lammps/lammps-17Apr2024/src/lmp_mpi[0x41a7bc]
[b08r4n08:32422] [ 7] /public/home/zzs000227/lammps/lammps-17Apr2024/src/lmp_mpi[0x40ab08]
[b08r4n08:32422] [ 8] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b958c3183d5]
[b08r4n08:32422] [ 9] /public/home/zzs000227/lammps/lammps-17Apr2024/src/lmp_mpi[0x40cac5]
[b08r4n08:32422] *** End of error message ***
slurmstepd: error: mpi/pmix_v3: _errhandler: b08r4n10 [2]: pmixp_client_v2.c:211: Error handler invoked: status = -25, source = [slurm.pmix.16950728.0:83]
slurmstepd: error: *** STEP 16950728.0 ON b08r4n08 CANCELLED AT 2024-05-02T00:11:43 ***
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd: error: mpi/pmix_v3: _errhandler: b08r4n09 [1]: pmixp_client_v2.c:211: Error handler invoked: status = -25, source = [slurm.pmix.16950728.0:62]
slurmstepd: error: mpi/pmix_v3: _errhandler: b08r4n08 [0]: pmixp_client_v2.c:211: Error handler invoked: status = -25, source = [slurm.pmix.16950728.0:21]
srun: error: b08r4n10: tasks 64-95: Segmentation fault
srun: launch/slurm: _step_signal: Terminating StepId=16950728.0
srun: error: b08r4n08: tasks 0-31: Segmentation fault
srun: error: b08r4n09: tasks 32-63: Segmentation fault
Would anyone please tell me why the calculation fails with suggestions/comments?
Thank you in advance.
