#-------------------------------------------------------------------------------
# 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 0.24366023459305097
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=45.863983
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) = 0.32489129
grid = 72 72 48
stencil order = 5
estimated absolute RMS force accuracy = 0.0034280733
estimated relative force accuracy = 1.0323541e-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) = 12.2 | 12.35 | 12.63 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 447148.7 278556.86 1.3074059 0 54212.576 9868.1664 0 0 692906.64 568123.35 -1345.0391 -589894.61 735216.12 0
Loop time of 5.94019e-06 on 32 procs for 0 steps with 27300 atoms
118.9% 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 | | 5.94e-06 | | |100.00
Nlocal: 853.125 ave 901 max 804 min
Histogram: 2 4 3 2 2 8 4 2 2 3
Nghost: 7260.16 ave 7375 max 7157 min
Histogram: 3 2 3 3 4 7 5 3 1 1
Neighs: 266318 ave 288566 max 236730 min
Histogram: 1 1 2 6 4 3 4 3 4 4
Total # of neighbors = 8522170
Ave neighs/atom = 312.1674
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=45.863983
# Minimization stage to push all atoms above max or below min inwards
fix upper all indent 10.0 plane z 47.252440037912272 hi units box
fix lower all indent 10.0 plane z -1.3884565819122705 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) = 0.32489129
grid = 72 72 48
stencil order = 5
estimated absolute RMS force accuracy = 0.0034280733
estimated relative force accuracy = 1.0323541e-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 | 13.48 | 13.75 Mbytes
Step Fnorm Volume v_sysdensity Zlo Zhi
0 136968.31 278556.86 1.3074059 0 45.863983
3 48529391 278556.86 1.3074059 0 45.863983
WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:935)
Loop time of 0.901046 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 =
735216.120719332 182519.575226973 46682298.5938261
Force two-norm initial, final = 136968.31 48529391
Force max component initial, final = 15045.635 23603317
Final line search alpha, max atom move = 0.00012866983 3037.0346
Iterations, force evaluations = 3 60
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.36025 | 0.41097 | 0.4424 | 3.2 | 45.61
Bond | 0.0023929 | 0.0027362 | 0.0029111 | 0.2 | 0.30
Kspace | 0.34248 | 0.37338 | 0.4237 | 3.3 | 41.44
Neigh | 0.060103 | 0.060373 | 0.060674 | 0.1 | 6.70
Comm | 0.045213 | 0.046343 | 0.047282 | 0.2 | 5.14
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.00034729 | 0.00054397 | 0.00070938 | 0.0 | 0.06
Other | | 0.006698 | | | 0.74
Nlocal: 853.125 ave 901 max 803 min
Histogram: 3 3 2 4 1 6 4 3 3 3
Nghost: 7258.12 ave 7371 max 7145 min
Histogram: 3 1 3 3 5 6 5 3 2 1
Neighs: 266305 ave 289066 max 236680 min
Histogram: 1 2 2 6 3 3 5 2 4 4
Total # of neighbors = 8521767
Ave neighs/atom = 312.15264
Ave special neighs/atom = 1.892967
Neighbor list builds = 7
Dangerous builds = 2