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 1 by 1 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 = 0.003 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 = 2197 512
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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) = 5.625 | 5.625 | 5.625 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 22.604289 115.04411 385.4719
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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 5.78944e-05 64
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500 480.93508 -378.08914 36.26854 115.49018 2822.245
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600 457.38119 -381.9922 62.73272 115.65441 -387.65281
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700 488.20843 -393.89334 45.144546 115.47805 3086.293
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800 463.52123 -384.28537 59.827245 116.2942 3310.9672
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900 500.42748 -424.29715 64.614956 116.16348 -612.56056
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SHAKE stats (type/ave/delta/count) on step 1000
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1 2.00000 8.23271e-07 192
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1 328.410 5.98754e-05 64
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1000 522.46734 -424.93564 44.24152 116.1088 3948.9908
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1100 470.79532 -398.30875 66.721422 116.08177 2480.4521
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1200 515.87076 -433.25982 58.802584 116.07313 1913.2295
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1300 517.25521 -425.5203 49.308433 115.63494 3343.755
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1400 515.28471 -427.75141 53.078285 115.29997 2755.9048
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SHAKE stats (type/ave/delta/count) on step 1500
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1 2.00000 8.95165e-07 192
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1 328.410 7.19288e-05 64
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1500 514.22181 -421.99736 48.624007 115.58906 2400.1515
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1600 533.9392 -430.89564 38.263047 115.07866 4331.2167
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1700 529.29154 -424.02106 35.673551 114.94439 2973.3181
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1800 535.52166 -438.41572 43.952454 114.75272 1799.8588
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1900 519.40791 -413.30717 34.399008 114.9856 4270.415
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SHAKE stats (type/ave/delta/count) on step 2000
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1 2.00000 8.04353e-07 192
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1 328.410 7.97925e-05 64
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2000 553.26572 -446.67936 35.423618 114.83268 1729.4708
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2100 546.58793 -448.39367 43.475288 114.82028 1266.9778
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2200 536.17021 -442.03485 46.968579 114.76641 2419.0965
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2300 556.29724 -457.19766 43.217115 114.99049 1122.5796
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2400 529.02178 -437.66639 49.530498 114.89949 1714.4747
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SHAKE stats (type/ave/delta/count) on step 2500
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1 2.00000 6.70601e-07 192
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1 328.410 6.39002e-05 64
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2500 500.56024 -423.00108 62.368402 115.33925 3750.7564
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Loop time of 6.4485 on 1 procs for 2500 steps with 384 atoms
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Performance: 33.496 ns/day, 0.717 hours/ns, 387.687 timesteps/s
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99.4% CPU use with 1 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 | 4.9332 | 4.9332 | 4.9332 | 0.0 | 76.50
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Bond | 0.013685 | 0.013685 | 0.013685 | 0.0 | 0.21
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Kspace | 0.33226 | 0.33226 | 0.33226 | 0.0 | 5.15
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Neigh | 1.0663 | 1.0663 | 1.0663 | 0.0 | 16.54
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Comm | 0.062471 | 0.062471 | 0.062471 | 0.0 | 0.97
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Output | 0.00048861 | 0.00048861 | 0.00048861 | 0.0 | 0.01
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Modify | 0.030447 | 0.030447 | 0.030447 | 0.0 | 0.47
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Other | | 0.009605 | | | 0.15
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Nlocal: 384.000 ave 384 max 384 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5594.00 ave 5594 max 5594 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 129739.0 ave 129739 max 129739 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 129739
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Ave neighs/atom = 337.86198
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Ave special neighs/atom = 2.0000000
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Neighbor list builds = 320
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Dangerous builds = 0
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Total wall time: 0:00:06
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