forked from lijiext/lammps
228 lines
11 KiB
Groff
228 lines
11 KiB
Groff
LAMMPS (27 Nov 2018)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
units metal
|
|
atom_style charge
|
|
dimension 3
|
|
boundary p p p
|
|
|
|
read_data data.m-HfO2
|
|
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
|
|
1 by 2 by 2 MPI processor grid
|
|
reading atoms ...
|
|
1500 atoms
|
|
#read_data data.t-HfO2
|
|
#read_data data.c-HfO2
|
|
|
|
mass 1 178.0
|
|
group type1 type 1
|
|
500 atoms in group type1
|
|
compute charge1 type1 property/atom q
|
|
compute q1 type1 reduce ave c_charge1
|
|
mass 2 16.00
|
|
group type2 type 2
|
|
1000 atoms in group type2
|
|
compute charge2 type2 property/atom q
|
|
compute q2 type2 reduce ave c_charge2
|
|
|
|
pair_style comb
|
|
pair_coeff * * ffield.comb Hf O
|
|
Reading potential file ffield.comb with DATE: 2011-02-22
|
|
|
|
neighbor 0.5 bin
|
|
neigh_modify every 10 delay 10 check yes
|
|
|
|
timestep 0.00020
|
|
|
|
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
|
|
thermo_modify norm yes
|
|
|
|
fix 1 all nvt temp 300.0 300.0 0.1
|
|
thermo 1
|
|
run 1
|
|
Neighbor list info ...
|
|
update every 10 steps, delay 10 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 12.5
|
|
ghost atom cutoff = 12.5
|
|
binsize = 6.25, bins = 5 5 5
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair comb, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 7.595 | 7.595 | 7.596 Mbytes
|
|
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
|
0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
|
|
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
|
|
Loop time of 0.0343346 on 4 procs for 1 steps with 1500 atoms
|
|
|
|
Performance: 0.503 ns/day, 47.687 hours/ns, 29.125 timesteps/s
|
|
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.032358 | 0.033033 | 0.034117 | 0.4 | 96.21
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.00012684 | 0.0012044 | 0.0018878 | 2.0 | 3.51
|
|
Output | 4.3392e-05 | 4.6432e-05 | 5.1737e-05 | 0.0 | 0.14
|
|
Modify | 2.1935e-05 | 2.3842e-05 | 2.5511e-05 | 0.0 | 0.07
|
|
Other | | 2.718e-05 | | | 0.08
|
|
|
|
Nlocal: 375 ave 375 max 375 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 6075 ave 6075 max 6075 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 259375 ave 259375 max 259375 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 1037500
|
|
Ave neighs/atom = 691.667
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
fix 2 all qeq/comb 1 0.003 file fq.out
|
|
run 5
|
|
Per MPI rank memory allocation (min/avg/max) = 8.22 | 8.22 | 8.221 Mbytes
|
|
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
|
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
|
2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
|
3 0.2686308 -10.041388 -10.041423 2.7214912 -12.762914 -130800.39 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
|
4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
|
5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
|
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
|
Loop time of 0.264002 on 4 procs for 5 steps with 1500 atoms
|
|
|
|
Performance: 0.327 ns/day, 73.334 hours/ns, 18.939 timesteps/s
|
|
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.16374 | 0.17099 | 0.17738 | 1.2 | 64.77
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.0030768 | 0.0093628 | 0.016711 | 5.1 | 3.55
|
|
Output | 0.00022531 | 0.00034034 | 0.00068116 | 0.0 | 0.13
|
|
Modify | 0.083183 | 0.083188 | 0.083197 | 0.0 | 31.51
|
|
Other | | 0.0001165 | | | 0.04
|
|
|
|
Nlocal: 375 ave 375 max 375 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 6075 ave 6075 max 6075 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 259375 ave 259375 max 259375 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 1037500
|
|
Ave neighs/atom = 691.667
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
|
|
unfix 1
|
|
fix 1 all box/relax aniso 0.0 vmax 0.0002
|
|
|
|
# should minimize to higher tolerance in practice
|
|
|
|
#minimize 1.0e-12 1.0e-18 1000 10000
|
|
minimize 1.0e-4 1.0e-6 1000 10000
|
|
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
|
|
Per MPI rank memory allocation (min/avg/max) = 9.345 | 9.345 | 9.346 Mbytes
|
|
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
|
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
|
|
7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
Loop time of 0.15331 on 4 procs for 1 steps with 1500 atoms
|
|
|
|
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
Minimization stats:
|
|
Stopping criterion = energy tolerance
|
|
Energy initial, next-to-last, final =
|
|
-10.0414727016 -10.0414727016 -10.0419532985
|
|
Force two-norm initial, final = 2625.99 2625.45
|
|
Force max component initial, final = 1915.33 1916.61
|
|
Final line search alpha, max atom move = 1.04421e-07 0.000200134
|
|
Iterations, force evaluations = 1 1
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.065077 | 0.066851 | 0.06825 | 0.5 | 43.61
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.0013995 | 0.0027977 | 0.0045724 | 2.4 | 1.82
|
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
Modify | 0.083279 | 0.083284 | 0.083293 | 0.0 | 54.32
|
|
Other | | 0.0003769 | | | 0.25
|
|
|
|
Nlocal: 375 ave 375 max 375 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 6075 ave 6075 max 6075 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 259375 ave 259375 max 259375 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 1037500
|
|
Ave neighs/atom = 691.667
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
min_modify dmax 0.005 line quadratic
|
|
|
|
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
|
|
#dump_modify 1 element Hf O
|
|
|
|
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
|
#dump_modify 2 pad 2 element Hf O
|
|
|
|
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
|
#dump_modify 3 pad 2 element Hf O
|
|
|
|
velocity all create 300.1 2398378
|
|
run 10
|
|
Per MPI rank memory allocation (min/avg/max) = 8.22 | 8.22 | 8.221 Mbytes
|
|
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2
|
|
7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
9 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
10 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
11 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
12 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
13 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
14 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
|
|
Loop time of 0.555816 on 4 procs for 10 steps with 1500 atoms
|
|
|
|
Performance: 0.311 ns/day, 77.197 hours/ns, 17.992 timesteps/s
|
|
92.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.33358 | 0.35381 | 0.36898 | 2.2 | 63.66
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.005245 | 0.02059 | 0.041362 | 9.1 | 3.70
|
|
Output | 0.00058889 | 0.00082082 | 0.0015032 | 0.0 | 0.15
|
|
Modify | 0.1798 | 0.18018 | 0.18053 | 0.1 | 32.42
|
|
Other | | 0.0004114 | | | 0.07
|
|
|
|
Nlocal: 375 ave 375 max 375 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 6075 ave 6075 max 6075 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 259375 ave 259375 max 259375 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 1037500
|
|
Ave neighs/atom = 691.667
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:02
|