149 lines
5.7 KiB
Groff
149 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 = 0.000178751 secs
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read_data CPU = 0.0385782 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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dynamic group statted_grp_REACT 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) = 34.42 | 34.77 | 35.45 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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50 293.70542 -52.547388 0.0034851739 1 0
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100 276.36755 54.81826 0.0034851739 1 1
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150 448.65869 16.874435 0.0034851739 1 1
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200 379.84257 11.578545 0.0034851739 1 1
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250 298.21983 90.656585 0.0034851739 1 1
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300 333.3111 -30.139607 0.0034851739 1 1
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350 266.57108 6.4505134 0.0034851739 1 1
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400 264.05476 10.513204 0.0034851739 1 1
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450 250.70418 -18.635379 0.0034851739 1 1
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500 261.21632 10.231013 0.0034851739 1 1
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550 309.89024 -8.8299506 0.0034851739 1 1
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600 373.45851 30.368993 0.0034851739 1 1
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650 338.26242 9.0362267 0.0034851739 1 1
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700 295.67794 -5.6007538 0.0034851739 1 1
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750 310.86563 -59.228181 0.0034851739 1 1
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800 286.22678 -9.9022407 0.0034851739 1 1
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850 218.42135 27.845352 0.0034851739 1 1
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900 259.62551 24.216336 0.0034851739 1 1
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950 250.21307 -14.560985 0.0034851739 1 1
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1000 274.29245 -0.38768626 0.0034851739 1 1
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Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms
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Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s
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98.6% 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 | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85
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Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84
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Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16
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Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78
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Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03
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Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93
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Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10
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Other | | 0.0008281 | | | 0.31
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Nlocal: 11 ave 21 max 0 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 32.5 ave 43 max 23 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 185 ave 376 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 740
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Ave neighs/atom = 16.8182
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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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