forked from lijiext/lammps
137 lines
5.1 KiB
Groff
137 lines
5.1 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 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 pe/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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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 c_c2
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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 force/tally only called from pair style (../compute_force_tally.cpp:75)
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WARNING: Compute force/tally only called from pair style (../compute_force_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 = 8.16441 Mbytes
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Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2
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0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0
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10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0
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20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0
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30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0
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40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0
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50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0
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Loop time of 1.13658 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: 7.602 ns/day 3.157 hours/ns 43.991 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 | 0.85795 | 0.89088 | 0.93636 | 3.0 | 78.38
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Bond | 3.4571e-05 | 4.4644e-05 | 5.4598e-05 | 0.1 | 0.00
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Kspace | 0.059847 | 0.1051 | 0.1384 | 8.9 | 9.25
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Neigh | 0.085891 | 0.085954 | 0.086 | 0.0 | 7.56
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Comm | 0.01758 | 0.018091 | 0.019178 | 0.5 | 1.59
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Output | 0.013697 | 0.013725 | 0.013805 | 0.0 | 1.21
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Modify | 0.021068 | 0.021137 | 0.021205 | 0.0 | 1.86
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Other | | 0.001656 | | | 0.15
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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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