#------------------------------------------------------------------------------- # 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 -10.298644789527494 Displacing atoms ... # 1. Variable Indenter Stage, minimization to compress initial cell #------------------------------------------------------------------ variable lowz equal zlo print "INITIAL zlow=${lowz}" INITIAL zlow=-8.32197453282749 variable highz equal zhi print "INITIAL zhigh=${highz}" INITIAL zhigh=54.1859579537725 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 11 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) = 30.2 | 30.2 | 30.2 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 10942.519 379644.6 0.95928371 0 54168.331 9843.1961 0 0 141748.95 -16420.032 0 0 189340.44 0 Loop time of 2.123e-06 on 2 procs for 0 steps with 27300 atoms 141.3% CPU use with 2 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 | | 2.123e-06 | | |100.00 Nlocal: 13650 ave 13683 max 13617 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 14312 ave 14315 max 14309 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 2.99573e+06 ave 2.99791e+06 max 2.99355e+06 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 5991460 Ave neighs/atom = 219.4674 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=${lowz}" zlow=-8.32197453282749 print "zhigh=${highz}" zhigh=54.1859579537725 # Minimization stage to push all atoms above max or below min inwards fix upper all indent 10.0 plane z 54.179707796108509 hi units box fix lower all indent 10.0 plane z -8.3157243401164926 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) = 32.45 | 32.45 | 32.45 Mbytes Step Fnorm Volume v_sysdensity Zlo Zhi 0 33625.84 379644.6 0.95928371 -8.3219745 54.185958 50 4427.4832 385704.37 0.94421248 -8.836488 54.669177 55 10682.055 385704.37 0.94421248 -8.836488 54.669177 Loop time of 17.361 on 2 procs for 55 steps with 27300 atoms 99.5% CPU use with 2 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 189340.441179322 -380049.974337232 -380206.230236769 Force two-norm initial, final = 33625.84 10682.055 Force max component initial, final = 4344.883 7131.8118 Final line search alpha, max atom move = 4.5061076e-05 0.32136711 Iterations, force evaluations = 55 299 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.643 | 14.703 | 14.762 | 1.5 | 84.69 Bond | 0.14052 | 0.14209 | 0.14366 | 0.4 | 0.82 Neigh | 2.3067 | 2.3067 | 2.3068 | 0.0 | 13.29 Comm | 0.072242 | 0.1329 | 0.19356 | 16.6 | 0.77 Output | 8.1642e-05 | 8.6443e-05 | 9.1244e-05 | 0.0 | 0.00 Modify | 0.0089982 | 0.0091601 | 0.009322 | 0.2 | 0.05 Other | | 0.06749 | | | 0.39 Nlocal: 13650 ave 13687 max 13613 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 14329.5 ave 14363 max 14296 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 2.99415e+06 ave 2.99551e+06 max 2.9928e+06 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 5988307 Ave neighs/atom = 219.3519 Ave special neighs/atom = 1.892967 Neighbor list builds = 39 Dangerous builds = 13 unfix upper unfix lower print "AFTER MINIMIZE WITH VARIABLE INDENTER..." AFTER MINIMIZE WITH VARIABLE INDENTER... print "zlow=${lowz}" zlow=-8.83648797382266 print "zhigh=${highz}" zhigh=54.669177194801 # 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 = 0.004 seconds variable zhigh equal "54.179707796108509 - elapsed * 0.000113157243" variable zlow equal "-8.3157243401164926 + elapsed * 0.000113157243" 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 0.990552 0.868779 24909 2 97.7085 45.3709 8303 Per MPI rank memory allocation (min/avg/max) = 31.95 | 31.95 | 31.95 Mbytes Step v_time Press Volume v_sysdensity Temp E_vdwl E_coul PotEng KinEng v_zlow v_zhigh Zlo Zhi 0 1e-06 2.6685398e+262 386022.52 0.94343428 428.46899 49729.859 -442441.6 -391782.9 24261.4 -8.3157243 54.179708 -8.8818363 54.676212 ERROR: Domain too large for neighbor bins (../nbin_standard.cpp:133) Last command: run 100000