forked from lijiext/lammps
178 lines
6.7 KiB
Groff
178 lines
6.7 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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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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# 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 = 8000 3375
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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) = 26.54 | 26.54 | 26.54 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 3e-06 on 1 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 force/tally compute and other computes and thermo keywords
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# compute pairwise force between two molecules and everybody
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compute fpa one group/group all pair yes kspace no boundary no
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# tally pairwise force between two molecules and the all molecules
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compute c1 one force/tally all
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# tally the force of all with all (should be zero)
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compute c2 all force/tally all
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# collect per atom data. only reduce over the first group.
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compute one one reduce sum c_c1[1] c_c1[2] c_c1[3]
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compute red all reduce sum c_c2[1] c_c2[2] c_c2[3]
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# determine magnitude of force
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variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3])
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variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3])
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# round to 10**-10 absolute precision.
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variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10
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variable all equal round(1e10*c_c2)*1e-10
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velocity all create 300 432567 dist uniform
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timestep 2.0
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# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero
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thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all
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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 = 8000 3375
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WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77)
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WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77)
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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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2 neighbor lists, perpetual/occasional/extra = 1 1 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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(2) compute group/group, 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) = 28.47 | 28.47 | 28.47 Mbytes
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Step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all
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0 22.7331 22.7331 22.7331 -17.068295 -17.068295 -8.8348335 -8.8348334 -12.141369 -12.141369 0 0
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10 11.736901 11.736901 11.736901 -3.3897029 -3.3897029 9.1193856 9.1193856 -6.5651786 -6.5651786 0 0
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20 5.6120339 5.6120339 5.6120339 -0.60046861 -0.60046861 -4.4481306 -4.4481306 3.3687528 3.3687528 0 0
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30 17.29261 17.29261 17.29261 6.179302 6.179302 -10.593979 -10.593979 12.190906 12.190906 0 0
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40 18.664433 18.664433 18.664433 5.4727782 5.4727782 -6.9329319 -6.9329319 16.442148 16.442148 0 0
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50 12.130407 12.130407 12.130407 -1.0321196 -1.0321196 8.0035558 8.0035558 -9.0567428 -9.0567428 0 0
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Loop time of 13.9507 on 1 procs for 50 steps with 4500 atoms
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Performance: 0.619 ns/day, 38.752 hours/ns, 3.584 timesteps/s
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32.0% CPU use with 1 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 | 12.594 | 12.594 | 12.594 | 0.0 | 90.27
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Bond | 7.3e-05 | 7.3e-05 | 7.3e-05 | 0.0 | 0.00
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Kspace | 0.56296 | 0.56296 | 0.56296 | 0.0 | 4.04
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Neigh | 0.65858 | 0.65858 | 0.65858 | 0.0 | 4.72
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Comm | 0.019093 | 0.019093 | 0.019093 | 0.0 | 0.14
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Output | 0.055025 | 0.055025 | 0.055025 | 0.0 | 0.39
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Modify | 0.057276 | 0.057276 | 0.057276 | 0.0 | 0.41
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Other | | 0.004003 | | | 0.03
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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: 21131 ave 21131 max 21131 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2601983
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Ave neighs/atom = 578.218
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Ave special neighs/atom = 2
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Neighbor list builds = 4
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Dangerous builds = 1
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Total wall time: 0:00:15
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