forked from lijiext/lammps
145 lines
5.2 KiB
Groff
145 lines
5.2 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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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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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 beween 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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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:75)
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WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75)
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Neighbor list info ...
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2 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 = 8.44413 Mbytes
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Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair
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0 -516632.19 -516632.19 3169.9382 3169.9382 46213.889 46213.889 49383.827 49383.827 49383.827 49383.827
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10 -517027.36 -517027.36 3099.1322 3099.1322 45891.84 45891.84 48990.972 48990.972 48990.972 48990.972
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20 -516828.06 -516828.06 3101.4321 3101.4321 45884.14 45884.14 48985.572 48985.572 48985.572 48985.572
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30 -517032.1 -517032.1 3198.5939 3198.5939 45793.571 45793.571 48992.165 48992.165 48992.165 48992.165
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40 -517095.56 -517095.56 3244.0797 3244.0797 45715.265 45715.265 48959.345 48959.345 48959.345 48959.345
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50 -517273.54 -517273.54 3274.9142 3274.9142 45665.997 45665.997 48940.911 48940.911 48940.911 48940.911
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Loop time of 1.20533 on 4 procs for 50 steps with 4500 atoms
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100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
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Performance: 7.168 ns/day 3.348 hours/ns 41.482 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 | 0.87053 | 0.90325 | 0.94364 | 2.8 | 74.94
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Bond | 0.00015402 | 0.00018191 | 0.00020909 | 0.2 | 0.02
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Kspace | 0.061657 | 0.10164 | 0.13394 | 8.4 | 8.43
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Neigh | 0.088292 | 0.088332 | 0.088373 | 0.0 | 7.33
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Comm | 0.017319 | 0.017806 | 0.018291 | 0.4 | 1.48
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Output | 0.07067 | 0.070706 | 0.070813 | 0.0 | 5.87
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Modify | 0.021655 | 0.021694 | 0.02173 | 0.0 | 1.80
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Other | | 0.001719 | | | 0.14
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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 = 2601984
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Ave neighs/atom = 578.219
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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: 0:00:01
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