#------------------------------------------------------------------------------- # 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 -9.861649974887591 Displacing atoms ... # 1. Variable Indenter Stage, minimization to compress initial cell #------------------------------------------------------------------ variable lowz equal zlo print "INITIAL zlow=${lowz}" INITIAL zlow=-8.93252880458759 variable highz equal zhi print "INITIAL zhigh=${highz}" INITIAL zhigh=54.7965118548124 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 = 14 14 12 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) = 9.814 | 9.985 | 10.4 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 191639.51 387061.05 0.94090293 0 54469.214 9882.2208 0 0 467327.78 -14637.405 0 0 517041.81 0 Loop time of 1.28991e-05 on 32 procs for 0 steps with 27300 atoms 108.1% 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 | | 1.29e-05 | | |100.00 Nlocal: 853.125 ave 915 max 790 min Histogram: 2 1 3 6 5 4 2 5 2 2 Nghost: 4759.84 ave 4875 max 4587 min Histogram: 1 1 2 1 4 5 5 7 3 3 Neighs: 186818 ave 220419 max 152475 min Histogram: 1 3 4 3 6 5 2 2 3 3 Total # of neighbors = 5978191 Ave neighs/atom = 218.98136 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=${lowz}" zlow=-8.93252880458759 print "zhigh=${highz}" zhigh=54.7965118548124 # Minimization stage to push all atoms above max or below min inwards fix upper all indent 10.0 plane z 54.790140171990409 hi units box fix lower all indent 10.0 plane z -8.9261567159983919 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) = 10.94 | 11.11 | 11.53 Mbytes Step Fnorm Volume v_sysdensity Zlo Zhi 0 103045.74 387061.05 0.94090293 -8.9325288 54.796512 48 150595.12 389164.41 0.93581755 -8.9748058 55.100548 Loop time of 1.7525 on 32 procs for 48 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 = 517041.811518927 -379417.484220426 -382863.924531272 Force two-norm initial, final = 103045.74 150595.12 Force max component initial, final = 11815.488 71863.524 Final line search alpha, max atom move = 4.8399711e-06 0.34781738 Iterations, force evaluations = 48 247 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89585 | 1.0858 | 1.2657 | 9.4 | 61.96 Bond | 0.0091492 | 0.010211 | 0.011478 | 0.6 | 0.58 Neigh | 0.38188 | 0.38277 | 0.38375 | 0.1 | 21.84 Comm | 0.07145 | 0.24933 | 0.43744 | 19.5 | 14.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.0007401 | 0.0011619 | 0.0020213 | 1.4 | 0.07 Other | | 0.02325 | | | 1.33 Nlocal: 853.125 ave 917 max 793 min Histogram: 2 2 4 7 3 3 4 3 2 2 Nghost: 4758.47 ave 4870 max 4572 min Histogram: 1 1 3 1 4 1 5 7 7 2 Neighs: 186715 ave 218330 max 153718 min Histogram: 1 3 4 2 7 4 2 3 2 4 Total # of neighbors = 5974892 Ave neighs/atom = 218.86051 Ave special neighs/atom = 1.892967 Neighbor list builds = 60 Dangerous builds = 25 unfix upper unfix lower print "AFTER MINIMIZE WITH VARIABLE INDENTER..." AFTER MINIMIZE WITH VARIABLE INDENTER... print "zlow=${lowz}" zlow=-8.97480580439379 print "zhigh=${highz}" zhigh=55.1005484856222 # 2. Fixed Indenter Stage with NVT dynamics to compress initial cell #------------------------------------------------------------------- reset_timestep 0 velocity all create 298.15 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 8303 = # of frozen angles find clusters CPU = 0.002 seconds variable zhigh equal "54.790140171990409 - elapsed * 0.000119261567" variable zlow equal "-8.9261567159983919 + elapsed * 0.000119261567" 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 20 298.15 298.15 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 0.989509 0.979258 24909 2 97.6195 36.1427 8303 Per MPI rank memory allocation (min/avg/max) = 10.69 | 10.87 | 11.28 Mbytes Step v_time Press Volume v_sysdensity Temp E_vdwl E_coul PotEng KinEng v_zlow v_zhigh Zlo Zhi 0 1e-06 -2.6609531e+73 389069.18 0.93604659 428.46899 47547.708 -444038.91 -395579.79 24261.4 -8.9261567 54.79014 -8.9735242 55.086152 ERROR: Domain too large for neighbor bins (../nbin_standard.cpp:133) Last command: run 100000