254 lines
13 KiB
Groff
254 lines
13 KiB
Groff
LAMMPS (19 Nov 2024)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
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using 1 OpenMP thread(s) per MPI task
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# Removing Binned Velocities of Center of Mass (VCM) from Stress
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# This example shows how to remove rigid body motion from
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# binned stress calculations. This uses a combination of commands
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# from compute chunk/atom, compute temp/chunk, compute
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# stress/atom and fix ave/time. We'll show how these commands
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# work in the context of a shockwave experiment on a cube of
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# atoms. To shock the cube, a rectangular region of atoms is
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# frozen, moved into the cube with a constant velocity along the
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# x direction, and then unfrozen. As the shockwave begins
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# propagating, the body of the cube also moves along the x
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# direction. To better understand the stress dynamics of the
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# cube we remove the velocity component belonging to the overall
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# motion of each bin.
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units metal
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boundary p p p
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atom_style atomic
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lattice fcc 5.3589
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Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
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processors 1 * *
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# Defining regions for box and atoms.
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# In this experiment an elongated simulation cell is
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# defined in the x direction to allow for non-periodic
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# motion of the atoms.
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region box1 block -3 24 0 12 0 12 units lattice
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region box2 block 0 12 0 12 0 12 units lattice
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# Creating box and atoms
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create_box 1 box1
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Created orthogonal box = (-16.0767 0 0) to (128.6136 64.3068 64.3068)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 region box2
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Created 7200 atoms
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using lattice units in orthogonal box = (-16.0767 0 0) to (128.6136 64.3068 64.3068)
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create_atoms CPU = 0.002 seconds
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mass 1 40.00
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# Adding energy to the system
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velocity all create 600.0 9999
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pair_style lj/cut 10
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pair_coeff 1 1 0.04 3.405
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# Begin time integration
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timestep 2e-3
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fix fix_nve all nve
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thermo 100
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run 500
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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 = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 25 11 11
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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) = 5.721 | 5.721 | 5.721 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 600 -2252.7567 0 -1694.4304 -974.62456
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100 284.72172 -1977.4291 0 -1712.483 2453.7429
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200 304.44519 -1994.7937 0 -1711.4941 1822.2699
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300 304.28012 -1993.2958 0 -1710.1498 1498.3794
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400 296.76492 -1985.1364 0 -1708.9836 1259.9474
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500 295.00895 -1982.4224 0 -1707.9036 964.9526
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Loop time of 3.01696 on 1 procs for 500 steps with 7200 atoms
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Performance: 28.638 ns/day, 0.838 hours/ns, 165.730 timesteps/s, 1.193 Matom-step/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 | 2.8439 | 2.8439 | 2.8439 | 0.0 | 94.26
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Neigh | 0.11212 | 0.11212 | 0.11212 | 0.0 | 3.72
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Comm | 0.015585 | 0.015585 | 0.015585 | 0.0 | 0.52
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Output | 0.003747 | 0.003747 | 0.003747 | 0.0 | 0.12
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Modify | 0.026097 | 0.026097 | 0.026097 | 0.0 | 0.87
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Other | | 0.01551 | | | 0.51
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Nlocal: 7200 ave 7200 max 7200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 6410 ave 6410 max 6410 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 615095 ave 615095 max 615095 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 615095
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Ave neighs/atom = 85.429861
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Neighbor list builds = 9
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Dangerous builds = 0
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#------------------------------------#
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# Chunk, Stress, and VCM removal steps
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#------------------------------------#
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# 1. Create 20 equispaced bins sliced along the x direction.
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# "units reduced" normalizes the distance from 0 to 1
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variable nbins index 20
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variable fraction equal 1.0/v_nbins
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variable volfrac equal 1/(vol*${fraction})
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variable volfrac equal 1/(vol*0.05)
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compute ch_id all chunk/atom bin/1d x lower ${fraction} units reduced
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compute ch_id all chunk/atom bin/1d x lower 0.05 units reduced
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# 2. Calculate temperature bins with VCM aka COM velocities removed.
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compute ch_temp_vcm all temp/chunk ch_id com yes
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# 3. Compute per atom stress with VCM removed via temp-ID.
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# The velocities from specified temp-ID are used to compute stress
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# Stress/atom units are pressure*volume! Optionally handled next step.
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compute atom_stress_vcm all stress/atom ch_temp_vcm
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# 4. Divide out bin volume from xx stress component.
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variable stress atom -(c_atom_stress_vcm[1])/(vol*${fraction})
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variable stress atom -(c_atom_stress_vcm[1])/(vol*0.05)
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# 5. Sum the per atom stresses in each bin.
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compute ch_stress_vcm all reduce/chunk ch_id sum v_stress
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# 6. Average and output to file.
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# The average output is every 100 steps with samples collected 20 times with 5 step intervals
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# fix ave_stress_vcm all ave/time 5 20 100 c_ch_stress_vcm mode vector file stress_xx.out
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#------------------------------------#
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# Piston compressing along x direction
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region piston block -1 1 INF INF INF INF units lattice
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group piston region piston
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863 atoms in group piston
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fix fix_piston piston move linear 5 0 0 units box # strain rate ~ 8e10 1/s
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thermo_style custom step temp ke pe lx ly lz pxx pyy pzz econserve
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# Atom dump
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# dump atom_dump all atom 50 dump.vcm
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# # Image dumps
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# dump 2 all image 250 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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# dump_modify 2 pad 1
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# # Movie dump
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# dump 3 all movie 125 movie.avi type type # axes yes 0.8 0.02 view 60 -30
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# dump_modify 3 pad 1
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run 500
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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WARNING: One or more atoms are time integrated more than once (src/modify.cpp:296)
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Per MPI rank memory allocation (min/avg/max) = 6.975 | 6.975 | 6.975 Mbytes
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Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve
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500 295.00895 274.51875 -1982.4224 144.6903 64.3068 64.3068 631.89976 1127.2965 1135.6616 -1707.9036
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600 357.38902 332.56613 -1951.3422 144.6903 64.3068 64.3068 2236.6706 2003.2726 1943.6815 -1618.7761
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700 420.30268 391.11005 -1911.8178 144.6903 64.3068 64.3068 3761.5011 3065.4699 3140.3169 -1520.7077
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800 484.96279 451.27911 -1875.379 144.6903 64.3068 64.3068 5362.254 4174.4201 4166.0818 -1424.0999
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900 587.78954 546.96391 -1871.217 144.6903 64.3068 64.3068 6481.4714 4875.705 4676.6083 -1324.2531
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1000 684.07997 636.56636 -1868.1639 144.6903 64.3068 64.3068 7734.6158 5271.3524 5272.1276 -1231.5975
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Loop time of 3.09383 on 1 procs for 500 steps with 7200 atoms
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Performance: 27.927 ns/day, 0.859 hours/ns, 161.612 timesteps/s, 1.164 Matom-step/s
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100.0% 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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Pair | 2.8485 | 2.8485 | 2.8485 | 0.0 | 92.07
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Neigh | 0.18767 | 0.18767 | 0.18767 | 0.0 | 6.07
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Comm | 0.011533 | 0.011533 | 0.011533 | 0.0 | 0.37
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Output | 0.003323 | 0.003323 | 0.003323 | 0.0 | 0.11
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Modify | 0.031777 | 0.031777 | 0.031777 | 0.0 | 1.03
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Other | | 0.01107 | | | 0.36
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Nlocal: 7200 ave 7200 max 7200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 6409 ave 6409 max 6409 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 646408 ave 646408 max 646408 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 646408
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Ave neighs/atom = 89.778889
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Neighbor list builds = 15
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Dangerous builds = 0
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unfix fix_piston
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run 1500
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 6.6 | 6.6 | 6.6 Mbytes
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Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve
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1000 684.07997 636.56636 -1868.1639 144.6903 64.3068 64.3068 7734.6158 5271.3524 5272.1276 -1231.5975
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1100 710.19886 660.87113 -1894.0485 144.6903 64.3068 64.3068 8048.3485 5396.6668 5376.5956 -1233.1774
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1200 717.16487 667.35331 -1901.3849 144.6903 64.3068 64.3068 8009.7984 5634.5121 5349.4113 -1234.0316
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1300 710.26037 660.92837 -1894.9802 144.6903 64.3068 64.3068 8063.4125 5572.1245 5530.174 -1234.0519
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1400 715.93921 666.21278 -1898.8885 144.6903 64.3068 64.3068 7752.0927 5293.5463 5322.2312 -1232.6757
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1500 748.85411 696.84154 -1926.4891 144.6903 64.3068 64.3068 6030.5428 4076.8886 4012.7653 -1229.6475
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1600 767.98982 714.64815 -1939.8556 144.6903 64.3068 64.3068 4200.3475 2532.5711 2530.5518 -1225.2075
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1700 757.22042 704.62675 -1925.553 144.6903 64.3068 64.3068 2686.7843 1482.2796 1505.8073 -1220.9262
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1800 727.30327 676.78754 -1894.6635 144.6903 64.3068 64.3068 1764.2793 781.37451 801.18668 -1217.8759
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1900 688.82146 640.97853 -1856.5007 144.6903 64.3068 64.3068 1022.805 417.32394 359.74951 -1215.5221
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2000 655.91228 610.35509 -1823.954 144.6903 64.3068 64.3068 551.98825 -20.148643 -56.976652 -1213.5989
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2100 620.22468 577.14622 -1789.1761 144.6903 64.3068 64.3068 264.05975 -266.8323 -314.45533 -1212.0299
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2200 589.13325 548.21428 -1758.9252 144.6903 64.3068 64.3068 41.369707 -533.503 -525.69401 -1210.7109
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2300 563.20394 524.08593 -1733.6036 144.6903 64.3068 64.3068 -220.99189 -810.90513 -774.65084 -1209.5176
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2400 540.44236 502.90528 -1711.3384 144.6903 64.3068 64.3068 -358.01508 -962.31635 -977.3253 -1208.4332
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2500 523.5718 487.20648 -1694.7088 144.6903 64.3068 64.3068 -521.87444 -1152.8386 -1231.7615 -1207.5023
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Loop time of 9.34327 on 1 procs for 1500 steps with 7200 atoms
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Performance: 27.742 ns/day, 0.865 hours/ns, 160.543 timesteps/s, 1.156 Matom-step/s
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98.5% 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 | 8.4692 | 8.4692 | 8.4692 | 0.0 | 90.65
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Neigh | 0.7512 | 0.7512 | 0.7512 | 0.0 | 8.04
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Comm | 0.031189 | 0.031189 | 0.031189 | 0.0 | 0.33
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Output | 0.010584 | 0.010584 | 0.010584 | 0.0 | 0.11
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Modify | 0.053052 | 0.053052 | 0.053052 | 0.0 | 0.57
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Other | | 0.02803 | | | 0.30
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Nlocal: 7200 ave 7200 max 7200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 6380 ave 6380 max 6380 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 515773 ave 515773 max 515773 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 515773
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Ave neighs/atom = 71.635139
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Neighbor list builds = 57
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Dangerous builds = 0
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Total wall time: 0:00:15
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