103 lines
5.1 KiB
Groff
103 lines
5.1 KiB
Groff
LAMMPS (7 Jan 2022)
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# Numerical difference calculation
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# of Born matrix
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# adjustable parameters
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variable nsteps index 50 # length of run
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variable nthermo index 10 # thermo output interval
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variable nlat index 3 # size of box
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variable delta index 1.0e-6 # strain size
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variable temp index 0.3 # temperature
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
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region box block 0 3 0 ${nlat} 0 ${nlat}
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region box block 0 3 0 3 0 ${nlat}
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region box block 0 3 0 3 0 3
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create_box 1 box
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Created orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
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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 108 atoms
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using lattice units in orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
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create_atoms CPU = 0.000 seconds
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mass 1 1.0
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velocity all create ${temp} 87287 loop geom
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velocity all create 0.3 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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neighbor 0.0 bin
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neigh_modify every 1 delay 0 check no
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fix 1 all nve
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compute born all born/matrix
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thermo ${nthermo}
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thermo 10
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thermo_style custom step temp pe press c_born[*]
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run ${nsteps}
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run 50
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.5
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ghost atom cutoff = 2.5
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binsize = 1.25, bins = 5 5 5
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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
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bin: standard
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(2) compute born/matrix, occasional, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 2.561 | 2.561 | 2.561 Mbytes
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Step Temp PotEng Press c_born[1] c_born[2] c_born[3] c_born[4] c_born[5] c_born[6] c_born[7] c_born[8] c_born[9] c_born[10] c_born[11] c_born[12] c_born[13] c_born[14] c_born[15] c_born[16] c_born[17] c_born[18] c_born[19] c_born[20] c_born[21]
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0 0.3 -6.7733681 -5.9844023 411.5161 411.5161 411.5161 595.57522 595.57522 595.57522 595.57522 595.57522 -2.9143354e-15 -1.9984014e-15 1.8873791e-15 595.57522 -9.7560848e-15 -3.3029135e-15 -9.6311847e-15 -1.2281842e-14 -5.3568261e-15 -2.5257574e-15 -3.2196468e-15 -3.5804693e-15 -2.553513e-15
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10 0.25283594 -6.703292 -5.5569889 891.93989 928.15437 944.55768 872.69866 852.24088 816.0675 816.0675 852.24088 10.111334 3.6921122 -6.3839362 872.69866 -4.6709643 4.4335317 -9.7018557 -4.5201548 3.7624526 11.200776 11.200776 4.4335317 10.111334
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20 0.13298345 -6.5218396 -4.5683635 1958.2215 2130.5784 2172.9636 1516.3032 1426.6019 1323.0834 1323.0834 1426.6019 39.867158 11.406477 -25.845853 1516.3032 3.3483658 27.179119 -36.809191 10.147948 7.0018777 41.995438 41.995438 27.179119 39.867158
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30 0.089302796 -6.4604227 -4.1807379 2401.2346 2625.1676 2638.9312 1724.973 1625.4639 1602.8817 1602.8817 1625.4639 55.594925 -101.03316 -41.689385 1724.973 35.280816 26.589804 -40.046683 63.973353 -78.086653 41.559746 41.559746 26.589804 55.594925
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40 0.12149354 -6.5076059 -4.4000835 2234.612 2345.8821 2337.9552 1513.845 1486.9674 1564.2263 1564.2263 1486.9674 56.775913 -199.0226 -45.302207 1513.845 27.333643 -9.5839331 -16.768077 120.5015 -141.06684 17.802047 17.802047 -9.5839331 56.775913
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50 0.13053032 -6.5204024 -4.5064456 2097.1985 2270.3252 2180.7348 1458.5923 1396.6336 1507.4402 1507.4402 1396.6336 37.603097 -213.85355 22.82129 1458.5923 47.47204 -20.546302 54.328025 195.36071 -169.33495 -24.624815 -24.624815 -20.546302 37.603097
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Loop time of 0.00293746 on 4 procs for 50 steps with 108 atoms
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Performance: 7353280.980 tau/day, 17021.484 timesteps/s
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99.2% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.00037884 | 0.00040147 | 0.00041828 | 0.0 | 13.67
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Neigh | 0.0010222 | 0.0011142 | 0.0011623 | 0.2 | 37.93
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Comm | 0.00098867 | 0.0010309 | 0.0011341 | 0.2 | 35.09
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Output | 0.00030288 | 0.00031473 | 0.00034979 | 0.0 | 10.71
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Modify | 2.0147e-05 | 2.218e-05 | 2.3691e-05 | 0.0 | 0.76
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Other | | 5.406e-05 | | | 1.84
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Nlocal: 27 ave 31 max 25 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Nghost: 429.75 ave 450 max 409 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 727.25 ave 845 max 651 min
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Histogram: 1 0 1 1 0 0 0 0 0 1
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Total # of neighbors = 2909
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Ave neighs/atom = 26.935185
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Neighbor list builds = 50
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Dangerous builds not checked
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Total wall time: 0:00:00
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