forked from lijiext/lammps
199 lines
10 KiB
Groff
199 lines
10 KiB
Groff
LAMMPS (27 Nov 2018)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
units real
|
|
atom_style full
|
|
boundary p p p
|
|
dielectric 1
|
|
special_bonds lj/coul 0.0 0.0 1.0
|
|
|
|
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
|
|
bond_style harmonic
|
|
angle_style harmonic
|
|
dihedral_style harmonic
|
|
improper_style none
|
|
kspace_style pppm 0.001
|
|
|
|
read_data data.dreiding
|
|
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
384 atoms
|
|
scanning bonds ...
|
|
4 = max bonds/atom
|
|
scanning angles ...
|
|
6 = max angles/atom
|
|
scanning dihedrals ...
|
|
3 = max dihedrals/atom
|
|
reading bonds ...
|
|
320 bonds
|
|
reading angles ...
|
|
448 angles
|
|
reading dihedrals ...
|
|
192 dihedrals
|
|
4 = max # of 1-2 neighbors
|
|
3 = max # of 1-3 neighbors
|
|
5 = max # of special neighbors
|
|
|
|
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
|
|
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
|
|
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
|
|
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
|
|
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
|
|
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
|
|
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
|
|
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
|
|
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
|
|
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
|
|
pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4
|
|
pair_modify mix arithmetic
|
|
neighbor 2.0 multi
|
|
neigh_modify every 2 delay 4 check yes
|
|
variable input index in.ch3oh.box.dreiding
|
|
variable sname index ch3oh.box.dreiding
|
|
|
|
compute hb all pair hbond/dreiding/lj
|
|
variable C_hbond equal c_hb[1] #number hbonds
|
|
variable E_hbond equal c_hb[2] #hbond energy
|
|
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
|
|
thermo_modify line multi format float %14.6f
|
|
|
|
fix 1 all nve
|
|
|
|
thermo 10
|
|
|
|
run 100
|
|
PPPM initialization ...
|
|
WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302)
|
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
G vector (1/distance) = 0.142073
|
|
grid = 3 3 3
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.154715
|
|
estimated relative force accuracy = 0.00046592
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 512 27
|
|
Neighbor list info ...
|
|
update every 2 steps, delay 4 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 13.5
|
|
ghost atom cutoff = 13.5
|
|
binsize = 6.75, bins = 3 3 3
|
|
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
|
(1) pair hbond/dreiding/lj, perpetual, skip from (3)
|
|
attributes: full, newton on
|
|
pair build: skip
|
|
stencil: none
|
|
bin: none
|
|
(2) pair lj/cut/coul/long, perpetual, half/full from (3)
|
|
attributes: half, newton on
|
|
pair build: halffull/newton
|
|
stencil: none
|
|
bin: none
|
|
(3) neighbor class addition, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/multi
|
|
stencil: full/multi/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
|
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
|
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
|
|
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
|
|
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
|
|
E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152
|
|
v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
|
|
---------------- Step 10 ----- CPU = 0.0306 (sec) ----------------
|
|
TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522
|
|
PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481
|
|
E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883
|
|
E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278
|
|
v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335
|
|
---------------- Step 20 ----- CPU = 0.0597 (sec) ----------------
|
|
TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407
|
|
PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582
|
|
E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103
|
|
E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343
|
|
v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335
|
|
---------------- Step 30 ----- CPU = 0.0889 (sec) ----------------
|
|
TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412
|
|
PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630
|
|
E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697
|
|
E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068
|
|
v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335
|
|
---------------- Step 40 ----- CPU = 0.1178 (sec) ----------------
|
|
TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037
|
|
PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583
|
|
E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713
|
|
E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393
|
|
v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335
|
|
---------------- Step 50 ----- CPU = 0.1467 (sec) ----------------
|
|
TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734
|
|
PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041
|
|
E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518
|
|
E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967
|
|
v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335
|
|
---------------- Step 60 ----- CPU = 0.1755 (sec) ----------------
|
|
TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489
|
|
PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008
|
|
E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312
|
|
E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165
|
|
v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335
|
|
---------------- Step 70 ----- CPU = 0.2044 (sec) ----------------
|
|
TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019
|
|
PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999
|
|
E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572
|
|
E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544
|
|
v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335
|
|
---------------- Step 80 ----- CPU = 0.2333 (sec) ----------------
|
|
TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689
|
|
PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918
|
|
E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346
|
|
E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370
|
|
v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335
|
|
---------------- Step 90 ----- CPU = 0.2622 (sec) ----------------
|
|
TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574
|
|
PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914
|
|
E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267
|
|
E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223
|
|
v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335
|
|
---------------- Step 100 ----- CPU = 0.2911 (sec) ----------------
|
|
TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054
|
|
PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059
|
|
E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719
|
|
E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795
|
|
v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335
|
|
Loop time of 0.291149 on 1 procs for 100 steps with 384 atoms
|
|
|
|
Performance: 29.676 ns/day, 0.809 hours/ns, 343.467 timesteps/s
|
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.255 | 0.255 | 0.255 | 0.0 | 87.59
|
|
Bond | 0.0042725 | 0.0042725 | 0.0042725 | 0.0 | 1.47
|
|
Kspace | 0.027151 | 0.027151 | 0.027151 | 0.0 | 9.33
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.0034399 | 0.0034399 | 0.0034399 | 0.0 | 1.18
|
|
Output | 0.00025988 | 0.00025988 | 0.00025988 | 0.0 | 0.09
|
|
Modify | 0.00059223 | 0.00059223 | 0.00059223 | 0.0 | 0.20
|
|
Other | | 0.0004294 | | | 0.15
|
|
|
|
Nlocal: 384 ave 384 max 384 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 4637 ave 4637 max 4637 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 101854 ave 101854 max 101854 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 5624 ave 5624 max 5624 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 101854
|
|
Ave neighs/atom = 265.245
|
|
Ave special neighs/atom = 4
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
|
|
Please see the log.cite file for references relevant to this simulation
|
|
|
|
Total wall time: 0:00:00
|