159 lines
6.5 KiB
Groff
159 lines
6.5 KiB
Groff
LAMMPS (22 Oct 2020)
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using 1 OpenMP thread(s) per MPI task
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# demo using atom style hybrid template charge to simulate a h2o/co2 mixture
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units real
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molecule twomols h2o.mol co2.mol offset 2 1 1 0 0
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Read molecule template twomols:
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1 molecules
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3 atoms with max type 2
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2 bonds with max type 1
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1 angles with max type 1
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0 dihedrals with max type 0
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0 impropers with max type 0
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Read molecule template twomols:
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1 molecules
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3 atoms with max type 4
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2 bonds with max type 2
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1 angles with max type 2
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0 dihedrals with max type 0
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0 impropers with max type 0
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atom_style hybrid template twomols charge
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boundary p p p
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pair_style lj/cut/coul/long 12
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pair_modify mix arithmetic tail yes
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kspace_style pppm 0.0001
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pair_style lj/cut/coul/long 12
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bond_style harmonic
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angle_style harmonic
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read_data h2o-co2.data
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Reading data file ...
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orthogonal box = (-10.000000 -10.000000 -10.000000) to (10.000000 10.000000 10.000000)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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384 atoms
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256 template bonds
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128 template angles
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read_data CPU = 0.002 seconds
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group h2o type 1 2
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192 atoms in group h2o
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group co2 type 3 4
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192 atoms in group co2
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neighbor 1.0 bin
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neigh_modify every 1 delay 1 check yes
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timestep 1.0
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velocity all create 300.0 34672
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thermo 100
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fix 1 all nve
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fix 2 all shake 1.0e-4 1000 500 b 1 a 1 mol twomols
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WARNING: Molecule template for fix shake has multiple molecules (src/RIGID/fix_shake.cpp:174)
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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64 = # of frozen angles
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find clusters CPU = 0.000 seconds
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#dump 1 all custom 100 h2o-co2.lammpstrj id mol xu yu zu
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run 2500
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
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G vector (1/distance) = 0.21452218
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grid = 8 8 8
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0237525
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estimated relative force accuracy = 7.1529949e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 1053 128
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Neighbor list info ...
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update every 1 steps, delay 1 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 15
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ghost atom cutoff = 15
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binsize = 7.5, bins = 3 3 3
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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SHAKE stats (type/ave/delta/count) on step 0
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1 1.99995 1.29379e-05 192
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1 328.411 6.25278e-13 64
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Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 360.18809 -173.24472 3.5527137e-13 169.25036 2429.6019
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100 363.1919 -274.40147 44.351072 115.30094 -883.3694
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200 427.79493 -329.78833 38.354106 115.34674 1523.3792
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300 465.88637 -350.56147 22.60429 115.0441 385.47189
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400 436.9596 -357.24661 57.161471 115.41032 2307.0158
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SHAKE stats (type/ave/delta/count) on step 500
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1 2.00000 4.02911e-07 192
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1 328.410 5.78945e-05 64
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500 480.93505 -378.08914 36.268541 115.49016 2822.245
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600 457.38144 -381.99241 62.732739 115.65446 -387.65505
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700 488.20801 -393.89265 45.144482 115.47829 3086.2987
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800 463.5234 -384.28682 59.826927 116.2945 3310.9691
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900 500.48024 -424.35693 64.621298 116.16022 -612.4406
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SHAKE stats (type/ave/delta/count) on step 1000
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1 2.00000 8.21157e-07 192
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1 328.410 5.79572e-05 64
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1000 522.3905 -424.85292 44.232122 116.10905 3948.1535
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1100 466.7856 -395.03916 67.204265 116.02145 2555.2069
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1200 505.58079 -424.30563 59.681049 116.12127 1919.2701
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1300 510.78441 -418.28838 48.398524 115.804 3476.7443
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1400 494.39282 -407.60176 52.9665 115.47219 2343.5129
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SHAKE stats (type/ave/delta/count) on step 1500
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1 2.00000 7.21617e-07 192
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1 328.410 8.01168e-05 64
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1500 533.48096 -444.9571 53.263393 115.58182 1055.8053
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1600 548.84084 -449.81134 43.134527 115.20409 3084.0678
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1700 522.65205 -419.10648 37.279839 115.1519 1813.2589
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1800 497.72839 -403.88156 45.774501 115.17212 1822.8113
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1900 535.04509 -434.52042 40.685094 114.9275 4216.4353
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SHAKE stats (type/ave/delta/count) on step 2000
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1 2.00000 1.03652e-06 192
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1 328.410 5.49305e-05 64
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2000 540.42903 -436.41996 37.284032 114.74637 1422.0078
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2100 534.80707 -439.51681 46.068646 115.08833 1460.2864
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2200 507.8413 -419.62464 51.912776 115.18345 3790.8003
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2300 553.37305 -456.23124 45.592723 115.55197 515.72888
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2400 538.60716 -447.65657 51.130476 115.62382 2087.6217
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SHAKE stats (type/ave/delta/count) on step 2500
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1 2.00000 6.38759e-07 192
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1 328.410 5.54712e-05 64
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2500 507.38323 -436.58125 69.949293 115.8278 3313.9095
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Loop time of 2.62759 on 4 procs for 2500 steps with 384 atoms
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Performance: 82.205 ns/day, 0.292 hours/ns, 951.443 timesteps/s
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93.7% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 1.1769 | 1.3595 | 1.5961 | 13.1 | 51.74
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Bond | 0.0040634 | 0.0042451 | 0.0044163 | 0.2 | 0.16
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Kspace | 0.37643 | 0.62177 | 0.8124 | 20.0 | 23.66
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Neigh | 0.35517 | 0.35603 | 0.35688 | 0.1 | 13.55
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Comm | 0.15521 | 0.16781 | 0.18101 | 2.8 | 6.39
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Output | 0.00039921 | 0.00083364 | 0.0018058 | 0.0 | 0.03
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Modify | 0.081231 | 0.095032 | 0.10957 | 3.5 | 3.62
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Other | | 0.02238 | | | 0.85
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Nlocal: 96.0000 ave 105 max 84 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Nghost: 3764.00 ave 3776 max 3755 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Neighs: 32527.2 ave 34260 max 29030 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Total # of neighbors = 130109
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Ave neighs/atom = 338.82552
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Ave special neighs/atom = 2.0000000
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Neighbor list builds = 321
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Dangerous builds = 0
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Total wall time: 0:00:02
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