#------------------------------------------------------------------------------- # 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 7.22825e-06 on 32 procs for 0 steps with 27300 atoms 103.3% 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 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 | | 7.228e-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 0.91297 on 32 procs for 3 steps with 27300 atoms 99.1% 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 | 0.3803 | 0.42401 | 0.47852 | 4.2 | 46.44 Bond | 0.0024612 | 0.0026619 | 0.0029243 | 0.2 | 0.29 Kspace | 0.3428 | 0.39804 | 0.4413 | 4.4 | 43.60 Neigh | 0.035656 | 0.035818 | 0.036018 | 0.1 | 3.92 Comm | 0.043894 | 0.04527 | 0.046628 | 0.3 | 4.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00038216 | 0.00050911 | 0.00073223 | 0.0 | 0.06 Other | | 0.006659 | | | 0.73 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