#------------------------------------------------------------------------------- # 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 -0.24716176154885616 Displacing atoms ... # 1. Variable Indenter Stage, minimization to compress initial cell #------------------------------------------------------------------ variable lowz equal zlo print "INITIAL zlow=${lowz}" INITIAL zlow=0.767657941551144 variable highz equal zhi print "INITIAL zhigh=${highz}" INITIAL zhigh=39.6464015353511 run 0 WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) generated 0 of 1 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 = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 6 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) = 8.393 | 8.778 | 9.163 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 19349248 63500.506 1.0364237 0 12754.578 1675.4358 0 0 5988340.4 -6705.3397 0 0 5996065.1 0 Loop time of 3.84313e-06 on 8 procs for 0 steps with 6600 atoms 100.8% CPU use with 8 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 | | 3.843e-06 | | |100.00 Nlocal: 825 ave 881 max 774 min Histogram: 1 2 0 0 2 0 1 0 0 2 Nghost: 7579.75 ave 7789 max 7397 min Histogram: 1 3 0 0 0 0 0 2 1 1 Neighs: 447864 ave 549575 max 342578 min Histogram: 1 2 1 0 0 0 0 1 1 2 Total # of neighbors = 3582916 Ave neighs/atom = 542.86606 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 print "BEFORE MINIMIZE WITH VARIABLE INDENTER" BEFORE MINIMIZE WITH VARIABLE INDENTER print "zlow=${lowz}" zlow=0.767657941551144 print "zhigh=${highz}" zhigh=39.6464015353511 # Minimization stage to push all atoms above max or below min inwards fix upper all indent 10.0 plane z 39.64251465295834 hi units box fix lower all indent 10.0 plane z 0.77154568590021699 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 1 mixed pair_coeff terms from geometric mixing rule WARNING: Inconsistent image flags (../domain.cpp:814) Per MPI rank memory allocation (min/avg/max) = 9.518 | 9.903 | 10.29 Mbytes Step Fnorm Volume v_sysdensity Zlo Zhi 0 1.2933143e+08 63500.506 1.0364237 0.76765794 39.646402 11 82729.273 64730.169 1.0167351 0.72768591 40.359301 Loop time of 1.2734 on 8 procs for 11 steps with 6600 atoms 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 5996065.07494453 2790.31852773137 1388.63968597071 Force two-norm initial, final = 1.2933143e+08 82729.273 Force max component initial, final = 90793276 48614.135 Final line search alpha, max atom move = 5.1481591e-06 0.2502733 Iterations, force evaluations = 11 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73765 | 0.95646 | 1.181 | 17.3 | 75.11 Bond | 0.0031998 | 0.0034673 | 0.003909 | 0.4 | 0.27 Neigh | 0.062014 | 0.062057 | 0.062111 | 0.0 | 4.87 Comm | 0.020767 | 0.24597 | 0.46469 | 34.2 | 19.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00029066 | 0.00033466 | 0.00037972 | 0.0 | 0.03 Other | | 0.005109 | | | 0.40 Nlocal: 825 ave 898 max 760 min Histogram: 2 1 0 1 0 0 2 0 0 2 Nghost: 7584.62 ave 7863 max 7326 min Histogram: 2 2 0 0 0 0 0 1 1 2 Neighs: 447752 ave 560710 max 335078 min Histogram: 1 3 0 0 0 0 0 1 1 2 Total # of neighbors = 3582014 Ave neighs/atom = 542.72939 Ave special neighs/atom = 2 Neighbor list builds = 4 Dangerous builds = 1 unfix upper unfix lower print "AFTER MINIMIZE WITH VARIABLE INDENTER..." AFTER MINIMIZE WITH VARIABLE INDENTER... print "zlow=${lowz}" zlow=0.727685909348623 print "zhigh=${highz}" zhigh=40.3593012334731 # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2200 = # of frozen angles find clusters CPU = 0.000 seconds variable zhigh equal "39.64251465295834 - elapsed * 0.000002228454" variable zlow equal "0.77154568590021699 + elapsed * 0.000002228454" 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 10000 fix movable1 movable nve fix movable2 movable temp/rescale 20 298.2 298.2 10 1.0 timestep 1 run 1000000 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.988402 1.07338 6600 1 100.174 68.6113 2200 Per MPI rank memory allocation (min/avg/max) = 9.268 | 9.654 | 10.04 Mbytes Step v_time Press Volume v_sysdensity Temp E_vdwl E_coul PotEng KinEng v_zlow v_zhigh Zlo Zhi 0 1e-06 -2.6851045e+217 64639.7 1.0181581 447.33389 11063.823 -14199.116 -3135.2932 5865.703 0.77154569 39.642515 0.7514913 40.327716 ERROR: Domain too large for neighbor bins (../nbin_standard.cpp:133) Last command: run 1000000