147 lines
6.3 KiB
Groff
147 lines
6.3 KiB
Groff
LAMMPS (8 Feb 2023)
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Processor partition = 6
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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variable ibead uloop 8 pad
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units real
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neigh_modify delay 2 every 1
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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pair_style lj/charmm/coul/long 11 12
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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read_data system.data
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Reading data file ...
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orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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8674 atoms
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reading velocities ...
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8674 velocities
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scanning bonds ...
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4 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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18 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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reading bonds ...
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5869 bonds
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reading angles ...
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3264 angles
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reading dihedrals ...
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708 dihedrals
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reading impropers ...
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38 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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9 = max # of 1-3 neighbors
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17 = max # of 1-4 neighbors
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21 = max # of special neighbors
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special bonds CPU = 0.004 seconds
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read_data CPU = 0.139 seconds
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#read_restart system_${ibead}.rest1
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special_bonds charmm
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fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
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thermo 10
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thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3]
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thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
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timestep 0.08
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# restart 100 system_${ibead}.rest1 system_${ibead}.rest2
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group prot id <= 256
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256 atoms in group prot
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# dump 1 prot dcd 100 prot_${ibead}.dcd
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run 200
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.22071363
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grid = 20 20 20
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stencil order = 5
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estimated absolute RMS force accuracy = 0.024910591
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estimated relative force accuracy = 7.5017505e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 15625 8000
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Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 2 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 = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmm/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
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bin: standard
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WARNING: Inconsistent image flags (src/domain.cpp:815)
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Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
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Step Temp PotEng TotEng espring T_ring virial
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0 306.20099 -26166.171 -18250.089 0 0 -676.31071
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10 14.02002 -25861.333 -25498.879 45.268744 382.8946 -722.47561
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20 15.752886 -25289.441 -24882.188 135.42322 430.22014 -482.48877
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30 17.181691 -24659.071 -24214.881 316.76011 469.24159 115.80651
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40 11.76983 -24165.345 -23861.065 544.21259 321.44065 710.32531
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50 11.904289 -24034.29 -23726.534 812.12301 325.1128 1057.7309
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60 12.409559 -23964.986 -23644.167 1115.614 338.91201 1490.6948
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70 11.53241 -23718.204 -23420.061 1442.0767 314.95657 1654.3805
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80 12.377693 -23123.366 -22803.371 1794.1167 338.04173 2019.537
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90 11.21341 -22129.26 -21839.365 2172.5974 306.24451 2037.5349
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100 10.778526 -20922.126 -20643.474 2553.3173 294.36759 1922.6067
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110 10.656113 -19666.579 -19391.091 2944.1884 291.02442 1115.4533
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120 10.374573 -18508.305 -18240.096 3331.7564 283.3354 401.15223
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130 10.057534 -17613.953 -17353.939 3714.254 274.67688 -248.49945
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140 9.7972276 -16953.726 -16700.443 4076.4386 267.56777 -841.79062
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150 9.8266474 -16502.516 -16248.472 4422.7241 268.37124 -1155.8854
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160 9.9655308 -16127.142 -15869.507 4748.4514 272.16422 -1094.1994
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170 9.9292831 -15818.923 -15562.225 5045.9331 271.17428 -884.00102
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180 10.157102 -15473.205 -15210.618 5313.5511 277.39613 -553.25499
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190 10.068063 -15095.751 -14835.466 5545.0144 274.96443 -237.36247
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200 10.155151 -14754.017 -14491.48 5742.1288 277.34285 -332.89648
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Loop time of 35.3338 on 1 procs for 200 steps with 8674 atoms
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Performance: 0.039 ns/day, 613.434 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
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97.5% CPU use with 1 MPI tasks x 1 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 | 27.875 | 27.875 | 27.875 | 0.0 | 78.89
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Bond | 0.12707 | 0.12707 | 0.12707 | 0.0 | 0.36
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Kspace | 2.4348 | 2.4348 | 2.4348 | 0.0 | 6.89
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.11906 | 0.11906 | 0.11906 | 0.0 | 0.34
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Output | 0.0021503 | 0.0021503 | 0.0021503 | 0.0 | 0.01
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Modify | 4.7164 | 4.7164 | 4.7164 | 0.0 | 13.35
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Other | | 0.05955 | | | 0.17
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Nlocal: 8674 ave 8674 max 8674 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 27366 ave 27366 max 27366 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 4485849
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Ave neighs/atom = 517.16036
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Ave special neighs/atom = 2.2573207
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:35
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