forked from lijiext/lammps
118 lines
4.8 KiB
Groff
118 lines
4.8 KiB
Groff
LAMMPS (15 Feb 2016)
|
|
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)
|
|
2 by 1 by 2 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 0.4000E+01 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
|
|
|
|
run 0
|
|
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
|
PPPM initialization ...
|
|
WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297)
|
|
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 = 392 12
|
|
Neighbor list info ...
|
|
3 neighbor list requests
|
|
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
|
|
Memory usage per processor = 8.55822 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 E_hbond = -69.322152
|
|
C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
|
|
Loop time of 3.33786e-06 on 4 procs for 0 steps with 384 atoms
|
|
|
|
0.0% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
|
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
|
Kspace | 0 | 0 | 0 | 0.0 | 0.00
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
Other | | 3.338e-06 | | |100.00
|
|
|
|
Nlocal: 96 ave 104 max 87 min
|
|
Histogram: 1 1 0 0 0 0 0 0 0 2
|
|
Nghost: 3063.25 ave 3108 max 3024 min
|
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
|
Neighs: 25463.5 ave 28799 max 22471 min
|
|
Histogram: 1 0 0 1 0 1 0 0 0 1
|
|
FullNghs: 50927 ave 55516 max 46073 min
|
|
Histogram: 1 1 0 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 203708
|
|
Ave neighs/atom = 530.49
|
|
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
|