136 lines
4.4 KiB
Groff
136 lines
4.4 KiB
Groff
LAMMPS (21 Aug 2015-ICMS)
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using 1 OpenMP thread(s) per MPI task
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units real
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atom_style full
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read_data data.spce
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orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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4500 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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3000 bonds
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reading angles ...
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1500 angles
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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pair_style lj/cut/coul/long 12.0 12.0
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kspace_style pppm 1.0e-4
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pair_coeff 1 1 0.15535 3.166
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pair_coeff * 2 0.0000 0.0000
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 1.0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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2 = max # of special neighbors
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neighbor 2.0 bin
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fix 1 all shake 0.0001 20 0 b 1 a 1
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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1500 = # of frozen angles
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fix 2 all nvt temp 300.0 300.0 100.0
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group one molecule 1 2
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6 atoms in group one
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# the following section shows equivalences between using the stress/tally compute and other computes and thermo keywords
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# compute per atom stress contributions
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compute spa all stress/atom NULL pair
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compute press all pressure NULL pair
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# compute stress contributions from one group with all
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compute c1 one stress/tally all
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# collect stress contributions from all with all
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compute c2 all stress/tally all
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compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] c_spa[1] c_spa[2] c_spa[3]
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compute red all reduce sum c_spa[1] c_spa[2] c_spa[3] c_c2[1] c_c2[2] c_c2[3]
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#
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variable spa equal -(c_red[1]+c_red[2]+c_red[3])/(3.0*vol)
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variable press equal -(c_red[4]+c_red[5]+c_red[6])/(3.0*vol)
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variable one equal (c_one[1]+c_one[2]+c_one[3])/3.0
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variable ref equal (c_one[4]+c_one[5]+c_one[6])/3.0
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#velocity all create 300 432567 dist uniform
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timestep 2.0
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thermo_style custom step c_press v_spa v_press v_one v_ref
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thermo 10
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run 50
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PPPM initialization ...
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G vector (1/distance) = 0.218482
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0319435
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estimated relative force accuracy = 9.61968e-05
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using double precision FFTs
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3d grid and FFT values/proc = 8000 3375
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WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
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WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75)
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 10 steps, check yes
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7 -> bins = 6 6 6
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Memory usage per processor = 24.631 Mbytes
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Step press spa press one ref
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0 26497.547 26497.547 26497.547 -2357033.6 -2357033.6
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10 23665.073 23665.073 23665.073 -2096057.3 -2096057.3
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20 23338.149 23338.149 23338.149 -2034283 -2034283
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30 25946.4 25946.4 25946.4 -2002817 -2002817
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40 27238.349 27238.349 27238.349 -2155411.5 -2155411.5
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50 27783.092 27783.092 27783.092 -1862190.3 -1862190.3
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Loop time of 4.15609 on 1 procs for 50 steps with 4500 atoms
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100.1% CPU use with 1 MPI tasks x 1 OpenMP threads
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Performance: 2.079 ns/day 11.545 hours/ns 12.031 timesteps/s
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MPI task timings breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 3.6444 | 3.6444 | 3.6444 | 0.0 | 87.69
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Bond | 0.0016105 | 0.0016105 | 0.0016105 | 0.0 | 0.04
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Kspace | 0.22345 | 0.22345 | 0.22345 | 0.0 | 5.38
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Neigh | 0.23588 | 0.23588 | 0.23588 | 0.0 | 5.68
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Comm | 0.010035 | 0.010035 | 0.010035 | 0.0 | 0.24
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Output | 0.0084085 | 0.0084085 | 0.0084085 | 0.0 | 0.20
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Modify | 0.029978 | 0.029978 | 0.029978 | 0.0 | 0.72
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Other | | 0.002368 | | | 0.06
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Nlocal: 4500 ave 4500 max 4500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 21226 ave 21226 max 21226 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2.60175e+06 ave 2.60175e+06 max 2.60175e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2601750
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Ave neighs/atom = 578.167
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Ave special neighs/atom = 2
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Neighbor list builds = 3
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Dangerous builds = 0
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Total wall time: 0:00:04
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