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LAMMPS (6 Apr 2015-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:89)
using 1 OpenMP thread(s) per MPI task
units real
atom_style hybrid sphere dipole molecular
# this is equivalent to special_bonds amber,
# but also compatible with the per-style overrides below.
special_bonds lj 0.0 1.0e-100 0.5 coul 0.0 1.0e-100 0.8333333333333333
pair_style hybrid lj/sf/dipole/sf 12.0 lj/sf/dipole/sf 12.0 lj/charmm/coul/long 11.0 12.0
pair_modify mix arithmetic
pair_modify pair lj/sf/dipole/sf 1 special lj/coul 0.0 1.0 1.0
pair_modify pair lj/sf/dipole/sf 2 special lj/coul 0.0 1.0 1.0
kspace_style pppm/cg 1.0e-5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data data.bnzwbox
orthogonal box = (-11.3621 -13.9039 -13.1983) to (18.0429 16.0051 16.7857)
1 by 1 by 1 MPI processor grid
reading atoms ...
587 atoms
scanning bonds ...
3 = max bonds/atom
scanning angles ...
3 = max angles/atom
scanning dihedrals ...
9 = max dihedrals/atom
reading bonds ...
12 bonds
reading angles ...
18 angles
reading dihedrals ...
30 dihedrals
3 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
8 = max # of 1-4 neighbors
10 = max # of special neighbors
# pair_coeffs:
pair_coeff 1 1 lj/charmm/coul/long 0.0860 3.39967 0.0860 3.39967 # AA-AA
pair_coeff 2 2 lj/charmm/coul/long 0.015000 2.59964 0.015000 2.59964 # AA-AA
pair_coeff 3 3 lj/sf/dipole/sf 1 0.550000 3.050000 # CG-CG, this will be propagated with the longer timestep
pair_coeff 1 2 lj/charmm/coul/long 0.0359 2.9997 0.0359 2.9997 # AA-AA
pair_coeff 1 3 lj/sf/dipole/sf 2 0.2175 3.2248 # CG-AA, this will be propagated with the shorter timestep
pair_coeff 2 3 lj/sf/dipole/sf 2 0.0908 2.8248 # CG-AA, this will be propagated with the shorter timestep
# this will set individual per-atom masses - as required by
# atom style sphere - to the same value as the per-type masses.
set type 1 mass 12.011000
6 settings made for mass
set type 2 mass 1.008000
6 settings made for mass
set type 3 mass 40.00
575 settings made for mass
group solute molecule 1
12 atoms in group solute
group water molecule > 1
575 atoms in group water
set group solute diameter 0.0
12 settings made for diameter
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
#timestep 8
#run_style respa 2 4 hybrid 2 1 1 kspace 1 improper 2
timestep 2.0
run_style verlet
fix integrateSolute solute nve
fix integrateWater water nve/sphere update dipole
fix thermostatWater water langevin 298 298 100 9 omega yes zero yes
fix thermostatSolute solute langevin 298 298 100 9 zero yes
thermo 100
minimize 1.0E-4 1.0E-6 100 1000
PPPM initialization ...
G vector (1/distance) = 0.107059
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.00268661
estimated relative force accuracy = 8.09066e-06
using double precision FFTs
3d grid and FFT values/proc = 512 27
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 14
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 2.0%
Min/max charged atoms/proc: 2.0% 2.0%
Memory usage per processor = 13.1326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 1229.2095 0.19819566 1229.4077 33888.578
100 0 -2841.678 2.1349864 -2839.543 1363.0469
Loop time of 1.24367 on 1 procs for 100 steps with 587 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
1229.4076721 -2835.11740182 -2839.54299044
Force two-norm initial, final = 1311.12 92.7793
Force max component initial, final = 529.28 52.5897
Final line search alpha, max atom move = 0.00240725 0.126597
Iterations, force evaluations = 100 181
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2039 | 1.2039 | 1.2039 | 0.0 | 96.80
Bond | 0.0011945 | 0.0011945 | 0.0011945 | 0.0 | 0.10
Kspace | 0.0033362 | 0.0033362 | 0.0033362 | 0.0 | 0.27
Neigh | 0.015982 | 0.015982 | 0.015982 | 0.0 | 1.29
Comm | 0.015237 | 0.015237 | 0.015237 | 0.0 | 1.23
Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003967 | | | 0.32
Nlocal: 587 ave 587 max 587 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3599 ave 3599 max 3599 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 75832 ave 75832 max 75832 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 75832
Ave neighs/atom = 129.186
Ave special neighs/atom = 0.173765
Neighbor list builds = 5
Dangerous builds = 0
run 1000
PPPM initialization ...
G vector (1/distance) = 0.107059
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.00268661
estimated relative force accuracy = 8.09066e-06
using double precision FFTs
3d grid and FFT values/proc = 512 27
Memory usage per processor = 12.0076 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0 -2841.678 2.1349864 -2839.543 1363.0469
200 285.39211 -2675.81 14.315456 -2162.9845 3732.8229
300 291.58808 -2733.738 13.268339 -2211.1368 3040.2089
400 298.44197 -2860.0383 15.480615 -2323.2528 2646.7134
500 296.79448 -2966.7422 11.311007 -2437.004 1958.8059
600 308.29218 -3120.7411 15.267691 -2566.9626 1558.7607
700 312.67712 -3194.7043 8.7624891 -2639.7716 1212.4966
800 308.86454 -3385.1928 14.905594 -2830.7766 204.85265
900 296.81418 -3545.2909 13.78069 -3013.0487 528.53145
1000 311.33831 -3682.4629 10.590424 -3128.0408 309.35302
1100 296.60224 -3749.0433 14.01717 -3216.9347 -102.75834
Loop time of 5.87081 on 1 procs for 1000 steps with 587 atoms
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 29.434 ns/day 0.815 hours/ns 170.334 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.5785 | 5.5785 | 5.5785 | 0.0 | 95.02
Bond | 0.0061142 | 0.0061142 | 0.0061142 | 0.0 | 0.10
Kspace | 0.020182 | 0.020182 | 0.020182 | 0.0 | 0.34
Neigh | 0.051474 | 0.051474 | 0.051474 | 0.0 | 0.88
Comm | 0.088405 | 0.088405 | 0.088405 | 0.0 | 1.51
Output | 0.0004251 | 0.0004251 | 0.0004251 | 0.0 | 0.01
Modify | 0.11323 | 0.11323 | 0.11323 | 0.0 | 1.93
Other | | 0.01249 | | | 0.21
Nlocal: 587 ave 587 max 587 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3622 ave 3622 max 3622 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 75556 ave 75556 max 75556 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 75556
Ave neighs/atom = 128.716
Ave special neighs/atom = 0.173765
Neighbor list builds = 15
Dangerous builds = 0
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