#-------------------------------------------------------------------------------
# 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 -0.70179663773723888
Displacing atoms ...
# 1. Variable Indenter Stage, minimization to compress initial cell
#------------------------------------------------------------------
variable lowz equal zlo
print "INITIAL zlow=${lowz}"
INITIAL zlow=0
variable highz equal zhi
print "INITIAL zhigh=${highz}"
INITIAL zhigh=55.3706
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 0.0216 (../kspace.cpp:325)
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.32370376
grid = 48 48 50
stencil order = 5
estimated absolute RMS force accuracy = 0.0035069416
estimated relative force accuracy = 1.056105e-05
using double precision KISS FFT
3d grid and FFT values/proc = 11191 4608
generated 0 of 36 mixed pair_coeff terms from sixthpower 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 = 9 9 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.65 | 11.07 | 11.38 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 506429.68 134171.42 1.2788699 0 25482.039 4664.4174 0 0 375004.19 267083.82 -626.07893 -280588.35 391646.12 0
Loop time of 6.43928e-06 on 32 procs for 0 steps with 13126 atoms
90.8% 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
Kspace | 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 | | 6.439e-06 | | |100.00
Nlocal: 410.188 ave 476 max 333 min
Histogram: 3 2 4 3 2 2 4 3 6 3
Nghost: 5715.25 ave 6210 max 5338 min
Histogram: 12 4 0 0 0 1 5 2 0 8
Neighs: 130272 ave 165970 max 79483 min
Histogram: 5 2 1 0 0 5 4 4 5 6
Total # of neighbors = 4168708
Ave neighs/atom = 317.59165
Ave special neighs/atom = 1.9037026
Neighbor list builds = 0
Dangerous builds = 0
print "BEFORE MINIMIZE WITH VARIABLE INDENTER"
BEFORE MINIMIZE WITH VARIABLE INDENTER
print "zlow=${lowz}"
zlow=0
print "zhigh=${highz}"
zhigh=55.3706
# Minimization stage to push all atoms above max or below min inwards
fix upper all indent 10.0 plane z 54.621446743994539 hi units box
fix lower all indent 10.0 plane z 0.7491532560054619 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
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.32370376
grid = 48 48 50
stencil order = 5
estimated absolute RMS force accuracy = 0.0035069416
estimated relative force accuracy = 1.056105e-05
using double precision KISS FFT
3d grid and FFT values/proc = 11191 4608
generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.77 | 12.2 | 12.51 Mbytes
Step Fnorm Volume v_sysdensity Zlo Zhi
0 2156404.8 134171.42 1.2788699 0 55.3706
30 1559666.8 134171.42 1.2788699 0 55.3706
Loop time of 1.51943 on 32 procs for 30 steps with 13126 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 =
391646.11598422 -149800.911647561 961434.92909566
Force two-norm initial, final = 2156404.8 1559666.8
Force max component initial, final = 1482332.9 612025.78
Final line search alpha, max atom move = 0.00077965361 477.16811
Iterations, force evaluations = 30 191
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.39894 | 0.63979 | 0.80161 | 15.6 | 42.11
Bond | 0.0032851 | 0.0041217 | 0.0048068 | 0.7 | 0.27
Kspace | 0.49806 | 0.65964 | 0.90053 | 15.5 | 43.41
Neigh | 0.099074 | 0.09986 | 0.10037 | 0.1 | 6.57
Comm | 0.098718 | 0.10258 | 0.10613 | 0.8 | 6.75
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.0004666 | 0.00059558 | 0.00077322 | 0.0 | 0.04
Other | | 0.01285 | | | 0.85
Nlocal: 410.188 ave 478 max 327 min
Histogram: 2 3 3 2 4 2 6 2 4 4
Nghost: 5707.47 ave 6195 max 5340 min
Histogram: 12 4 0 0 0 2 4 2 2 6
Neighs: 130194 ave 164210 max 78016 min
Histogram: 2 5 0 1 1 4 4 5 4 6
Total # of neighbors = 4166220
Ave neighs/atom = 317.4021
Ave special neighs/atom = 1.9037026
Neighbor list builds = 21
Dangerous builds = 7