147 lines
6.3 KiB
Groff
147 lines
6.3 KiB
Groff
LAMMPS (8 Feb 2023)
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Processor partition = 5
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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 14.020019 -26051.605 -25689.152 7.3596437 382.89455 -789.8534
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20 15.752865 -25975.95 -25568.698 25.331469 430.21956 -594.00538
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30 17.181375 -25873.108 -25428.926 57.426817 469.23297 -181.78718
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40 11.772036 -25785.82 -25481.483 101.0172 321.50089 318.12089
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50 11.907234 -25813.038 -25505.205 157.46734 325.19321 630.72419
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60 12.407378 -25738.74 -25417.978 232.72881 338.85245 1042.2805
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70 11.569463 -25485.646 -25186.546 331.59654 315.9685 1219.4474
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80 12.423569 -25007.927 -24686.746 455.84829 339.29462 1585.4189
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90 11.222078 -24360.128 -24070.009 610.51406 306.48124 1770.0165
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100 10.746584 -23649.481 -23371.654 794.88729 293.49524 1751.0868
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110 10.688659 -22906.499 -22630.17 1011.4935 291.91326 1164.4167
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120 10.413653 -22131.25 -21862.03 1258.7802 284.40268 494.75639
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130 10.207431 -21354.621 -21090.733 1532.012 278.77066 -85.33744
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140 9.9484212 -20506.422 -20249.23 1833.2006 271.69695 -582.25635
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150 9.8592991 -19641.288 -19386.399 2150.5002 269.26298 -860.97106
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160 9.9476229 -18750.371 -18493.199 2484.32 271.67515 -781.67257
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170 9.9050652 -17855.648 -17599.576 2822.3305 270.51287 -564.01235
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180 9.9461836 -17049.565 -16792.431 3164.947 271.63584 -414.44888
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190 9.9650455 -16346.398 -16088.776 3500.8641 272.15097 -250.509
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200 10.114117 -15721.822 -15460.346 3824.3372 276.22219 -539.50977
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Loop time of 35.3336 on 1 procs for 200 steps with 8674 atoms
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Performance: 0.039 ns/day, 613.431 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
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98.8% 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 | 27.569 | 27.569 | 27.569 | 0.0 | 78.03
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Bond | 0.13166 | 0.13166 | 0.13166 | 0.0 | 0.37
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Kspace | 2.4398 | 2.4398 | 2.4398 | 0.0 | 6.91
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.12114 | 0.12114 | 0.12114 | 0.0 | 0.34
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Output | 0.0022707 | 0.0022707 | 0.0022707 | 0.0 | 0.01
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Modify | 5.0103 | 5.0103 | 5.0103 | 0.0 | 14.18
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Other | | 0.05914 | | | 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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