185 lines
6.7 KiB
Groff
185 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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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 1.75e-06 on 4 procs for 0 steps with 4500 atoms
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group oxy type 1
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1500 atoms in group oxy
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group hyd type 2
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3000 atoms in group hyd
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# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords
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# compute pairwise energy between all oxygen and all hydrogen
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compute epa oxy group/group hyd pair yes kspace no boundary no
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# tally pairwise energy between all oygen and all hydrogen
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compute c1 oxy pe/tally hyd
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# tally pairwise energy between all atoms to compare with globals
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compute c2 all pe/tally all
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# collect per atom energies
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compute c3 all pe/atom pair
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# reduce over the first group only the per-atom data is storing VDW and Coulomb separately...
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compute oxy oxy reduce sum c_c1[1] c_c1[2]
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compute red all reduce sum c_c2[1] c_c2[2] c_c3
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# ... thus to get the same as compute group/group, we need to add the two
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# ... and multiply by 2.0 since compute group/group sums the pair energy, while we collect only for the first group.
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variable epa equal 2.0*(c_oxy[1]+c_oxy[2])
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# compute equivalent values to globals
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variable vdwl equal c_red[1]
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variable coul equal c_red[2]
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variable pe equal c_red[3]
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variable pair equal v_vdwl+v_coul
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variable eref equal epair-elong
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velocity all create 300 432567 dist uniform
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timestep 2.0
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# c_epa and v_epa, evdwl and v_vdwl, ecoul and v_coul, and the last 4 columns each should have identical value
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thermo_style custom step c_epa v_epa evdwl v_vdwl ecoul v_coul v_eref v_pe c_c2 v_pair
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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 pe/tally only called from pair style (../compute_pe_tally.cpp:77)
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WARNING: Compute pe/tally only called from pair style (../compute_pe_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) = 11.86 | 11.87 | 11.88 Mbytes
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Step c_epa v_epa E_vdwl v_vdwl E_coul v_coul v_eref v_pe c_c2 v_pair
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0 -516634.27 -516634.27 3169.9427 3169.9427 46212.482 46212.482 49382.425 49382.425 49382.425 49382.425
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10 -517027.35 -517027.35 3099.1374 3099.1374 45891.866 45891.866 48991.003 48991.003 48991.003 48991.003
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20 -516828.05 -516828.05 3101.4373 3101.4373 45884.156 45884.156 48985.594 48985.594 48985.594 48985.594
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30 -517032.07 -517032.07 3198.5951 3198.5951 45793.595 45793.595 48992.191 48992.191 48992.191 48992.191
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40 -517095.54 -517095.54 3244.0771 3244.0771 45715.292 45715.292 48959.369 48959.369 48959.369 48959.369
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50 -517273.5 -517273.5 3274.9097 3274.9097 45666.025 45666.025 48940.935 48940.935 48940.935 48940.935
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Loop time of 2.32344 on 4 procs for 50 steps with 4500 atoms
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Performance: 3.719 ns/day, 6.454 hours/ns, 21.520 timesteps/s
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64.0% 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 | 1.5561 | 1.8883 | 2.0327 | 14.1 | 81.27
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Bond | 8.8e-05 | 0.000116 | 0.000135 | 0.0 | 0.00
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Kspace | 0.094718 | 0.1933 | 0.26055 | 14.1 | 8.32
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Neigh | 0.085117 | 0.1073 | 0.1147 | 3.9 | 4.62
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Comm | 0.014156 | 0.017907 | 0.020005 | 1.8 | 0.77
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Output | 0.071634 | 0.090599 | 0.097665 | 3.6 | 3.90
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Modify | 0.019447 | 0.024101 | 0.026277 | 1.8 | 1.04
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Other | | 0.001804 | | | 0.08
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Nlocal: 1125 ave 1148 max 1097 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Nghost: 12212.5 ave 12269 max 12162 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Neighs: 650496 ave 675112 max 631353 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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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: 0:00:02
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