#-------------------------------------------------------------------------------
# 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 -0.21477411639986954
Displacing atoms ...
# 1. Variable Indenter Stage, minimization to compress initial cell
#------------------------------------------------------------------
variable lowz equal zlo
print "INITIAL zlow=${lowz}"
INITIAL zlow=0.37799680150013
variable highz equal zhi
print "INITIAL zhigh=${highz}"
INITIAL zhigh=44.9057219657001
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) = 9.417 | 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 193494.21 91309.234 1.329603 0 18029.891 3282.8808 0 0 118712.34 -11681.654 0 0 128343.46 0
Loop time of 7.67528e-06 on 32 procs for 0 steps with 9101 atoms
18.3% 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 | | 7.675e-06 | | |100.00
Nlocal: 284.406 ave 321 max 250 min
Histogram: 1 2 3 6 7 5 2 3 1 2
Nghost: 3804.09 ave 3929 max 3682 min
Histogram: 2 2 5 7 1 1 5 4 3 2
Neighs: 87882.3 ave 111342 max 65434 min
Histogram: 1 5 4 6 1 2 5 3 2 3
Total # of neighbors = 2812234
Ave neighs/atom = 309.00275
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=${lowz}"
zlow=0.37799680150013
print "zhigh=${highz}"
zhigh=44.9057219657001
# Minimization stage to push all atoms above max or below min inwards
fix upper all indent 10.0 plane z 44.901270341540524 hi units box
fix lower all indent 10.0 plane z 0.38244915935948021 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 29414.809 91309.234 1.329603 0.3779968 44.905722
31 1.0709202e+08 91769.63 1.3229326 0.26057065 45.012812
Loop time of 0.581377 on 32 procs for 31 steps with 9101 atoms
98.8% CPU use with 32 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
128343.456683488 -126893.06873242 47906460.9266372
Force two-norm initial, final = 29414.809 1.0709202e+08
Force max component initial, final = 4421.2349 51865899
Final line search alpha, max atom move = 0.00054965611 28508.408
Iterations, force evaluations = 31 171
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.29634 | 0.37293 | 0.46796 | 7.8 | 64.15
Bond | 0.0020774 | 0.0023907 | 0.0027541 | 0.4 | 0.41
Neigh | 0.066703 | 0.06697 | 0.067276 | 0.1 | 11.52
Comm | 0.036774 | 0.13182 | 0.2088 | 13.3 | 22.67
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.00020084 | 0.00023161 | 0.00036831 | 0.0 | 0.04
Other | | 0.007036 | | | 1.21
Nlocal: 284.406 ave 326 max 255 min
Histogram: 2 5 3 7 5 4 3 1 1 1
Nghost: 3802.09 ave 3940 max 3682 min
Histogram: 3 2 6 6 1 0 6 4 2 2
Neighs: 87636.4 ave 112777 max 68994 min
Histogram: 3 7 4 2 3 2 4 4 0 3
Total # of neighbors = 2804365
Ave neighs/atom = 308.13812
Ave special neighs/atom = 1.8929788
Neighbor list builds = 19
Dangerous builds = 4