#-------------------------------------------------------------------------------
# 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 0.10958717501163662
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=45.865231
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 = 0.0616 (../kspace.cpp:325)
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.32489059
grid = 72 72 48
stencil order = 5
estimated absolute RMS force accuracy = 0.003428169
estimated relative force accuracy = 1.0323829e-05
using double precision KISS FFT
3d grid and FFT values/proc = 19375 10368
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 = 14 14 8
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) = 12.19 | 12.4 | 12.78 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 423498.27 278564.44 1.3073703 0 54307.952 9865.1944 0 0 658583.21 564914.12 -1345.0025 -596239.3 691431.18 0
Loop time of 6.8135e-06 on 32 procs for 0 steps with 27300 atoms
42.7% 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 | | 6.814e-06 | | |100.00
Nlocal: 853.125 ave 886 max 818 min
Histogram: 1 6 2 1 4 5 5 1 4 3
Nghost: 7288.59 ave 7389 max 7183 min
Histogram: 7 2 0 1 2 6 5 3 1 5
Neighs: 272943 ave 303402 max 244317 min
Histogram: 4 3 4 2 4 3 3 1 5 3
Total # of neighbors = 8734174
Ave neighs/atom = 319.93311
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=${lowz}"
zlow=0
print "zhigh=${highz}"
zhigh=45.865231
# Minimization stage to push all atoms above max or below min inwards
fix upper all indent 10.0 plane z 45.315590029014587 hi units box
fix lower all indent 10.0 plane z 0.54964082948541626 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) = 0.32489059
grid = 72 72 48
stencil order = 5
estimated absolute RMS force accuracy = 0.003428169
estimated relative force accuracy = 1.0323829e-05
using double precision KISS FFT
3d grid and FFT values/proc = 19375 10368
generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.53 | 13.9 Mbytes
Step Fnorm Volume v_sysdensity Zlo Zhi
0 100647.71 278564.44 1.3073703 0 45.865231
3 1.3304282e+08 278564.44 1.3073703 0 45.865231
Loop time of 0.880944 on 32 procs for 3 steps with 27300 atoms
99.2% CPU use with 32 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
691431.179127002 197755.305524909 8844199.89829102
Force two-norm initial, final = 100647.71 1.3304282e+08
Force max component initial, final = 7087.2508 88904580
Final line search alpha, max atom move = 2.7728159e-05 2465.1603
Iterations, force evaluations = 3 60
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.37614 | 0.42304 | 0.46452 | 3.9 | 48.02
Bond | 0.002492 | 0.0026548 | 0.0028813 | 0.2 | 0.30
Kspace | 0.3267 | 0.36763 | 0.41445 | 4.1 | 41.73
Neigh | 0.035337 | 0.035442 | 0.035641 | 0.0 | 4.02
Comm | 0.04354 | 0.045032 | 0.046724 | 0.4 | 5.11
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.00033989 | 0.00051618 | 0.00067481 | 0.0 | 0.06
Other | | 0.006636 | | | 0.75
Nlocal: 853.125 ave 887 max 819 min
Histogram: 2 5 2 2 4 6 1 5 1 4
Nghost: 7288.47 ave 7383 max 7189 min
Histogram: 7 2 0 1 1 4 9 2 1 5
Neighs: 272917 ave 302212 max 243402 min
Histogram: 4 3 1 4 5 2 3 2 4 4
Total # of neighbors = 8733349
Ave neighs/atom = 319.90289
Ave special neighs/atom = 1.892967
Neighbor list builds = 4
Dangerous builds = 2