#-------------------------------------------------------------------------------
# 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 -0.25874789341437676
Displacing atoms ...
# 1. Variable Indenter Stage, minimization to compress initial cell
#------------------------------------------------------------------
variable lowz equal zlo
print "INITIAL zlow=${lowz}"
INITIAL zlow=0.435512525285623
variable highz equal zhi
print "INITIAL zhigh=${highz}"
INITIAL zhigh=44.8482066878856
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 = 8 8 8
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) = 9.416 | 9.571 | 9.997 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 198428.08 91073.35 1.3330468 0 18016.691 3282.0657 0 0 120759.26 -13412.558 0 0 128645.46 0
Loop time of 9.54122e-06 on 32 procs for 0 steps with 9101 atoms
103.5% CPU use with 32 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 | | 9.541e-06 | | |100.00
Nlocal: 284.406 ave 321 max 248 min
Histogram: 1 1 4 5 7 5 3 2 2 2
Nghost: 3803.06 ave 3935 max 3675 min
Histogram: 3 1 6 6 1 1 5 3 4 2
Neighs: 87883.6 ave 111350 max 64635 min
Histogram: 1 4 5 6 1 2 5 1 4 3
Total # of neighbors = 2812275
Ave neighs/atom = 309.00725
Ave special neighs/atom = 1.8929788
Neighbor list builds = 0
Dangerous builds = 0
print "BEFORE MINIMIZE WITH VARIABLE INDENTER"
BEFORE MINIMIZE WITH VARIABLE INDENTER
print "zlow=${lowz}"
zlow=0.435512525285623
print "zhigh=${highz}"
zhigh=44.8482066878856
# Minimization stage to push all atoms above max or below min inwards
fix upper all indent 10.0 plane z 44.843766528078874 hi units box
fix lower all indent 10.0 plane z 0.43995297282112189 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) = 10.54 | 10.7 | 11.12 Mbytes
Step Fnorm Volume v_sysdensity Zlo Zhi
0 30486.879 91073.35 1.3330468 0.43551253 44.848207
27 1.4378507e+09 91672.171 1.324339 0.27763697 44.982351
Loop time of 0.47957 on 32 procs for 27 steps with 9101 atoms
98.5% CPU use with 32 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
128645.457549066 -119513.005692665 52571005.3063201
Force two-norm initial, final = 30486.879 1.4378507e+09
Force max component initial, final = 4769.5066 7.2369727e+08
Final line search alpha, max atom move = 0.00068627994 496658.92
Iterations, force evaluations = 27 130
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.22541 | 0.28329 | 0.35638 | 6.9 | 59.07
Bond | 0.001597 | 0.0018242 | 0.0021253 | 0.3 | 0.38
Neigh | 0.080756 | 0.080984 | 0.081206 | 0.0 | 16.89
Comm | 0.03431 | 0.10748 | 0.16565 | 11.5 | 22.41
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.00015686 | 0.00018132 | 0.0002863 | 0.0 | 0.04
Other | | 0.005807 | | | 1.21
Nlocal: 284.406 ave 327 max 256 min
Histogram: 1 7 4 4 6 5 1 2 0 2
Nghost: 3800.97 ave 3938 max 3684 min
Histogram: 5 3 3 6 0 2 5 4 1 3
Neighs: 87669.2 ave 113016 max 69784 min
Histogram: 4 6 5 2 2 2 5 3 0 3
Total # of neighbors = 2805416
Ave neighs/atom = 308.2536
Ave special neighs/atom = 1.8929788
Neighbor list builds = 22
Dangerous builds = 9