#-------------------------------------------------------------------------------
# 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 -0.18775290072277429
Displacing atoms ...
# 1. Variable Indenter Stage, minimization to compress initial cell
#------------------------------------------------------------------
variable lowz equal zlo
print "INITIAL zlow=${lowz}"
INITIAL zlow=0.337152710477226
variable highz equal zhi
print "INITIAL zhigh=${highz}"
INITIAL zhigh=45.5280774880772
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 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) = 10.41 | 10.54 | 11.01 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 511978.35 274469.01 1.3268779 0 54221.091 9872.4125 0 0 761482.1 7984.9893 0 0 833560.6 0
Loop time of 7.96047e-06 on 32 procs for 0 steps with 27300 atoms
95.8% 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 | | 7.96e-06 | | |100.00
Nlocal: 853.125 ave 922 max 794 min
Histogram: 2 2 4 7 2 5 5 1 2 2
Nghost: 5451.69 ave 5614 max 5287 min
Histogram: 2 3 3 4 4 3 5 4 1 3
Neighs: 263277 ave 313774 max 215500 min
Histogram: 5 3 5 3 0 0 4 5 3 4
Total # of neighbors = 8424856
Ave neighs/atom = 308.60278
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=${lowz}"
zlow=0.337152710477226
print "zhigh=${highz}"
zhigh=45.5280774880772
# Minimization stage to push all atoms above max or below min inwards
fix upper all indent 10.0 plane z 45.523559411935892 hi units box
fix lower all indent 10.0 plane z 0.34167144656411308 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) = 11.54 | 11.66 | 12.13 Mbytes
Step Fnorm Volume v_sysdensity Zlo Zhi
0 134923.63 274469.01 1.3268779 0.33715271 45.528077
50 2739.3764 277399.4 1.3128611 -0.017894645 45.655514
58 9320.3675 277197.41 1.3138178 -0.016509312 45.623641
Loop time of 4.22861 on 32 procs for 58 steps with 27300 atoms
99.0% CPU use with 32 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
833560.597642739 -407576.532643848 -407615.606332536
Force two-norm initial, final = 134923.63 9320.3675
Force max component initial, final = 14158.989 6189.4959
Final line search alpha, max atom move = 9.5067906e-07 0.0058842241
Iterations, force evaluations = 58 472
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.4458 | 2.9286 | 3.4509 | 18.5 | 69.26
Bond | 0.018222 | 0.019682 | 0.022276 | 0.7 | 0.47
Neigh | 0.57735 | 0.57866 | 0.58042 | 0.1 | 13.68
Comm | 0.14103 | 0.63927 | 1.148 | 40.1 | 15.12
Output | 8.825e-05 | 8.9578e-05 | 0.00010542 | 0.0 | 0.00
Modify | 0.0014422 | 0.0023197 | 0.0041311 | 1.9 | 0.05
Other | | 0.05998 | | | 1.42
Nlocal: 853.125 ave 915 max 809 min
Histogram: 4 4 2 8 2 3 5 1 2 1
Nghost: 5457.31 ave 5599 max 5313 min
Histogram: 2 0 5 5 4 6 4 2 1 3
Neighs: 262356 ave 309558 max 219308 min
Histogram: 6 4 3 3 0 1 4 4 3 4
Total # of neighbors = 8395394
Ave neighs/atom = 307.52359
Ave special neighs/atom = 1.892967
Neighbor list builds = 62
Dangerous builds = 24