./Stage_2/2.2_CompressLayer.out output for 777: H2O-compress layer 1ns
Status:
finished
#-------------------------------------------------------------------------------
# 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