#------------------------------------------------------------------------------- # 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 0.24366023458905772 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 6.68991e-06 on 32 procs for 0 steps with 27300 atoms 117.2% 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 | | 6.69e-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 47.252440037908279 hi units box fix lower all indent 10.0 plane z -1.3884565819162638 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 0.89383 on 32 procs for 3 steps with 27300 atoms 99.3% 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 | 0.36106 | 0.41024 | 0.44381 | 3.3 | 45.90 Bond | 0.0023874 | 0.0027325 | 0.0029735 | 0.2 | 0.31 Kspace | 0.3349 | 0.36811 | 0.41687 | 3.4 | 41.18 Neigh | 0.059245 | 0.05942 | 0.059532 | 0.0 | 6.65 Comm | 0.045176 | 0.04596 | 0.046833 | 0.2 | 5.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00040399 | 0.00052764 | 0.00067853 | 0.0 | 0.06 Other | | 0.006845 | | | 0.77 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