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update examples. add abcfire variants

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Axel Kohlmeyer
2023-01-10 16:28:18 -05:00
parent 8800adf1cd
commit f5a8a0c398
16 changed files with 1864 additions and 454 deletions
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LAMMPS (22 Dec 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.5391903 1.5391903 1.5391903
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.15391903) to (30.783806 30.783806 0.15391903)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
using lattice units in orthogonal box = (0 0 -0.15391903) to (30.783806 30.783806 0.15391903)
create_atoms CPU = 0.000 seconds
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
#dump 1 all atom 100 dump.min
#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
thermo 100
run 1000
Generated 0 of 0 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 = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 22 22 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.057 | 3.057 | 3.057 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935263 0 2.5301106 15.833296
600 3.3888915 -0.85213743 0 2.532518 15.162759
700 3.2123675 -0.67642318 0 2.5319289 16.310565
800 3.3016275 -0.76569171 0 2.5318087 15.639335
900 3.4639203 -0.92788002 0 2.5317104 14.765912
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
Loop time of 0.171947 on 1 procs for 1000 steps with 800 atoms
Performance: 2512398.512 tau/day, 5815.737 timesteps/s, 4.653 Matom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10856 | 0.10856 | 0.10856 | 0.0 | 63.13
Neigh | 0.044014 | 0.044014 | 0.044014 | 0.0 | 25.60
Comm | 0.0042309 | 0.0042309 | 0.0042309 | 0.0 | 2.46
Output | 0.00030427 | 0.00030427 | 0.00030427 | 0.0 | 0.18
Modify | 0.010256 | 0.010256 | 0.010256 | 0.0 | 5.96
Other | | 0.004584 | | | 2.67
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 317 ave 317 max 317 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7743 ave 7743 max 7743 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7743
Ave neighs/atom = 9.67875
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
#dump_modify 1 every 25
thermo 50
min_style fire
min_modify alpha0 0.10 integrator verlet
minimize 0.0 1.0e-6 10000 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback abcfire
0.1 20 1.1 0.5 0.1 0.99 10 0.02 verlet yes no
Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.79078181 0 -0.79078181 12.79527
1050 0.078268931 -2.7183168 0 -2.6401457 -0.41989487
1100 0.0041272325 -2.843344 0 -2.839222 -1.3055655
1150 0.0050029044 -2.8770425 0 -2.8720459 -1.270977
1200 0.0025368218 -2.8883676 0 -2.8858339 -1.2772875
1250 0.00052248085 -2.8935826 0 -2.8930608 -1.2649988
1300 0.0027712804 -2.898842 0 -2.8960742 -1.2669316
1350 0.00058765348 -2.9014204 0 -2.9008335 -1.2598231
1400 0.00010378673 -2.9041687 0 -2.9040651 -1.2413645
1450 0.00023627389 -2.9048032 0 -2.9045672 -1.2352329
1500 5.2020247e-05 -2.9057308 0 -2.9056788 -1.2239923
1550 1.6800749e-05 -2.9058345 0 -2.9058177 -1.2182086
1600 2.5535502e-07 -2.9058623 0 -2.905862 -1.2165945
1650 9.0070188e-07 -2.905866 0 -2.9058651 -1.2161655
1700 5.2795357e-07 -2.905868 0 -2.9058674 -1.2150157
1750 6.4210837e-07 -2.9058696 0 -2.9058689 -1.2132824
1800 2.5157801e-08 -2.9058697 0 -2.9058697 -1.2132316
1850 5.8718638e-09 -2.9058697 0 -2.9058697 -1.213182
1900 2.0591585e-09 -2.9058697 0 -2.9058697 -1.2131855
1950 6.7576932e-12 -2.9058697 0 -2.9058697 -1.2131761
2000 2.4998566e-13 -2.9058697 0 -2.9058697 -1.2131762
2050 8.7057136e-15 -2.9058697 0 -2.9058697 -1.2131761
2100 2.5253484e-15 -2.9058697 0 -2.9058697 -1.2131761
2117 2.1356326e-15 -2.9058697 0 -2.9058697 -1.2131761
Loop time of 0.203389 on 1 procs for 1117 steps with 800 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-0.790781812776473 -2.90586971958912 -2.9058697195891
Force two-norm initial, final = 1905.4669 9.9910235e-07
Force max component initial, final = 343.39191 4.5108834e-07
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 1117 1127
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15606 | 0.15606 | 0.15606 | 0.0 | 76.73
Neigh | 0.010678 | 0.010678 | 0.010678 | 0.0 | 5.25
Comm | 0.002841 | 0.002841 | 0.002841 | 0.0 | 1.40
Output | 0.00034344 | 0.00034344 | 0.00034344 | 0.0 | 0.17
Modify | 0.0020471 | 0.0020471 | 0.0020471 | 0.0 | 1.01
Other | | 0.03142 | | | 15.45
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 322 ave 322 max 322 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7000 ave 7000 max 7000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7000
Ave neighs/atom = 8.75
Neighbor list builds = 54
Dangerous builds = 0
Total wall time: 0:00:00