forked from lijiext/lammps
236 lines
8.2 KiB
Groff
236 lines
8.2 KiB
Groff
LAMMPS (7 Aug 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
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using 1 OpenMP thread(s) per MPI task
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# Steinhardt-Nelson bond orientational order parameters for icosahedral cluster
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# W_6_hat is sensitive to icosohedral order
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variable rcut equal 1.2 # a bit bigger than LJ Rmin
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variable rcutred equal 0.75 # a bit bigger than 1/sqrt(2)
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# create a perfect fcc crystallite
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atom_style atomic
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boundary s s s
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lattice fcc 1.0 # neighbors at LJ Rmin
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Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
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region box block 0 2 0 2 0 2
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create_box 1 box
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Created orthogonal box = (0 0 0) to (3.1748 3.1748 3.1748)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 63 atoms
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create_atoms CPU = 0.000592947 secs
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mass 1 1.0
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region centralatom sphere 1 1 1 0.0 side in
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group centralatom region centralatom
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1 atoms in group centralatom
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region mysphere sphere 1 1 1 ${rcutred} side out
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region mysphere sphere 1 1 1 0.75 side out
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delete_atoms region mysphere
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Deleted 50 atoms, new total = 13
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# LJ potential
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pair_style lj/cut 100.0
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pair_coeff * * 1.0 1.0 100.0
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# define output for central atom
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compute qlwlhat all orientorder/atom wl/hat yes cutoff ${rcut} nnn NULL
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compute qlwlhat all orientorder/atom wl/hat yes cutoff 1.2 nnn NULL
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compute avql centralatom reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5]
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compute avwlhat centralatom reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10]
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variable q6 equal c_avql[2]
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variable w6hat equal c_avwlhat[2]
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compute mype all pe/atom
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compute centralatompe centralatom reduce ave c_mype
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# gently equilibrate the crystallite
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velocity all create 0.001 482748
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fix 1 all nve
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neighbor 0.3 bin
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neigh_modify every 1 check no delay 0
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timestep 0.003
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thermo_style custom step temp epair etotal c_centralatompe v_q6 v_w6hat
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thermo 10
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run 10
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 100.3
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ghost atom cutoff = 100.3
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binsize = 50.15, bins = 1 1 1
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) compute orientorder/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 60.76 | 60.76 | 60.76 Mbytes
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Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat
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0 0.001 -3.134107 -3.1327224 -6 0.57452426 -0.013160601
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10 0.0021821015 -3.1357444 -3.132723 -5.9994885 0.57450756 -0.013160431
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Loop time of 0.15387 on 4 procs for 10 steps with 13 atoms
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Performance: 16845.410 tau/day, 64.990 timesteps/s
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99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 9.7752e-06 | 1.7285e-05 | 2.9087e-05 | 0.0 | 0.01
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Neigh | 0.055218 | 0.065482 | 0.073829 | 2.9 | 42.56
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Comm | 0.0061202 | 0.018279 | 0.028283 | 6.3 | 11.88
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Output | 0.020282 | 0.020287 | 0.020298 | 0.0 | 13.18
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Modify | 2.7895e-05 | 2.8968e-05 | 2.9802e-05 | 0.0 | 0.02
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Other | | 0.04978 | | | 32.35
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Nlocal: 3.25 ave 4 max 2 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Nghost: 9.75 ave 11 max 9 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Neighs: 19.5 ave 35 max 7 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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FullNghs: 39 ave 48 max 24 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Total # of neighbors = 156
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Ave neighs/atom = 12
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Neighbor list builds = 10
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Dangerous builds not checked
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# quench to icosehedral cluster
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minimize 1.0e-10 1.0e-6 100 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
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Per MPI rank memory allocation (min/avg/max) = 112.9 | 112.9 | 112.9 Mbytes
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Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat
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10 0.0021821015 -3.1357444 -3.132723 -5.9994885 0.57450756 -0.013160431
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20 0.0021821015 -3.1449613 -3.1419399 -5.9764731 0.57452454 -0.01316152
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30 0.0021821015 -3.3366586 -3.3336372 -5.7717004 0.63679987 -0.16411081
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40 0.0021821015 -3.4097262 -3.4067048 -5.6321229 0.66331761 -0.16975374
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49 0.0021821015 -3.409754 -3.4067326 -5.6323347 0.66332496 -0.16975389
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Loop time of 0.0932837 on 4 procs for 39 steps with 13 atoms
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97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-3.13574438249 -3.40975395519 -3.40975395529
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Force two-norm initial, final = 6.46606 0.000429142
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Force max component initial, final = 1.45519 0.000196446
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Final line search alpha, max atom move = 1 0.000196446
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Iterations, force evaluations = 39 98
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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 | 5.4121e-05 | 9.0897e-05 | 0.00014281 | 0.0 | 0.10
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Neigh | 0.019662 | 0.02379 | 0.03176 | 3.0 | 25.50
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Comm | 0.0072601 | 0.014304 | 0.019575 | 3.8 | 15.33
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Output | 0.033646 | 0.033654 | 0.03368 | 0.0 | 36.08
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.02144 | | | 22.99
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Nlocal: 3.25 ave 6 max 1 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Nghost: 9.75 ave 12 max 7 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 19.5 ave 49 max 1 min
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Histogram: 2 0 0 0 1 0 0 0 0 1
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FullNghs: 39 ave 72 max 12 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Total # of neighbors = 156
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Ave neighs/atom = 12
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Neighbor list builds = 5
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Dangerous builds not checked
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# check Q_l values
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print " "
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print "*******************************************************************"
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*******************************************************************
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print " "
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print "Comparison with reference values of Q_l "
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Comparison with reference values of Q_l
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print " [Table I in W. Mickel, S. C. Kapfer,"
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[Table I in W. Mickel, S. C. Kapfer,
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print " G. E. Schroeder-Turkand, K. Mecke, "
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G. E. Schroeder-Turkand, K. Mecke,
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print " J. Chem. Phys. 138, 044501 (2013).]"
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J. Chem. Phys. 138, 044501 (2013).]
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print " "
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variable q4ref equal 0.0
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variable q6ref equal 0.663
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variable q8ref equal 0.0
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variable q10ref equal 0.363
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variable q12ref equal 0.585
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variable q4 equal c_avql[1]
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variable q6 equal c_avql[2]
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variable q8 equal c_avql[3]
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variable q10 equal c_avql[4]
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variable q12 equal c_avql[5]
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print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)"
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q4 = 0.000001 delta = 0.0000
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print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
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q6 = 0.663325 delta = 0.0003
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print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
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q8 = 0.000002 delta = 0.0000
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print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
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q10 = 0.362951 delta = -0.0000
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print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
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q12 = 0.585423 delta = 0.0004
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# check W_l_hat values
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print " "
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print "Comparison with reference values of W_l_hat"
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Comparison with reference values of W_l_hat
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print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, "
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[Table I in P. Steinhardt, D. Nelson, and M. Ronchetti,
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print " Phys. Rev. B 28, 784 (1983).]"
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Phys. Rev. B 28, 784 (1983).]
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print " "
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variable w6hatref equal -0.169754
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variable w10hatref equal -0.093967
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variable w4hat equal c_avwlhat[1]
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variable w6hat equal c_avwlhat[2]
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variable w8hat equal c_avwlhat[3]
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variable w10hat equal c_avwlhat[4]
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variable w12hat equal c_avwlhat[5]
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print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
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w6hat = -0.169754 delta = 0.000000
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print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
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w10hat = -0.093968 delta = -0.000001
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print " "
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print "*******************************************************************"
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*******************************************************************
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print " "
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Total wall time: 0:00:00
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