257 lines
12 KiB
Plaintext
257 lines
12 KiB
Plaintext
LAMMPS (5 Oct 2016)
|
|
package omp 0
|
|
WARNING: OpenMP support not enabled during compilation; using 1 thread only. (../fix_omp.cpp:123)
|
|
# Created by charmm2lammps v1.9.1 on Wed Oct 5 18:18:20 EDT 2016
|
|
# Command: charmm2lammps.pl -water -ions -border=2.0 all27_na 1ac7
|
|
|
|
units real
|
|
neigh_modify delay 2 every 1
|
|
|
|
atom_style full
|
|
bond_style harmonic
|
|
angle_style charmm
|
|
dihedral_style charmm
|
|
improper_style harmonic
|
|
|
|
pair_style lj/charmm/coul/long 8 12
|
|
pair_modify mix arithmetic
|
|
kspace_style pppm 1e-6
|
|
|
|
read_data 1ac7.data
|
|
orthogonal box = (-14.087 -1.88253 -5.44214) to (10.545 22.7495 33.9691)
|
|
2 by 2 by 2 MPI processor grid
|
|
reading atoms ...
|
|
1968 atoms
|
|
scanning bonds ...
|
|
3 = max bonds/atom
|
|
scanning angles ...
|
|
6 = max angles/atom
|
|
scanning dihedrals ...
|
|
14 = max dihedrals/atom
|
|
scanning impropers ...
|
|
1 = max impropers/atom
|
|
reading bonds ...
|
|
1516 bonds
|
|
reading angles ...
|
|
1491 angles
|
|
reading dihedrals ...
|
|
1659 dihedrals
|
|
reading impropers ...
|
|
43 impropers
|
|
4 = max # of 1-2 neighbors
|
|
7 = max # of 1-3 neighbors
|
|
18 = max # of 1-4 neighbors
|
|
20 = max # of special neighbors
|
|
|
|
special_bonds charmm
|
|
thermo 10
|
|
thermo_style multi
|
|
timestep 1.0
|
|
|
|
minimize 0.0 0.0 50 200
|
|
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
|
PPPM initialization ...
|
|
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
|
G vector (1/distance) = 0.280406
|
|
grid = 30 30 40
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.000302577
|
|
estimated relative force accuracy = 9.11202e-07
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 13068 4500
|
|
Last active /omp style is kspace_style pppm/omp
|
|
Neighbor list info ...
|
|
1 neighbor list requests
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 14
|
|
ghost atom cutoff = 14
|
|
binsize = 7 -> bins = 4 4 6
|
|
Memory usage per processor = 15.8614 Mbytes
|
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
|
TotEng = 16313.1962 KinEng = 0.0000 Temp = 0.0000
|
|
PotEng = 16313.1962 E_bond = 12014.3479 E_angle = 5414.5475
|
|
E_dihed = 557.2338 E_impro = 0.0516 E_vdwl = 1176.0283
|
|
E_coul = 28218.0485 E_long = -31067.0615 Press = -18022.1296
|
|
---------------- Step 10 ----- CPU = 0.1081 (sec) ----------------
|
|
TotEng = -1447.9072 KinEng = 0.0000 Temp = 0.0000
|
|
PotEng = -1447.9072 E_bond = 247.8926 E_angle = 2176.8245
|
|
E_dihed = 555.8870 E_impro = 1.7628 E_vdwl = -407.3892
|
|
E_coul = 27746.6549 E_long = -31769.5399 Press = -1411.7232
|
|
---------------- Step 20 ----- CPU = 0.2182 (sec) ----------------
|
|
TotEng = -4807.5054 KinEng = 0.0000 Temp = 0.0000
|
|
PotEng = -4807.5054 E_bond = 177.3593 E_angle = 555.9353
|
|
E_dihed = 551.4306 E_impro = 2.6640 E_vdwl = -581.3001
|
|
E_coul = 27120.3184 E_long = -32633.9130 Press = -13576.9371
|
|
---------------- Step 30 ----- CPU = 0.3443 (sec) ----------------
|
|
TotEng = -5555.1803 KinEng = 0.0000 Temp = 0.0000
|
|
PotEng = -5555.1803 E_bond = 147.6057 E_angle = 459.3239
|
|
E_dihed = 539.1126 E_impro = 2.8843 E_vdwl = -576.4747
|
|
E_coul = 26797.8386 E_long = -32925.4706 Press = -12870.0319
|
|
---------------- Step 40 ----- CPU = 0.4657 (sec) ----------------
|
|
TotEng = -5973.0779 KinEng = 0.0000 Temp = 0.0000
|
|
PotEng = -5973.0779 E_bond = 150.6611 E_angle = 441.4999
|
|
E_dihed = 528.1431 E_impro = 3.1819 E_vdwl = -519.1875
|
|
E_coul = 26477.1520 E_long = -33054.5284 Press = -13277.6629
|
|
---------------- Step 50 ----- CPU = 0.5988 (sec) ----------------
|
|
TotEng = -6363.9506 KinEng = 0.0000 Temp = 0.0000
|
|
PotEng = -6363.9506 E_bond = 165.0850 E_angle = 401.3082
|
|
E_dihed = 518.3931 E_impro = 3.2379 E_vdwl = -463.1261
|
|
E_coul = 26138.9684 E_long = -33127.8170 Press = -13085.4188
|
|
Loop time of 0.598905 on 8 procs for 50 steps with 1968 atoms
|
|
|
|
99.2% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
|
|
Minimization stats:
|
|
Stopping criterion = max iterations
|
|
Energy initial, next-to-last, final =
|
|
16313.1961904 -6328.33883947 -6363.95060584
|
|
Force two-norm initial, final = 9108.55 292.099
|
|
Force max component initial, final = 2254.31 67.3492
|
|
Final line search alpha, max atom move = 0.00149026 0.100368
|
|
Iterations, force evaluations = 50 75
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.24051 | 0.28255 | 0.35023 | 7.1 | 47.18
|
|
Bond | 0.0022576 | 0.0057876 | 0.0081606 | 2.6 | 0.97
|
|
Kspace | 0.18978 | 0.25595 | 0.29717 | 7.2 | 42.74
|
|
Neigh | 0.015369 | 0.01561 | 0.015768 | 0.1 | 2.61
|
|
Comm | 0.031344 | 0.032818 | 0.034241 | 0.5 | 5.48
|
|
Output | 0.00034261 | 0.00035512 | 0.00043511 | 0.2 | 0.06
|
|
Modify | 0.0011175 | 0.001414 | 0.0016975 | 0.5 | 0.24
|
|
Other | | 0.00442 | | | 0.74
|
|
|
|
Nlocal: 246 ave 274 max 226 min
|
|
Histogram: 2 1 0 1 1 0 1 1 0 1
|
|
Nghost: 6331 ave 6591 max 6075 min
|
|
Histogram: 1 1 0 0 2 2 0 0 1 1
|
|
Neighs: 116074 ave 137552 max 99519 min
|
|
Histogram: 1 2 1 1 0 0 0 1 0 2
|
|
|
|
Total # of neighbors = 928592
|
|
Ave neighs/atom = 471.846
|
|
Ave special neighs/atom = 4.4065
|
|
Neighbor list builds = 3
|
|
Dangerous builds = 0
|
|
|
|
reset_timestep 0
|
|
fix 1 all nve
|
|
fix 2 all shake 1e-6 500 0 m 1.0 a 93
|
|
112 = # of size 2 clusters
|
|
26 = # of size 3 clusters
|
|
6 = # of size 4 clusters
|
|
475 = # of frozen angles
|
|
velocity all create 0.0 12345678 dist uniform
|
|
|
|
restart 500 1ac7.restart1 1ac7.restart2
|
|
dump 1 all atom 100 1ac7.dump
|
|
dump_modify 1 image yes scale yes
|
|
|
|
thermo 100
|
|
run 1000
|
|
PPPM initialization ...
|
|
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
|
G vector (1/distance) = 0.280406
|
|
grid = 30 30 40
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.000302577
|
|
estimated relative force accuracy = 9.11202e-07
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 13068 4500
|
|
Last active /omp style is kspace_style pppm/omp
|
|
Neighbor list info ...
|
|
1 neighbor list requests
|
|
update every 1 steps, delay 2 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 14
|
|
ghost atom cutoff = 14
|
|
binsize = 7 -> bins = 4 4 6
|
|
Memory usage per processor = 16.6281 Mbytes
|
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
|
TotEng = -6507.5910 KinEng = 0.0000 Temp = 0.0000
|
|
PotEng = -6507.5910 E_bond = 107.6907 E_angle = 315.0621
|
|
E_dihed = 518.3931 E_impro = 3.2379 E_vdwl = -463.1261
|
|
E_coul = 26138.9684 E_long = -33127.8170 Press = -12385.0996
|
|
---------------- Step 100 ----- CPU = 0.6002 (sec) ----------------
|
|
TotEng = -6239.1679 KinEng = 693.7285 Temp = 162.5977
|
|
PotEng = -6932.8964 E_bond = 97.8328 E_angle = 278.8843
|
|
E_dihed = 517.0395 E_impro = 2.5171 E_vdwl = 25.4169
|
|
E_coul = 25297.7912 E_long = -33152.3783 Press = -7082.4023
|
|
---------------- Step 200 ----- CPU = 1.2143 (sec) ----------------
|
|
TotEng = -6239.2467 KinEng = 973.1878 Temp = 228.0980
|
|
PotEng = -7212.4345 E_bond = 100.5993 E_angle = 320.4657
|
|
E_dihed = 524.2274 E_impro = 2.4292 E_vdwl = 599.6228
|
|
E_coul = 24399.1819 E_long = -33158.9608 Press = -876.3929
|
|
---------------- Step 300 ----- CPU = 1.8629 (sec) ----------------
|
|
TotEng = -6239.3074 KinEng = 1080.8940 Temp = 253.3425
|
|
PotEng = -7320.2014 E_bond = 109.8163 E_angle = 341.6580
|
|
E_dihed = 522.9161 E_impro = 3.3533 E_vdwl = 548.9557
|
|
E_coul = 24315.8677 E_long = -33162.7685 Press = -2189.9473
|
|
---------------- Step 400 ----- CPU = 2.5209 (sec) ----------------
|
|
TotEng = -6239.4210 KinEng = 1085.2885 Temp = 254.3725
|
|
PotEng = -7324.7096 E_bond = 95.4880 E_angle = 333.0840
|
|
E_dihed = 531.5762 E_impro = 4.2236 E_vdwl = 547.4841
|
|
E_coul = 24332.2081 E_long = -33168.7736 Press = -1741.7706
|
|
---------------- Step 500 ----- CPU = 3.1762 (sec) ----------------
|
|
TotEng = -6239.4511 KinEng = 1151.8207 Temp = 269.9665
|
|
PotEng = -7391.2719 E_bond = 108.9390 E_angle = 328.6496
|
|
E_dihed = 528.8096 E_impro = 3.4706 E_vdwl = 499.9982
|
|
E_coul = 24309.7254 E_long = -33170.8642 Press = -2725.2316
|
|
---------------- Step 600 ----- CPU = 3.8115 (sec) ----------------
|
|
TotEng = -6239.4095 KinEng = 1129.5086 Temp = 264.7369
|
|
PotEng = -7368.9182 E_bond = 102.3632 E_angle = 346.1347
|
|
E_dihed = 534.3048 E_impro = 3.7134 E_vdwl = 473.9210
|
|
E_coul = 24346.7523 E_long = -33176.1075 Press = -2684.1848
|
|
---------------- Step 700 ----- CPU = 4.4501 (sec) ----------------
|
|
TotEng = -6239.4955 KinEng = 1132.8803 Temp = 265.5272
|
|
PotEng = -7372.3758 E_bond = 103.5625 E_angle = 340.8027
|
|
E_dihed = 535.9840 E_impro = 4.0448 E_vdwl = 488.9549
|
|
E_coul = 24323.6826 E_long = -33169.4072 Press = -2041.9019
|
|
---------------- Step 800 ----- CPU = 5.0783 (sec) ----------------
|
|
TotEng = -6239.5236 KinEng = 1192.2677 Temp = 279.4465
|
|
PotEng = -7431.7912 E_bond = 110.5122 E_angle = 329.8173
|
|
E_dihed = 534.5353 E_impro = 5.5900 E_vdwl = 541.3805
|
|
E_coul = 24227.6695 E_long = -33181.2961 Press = -1628.5627
|
|
---------------- Step 900 ----- CPU = 5.7072 (sec) ----------------
|
|
TotEng = -6239.5270 KinEng = 1162.7914 Temp = 272.5378
|
|
PotEng = -7402.3184 E_bond = 104.9538 E_angle = 347.6531
|
|
E_dihed = 536.4713 E_impro = 4.6832 E_vdwl = 483.3306
|
|
E_coul = 24295.7423 E_long = -33175.1528 Press = -1959.1567
|
|
---------------- Step 1000 ----- CPU = 6.3345 (sec) ----------------
|
|
TotEng = -6239.5020 KinEng = 1128.3312 Temp = 264.4609
|
|
PotEng = -7367.8332 E_bond = 102.9814 E_angle = 352.0690
|
|
E_dihed = 540.5086 E_impro = 3.6712 E_vdwl = 495.7763
|
|
E_coul = 24316.4138 E_long = -33179.2534 Press = -1881.5655
|
|
Loop time of 6.33458 on 8 procs for 1000 steps with 1968 atoms
|
|
|
|
Performance: 13.639 ns/day, 1.760 hours/ns, 157.864 timesteps/s
|
|
99.6% CPU use with 8 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 2.2335 | 2.5532 | 3.1707 | 18.5 | 40.31
|
|
Bond | 0.01158 | 0.051889 | 0.080867 | 9.9 | 0.82
|
|
Kspace | 2.1965 | 2.7773 | 3.0728 | 16.7 | 43.84
|
|
Neigh | 0.24407 | 0.24588 | 0.24863 | 0.3 | 3.88
|
|
Comm | 0.36894 | 0.37849 | 0.39142 | 1.3 | 5.97
|
|
Output | 0.0083764 | 0.0085732 | 0.0087767 | 0.1 | 0.14
|
|
Modify | 0.25864 | 0.28389 | 0.2976 | 2.5 | 4.48
|
|
Other | | 0.03539 | | | 0.56
|
|
|
|
Nlocal: 246 ave 290 max 210 min
|
|
Histogram: 1 1 0 1 2 0 2 0 0 1
|
|
Nghost: 6160.5 ave 6438 max 5877 min
|
|
Histogram: 2 0 0 1 0 2 0 1 1 1
|
|
Neighs: 116321 ave 144703 max 98946 min
|
|
Histogram: 1 2 1 1 0 2 0 0 0 1
|
|
|
|
Total # of neighbors = 930570
|
|
Ave neighs/atom = 472.851
|
|
Ave special neighs/atom = 4.4065
|
|
Neighbor list builds = 46
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:07
|