LAMMPS (2 Aug 2023 - Update 1)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000
# For Simulator : LAMMPS Stable release 29 September 2021
# Running on : LAMMPS 2 Aug 2023
#
Lattice spacing in x,y,z = 5.1529356 5.1529356 5.1529356
Created orthogonal box = (0 0 0) to (51.529356 51.529356 51.529356)
1 by 1 by 1 MPI processor grid
Created 4000 atoms
using lattice units in orthogonal box = (0 0 0) to (51.529356 51.529356 51.529356)
create_atoms CPU = 0.001 seconds
WARNING: Van der Waals parameters for element SI indicate inner wall+shielding, but earlier atoms indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (src/REAXFF/reaxff_ffield.cpp:251)
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:296)
Initial system volume: 136824.58903756 Angstroms^3
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM Project: doi:10.1007/s11837-011-0102-6
- OpenKIM potential: https://openkim.org/cite/SM_282799919035_000#item-citation
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 4000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 9 9 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 302 | 302 | 302 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal
0 -365743.67 -15860.146 -369238.09 -16011.679 293.15 293.15 136824.59 136824.59 1167.4846 1182.9538
1000 -362482.08 -15718.711 -365912.6 -15867.472 287.78827 287.78827 160391.67 160391.67 132.29948 134.05245
Loop time of 171.991 on 1 procs for 1000 steps with 4000 atoms
Performance: 0.502 ns/day, 47.775 hours/ns, 5.814 timesteps/s, 23.257 katom-step/s
88.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 155.42 | 155.42 | 155.42 | 0.0 | 90.37
Neigh | 0.36711 | 0.36711 | 0.36711 | 0.0 | 0.21
Comm | 0.036638 | 0.036638 | 0.036638 | 0.0 | 0.02
Output | 0.00010793 | 0.00010793 | 0.00010793 | 0.0 | 0.00
Modify | 16.122 | 16.122 | 16.122 | 0.0 | 9.37
Other | | 0.04196 | | | 0.02
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8195 ave 8195 max 8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 447327 ave 447327 max 447327 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 447327
Ave neighs/atom = 111.83175
Neighbor list builds = 9
Dangerous builds = 0
flag: Temp = 292.666646859522, Press = 5.98926572843805
Setting up Verlet run ...
Unit style : real
Current step : 1000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal
1000 -362482.08 -15718.711 -365912.6 -15867.472 287.78827 287.78827 160391.67 160391.67 132.29948 134.05245
2000 -362301.97 -15710.9 -365791.12 -15862.204 292.70762 292.70762 160765.19 160765.19 -1581.6082 -1602.5645
Loop time of 140.814 on 1 procs for 1000 steps with 4000 atoms
Performance: 0.614 ns/day, 39.115 hours/ns, 7.102 timesteps/s, 28.406 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 126.77 | 126.77 | 126.77 | 0.0 | 90.03
Neigh | 0.13801 | 0.13801 | 0.13801 | 0.0 | 0.10
Comm | 0.033369 | 0.033369 | 0.033369 | 0.0 | 0.02
Output | 6.2026e-05 | 6.2026e-05 | 6.2026e-05 | 0.0 | 0.00
Modify | 13.852 | 13.852 | 13.852 | 0.0 | 9.84
Other | | 0.01897 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8195 ave 8195 max 8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 446625 ave 446625 max 446625 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 446625
Ave neighs/atom = 111.65625
Neighbor list builds = 5
Dangerous builds = 0
flag: Temp = 293.301561621513, Press = -14.0958995817587
Setting up Verlet run ...
Unit style : real
Current step : 2000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal
2000 -362301.97 -15710.9 -365791.12 -15862.204 292.70762 292.70762 160765.19 160765.19 -1581.6082 -1602.5645
3000 -362191.51 -15706.11 -365597.6 -15853.812 285.73919 285.73919 160593.1 160593.1 -267.79341 -271.34167
Loop time of 147.558 on 1 procs for 1000 steps with 4000 atoms
Performance: 0.586 ns/day, 40.988 hours/ns, 6.777 timesteps/s, 27.108 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 133.53 | 133.53 | 133.53 | 0.0 | 90.49
Neigh | 0.11138 | 0.11138 | 0.11138 | 0.0 | 0.08
Comm | 0.03477 | 0.03477 | 0.03477 | 0.0 | 0.02
Output | 5.849e-05 | 5.849e-05 | 5.849e-05 | 0.0 | 0.00
Modify | 13.865 | 13.865 | 13.865 | 0.0 | 9.40
Other | | 0.02065 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8195 ave 8195 max 8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 446598 ave 446598 max 446598 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 446598
Ave neighs/atom = 111.6495
Neighbor list builds = 4
Dangerous builds = 0
flag: Temp = 293.255787844148, Press = -9.91669741643013
Setting up Verlet run ...
Unit style : real
Current step : 3000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal
3000 -362191.51 -15706.11 -365597.6 -15853.812 285.73919 285.73919 160593.1 160593.1 -267.79341 -271.34167
4000 -362173.42 -15705.326 -365688.03 -15857.734 294.84272 294.84272 160808.77 160808.77 -910.01843 -922.07618
Loop time of 144.911 on 1 procs for 1000 steps with 4000 atoms
Performance: 0.596 ns/day, 40.253 hours/ns, 6.901 timesteps/s, 27.603 katom-step/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 130.98 | 130.98 | 130.98 | 0.0 | 90.38
Neigh | 0.13908 | 0.13908 | 0.13908 | 0.0 | 0.10
Comm | 0.034599 | 0.034599 | 0.034599 | 0.0 | 0.02
Output | 5.3921e-05 | 5.3921e-05 | 5.3921e-05 | 0.0 | 0.00
Modify | 13.74 | 13.74 | 13.74 | 0.0 | 9.48
Other | | 0.02017 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8195 ave 8195 max 8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 446581 ave 446581 max 446581 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 446581
Ave neighs/atom = 111.64525
Neighbor list builds = 5
Dangerous builds = 0
flag: Temp = 293.066158942026, Press = -9.65459789880963
Setting up Verlet run ...
Unit style : real
Current step : 4000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal
4000 -362173.42 -15705.326 -365688.03 -15857.734 294.84272 294.84272 160808.77 160808.77 -910.01843 -922.07618
5000 -362523.28 -15720.497 -365971.48 -15870.025 289.2717 289.2717 160778.73 160778.73 429.40803 435.09769
Loop time of 148.588 on 1 procs for 1000 steps with 4000 atoms
Performance: 0.581 ns/day, 41.274 hours/ns, 6.730 timesteps/s, 26.920 katom-step/s
97.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 134.24 | 134.24 | 134.24 | 0.0 | 90.34
Neigh | 0.10992 | 0.10992 | 0.10992 | 0.0 | 0.07
Comm | 0.03421 | 0.03421 | 0.03421 | 0.0 | 0.02
Output | 6.4541e-05 | 6.4541e-05 | 6.4541e-05 | 0.0 | 0.00
Modify | 14.189 | 14.189 | 14.189 | 0.0 | 9.55
Other | | 0.01957 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8195 ave 8195 max 8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 446798 ave 446798 max 446798 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 446798
Ave neighs/atom = 111.6995
Neighbor list builds = 4
Dangerous builds = 0
flag: Temp = 293.136864510705, Press = -6.63090378071233
Setting up Verlet run ...
Unit style : real
Current step : 5000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal
5000 -362523.28 -15720.497 -365971.48 -15870.025 289.2717 289.2717 160778.73 160778.73 429.40803 435.09769
6000 -362392.46 -15714.824 -365842.89 -15864.449 289.4594 289.4594 160460.14 160460.14 1400.8477 1419.409
Loop time of 148.118 on 1 procs for 1000 steps with 4000 atoms
Performance: 0.583 ns/day, 41.144 hours/ns, 6.751 timesteps/s, 27.006 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 134.15 | 134.15 | 134.15 | 0.0 | 90.57
Neigh | 0.1385 | 0.1385 | 0.1385 | 0.0 | 0.09
Comm | 0.034979 | 0.034979 | 0.034979 | 0.0 | 0.02
Output | 5.9151e-05 | 5.9151e-05 | 5.9151e-05 | 0.0 | 0.00
Modify | 13.773 | 13.773 | 13.773 | 0.0 | 9.30
Other | | 0.02062 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8195 ave 8195 max 8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 446674 ave 446674 max 446674 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 446674
Ave neighs/atom = 111.6685
Neighbor list builds = 5
Dangerous builds = 0
flag: Temp = 293.097061707177, Press = -6.56495067269021
Setting up Verlet run ...
Unit style : real
Current step : 6000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal
6000 -362392.46 -15714.824 -365842.89 -15864.449 289.4594 289.4594 160460.14 160460.14 1400.8477 1419.409
7000 -362223.61 -15707.502 -365763.85 -15861.022 296.99318 296.99318 160646.22 160646.22 382.21941 387.28382
Loop time of 146.763 on 1 procs for 1000 steps with 4000 atoms
Performance: 0.589 ns/day, 40.767 hours/ns, 6.814 timesteps/s, 27.255 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 132.84 | 132.84 | 132.84 | 0.0 | 90.51
Neigh | 0.13849 | 0.13849 | 0.13849 | 0.0 | 0.09
Comm | 0.035175 | 0.035175 | 0.035175 | 0.0 | 0.02
Output | 5.7528e-05 | 5.7528e-05 | 5.7528e-05 | 0.0 | 0.00
Modify | 13.728 | 13.728 | 13.728 | 0.0 | 9.35
Other | | 0.0205 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8195 ave 8195 max 8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 447208 ave 447208 max 447208 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 447208
Ave neighs/atom = 111.802
Neighbor list builds = 5
Dangerous builds = 0
flag: Temp = 293.124937098236, Press = -7.41616484114544
Setting up Verlet run ...
Unit style : real
Current step : 7000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal
7000 -362223.61 -15707.502 -365763.85 -15861.022 296.99318 296.99318 160646.22 160646.22 382.21941 387.28382
8000 -362183.89 -15705.78 -365724.49 -15859.315 297.02423 297.02423 160435.21 160435.21 1287.8473 1304.9113
Loop time of 146.493 on 1 procs for 1000 steps with 4000 atoms
Performance: 0.590 ns/day, 40.692 hours/ns, 6.826 timesteps/s, 27.305 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 132.55 | 132.55 | 132.55 | 0.0 | 90.48
Neigh | 0.11128 | 0.11128 | 0.11128 | 0.0 | 0.08
Comm | 0.034613 | 0.034613 | 0.034613 | 0.0 | 0.02
Output | 7.3197e-05 | 7.3197e-05 | 7.3197e-05 | 0.0 | 0.00
Modify | 13.776 | 13.776 | 13.776 | 0.0 | 9.40
Other | | 0.02021 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8195 ave 8195 max 8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 446419 ave 446419 max 446419 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 446419
Ave neighs/atom = 111.60475
Neighbor list builds = 4
Dangerous builds = 0
flag: Temp = 293.12998389071, Press = -6.45095876278958
Setting up Verlet run ...
Unit style : real
Current step : 8000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal
8000 -362183.89 -15705.78 -365724.49 -15859.315 297.02423 297.02423 160435.21 160435.21 1287.8473 1304.9113
9000 -362323.71 -15711.843 -365850.7 -15864.788 295.88204 295.88204 160647.09 160647.09 152.95841 154.98511
Loop time of 147.604 on 1 procs for 1000 steps with 4000 atoms
Performance: 0.585 ns/day, 41.001 hours/ns, 6.775 timesteps/s, 27.099 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 133.61 | 133.61 | 133.61 | 0.0 | 90.52
Neigh | 0.14554 | 0.14554 | 0.14554 | 0.0 | 0.10
Comm | 0.035617 | 0.035617 | 0.035617 | 0.0 | 0.02
Output | 6.927e-05 | 6.927e-05 | 6.927e-05 | 0.0 | 0.00
Modify | 13.794 | 13.794 | 13.794 | 0.0 | 9.35
Other | | 0.02045 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8195 ave 8195 max 8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 447088 ave 447088 max 447088 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 447088
Ave neighs/atom = 111.772
Neighbor list builds = 5
Dangerous builds = 0
flag: Temp = 293.102880008371, Press = -5.23333947104644
Setting up Verlet run ...
Unit style : real
Current step : 9000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal
9000 -362323.71 -15711.843 -365850.7 -15864.788 295.88204 295.88204 160647.09 160647.09 152.95841 154.98511
10000 -362231.63 -15707.85 -365728.16 -15859.474 293.32683 293.32683 160680.88 160680.88 -370.13647 -375.04078
Loop time of 147.938 on 1 procs for 1000 steps with 4000 atoms
Performance: 0.584 ns/day, 41.094 hours/ns, 6.760 timesteps/s, 27.038 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 133.81 | 133.81 | 133.81 | 0.0 | 90.45
Neigh | 0.11014 | 0.11014 | 0.11014 | 0.0 | 0.07
Comm | 0.03664 | 0.03664 | 0.03664 | 0.0 | 0.02
Output | 7.8217e-05 | 7.8217e-05 | 7.8217e-05 | 0.0 | 0.00
Modify | 13.955 | 13.955 | 13.955 | 0.0 | 9.43
Other | | 0.02092 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8195 ave 8195 max 8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 446929 ave 446929 max 446929 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 446929
Ave neighs/atom = 111.73225
Neighbor list builds = 4
Dangerous builds = 0
160666.062429485
LAMMPS calculation completed