mirror of https://github.com/lammps/lammps.git
add examples for using fix rigid/nv?/small with fix deposit
This commit is contained in:
Axel Kohlmeyer
parent
8e28252ac9
commit
1fe284dbba
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# sample surface deposition script for molecules
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units lj
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atom_style bond
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boundary p p f
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lattice fcc 1.0
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region box block 0 5 0 5 0 10
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create_box 3 box bond/types 1 extra/bond/per/atom 1
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region substrate block INF INF INF INF INF 3
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create_atoms 1 region substrate
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 1.0 1.0 5.0
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mass * 1.0
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bond_style harmonic
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bond_coeff 1 5.0 1.0
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neigh_modify delay 0
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molecule dimer molecule.dimer
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region slab block 0 5 0 5 8 9
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group addatoms empty
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region mobile block 0 5 0 5 2 INF
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group mobile region mobile
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compute add addatoms temp
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compute_modify add dynamic/dof yes extra/dof 0
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fix 1 addatoms rigid/nve/small molecule mol dimer
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fix 2 mobile langevin 0.1 0.1 0.1 587283
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fix 3 mobile nve
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fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 &
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mol dimer vz -1.0 -1.0 rigid 1
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fix 5 addatoms wall/reflect zhi EDGE
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thermo_style custom step atoms temp epair etotal press
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thermo 100
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thermo_modify temp add lost/bond ignore lost warn
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#dump 1 all atom 50 dump.deposit.atom
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#dump 2 all image 50 image.*.jpg type type &
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# axes yes 0.8 0.02 view 80 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 50 tmp.mpg type type &
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# axes yes 0.8 0.02 view 80 -30
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#dump_modify 3 pad 5
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run 10000
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@ -0,0 +1,56 @@
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# sample surface deposition script for molecules
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units lj
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atom_style bond
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boundary p p f
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lattice fcc 1.0
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region box block 0 5 0 5 0 10
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create_box 3 box bond/types 1 extra/bond/per/atom 1
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region substrate block INF INF INF INF INF 3
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create_atoms 1 region substrate
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 1.0 1.0 5.0
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mass * 1.0
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bond_style harmonic
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bond_coeff 1 5.0 1.0
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neigh_modify delay 0
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molecule dimer molecule.dimer
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region slab block 0 5 0 5 8 9
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group addatoms empty
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region mobile block 0 5 0 5 2 INF
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group mobile region mobile
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compute add addatoms temp
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compute_modify add dynamic/dof yes extra/dof 0
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fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer
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fix 2 mobile langevin 0.1 0.1 0.1 587283
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fix 3 mobile nve
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fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 &
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mol dimer vz -1.0 -1.0 rigid 1
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fix 5 addatoms wall/reflect zhi EDGE
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thermo_style custom step atoms temp epair etotal press
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thermo 100
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thermo_modify temp add lost/bond ignore lost warn
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#dump 1 all atom 50 dump.deposit.atom
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#dump 2 all image 50 image.*.jpg type type &
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# axes yes 0.8 0.02 view 80 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 50 tmp.mpg type type &
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# axes yes 0.8 0.02 view 80 -30
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#dump_modify 3 pad 5
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run 10000
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@ -0,0 +1,218 @@
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LAMMPS (10 Mar 2021)
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using 1 OpenMP thread(s) per MPI task
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# sample surface deposition script for molecules
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units lj
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atom_style bond
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boundary p p f
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
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region box block 0 5 0 5 0 10
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create_box 3 box bond/types 1 extra/bond/per/atom 1
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
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1 by 1 by 1 MPI processor grid
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region substrate block INF INF INF INF INF 3
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create_atoms 1 region substrate
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Created 350 atoms
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create_atoms CPU = 0.001 seconds
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 1.0 1.0 5.0
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mass * 1.0
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bond_style harmonic
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bond_coeff 1 5.0 1.0
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neigh_modify delay 0
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molecule dimer molecule.dimer
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Read molecule template dimer:
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1 molecules
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2 atoms with max type 3
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1 bonds with max type 1
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0 angles with max type 0
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0 dihedrals with max type 0
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0 impropers with max type 0
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region slab block 0 5 0 5 8 9
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group addatoms empty
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0 atoms in group addatoms
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region mobile block 0 5 0 5 2 INF
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group mobile region mobile
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150 atoms in group mobile
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compute add addatoms temp
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compute_modify add dynamic/dof yes extra/dof 0
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fix 1 addatoms rigid/nve/small molecule mol dimer
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create bodies CPU = 0.000 seconds
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0 rigid bodies with 0 atoms
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1.0000000 = max distance from body owner to body atom
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fix 2 mobile langevin 0.1 0.1 0.1 587283
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fix 3 mobile nve
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fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
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fix 5 addatoms wall/reflect zhi EDGE
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thermo_style custom step atoms temp epair etotal press
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thermo 100
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thermo_modify temp add lost/bond ignore lost warn
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WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
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#dump 1 all atom 50 dump.deposit.atom
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#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
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#dump_modify 3 pad 5
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run 10000
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WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
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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 = 5.3
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ghost atom cutoff = 5.3
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binsize = 2.65, bins = 3 3 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/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes
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Step Atoms Temp E_pair TotEng Press
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0 350 0 -6.9215833 -6.9215833 -1.0052629
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100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914
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200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276
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300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826
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400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699
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500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307
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600 362 1.026148 -6.7105231 -6.6680032 -0.68314418
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700 364 1.0683344 -6.6725162 -6.621154 -0.65747369
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800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615
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900 368 1.1250034 -6.6101882 -6.541404 -0.66674346
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1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655
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1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041
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1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272
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1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641
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1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595
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1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503
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1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922
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1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709
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1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665
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1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025
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2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647
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2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526
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2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284
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2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436
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2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839
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2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448
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2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222
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2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856
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2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872
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2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283
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3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953
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3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935
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3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713
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3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674
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3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626
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3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941
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3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484
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3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147
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3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799
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3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878
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4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433
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4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822
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4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778
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4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913
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4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275
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4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051
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4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572
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4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509
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4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049
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4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429
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5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531
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5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403
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5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239
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5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702
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5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883
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5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171
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5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419
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5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563
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5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625
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5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757
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6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047
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6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913
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6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083
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6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967
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6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489
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6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516
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6600 482 0.354106 -6.6890268 -6.567808 -0.81897158
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6700 484 0.3504816 -6.681739 -6.5604463 -0.811609
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6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296
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6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651
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7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078
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7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001
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7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767
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7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121
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7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584
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7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602
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7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497
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7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548
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7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084
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7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684
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8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575
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8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457
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8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287
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8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937
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8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496
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8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738
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8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327
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8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016
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8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456
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8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919
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9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061
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9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298
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9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671
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9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602
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9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131
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9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326
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9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105
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9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932
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9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759
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9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312
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10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213
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Loop time of 16.7275 on 1 procs for 10000 steps with 550 atoms
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Performance: 258256.688 tau/day, 597.816 timesteps/s
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99.9% 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 | 9.2508 | 9.2508 | 9.2508 | 0.0 | 55.30
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Bond | 0.021603 | 0.021603 | 0.021603 | 0.0 | 0.13
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Neigh | 4.5325 | 4.5325 | 4.5325 | 0.0 | 27.10
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Comm | 0.62777 | 0.62777 | 0.62777 | 0.0 | 3.75
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Output | 0.006916 | 0.006916 | 0.006916 | 0.0 | 0.04
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Modify | 2.218 | 2.218 | 2.218 | 0.0 | 13.26
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Other | | 0.07002 | | | 0.42
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Nlocal: 550.000 ave 550 max 550 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2344.00 ave 2344 max 2344 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 36607.0 ave 36607 max 36607 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 36607
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Ave neighs/atom = 66.558182
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Ave special neighs/atom = 0.36363636
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Neighbor list builds = 847
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Dangerous builds = 0
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Total wall time: 0:00:16
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@ -0,0 +1,218 @@
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LAMMPS (10 Mar 2021)
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using 1 OpenMP thread(s) per MPI task
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# sample surface deposition script for molecules
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units lj
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atom_style bond
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boundary p p f
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
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region box block 0 5 0 5 0 10
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create_box 3 box bond/types 1 extra/bond/per/atom 1
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
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1 by 1 by 4 MPI processor grid
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region substrate block INF INF INF INF INF 3
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create_atoms 1 region substrate
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Created 350 atoms
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create_atoms CPU = 0.002 seconds
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 1.0 1.0 5.0
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mass * 1.0
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bond_style harmonic
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bond_coeff 1 5.0 1.0
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neigh_modify delay 0
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molecule dimer molecule.dimer
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Read molecule template dimer:
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1 molecules
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2 atoms with max type 3
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1 bonds with max type 1
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0 angles with max type 0
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
region slab block 0 5 0 5 8 9
|
||||
|
||||
group addatoms empty
|
||||
0 atoms in group addatoms
|
||||
region mobile block 0 5 0 5 2 INF
|
||||
group mobile region mobile
|
||||
150 atoms in group mobile
|
||||
|
||||
compute add addatoms temp
|
||||
compute_modify add dynamic/dof yes extra/dof 0
|
||||
|
||||
fix 1 addatoms rigid/nve/small molecule mol dimer
|
||||
create bodies CPU = 0.000 seconds
|
||||
0 rigid bodies with 0 atoms
|
||||
1.0000000 = max distance from body owner to body atom
|
||||
fix 2 mobile langevin 0.1 0.1 0.1 587283
|
||||
fix 3 mobile nve
|
||||
|
||||
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
|
||||
fix 5 addatoms wall/reflect zhi EDGE
|
||||
|
||||
thermo_style custom step atoms temp epair etotal press
|
||||
thermo 100
|
||||
thermo_modify temp add lost/bond ignore lost warn
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
|
||||
|
||||
#dump 1 all atom 50 dump.deposit.atom
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 10000
|
||||
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65, bins = 3 3 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes
|
||||
Step Atoms Temp E_pair TotEng Press
|
||||
0 350 0 -6.9215833 -6.9215833 -1.0052629
|
||||
100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337
|
||||
200 354 1.0081552 -6.8645575 -6.850318 -0.69629729
|
||||
300 356 1.0085803 -6.821677 -6.8004288 -0.69532657
|
||||
400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568
|
||||
500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641
|
||||
600 362 1.026146 -6.7129201 -6.6704003 -0.67063836
|
||||
700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472
|
||||
800 366 1.0958894 -6.6402029 -6.5803182 -0.66307282
|
||||
900 368 1.1231769 -6.6050912 -6.5364187 -0.64076928
|
||||
1000 370 1.1976289 -6.5942508 -6.51333 -0.69249047
|
||||
1100 372 1.05061 -6.5772306 -6.4995645 -0.6307289
|
||||
1200 374 0.93723829 -6.5732962 -6.4981166 -0.64963821
|
||||
1300 376 0.93899122 -6.5578418 -6.476679 -0.65096688
|
||||
1400 378 0.87050694 -6.546852 -6.4662495 -0.67613401
|
||||
1500 380 0.84462904 -6.5400883 -6.4567368 -0.64376986
|
||||
1600 382 0.92417795 -6.5611292 -6.4643567 -0.62092779
|
||||
1700 384 0.67296541 -6.5589985 -6.4845167 -0.6779111
|
||||
1800 386 0.87159158 -6.5655058 -6.4638954 -0.6582786
|
||||
1900 388 0.67504975 -6.5772537 -6.4946123 -0.665098
|
||||
2000 390 0.65034978 -6.5717854 -6.4884072 -0.73162072
|
||||
2100 392 0.63389859 -6.5652907 -6.4803935 -0.64937411
|
||||
2200 394 0.6265637 -6.5582412 -6.4707767 -0.70819854
|
||||
2300 396 0.85352983 -6.5750751 -6.4511408 -0.69995918
|
||||
2400 398 0.69792348 -6.5938659 -6.4886513 -0.63755214
|
||||
2500 400 0.45320495 -6.595022 -6.5242087 -0.70462183
|
||||
2600 402 0.46824374 -6.5697613 -6.4940502 -0.75497893
|
||||
2700 404 0.46605975 -6.5599272 -6.4820583 -0.66778506
|
||||
2800 406 0.50637604 -6.5700492 -6.482743 -0.63812082
|
||||
2900 408 0.55335921 -6.5873352 -6.4890054 -0.62891652
|
||||
3000 410 0.51731142 -6.5890566 -6.4944264 -0.64305355
|
||||
3100 412 0.59439734 -6.6003127 -6.4885025 -0.67140541
|
||||
3200 414 0.53413632 -6.595564 -6.4923492 -0.76242248
|
||||
3300 416 0.49221593 -6.5990831 -6.5014681 -0.71330819
|
||||
3400 418 0.55006126 -6.6015725 -6.4897179 -0.72044309
|
||||
3500 420 0.49065348 -6.6329864 -6.5307669 -0.65775397
|
||||
3600 422 0.41907335 -6.6219753 -6.5325995 -0.75936391
|
||||
3700 424 0.38720116 -6.6153349 -6.5308629 -0.74166397
|
||||
3800 426 0.40625994 -6.6150209 -6.5244231 -0.7595111
|
||||
3900 428 0.40460547 -6.6122642 -6.5200936 -0.70484465
|
||||
4000 430 0.45014991 -6.6254404 -6.5207544 -0.70069933
|
||||
4100 432 0.44820466 -6.640222 -6.5338771 -0.805972
|
||||
4200 434 0.39767521 -6.6450316 -6.5488199 -0.72841414
|
||||
4300 436 0.4155331 -6.6547917 -6.5523381 -0.6894484
|
||||
4400 438 0.43034353 -6.6615074 -6.5534303 -0.74026062
|
||||
4500 440 0.38062977 -6.6541618 -6.5568417 -0.85911194
|
||||
4600 442 0.39357419 -6.6522517 -6.5498512 -0.66232114
|
||||
4700 444 0.40296801 -6.6647029 -6.5580616 -0.67307577
|
||||
4800 446 0.38194993 -6.6510248 -6.548258 -0.77887746
|
||||
4900 448 0.40739835 -6.6601751 -6.5487771 -0.84146416
|
||||
5000 450 0.38392807 -6.6560665 -6.5494198 -0.77343399
|
||||
5100 452 0.35209286 -6.6481476 -6.5488294 -0.68065755
|
||||
5200 454 0.41355143 -6.6615988 -6.543181 -0.81611092
|
||||
5300 456 0.42200484 -6.6627494 -6.5401273 -0.7774134
|
||||
5400 458 0.37764326 -6.661431 -6.550117 -0.72187808
|
||||
5500 460 0.41857405 -6.6674232 -6.542306 -0.74929745
|
||||
5600 462 0.41682611 -6.6710961 -6.5447852 -0.7557454
|
||||
5700 464 0.44396148 -6.6924346 -6.5560887 -0.78018312
|
||||
5800 466 0.37058077 -6.6865013 -6.5711919 -0.74146125
|
||||
5900 468 0.346812 -6.681215 -6.57191 -0.81184233
|
||||
6000 470 0.34919462 -6.6827931 -6.571348 -0.87330821
|
||||
6100 472 0.39360936 -6.6933359 -6.5661634 -0.79237598
|
||||
6200 474 0.33270778 -6.6847095 -6.5759127 -0.77978526
|
||||
6300 476 0.35973804 -6.6951254 -6.5760944 -0.80340174
|
||||
6400 478 0.38124318 -6.7045984 -6.5769857 -0.81628407
|
||||
6500 480 0.41188302 -6.7133356 -6.573896 -0.7940289
|
||||
6600 482 0.36998039 -6.7079555 -6.5813025 -0.75055442
|
||||
6700 484 0.37615026 -6.722917 -6.592741 -0.76534055
|
||||
6800 486 0.3466597 -6.7188712 -6.5976116 -0.77986211
|
||||
6900 488 0.32902492 -6.7247054 -6.6084005 -0.75702458
|
||||
7000 490 0.31856427 -6.7167709 -6.6029979 -0.76014555
|
||||
7100 492 0.30233891 -6.7144406 -6.6053651 -0.96246708
|
||||
7200 494 0.32557309 -6.7315347 -6.6129049 -0.8122153
|
||||
7300 496 0.29919611 -6.7186327 -6.6085455 -0.71917931
|
||||
7400 498 0.29778169 -6.7259455 -6.6153238 -0.88199391
|
||||
7500 500 0.35535305 -6.7419073 -6.6086499 -0.90344083
|
||||
7600 502 0.31979187 -6.7326802 -6.6116434 -0.78324572
|
||||
7700 504 0.30821359 -6.72895 -6.6112295 -0.81363335
|
||||
7800 506 0.31374993 -6.7255461 -6.6046346 -0.89904197
|
||||
7900 508 0.29072338 -6.7177355 -6.6047082 -0.81423073
|
||||
8000 510 0.30557494 -6.7208283 -6.600995 -0.85853575
|
||||
8100 512 0.30521237 -6.726874 -6.6061601 -0.75361257
|
||||
8200 514 0.29622226 -6.7152225 -6.5970794 -0.85766132
|
||||
8300 516 0.28337698 -6.7023552 -6.5884003 -0.8985415
|
||||
8400 518 0.32860902 -6.7211074 -6.5878875 -0.89758921
|
||||
8500 520 0.35483743 -6.7406183 -6.5956126 -0.77602077
|
||||
8600 522 0.32928486 -6.7326607 -6.5970358 -0.75070137
|
||||
8700 524 0.36008106 -6.7474714 -6.5980103 -0.87093836
|
||||
8800 526 0.36082301 -6.743579 -6.5926644 -0.90132107
|
||||
8900 528 0.35010285 -6.7501553 -6.6026214 -0.85238959
|
||||
9000 530 0.31513985 -6.7411795 -6.6073937 -0.75884529
|
||||
9100 532 0.30895083 -6.7421063 -6.6099891 -0.74482692
|
||||
9200 534 0.33631849 -6.751265 -6.6064087 -0.95632911
|
||||
9300 536 0.33306096 -6.759187 -6.6147156 -0.76275935
|
||||
9400 538 0.34582537 -6.7706766 -6.619619 -0.72251598
|
||||
9500 540 0.32003146 -6.772057 -6.6313024 -0.88195851
|
||||
9600 542 0.32439637 -6.7743569 -6.6307127 -0.90233104
|
||||
9700 544 0.33988235 -6.7763721 -6.624862 -0.85185581
|
||||
9800 546 0.32877587 -6.7744977 -6.62697 -0.8550905
|
||||
9900 548 0.29570051 -6.7623752 -6.6288243 -1.0371157
|
||||
10000 550 0.33675914 -6.7757315 -6.6226591 -1.0082157
|
||||
Loop time of 16.2553 on 4 procs for 10000 steps with 550 atoms
|
||||
|
||||
Performance: 265759.101 tau/day, 615.183 timesteps/s
|
||||
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0034051 | 2.6646 | 8.0317 | 200.7 | 16.39
|
||||
Bond | 0.0022626 | 0.0072971 | 0.019437 | 8.3 | 0.04
|
||||
Neigh | 0.018657 | 1.218 | 3.7621 | 137.5 | 7.49
|
||||
Comm | 1.1497 | 6.7957 | 12.192 | 164.2 | 41.81
|
||||
Output | 0.010692 | 0.01431 | 0.019901 | 3.2 | 0.09
|
||||
Modify | 3.1502 | 5.3779 | 11.342 | 149.0 | 33.08
|
||||
Other | | 0.1775 | | | 1.09
|
||||
|
||||
Nlocal: 137.500 ave 299 max 2 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 1903.75 ave 2686 max 529 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 9209.75 ave 23206 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 36839
|
||||
Ave neighs/atom = 66.980000
|
||||
Ave special neighs/atom = 0.36363636
|
||||
Neighbor list builds = 829
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:16
|
||||
|
|
@ -0,0 +1,218 @@
|
|||
LAMMPS (10 Mar 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# sample surface deposition script for molecules
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
boundary p p f
|
||||
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block 0 5 0 5 0 10
|
||||
create_box 3 box bond/types 1 extra/bond/per/atom 1
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
region substrate block INF INF INF INF INF 3
|
||||
create_atoms 1 region substrate
|
||||
Created 350 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 2 1.0 1.0 5.0
|
||||
mass * 1.0
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 5.0 1.0
|
||||
|
||||
neigh_modify delay 0
|
||||
|
||||
molecule dimer molecule.dimer
|
||||
Read molecule template dimer:
|
||||
1 molecules
|
||||
2 atoms with max type 3
|
||||
1 bonds with max type 1
|
||||
0 angles with max type 0
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
region slab block 0 5 0 5 8 9
|
||||
|
||||
group addatoms empty
|
||||
0 atoms in group addatoms
|
||||
region mobile block 0 5 0 5 2 INF
|
||||
group mobile region mobile
|
||||
150 atoms in group mobile
|
||||
|
||||
compute add addatoms temp
|
||||
compute_modify add dynamic/dof yes extra/dof 0
|
||||
|
||||
fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer
|
||||
create bodies CPU = 0.000 seconds
|
||||
0 rigid bodies with 0 atoms
|
||||
1.0000000 = max distance from body owner to body atom
|
||||
fix 2 mobile langevin 0.1 0.1 0.1 587283
|
||||
fix 3 mobile nve
|
||||
|
||||
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
|
||||
fix 5 addatoms wall/reflect zhi EDGE
|
||||
|
||||
thermo_style custom step atoms temp epair etotal press
|
||||
thermo 100
|
||||
thermo_modify temp add lost/bond ignore lost warn
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
|
||||
|
||||
#dump 1 all atom 50 dump.deposit.atom
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 10000
|
||||
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65, bins = 3 3 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes
|
||||
Step Atoms Temp E_pair TotEng Press
|
||||
0 350 0 -6.9215833 -6.9215833 -1.0052629
|
||||
100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914
|
||||
200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276
|
||||
300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826
|
||||
400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699
|
||||
500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307
|
||||
600 362 1.026148 -6.7105231 -6.6680032 -0.68314418
|
||||
700 364 1.0683344 -6.6725162 -6.621154 -0.65747369
|
||||
800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615
|
||||
900 368 1.1250034 -6.6101882 -6.541404 -0.66674346
|
||||
1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655
|
||||
1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041
|
||||
1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272
|
||||
1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641
|
||||
1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595
|
||||
1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503
|
||||
1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922
|
||||
1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709
|
||||
1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665
|
||||
1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025
|
||||
2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647
|
||||
2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526
|
||||
2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284
|
||||
2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436
|
||||
2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839
|
||||
2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448
|
||||
2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222
|
||||
2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856
|
||||
2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872
|
||||
2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283
|
||||
3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953
|
||||
3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935
|
||||
3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713
|
||||
3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674
|
||||
3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626
|
||||
3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941
|
||||
3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484
|
||||
3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147
|
||||
3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799
|
||||
3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878
|
||||
4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433
|
||||
4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822
|
||||
4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778
|
||||
4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913
|
||||
4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275
|
||||
4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051
|
||||
4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572
|
||||
4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509
|
||||
4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049
|
||||
4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429
|
||||
5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531
|
||||
5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403
|
||||
5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239
|
||||
5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702
|
||||
5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883
|
||||
5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171
|
||||
5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419
|
||||
5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563
|
||||
5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625
|
||||
5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757
|
||||
6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047
|
||||
6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913
|
||||
6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083
|
||||
6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967
|
||||
6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489
|
||||
6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516
|
||||
6600 482 0.354106 -6.6890268 -6.567808 -0.81897158
|
||||
6700 484 0.3504816 -6.681739 -6.5604463 -0.811609
|
||||
6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296
|
||||
6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651
|
||||
7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078
|
||||
7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001
|
||||
7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767
|
||||
7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121
|
||||
7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584
|
||||
7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602
|
||||
7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497
|
||||
7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548
|
||||
7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084
|
||||
7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684
|
||||
8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575
|
||||
8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457
|
||||
8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287
|
||||
8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937
|
||||
8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496
|
||||
8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738
|
||||
8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327
|
||||
8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016
|
||||
8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456
|
||||
8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919
|
||||
9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061
|
||||
9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298
|
||||
9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671
|
||||
9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602
|
||||
9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131
|
||||
9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326
|
||||
9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105
|
||||
9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932
|
||||
9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759
|
||||
9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312
|
||||
10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213
|
||||
Loop time of 16.6615 on 1 procs for 10000 steps with 550 atoms
|
||||
|
||||
Performance: 259279.806 tau/day, 600.185 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.2639 | 9.2639 | 9.2639 | 0.0 | 55.60
|
||||
Bond | 0.021559 | 0.021559 | 0.021559 | 0.0 | 0.13
|
||||
Neigh | 4.544 | 4.544 | 4.544 | 0.0 | 27.27
|
||||
Comm | 0.62792 | 0.62792 | 0.62792 | 0.0 | 3.77
|
||||
Output | 0.0069666 | 0.0069666 | 0.0069666 | 0.0 | 0.04
|
||||
Modify | 2.1282 | 2.1282 | 2.1282 | 0.0 | 12.77
|
||||
Other | | 0.06897 | | | 0.41
|
||||
|
||||
Nlocal: 550.000 ave 550 max 550 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2344.00 ave 2344 max 2344 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 36607.0 ave 36607 max 36607 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 36607
|
||||
Ave neighs/atom = 66.558182
|
||||
Ave special neighs/atom = 0.36363636
|
||||
Neighbor list builds = 847
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:16
|
||||
|
|
@ -0,0 +1,218 @@
|
|||
LAMMPS (10 Mar 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# sample surface deposition script for molecules
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
boundary p p f
|
||||
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block 0 5 0 5 0 10
|
||||
create_box 3 box bond/types 1 extra/bond/per/atom 1
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
|
||||
region substrate block INF INF INF INF INF 3
|
||||
create_atoms 1 region substrate
|
||||
Created 350 atoms
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 2 1.0 1.0 5.0
|
||||
mass * 1.0
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 5.0 1.0
|
||||
|
||||
neigh_modify delay 0
|
||||
|
||||
molecule dimer molecule.dimer
|
||||
Read molecule template dimer:
|
||||
1 molecules
|
||||
2 atoms with max type 3
|
||||
1 bonds with max type 1
|
||||
0 angles with max type 0
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
region slab block 0 5 0 5 8 9
|
||||
|
||||
group addatoms empty
|
||||
0 atoms in group addatoms
|
||||
region mobile block 0 5 0 5 2 INF
|
||||
group mobile region mobile
|
||||
150 atoms in group mobile
|
||||
|
||||
compute add addatoms temp
|
||||
compute_modify add dynamic/dof yes extra/dof 0
|
||||
|
||||
fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer
|
||||
create bodies CPU = 0.000 seconds
|
||||
0 rigid bodies with 0 atoms
|
||||
1.0000000 = max distance from body owner to body atom
|
||||
fix 2 mobile langevin 0.1 0.1 0.1 587283
|
||||
fix 3 mobile nve
|
||||
|
||||
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
|
||||
fix 5 addatoms wall/reflect zhi EDGE
|
||||
|
||||
thermo_style custom step atoms temp epair etotal press
|
||||
thermo 100
|
||||
thermo_modify temp add lost/bond ignore lost warn
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
|
||||
|
||||
#dump 1 all atom 50 dump.deposit.atom
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 10000
|
||||
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.3
|
||||
ghost atom cutoff = 5.3
|
||||
binsize = 2.65, bins = 3 3 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes
|
||||
Step Atoms Temp E_pair TotEng Press
|
||||
0 350 0 -6.9215833 -6.9215833 -1.0052629
|
||||
100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337
|
||||
200 354 1.0081552 -6.8645575 -6.850318 -0.69629729
|
||||
300 356 1.0085803 -6.821677 -6.8004288 -0.69532657
|
||||
400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568
|
||||
500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641
|
||||
600 362 1.026146 -6.7129201 -6.6704003 -0.67063836
|
||||
700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472
|
||||
800 366 1.0958894 -6.6402029 -6.5803182 -0.66307282
|
||||
900 368 1.1231769 -6.6050912 -6.5364187 -0.64076928
|
||||
1000 370 1.1976289 -6.5942508 -6.51333 -0.69249047
|
||||
1100 372 1.05061 -6.5772306 -6.4995645 -0.6307289
|
||||
1200 374 0.93723829 -6.5732962 -6.4981166 -0.64963821
|
||||
1300 376 0.93899122 -6.5578418 -6.476679 -0.65096688
|
||||
1400 378 0.87050694 -6.546852 -6.4662495 -0.67613401
|
||||
1500 380 0.84462904 -6.5400883 -6.4567368 -0.64376986
|
||||
1600 382 0.92417795 -6.5611292 -6.4643567 -0.62092779
|
||||
1700 384 0.67296541 -6.5589985 -6.4845167 -0.6779111
|
||||
1800 386 0.87159158 -6.5655058 -6.4638954 -0.6582786
|
||||
1900 388 0.67504975 -6.5772537 -6.4946123 -0.665098
|
||||
2000 390 0.65034978 -6.5717854 -6.4884072 -0.73162072
|
||||
2100 392 0.63389859 -6.5652907 -6.4803935 -0.64937411
|
||||
2200 394 0.6265637 -6.5582412 -6.4707767 -0.70819854
|
||||
2300 396 0.85352983 -6.5750751 -6.4511408 -0.69995918
|
||||
2400 398 0.69792348 -6.5938659 -6.4886513 -0.63755214
|
||||
2500 400 0.45320495 -6.595022 -6.5242087 -0.70462183
|
||||
2600 402 0.46824374 -6.5697613 -6.4940502 -0.75497893
|
||||
2700 404 0.46605975 -6.5599272 -6.4820583 -0.66778506
|
||||
2800 406 0.50637604 -6.5700492 -6.482743 -0.63812082
|
||||
2900 408 0.55335921 -6.5873352 -6.4890054 -0.62891652
|
||||
3000 410 0.51731142 -6.5890566 -6.4944264 -0.64305355
|
||||
3100 412 0.59439734 -6.6003127 -6.4885025 -0.67140541
|
||||
3200 414 0.53413632 -6.595564 -6.4923492 -0.76242248
|
||||
3300 416 0.49221593 -6.5990831 -6.5014681 -0.71330819
|
||||
3400 418 0.55006126 -6.6015725 -6.4897179 -0.72044309
|
||||
3500 420 0.49065348 -6.6329864 -6.5307669 -0.65775397
|
||||
3600 422 0.41907335 -6.6219753 -6.5325995 -0.75936391
|
||||
3700 424 0.38720116 -6.6153349 -6.5308629 -0.74166397
|
||||
3800 426 0.40625994 -6.6150209 -6.5244231 -0.7595111
|
||||
3900 428 0.40460547 -6.6122642 -6.5200936 -0.70484465
|
||||
4000 430 0.45014991 -6.6254404 -6.5207544 -0.70069933
|
||||
4100 432 0.44820466 -6.640222 -6.5338771 -0.805972
|
||||
4200 434 0.39767521 -6.6450316 -6.5488199 -0.72841414
|
||||
4300 436 0.4155331 -6.6547917 -6.5523381 -0.6894484
|
||||
4400 438 0.43034353 -6.6615074 -6.5534303 -0.74026062
|
||||
4500 440 0.38062977 -6.6541618 -6.5568417 -0.85911194
|
||||
4600 442 0.39357419 -6.6522517 -6.5498512 -0.66232114
|
||||
4700 444 0.40296801 -6.6647029 -6.5580616 -0.67307577
|
||||
4800 446 0.38194993 -6.6510248 -6.548258 -0.77887746
|
||||
4900 448 0.40739835 -6.6601751 -6.5487771 -0.84146416
|
||||
5000 450 0.38392807 -6.6560665 -6.5494198 -0.77343399
|
||||
5100 452 0.35209286 -6.6481476 -6.5488294 -0.68065755
|
||||
5200 454 0.41355143 -6.6615988 -6.543181 -0.81611092
|
||||
5300 456 0.42200484 -6.6627494 -6.5401273 -0.7774134
|
||||
5400 458 0.37764326 -6.661431 -6.550117 -0.72187808
|
||||
5500 460 0.41857405 -6.6674232 -6.542306 -0.74929745
|
||||
5600 462 0.41682611 -6.6710961 -6.5447852 -0.7557454
|
||||
5700 464 0.44396148 -6.6924346 -6.5560887 -0.78018312
|
||||
5800 466 0.37058077 -6.6865013 -6.5711919 -0.74146125
|
||||
5900 468 0.346812 -6.681215 -6.57191 -0.81184233
|
||||
6000 470 0.34919462 -6.6827931 -6.571348 -0.87330821
|
||||
6100 472 0.39360936 -6.6933359 -6.5661634 -0.79237598
|
||||
6200 474 0.33270778 -6.6847095 -6.5759127 -0.77978526
|
||||
6300 476 0.35973804 -6.6951254 -6.5760944 -0.80340174
|
||||
6400 478 0.38124318 -6.7045984 -6.5769857 -0.81628407
|
||||
6500 480 0.41188302 -6.7133356 -6.573896 -0.7940289
|
||||
6600 482 0.36998039 -6.7079555 -6.5813025 -0.75055442
|
||||
6700 484 0.37615026 -6.722917 -6.592741 -0.76534055
|
||||
6800 486 0.3466597 -6.7188712 -6.5976116 -0.77986211
|
||||
6900 488 0.32902492 -6.7247054 -6.6084005 -0.75702458
|
||||
7000 490 0.31856427 -6.7167709 -6.6029979 -0.76014555
|
||||
7100 492 0.30233891 -6.7144406 -6.6053651 -0.96246708
|
||||
7200 494 0.32557309 -6.7315347 -6.6129049 -0.8122153
|
||||
7300 496 0.29919611 -6.7186327 -6.6085455 -0.71917931
|
||||
7400 498 0.29778169 -6.7259455 -6.6153238 -0.88199391
|
||||
7500 500 0.35535305 -6.7419073 -6.6086499 -0.90344083
|
||||
7600 502 0.31979187 -6.7326802 -6.6116434 -0.78324572
|
||||
7700 504 0.30821359 -6.72895 -6.6112295 -0.81363335
|
||||
7800 506 0.31374993 -6.7255461 -6.6046346 -0.89904197
|
||||
7900 508 0.29072338 -6.7177355 -6.6047082 -0.81423073
|
||||
8000 510 0.30557494 -6.7208283 -6.600995 -0.85853575
|
||||
8100 512 0.30521237 -6.726874 -6.6061601 -0.75361257
|
||||
8200 514 0.29622226 -6.7152225 -6.5970794 -0.85766132
|
||||
8300 516 0.28337698 -6.7023552 -6.5884003 -0.8985415
|
||||
8400 518 0.32860902 -6.7211074 -6.5878875 -0.89758921
|
||||
8500 520 0.35483743 -6.7406183 -6.5956126 -0.77602077
|
||||
8600 522 0.32928486 -6.7326607 -6.5970358 -0.75070137
|
||||
8700 524 0.36008106 -6.7474714 -6.5980103 -0.87093836
|
||||
8800 526 0.36082301 -6.743579 -6.5926644 -0.90132107
|
||||
8900 528 0.35010285 -6.7501553 -6.6026214 -0.85238959
|
||||
9000 530 0.31513985 -6.7411795 -6.6073937 -0.75884529
|
||||
9100 532 0.30895083 -6.7421063 -6.6099891 -0.74482692
|
||||
9200 534 0.33631849 -6.751265 -6.6064087 -0.95632911
|
||||
9300 536 0.33306096 -6.759187 -6.6147156 -0.76275935
|
||||
9400 538 0.34582537 -6.7706766 -6.619619 -0.72251598
|
||||
9500 540 0.32003146 -6.772057 -6.6313024 -0.88195851
|
||||
9600 542 0.32439637 -6.7743569 -6.6307127 -0.90233104
|
||||
9700 544 0.33988235 -6.7763721 -6.624862 -0.85185581
|
||||
9800 546 0.32877587 -6.7744977 -6.62697 -0.8550905
|
||||
9900 548 0.29570051 -6.7623752 -6.6288243 -1.0371157
|
||||
10000 550 0.33675914 -6.7757315 -6.6226591 -1.0082157
|
||||
Loop time of 16.1559 on 4 procs for 10000 steps with 550 atoms
|
||||
|
||||
Performance: 267395.139 tau/day, 618.970 timesteps/s
|
||||
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035574 | 2.5467 | 7.5373 | 192.6 | 15.76
|
||||
Bond | 0.0022929 | 0.0073138 | 0.019471 | 8.3 | 0.05
|
||||
Neigh | 0.018645 | 1.2357 | 3.8167 | 138.4 | 7.65
|
||||
Comm | 1.1946 | 6.6335 | 11.87 | 158.8 | 41.06
|
||||
Output | 0.010714 | 0.014391 | 0.020006 | 3.2 | 0.09
|
||||
Modify | 3.4474 | 5.6081 | 11.47 | 143.2 | 34.71
|
||||
Other | | 0.1102 | | | 0.68
|
||||
|
||||
Nlocal: 137.500 ave 299 max 2 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 1903.75 ave 2686 max 529 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 9209.75 ave 23206 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 36839
|
||||
Ave neighs/atom = 66.980000
|
||||
Ave special neighs/atom = 0.36363636
|
||||
Neighbor list builds = 829
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:16
|
||||
Loading…
Reference in New Issue