#------------------------------------------------------------------------------- # 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 -0.24960112987225713 Displacing atoms ... # 1. Variable Indenter Stage, minimization to compress initial cell #------------------------------------------------------------------ variable lowz equal zlo print "INITIAL zlow=${lowz}" INITIAL zlow=0.431115409527743 variable highz equal zhi print "INITIAL zhigh=${highz}" INITIAL zhigh=44.8526043307277 run 0 WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) generated 0 of 36 mixed pair_coeff terms from geometric 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 = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard WARNING: Inconsistent image flags (../domain.cpp:814) Per MPI rank memory allocation (min/avg/max) = 9.417 | 9.571 | 9.997 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 200599.39 91091.385 1.3327828 0 18025.238 3282.9057 0 0 121669.63 -13122.786 0 0 129854.98 0 Loop time of 1.05777e-05 on 32 procs for 0 steps with 9101 atoms 91.6% 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 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 | | 1.058e-05 | | |100.00 Nlocal: 284.406 ave 321 max 248 min Histogram: 1 1 4 6 6 5 3 3 1 2 Nghost: 3804 ave 3935 max 3677 min Histogram: 3 1 6 6 1 1 5 3 4 2 Neighs: 87885.7 ave 111479 max 64630 min Histogram: 1 4 5 6 1 2 5 1 4 3 Total # of neighbors = 2812341 Ave neighs/atom = 309.0145 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 print "BEFORE MINIMIZE WITH VARIABLE INDENTER" BEFORE MINIMIZE WITH VARIABLE INDENTER print "zlow=${lowz}" zlow=0.431115409527743 print "zhigh=${highz}" zhigh=44.8526043307277 # Minimization stage to push all atoms above max or below min inwards fix upper all indent 10.0 plane z 44.848162609438859 hi units box fix lower all indent 10.0 plane z 0.43555689144321685 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 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule WARNING: Inconsistent image flags (../domain.cpp:814) Per MPI rank memory allocation (min/avg/max) = 10.54 | 10.7 | 11.12 Mbytes Step Fnorm Volume v_sysdensity Zlo Zhi 0 30968.112 91091.385 1.3327828 0.43111541 44.852604 29 35117.171 91565.343 1.3258841 0.33191787 44.984536 Loop time of 0.464989 on 32 procs for 29 steps with 9101 atoms 98.6% CPU use with 32 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 129854.984922331 -128801.29604899 -130229.354944418 Force two-norm initial, final = 30968.112 35117.171 Force max component initial, final = 4914.1711 22705.737 Final line search alpha, max atom move = 2.6309692e-05 0.59738095 Iterations, force evaluations = 29 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22816 | 0.28568 | 0.36043 | 6.9 | 61.44 Bond | 0.0016095 | 0.0018299 | 0.0021047 | 0.3 | 0.39 Neigh | 0.066713 | 0.066988 | 0.067402 | 0.1 | 14.41 Comm | 0.030073 | 0.10478 | 0.16276 | 11.7 | 22.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00015289 | 0.0001781 | 0.00020904 | 0.0 | 0.04 Other | | 0.005535 | | | 1.19 Nlocal: 284.406 ave 327 max 253 min Histogram: 1 3 7 3 6 6 2 2 1 1 Nghost: 3802.06 ave 3948 max 3678 min Histogram: 4 2 7 3 2 0 6 4 2 2 Neighs: 87688.1 ave 112718 max 69299 min Histogram: 4 6 5 1 3 1 5 4 0 3 Total # of neighbors = 2806018 Ave neighs/atom = 308.31975 Ave special neighs/atom = 1.8929788 Neighbor list builds = 19 Dangerous builds = 6 unfix upper unfix lower print "AFTER MINIMIZE WITH VARIABLE INDENTER..." AFTER MINIMIZE WITH VARIABLE INDENTER... print "zlow=${lowz}" zlow=0.331917865393975 print "zhigh=${highz}" zhigh=44.9845363871369 # 2. Fixed Indenter Stage with NVT dynamics to compress initial cell #------------------------------------------------------------------- reset_timestep 0 velocity all create 298.2 72489 dist gaussian mom yes rot no # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2768 = # of frozen angles find clusters CPU = 0.001 seconds variable zhigh equal "44.848162609438859 - elapsed * 0.000025644431" variable zlow equal "0.43555689144321685 + elapsed * 0.000025644431" fix upper all indent 10.0 plane z v_zhigh hi units box fix lower all indent 10.0 plane z v_zlow lo units box thermo_style custom step v_time press vol v_sysdensity temp evdwl ecoul pe ke v_zlow v_zhigh zlo zhi thermo 1000 fix movable1 movable nve fix movable2 movable temp/rescale 20 298.2 298.2 10 1.0 timestep 1 run 100000 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule WARNING: Inconsistent image flags (../domain.cpp:814) SHAKE stats (type/ave/delta/count) on step 0 2 0.99636 0.829646 8304 2 96.9089 52.2949 2768 Per MPI rank memory allocation (min/avg/max) = 10.29 | 10.48 | 10.87 Mbytes Step v_time Press Volume v_sysdensity Temp E_vdwl E_coul PotEng KinEng v_zlow v_zhigh Zlo Zhi 0 1e-06 -1.5323571e+277 91580.994 1.3256575 428.55654 30202.558 -167019.7 -136280.44 8088.7858 0.43555689 44.848163 0.32567025 44.985921 ERROR: Domain too large for neighbor bins (../nbin_standard.cpp:133) Last command: run 100000