mirror of https://github.com/lammps/lammps.git
update examples and log files for cases affected by the fix_modify changes
This commit is contained in:
Axel Kohlmeyer
parent
72ce5c6238
commit
82dc03ab3d
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@ -67,10 +67,6 @@ fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Add fix energy to output etotal
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fix_modify myhug energy yes
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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@ -81,7 +77,7 @@ variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
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thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
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@ -115,10 +111,6 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Add fix energy to output etotal
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fix_modify myhug energy yes
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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@ -129,7 +121,7 @@ variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
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thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
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@ -153,10 +145,6 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Add fix energy to output etotal
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fix_modify myhug energy yes
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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@ -167,7 +155,7 @@ variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
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thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
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@ -0,0 +1,399 @@
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LAMMPS (24 Dec 2020)
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using 1 OpenMP thread(s) per MPI task
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# This script reproduces stress trajectories from Fig. 1 in
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# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
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#
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# Three thermostatting scenarios are visited: undamped (nodrag),
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# damped (drag) and Nose-Hoover chain (nhchains).
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#
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# The axial and shear stress trajectories are printed to the
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# file "stress_vs_t.dat". For the damped case, the original figure
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# seems to be a plot of 2*tau, rather than tau.
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#
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# The script also demonstrates how to
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# orient a crystal along <110>,
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# and how to use the lj/cubic pair style.
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units lj
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boundary p p p
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atom_style atomic
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# Set up FCC lattice with z axis along <110>
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lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
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Lattice spacing in x,y,z = 1.4142135 2.0000000 2.0000000
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region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
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create_box 1 mycell
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.0710677 9.9999999 9.9999999)
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1 by 1 by 1 MPI processor grid
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mass * 1.0
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create_atoms 1 box
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Created 1000 atoms
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create_atoms CPU = 0.001 seconds
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# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
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pair_style lj/cubic
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pair_coeff * * 1.0 0.8908987
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# Relax box dimensions
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fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
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thermo 100
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thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
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min_modify line quadratic
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minimize 0.0 1.0e-6 10000 100000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188)
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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 = 1.8475372
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ghost atom cutoff = 1.8475372
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binsize = 0.92376862, bins = 8 11 11
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, 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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.247 | 4.247 | 4.247 Mbytes
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Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
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0 0 -6.2937536 -6.2937536 -2.7722424 -2.7722424 -2.7722424 7.0710677 9.9999999 9.9999999
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100 0 -6.3319014 -6.3319014 -0.75971257 -0.75971257 -0.75971257 7.0003571 9.8999999 9.8999999
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134 0 -6.3344253 -6.3344253 -4.3330648e-13 -4.7530261e-13 -4.7130069e-13 6.9780267 9.8684199 9.8684199
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Loop time of 0.200013 on 1 procs for 134 steps with 1000 atoms
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = force tolerance
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Energy initial, next-to-last, final =
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-6.29375358358557 -6.33442531515503 -6.33442531515503
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Force two-norm initial, final = 3395.2895 5.5740327e-10
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Force max component initial, final = 1960.2713 3.2730334e-10
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Final line search alpha, max atom move = 1.0000000 3.2730334e-10
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Iterations, force evaluations = 134 137
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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 | 0.14357 | 0.14357 | 0.14357 | 0.0 | 71.78
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Neigh | 0.0017562 | 0.0017562 | 0.0017562 | 0.0 | 0.88
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Comm | 0.0049057 | 0.0049057 | 0.0049057 | 0.0 | 2.45
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Output | 5.126e-05 | 5.126e-05 | 5.126e-05 | 0.0 | 0.03
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.04973 | | | 24.86
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Nlocal: 1000.00 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1724.00 ave 1724 max 1724 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 21000.0 ave 21000 max 21000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 21000
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Ave neighs/atom = 21.000000
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Neighbor list builds = 1
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Dangerous builds = 0
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# Define initial velocity
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velocity all create 0.01 87287 mom yes rot yes dist gaussian
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write_restart restart.equil
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System init for write_restart ...
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# Start Run #1
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
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restoring atom style atomic from restart
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orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
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1 by 1 by 1 MPI processor grid
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restoring pair style lj/cubic from restart
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1000 atoms
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read_restart CPU = 0.001 seconds
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neighbor 0.2 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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reset_timestep 0
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# Pzz = 40.0, drag/damping term off
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fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
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# Specify reference state from paper, times 1000 atoms
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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variable us equal f_myhug[2] # shock velocity [distance/time]
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variable up equal f_myhug[3] # particle velocity [distance/time]
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variable pzz equal pzz # axial stress
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variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
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#dump id all atom 500 dump.hugoniostat
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#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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run 10000
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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 = 1.7475372
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ghost atom cutoff = 1.7475372
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binsize = 0.87376862, bins = 8 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, 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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.124 | 3.124 Mbytes
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Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344253 -6.3194403 0.014381062 -0.00023971829 9.8684199 0 -0.004855267 2.3814248 0.0041108563
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1000 0.0093381492 0.013993217 -2.1704431 -4183.8284 129.15284 58.544409 8.3142517 -4.1816719 0.93744212 23.519052 3.7381985
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2000 0.24794859 0.37155095 -5.8915826 -528.38691 8.3849811 1.3744297 9.5938806 -0.52286688 -0.24350394 13.910493 0.41033425
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3000 0.3892042 0.5832225 -3.7686896 -3442.3257 72.742382 28.486576 8.6238082 -3.4391402 0.0038227739 19.697354 2.5139569
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4000 0.67010303 1.0041494 -4.2080956 -2935.8105 35.596234 3.9346859 8.7508489 -2.9326065 -0.58038927 14.529876 1.6677093
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5000 0.41845028 0.62704774 -4.8392822 -1894.6664 30.624319 4.6370699 8.7827304 -1.8904542 -0.31998377 13.670423 1.5249748
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6000 0.22409652 0.33580864 -3.7653422 -2666.4156 50.804071 7.220865 8.25496 -2.6629861 -0.017448126 14.48017 2.3883779
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7000 0.094832866 0.14210705 -4.5432169 -2337.0271 35.853414 3.4750842 8.4475655 -2.332626 -0.052659776 12.95347 1.8841809
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8000 0.043338745 0.06494311 -4.6249403 -1687.4892 39.679004 6.7256868 8.4321684 -1.6829292 0.070571417 13.554654 1.9927395
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9000 0.018233343 0.027322664 -4.425909 -1916.4941 41.680023 5.9079935 8.3470382 -1.9120955 0.090887676 13.502397 2.1013348
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10000 0.0082616415 0.01238007 -4.6221264 -1723.6542 39.842157 6.5678795 8.41093 -1.7190444 0.099616538 13.484322 2.0113699
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Loop time of 15.2001 on 1 procs for 10000 steps with 1000 atoms
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Performance: 56841.813 tau/day, 657.891 timesteps/s
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99.8% 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 | 11.69 | 11.69 | 11.69 | 0.0 | 76.91
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Neigh | 0.34087 | 0.34087 | 0.34087 | 0.0 | 2.24
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Comm | 0.41211 | 0.41211 | 0.41211 | 0.0 | 2.71
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Output | 0.001153 | 0.001153 | 0.001153 | 0.0 | 0.01
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Modify | 2.6404 | 2.6404 | 2.6404 | 0.0 | 17.37
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Other | | 0.1158 | | | 0.76
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Nlocal: 1000.00 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1886.00 ave 1886 max 1886 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 20874.0 ave 20874 max 20874 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 20874
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Ave neighs/atom = 20.874000
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Neighbor list builds = 188
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Dangerous builds = 0
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# Start Run #2
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
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restoring atom style atomic from restart
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orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
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1 by 1 by 1 MPI processor grid
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restoring pair style lj/cubic from restart
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1000 atoms
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read_restart CPU = 0.001 seconds
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neighbor 0.2 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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reset_timestep 0
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# Pzz = 40.0, drag/damping term on
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fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
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# Specify reference state from paper, times 1000 atoms
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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variable us equal f_myhug[2] # shock velocity [distance/time]
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variable up equal f_myhug[3] # particle velocity [distance/time]
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variable pzz equal pzz # axial stress
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variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
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run 10000
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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 = 1.7475372
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ghost atom cutoff = 1.7475372
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binsize = 0.87376862, bins = 8 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, 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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.124 | 3.124 Mbytes
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Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344253 -6.3194403 0.014381062 -0.00023971829 9.8684199 0 -0.004855267 2.3814248 0.0041108563
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1000 0.0062572988 0.0093765623 -5.989087 -1670.9191 18.918118 7.5844401 9.2338165 -1.6649394 0.023419337 13.976997 0.92138738
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2000 0.0068451081 0.010257394 -5.456581 -2537.81 37.064253 15.537266 8.9496405 -2.5323637 0.10230605 16.325406 1.5455016
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3000 0.0073276099 0.010980423 -5.3663421 -2643.8751 39.907292 16.807489 8.9154852 -2.6385198 0.11818116 16.63905 1.6326832
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4000 0.0069296906 0.010384141 -5.36234 -2655.7228 40.010742 16.851482 8.9144328 -2.6503709 0.11868137 16.651571 1.6356847
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5000 0.0076142461 0.011409948 -5.3631443 -2664.4499 39.997648 16.846756 8.9145416 -2.6590982 0.1184114 16.649779 1.6353254
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6000 0.0077053831 0.011546517 -5.3628538 -2673.2444 39.991598 16.840314 8.9145803 -2.667893 0.11818361 16.648852 1.6351691
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7000 0.0077405663 0.011599239 -5.3623531 -2682.1589 40.000448 16.844009 8.9145774 -2.6768081 0.11809899 16.650669 1.6353525
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8000 0.0080673569 0.012088934 -5.3623755 -2691.0104 39.995327 16.840134 8.9146099 -2.6856601 0.11787103 16.649882 1.6352204
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9000 0.0083223083 0.012470979 -5.3622988 -2699.8929 40.00571 16.847764 8.9146503 -2.6945431 0.11781523 16.652389 1.6353987
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10000 0.0091249116 0.01367368 -5.3630138 -2708.966 39.987197 16.837314 8.9146848 -2.7036167 0.11743014 16.648832 1.6349911
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Loop time of 13.6753 on 1 procs for 10000 steps with 1000 atoms
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Performance: 63179.754 tau/day, 731.247 timesteps/s
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99.8% 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 | 10.568 | 10.568 | 10.568 | 0.0 | 77.28
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Neigh | 0.019792 | 0.019792 | 0.019792 | 0.0 | 0.14
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Comm | 0.33708 | 0.33708 | 0.33708 | 0.0 | 2.46
|
||||
Output | 0.0011928 | 0.0011928 | 0.0011928 | 0.0 | 0.01
|
||||
Modify | 2.639 | 2.639 | 2.639 | 0.0 | 19.30
|
||||
Other | | 0.1101 | | | 0.81
|
||||
|
||||
Nlocal: 1000.00 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1724.00 ave 1724 max 1724 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 21000.0 ave 21000 max 21000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21.000000
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
|
||||
# Start Run #3
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style lj/cubic from restart
|
||||
1000 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.001
|
||||
reset_timestep 0
|
||||
|
||||
# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
|
||||
|
||||
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
|
||||
|
||||
# Specify reference state from paper, times 1000 atoms
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Define output
|
||||
|
||||
variable dele equal f_myhug[1] # energy delta [temperature]
|
||||
variable us equal f_myhug[2] # shock velocity [distance/time]
|
||||
variable up equal f_myhug[3] # particle velocity [distance/time]
|
||||
variable pzz equal pzz # axial stress
|
||||
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
|
||||
variable time equal dt*step
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
|
||||
|
||||
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.7475372
|
||||
ghost atom cutoff = 1.7475372
|
||||
binsize = 0.87376862, bins = 8 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.124 | 3.124 Mbytes
|
||||
Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
|
||||
0 0.01 0.014985 -6.3344253 -6.3194403 0.014381062 -0.00023971829 9.8684199 0 -0.004855267 2.3814248 0.0041108563
|
||||
1000 0.0083300318 0.012482553 -5.5023183 -838.99233 35.610078 14.886668 8.9677982 -0.83350249 0.093761717 16.159482 1.500112
|
||||
2000 0.020386436 0.030549075 -5.294934 -1021.4347 41.760404 17.563313 8.8960328 -1.0161703 0.1178086 16.852842 1.6868239
|
||||
3000 0.049693082 0.074465084 -5.3469418 -982.1922 39.030412 16.123502 8.9325589 -0.97691972 0.073097533 16.601991 1.6003728
|
||||
4000 0.11859524 0.17771497 -5.207074 -1299.948 40.941639 16.507821 8.9213137 -1.2949186 0.018189971 16.904165 1.6487306
|
||||
5000 0.130146 0.19502378 -5.261025 -1208.3405 39.059595 15.609328 8.9431689 -1.2032745 -0.00023811036 16.701434 1.5920334
|
||||
6000 0.13812959 0.20698719 -5.1710048 -1334.1421 40.904888 16.242199 8.9222846 -1.329178 -0.0044756362 16.90509 1.6471606
|
||||
7000 0.12107441 0.18143001 -5.2602562 -1170.0585 39.060849 15.577606 8.9397535 -1.1649797 0.005587398 16.671517 1.5949415
|
||||
8000 0.14333426 0.21478639 -5.1717109 -1352.635 40.876285 16.205871 8.9218128 -1.3476781 -0.0069373292 16.895041 1.6469877
|
||||
9000 0.12159783 0.18221435 -5.2591928 -1186.8604 39.22852 15.6778 8.9376658 -1.1817834 0.0077335044 16.68885 1.6001243
|
||||
10000 0.15321647 0.22959488 -5.188176 -1391.2245 40.666599 16.146259 8.9228489 -1.3862659 -0.0091900905 16.860718 1.6418747
|
||||
Loop time of 13.963 on 1 procs for 10000 steps with 1000 atoms
|
||||
|
||||
Performance: 61877.846 tau/day, 716.179 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.667 | 10.667 | 10.667 | 0.0 | 76.40
|
||||
Neigh | 0.16763 | 0.16763 | 0.16763 | 0.0 | 1.20
|
||||
Comm | 0.36182 | 0.36182 | 0.36182 | 0.0 | 2.59
|
||||
Output | 0.0011809 | 0.0011809 | 0.0011809 | 0.0 | 0.01
|
||||
Modify | 2.6516 | 2.6516 | 2.6516 | 0.0 | 18.99
|
||||
Other | | 0.1135 | | | 0.81
|
||||
|
||||
Nlocal: 1000.00 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1724.00 ave 1724 max 1724 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 20654.0 ave 20654 max 20654 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 20654
|
||||
Ave neighs/atom = 20.654000
|
||||
Neighbor list builds = 94
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:43
|
||||
|
|
@ -0,0 +1,399 @@
|
|||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# This script reproduces stress trajectories from Fig. 1 in
|
||||
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
|
||||
#
|
||||
# Three thermostatting scenarios are visited: undamped (nodrag),
|
||||
# damped (drag) and Nose-Hoover chain (nhchains).
|
||||
#
|
||||
# The axial and shear stress trajectories are printed to the
|
||||
# file "stress_vs_t.dat". For the damped case, the original figure
|
||||
# seems to be a plot of 2*tau, rather than tau.
|
||||
#
|
||||
# The script also demonstrates how to
|
||||
# orient a crystal along <110>,
|
||||
# and how to use the lj/cubic pair style.
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
# Set up FCC lattice with z axis along <110>
|
||||
|
||||
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
|
||||
Lattice spacing in x,y,z = 1.4142135 2.0000000 2.0000000
|
||||
|
||||
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
|
||||
create_box 1 mycell
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.0710677 9.9999999 9.9999999)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0
|
||||
create_atoms 1 box
|
||||
Created 1000 atoms
|
||||
create_atoms CPU = 0.105 seconds
|
||||
|
||||
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 1.0 0.8908987
|
||||
|
||||
# Relax box dimensions
|
||||
|
||||
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
|
||||
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-6 10000 100000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.8475372
|
||||
ghost atom cutoff = 1.8475372
|
||||
binsize = 0.92376862, bins = 8 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.211 | 4.211 | 4.211 Mbytes
|
||||
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
|
||||
0 0 -6.2937536 -6.2937536 -2.7722424 -2.7722424 -2.7722424 7.0710677 9.9999999 9.9999999
|
||||
100 0 -6.3319014 -6.3319014 -0.75971257 -0.75971257 -0.75971257 7.0003571 9.8999999 9.8999999
|
||||
134 0 -6.3344253 -6.3344253 -4.303004e-13 -4.72443e-13 -4.7038971e-13 6.9780267 9.8684199 9.8684199
|
||||
Loop time of 0.38554 on 4 procs for 134 steps with 1000 atoms
|
||||
|
||||
75.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-6.29375358358589 -6.33442531515435 -6.33442531515435
|
||||
Force two-norm initial, final = 3395.2895 5.5617370e-10
|
||||
Force max component initial, final = 1960.2713 3.2533415e-10
|
||||
Final line search alpha, max atom move = 1.0000000 3.2533415e-10
|
||||
Iterations, force evaluations = 134 137
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.031873 | 0.042436 | 0.055233 | 4.3 | 11.01
|
||||
Neigh | 0.0004189 | 0.00049466 | 0.00058317 | 0.0 | 0.13
|
||||
Comm | 0.085755 | 0.095315 | 0.10484 | 2.7 | 24.72
|
||||
Output | 2.8372e-05 | 3.0637e-05 | 3.6955e-05 | 0.0 | 0.01
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.2473 | | | 64.13
|
||||
|
||||
Nlocal: 250.000 ave 305 max 205 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 829.000 ave 874 max 774 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 5250.00 ave 6445 max 4305 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21.000000
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Define initial velocity
|
||||
|
||||
velocity all create 0.01 87287 mom yes rot yes dist gaussian
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Start Run #1
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style lj/cubic from restart
|
||||
1000 atoms
|
||||
read_restart CPU = 0.006 seconds
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.001
|
||||
reset_timestep 0
|
||||
|
||||
# Pzz = 40.0, drag/damping term off
|
||||
|
||||
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
|
||||
|
||||
# Specify reference state from paper, times 1000 atoms
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Define output
|
||||
|
||||
variable dele equal f_myhug[1] # energy delta [temperature]
|
||||
variable us equal f_myhug[2] # shock velocity [distance/time]
|
||||
variable up equal f_myhug[3] # particle velocity [distance/time]
|
||||
variable pzz equal pzz # axial stress
|
||||
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
|
||||
variable time equal dt*step
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
|
||||
|
||||
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
|
||||
|
||||
#dump id all atom 500 dump.hugoniostat
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.7475372
|
||||
ghost atom cutoff = 1.7475372
|
||||
binsize = 0.87376862, bins = 8 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.086 | 3.086 | 3.086 Mbytes
|
||||
Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
|
||||
0 0.01 0.014985 -6.3344253 -6.3194403 0.014347835 -0.00026463907 9.8684199 0 -0.0048552735 2.378672 0.0041061045
|
||||
1000 0.010586669 0.015864123 -2.1721826 -4183.9265 129.03333 58.456619 8.3141284 -4.1817701 0.93542364 23.507245 3.7366151
|
||||
2000 0.33213628 0.49770621 -5.5847928 -972.65689 12.097176 1.2026574 9.4616027 -0.9675698 -0.35714344 13.85823 0.59422982
|
||||
3000 0.46981589 0.70401911 -3.9208694 -3177.4622 63.005615 22.559014 8.6828715 -3.1742453 -0.16959033 18.776506 2.284245
|
||||
4000 0.5486246 0.82211396 -4.170224 -2897.9717 38.4091 4.9062274 8.6573154 -2.8946236 -0.45434723 14.506949 1.8023381
|
||||
5000 0.30607733 0.45865688 -4.73528 -1914.3534 35.002193 6.2096608 8.6658138 -1.9100768 -0.19602135 13.896788 1.714585
|
||||
6000 0.13928238 0.20871465 -4.3038564 -1672.0118 50.372856 12.190245 8.3966652 -1.6679166 0.11455965 15.089171 2.2725288
|
||||
7000 0.055325106 0.082904671 -5.2030895 -1689.3101 30.859753 6.5561993 8.6850199 -1.6841899 0.020593532 13.15254 1.5972063
|
||||
8000 0.02793065 0.041854078 -4.5281755 -966.55101 48.144696 12.229149 8.4107035 -0.96206469 0.19920754 14.821718 2.2112004
|
||||
9000 0.018182543 0.02724654 -4.9847463 -1618.778 37.347471 8.7290944 8.5607031 -1.6138205 0.10912671 13.773572 1.8458347
|
||||
10000 0.0082850143 0.012415094 -5.0129769 -1686.404 36.462176 8.3390717 8.5689886 -1.6814034 0.10655037 13.652105 1.8181142
|
||||
Loop time of 22.212 on 4 procs for 10000 steps with 1000 atoms
|
||||
|
||||
Performance: 38897.956 tau/day, 450.208 timesteps/s
|
||||
76.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.4702 | 3.5904 | 3.684 | 4.4 | 16.16
|
||||
Neigh | 0.1001 | 0.10727 | 0.11784 | 2.0 | 0.48
|
||||
Comm | 5.1418 | 5.2862 | 5.3573 | 3.7 | 23.80
|
||||
Output | 0.083086 | 0.095493 | 0.11021 | 4.0 | 0.43
|
||||
Modify | 11.789 | 11.841 | 11.967 | 2.1 | 53.31
|
||||
Other | | 1.292 | | | 5.82
|
||||
|
||||
Nlocal: 250.000 ave 260 max 240 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 927.500 ave 934 max 921 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 5049.00 ave 5203 max 4889 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 20196
|
||||
Ave neighs/atom = 20.196000
|
||||
Neighbor list builds = 175
|
||||
Dangerous builds = 0
|
||||
|
||||
# Start Run #2
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style lj/cubic from restart
|
||||
1000 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.001
|
||||
reset_timestep 0
|
||||
|
||||
# Pzz = 40.0, drag/damping term on
|
||||
|
||||
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
|
||||
|
||||
# Specify reference state from paper, times 1000 atoms
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Define output
|
||||
|
||||
variable dele equal f_myhug[1] # energy delta [temperature]
|
||||
variable us equal f_myhug[2] # shock velocity [distance/time]
|
||||
variable up equal f_myhug[3] # particle velocity [distance/time]
|
||||
variable pzz equal pzz # axial stress
|
||||
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
|
||||
variable time equal dt*step
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
|
||||
|
||||
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.7475372
|
||||
ghost atom cutoff = 1.7475372
|
||||
binsize = 0.87376862, bins = 8 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.086 | 3.086 | 3.086 Mbytes
|
||||
Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
|
||||
0 0.01 0.014985 -6.3344253 -6.3194403 0.014347835 -0.00026463907 9.8684199 0 -0.0048552735 2.378672 0.0041061045
|
||||
1000 0.0063089135 0.0094539069 -5.9892322 -1671.0142 18.914957 7.5823225 9.2337797 -1.6650344 0.02342632 13.975435 0.92133641
|
||||
2000 0.006881368 0.01031173 -5.4566762 -2537.9852 37.064191 15.537213 8.9495783 -2.5325389 0.1023455 16.32485 1.5455517
|
||||
3000 0.0072427308 0.010853232 -5.3662814 -2644.0227 39.906002 16.80569 8.9154322 -2.6386673 0.1182133 16.638326 1.6327015
|
||||
4000 0.0070936511 0.010629836 -5.362616 -2655.9513 40.007995 16.850321 8.9143648 -2.6505993 0.11869211 16.650416 1.6356858
|
||||
5000 0.0074091959 0.01110268 -5.3628939 -2664.5927 39.998199 16.845204 8.9144816 -2.6592409 0.11846407 16.649379 1.6353872
|
||||
6000 0.0077388568 0.011596677 -5.362926 -2673.502 39.995216 16.842807 8.9145056 -2.6681507 0.11826568 16.648964 1.635306
|
||||
7000 0.0076023299 0.011392091 -5.3621079 -2682.3942 39.998343 16.839762 8.9144789 -2.6770435 0.1181081 16.649386 1.6353924
|
||||
8000 0.0076916892 0.011525996 -5.3617056 -2691.2334 40.000701 16.839078 8.9144843 -2.6858832 0.11795298 16.649924 1.635436
|
||||
9000 0.0082153298 0.012310672 -5.3620895 -2700.1796 40.006134 16.845865 8.914544 -2.6948298 0.11785245 16.651566 1.6354968
|
||||
10000 0.0088368733 0.013242055 -5.3625353 -2709.138 39.989575 16.835079 8.914577 -2.7037887 0.11749055 16.648403 1.6351305
|
||||
Loop time of 19.325 on 4 procs for 10000 steps with 1000 atoms
|
||||
|
||||
Performance: 44708.822 tau/day, 517.463 timesteps/s
|
||||
77.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.3012 | 3.4003 | 3.584 | 5.9 | 17.60
|
||||
Neigh | 0.0047636 | 0.0054044 | 0.0072584 | 1.5 | 0.03
|
||||
Comm | 4.5282 | 4.5961 | 4.651 | 2.1 | 23.78
|
||||
Output | 0.00071692 | 0.0062424 | 0.0086811 | 4.1 | 0.03
|
||||
Modify | 10.133 | 10.215 | 10.287 | 1.7 | 52.86
|
||||
Other | | 1.102 | | | 5.70
|
||||
|
||||
Nlocal: 250.000 ave 258 max 239 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 829.000 ave 840 max 821 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 5250.00 ave 5360 max 5090 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21.000000
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
# Start Run #3
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style lj/cubic from restart
|
||||
1000 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.001
|
||||
reset_timestep 0
|
||||
|
||||
# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
|
||||
|
||||
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
|
||||
|
||||
# Specify reference state from paper, times 1000 atoms
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Define output
|
||||
|
||||
variable dele equal f_myhug[1] # energy delta [temperature]
|
||||
variable us equal f_myhug[2] # shock velocity [distance/time]
|
||||
variable up equal f_myhug[3] # particle velocity [distance/time]
|
||||
variable pzz equal pzz # axial stress
|
||||
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
|
||||
variable time equal dt*step
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp ke epair econserve pzz v_tau lz f_myhug v_dele v_us v_up
|
||||
|
||||
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.7475372
|
||||
ghost atom cutoff = 1.7475372
|
||||
binsize = 0.87376862, bins = 8 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.086 | 3.086 | 3.086 Mbytes
|
||||
Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
|
||||
0 0.01 0.014985 -6.3344253 -6.3194403 0.014347835 -0.00026463907 9.8684199 0 -0.0048552735 2.378672 0.0041061045
|
||||
1000 0.0078345757 0.011740112 -5.5017136 -838.78091 35.616593 14.888102 8.9677603 -0.83329094 0.093891841 16.160627 1.5002802
|
||||
2000 0.019260442 0.028861773 -5.2936038 -1018.9574 41.771461 17.563025 8.8958988 -1.0136927 0.11811776 16.853931 1.6871615
|
||||
3000 0.04811126 0.072094723 -5.3454068 -976.69826 39.061528 16.137201 8.9322605 -0.97142494 0.073850795 16.606008 1.6012612
|
||||
4000 0.11854637 0.17764173 -5.2071392 -1296.5766 40.843143 16.426195 8.9202981 -1.2915471 0.017621672 16.874934 1.6476132
|
||||
5000 0.13634185 0.20430827 -5.2645154 -1258.4101 39.098283 15.627986 8.9407719 -1.2533499 -0.00067591716 16.688492 1.5948462
|
||||
6000 0.14222512 0.21312434 -5.1774698 -1369.5986 40.888661 16.260803 8.9214848 -1.3646342 -0.0041700902 16.894723 1.6475174
|
||||
7000 0.12683772 0.19006633 -5.2679854 -1210.973 39.084165 15.633846 8.9393379 -1.2058951 0.00572464 16.672829 1.595768
|
||||
8000 0.14531337 0.21775209 -5.1737911 -1372.667 40.861256 16.19118 8.9199953 -1.367711 -0.0065459838 16.876028 1.648237
|
||||
9000 0.12123505 0.18167072 -5.2546764 -1189.0875 39.276006 15.677923 8.9363537 -1.1840145 0.0075170176 16.687402 1.6022003
|
||||
10000 0.1477113 0.22134539 -5.1833959 -1353.4057 40.578404 16.080238 8.9245614 -1.3484436 -0.0098061873 16.857426 1.6386338
|
||||
Loop time of 18.9651 on 4 procs for 10000 steps with 1000 atoms
|
||||
|
||||
Performance: 45557.373 tau/day, 527.284 timesteps/s
|
||||
77.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.1152 | 3.3473 | 3.5591 | 10.0 | 17.65
|
||||
Neigh | 0.045731 | 0.056706 | 0.066921 | 3.7 | 0.30
|
||||
Comm | 3.9563 | 4.1638 | 4.4413 | 9.7 | 21.96
|
||||
Output | 0.00067329 | 0.0033167 | 0.011241 | 7.9 | 0.02
|
||||
Modify | 10.321 | 10.425 | 10.482 | 2.0 | 54.97
|
||||
Other | | 0.9693 | | | 5.11
|
||||
|
||||
Nlocal: 250.000 ave 257 max 244 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nghost: 832.250 ave 840 max 822 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 5144.25 ave 5282 max 4949 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 20577
|
||||
Ave neighs/atom = 20.577000
|
||||
Neighbor list builds = 95
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:01:01
|
||||
|
|
@ -1,401 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# This script reproduces stress trajectories from Fig. 1 in
|
||||
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
|
||||
#
|
||||
# Three thermostatting scenarios are visited: undamped (nodrag),
|
||||
# damped (drag) and Nose-Hoover chain (nhchains).
|
||||
#
|
||||
# The axial and shear stress trajectories are printed to the
|
||||
# file "stress_vs_t.dat". For the damped case, the original figure
|
||||
# seems to be a plot of 2*tau, rather than tau.
|
||||
#
|
||||
# The script also demonstrates how to
|
||||
# orient a crystal along <110>,
|
||||
# and how to use the lj/cubic pair style.
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
# Set up FCC lattice with z axis along <110>
|
||||
|
||||
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
|
||||
Lattice spacing in x,y,z = 1.41421 2 2
|
||||
|
||||
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
|
||||
create_box 1 mycell
|
||||
Created orthogonal box = (0 0 0) to (7.07107 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0
|
||||
create_atoms 1 box
|
||||
Created 1000 atoms
|
||||
Time spent = 0.000465155 secs
|
||||
|
||||
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 1.0 0.8908987
|
||||
|
||||
# Relax box dimensions
|
||||
|
||||
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
|
||||
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-6 10000 100000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.84754
|
||||
ghost atom cutoff = 1.84754
|
||||
binsize = 0.923769, bins = 8 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.247 | 4.247 | 4.247 Mbytes
|
||||
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
|
||||
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
|
||||
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
|
||||
134 0 -6.3344257 -6.3344257 -4.5005818e-13 -4.9677973e-13 -4.9219424e-13 6.9780266 9.8684199 9.8684199
|
||||
Loop time of 0.0724094 on 1 procs for 134 steps with 1000 atoms
|
||||
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-6.2937539309 -6.33442568056 -6.33442568056
|
||||
Force two-norm initial, final = 3395.29 5.83329e-10
|
||||
Force max component initial, final = 1960.27 3.42093e-10
|
||||
Final line search alpha, max atom move = 1 3.42093e-10
|
||||
Iterations, force evaluations = 134 137
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.054599 | 0.054599 | 0.054599 | 0.0 | 75.40
|
||||
Neigh | 0.0011106 | 0.0011106 | 0.0011106 | 0.0 | 1.53
|
||||
Comm | 0.002012 | 0.002012 | 0.002012 | 0.0 | 2.78
|
||||
Output | 1.955e-05 | 1.955e-05 | 1.955e-05 | 0.0 | 0.03
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01467 | | | 20.26
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1724 ave 1724 max 1724 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 21000 ave 21000 max 21000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Define initial velocity
|
||||
|
||||
velocity all create 0.01 87287 mom yes rot yes dist gaussian
|
||||
write_restart restart.equil
|
||||
|
||||
# Start Run #1
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style lj/cubic from restart
|
||||
1000 atoms
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.001
|
||||
reset_timestep 0
|
||||
|
||||
# Pzz = 40.0, drag/damping term off
|
||||
|
||||
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
|
||||
|
||||
# Specify reference state from paper, times 1000 atoms
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
# Define output
|
||||
|
||||
variable dele equal f_myhug[1] # energy delta [temperature]
|
||||
variable us equal f_myhug[2] # shock velocity [distance/time]
|
||||
variable up equal f_myhug[3] # particle velocity [distance/time]
|
||||
variable pzz equal pzz # axial stress
|
||||
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
|
||||
variable time equal dt*step
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
|
||||
|
||||
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
|
||||
|
||||
#dump id all atom 500 dump.hugoniostat
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.74754
|
||||
ghost atom cutoff = 1.74754
|
||||
binsize = 0.873769, bins = 8 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes
|
||||
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
|
||||
0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
|
||||
1000 0.0093381489 0.013993216 -2.170443 -6.3381216 129.15286 58.544417 8.3142516 -4.1816719 0.93744258 23.519053 3.7381989
|
||||
2000 0.24794909 0.37155171 -5.8915802 -6.0429087 8.3850692 1.3744507 9.5938765 -0.5228803 -0.2435043 13.910468 0.4103393
|
||||
3000 0.38920701 0.5832267 -3.768677 -6.6246124 72.742761 28.486747 8.623805 -3.439162 0.003825459 19.697379 2.5139668
|
||||
4000 0.67009971 1.0041444 -4.2080644 -6.1365367 35.596179 3.9344133 8.7508422 -2.9326167 -0.58039603 14.529822 1.6677129
|
||||
5000 0.41848975 0.62710689 -4.8393088 -6.1026724 30.626544 4.6387208 8.7827245 -1.8904705 -0.31996439 13.670884 1.5250343
|
||||
6000 0.22410139 0.33581594 -3.7652941 -6.0923259 50.807437 7.2229456 8.2549488 -2.6628477 -0.017396966 14.4806 2.3884652
|
||||
7000 0.095001485 0.14235972 -4.5436753 -6.7307217 35.8743 3.4938089 8.4476287 -2.3294061 -0.052272192 12.957528 1.8846881
|
||||
8000 0.043277437 0.064851239 -4.6264096 -6.2447456 39.658659 6.7266325 8.4327483 -1.6831873 0.070488482 13.553882 1.9918311
|
||||
9000 0.018271956 0.027380526 -4.4239627 -6.3085661 41.708324 5.9081923 8.3463321 -1.9119839 0.091057512 13.503882 2.1025305
|
||||
10000 0.0082840001 0.012413574 -4.622252 -6.3316699 39.830379 6.5596321 8.4109569 -1.7218314 0.099435465 13.482451 2.0110543
|
||||
Loop time of 6.20702 on 1 procs for 10000 steps with 1000 atoms
|
||||
|
||||
Performance: 139197.321 tau/day, 1611.080 timesteps/s
|
||||
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.0198 | 5.0198 | 5.0198 | 0.0 | 80.87
|
||||
Neigh | 0.21405 | 0.21405 | 0.21405 | 0.0 | 3.45
|
||||
Comm | 0.16164 | 0.16164 | 0.16164 | 0.0 | 2.60
|
||||
Output | 0.00053501 | 0.00053501 | 0.00053501 | 0.0 | 0.01
|
||||
Modify | 0.7419 | 0.7419 | 0.7419 | 0.0 | 11.95
|
||||
Other | | 0.06911 | | | 1.11
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1886 ave 1886 max 1886 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 20874 ave 20874 max 20874 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 20874
|
||||
Ave neighs/atom = 20.874
|
||||
Neighbor list builds = 188
|
||||
Dangerous builds = 0
|
||||
|
||||
# Start Run #2
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style lj/cubic from restart
|
||||
1000 atoms
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.001
|
||||
reset_timestep 0
|
||||
|
||||
# Pzz = 40.0, drag/damping term on
|
||||
|
||||
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
|
||||
|
||||
# Specify reference state from paper, times 1000 atoms
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
# Define output
|
||||
|
||||
variable dele equal f_myhug[1] # energy delta [temperature]
|
||||
variable us equal f_myhug[2] # shock velocity [distance/time]
|
||||
variable up equal f_myhug[3] # particle velocity [distance/time]
|
||||
variable pzz equal pzz # axial stress
|
||||
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
|
||||
variable time equal dt*step
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
|
||||
|
||||
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.74754
|
||||
ghost atom cutoff = 1.74754
|
||||
binsize = 0.873769, bins = 8 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes
|
||||
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
|
||||
0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
|
||||
1000 0.0062572991 0.0093765627 -5.9890874 -7.64465 18.918117 7.5844397 9.2338165 -1.6649392 0.02341947 13.976996 0.92138738
|
||||
2000 0.006845108 0.010257394 -5.4565813 -7.9786876 37.064254 15.537266 8.9496404 -2.5323637 0.1023062 16.325405 1.5455017
|
||||
3000 0.0073276109 0.010980425 -5.3663425 -7.9938818 39.907292 16.807488 8.9154852 -2.6385197 0.11818131 16.639049 1.6326833
|
||||
4000 0.0069296915 0.010384143 -5.3623404 -8.0023271 40.010741 16.851482 8.9144328 -2.6503708 0.11868152 16.651571 1.6356847
|
||||
5000 0.0076142476 0.01140995 -5.3631447 -8.0108329 39.997648 16.846756 8.9145416 -2.6590981 0.11841154 16.649778 1.6353255
|
||||
6000 0.0077053839 0.011546518 -5.3628542 -8.0192007 39.991597 16.840313 8.9145803 -2.6678931 0.11818376 16.648851 1.6351691
|
||||
7000 0.0077405662 0.011599239 -5.3623534 -8.0275624 40.000448 16.844008 8.9145774 -2.6768081 0.11809914 16.650669 1.6353525
|
||||
8000 0.008067359 0.012088937 -5.3623759 -8.0359471 39.995327 16.840134 8.9146099 -2.6856601 0.11787118 16.649881 1.6352204
|
||||
9000 0.0083223114 0.012470984 -5.3622992 -8.0443714 40.00571 16.847763 8.9146503 -2.6945431 0.11781538 16.652389 1.6353987
|
||||
10000 0.0091249143 0.013673684 -5.3630142 -8.0529573 39.987196 16.837314 8.9146848 -2.7036168 0.11743028 16.648831 1.6349911
|
||||
Loop time of 5.48047 on 1 procs for 10000 steps with 1000 atoms
|
||||
|
||||
Performance: 157650.687 tau/day, 1824.661 timesteps/s
|
||||
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.5166 | 4.5166 | 4.5166 | 0.0 | 82.41
|
||||
Neigh | 0.012162 | 0.012162 | 0.012162 | 0.0 | 0.22
|
||||
Comm | 0.14168 | 0.14168 | 0.14168 | 0.0 | 2.59
|
||||
Output | 0.00053787 | 0.00053787 | 0.00053787 | 0.0 | 0.01
|
||||
Modify | 0.74394 | 0.74394 | 0.74394 | 0.0 | 13.57
|
||||
Other | | 0.06553 | | | 1.20
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1724 ave 1724 max 1724 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 21000 ave 21000 max 21000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
|
||||
# Start Run #3
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style lj/cubic from restart
|
||||
1000 atoms
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.001
|
||||
reset_timestep 0
|
||||
|
||||
# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
|
||||
|
||||
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
|
||||
|
||||
# Specify reference state from paper, times 1000 atoms
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
# Define output
|
||||
|
||||
variable dele equal f_myhug[1] # energy delta [temperature]
|
||||
variable us equal f_myhug[2] # shock velocity [distance/time]
|
||||
variable up equal f_myhug[3] # particle velocity [distance/time]
|
||||
variable pzz equal pzz # axial stress
|
||||
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
|
||||
variable time equal dt*step
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
|
||||
|
||||
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.74754
|
||||
ghost atom cutoff = 1.74754
|
||||
binsize = 0.873769, bins = 8 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes
|
||||
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
|
||||
0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
|
||||
1000 0.0083300394 0.012482564 -5.5023188 -6.3233387 35.610076 14.886667 8.9677982 -0.83350251 0.093761848 16.159481 1.500112
|
||||
2000 0.020386462 0.030549113 -5.2949349 -6.2805556 41.760388 17.563305 8.896033 -1.0161699 0.11780863 16.85284 1.6868235
|
||||
3000 0.049693152 0.074465188 -5.3469434 -6.2493961 39.030372 16.123483 8.9325594 -0.9769179 0.073097387 16.601986 1.6003716
|
||||
4000 0.11859514 0.17771482 -5.207077 -6.3242752 40.941558 16.507785 8.9213147 -1.2949131 0.018189678 16.904156 1.6487282
|
||||
5000 0.13014573 0.19502337 -5.2610248 -6.269279 39.059628 15.609345 8.9431685 -1.2032776 -0.00023747376 16.701437 1.5920344
|
||||
6000 0.1381307 0.20698886 -5.171005 -6.2931942 40.904837 16.242165 8.9222854 -1.3291781 -0.0044770368 16.905086 1.6471589
|
||||
7000 0.12107326 0.18142828 -5.2602554 -6.2438099 39.060928 15.57765 8.9397525 -1.1649827 0.0055890257 16.671524 1.594944
|
||||
8000 0.14333636 0.21478954 -5.1717123 -6.304602 40.876188 16.205815 8.9218142 -1.3476793 -0.0069396327 16.895033 1.6469846
|
||||
9000 0.12159663 0.18221255 -5.2591911 -6.2587685 39.228648 15.677869 8.9376641 -1.18179 0.0077357066 16.688862 1.6001283
|
||||
10000 0.15321883 0.22959841 -5.1881787 -6.3448453 40.666451 16.146177 8.922851 -1.386265 -0.0091929687 16.860705 1.6418699
|
||||
Loop time of 5.6426 on 1 procs for 10000 steps with 1000 atoms
|
||||
|
||||
Performance: 153120.907 tau/day, 1772.233 timesteps/s
|
||||
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.5653 | 4.5653 | 4.5653 | 0.0 | 80.91
|
||||
Neigh | 0.10885 | 0.10885 | 0.10885 | 0.0 | 1.93
|
||||
Comm | 0.14695 | 0.14695 | 0.14695 | 0.0 | 2.60
|
||||
Output | 0.00055218 | 0.00055218 | 0.00055218 | 0.0 | 0.01
|
||||
Modify | 0.75364 | 0.75364 | 0.75364 | 0.0 | 13.36
|
||||
Other | | 0.0673 | | | 1.19
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1724 ave 1724 max 1724 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 20654 ave 20654 max 20654 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 20654
|
||||
Ave neighs/atom = 20.654
|
||||
Neighbor list builds = 94
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:17
|
||||
|
|
@ -1,401 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# This script reproduces stress trajectories from Fig. 1 in
|
||||
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
|
||||
#
|
||||
# Three thermostatting scenarios are visited: undamped (nodrag),
|
||||
# damped (drag) and Nose-Hoover chain (nhchains).
|
||||
#
|
||||
# The axial and shear stress trajectories are printed to the
|
||||
# file "stress_vs_t.dat". For the damped case, the original figure
|
||||
# seems to be a plot of 2*tau, rather than tau.
|
||||
#
|
||||
# The script also demonstrates how to
|
||||
# orient a crystal along <110>,
|
||||
# and how to use the lj/cubic pair style.
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
# Set up FCC lattice with z axis along <110>
|
||||
|
||||
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
|
||||
Lattice spacing in x,y,z = 1.41421 2 2
|
||||
|
||||
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
|
||||
create_box 1 mycell
|
||||
Created orthogonal box = (0 0 0) to (7.07107 10 10)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0
|
||||
create_atoms 1 box
|
||||
Created 1000 atoms
|
||||
Time spent = 0.0003438 secs
|
||||
|
||||
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 1.0 0.8908987
|
||||
|
||||
# Relax box dimensions
|
||||
|
||||
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
|
||||
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-6 10000 100000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.84754
|
||||
ghost atom cutoff = 1.84754
|
||||
binsize = 0.923769, bins = 8 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.211 | 4.211 | 4.211 Mbytes
|
||||
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
|
||||
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
|
||||
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
|
||||
134 0 -6.3344257 -6.3344257 -4.5046204e-13 -4.92206e-13 -4.9610344e-13 6.9780266 9.8684199 9.8684199
|
||||
Loop time of 0.0269771 on 4 procs for 134 steps with 1000 atoms
|
||||
|
||||
94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-6.2937539309 -6.33442568056 -6.33442568056
|
||||
Force two-norm initial, final = 3395.29 5.80609e-10
|
||||
Force max component initial, final = 1960.27 3.41627e-10
|
||||
Final line search alpha, max atom move = 1 3.41627e-10
|
||||
Iterations, force evaluations = 134 137
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.011534 | 0.013897 | 0.016008 | 1.3 | 51.51
|
||||
Neigh | 0.00024176 | 0.00029498 | 0.00035191 | 0.0 | 1.09
|
||||
Comm | 0.0029764 | 0.0050126 | 0.0073018 | 2.2 | 18.58
|
||||
Output | 1.8835e-05 | 1.9968e-05 | 2.2888e-05 | 0.0 | 0.07
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.007753 | | | 28.74
|
||||
|
||||
Nlocal: 250 ave 305 max 205 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 829 ave 874 max 774 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 5250 ave 6445 max 4305 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Define initial velocity
|
||||
|
||||
velocity all create 0.01 87287 mom yes rot yes dist gaussian
|
||||
write_restart restart.equil
|
||||
|
||||
# Start Run #1
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style lj/cubic from restart
|
||||
1000 atoms
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.001
|
||||
reset_timestep 0
|
||||
|
||||
# Pzz = 40.0, drag/damping term off
|
||||
|
||||
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
|
||||
|
||||
# Specify reference state from paper, times 1000 atoms
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
# Define output
|
||||
|
||||
variable dele equal f_myhug[1] # energy delta [temperature]
|
||||
variable us equal f_myhug[2] # shock velocity [distance/time]
|
||||
variable up equal f_myhug[3] # particle velocity [distance/time]
|
||||
variable pzz equal pzz # axial stress
|
||||
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
|
||||
variable time equal dt*step
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
|
||||
|
||||
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
|
||||
|
||||
#dump id all atom 500 dump.hugoniostat
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.74754
|
||||
ghost atom cutoff = 1.74754
|
||||
binsize = 0.873769, bins = 8 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes
|
||||
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
|
||||
0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
|
||||
1000 0.010586668 0.015864122 -2.1721826 -6.3380886 129.03334 58.456626 8.3141284 -4.1817701 0.93542408 23.507246 3.7366154
|
||||
2000 0.3321368 0.49770699 -5.584787 -6.0546694 12.097343 1.2026972 9.4615963 -0.96758935 -0.3571439 13.858218 0.5942385
|
||||
3000 0.46981685 0.70402055 -3.9208474 -6.3911005 63.005989 22.559106 8.6828663 -3.1742737 -0.16958917 18.776521 2.2842567
|
||||
4000 0.54866493 0.82217439 -4.1703408 -6.2427645 38.408608 4.9066022 8.6573289 -2.894598 -0.45434132 14.506935 1.8023166
|
||||
5000 0.30625495 0.45892304 -4.7355785 -6.186448 35.000599 6.2097986 8.6658098 -1.9097925 -0.19603125 13.896448 1.7145489
|
||||
6000 0.13938196 0.20886386 -4.303964 -5.7629121 50.370681 12.189231 8.3966581 -1.6678119 0.11451271 15.088809 2.2724852
|
||||
7000 0.055349516 0.082941249 -5.2031342 -6.8043199 30.859256 6.5562297 8.6850282 -1.684127 0.020586458 13.152479 1.5971879
|
||||
8000 0.027926794 0.0418483 -4.5281656 -5.4484008 48.145681 12.229919 8.4107051 -0.96208352 0.19922201 14.821877 2.2112219
|
||||
9000 0.018195086 0.027265336 -4.9847444 -6.5712684 37.347655 8.7291385 8.5606968 -1.6137894 0.10912534 13.773573 1.8458438
|
||||
10000 0.0082893467 0.012421586 -5.0130076 -6.6821423 36.46118 8.3386716 8.5689995 -1.6815563 0.1065388 13.651975 1.8180818
|
||||
Loop time of 2.01177 on 4 procs for 10000 steps with 1000 atoms
|
||||
|
||||
Performance: 429472.539 tau/day, 4970.747 timesteps/s
|
||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.2437 | 1.2651 | 1.2843 | 1.7 | 62.89
|
||||
Neigh | 0.051696 | 0.052503 | 0.053247 | 0.3 | 2.61
|
||||
Comm | 0.24826 | 0.26724 | 0.28867 | 3.5 | 13.28
|
||||
Output | 0.00058603 | 0.00085759 | 0.0016623 | 0.0 | 0.04
|
||||
Modify | 0.37363 | 0.37671 | 0.38189 | 0.5 | 18.73
|
||||
Other | | 0.04935 | | | 2.45
|
||||
|
||||
Nlocal: 250 ave 260 max 240 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 927.5 ave 934 max 921 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 5048.5 ave 5203 max 4889 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 20194
|
||||
Ave neighs/atom = 20.194
|
||||
Neighbor list builds = 175
|
||||
Dangerous builds = 0
|
||||
|
||||
# Start Run #2
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style lj/cubic from restart
|
||||
1000 atoms
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.001
|
||||
reset_timestep 0
|
||||
|
||||
# Pzz = 40.0, drag/damping term on
|
||||
|
||||
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
|
||||
|
||||
# Specify reference state from paper, times 1000 atoms
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
# Define output
|
||||
|
||||
variable dele equal f_myhug[1] # energy delta [temperature]
|
||||
variable us equal f_myhug[2] # shock velocity [distance/time]
|
||||
variable up equal f_myhug[3] # particle velocity [distance/time]
|
||||
variable pzz equal pzz # axial stress
|
||||
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
|
||||
variable time equal dt*step
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
|
||||
|
||||
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.74754
|
||||
ghost atom cutoff = 1.74754
|
||||
binsize = 0.873769, bins = 8 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes
|
||||
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
|
||||
0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
|
||||
1000 0.0063089138 0.0094539073 -5.9892326 -7.6448129 18.914956 7.5823222 9.2337797 -1.6650342 0.023426454 13.975434 0.92133642
|
||||
2000 0.0068813683 0.01031173 -5.4566765 -7.9789037 37.064192 15.537213 8.9495783 -2.5325388 0.10234565 16.32485 1.5455517
|
||||
3000 0.0072427316 0.010853233 -5.3662818 -7.9940958 39.906002 16.80569 8.9154322 -2.6386672 0.11821344 16.638326 1.6327015
|
||||
4000 0.0070936522 0.010629838 -5.3626164 -8.0025859 40.007994 16.850321 8.9143648 -2.6505993 0.11869226 16.650416 1.6356859
|
||||
5000 0.0074091958 0.01110268 -5.3628943 -8.0110325 39.998199 16.845204 8.9144816 -2.6592409 0.11846422 16.649379 1.6353872
|
||||
6000 0.0077388573 0.011596678 -5.3629264 -8.0194804 39.995216 16.842807 8.9145056 -2.6681507 0.11826582 16.648964 1.635306
|
||||
7000 0.0076023298 0.011392091 -5.3621083 -8.0277598 39.998343 16.839762 8.9144789 -2.6770435 0.11810824 16.649386 1.6353924
|
||||
8000 0.007691692 0.011526001 -5.361706 -8.0360632 40.000701 16.839078 8.9144843 -2.6858833 0.11795313 16.649923 1.6354361
|
||||
9000 0.0082153298 0.012310672 -5.3620899 -8.0446091 40.006134 16.845865 8.914544 -2.6948299 0.11785259 16.651566 1.6354969
|
||||
10000 0.0088368792 0.013242063 -5.3625357 -8.0530825 39.989575 16.835079 8.914577 -2.7037888 0.1174907 16.648402 1.6351306
|
||||
Loop time of 1.80214 on 4 procs for 10000 steps with 1000 atoms
|
||||
|
||||
Performance: 479429.980 tau/day, 5548.958 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1353 | 1.1591 | 1.1787 | 1.5 | 64.32
|
||||
Neigh | 0.0028975 | 0.0029137 | 0.0029218 | 0.0 | 0.16
|
||||
Comm | 0.20882 | 0.22752 | 0.25213 | 3.4 | 12.62
|
||||
Output | 0.00058103 | 0.0007953 | 0.0014329 | 0.0 | 0.04
|
||||
Modify | 0.36598 | 0.36908 | 0.37078 | 0.3 | 20.48
|
||||
Other | | 0.04277 | | | 2.37
|
||||
|
||||
Nlocal: 250 ave 258 max 239 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 829 ave 840 max 821 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 5250 ave 5360 max 5090 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
# Start Run #3
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style lj/cubic from restart
|
||||
1000 atoms
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.001
|
||||
reset_timestep 0
|
||||
|
||||
# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
|
||||
|
||||
fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
|
||||
|
||||
# Specify reference state from paper, times 1000 atoms
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
# Define output
|
||||
|
||||
variable dele equal f_myhug[1] # energy delta [temperature]
|
||||
variable us equal f_myhug[2] # shock velocity [distance/time]
|
||||
variable up equal f_myhug[3] # particle velocity [distance/time]
|
||||
variable pzz equal pzz # axial stress
|
||||
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
|
||||
variable time equal dt*step
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
|
||||
|
||||
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.74754
|
||||
ghost atom cutoff = 1.74754
|
||||
binsize = 0.873769, bins = 8 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes
|
||||
Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
|
||||
0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
|
||||
1000 0.0078345827 0.011740122 -5.501714 -6.3232649 35.616592 14.888101 8.9677603 -0.833291 0.093891974 16.160626 1.5002802
|
||||
2000 0.019260469 0.028861813 -5.2936047 -6.2784351 41.771445 17.563018 8.895899 -1.0136922 0.11811779 16.853929 1.687161
|
||||
3000 0.048111305 0.072094791 -5.3454082 -6.2447367 39.061491 16.137184 8.932261 -0.97142325 0.073850675 16.606004 1.6012602
|
||||
4000 0.11854629 0.17764161 -5.2071426 -6.3210422 40.843054 16.426156 8.9202992 -1.2915412 0.017621345 16.874925 1.6476105
|
||||
5000 0.13634167 0.204308 -5.2645153 -6.3135608 39.098316 15.628006 8.9407716 -1.2533534 -0.00067532215 16.688495 1.5948471
|
||||
6000 0.14222646 0.21312635 -5.1774703 -6.3289809 40.888616 16.260775 8.9214855 -1.3646369 -0.0041713956 16.89472 1.6475159
|
||||
7000 0.12683662 0.19006468 -5.2679846 -6.2838171 39.084233 15.633883 8.939337 -1.2058972 0.0057260888 16.672835 1.5957701
|
||||
8000 0.14531516 0.21775476 -5.1737923 -6.3237483 40.861161 16.191124 8.9199968 -1.3677107 -0.0065481979 16.876021 1.6482339
|
||||
9000 0.12123357 0.18166851 -5.2546748 -6.2570254 39.276123 15.677988 8.9363522 -1.1840191 0.0075191856 16.687414 1.6022039
|
||||
10000 0.14771416 0.22134967 -5.1833988 -6.3104954 40.578265 16.080163 8.9245634 -1.3484463 -0.0098090911 16.857414 1.6386293
|
||||
Loop time of 1.8702 on 4 procs for 10000 steps with 1000 atoms
|
||||
|
||||
Performance: 461983.152 tau/day, 5347.027 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1723 | 1.1812 | 1.1956 | 0.9 | 63.16
|
||||
Neigh | 0.028221 | 0.030409 | 0.035555 | 1.7 | 1.63
|
||||
Comm | 0.22963 | 0.24139 | 0.25155 | 1.6 | 12.91
|
||||
Output | 0.00055218 | 0.00077897 | 0.0014515 | 0.0 | 0.04
|
||||
Modify | 0.37165 | 0.37241 | 0.3732 | 0.1 | 19.91
|
||||
Other | | 0.04404 | | | 2.35
|
||||
|
||||
Nlocal: 250 ave 257 max 244 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nghost: 832.25 ave 840 max 822 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 5144.25 ave 5282 max 4949 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 20577
|
||||
Ave neighs/atom = 20.577
|
||||
Neighbor list builds = 95
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:05
|
||||
|
|
@ -1,110 +0,0 @@
|
|||
LAMMPS (5 Oct 2016)
|
||||
# This script reproduces stress trajectories from Fig. 1 in
|
||||
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
|
||||
#
|
||||
# Three thermostatting scenarios are visited: undamped (nodrag),
|
||||
# damped (drag) and Nose-Hoover chain (nhchains).
|
||||
#
|
||||
# The axial and shear stress trajectories are printed to the
|
||||
# file "stress_vs_t.dat". For the damped case, the original figure
|
||||
# seems to be a plot of 2*tau, rather than tau.
|
||||
#
|
||||
# The script also demonstrates how to
|
||||
# orient a crystal along <110>,
|
||||
# and how to use the lj/cubic pair style.
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
# Set up FCC lattice with z axis along <110>
|
||||
|
||||
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
|
||||
Lattice spacing in x,y,z = 1.41421 2 2
|
||||
|
||||
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
|
||||
create_box 1 mycell
|
||||
Created orthogonal box = (0 0 0) to (7.07107 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0
|
||||
create_atoms 1 box
|
||||
Created 1000 atoms
|
||||
|
||||
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 1.0 0.8908987
|
||||
|
||||
# Relax box dimensions
|
||||
|
||||
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
|
||||
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-6 10000 100000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.84754
|
||||
ghost atom cutoff = 1.84754
|
||||
binsize = 0.923769 -> bins = 8 11 11
|
||||
Memory usage per processor = 3.65406 Mbytes
|
||||
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
|
||||
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
|
||||
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
|
||||
134 0 -6.3344257 -6.3344257 -4.5005818e-13 -4.9677973e-13 -4.9219424e-13 6.9780266 9.8684199 9.8684199
|
||||
Loop time of 0.0817621 on 1 procs for 134 steps with 1000 atoms
|
||||
|
||||
100.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-6.2937539309 -6.33442568056 -6.33442568056
|
||||
Force two-norm initial, final = 3395.29 5.83329e-10
|
||||
Force max component initial, final = 1960.27 3.42093e-10
|
||||
Final line search alpha, max atom move = 1 3.42093e-10
|
||||
Iterations, force evaluations = 134 137
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.066955 | 0.066955 | 0.066955 | 0.0 | 81.89
|
||||
Neigh | 0.001004 | 0.001004 | 0.001004 | 0.0 | 1.23
|
||||
Comm | 0.0014298 | 0.0014298 | 0.0014298 | 0.0 | 1.75
|
||||
Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.02
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01236 | | | 15.11
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1724 ave 1724 max 1724 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 21000 ave 21000 max 21000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Define initial velocity
|
||||
|
||||
velocity all create 0.01 87287 mom yes rot yes dist gaussian
|
||||
write_restart restart.equil
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.84754
|
||||
ghost atom cutoff = 1.84754
|
||||
binsize = 0.923769 -> bins = 8 11 11
|
||||
|
||||
# Start Run #1
|
||||
|
||||
log log.nodrag
|
||||
|
|
@ -1,110 +0,0 @@
|
|||
LAMMPS (5 Oct 2016)
|
||||
# This script reproduces stress trajectories from Fig. 1 in
|
||||
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
|
||||
#
|
||||
# Three thermostatting scenarios are visited: undamped (nodrag),
|
||||
# damped (drag) and Nose-Hoover chain (nhchains).
|
||||
#
|
||||
# The axial and shear stress trajectories are printed to the
|
||||
# file "stress_vs_t.dat". For the damped case, the original figure
|
||||
# seems to be a plot of 2*tau, rather than tau.
|
||||
#
|
||||
# The script also demonstrates how to
|
||||
# orient a crystal along <110>,
|
||||
# and how to use the lj/cubic pair style.
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
# Set up FCC lattice with z axis along <110>
|
||||
|
||||
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
|
||||
Lattice spacing in x,y,z = 1.41421 2 2
|
||||
|
||||
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
|
||||
create_box 1 mycell
|
||||
Created orthogonal box = (0 0 0) to (7.07107 10 10)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0
|
||||
create_atoms 1 box
|
||||
Created 1000 atoms
|
||||
|
||||
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 1.0 0.8908987
|
||||
|
||||
# Relax box dimensions
|
||||
|
||||
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
|
||||
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-6 10000 100000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.84754
|
||||
ghost atom cutoff = 1.84754
|
||||
binsize = 0.923769 -> bins = 8 11 11
|
||||
Memory usage per processor = 3.63062 Mbytes
|
||||
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
|
||||
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
|
||||
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
|
||||
134 0 -6.3344257 -6.3344257 -4.5046204e-13 -4.92206e-13 -4.9610344e-13 6.9780266 9.8684199 9.8684199
|
||||
Loop time of 0.0299768 on 4 procs for 134 steps with 1000 atoms
|
||||
|
||||
98.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-6.2937539309 -6.33442568056 -6.33442568056
|
||||
Force two-norm initial, final = 3395.29 5.80609e-10
|
||||
Force max component initial, final = 1960.27 3.41627e-10
|
||||
Final line search alpha, max atom move = 1 3.41627e-10
|
||||
Iterations, force evaluations = 134 137
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.01485 | 0.017638 | 0.020133 | 1.4 | 58.84
|
||||
Neigh | 0.00022697 | 0.00027376 | 0.00033092 | 0.2 | 0.91
|
||||
Comm | 0.0026414 | 0.0050641 | 0.0078235 | 2.6 | 16.89
|
||||
Output | 1.502e-05 | 1.6749e-05 | 2.0027e-05 | 0.0 | 0.06
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.006985 | | | 23.30
|
||||
|
||||
Nlocal: 250 ave 305 max 205 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 829 ave 874 max 774 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 5250 ave 6445 max 4305 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Define initial velocity
|
||||
|
||||
velocity all create 0.01 87287 mom yes rot yes dist gaussian
|
||||
write_restart restart.equil
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.84754
|
||||
ghost atom cutoff = 1.84754
|
||||
binsize = 0.923769 -> bins = 8 11 11
|
||||
|
||||
# Start Run #1
|
||||
|
||||
log log.nodrag
|
||||
|
|
@ -36,15 +36,12 @@ unfix 2
|
|||
# MSST fix
|
||||
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
|
||||
|
||||
# this is needed to make etotal equal the MSST conserved quantity
|
||||
fix_modify msst energy yes
|
||||
|
||||
variable dhug equal f_msst[1]
|
||||
variable dray equal f_msst[2]
|
||||
variable lgr_vel equal f_msst[3]
|
||||
variable lgr_pos equal f_msst[4]
|
||||
|
||||
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal &
|
||||
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz econserve &
|
||||
v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
|
||||
#dump id all atom 50 dump.msst
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (30 Jun 2020)
|
||||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# LJ test of msst shock dynamics
|
||||
|
||||
|
|
@ -10,18 +10,18 @@ atom_style atomic
|
|||
timestep 1e-03
|
||||
|
||||
lattice fcc 5.3589
|
||||
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
|
||||
Lattice spacing in x,y,z = 5.3589000 5.3589000 5.3589000
|
||||
|
||||
## Specify the box as a given number of unit cells.
|
||||
region box1 block 0 18 0 18 0 18 units lattice
|
||||
|
||||
## Instantiate the system.
|
||||
create_box 1 box1
|
||||
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (96.460200 96.460200 96.460200)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region box1
|
||||
Created 23328 atoms
|
||||
create_atoms CPU = 0.007 seconds
|
||||
create_atoms CPU = 0.012 seconds
|
||||
|
||||
mass 1 40.00
|
||||
|
||||
|
|
@ -63,30 +63,30 @@ Step Temp E_pair E_mol TotEng Press
|
|||
80 300.28534 -1056.589 0 -151.15321 8324.8812
|
||||
90 305.83368 -1073.3097 0 -151.14426 8175.2478
|
||||
100 304.06857 -1067.9843 0 -151.14112 8191.234
|
||||
Loop time of 3.62419 on 1 procs for 100 steps with 23328 atoms
|
||||
Loop time of 8.29437 on 1 procs for 100 steps with 23328 atoms
|
||||
|
||||
Performance: 4.768 ns/day, 5.034 hours/ns, 27.592 timesteps/s
|
||||
Performance: 2.083 ns/day, 11.520 hours/ns, 12.056 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 | 3.4606 | 3.4606 | 3.4606 | 0.0 | 95.49
|
||||
Neigh | 0.065469 | 0.065469 | 0.065469 | 0.0 | 1.81
|
||||
Comm | 0.030757 | 0.030757 | 0.030757 | 0.0 | 0.85
|
||||
Output | 0.0024359 | 0.0024359 | 0.0024359 | 0.0 | 0.07
|
||||
Modify | 0.049582 | 0.049582 | 0.049582 | 0.0 | 1.37
|
||||
Other | | 0.01537 | | | 0.42
|
||||
Pair | 7.9896 | 7.9896 | 7.9896 | 0.0 | 96.33
|
||||
Neigh | 0.13503 | 0.13503 | 0.13503 | 0.0 | 1.63
|
||||
Comm | 0.053102 | 0.053102 | 0.053102 | 0.0 | 0.64
|
||||
Output | 0.0035691 | 0.0035691 | 0.0035691 | 0.0 | 0.04
|
||||
Modify | 0.091417 | 0.091417 | 0.091417 | 0.0 | 1.10
|
||||
Other | | 0.02167 | | | 0.26
|
||||
|
||||
Nlocal: 23328.0 ave 23328.0 max 23328.0 min
|
||||
Nlocal: 23328.0 ave 23328 max 23328 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 22235.0 ave 22235.0 max 22235.0 min
|
||||
Nghost: 22235.0 ave 22235 max 22235 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2183715.0 ave 2183715.0 max 2183715.0 min
|
||||
Neighs: 2.18372e+06 ave 2.18372e+06 max 2.18372e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2183715
|
||||
Ave neighs/atom = 93.60918209876543
|
||||
Ave neighs/atom = 93.609182
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
unfix 2
|
||||
|
|
@ -102,15 +102,12 @@ MSST parameters:
|
|||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
|
||||
# this is needed to make etotal equal the MSST conserved quantity
|
||||
fix_modify msst energy yes
|
||||
|
||||
variable dhug equal f_msst[1]
|
||||
variable dray equal f_msst[2]
|
||||
variable lgr_vel equal f_msst[3]
|
||||
variable lgr_pos equal f_msst[4]
|
||||
|
||||
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz econserve v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
|
||||
#dump id all atom 50 dump.msst
|
||||
|
||||
|
|
@ -126,42 +123,42 @@ Fix MSST p0 = 8106.7886
|
|||
Fix MSST e0 = -151.14112
|
||||
Fix MSST initial strain rate of -0.032011238 established by reducing temperature by factor of 0.01
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.98 | 18.98 | 18.98 Mbytes
|
||||
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
100 301.02788 907.67474 -1058.8159 96.4602 96.4602 96.4602 8242.1214 8202.9779 8095.8693 -151.14112 1.5203428 -10.919311 0 0 9.1684318
|
||||
110 297.71411 897.68288 -1048.8859 96.4602 96.4602 96.399397 8347.6253 8303.7121 8220.7572 -151.20299 1.439058 28.652258 0.017649501 -0.55980494 5.7336721
|
||||
120 295.64308 891.43821 -1042.72 96.4602 96.4602 96.340496 8431.6742 8379.2441 8331.5304 -151.28174 1.3655893 56.776734 0.034747125 -1.119263 2.3808018
|
||||
130 296.02228 892.5816 -1043.9407 96.4602 96.4602 96.283468 8456.2492 8412.6368 8392.5853 -151.35912 1.2945465 37.811981 0.05130089 -1.6783851 -0.87840575
|
||||
140 298.19024 899.11855 -1050.5482 96.4602 96.4602 96.228236 8430.5151 8415.6802 8414.2537 -151.42965 1.2243399 -18.01985 0.067333442 -2.2371818 -4.0330712
|
||||
150 300.86421 907.18122 -1058.6966 96.4602 96.4602 96.174681 8399.4697 8396.2236 8420.9004 -151.51534 1.1598278 -86.5197 0.082879112 -2.7956634 -7.0824881
|
||||
160 303.34119 914.64996 -1066.2388 96.4602 96.4602 96.122673 8388.3438 8360.5024 8428.751 -151.58881 1.0977647 -151.64553 0.097975827 -3.353839 -10.033902
|
||||
170 304.87769 919.28288 -1070.961 96.4602 96.4602 96.072088 8408.8694 8333.4337 8449.5665 -151.67812 1.044322 -201.80899 0.11265931 -3.9117174 -12.897768
|
||||
180 304.99 919.62151 -1071.3588 96.4602 96.4602 96.022824 8461.5542 8343.1436 8484.9824 -151.73733 0.99203387 -235.51793 0.12695926 -4.4693063 -15.685622
|
||||
190 305.1148 919.99782 -1071.7807 96.4602 96.4602 95.9748 8498.7562 8371.4217 8514.4473 -151.78288 0.93937416 -273.43964 0.1408996 -5.0266132 -18.403999
|
||||
200 306.45829 924.0488 -1075.8787 96.4602 96.4602 95.927931 8488.9509 8385.2408 8529.6443 -151.82991 0.88654815 -324.00777 0.15450451 -5.583645 -21.055149
|
||||
Loop time of 7.9807 on 1 procs for 100 steps with 23328 atoms
|
||||
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
100 301.02788 907.67474 -1067.9843 96.4602 96.4602 96.4602 8242.1214 8202.9779 8095.8693 -151.14112 1.5203428 -10.919311 0 0 9.1684318
|
||||
110 297.71411 897.68288 -1054.6195 96.4602 96.4602 96.399397 8347.6253 8303.7121 8220.7572 -151.20299 1.439058 28.652258 0.017649501 -0.55980494 5.7336721
|
||||
120 295.64308 891.43821 -1045.1008 96.4602 96.4602 96.340496 8431.6742 8379.2441 8331.5304 -151.28174 1.3655893 56.776734 0.034747125 -1.119263 2.3808018
|
||||
130 296.02228 892.5816 -1043.0623 96.4602 96.4602 96.283468 8456.2492 8412.6368 8392.5853 -151.35912 1.2945465 37.811981 0.05130089 -1.6783851 -0.87840575
|
||||
140 298.19024 899.11855 -1046.5151 96.4602 96.4602 96.228236 8430.5151 8415.6802 8414.2537 -151.42965 1.2243399 -18.01985 0.067333442 -2.2371818 -4.0330712
|
||||
150 300.86421 907.18122 -1051.6141 96.4602 96.4602 96.174681 8399.4697 8396.2236 8420.9004 -151.51534 1.1598278 -86.5197 0.082879112 -2.7956634 -7.0824881
|
||||
160 303.34119 914.64996 -1056.2049 96.4602 96.4602 96.122673 8388.3438 8360.5024 8428.751 -151.58881 1.0977647 -151.64553 0.097975827 -3.353839 -10.033902
|
||||
170 304.87769 919.28288 -1058.0632 96.4602 96.4602 96.072088 8408.8694 8333.4337 8449.5665 -151.67812 1.044322 -201.80899 0.11265931 -3.9117174 -12.897768
|
||||
180 304.99 919.62151 -1055.6732 96.4602 96.4602 96.022824 8461.5542 8343.1436 8484.9824 -151.73733 0.99203387 -235.51793 0.12695926 -4.4693063 -15.685622
|
||||
190 305.1148 919.99782 -1053.3767 96.4602 96.4602 95.9748 8498.7562 8371.4217 8514.4473 -151.78288 0.93937416 -273.43964 0.1408996 -5.0266132 -18.403999
|
||||
200 306.45829 924.0488 -1054.8236 96.4602 96.4602 95.927931 8488.9509 8385.2408 8529.6443 -151.82991 0.88654815 -324.00777 0.15450451 -5.583645 -21.055149
|
||||
Loop time of 13.2508 on 1 procs for 100 steps with 23328 atoms
|
||||
|
||||
Performance: 2.165 ns/day, 11.084 hours/ns, 12.530 timesteps/s
|
||||
Performance: 1.304 ns/day, 18.404 hours/ns, 7.547 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 | 6.8295 | 6.8295 | 6.8295 | 0.0 | 85.58
|
||||
Neigh | 0.13211 | 0.13211 | 0.13211 | 0.0 | 1.66
|
||||
Comm | 0.032946 | 0.032946 | 0.032946 | 0.0 | 0.41
|
||||
Output | 0.02301 | 0.02301 | 0.02301 | 0.0 | 0.29
|
||||
Modify | 0.94857 | 0.94857 | 0.94857 | 0.0 | 11.89
|
||||
Other | | 0.01452 | | | 0.18
|
||||
Pair | 11.716 | 11.716 | 11.716 | 0.0 | 88.41
|
||||
Neigh | 0.26843 | 0.26843 | 0.26843 | 0.0 | 2.03
|
||||
Comm | 0.056694 | 0.056694 | 0.056694 | 0.0 | 0.43
|
||||
Output | 0.029758 | 0.029758 | 0.029758 | 0.0 | 0.22
|
||||
Modify | 1.1599 | 1.1599 | 1.1599 | 0.0 | 8.75
|
||||
Other | | 0.02035 | | | 0.15
|
||||
|
||||
Nlocal: 23328.0 ave 23328.0 max 23328.0 min
|
||||
Nlocal: 23328.0 ave 23328 max 23328 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 22205.0 ave 22205.0 max 22205.0 min
|
||||
Nghost: 22205.0 ave 22205 max 22205 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2183494.0 ave 2183494.0 max 2183494.0 min
|
||||
Neighs: 2.18349e+06 ave 2.18349e+06 max 2.18349e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2183494
|
||||
Ave neighs/atom = 93.5997085048011
|
||||
Ave neighs/atom = 93.599709
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:11
|
||||
Total wall time: 0:00:22
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (30 Jun 2020)
|
||||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# LJ test of msst shock dynamics
|
||||
|
||||
|
|
@ -10,18 +10,18 @@ atom_style atomic
|
|||
timestep 1e-03
|
||||
|
||||
lattice fcc 5.3589
|
||||
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
|
||||
Lattice spacing in x,y,z = 5.3589000 5.3589000 5.3589000
|
||||
|
||||
## Specify the box as a given number of unit cells.
|
||||
region box1 block 0 18 0 18 0 18 units lattice
|
||||
|
||||
## Instantiate the system.
|
||||
create_box 1 box1
|
||||
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (96.460200 96.460200 96.460200)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region box1
|
||||
Created 23328 atoms
|
||||
create_atoms CPU = 0.003 seconds
|
||||
create_atoms CPU = 0.080 seconds
|
||||
|
||||
mass 1 40.00
|
||||
|
||||
|
|
@ -63,30 +63,30 @@ Step Temp E_pair E_mol TotEng Press
|
|||
80 299.37658 -1053.8476 0 -151.1519 8352.9467
|
||||
90 304.24026 -1068.4941 0 -151.13319 8218.1594
|
||||
100 301.9683 -1061.6332 0 -151.12284 8244.1277
|
||||
Loop time of 0.995305 on 4 procs for 100 steps with 23328 atoms
|
||||
Loop time of 5.66225 on 4 procs for 100 steps with 23328 atoms
|
||||
|
||||
Performance: 17.362 ns/day, 1.382 hours/ns, 100.472 timesteps/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 3.052 ns/day, 7.864 hours/ns, 17.661 timesteps/s
|
||||
78.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.88957 | 0.90144 | 0.91686 | 1.1 | 90.57
|
||||
Neigh | 0.016824 | 0.016945 | 0.017106 | 0.1 | 1.70
|
||||
Comm | 0.039949 | 0.054853 | 0.068734 | 4.8 | 5.51
|
||||
Output | 0.00076342 | 0.0010425 | 0.0018687 | 1.5 | 0.10
|
||||
Modify | 0.012839 | 0.012946 | 0.013153 | 0.1 | 1.30
|
||||
Other | | 0.008074 | | | 0.81
|
||||
Pair | 2.6416 | 2.7792 | 2.9335 | 6.4 | 49.08
|
||||
Neigh | 0.029522 | 0.037458 | 0.054701 | 5.3 | 0.66
|
||||
Comm | 2.1998 | 2.4099 | 2.5822 | 8.8 | 42.56
|
||||
Output | 0.10457 | 0.10816 | 0.11265 | 1.0 | 1.91
|
||||
Modify | 0.023462 | 0.033517 | 0.044696 | 4.9 | 0.59
|
||||
Other | | 0.294 | | | 5.19
|
||||
|
||||
Nlocal: 5832.0 ave 5850.0 max 5813.0 min
|
||||
Nlocal: 5832.00 ave 5850 max 5813 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 10571.0 ave 10590.0 max 10553.0 min
|
||||
Nghost: 10571.0 ave 10590 max 10553 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 545761.75 ave 548069.0 max 543643.0 min
|
||||
Neighs: 545762.0 ave 548069 max 543643 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2183047
|
||||
Ave neighs/atom = 93.58054698216735
|
||||
Ave neighs/atom = 93.580547
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
unfix 2
|
||||
|
|
@ -102,15 +102,12 @@ MSST parameters:
|
|||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
|
||||
# this is needed to make etotal equal the MSST conserved quantity
|
||||
fix_modify msst energy yes
|
||||
|
||||
variable dhug equal f_msst[1]
|
||||
variable dray equal f_msst[2]
|
||||
variable lgr_vel equal f_msst[3]
|
||||
variable lgr_pos equal f_msst[4]
|
||||
|
||||
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz econserve v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
|
||||
#dump id all atom 50 dump.msst
|
||||
|
||||
|
|
@ -126,42 +123,42 @@ Fix MSST p0 = 8186.2393
|
|||
Fix MSST e0 = -151.12284
|
||||
Fix MSST initial strain rate of -0.031900492 established by reducing temperature by factor of 0.01
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.535 | 8.535 | 8.535 Mbytes
|
||||
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
100 298.94862 901.40524 -1052.5281 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034
|
||||
110 296.49826 894.01679 -1045.224 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557
|
||||
120 295.97607 892.44225 -1043.7239 96.4602 96.4602 96.340904 8377.6797 8385.921 8378.3042 -151.28169 1.3584606 24.672199 0.034628719 -1.1192655 2.2953307
|
||||
130 297.34893 896.58179 -1047.945 96.4602 96.4602 96.284029 8379.2516 8394.8806 8416.2669 -151.36322 1.2881444 -17.170168 0.051138087 -1.6783905 -0.96527961
|
||||
140 299.71946 903.72952 -1055.1787 96.4602 96.4602 96.22888 8357.0358 8388.6743 8424.3188 -151.44922 1.221125 -86.501161 0.067146366 -2.2371908 -4.1195182
|
||||
150 301.79241 909.97998 -1061.4976 96.4602 96.4602 96.175327 8332.7118 8393.7027 8434.6177 -151.51765 1.1560248 -151.34689 0.082691635 -2.7956762 -7.172084
|
||||
160 303.18249 914.17141 -1065.7667 96.4602 96.4602 96.123244 8321.1154 8413.1248 8454.5596 -151.59527 1.0977348 -204.4864 0.097810061 -3.3538554 -10.134387
|
||||
170 304.34089 917.66428 -1069.3198 96.4602 96.4602 96.072522 8327.6227 8431.1177 8467.92 -151.65554 1.0390628 -262.29751 0.11253339 -3.9117366 -13.01442
|
||||
180 305.86343 922.25514 -1073.9633 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462
|
||||
190 307.44054 927.01052 -1078.7892 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801
|
||||
200 308.43619 930.01265 -1081.8521 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378
|
||||
Loop time of 2.16596 on 4 procs for 100 steps with 23328 atoms
|
||||
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
100 298.94862 901.40524 -1061.6332 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034
|
||||
110 296.49826 894.01679 -1050.8801 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557
|
||||
120 295.97607 892.44225 -1046.0193 96.4602 96.4602 96.340904 8377.6797 8385.921 8378.3042 -151.28169 1.3584606 24.672199 0.034628719 -1.1192655 2.2953307
|
||||
130 297.34893 896.58179 -1046.9797 96.4602 96.4602 96.284029 8379.2516 8394.8806 8416.2669 -151.36322 1.2881444 -17.170168 0.051138087 -1.6783905 -0.96527961
|
||||
140 299.71946 903.72952 -1051.0592 96.4602 96.4602 96.22888 8357.0358 8388.6743 8424.3188 -151.44922 1.221125 -86.501161 0.067146366 -2.2371908 -4.1195182
|
||||
150 301.79241 909.97998 -1054.3256 96.4602 96.4602 96.175327 8332.7118 8393.7027 8434.6177 -151.51765 1.1560248 -151.34689 0.082691635 -2.7956762 -7.172084
|
||||
160 303.18249 914.17141 -1055.6323 96.4602 96.4602 96.123244 8321.1154 8413.1248 8454.5596 -151.59527 1.0977348 -204.4864 0.097810061 -3.3538554 -10.134387
|
||||
170 304.34089 917.66428 -1056.3054 96.4602 96.4602 96.072522 8327.6227 8431.1177 8467.92 -151.65554 1.0390628 -262.29751 0.11253339 -3.9117366 -13.01442
|
||||
180 305.86343 922.25514 -1058.1478 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462
|
||||
190 307.44054 927.01052 -1060.2474 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801
|
||||
200 308.43619 930.01265 -1060.6483 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378
|
||||
Loop time of 11.445 on 4 procs for 100 steps with 23328 atoms
|
||||
|
||||
Performance: 7.978 ns/day, 3.008 hours/ns, 46.169 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 1.510 ns/day, 15.896 hours/ns, 8.737 timesteps/s
|
||||
77.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.7569 | 1.7822 | 1.8059 | 1.6 | 82.28
|
||||
Neigh | 0.034235 | 0.03546 | 0.037677 | 0.7 | 1.64
|
||||
Comm | 0.065427 | 0.091172 | 0.11833 | 7.4 | 4.21
|
||||
Output | 0.0062776 | 0.0065615 | 0.0074117 | 0.6 | 0.30
|
||||
Modify | 0.24069 | 0.2423 | 0.24655 | 0.5 | 11.19
|
||||
Other | | 0.008271 | | | 0.38
|
||||
Pair | 3.7358 | 4.0193 | 4.3315 | 10.5 | 35.12
|
||||
Neigh | 0.05921 | 0.078071 | 0.089958 | 4.1 | 0.68
|
||||
Comm | 2.3136 | 2.683 | 3.054 | 16.3 | 23.44
|
||||
Output | 0.038525 | 0.040035 | 0.044559 | 1.3 | 0.35
|
||||
Modify | 4.2814 | 4.3709 | 4.4749 | 4.1 | 38.19
|
||||
Other | | 0.2537 | | | 2.22
|
||||
|
||||
Nlocal: 5832.0 ave 5874.0 max 5803.0 min
|
||||
Nlocal: 5832.00 ave 5874 max 5803 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 10563.75 ave 10588.0 max 10526.0 min
|
||||
Nghost: 10563.8 ave 10588 max 10526 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 545708.5 ave 550787.0 max 542668.0 min
|
||||
Neighs: 545708.0 ave 550787 max 542668 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2182834
|
||||
Ave neighs/atom = 93.57141632373114
|
||||
Ave neighs/atom = 93.571416
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
Total wall time: 0:00:17
|
||||
|
|
@ -53,9 +53,9 @@ velocity all create $t 5287287 loop geom
|
|||
pair_style sw
|
||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -71,9 +71,9 @@ read_restart restart.equil
|
|||
pair_style sw
|
||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -87,9 +87,9 @@ read_restart restart.equil
|
|||
pair_style vashishta
|
||||
pair_coeff * * InP.vashishta In In In In P P P P
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
@ -106,9 +106,9 @@ change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
|||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
|
|
|||
|
|
@ -0,0 +1,373 @@
|
|||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for threebody potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Stillinger-Weber model for silicon
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.77118
|
||||
ghost atom cutoff = 4.77118
|
||||
binsize = 2.38559, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.983 | 2.983 | 2.983 Mbytes
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
0 1800 -2220.3392 -2101.4457 -2101.4457 12358.626
|
||||
10 1006.0192 -2167.7053 -2101.2558 -2101.3286 13892.426
|
||||
20 588.26396 -2139.7132 -2100.8573 -2101.3117 11295.566
|
||||
30 990.55956 -2165.2164 -2099.788 -2101.3931 6279.0239
|
||||
40 700.12917 -2144.4279 -2098.183 -2101.3427 5594.2388
|
||||
50 523.64239 -2131.7796 -2097.192 -2101.3122 6013.0994
|
||||
60 989.47092 -2161.3716 -2096.0152 -2101.3839 5819.2688
|
||||
70 877.27433 -2152.4432 -2094.4975 -2101.3461 9116.6569
|
||||
80 800.80221 -2146.1371 -2093.2426 -2101.313 11995.66
|
||||
90 1293.9689 -2176.9021 -2091.4329 -2101.3848 11692.45
|
||||
100 1112.9699 -2162.7259 -2089.2121 -2101.3478 12263.758
|
||||
Loop time of 0.157871 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 54.728 ns/day, 0.439 hours/ns, 633.430 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14704 | 0.14704 | 0.14704 | 0.0 | 93.14
|
||||
Neigh | 0.00247 | 0.00247 | 0.00247 | 0.0 | 1.56
|
||||
Comm | 0.0024729 | 0.0024729 | 0.0024729 | 0.0 | 1.57
|
||||
Output | 0.0002656 | 0.0002656 | 0.0002656 | 0.0 | 0.17
|
||||
Modify | 0.0050237 | 0.0050237 | 0.0050237 | 0.0 | 3.18
|
||||
Other | | 0.0006011 | | | 0.38
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017.00 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13988.0 ave 13988 max 13988 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13988
|
||||
Ave neighs/atom = 27.320312
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.6320004
|
||||
ghost atom cutoff = 5.6320004
|
||||
binsize = 2.8160002, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.001 | 3.001 | 3.001 Mbytes
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 1112.9699 -625.76163 -552.24781 -564.38354 462129.66
|
||||
110 1502.8461 -649.55768 -550.29179 -564.45814 463413.45
|
||||
120 1926.4523 -674.71265 -547.46675 -564.53612 486338.88
|
||||
130 1152.6663 -621.47264 -545.33681 -564.37203 514892.2
|
||||
140 1762.244 -659.86941 -543.46979 -564.4985 488159.88
|
||||
150 1767.8665 -657.67178 -540.90078 -564.48386 466721.31
|
||||
160 1075.2874 -610.12809 -539.10328 -564.36709 470151.9
|
||||
170 1697.9313 -649.3684 -537.21675 -564.47207 467953.71
|
||||
180 1856.1197 -657.14338 -534.54309 -564.48754 488372.27
|
||||
190 1346.1107 -621.42431 -532.5111 -564.38065 511750.04
|
||||
200 1919.5266 -657.26587 -530.47743 -564.47797 488684.56
|
||||
Loop time of 0.455825 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 18.955 ns/day, 1.266 hours/ns, 219.382 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 | 0.44091 | 0.44091 | 0.44091 | 0.0 | 96.73
|
||||
Neigh | 0.0054555 | 0.0054555 | 0.0054555 | 0.0 | 1.20
|
||||
Comm | 0.0035784 | 0.0035784 | 0.0035784 | 0.0 | 0.79
|
||||
Output | 0.00024486 | 0.00024486 | 0.00024486 | 0.0 | 0.05
|
||||
Modify | 0.0050471 | 0.0050471 | 0.0050471 | 0.0 | 1.11
|
||||
Other | | 0.000592 | | | 0.13
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1428.00 ave 1428 max 1428 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 17344.0 ave 17344 max 17344 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 17344
|
||||
Ave neighs/atom = 33.875000
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Vashishta model for In/P
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * InP.vashishta In In In In P P P P
|
||||
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7
|
||||
ghost atom cutoff = 7
|
||||
binsize = 3.5, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair vashishta, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 1112.9699 -1497.2988 -1423.785 -1435.9207 355619.19
|
||||
110 1250.545 -1504.5795 -1421.9785 -1435.9786 345188.52
|
||||
120 1360.2275 -1509.3443 -1419.4986 -1435.9801 333306.3
|
||||
130 1066.4516 -1487.9076 -1417.4664 -1435.9076 334465.11
|
||||
140 1481.0477 -1513.0511 -1415.2251 -1435.988 308725.1
|
||||
150 1216.1167 -1493.0774 -1412.7505 -1435.9217 304249.09
|
||||
160 1211.4398 -1490.7459 -1410.728 -1435.9164 288897.09
|
||||
170 1542.2025 -1510.0774 -1408.212 -1435.9608 260104.14
|
||||
180 1302.9041 -1491.7765 -1405.7172 -1435.8971 249514.04
|
||||
190 1332.3326 -1491.5271 -1403.524 -1435.9213 227537.99
|
||||
200 1352.1813 -1490.4513 -1401.1371 -1435.9049 207626.42
|
||||
Loop time of 0.217808 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 39.668 ns/day, 0.605 hours/ns, 459.121 timesteps/s
|
||||
98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.19635 | 0.19635 | 0.19635 | 0.0 | 90.15
|
||||
Neigh | 0.01054 | 0.01054 | 0.01054 | 0.0 | 4.84
|
||||
Comm | 0.0051923 | 0.0051923 | 0.0051923 | 0.0 | 2.38
|
||||
Output | 0.00027919 | 0.00027919 | 0.00027919 | 0.0 | 0.13
|
||||
Modify | 0.0048637 | 0.0048637 | 0.0048637 | 0.0 | 2.23
|
||||
Other | | 0.0005858 | | | 0.27
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1838.00 ave 1838 max 1838 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 36482.0 ave 36482 max 36482 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 36482
|
||||
Ave neighs/atom = 71.253906
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 1112.9699 -3259.7676 -3186.2538 -3198.3895 1912461.3
|
||||
110 1772.8268 -3301.5479 -3184.4493 -3198.8218 1885295.6
|
||||
120 1169.7287 -3258.74 -3181.4772 -3197.9294 1898705.2
|
||||
130 1308.5623 -3265.1338 -3178.7007 -3197.5922 1894187.5
|
||||
140 1486.0361 -3274.951 -3176.7954 -3197.776 1871927.6
|
||||
150 1419.0362 -3267.7302 -3174.0002 -3197.2296 1925234.6
|
||||
160 1196.6689 -3250.1492 -3171.1069 -3196.7078 1902235.1
|
||||
170 1707.5846 -3281.7658 -3168.9766 -3196.9721 1863047.3
|
||||
180 1337.4358 -3254.9844 -3166.6442 -3196.8222 1880420.9
|
||||
190 1441.8052 -3259.0364 -3163.8023 -3196.3556 1904512.1
|
||||
200 1569.0317 -3265.0089 -3161.3714 -3196.3328 1899462.7
|
||||
Loop time of 0.487425 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 17.726 ns/day, 1.354 hours/ns, 205.160 timesteps/s
|
||||
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.47762 | 0.47762 | 0.47762 | 0.0 | 97.99
|
||||
Neigh | 0.0014286 | 0.0014286 | 0.0014286 | 0.0 | 0.29
|
||||
Comm | 0.0024068 | 0.0024068 | 0.0024068 | 0.0 | 0.49
|
||||
Output | 0.00028992 | 0.00028992 | 0.00028992 | 0.0 | 0.06
|
||||
Modify | 0.0050635 | 0.0050635 | 0.0050635 | 0.0 | 1.04
|
||||
Other | | 0.0006182 | | | 0.13
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1028.00 ave 1028 max 1028 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 14604.0 ave 14604 max 14604 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14604
|
||||
Ave neighs/atom = 28.523438
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:01
|
||||
|
|
@ -0,0 +1,373 @@
|
|||
LAMMPS (24 Dec 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for threebody potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.074 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Stillinger-Weber model for silicon
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.77118
|
||||
ghost atom cutoff = 4.77118
|
||||
binsize = 2.38559, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
0 1800 -2220.3392 -2101.4457 -2101.4457 12358.626
|
||||
10 1006.0192 -2167.7053 -2101.2558 -2101.3286 13892.426
|
||||
20 588.26396 -2139.7132 -2100.8573 -2101.3117 11295.566
|
||||
30 990.55956 -2165.2164 -2099.788 -2101.3931 6279.0239
|
||||
40 700.12917 -2144.4279 -2098.183 -2101.3427 5594.2388
|
||||
50 523.64239 -2131.7796 -2097.192 -2101.3122 6013.0994
|
||||
60 989.47092 -2161.3716 -2096.0152 -2101.3839 5819.2688
|
||||
70 877.27433 -2152.4432 -2094.4975 -2101.3461 9116.6569
|
||||
80 800.80221 -2146.1371 -2093.2426 -2101.313 11995.66
|
||||
90 1293.9689 -2176.9021 -2091.4329 -2101.3848 11692.45
|
||||
100 1112.9699 -2162.7259 -2089.2121 -2101.3478 12263.758
|
||||
Loop time of 0.0998364 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 86.542 ns/day, 0.277 hours/ns, 1001.639 timesteps/s
|
||||
81.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.037337 | 0.049389 | 0.069239 | 5.9 | 49.47
|
||||
Neigh | 0.00067854 | 0.00068814 | 0.00070286 | 0.0 | 0.69
|
||||
Comm | 0.025239 | 0.04504 | 0.056869 | 6.1 | 45.11
|
||||
Output | 0.00015712 | 0.00082219 | 0.0028148 | 0.0 | 0.82
|
||||
Modify | 0.0014369 | 0.0015754 | 0.0016632 | 0.2 | 1.58
|
||||
Other | | 0.002321 | | | 2.33
|
||||
|
||||
Nlocal: 128.000 ave 132 max 125 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 525.000 ave 528 max 521 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3497.00 ave 3619 max 3397 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 13988
|
||||
Ave neighs/atom = 27.320312
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.6320004
|
||||
ghost atom cutoff = 5.6320004
|
||||
binsize = 2.8160002, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.967 | 2.967 | 2.968 Mbytes
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 1112.9699 -625.76163 -552.24782 -564.38354 462129.66
|
||||
110 1502.8461 -649.55768 -550.29179 -564.45814 463413.45
|
||||
120 1926.4523 -674.71265 -547.46675 -564.53613 486338.88
|
||||
130 1152.6663 -621.47265 -545.33681 -564.37203 514892.19
|
||||
140 1762.244 -659.86941 -543.46979 -564.4985 488159.88
|
||||
150 1767.8665 -657.67179 -540.90079 -564.48386 466721.31
|
||||
160 1075.2874 -610.1281 -539.10328 -564.36709 470151.9
|
||||
170 1697.9313 -649.3684 -537.21676 -564.47208 467953.7
|
||||
180 1856.1197 -657.14338 -534.54309 -564.48754 488372.26
|
||||
190 1346.1107 -621.42432 -532.5111 -564.38065 511750.03
|
||||
200 1919.5266 -657.26587 -530.47743 -564.47797 488684.56
|
||||
Loop time of 0.286556 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 30.151 ns/day, 0.796 hours/ns, 348.971 timesteps/s
|
||||
81.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11093 | 0.139 | 0.16864 | 5.8 | 48.51
|
||||
Neigh | 0.0014305 | 0.0014756 | 0.0015156 | 0.1 | 0.51
|
||||
Comm | 0.10154 | 0.12374 | 0.16907 | 7.8 | 43.18
|
||||
Output | 0.0001862 | 0.00030428 | 0.0006578 | 0.0 | 0.11
|
||||
Modify | 0.0038164 | 0.019159 | 0.034146 | 10.8 | 6.69
|
||||
Other | | 0.002872 | | | 1.00
|
||||
|
||||
Nlocal: 128.000 ave 135 max 122 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 759.750 ave 770 max 751 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4336.00 ave 4563 max 4128 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 17344
|
||||
Ave neighs/atom = 33.875000
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Vashishta model for In/P
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * InP.vashishta In In In In P P P P
|
||||
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7
|
||||
ghost atom cutoff = 7
|
||||
binsize = 3.5, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair vashishta, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.988 | 2.988 | 2.988 Mbytes
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 1112.9699 -1497.2988 -1423.785 -1435.9207 355619.19
|
||||
110 1250.545 -1504.5795 -1421.9785 -1435.9786 345188.52
|
||||
120 1360.2275 -1509.3443 -1419.4986 -1435.9801 333306.3
|
||||
130 1066.4516 -1487.9076 -1417.4664 -1435.9076 334465.11
|
||||
140 1481.0477 -1513.0511 -1415.2251 -1435.988 308725.1
|
||||
150 1216.1167 -1493.0774 -1412.7505 -1435.9217 304249.09
|
||||
160 1211.4398 -1490.7459 -1410.728 -1435.9164 288897.09
|
||||
170 1542.2025 -1510.0774 -1408.212 -1435.9608 260104.14
|
||||
180 1302.9041 -1491.7765 -1405.7172 -1435.8971 249514.04
|
||||
190 1332.3326 -1491.5271 -1403.524 -1435.9213 227537.99
|
||||
200 1352.1813 -1490.4513 -1401.1371 -1435.9049 207626.42
|
||||
Loop time of 0.14468 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 59.718 ns/day, 0.402 hours/ns, 691.179 timesteps/s
|
||||
81.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.047903 | 0.058669 | 0.086091 | 6.6 | 40.55
|
||||
Neigh | 0.0027876 | 0.002852 | 0.0028808 | 0.1 | 1.97
|
||||
Comm | 0.034642 | 0.066142 | 0.078599 | 7.1 | 45.72
|
||||
Output | 0.00018477 | 0.0049147 | 0.019101 | 11.7 | 3.40
|
||||
Modify | 0.0015709 | 0.0022651 | 0.0029545 | 1.4 | 1.57
|
||||
Other | | 0.009837 | | | 6.80
|
||||
|
||||
Nlocal: 128.000 ave 131 max 124 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Nghost: 1013.25 ave 1025 max 1002 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 9120.50 ave 9356 max 8868 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 36482
|
||||
Ave neighs/atom = 71.253906
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.005 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo_style custom step temp epair etotal econserve press
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.948 | 2.948 | 2.948 Mbytes
|
||||
Step Temp E_pair TotEng Econserve Press
|
||||
100 1112.9699 -3259.7676 -3186.2538 -3198.3895 1912461.3
|
||||
110 1772.8268 -3301.5479 -3184.4493 -3198.8218 1885295.6
|
||||
120 1169.7287 -3258.74 -3181.4772 -3197.9294 1898705.2
|
||||
130 1308.5623 -3265.1338 -3178.7007 -3197.5922 1894187.5
|
||||
140 1486.0361 -3274.951 -3176.7954 -3197.776 1871927.6
|
||||
150 1419.0362 -3267.7302 -3174.0002 -3197.2296 1925234.6
|
||||
160 1196.6689 -3250.1492 -3171.1069 -3196.7078 1902235.1
|
||||
170 1707.5846 -3281.7658 -3168.9766 -3196.9721 1863047.3
|
||||
180 1337.4358 -3254.9844 -3166.6442 -3196.8222 1880420.9
|
||||
190 1441.8052 -3259.0364 -3163.8023 -3196.3556 1904512.1
|
||||
200 1569.0317 -3265.0089 -3161.3714 -3196.3328 1899462.7
|
||||
Loop time of 0.348631 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 24.783 ns/day, 0.968 hours/ns, 286.836 timesteps/s
|
||||
81.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.13281 | 0.15657 | 0.20106 | 6.9 | 44.91
|
||||
Neigh | 0.00037527 | 0.00039309 | 0.00040412 | 0.0 | 0.11
|
||||
Comm | 0.12177 | 0.16672 | 0.19154 | 6.8 | 47.82
|
||||
Output | 0.00019097 | 0.000462 | 0.0012722 | 0.0 | 0.13
|
||||
Modify | 0.018353 | 0.020198 | 0.02302 | 1.3 | 5.79
|
||||
Other | | 0.004286 | | | 1.23
|
||||
|
||||
Nlocal: 128.000 ave 132 max 123 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 529.500 ave 533 max 524 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3651.00 ave 3783 max 3494 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 14604
|
||||
Ave neighs/atom = 28.523438
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:01
|
||||
|
|
@ -1,547 +0,0 @@
|
|||
LAMMPS (30 Nov 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for threebody potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Stillinger-Weber model for silicon
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.77118
|
||||
ghost atom cutoff = 4.77118
|
||||
binsize = 2.38559, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.983 | 2.983 | 2.983 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2220.3392 0 -2101.4457 12358.626
|
||||
10 1006.0192 -2167.7053 0 -2101.3286 13892.426
|
||||
20 588.26396 -2139.7132 0 -2101.3117 11295.566
|
||||
30 990.55956 -2165.2164 0 -2101.3931 6279.0239
|
||||
40 700.12917 -2144.4279 0 -2101.3427 5594.2388
|
||||
50 523.64239 -2131.7796 0 -2101.3122 6013.0994
|
||||
60 989.47092 -2161.3716 0 -2101.3839 5819.2688
|
||||
70 877.27433 -2152.4432 0 -2101.3461 9116.6569
|
||||
80 800.80221 -2146.1371 0 -2101.313 11995.66
|
||||
90 1293.9689 -2176.9021 0 -2101.3848 11692.45
|
||||
100 1112.9699 -2162.7259 0 -2101.3478 12263.758
|
||||
Loop time of 0.092666 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 93.238 ns/day, 0.257 hours/ns, 1079.144 timesteps/s
|
||||
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.089633 | 0.089633 | 0.089633 | 0.0 | 96.73
|
||||
Neigh | 0.001474 | 0.001474 | 0.001474 | 0.0 | 1.59
|
||||
Comm | 0.00041 | 0.00041 | 0.00041 | 0.0 | 0.44
|
||||
Output | 0.000153 | 0.000153 | 0.000153 | 0.0 | 0.17
|
||||
Modify | 0.000782 | 0.000782 | 0.000782 | 0.0 | 0.84
|
||||
Other | | 0.000214 | | | 0.23
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017.00 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13988.0 ave 13988 max 13988 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13988
|
||||
Ave neighs/atom = 27.320312
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.002 seconds
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.6320004
|
||||
ghost atom cutoff = 5.6320004
|
||||
binsize = 2.8160002, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.001 | 3.001 | 3.001 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -625.76163 0 -564.38354 462129.66
|
||||
110 1502.8461 -649.55768 0 -564.45814 463413.45
|
||||
120 1926.4523 -674.71265 0 -564.53612 486338.88
|
||||
130 1152.6663 -621.47264 0 -564.37203 514892.2
|
||||
140 1762.244 -659.86941 0 -564.4985 488159.88
|
||||
150 1767.8665 -657.67178 0 -564.48386 466721.31
|
||||
160 1075.2874 -610.12809 0 -564.36709 470151.9
|
||||
170 1697.9313 -649.3684 0 -564.47207 467953.71
|
||||
180 1856.1197 -657.14338 0 -564.48754 488372.27
|
||||
190 1346.1107 -621.42431 0 -564.38065 511750.04
|
||||
200 1919.5266 -657.26587 0 -564.47797 488684.56
|
||||
Loop time of 0.289193 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 29.876 ns/day, 0.803 hours/ns, 345.790 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.28463 | 0.28463 | 0.28463 | 0.0 | 98.42
|
||||
Neigh | 0.002821 | 0.002821 | 0.002821 | 0.0 | 0.98
|
||||
Comm | 0.000605 | 0.000605 | 0.000605 | 0.0 | 0.21
|
||||
Output | 0.000176 | 0.000176 | 0.000176 | 0.0 | 0.06
|
||||
Modify | 0.000769 | 0.000769 | 0.000769 | 0.0 | 0.27
|
||||
Other | | 0.000188 | | | 0.07
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1428.00 ave 1428 max 1428 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 17344.0 ave 17344 max 17344 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 17344
|
||||
Ave neighs/atom = 33.875000
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Vashishta model for In/P
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * InP.vashishta In In In In P P P P
|
||||
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7
|
||||
ghost atom cutoff = 7
|
||||
binsize = 3.5, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair vashishta, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -1497.2988 0 -1435.9207 355619.19
|
||||
110 1250.545 -1504.5795 0 -1435.9786 345188.52
|
||||
120 1360.2275 -1509.3443 0 -1435.9801 333306.3
|
||||
130 1066.4516 -1487.9076 0 -1435.9076 334465.11
|
||||
140 1481.0477 -1513.0511 0 -1435.988 308725.1
|
||||
150 1216.1167 -1493.0774 0 -1435.9217 304249.09
|
||||
160 1211.4398 -1490.7459 0 -1435.9164 288897.09
|
||||
170 1542.2025 -1510.0774 0 -1435.9608 260104.14
|
||||
180 1302.9041 -1491.7765 0 -1435.8971 249514.04
|
||||
190 1332.3326 -1491.5271 0 -1435.9213 227537.99
|
||||
200 1352.1813 -1490.4513 0 -1435.9049 207626.42
|
||||
Loop time of 0.126684 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 68.201 ns/day, 0.352 hours/ns, 789.366 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11981 | 0.11981 | 0.11981 | 0.0 | 94.57
|
||||
Neigh | 0.004903 | 0.004903 | 0.004903 | 0.0 | 3.87
|
||||
Comm | 0.000846 | 0.000846 | 0.000846 | 0.0 | 0.67
|
||||
Output | 0.000145 | 0.000145 | 0.000145 | 0.0 | 0.11
|
||||
Modify | 0.000772 | 0.000772 | 0.000772 | 0.0 | 0.61
|
||||
Other | | 0.000207 | | | 0.16
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1838.00 ave 1838 max 1838 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 36482.0 ave 36482 max 36482 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 36482
|
||||
Ave neighs/atom = 71.253906
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -3259.7676 0 -3198.3895 1912461.3
|
||||
110 1772.8268 -3301.5479 0 -3198.8218 1885295.6
|
||||
120 1169.7287 -3258.74 0 -3197.9294 1898705.2
|
||||
130 1308.5623 -3265.1338 0 -3197.5922 1894187.5
|
||||
140 1486.0361 -3274.951 0 -3197.776 1871927.6
|
||||
150 1419.0362 -3267.7302 0 -3197.2296 1925234.6
|
||||
160 1196.6689 -3250.1492 0 -3196.7078 1902235.1
|
||||
170 1707.5846 -3281.7658 0 -3196.9721 1863047.3
|
||||
180 1337.4358 -3254.9844 0 -3196.8222 1880420.9
|
||||
190 1441.8052 -3259.0364 0 -3196.3556 1904512.1
|
||||
200 1569.0317 -3265.0089 0 -3196.3328 1899462.7
|
||||
Loop time of 0.114312 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 75.583 ns/day, 0.318 hours/ns, 874.799 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.1121 | 0.1121 | 0.1121 | 0.0 | 98.06
|
||||
Neigh | 0.000773 | 0.000773 | 0.000773 | 0.0 | 0.68
|
||||
Comm | 0.000415 | 0.000415 | 0.000415 | 0.0 | 0.36
|
||||
Output | 0.000136 | 0.000136 | 0.000136 | 0.0 | 0.12
|
||||
Modify | 0.000703 | 0.000703 | 0.000703 | 0.0 | 0.61
|
||||
Other | | 0.000186 | | | 0.16
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1028.00 ave 1028 max 1028 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 14604.0 ave 14604 max 14604 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14604
|
||||
Ave neighs/atom = 28.523438
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.986 | 2.986 | 2.986 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -2309.6047 0 -2248.2266 17662.891
|
||||
110 835.77436 -2289.6119 0 -2248.1918 19964.211
|
||||
120 1067.0735 -2303.0587 0 -2248.2414 13767.101
|
||||
130 957.60664 -2293.7047 0 -2248.2139 14850.338
|
||||
140 865.12471 -2285.7774 0 -2248.1971 17101.553
|
||||
150 1104.7368 -2299.5468 0 -2248.2286 13031.988
|
||||
160 1077.1682 -2295.3841 0 -2248.2227 13615.019
|
||||
170 843.8591 -2277.9713 0 -2248.1911 18966.532
|
||||
180 1008.7412 -2286.922 0 -2248.2075 17275.649
|
||||
190 1237.9346 -2299.5487 0 -2248.2305 14334.006
|
||||
200 1060.2161 -2285.3352 0 -2248.1952 18999.834
|
||||
Loop time of 0.12412 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 69.610 ns/day, 0.345 hours/ns, 805.672 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12079 | 0.12079 | 0.12079 | 0.0 | 97.32
|
||||
Neigh | 0.001821 | 0.001821 | 0.001821 | 0.0 | 1.47
|
||||
Comm | 0.000407 | 0.000407 | 0.000407 | 0.0 | 0.33
|
||||
Output | 0.000159 | 0.000159 | 0.000159 | 0.0 | 0.13
|
||||
Modify | 0.000736 | 0.000736 | 0.000736 | 0.0 | 0.59
|
||||
Other | | 0.000203 | | | 0.16
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1007.00 ave 1007 max 1007 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 8884.00 ave 8884 max 8884 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8884
|
||||
Ave neighs/atom = 17.351562
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.205694
|
||||
ghost atom cutoff = 4.205694
|
||||
binsize = 2.102847, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod/c, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.980 | 2.980 | 2.980 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -2309.1331 0 -2247.755 20346.718
|
||||
110 831.93715 -2288.8853 0 -2247.7187 21758.195
|
||||
120 1077.6698 -2303.2846 0 -2247.7693 16036.053
|
||||
130 972.43247 -2294.1847 0 -2247.7467 16614.835
|
||||
140 815.76148 -2282.0495 0 -2247.7194 18310.116
|
||||
150 1072.7096 -2297.0491 0 -2247.7574 13896.767
|
||||
160 1061.8824 -2294.0028 0 -2247.7522 13663.179
|
||||
170 787.17244 -2273.8946 0 -2247.7175 18586.606
|
||||
180 932.5662 -2281.6828 0 -2247.7315 18154.167
|
||||
190 1205.7299 -2297.2769 0 -2247.7608 14504.136
|
||||
200 1022.5285 -2282.7039 0 -2247.7245 18710.495
|
||||
Loop time of 0.12973 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 66.600 ns/day, 0.360 hours/ns, 770.832 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12643 | 0.12643 | 0.12643 | 0.0 | 97.45
|
||||
Neigh | 0.001798 | 0.001798 | 0.001798 | 0.0 | 1.39
|
||||
Comm | 0.000421 | 0.000421 | 0.000421 | 0.0 | 0.32
|
||||
Output | 0.00016 | 0.00016 | 0.00016 | 0.0 | 0.12
|
||||
Modify | 0.000733 | 0.000733 | 0.000733 | 0.0 | 0.57
|
||||
Other | | 0.000192 | | | 0.15
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 958.000 ave 958 max 958 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 8416.00 ave 8416 max 8416 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8416
|
||||
Ave neighs/atom = 16.437500
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,547 +0,0 @@
|
|||
LAMMPS (30 Nov 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for threebody potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Stillinger-Weber model for silicon
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.77118
|
||||
ghost atom cutoff = 4.77118
|
||||
binsize = 2.38559, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2220.3392 0 -2101.4457 12358.626
|
||||
10 1006.0192 -2167.7053 0 -2101.3286 13892.426
|
||||
20 588.26396 -2139.7132 0 -2101.3117 11295.566
|
||||
30 990.55956 -2165.2164 0 -2101.3931 6279.0239
|
||||
40 700.12917 -2144.4279 0 -2101.3427 5594.2388
|
||||
50 523.64239 -2131.7796 0 -2101.3122 6013.0994
|
||||
60 989.47092 -2161.3716 0 -2101.3839 5819.2688
|
||||
70 877.27433 -2152.4432 0 -2101.3461 9116.6569
|
||||
80 800.80221 -2146.1371 0 -2101.313 11995.66
|
||||
90 1293.9689 -2176.9021 0 -2101.3848 11692.45
|
||||
100 1112.9699 -2162.7259 0 -2101.3478 12263.758
|
||||
Loop time of 0.0284905 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 303.259 ns/day, 0.079 hours/ns, 3509.942 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.022257 | 0.023383 | 0.025192 | 0.7 | 82.07
|
||||
Neigh | 0.00036 | 0.00037475 | 0.000387 | 0.0 | 1.32
|
||||
Comm | 0.002084 | 0.0039075 | 0.005034 | 1.8 | 13.72
|
||||
Output | 9.9e-05 | 0.00011525 | 0.00016 | 0.0 | 0.40
|
||||
Modify | 0.000428 | 0.00043675 | 0.000443 | 0.0 | 1.53
|
||||
Other | | 0.0002728 | | | 0.96
|
||||
|
||||
Nlocal: 128.000 ave 132 max 125 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 525.000 ave 528 max 521 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3497.00 ave 3619 max 3397 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 13988
|
||||
Ave neighs/atom = 27.320312
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.000 seconds
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
|
||||
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.6320004
|
||||
ghost atom cutoff = 5.6320004
|
||||
binsize = 2.8160002, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.967 | 2.967 | 2.968 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -625.76163 0 -564.38354 462129.66
|
||||
110 1502.8461 -649.55768 0 -564.45814 463413.45
|
||||
120 1926.4523 -674.71265 0 -564.53613 486338.88
|
||||
130 1152.6663 -621.47265 0 -564.37203 514892.19
|
||||
140 1762.244 -659.86941 0 -564.4985 488159.88
|
||||
150 1767.8665 -657.67179 0 -564.48386 466721.31
|
||||
160 1075.2874 -610.1281 0 -564.36709 470151.9
|
||||
170 1697.9313 -649.3684 0 -564.47208 467953.7
|
||||
180 1856.1197 -657.14338 0 -564.48754 488372.26
|
||||
190 1346.1107 -621.42432 0 -564.38065 511750.03
|
||||
200 1919.5266 -657.26587 0 -564.47797 488684.56
|
||||
Loop time of 0.084576 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 102.157 ns/day, 0.235 hours/ns, 1182.369 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.072089 | 0.074912 | 0.076672 | 0.7 | 88.57
|
||||
Neigh | 0.000745 | 0.0008125 | 0.000883 | 0.0 | 0.96
|
||||
Comm | 0.006054 | 0.0077975 | 0.010598 | 2.1 | 9.22
|
||||
Output | 0.000129 | 0.00015525 | 0.000219 | 0.0 | 0.18
|
||||
Modify | 0.000523 | 0.000578 | 0.000641 | 0.0 | 0.68
|
||||
Other | | 0.0003213 | | | 0.38
|
||||
|
||||
Nlocal: 128.000 ave 135 max 122 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 759.750 ave 770 max 751 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4336.00 ave 4563 max 4128 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 17344
|
||||
Ave neighs/atom = 33.875000
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Vashishta model for In/P
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style vashishta
|
||||
pair_coeff * * InP.vashishta In In In In P P P P
|
||||
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7
|
||||
ghost atom cutoff = 7
|
||||
binsize = 3.5, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair vashishta, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.988 | 2.988 | 2.988 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -1497.2988 0 -1435.9207 355619.19
|
||||
110 1250.545 -1504.5795 0 -1435.9786 345188.52
|
||||
120 1360.2275 -1509.3443 0 -1435.9801 333306.3
|
||||
130 1066.4516 -1487.9076 0 -1435.9076 334465.11
|
||||
140 1481.0477 -1513.0511 0 -1435.988 308725.1
|
||||
150 1216.1167 -1493.0774 0 -1435.9217 304249.09
|
||||
160 1211.4398 -1490.7459 0 -1435.9164 288897.09
|
||||
170 1542.2025 -1510.0774 0 -1435.9608 260104.14
|
||||
180 1302.9041 -1491.7765 0 -1435.8971 249514.04
|
||||
190 1332.3326 -1491.5271 0 -1435.9213 227537.99
|
||||
200 1352.1813 -1490.4513 0 -1435.9049 207626.42
|
||||
Loop time of 0.0404882 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 213.395 ns/day, 0.112 hours/ns, 2469.852 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.032713 | 0.033094 | 0.033544 | 0.2 | 81.74
|
||||
Neigh | 0.001251 | 0.0012875 | 0.001308 | 0.1 | 3.18
|
||||
Comm | 0.004788 | 0.005204 | 0.00557 | 0.4 | 12.85
|
||||
Output | 0.000123 | 0.0001385 | 0.000182 | 0.0 | 0.34
|
||||
Modify | 0.000492 | 0.00050725 | 0.000533 | 0.0 | 1.25
|
||||
Other | | 0.0002565 | | | 0.63
|
||||
|
||||
Nlocal: 128.000 ave 131 max 124 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Nghost: 1013.25 ave 1025 max 1002 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 9120.50 ave 9356 max 8868 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 36482
|
||||
Ave neighs/atom = 71.253906
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.948 | 2.948 | 2.948 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -3259.7676 0 -3198.3895 1912461.3
|
||||
110 1772.8268 -3301.5479 0 -3198.8218 1885295.6
|
||||
120 1169.7287 -3258.74 0 -3197.9294 1898705.2
|
||||
130 1308.5623 -3265.1338 0 -3197.5922 1894187.5
|
||||
140 1486.0361 -3274.951 0 -3197.776 1871927.6
|
||||
150 1419.0362 -3267.7302 0 -3197.2296 1925234.6
|
||||
160 1196.6689 -3250.1492 0 -3196.7078 1902235.1
|
||||
170 1707.5846 -3281.7658 0 -3196.9721 1863047.3
|
||||
180 1337.4358 -3254.9844 0 -3196.8222 1880420.9
|
||||
190 1441.8052 -3259.0364 0 -3196.3556 1904512.1
|
||||
200 1569.0317 -3265.0089 0 -3196.3328 1899462.7
|
||||
Loop time of 0.03452 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 250.290 ns/day, 0.096 hours/ns, 2896.871 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.029269 | 0.029729 | 0.030688 | 0.3 | 86.12
|
||||
Neigh | 0.000203 | 0.00023375 | 0.000271 | 0.0 | 0.68
|
||||
Comm | 0.00275 | 0.0036492 | 0.004132 | 0.9 | 10.57
|
||||
Output | 0.000104 | 0.000121 | 0.000165 | 0.0 | 0.35
|
||||
Modify | 0.000456 | 0.0004605 | 0.000463 | 0.0 | 1.33
|
||||
Other | | 0.000326 | | | 0.94
|
||||
|
||||
Nlocal: 128.000 ave 132 max 123 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 529.500 ave 533 max 524 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3651.00 ave 3783 max 3494 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 14604
|
||||
Ave neighs/atom = 28.523438
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.950 | 2.950 | 2.950 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -2309.6047 0 -2248.2266 17662.891
|
||||
110 835.77436 -2289.6119 0 -2248.1918 19964.211
|
||||
120 1067.0735 -2303.0587 0 -2248.2414 13767.101
|
||||
130 957.60664 -2293.7047 0 -2248.2139 14850.338
|
||||
140 865.12471 -2285.7774 0 -2248.1971 17101.553
|
||||
150 1104.7368 -2299.5468 0 -2248.2286 13031.988
|
||||
160 1077.1682 -2295.3841 0 -2248.2227 13615.019
|
||||
170 843.8591 -2277.9713 0 -2248.1911 18966.532
|
||||
180 1008.7412 -2286.922 0 -2248.2075 17275.649
|
||||
190 1237.9346 -2299.5487 0 -2248.2305 14334.006
|
||||
200 1060.2161 -2285.3352 0 -2248.1952 18999.834
|
||||
Loop time of 0.043388 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 199.133 ns/day, 0.121 hours/ns, 2304.785 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.033874 | 0.036197 | 0.037433 | 0.7 | 83.43
|
||||
Neigh | 0.000538 | 0.00055575 | 0.000575 | 0.0 | 1.28
|
||||
Comm | 0.004381 | 0.0055505 | 0.007783 | 1.8 | 12.79
|
||||
Output | 0.000141 | 0.0001635 | 0.000228 | 0.0 | 0.38
|
||||
Modify | 0.000532 | 0.000615 | 0.000692 | 0.0 | 1.42
|
||||
Other | | 0.000306 | | | 0.71
|
||||
|
||||
Nlocal: 128.000 ave 135 max 121 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 515.000 ave 518 max 508 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2221.00 ave 2328 max 2103 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 8884
|
||||
Ave neighs/atom = 17.351562
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style sw stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.205694
|
||||
ghost atom cutoff = 4.205694
|
||||
binsize = 2.102847, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod/c, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.950 | 2.950 | 2.950 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 1112.9699 -2309.1331 0 -2247.755 20346.718
|
||||
110 831.93715 -2288.8853 0 -2247.7187 21758.195
|
||||
120 1077.6698 -2303.2846 0 -2247.7693 16036.053
|
||||
130 972.43247 -2294.1847 0 -2247.7467 16614.835
|
||||
140 815.76148 -2282.0495 0 -2247.7194 18310.116
|
||||
150 1072.7096 -2297.0491 0 -2247.7574 13896.767
|
||||
160 1061.8824 -2294.0028 0 -2247.7522 13663.179
|
||||
170 787.17244 -2273.8946 0 -2247.7175 18586.606
|
||||
180 932.5662 -2281.6828 0 -2247.7315 18154.167
|
||||
190 1205.7299 -2297.2769 0 -2247.7608 14504.136
|
||||
200 1022.5285 -2282.7039 0 -2247.7245 18710.495
|
||||
Loop time of 0.0526065 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 164.238 ns/day, 0.146 hours/ns, 1900.906 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.044962 | 0.045875 | 0.046737 | 0.3 | 87.20
|
||||
Neigh | 0.000603 | 0.00062075 | 0.000646 | 0.0 | 1.18
|
||||
Comm | 0.003882 | 0.0047085 | 0.005598 | 1.0 | 8.95
|
||||
Output | 0.000159 | 0.0001995 | 0.000321 | 0.0 | 0.38
|
||||
Modify | 0.000767 | 0.0007775 | 0.000792 | 0.0 | 1.48
|
||||
Other | | 0.0004255 | | | 0.81
|
||||
|
||||
Nlocal: 128.000 ave 131 max 122 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 483.000 ave 485 max 479 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2104.00 ave 2169 max 2008 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 8416
|
||||
Ave neighs/atom = 16.437500
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
Loading…
Reference in New Issue