148 lines
5.7 KiB
Groff
148 lines
5.7 KiB
Groff
LAMMPS (5 Jun 2019)
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Reading data file ...
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orthogonal box = (-25 -25 -25) to (25 25 25)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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44 atoms
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reading velocities ...
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44 velocities
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scanning bonds ...
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9 = max bonds/atom
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scanning angles ...
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21 = max angles/atom
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scanning dihedrals ...
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29 = max dihedrals/atom
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scanning impropers ...
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29 = max impropers/atom
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reading bonds ...
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42 bonds
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reading angles ...
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74 angles
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reading dihedrals ...
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100 dihedrals
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reading impropers ...
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44 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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4 = max # of 1-2 neighbors
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6 = max # of 1-3 neighbors
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12 = max # of 1-4 neighbors
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41 = max # of special neighbors
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special bonds CPU = 0.000163256 secs
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read_data CPU = 0.0244579 secs
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Read molecule mol1:
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18 atoms with max type 8
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16 bonds with max type 14
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25 angles with max type 28
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23 dihedrals with max type 36
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14 impropers with max type 11
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Read molecule mol2:
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18 atoms with max type 9
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17 bonds with max type 13
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31 angles with max type 27
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39 dihedrals with max type 33
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20 impropers with max type 1
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Read molecule mol3:
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15 atoms with max type 9
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14 bonds with max type 13
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25 angles with max type 27
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30 dihedrals with max type 33
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16 impropers with max type 1
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Read molecule mol4:
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15 atoms with max type 11
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13 bonds with max type 15
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19 angles with max type 29
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16 dihedrals with max type 32
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10 impropers with max type 13
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WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
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WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
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dynamic group bond_react_MASTER_group defined
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:319)
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G vector (1/distance) = 0.0534597
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grid = 2 2 2
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0402256
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estimated relative force accuracy = 0.000121138
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using double precision FFTs
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3d grid and FFT values/proc = 252 2
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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 = 10.5
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ghost atom cutoff = 10.5
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binsize = 5.25, bins = 10 10 10
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) pair lj/class2/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) fix bond/react, 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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Setting up Verlet run ...
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Unit style : real
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Current step : 0
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Time step : 1
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WARNING: Inconsistent image flags (../domain.cpp:784)
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Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
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Step Temp Press Density f_myrxns[1] f_myrxns[2]
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0 300 346.78165 0.0034851739 0 0
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50 416.49412 -20.293038 0.0034851739 1 0
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100 746.49323 91.912227 0.0034851739 1 1
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150 515.15907 -1.4024709 0.0034851739 1 1
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200 441.14572 -19.333087 0.0034851739 1 1
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250 376.40996 30.717679 0.0034851739 1 1
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300 326.15127 -3.0433799 0.0034851739 1 1
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350 326.21116 6.235391 0.0034851739 1 1
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400 366.48556 3.9807338 0.0034851739 1 1
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450 313.79097 7.6674629 0.0034851739 1 1
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500 278.89836 14.102052 0.0034851739 1 1
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550 267.50214 18.241417 0.0034851739 1 1
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600 276.28064 7.4649611 0.0034851739 1 1
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650 255.26713 -8.5258573 0.0034851739 1 1
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700 258.59752 -5.3341215 0.0034851739 1 1
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750 263.71264 33.369869 0.0034851739 1 1
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800 246.22976 -15.349137 0.0034851739 1 1
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850 255.93887 16.331669 0.0034851739 1 1
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900 239.72525 -0.20075789 0.0034851739 1 1
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950 213.73064 12.17619 0.0034851739 1 1
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1000 218.25094 -9.0955642 0.0034851739 1 1
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Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms
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Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s
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99.8% 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 | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56
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Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62
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Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04
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Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16
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Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31
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Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13
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Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91
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Other | | 0.0007123 | | | 0.28
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Nlocal: 11 ave 29 max 0 min
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Histogram: 1 1 0 0 1 0 0 0 0 1
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Nghost: 25 ave 31 max 12 min
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Histogram: 1 0 0 0 0 0 0 0 2 1
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Neighs: 204.5 ave 443 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Total # of neighbors = 818
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Ave neighs/atom = 18.5909
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Ave special neighs/atom = 9.77273
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Neighbor list builds = 1000
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:00
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