119 lines
4.8 KiB
Groff
119 lines
4.8 KiB
Groff
LAMMPS (2 Jun 2022)
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# 3d Lennard-Jones melt - MDI driver script
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variable x index 5
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variable y index 5
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variable z index 5
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units lj
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atom_style atomic
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read_data data.snapshot
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Reading data file ...
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orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
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1 by 1 by 3 MPI processor grid
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reading atoms ...
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500 atoms
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reading velocities ...
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500 velocities
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read_data CPU = 0.004 seconds
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 all nve
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fix 2 all mdi/qm add no every 100 virial yes
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compute 1 all pressure NULL virial
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variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
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thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
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thermo 100
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dump 1 all custom 100 dump.snapshot.driver.plugin id type x y z f_2[1] f_2[2] f_2[3]
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dump_modify 1 sort id
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mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.snapshot.engine extra "-log log.snapshot.engine.plugin" command """
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run 300 pre no post no every 100
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"print 'QM eng = $(f_2/atoms)'"
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"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
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"""
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run 300 pre no post no every 100
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"print 'QM eng = $(f_2/atoms)'"
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"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 6 6 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.417 | 4.422 | 4.425 Mbytes
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Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
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0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
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100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
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Loop time of 0.0245664 on 3 procs for 100 steps with 500 atoms
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print 'QM eng = $(f_2/atoms)'
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QM eng = -5.7579933325734442562
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print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
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QM virial = -0.41840219542566498001 -0.48020228608205661747 -0.33571704057970125357 -0.43928725961523629184
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Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
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100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
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200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
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Loop time of 0.0221302 on 3 procs for 100 steps with 500 atoms
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print 'QM eng = $(f_2/atoms)'
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QM eng = -5.7528640103266690531
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print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
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QM virial = -0.40524505957305301251 -0.51524577748319111414 -0.27940441114042025017 -0.42108499009554783976
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Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
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200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
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300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
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Loop time of 0.0224519 on 3 procs for 100 steps with 500 atoms
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Performance: 1924114.069 tau/day, 4453.968 timesteps/s
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100.0% CPU use with 3 MPI tasks x no 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 | 0.0096043 | 0.010493 | 0.011044 | 0.6 | 46.74
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Neigh | 0.0037658 | 0.0041299 | 0.004422 | 0.4 | 18.39
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Comm | 0.0048946 | 0.0055617 | 0.0068824 | 1.3 | 24.77
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Output | 0.00063471 | 0.00063884 | 0.00064691 | 0.0 | 2.85
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Modify | 0.0010632 | 0.0010754 | 0.0010895 | 0.0 | 4.79
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Other | | 0.0005531 | | | 2.46
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Nlocal: 166.667 ave 175 max 157 min
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Histogram: 1 0 0 0 0 0 1 0 0 1
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Nghost: 1254.33 ave 1264 max 1246 min
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Histogram: 1 0 0 1 0 0 0 0 0 1
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Neighs: 6248 ave 6632 max 5774 min
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Histogram: 1 0 0 0 0 0 1 0 0 1
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Total # of neighbors = 18744
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Ave neighs/atom = 37.488
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Neighbor list builds = 31
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Dangerous builds = 0
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print 'QM eng = $(f_2/atoms)'
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QM eng = -5.7527974697327239895
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print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
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QM virial = -0.41843911315521697958 -0.24280603320323956851 -0.42189158691169470483 -0.59061971935071611028
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Total wall time: 0:00:00
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