forked from lijiext/lammps
159 lines
5.3 KiB
Groff
159 lines
5.3 KiB
Groff
LAMMPS (19 May 2017)
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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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2 by 2 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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# make certain that shake constraints are satisfied
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run 0 post no
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PPPM initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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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 = 3380 960
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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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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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/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) = 10.6 | 10.61 | 10.61 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -16692.358 0 -16692.358 -1289.8319
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Loop time of 4e-06 on 4 procs for 0 steps with 4500 atoms
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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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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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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 = 3380 960
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WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79)
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WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79)
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Per MPI rank memory allocation (min/avg/max) = 15.25 | 15.26 | 15.27 Mbytes
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Step c_press v_spa v_press v_one v_ref
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0 26496.811 26496.811 26496.811 -2356992.7 -2356992.7
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10 23665.129 23665.129 23665.129 -2096059 -2096059
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20 23338.197 23338.197 23338.197 -2034284.1 -2034284.1
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30 25946.434 25946.434 25946.434 -2002815.3 -2002815.3
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40 27238.374 27238.374 27238.374 -2155408.7 -2155408.7
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50 27783.107 27783.107 27783.107 -1862191.5 -1862191.5
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Loop time of 4.32017 on 4 procs for 50 steps with 4500 atoms
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Performance: 2.000 ns/day, 12.000 hours/ns, 11.574 timesteps/s
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31.8% 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 | 3.5816 | 3.6917 | 3.839 | 4.9 | 85.45
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Bond | 0.001579 | 0.0016563 | 0.001709 | 0.1 | 0.04
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Kspace | 0.22505 | 0.3716 | 0.48023 | 15.3 | 8.60
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Neigh | 0.14558 | 0.14568 | 0.14575 | 0.0 | 3.37
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Comm | 0.032009 | 0.03441 | 0.036274 | 0.8 | 0.80
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Output | 0.02253 | 0.023115 | 0.024844 | 0.7 | 0.54
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Modify | 0.046954 | 0.047086 | 0.047132 | 0.0 | 1.09
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Other | | 0.004935 | | | 0.11
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Nlocal: 1125 ave 1154 max 1092 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Nghost: 12263.5 ave 12300 max 12219 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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Neighs: 650438 ave 678787 max 626279 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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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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