#-------------------------------------------------------------------------------
# Stage 2.2: Compress Layer
#-------------------------------------------------------------------------------
min_style cg
min_modify dmax 0.1 line fast
reset_timestep 0
displace_atoms all move 0.0 0.0 -10.281631167422894
Displacing atoms ...
# 1. Variable Indenter Stage, minimization to compress initial cell
#------------------------------------------------------------------
variable lowz equal zlo
print "INITIAL zlow=${lowz}"
INITIAL zlow=-8.84435536592289
variable highz equal zhi
print "INITIAL zhigh=${highz}"
INITIAL zhigh=54.7083380310771
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 36 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5
ghost atom cutoff = 11.5
binsize = 5.75, bins = 14 14 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/class2/coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Inconsistent image flags (../domain.cpp:814)
Per MPI rank memory allocation (min/avg/max) = 23.68 | 23.97 | 24.07 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
0 1e-06 162203.38 385990 0.94351377 0 54461.486 9880.5493 0 0 414737.15 -15370.197 0 0 463708.99 0
Loop time of 2.50025e-06 on 4 procs for 0 steps with 27300 atoms
60.0% 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 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.5e-06 | | |100.00
Nlocal: 6825 ave 6907 max 6773 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 10431.2 ave 10477 max 10396 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 1.49501e+06 ave 1.54302e+06 max 1.44503e+06 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 5980022
Ave neighs/atom = 219.04842
Ave special neighs/atom = 1.892967
Neighbor list builds = 0
Dangerous builds = 0
print "BEFORE MINIMIZE WITH VARIABLE INDENTER"
BEFORE MINIMIZE WITH VARIABLE INDENTER
print "zlow=${lowz}"
zlow=-8.84435536592289
print "zhigh=${highz}"
zhigh=54.7083380310771
# Minimization stage to push all atoms above max or below min inwards
fix upper all indent 10.0 plane z 54.701984298093102 hi units box
fix lower all indent 10.0 plane z -8.8380008421010938 lo units box
thermo_style custom step fnorm vol v_sysdensity zlo zhi
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888)
thermo 50
minimize 0.0 1.0 5000 10000
generated 0 of 36 mixed pair_coeff terms from geometric mixing rule
WARNING: Inconsistent image flags (../domain.cpp:814)
Per MPI rank memory allocation (min/avg/max) = 25.93 | 26.22 | 26.32 Mbytes
Step Fnorm Volume v_sysdensity Zlo Zhi
0 107405.56 385990 0.94351377 -8.8443554 54.708338
3 584355.75 385870.38 0.94380626 -8.8481587 54.68484
Loop time of 2.65215 on 4 procs for 3 steps with 27300 atoms
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
463708.991643462 150242.189089001 492448.693487977
Force two-norm initial, final = 107405.56 584355.75
Force max component initial, final = 14501.05 320567
Final line search alpha, max atom move = 8.9191763e-05 28.591936
Iterations, force evaluations = 3 79
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9537 | 2.0104 | 2.1347 | 5.2 | 75.80
Bond | 0.01875 | 0.019509 | 0.020335 | 0.5 | 0.74
Neigh | 0.46253 | 0.46264 | 0.46275 | 0.0 | 17.44
Comm | 0.022305 | 0.14717 | 0.2045 | 19.3 | 5.55
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.0014503 | 0.0015753 | 0.0017066 | 0.2 | 0.06
Other | | 0.01083 | | | 0.41
Nlocal: 6825 ave 6917 max 6758 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 10440.8 ave 10479 max 10408 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 1.49498e+06 ave 1.54528e+06 max 1.44149e+06 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 5979935
Ave neighs/atom = 219.04524
Ave special neighs/atom = 1.892967
Neighbor list builds = 15
Dangerous builds = 5