forked from lijiext/lammps
253 lines
12 KiB
Plaintext
253 lines
12 KiB
Plaintext
LAMMPS (17 Jan 2018)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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using 1 OpenMP thread(s) per MPI task
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# Created by charmm2lammps v1.9.1 on Sun Jan 28 05:46:18 EST 2018
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# Command: charmm2lammps.pl -water -ions -border=2.0 all27_na 1ac7
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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 8 12
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pair_modify mix arithmetic
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kspace_style pppm 1e-6
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read_data 1ac7.data
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orthogonal box = (-14.087 -1.88253 -5.44214) to (10.545 22.7495 33.9691)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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1968 atoms
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scanning bonds ...
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3 = 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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14 = 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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1516 bonds
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reading angles ...
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1491 angles
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reading dihedrals ...
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1659 dihedrals
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reading impropers ...
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43 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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18 = max # of 1-4 neighbors
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20 = max # of special neighbors
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special_bonds charmm
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thermo 10
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thermo_style multi
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timestep 1.0
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minimize 0.0 0.0 50 200
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
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PPPM initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.280406
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grid = 30 30 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000302577
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estimated relative force accuracy = 9.11202e-07
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using double precision FFTs
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3d grid and FFT values/proc = 21978 9000
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Neighbor list info ...
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update every 1 steps, delay 0 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 = 4 4 6
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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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 17.89 | 17.89 | 17.9 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = 16382.0106 KinEng = 0.0000 Temp = 0.0000
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PotEng = 16382.0106 E_bond = 12014.3479 E_angle = 5414.5475
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E_dihed = 557.2338 E_impro = 0.0516 E_vdwl = 1174.9839
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E_coul = 28273.7003 E_long = -31052.8544 Press = -17947.7297
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---------------- Step 10 ----- CPU = 0.2030 (sec) ----------------
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TotEng = -1386.3677 KinEng = 0.0000 Temp = 0.0000
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PotEng = -1386.3677 E_bond = 238.0964 E_angle = 2167.9109
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E_dihed = 556.7458 E_impro = 2.3622 E_vdwl = -407.1366
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E_coul = 27803.2765 E_long = -31747.6229 Press = -902.5957
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---------------- Step 20 ----- CPU = 0.4523 (sec) ----------------
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TotEng = -4643.9749 KinEng = 0.0000 Temp = 0.0000
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PotEng = -4643.9749 E_bond = 186.6424 E_angle = 546.1482
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E_dihed = 557.6115 E_impro = 3.7530 E_vdwl = -572.4168
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E_coul = 27184.6593 E_long = -32550.3724 Press = -13499.9676
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---------------- Step 30 ----- CPU = 0.7954 (sec) ----------------
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TotEng = -5356.2261 KinEng = 0.0000 Temp = 0.0000
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PotEng = -5356.2261 E_bond = 150.5494 E_angle = 451.1209
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E_dihed = 548.4804 E_impro = 3.8629 E_vdwl = -587.7229
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E_coul = 26908.1173 E_long = -32830.6340 Press = -12635.5249
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---------------- Step 40 ----- CPU = 1.1432 (sec) ----------------
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TotEng = -5814.9675 KinEng = 0.0000 Temp = 0.0000
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PotEng = -5814.9675 E_bond = 145.1741 E_angle = 424.9449
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E_dihed = 539.7599 E_impro = 3.8304 E_vdwl = -559.2034
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E_coul = 26618.2861 E_long = -32987.7596 Press = -13254.1066
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---------------- Step 50 ----- CPU = 1.4855 (sec) ----------------
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TotEng = -6207.1556 KinEng = 0.0000 Temp = 0.0000
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PotEng = -6207.1556 E_bond = 172.5209 E_angle = 400.9621
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E_dihed = 532.0702 E_impro = 3.4517 E_vdwl = -491.3979
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E_coul = 26261.2546 E_long = -33086.0173 Press = -13942.2342
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Loop time of 1.48576 on 4 procs for 50 steps with 1968 atoms
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98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = max iterations
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Energy initial, next-to-last, final =
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16382.0106166 -6167.68761847 -6207.15563509
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Force two-norm initial, final = 9111.03 289.249
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Force max component initial, final = 2253.01 63.7887
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Final line search alpha, max atom move = 0.000835537 0.0532979
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Iterations, force evaluations = 50 75
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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 | 0.86139 | 0.95604 | 1.1156 | 10.8 | 64.35
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Bond | 0.0054429 | 0.012373 | 0.015879 | 3.7 | 0.83
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Kspace | 0.29818 | 0.45076 | 0.54304 | 15.1 | 30.34
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Neigh | 0.037995 | 0.038014 | 0.038038 | 0.0 | 2.56
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Comm | 0.021986 | 0.022179 | 0.022257 | 0.1 | 1.49
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Output | 0.00028157 | 0.00048172 | 0.0010796 | 0.0 | 0.03
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.005911 | | | 0.40
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Nlocal: 492 ave 538 max 472 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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Nghost: 8001.25 ave 8242 max 7756 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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Neighs: 232207 ave 275971 max 203927 min
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Histogram: 2 0 0 0 1 0 0 0 0 1
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Total # of neighbors = 928828
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Ave neighs/atom = 471.965
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Ave special neighs/atom = 4.4065
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Neighbor list builds = 3
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Dangerous builds = 0
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reset_timestep 0
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fix 1 all nve
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fix 2 all shake 1e-6 500 0 m 1.0 a 93
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112 = # of size 2 clusters
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26 = # of size 3 clusters
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6 = # of size 4 clusters
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475 = # of frozen angles
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velocity all create 0.0 12345678 dist uniform
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restart 500 1ac7.restart1 1ac7.restart2
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dump 1 all atom 100 1ac7.dump
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dump_modify 1 image yes scale yes
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thermo 100
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run 1000
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PPPM initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.280406
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grid = 30 30 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000302577
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estimated relative force accuracy = 9.11202e-07
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using double precision FFTs
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3d grid and FFT values/proc = 21978 9000
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Per MPI rank memory allocation (min/avg/max) = 18.67 | 18.68 | 18.68 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -6345.9602 KinEng = 0.0000 Temp = 0.0000
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PotEng = -6345.9602 E_bond = 118.9251 E_angle = 315.7533
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E_dihed = 532.0702 E_impro = 3.4517 E_vdwl = -491.3979
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E_coul = 26261.2546 E_long = -33086.0173 Press = -13274.6498
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---------------- Step 100 ----- CPU = 1.5587 (sec) ----------------
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TotEng = -6089.2059 KinEng = 737.9545 Temp = 172.9635
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PotEng = -6827.1604 E_bond = 99.2610 E_angle = 293.4796
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E_dihed = 518.3926 E_impro = 3.4260 E_vdwl = -53.1737
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E_coul = 25455.9659 E_long = -33144.5118 Press = -7582.0585
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---------------- Step 200 ----- CPU = 3.1808 (sec) ----------------
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TotEng = -6089.3334 KinEng = 1048.0815 Temp = 245.6518
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PotEng = -7137.4150 E_bond = 105.4181 E_angle = 314.1091
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E_dihed = 525.7575 E_impro = 2.0633 E_vdwl = 549.1716
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E_coul = 24511.2323 E_long = -33145.1669 Press = -1214.5095
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---------------- Step 300 ----- CPU = 4.8699 (sec) ----------------
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TotEng = -6089.3928 KinEng = 1163.3028 Temp = 272.6576
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PotEng = -7252.6956 E_bond = 101.6270 E_angle = 351.8828
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E_dihed = 525.2212 E_impro = 3.1286 E_vdwl = 516.2458
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E_coul = 24404.4712 E_long = -33155.2722 Press = -2323.5317
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---------------- Step 400 ----- CPU = 6.5652 (sec) ----------------
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TotEng = -6089.4987 KinEng = 1182.3885 Temp = 277.1310
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PotEng = -7271.8872 E_bond = 114.0720 E_angle = 325.6458
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E_dihed = 516.7310 E_impro = 3.1876 E_vdwl = 522.6196
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E_coul = 24402.0712 E_long = -33156.2144 Press = -2169.9377
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---------------- Step 500 ----- CPU = 8.2547 (sec) ----------------
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TotEng = -6089.4538 KinEng = 1158.7955 Temp = 271.6012
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PotEng = -7248.2493 E_bond = 103.0865 E_angle = 339.1037
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E_dihed = 522.7155 E_impro = 2.6322 E_vdwl = 439.8428
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E_coul = 24513.5109 E_long = -33169.1409 Press = -1803.4201
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---------------- Step 600 ----- CPU = 9.9107 (sec) ----------------
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TotEng = -6089.5529 KinEng = 1205.1352 Temp = 282.4624
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PotEng = -7294.6881 E_bond = 108.2588 E_angle = 346.6746
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E_dihed = 531.5390 E_impro = 3.2909 E_vdwl = 459.2427
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E_coul = 24426.5336 E_long = -33170.2276 Press = -2567.6797
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---------------- Step 700 ----- CPU = 11.5432 (sec) ----------------
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TotEng = -6089.5542 KinEng = 1192.6231 Temp = 279.5298
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PotEng = -7282.1773 E_bond = 111.1701 E_angle = 368.3148
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E_dihed = 531.3469 E_impro = 3.6338 E_vdwl = 526.5919
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E_coul = 24341.9242 E_long = -33165.1590 Press = -1918.0534
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---------------- Step 800 ----- CPU = 13.1827 (sec) ----------------
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TotEng = -6089.6409 KinEng = 1211.1193 Temp = 283.8650
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PotEng = -7300.7601 E_bond = 104.1488 E_angle = 343.9467
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E_dihed = 536.0043 E_impro = 5.1288 E_vdwl = 507.6841
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E_coul = 24380.9222 E_long = -33178.5951 Press = -1535.2124
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---------------- Step 900 ----- CPU = 14.8342 (sec) ----------------
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TotEng = -6089.6435 KinEng = 1219.9414 Temp = 285.9327
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PotEng = -7309.5848 E_bond = 106.3702 E_angle = 362.6403
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E_dihed = 531.9023 E_impro = 4.1736 E_vdwl = 532.4576
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E_coul = 24326.4696 E_long = -33173.5985 Press = -694.2393
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---------------- Step 1000 ----- CPU = 16.5041 (sec) ----------------
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TotEng = -6089.6045 KinEng = 1204.4192 Temp = 282.2946
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PotEng = -7294.0238 E_bond = 108.7432 E_angle = 365.2088
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E_dihed = 541.1125 E_impro = 5.8781 E_vdwl = 533.2755
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E_coul = 24329.0904 E_long = -33177.3322 Press = -1373.0623
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Loop time of 16.5043 on 4 procs for 1000 steps with 1968 atoms
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Performance: 5.235 ns/day, 4.585 hours/ns, 60.590 timesteps/s
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98.8% CPU use with 4 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 | 8.2128 | 9.5121 | 11.127 | 36.9 | 57.63
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Bond | 0.035131 | 0.11618 | 0.15792 | 14.0 | 0.70
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Kspace | 4.0276 | 5.4843 | 6.6741 | 44.1 | 33.23
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Neigh | 0.66517 | 0.66553 | 0.66594 | 0.0 | 4.03
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Comm | 0.28238 | 0.35525 | 0.41804 | 9.9 | 2.15
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Output | 0.01374 | 0.014323 | 0.015721 | 0.7 | 0.09
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Modify | 0.28166 | 0.28593 | 0.29397 | 0.9 | 1.73
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Other | | 0.07076 | | | 0.43
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Nlocal: 492 ave 517 max 456 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Nghost: 7866 ave 8035 max 7664 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Neighs: 232474 ave 255787 max 198462 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Total # of neighbors = 929895
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Ave neighs/atom = 472.508
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Ave special neighs/atom = 4.4065
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Neighbor list builds = 47
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Dangerous builds = 0
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Total wall time: 0:00:18
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